Home
References
Go to the relevant journal site, clicking button.
1. Hiraoka, A., Ohkubo, T. and Fukuda, M. Human hematopoietic survival and growth factor. Cell Biol. Int. Rep. 10:
347-355, 1986
2. Hiraoka, A., Ohkubo, T. and Fukuda, M. Production of human hematopoietic survival and growth factor by a
myeloid leukemia cell line (KPB-M15) and placenta as detected by a monoclonal antibody. Cancer Res. 47:
5025-5030, 1987
3. Hiraoka, A., Ohkubo, T. and Fukuda, M. Monoclonal antibodies against human hematopoietic survival and
growth factor. Biomed. Biochim. Acta 46:419-427, 1987
4.Hiraoka, A., Ohkubo, T. and Fukuda, M. Further characterization of the biological properties of human
hematopoietic survival and growth factor. Exp. Cell Biol. 57:27-34, 1989
5. Kamamoto, T., Ohkubo, T., Sakoda, H., Taniguchi, Y., Kita, K., Yoshida, Y. and Uchino, H. Establishment of two
Ph1 chromosome-positive cell lines, KPB-M8 and KPB-M15 Jpn. J. Clin. Oncol. 16:107-115, 1986
6. Hiraoka, A., Sugimura, A., Seki, T., Nagasawa, T., Ohta, N., Shimonishi, M., Hagiya, M. and Shimizu, S. Cloning,
expression and characterization of a cDNA encoding a novel human growth factor for primitive hematopoietic
progenitor cells. Proc. Natl. Acad. Sci. USA 94:7577-7582, 1997
7. Mio, H., Kagami, N., Yokokawa, S., Kawai, H., Nakagawa, S., Takeuchi, K., Sekine, S. and Hiraoka, A.Isolation and
characterization of a cDNA for human, mouse and rat full length stem cell growth factor (SCGF), a new
member of C-type lectin superfamily. Biochem. Biophys. Res. Commun. 249:124-130, 1998
8. Wewer, U.M. and Albrechtsen, R. Tetranectin, a plasminogen kringle4-binding protein. Cloning and gene
expression pattern in human colon cancer Lab. Invest. 67:253-262, 1992
9. Serensen, C.B., Berglund, L. and Peterson, T.E. Cloning of a cDNA encoding murine tetranectin Gene 152:243-
245, 1995
10. Neame, P.J., Young, C.N. and Treep, J.T. Primary structure of a protein isolated from reef shark
(Carcharhinus springeri)cartilage that is similar to the mammalian C-type lectin homolog, tetranectin
Protein Sci. 1:161-168, 1992
11. Hiraoka, A., Yano, K., Kagami, N., Takeshige, K., Mio, H., Anazawa, H. and Sugimoto,S. Stem cell growth factor:
in situ hybridization analysis on the gene expression, molecular characterization and in vitro proliferative
activity of a recombinant preparation on primitive hematopoietic progenitor cells. Hematol. J. 2:307-315,
2001 11.pdf
12. Holtet, T.L., Graversen, J.H., Clemmensen, I., Thogersen, H.C. and Etzerodt, M. Tetranectin, a trimeric
plasminogen-binding C-type lectin. Protein Sci. 6:1511-1515, 1997
13. Zelensky, A.N. and Gready, J.E. The C-type lectin-like domain superfamily FEBS J. 272:6179-6217, 2005
14. Kastrup, J.S., Nielsen, B.B., Rasmussen, H., Holtet, T.L., Graversen, J.H., Etzerodt, M., Thogersen, H.C. and
Larsen, I.K. Structure of the C-type lectin carbohydrate recognition domain of human tetranectin Acta
Crystallogr., Sect. D 54:757-766, 1998
15. Nielsen, B.B., Kastrup, J.S., Rasmussen, H., Holtet, T.L., Graversen, J.H., Etzerodt, M., Thogersen, H.C. and
Larsen, I.K. Crystal structure of tetranectin, a trimeric plasminogen-binding protein with an alpha-helical
coiled coil FEBS Lett. 412:388-396, 1997
16. Nielbo, S., Thomsen, J.K., Graversen, J.H., Jensen, P.H., Etzerodt, M., Poulsen, F.M. and Thoegersen, H.C.
Structure of the plasminogen kringle 4 binding calcium-free form of the C-type lectin-like domain of
tetranectin Biochemistry 43:8636-8643, 2004
17. Lyman, S.D., James, L., Escobar, S., Downey, H., de Vries, P., Brasel, K., Stocking, K., Beckmann, M.P.,
Copeland, N.G. and Cleveland, L.S. Identification of soluble and membrane-bound isoforms of the murine flt3
ligand generated by alternative splicing of mRNAs Oncogene 10:149-157, 1995
18. Dressman, M.A., Malinowski, R., McLean, L.A., Gathmann, I., Capdeville, R., Hensley, M., IRIS(International
Randomized Study of Interleron-ΑversusSTI571) Study Group and Polymeropoulos, M.H. Correlation of
major cytogenetic response with a pharmacogenetic marker in chronic myeloid leukemia patients treated
with imatinib (STI571) Clin. Cancer Res. 10:2265-2271, 2004
19. Zelensky, A.N.& Gready, J.E. C-type lectin-like domains in Fugu rubripes BMC Genomics 5:51, 2004
20. Aparicio, S., Chapman, J., Stupka, E., Putnam, N., Chia, J.-M., Dehal, P.,Christoffels, A., Rash, S., Hoon, S.,
Smit, A., Gelpke, M.D.S., Roach, J., 0h, T., Ho, I.Y., Wong, M., Detter, C., Verhoef, F., Predki, P., Tay, A., Lucas,
S., Richardson, P., Smith, S.F., Clark, M.S., Edwards, Y.J.K., Doggett, N., Zharkikh, A., Tavtigian, S.V.,
Pruss, D., Barnstead, M., Evans, C., Baden, H., Powell, J.,Glusman, G., Rowen, L., Hood, L., Tan, Y.H.,
Elgar, G., Hawkins, T., Venkatesh, B., Rokhsar, D. and Brenner, S. Whole-genome shotgun assembly and
analysis of the genome of Fugu rubripes Science 297:1301-1310, 2002
21.Miki, R., Kadota, K., Bono, H., Mizuno, Y., Tomaru, Y., Carninci, P., Itoh, M., Shibata, K., Kawai, J., Konno, H.,
Watanabe, S., Sato, K., Tokusumi, Y., Kikuchi, N., Ishii, Y., Hamaguchi, Y., Nishizuka, I., Goto, H., Nitanda, H.,
Satomi, S., Yoshiki, A., Kusakabe, M., DeRisi, J.L., Eisen, M.B., Iyer, V.R., Brown, P.O., Muramatsu, M., Shimada,
H., Okazaki, Y. and Hayashizaki, Y. Delineating developmental and metabolic pathways in vivo by expression
profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays Proc. Natl. Acad. Sci. USA 98
:2199-2204, 2001
22.Su, A.I., Cooke, M.P., Ching, K.A., Hakak, Y., Walker, J.R., Wiltshire, T., 0rth, A.P., Vega, R.G., Sapinoso, L.M.,
Moqrich, A., Patapoutian, A., Hampton, G.M.,Schultz, P.G. and Hogenesch, J.B. Large-scale analysis of the
human and mouse transcriptomes Proc. Natl. Acad. Scj. USA 99:4465-4470, 2002
23.Brandenberger, R., Wei, H., Zhang, S., Lei, S., Murage, J., Fisk, G.J., Li, Y., Xu, C., Fang, R., Guegler, K., Rao, M.
S., Mandalam, R., Lebkowski, J. and Stanton, L.W. Transcriptome characterization elucidates signaling
networks that control human ES cell growth and differentiation Nat. Biotechnol. 22:707-716, 2004
24.Sun, Y., Li, H., Liu, Y., Shin, S., Mattson, M.P., Rao, M.S. and Zhan, M. Cross-species transcriptional profiles
establish a functional portrait of embryonic stem cells Genomics 89:22-35, 2007
25.Zhou, Q., Chipperfield, H., Melton, D.A. and Wong, W.H. A gene regulatory network in mouse embryonic stem
cells Proc. Natl. Acad. Sci. USA 104:16438-16443, 2007
26.Chen, S., Choo, A., Chin, A. and Oh, S.K.W. TGF-Β2 allows pluripotent human embryonic stem cell
proliferation on E6/E7 immortalized mouse embryonic fibroblasts J. Biotechnol. 122:341-361, 2006
27.Baross A, Schertzer M, Zuyderduyn SD, Jones SJ, Marra MA and Lansdorp PM Effect of TERT and ATM on
gene expression profiles in human fibroblasts Genes Chromosomes Cancer 39:298-310, 2004
28.Castellano, E., De Las Rivas, J., Guerrero, C. and Santos, E. Transcriptional networks of knockout cell lines
identify functional specificities of H-Ras and N-Ras: significant involvement of N-Ras in biotic and defense
responses Oncogene 26:917-933, 2007
29.Dumortier, J., Streblow, D.N., Moses, A.V., Jacobs, J.M., Kreklywich, C.N., Camp, D., Smith, R.D., Orloff, S.L. and
Nelson, J.A. Human cytomegalovirus secretome contains factors that induce angiogenesis and wound healing
J. Virol. 82:6524-6535, 2008
30.Jiang, Y., Vaessen, B., Lenvik, T., Blackstad, M., Reyes, M. and Verfaillie, C.M. Multipotent progenitor cells
can be isolated from postnatal murine bone marrow, muscle, and brain Exp. Hematol. 30:896-904, 2002
31.Silva, Jr., W.A., Covas, D.T.,Panepucci, R.A., Proto-Siqueira, R., Siufi, J.L.C.,Zanette, D.L., Santos, A.R.D. and
Zago, M.A. The profile of gene expression of human marrow mesenchymal stem cells Stem Cells 21:661-669,
2003
32.Baddoo, M., Hill, K., Wilkinson, R., Gaupp, D., Hughes, C., Kopen, G.C. and Phinney,D.G. Characterization of
mesenchymal stem cells isolated from murine bone marrow by negative selection J. Cell. Biochem. 89:1235-
1249, 2003
33.Liu, C.-H. and Hwang, S.-M. Cytokine interactions in mesenchymal stem cells from cord blood Cytokine 32:
270-279, 2005
34.lto, C., Sato, H., Ando, K., Watanabe, S., Yoshiba, F., Kishi, K., Furuya, A., Shitara, K., Sugimoto, S., Kohno,
H., Hiraoka, A. and Hotta, T. Serum stem cell growth factor for monitoring hematopoietic recovery following
stem cell transplantation Bone Marrow Transplant. 32:391-398,2003
35.Ma, X., Husain, T., Peng, H., Lin, S., Mironenko, O., Maun, N., Johnson, S., Tuck,D., Berliner, N., Krause, D.S.
and Perkins, A.S. Development of a murine hematopoietic progenitor complementary DNA microarray using a
subtracted complementary DNA library Blood 100:833-844, 2002
36.Ng, Y.Y., van Kessel, B., Lokhorst, H.M., Baert, M.R.M., van den Burg, C.M.M., Bloem, A.C. and Staal, F.J.T.
Gene-expression profiling of CD34+cells from various hematopoietic stem-cell sources reveals functional
differences in stem-cell activity J. Leuk. Biol. 75:314-323, 2004
37.Bartolovic, K., Balabanov, S., Berner, B., Buhring, H.J., Komor, M., Becker, S., Hoelzer, D., Kanz, L., Hofmann, W.
K. and Brummendorf, T.H. Clonal heterogeneity in growth kinetics of CD34+CD38- human cord blood cells in
vitro is correlated with gene expression pattern and telomere length Stem Cells 23:946-957, 2005
38.Panepucci, R.A., Calado, R.T., Rocha, V., Proto-Siqueira, R., Silva, Jr., W.A. and Zago, M.A. Higher expression
of transcription targets and components of the nuclear factor-ΚB pathway is a distinctive feature of
umbilical cord blood CD34+ precursors Stem Cells 25:189-196, 2007
39. Shen, S., Passioura, T., Symonds, G. and Dolnikov, A. N-ras oncogene-induced gene expression in human
hematopoietic progenitor cells: Upregulation ofp16INK4aandp21CIP1/WAF1correlates with myeloid
differentiation Exp. Hematol. 35:908-919, 2007
40. Vaes, B.L., Ducy, P., Sijbers, A.M., Hendriks, J.M., van Someren, E.P., de Jong, N.G., van den Heuvel, E.R.,
Olijve, W., van Zoelen, E.J. and Dechering, K.J. Microarray analysis on Runx2-deficient mouse embryos
reveals novel Runx2 functions and target genes during intramembranous and endochondral bone formation
Bone 39:724-738, 2006
41. Schroeder, T.M., Nair, A.K., Staggs, R., Lamblin, A.F. and Westendorf, J.J. Gene profile analysis of osteoblast
genes differentially regulated by histone deacetylase inhibitors BMC Genomics 8:362, 2007
42. Li, X., Liu, H., Qin, L., Tamasi, J., Bergenstock, M., Shapses, S., Feyen, J.H.M., Notterman, D.A. and Partridge,
N.C. Determination of dual effects of parathyroid hormone on skeletal gene expression in vivo by microarray
and network analysis J. Biol. Chem. 282:33086-33097, 2007
43. Guo, J., Jin, J. and Cooper, L.F. Dissection of sets of genes that control the character of wnt5a-deficient
mouse calvarial cells Bone 43:961-971, 2008
44. de Jong, N.G. Discovering the BMP signaling pathway by using motif enrichment and conservation ICT-TU
Delft pp1-19, 2007 44.pdf
45. Osawa, A., Kato, M., Matsumoto, E., Iwase, K., Sugimoto, T., Matsui, T., Ishikura, H., Sugano, S., Kurosawa, H.,
Takiguchi, M. and Seki, N. Activation of genes for growth factor and cytokine pathways late in chondrogenic
differentiation of ATDC5 cells Genomics 88:52-64, 2006
46. Zheng, H., Martin, J.A., Duwayri, Y., Falcon, G. and Buckwalter, J.A. Impact of aging on rat bone marrow-
derived stem cell chondrogenesis J. Gerontol. Biol. Sci. 62A:136-148, 2007
47. Chan, C.K.F., Chen, C.-C., Luppen, C.A., Kim, J.-B., DeBoer, A.T., Wei, K., Helms, J.A., Kuo, C.J., Kraft, D.L.
and Weissman, I.L. Endochondral ossification is required for haematopoietic stem-cell niche formation Nature
457:490-494, 2009
48. Dontu, G., Abdallah, W.M., Foley, J.M., Jackson, K.W., Clarke, M.F., Kawamura, M.J. and Wicha, M.S. In vitro
propagation and transcriptional profiling of human mammary stem/progenitor cells Genes Dev. 17:1253-
1270, 2003
49. Li, R.W., Meyer, M.J., Van Tassell, C.P., Sonstegard,T.S., Connor, E.E., Van Amburgh, M.E., Boisclair, Y.R. and
Capuco, A.V. Identification of estrogen-responsive genes in the parenchyma and fat pad of the bovine
mammary gland by microarray analysis Physiol. Genomics 27:42-53, 2006
50. Iguchi, M., Tobias, J.W. and Hecht, N.B. Expression profiling reveals meiotic male germ cell mRNAs that are
translationally up- and down-regulated Proc. Natl. Acad. Sci. USA 103:7712-7717, 2006
51. O'Shaughnessy, P.J., Fleming, L., Baker, P.J., Jackson, G. and Johnston, H. Identification of developmentally
regulated genes in the somatic cells of the mouse testis using serial analysis of gene expression Biol. Reprod.
69:797-808,2003
52. Hawrylycz, M.J., Lein, E.S., Guillozet-Bongaarts, A.L., Shen, E.H., Ng, L., Miller, J.A., van de Lagemaat, L.N.,
Smith, K.A., Ebbert, A., Riley, Z.L., Abajian, C., Beckmann, C.F., Bernard, A., Bertagnolli, D., Boe, A.F.,
Cartagena, P.M., Chakravarty, M.M., Chapin, M., Chong, J., Dalley, R.A., Daly, B.D., Dang, C., Datta, S., Dee, N.,
Dolbeare, T.A., Faber, V., Feng, D., Fowler, D.R., Goldy, J., Gregor, B.W., Haradon, Z., Haynor, D.R., Hohmann, J.
G., Horvath, S., Howard, R.E., Jeromin, A., Jochim, J.M., Kinnunen, M., Lau, C., Lazarz, E.T., Lee, C., Lemon, T.
A., Li, L., Li, Y., Morris, J.A., Overly, C.C., Parker, P.D., Parry, S.E., Reding, M., Royall, J.J., Schulkin, J.,
Sequeira, P.A., Slaughterbeck, C.R., Smith, S.C., Sodt, A.J., Sunkin, S.M., Swanson, B.E., Vawter, M.P., Williams,
D., Wohnoutka, P., Zielke, H.R., Geschwind, D.H., Hof, P.R., Smith, S.M., Koch, C., Grant, S.G.N. and Jones, A.R.
An anatomically comprehensive atlas of the adult human brain transcriptome Nature 489:391-399, 2012
53. Kagami, Y., Mitsui, T., Akane, H. and Maeda, S. Sexually dimorphic gene expression profile of the developing
mouse embryonic brain exposed in utero to 2,3,7,8-tetrachlorodibenzo-p-dioxin 22nd International
Neurotoxicology Conference P-111 (September 11-14, 2005)
54. Yan, J., Jiao, Y., Jiao, F., Stuart, J., Donahue, L.R., Beamer, W.G., Li, X., Roe, B.A., LeDoux, M.S. and Gu, W.
Effects of carbonic anhydrase VIII deficiency on cerebellar gene expression profiles in the wdl mouse
Neurosci. Lett. 413:196-201, 2007
55. Cadet J.L., McCoy,M.T. and Ladenheim, B. Distinct gene expression signatures in the striata of wild-type and
heterozygous c-fos knockout mice following methamphetamine administration: evidence from cDNA array
analyses Synapse 44:211-226,2002
56. Stanimirovic, D., Haqqani, A., Zhang, W., Ball, R., Freitas-Andrade, M., Nesic, M. and Moreno, M. Molecular
fingerprinting of cellular and acellular components of the neurovascular unit using genomics and proteomics
techniques 5th International Conference on Cerebral Vascular Biology (CVB 2003) Amarillo, Texas June
16th, 2003 Session 1-Genomics and Proteomics of The Cerebrovascular Barrier
57. Norman, B., Davis, J. and Piatigorsky, J. Postnatal gene expression in the normal mouse cornea by SAGE
Invest. Ophthalmol. Vis. Sci. 45:429-440, 2004
58. James, E.R., Fresco, V.M. and Robertson, L.L. Glucocorticoid-induced changes in the global gene expression
of lens epithelial cells J. Ocular Pharm. Therapeutics 21:11-27, 2005
59. Esson, D.W., Popp, M.P., Liu, L., Schultz, G.S. and Sherwood, M.B. Microarray analysis of the failure of
filtering blebs in a rat model of glaucoma filtering surgery Invest. Ophthalmol. Vis. Sci. 45:4450-4462, 2004
60. Wistow, G., Bernstein, S.L., Ray, S., Wyatt, M.K., Behal, A., Touchman, J.W., Bouffard, G., Smith, D. and
Peterson, K. Expressed sequence tag analysis of adult human iris for the NEIBank Project: Steroid-response
factors and similarities with retinal pigment epithelium Mol. Vision 8:185-195, 2002
61. Bhattacharya, S.K., Rockwood, E.J., Smith, S.D., Bonilha, V.L., Crabb, J.S., Kuchtey, R.W., Robertson, N.G.,
Peachey, N.S., Morton, C.C. and Crabb, J.W. Proteomics reveal cochlin deposits associated with
glaucomatous trabecular meshwork J. Biol. Chem. 280:6080-6084, 2005
62. Blackshaw, S., Harpavat, S., Trimarchi, J., Cai, L., Huang, H., Kuo, W.P., Weber, G., Lee, K., Fraioli, R.E., Cho, S.-
H., Yung, R., Asch, E., Ohno-Machado, L., Wong, W.H. and Cepko, C.L. Genomic analysis of mouse retinal
development PLoS Biol. 2:e247:1411-1431, 2004
63. Otani, A., Dorrell, M.I., Kjnder, K., Moreno, S.K., Nusinowitz, S., Banin, E., Heckenlively, J. and Friedlander,
M Rescue of retinal degeneration by intravitreally injected adult bone marrow-derived lineage-negative
hematopoietic stem cells J. Clin. Invest. 114:765-774, 2004
64. Sugita, S., Horie, S., Nakamura, O., Futagami, T., Takase, H., Keino, H., Aburatani, H., Katunuma, N., Ishidoh, K.,
Yamamoto, Y. and Mochizuki, M. Retinal pigment epithelium-derived CTLA-2 induces TGF-producing T
regulatory cells1 J. Immunol. 181:7525-7536, 2008
65. Banno, T., Gazel, A. and Blumenberg, M. Effects of tumor necrosis factor-Α(TNFΑ)in epidermal
keratinocytes revealed using global transcriptional profiling J. Biol. Chem. 279:32633-32642, 2004
66. Gazel, A., Ramphal, P., Rosdy, M., De wever, B., Tornier, C., Hosein, N., Lee, B., Tomic-Canic, M. and
Blumenberg, M. Transcriptional profiling of epidermal keratinocytes: Comparison of genes expressed in skin,
cultured keratinocytes, and reconstituted epidermis, using large DNA microarrays J. Inves. Dermatol. 121:
1459-1468, 2003
67. Billing, A.M., Fack, F., Renaut, J., Olinger, C.M., Schote, A.B., Turner, J.D. and Muller, C.P. Proteomic analysis
of the cortisol-mediated stress response in THP-1 monocytes using DIGE technology J. Mass Spectrom. 42:
1433-1444, 2007
68. Chebotaev, D., Yemelyanov, A., Zhu, L., Lavker, R.M. and Budunova, I. The tumor suppressor effect of the
glucocorticoid receptor in skin is mediated via its effect on follicular epithelial stem cells Oncogene 26:3060-
3068, 2007
69. Liang, X., Huuskonen, J., Hajivandi, M., Manzanedo, R., Predki, P., Amshey, J.R. and Pope, R.M. Identification
and quantification of proteins differentially secreted by a pair of normal and malignant breast-cancer cell
lines. Proteomics 9:182-193, 2009
70. Palmer, D.J., Kelly, V.C., Smit, A.-M., Kuy, S., Knight, C.G. and Cooper, G.J. Human colostrum: Identification of
minor proteins in the aqueousphase by proteomics Proteomics 6:2208-2216, 2006
71. Bordoni, A., Astolfi, A., Morandi, L., Pession, A., Danesi, F., Di Nunzio, M., Franzoni, M., Biagi,P.-L. and Pession,
A. N-3 PUFAs modulate global gene expression profile in cultured rat cardiomyocytes. Implications in cardiac
hypertrophy and heart failure FEBS Lett. 581:923-929, 2007
72. Kong, B., Liu, Y.-L. and Lu, X.-D. Microarray-bioinformatics analysis of altered genomic expression profiles
between human fetal and infant myocardium Chn. Med. J. 121:1257-1264, 2008
73. van Lunteren, E., Spiegler, S. and Moyer, M. Contrast between cardiac left ventricle and diaphragm muscle in
expression of genes involved in carbohydrate and lipid metabolism Resp. Physiol. Neurobiol. 161:41-53, 2008
74. Chen, B.P.C., Li, Y.-S., Zhao, Y., Chen, K.-D., Li,S., Lao, J., Yuan, S., Shyy, J.Y.-J. and Chien, S. DNA
microarray analysis of gene expression in endothelial cells in response to 24-h shear stress Physiol.
Genomics 7:55-63, 2001
75. Lunardi, C., Dolcino, M., Peterlana, D., Bason, C., Navone, R., Tamassia, N., Tinazzi, E., Beri, R., Corrocher, R.
and Puccetti, A. Endothelial cells' activation and apoptosis induced by a subset of antibodies against human
cytomegalovirus: Relevance to the pathogenesis of atherosclerosis PLoS ONE 5:e473, 2007
76. Igreja, C., Fragoso, R., Caiado, F., Clode, N., Henriques, A., Camargo, L., Reis, E.M. and Dias, S. Detailed
molecular characterization of cord blood-derived endothelial progenitors Exp. Hematol. 36:193-203, 2008
77. Michalopoulos, G.K., Bowen, W.C., MulÉ, K. and Luo, J. HGF-, EGF-, and dexamethasone-induced gene
expression patterns during formation of tissue in hepatic organoid cultures Gene Expr. 11:55-75, 2003
78. Kordes, C., Sawitza, I., MÜller-Marbach, A., Ale-Agha, N., Keitel, V., Klonowski-Stumpe, H. and HÄussinger, D.
CD133+ hepatic stellate cells are progenitor cells Biochem. Biophys. Res. Commun. 352:410-417, 2006
79. De Minicis, S., Seki, E., Uchinami, H., Kluwe, J., Zhang, Y., Brenner, D.A. and Schwabe, R.F. Gene expression
profiles during hepatic stellate cell activation in culture and in vivo Gastroenterology 132:1937-1946, 2007
80. Pederson, L., Ruan, M., Westendorf, J.J., Khosla, S. and Oursler, M.J. Regulation of bone formation by
osteoclasts involves Wnt/BMP signaling and the chemokine sphingosine-1-phosphate Proc. Natl. Acad. Sci.
USA 105:20764-20769, 2008
81. Cappellen, D., Luong-Nguyen, N.-H., Bongiovanni, S., Grenet, O., Wanke, C. and Susa, M. Transcriptional
program of mouse osteoclast differentiation governed by the macrophage colony-stimulating factor and the
ligand for the receptor activator of NFkB J. Biol. Chem. 277:21971-21982, 2002
82. Haddad, R., Guardiola, P., Izac, B., Thibault, C., Radich, J., Delezoide, A.-L., Baillou, C., Lemoine, F.M.,
Gluckman, J.C., Pflumio, F. and Canque, B. Molecular characterization of early human T/NK and B-lymphoid
progenitor cells in umbilical cord blood Blood 104:3918-3926, 2004
83. Wieczorek, G., Steinhoff, C., Schulz, R., Scheller, M., Vingron, M., Ropers, H.H. and Nuber, U.A. Gene
expression profile of mouse bone marrow stromal cells determined by cDNA microarray analysis Cell Tissue
Res. 311:227-237, 2003
84. Higashi, N., Fujioka, K., Denda-Nagai,K., Hashimoto, S., Nagai, S., Sato, T., Fujita, Y., Morikawa, A., Tsuiji, M.,
Miyata-Takeuchi, M., Sano, Y., Suzuki, N., Yamamoto, K., Matsushima, K. and Irimura, T. The macrophage C-
type lectin specific for galactose/N-acety1galactosamine is an endocytic receptor expressed on monocyte-
derived immature dendritic cells J. Biol. Chem. 277:20686-20693, 2002
85. Volpe, E., Cappelli, G., Grassi, M., Martino, A., Serafino, A., Colizzi, V., Sanarico, N. and Mariani, F. Gene
expression profiling of human macrophages at late time of infection with Mycobacterium tuberculosis
Immunology 118:449-460, 2006
86. Garaci, E., Pica, F., Sinibaldi-Vallebona, P., Pierimarchi, P., Mastino, A., Matteuccj, C. and Rasi, G. ThymosinΑ
1 in combination with cytokines and chemotherapy for the treatment of cancer Int. Immunopharmacol. 3:1145
-1150, 2003
87. Ng, L.F.P., Hibberd, M.L., Ooi, E.-E., Tang, K.-F., Neo, S.-Y., Tan, J., Murthy, K.R.K., Vega, V.B., Chia, J.-M., Liu,
E.T. and Ren, E.-C. A human in vitro model system for investigating genome-wide host responses to SARS
coronavirus infection BMC Infect. Dis. 4:34, 2004
88. AhrÉn, I.L., Eriksson, E., Egesten, A. and Riesbeck, K. Nontypeable haemophilus influenzae activates human
eosinophils throughΒ-glucan receptors Am. J. Respir. Cell Mol. Biol. 29:598-605, 2003
89. Vuillemonot, B.R., Rodriguez, J.F. and Hoyle, G.W. Lymphoid tissue and emphysema in the lungs of transgenic
mice inducibly expressing tumor necrosis factor-ΑAm. J. Respir. Cell Mol. Biol. 30:438-448, 2004
90. Jacquel, A., Herrant, M., Defamie, V., Belhacene, N., Colosetti, P., Marchetti, S., Legros, L., Deckert, M., Mari,
B., Cassuto, J.P., Hofman, P. and Auberger, P. A survey of the signaling pathways involved in megakaryocytic
differentiation of the human K562 leukemia cell line by molecular and c-DNA array analysis Oncogene 25:781
-794, 2006
91. GarcÍa-PiÑeres, A.J., Hildesheim, A., Dodd, L., Kemp, T.J., Yang, J., Fullmer, B., Harro, C., Lowy, D.R.,
Lempicki, R.A. and Pinto, L.A. Gene expression patterns induced by HPV-16 L1 virus-like particles in
leukocytes from vaccine recipients J. Immunol. 182:1706-1729, 2009
92. Burch, L.H., Yang, I.V., Whitehead, G.S., Chao, F.G., Katherine G. Berman, K.G. and Schwartz, D.A. The
transcriptional response to lipopolysaccharide reveals a role for interferon-Γin lung neutrophil recruitment
Am. J. Physiol. Lung Cell. Mol. Physiol. 291:L677-L682, 2006
93. Jiang, F. and Wang, Z. Identification of androgen-responsive genes in the rat ventral prostate by
complementary deoxyribonucleic acid subtraction and microarray Endocrinology 144:1257-1265,2003
94. Suzuki, T., Fujimoto, N., Kitamura, S. and Ohta, S. Quantitative determination of lobe specificity of mRNA
expression of androgen-dependent genes in the rat prostate gland Endocr. J. 54:123-132, 2007
95. Suzuki, T., Fujimoto, N., Kitamura, S. and Ohta, S. Effects of environmental antiandrogenic chemicals on
expression of androgen-responsive genes in rat prostate lobes J. Health Sci. 53:401-405, 2007
96. Hemberger, M., Cross, J.C., Ropers, H.-H., Lehrach, H., Fundele, R. and Himmelbauer, H. UniGene cDNA array-
based monitoring of transcriptome changes during mouse placental development Proc. Natl. Acad. Sci. USA
98:13126-13131,2001
97. Talbi, S., Hamilton, A.E., Vo, K.C., Tulac, S., Overgaard, M.T., Dosiou, C., Le Shay, N., Nezhat, C.N., Kempson,
R., Lessey, B.A., Nayak, N.R. and Giudice, L.C. Molecular phenotyping of human endometrium distinguishes
menstrual cycle phases and underlying biological processes in normo-ovulatory women Endocrinology 147:
1097-1121, 2006
98. Skinner, M.K., Schmidt, M., Savenkova, M.I., Sadler-Riggleman, I. and Nilsson, E.E. Regulation of granulosa and
theca cell transcriptomes during ovarian antral follicle development Mol. Reprod. Dev.75:1457-1472, 2008
99. Benchaouir, R., Rameau, P., Decraene, C., Dreyfus, P., Israeli, D., Pietu, G., Danos, O. and Garcia, L. Evidence
for a resident subset of cells with SP phenotype in the C2C12 myogenic line: a tool to explore muscle stem
cell biology Exp. Cell Res. 294:254-268, 2004
100. Decraene, C., Benchaouir, R., Dillies, M.A., Israeli, D., Bortoli, S., Rochon, C., Rameau, P., Pitaval, A., Tronik-
Le Roux, D., Danos, O., Gidrol, X., Garcia, L. and Pietu, G. Global transcriptional characterization of SP and
MP cells from the myogenic C2C12 cell line: effect of FGF6 Physiol. Genomics 23:132-149, 2005
101. Buteau, J., Shlien, A., Foisy, S. and Accili, D. Metabolic diapause in pancreaticΒ-cells expressing a gain-of-
function mutant of the forkhead protein foxo1 J. Biol. Chem. 282:287-293, 2007
102. Tabuchi, Y., Takasaki, I., Doi, T., Ishii, Y., Sakai, H. and Kondo, T. Genetic networks responsive to sodium
butyrate in colonic epithelial cells FEBS Lett. 580:3035-3041, 2006
103. Kidd, M., Modlin, I.M., Eick, G.N. and Champaneria, M.C. Isolation, functional characterization, and
transcriptome of Mastomys ileal enterochromaffin cells Am. J. Physiol. Gastrointest. Liver Physiol. 291:G778-
G791, 2006
104. ChabardÈs-Garonne, D., MÉjean, A., Aude, J.-C., Cheval, L., Di Stefano, A., Gaillard, M.-C., Imbert-Teboul,
M., Wittner, M., Balian, C., Anthouard, V., Robert, C., SÉgurens, B., Wincker, P., Weissenbach, J., Doucet, A.
and Elalouf, J.-M. A panoramic view of gene expression in the human kidney Proc. Natl. Acad. Sci. USA 100:
13710-13715, 2003
105. Moreno, C.S., Ramachandran, S., Ashby, D.G., Laycock, N., Plattner, C.A., Chen, W., Hahn, W.C. and Pallas, D.
C. Signaling and transcriptional changes critical for transformation of human cells by simian virus 40 small
tumor antigen or protein phosphatase 2A B56 knockdown Cancer Res. 64:6978-6988, 2004
106. Mukhopadhyay, P., Greene, R.M., Zacharias, W., Weinrich, M.C., Singh, S., Young Jr., W.W. and Pisano, M.M.
Developmental gene expression profiling of mammalian, fetal orofacial tissue Birth Defects Res. Pt. A 70:912-
926, 2004
107. Moffatt, P., Smith, C.E., Sooknanan, R., St-Arnaud, R. and Nanci, A. Identification of secreted and
membrane proteins in the rat incisor enamel organ using a signal-trap screening approach Eur. J. Oral Sci.
114(Suppl. S1):139-146, 2006
108. Pemberton, T.J., Li, F.-Y., Oka, S., Mendoza-Fandino, G.A., Hsu, Y.-H., Bringas, Jr., P., Chai, Y., Snead, M.L.,
Mehrian-Shai, R. and Patel1, P.I. Identification of novel genes expressed during mouse tooth development by
microarray gene expression analysis Dev. Dynamics 236:2245-2257, 2007
109. Tian, B., Nowak, D.E., Jamaluddin, M., Wang, S. and Brasier, A.R. Identification of direct genomic targets
downstream of the nuclear factor-B transcription factor mediating tumor necrosis factor signaling J. Biol.
Chem. 280:17435-17448, 2005
110. Tian, B., Nowak, D.E. and Brasier, A.R. A TNF-induced gene expression program under oscillatory NF-ΚB
control BMC Genomics 6:137, 2005
111. Huang, S.-T.J., Vo, K.C.T., Lyell, D.J., Faessen, G.H., Tulac, S., Tibshirani, R.,Giaccia, A.J. and Giudice, L.C.
Developmental response to hypoxia FASEB J. 18:1348-1365, 2004
112. Hu, R., Xu, C., Shen, G., Jain, M.R., Khor, T.O., Gopalkrishnan, A., Lin, W., Reddy, B., Jefferson Y. Chan, J.Y.
and Kong, A.-N.T. Gene expression profiles induced by cancer chemopreventive isothiocyanate sulforaphane
in the liver of C57BL/6J mice and C57BL/6J/Nrf2 (-/-) mice Cancer Lett. 243:170-192, 2006
113. Hu, R., Xu, C., Shen, G., Jain, M.R., Khor, T.O., Gopalkrishnan, A., Lin, W., Reddy, B., Chan, J.Y. and Kong,
A.-N.T. Identification of Nrf2-regulated genes induced by chemopreventive isothiocyanate PEITC by
oligonucleotide microarray Life Sci. 79:1944-1955, 2006
114. Nair, S., Xu, C., Shen, G., Hebbar, V., Gopalakrishnan, A., Hu, R., Jain, M.R., Liew, C., Chan, J.Y. and Kong, A.-
N.T. Toxicogenomics of endoplasmic reticulum stress inducer tunicamycin in the small intestine and liver of
Nrf2 knockout and C57BL/6J mice Toxicol. Lett. 168:21-39, 2007
115. Shachaf, C.M., Gentles, A.J., Elchuri, S., Sahoo, D., Soen, Y., Sharpe, O., Perez, O.D., Chang, M., Mitchel, D.,
Robinson, W.H., Dill, D., Nolan, G.P., Sylvia K. Plevritis, S.K. and Felsher, D.W. Genomic and proteomic analysis
reveals a threshold level of MYC required for tumor maintenance Cancer Res. 68:5132-5142, 2008
116. Knights, C.D, Catania, J., Di Giovanni, S., Muratoglu, S., Perez, R., Swartzbeck, A., Quong, A.A., Zhang, X.,
Beerman, T., Pestell, R.G. and Avantaggiati, M.L. Distinct p53 acetylation cassettes differentially influence
gene-expression patterns and cell fate J. Cell Biol. 173:533-544, 2006
117. Gehling, U.M., Ergun, S., Schumacher, U., Wagener, C., Pantel, K., 0tte, M., Schuch, G., Schafhausen, P.,
Mende, T., Kilic, N., Kluge, K., Schafer, B., Hossfeld, D.K. and Fiedler, W. ln vitro differentiation of endothelial
cells from AC133-positive progenitor cells Blood 95:3106-3112, 2000
118. Yao, C.-L., Chu, I.-M., Hsieh, T.-B. and Hwang, S.-M. A systematic strategy to optimize ex vivo expansion
medium for human hematopoietic stem cells derived from umbilical cord blood mononuclear cells Exp.
Hematol. 32:720-727, 2004
119. Loges, S., Butzal, M., Fischer, U., Gehling, U.M., Hossfeld, D.K. and Fiedler, W. Ex-vivo expansion of
multipotent CD133+stem cells with VEGF, FLT3L and SCGF American Society of Hematology 46th Annual
Meeting, San Diego, December 4-7, 2004 Abstract #4147 Blood 104:123b-124b, 2004
120. Zygmunt, M., Liang, O., Tinneberg, H.R., Preissner, K. and Ball, N. Isolierung, Charakterisierung und
Kultivierung von fetalen Stammzellen aus der Nabelschnur - Rolle der fetalen Faktoren in ihre
Differenzierung Geburtshilfe und Frauenheilkunde 63:H-GM 08, 2003 XVIII. Akademische Tagung
deutschsprechender Hochschullehrer in der Gynaekologie und Geburtshilfe Potsdam 2.-5. Oktober 2003
121. Gunsilius, E., Duba, H.C., Petzer, A.L., Kahler, C.M., Grunewald, K., Stockhammer, G., Gabl, C., Dirnhofer, S.,
Clausen, J. and Gastl, G. Evidence from a leukaemia model for maintenance of vascular endothelium by bone
-marrow-derived endothelial cells Lancet 355:1688-1691, 2000
122. Keller, U., Goetze, K.S., Oostendorp, R., Wimmer, M., von Bubnoff, N., Valina, C. and Peschell, C.
Characterization and expansion of endothelial cells cultured from cord blood, bone marrow and peripheral
blood CD34+ cells Blood 98, 32a; Abstract #127, 2001
123. Gehling, U.M., Guckenbiehl, M., Loges, S., Koester, R., lto, W., Muenzel, T., Hossfeld, D.K. and Fiedler, W. Use
of AC133-derived endothelial progenitor cells for coating of intracoronary stents Onkologie 25(S4), 24:83,
2002
124. Herder, C., Tonn, T., Oostendorp, R., Becker, S., Keller, U., Peschel, C., Grez, M. and Seifried, E. Sustained
expansion and transgene expression of coagulation factor VIII-transduced cord blood-derived endothelial
progenitor cells Arterioscler. Thromb. Vasc. Biol. 23:2266-2272, 2003
125. Lu, X., Chishti, A., Fulton, B., Bullock, R., Batchelor, A., Gascoigne, A., Gillespie, J.I. and Baudouin, S.V.
Circulating endothelial progenitor cells in human sepsis Proceedings of the Intensive Care Society and
Riverside Group 'State of the Art' Meeting, South Bank Centre, London, December 7-8, 2000 Br. J.
Anaesth. 87:333P-334P, 2001
126. Pomyje, J., Schweighofer, B., Muller, H.D., Ruf, W. and Hofer, E. Angiogenesis 16 Hematopoietic progenitor
cells expressing tissue factor support endothelial cell survival and tube formation in vitro Department of
Vascular Biology and Thrombosis Research, Medical University of Vienna, Brunnerstrasse 59, A-1230 Vienna,
Austria Deutsche, Osterreichische und Schweizerische Gesellschaften fur Angiologie, Gemeinsame
Jahrestagung Wien-Hofburg, Kongresszentrum 31. August bis 3. September 2004
127. Ma, N., Ladilov, Y., Moebius, J.M., Ong, L., Piechaczek, C., David, A., Kaminski, A., Choi, Y.-H., Li, W., Egger, D.,
Stamma, C. and Gustav, S. Intramyocardial delivery of human CD133+ cells in a SCID mouse cryoinjury
model: Bone marrow vs. cord blood-derived cells Cardiovasc. Res. 71:158-169, 2006
128. Butzal, M., Loges, S., Schweizer, M., Fischer, U., Gehling, U.M., Hossfeld, D.K. and Fiedler, W. Rapamycin
inhibits proliferation and differentiation of human endothelial progenitor cells in vitro Exp. Cell Res. 300:65-71,
2004
129. Wosnitza, M., Hemmrich, K., Groger, A., GrÄber, S. and Pallua, N. Plasticity of human adipose stem cells to
perform adipogenic and endothelial differentiation Differentiation 75:12-23, 2007
130. Loges, S., Butzal, M., Otten, J., Schweizer, M., Fischer, U., Bokemeyer, C., Hossfeld, D.K., Schuch, G. and
Fiedler, W. Cilengitide inhibits proliferation and differentiation of human endothelial progenitor cells in vitro
Biochem. Biophys. Res. Commun. 357:1016-1020, 2007
131. Kahler, C.M., Wechselberger, J., Hilbe, W., Gschwendtner, A., Colleselli, D., Niederegger, H., Boneberg, E.M.,
Spizzo, G., Wendel, A., Gunsilius, E., Patsch, J.R., and Hamacher, J. Peripheral infusion of rat bone marrow
derived endothelial progenitor cells leads to homing in acute lung injury Respir. Res. 8:50, 2007
132. Ma, F.X., Zhou, B., Chen, Z., Ren, Q., Lu, S.H., Sawamura, T. and Han, Z.C. Oxidized low density lipoprotein
impairs endothelial progenitor cells by regulation of endothelial nitric oxide synthase J. Lipid Res. 47:1227-
1237, 2006
133. Petzer, A.L., Woeginger, A., Wolf, D., Hoflehner, E., Hoelzler, K., Gastl, G. and Gunsilius, E. Individual adult
myelomonocytic and pluripotent hematopoietic progenitors are capable to generate cells of the endothelial
cell lineage Onkologie V154, 26:6, 2003
134. Loges, S., Fehse, B., Brockmann, M.A., Lamszus, K., Butzal, M., Guckenbiehl, M.,Schuch, G., Ergun, S., Fischer,
U., Zander, A.R., Hossfeld, D.K., Fiedler, W. and Gehling, U.M. Identification of the adult human hemangioblast
Stem Cells Dev. 13:229-242, 2004
135. Yuan, Y., Zhang, Y.S., Li, X.S., Guo, Z.K., Liu, X.D., Hou, C.M., Tang, P.X. and Mao, N. Cloning, expression and
purification of human stem cell growth factor cDNA and its species-specificity in hematopoiesis Zhongguo
Shi Yan Xue Ye Xue Za Zhi 14:379-383, 2006
136. Colleselli, D., Bijuklic, K., Mosheimer, B.A. and KÄhler, C.M. Inhibition of cyclooxygenase (COX)-2 affects
endothelial progenitor cell proliferation Exp. Cell Res. 312:2933-2941, 2006
137. Ozaki, Y., Nishimura, M., Sekiya, K., Suehiro, F., Kanawa, M., Nikawa, H., Hamada, T. and Kato, Y.
Comprehensive analysis of chemotactic factors for bone marrow mesenchymal stem cells Stem Cells Dev.
16:119-130, 2007
138. Gehling, U.M., Willems, M., Dandri, M., Petersen, J., Berna, M., Thill, M., Wulf, T., Muller, L., Pollok, J.M.,
Schlagner, K., Faltz, C., Hossfeld, D.K. and Rogiers, X. Partial hepatectomy induces mobilization of a unique
population of haematopoietic progenitor cells in human healthy liver donors J. Hepatol. 43:845-853, 2005
139. Thill, M., Schlagner, K., AltenÄhr, S., ErgÜn, S., Faragher, R.G.A., Kilic, N., Bednarz, J., Vohwinkel, G., Rogiers,
X., Hossfeld, D.K., Richard, G. and Gehling, U.M. A novel population of repair cells identified in the stroma of
the human cornea Stem Cells Dev. 16:733-746, 2007
140. Ochieng, J., Pratap, S., Khatua, A.K. & Sakwe, A.M. Anchorage-independent growth of breast carcinoma
cells is mediated by serum exosomes Exp. Cell Res. 315:1875-1888, 2009
141. Hiraoka, A. Leukemia cell lines require self-secreted stem cell growth factor (SCGF) for their proliferation
Leuk. Res. 32:1623-1625, 2008
142. Holleman, A., Cheok, M.H., den Boer, M.L., Yang, W., Veerman, A.J.P., Kazemier, K.M., Pei, D., Cheng, C., Pui,
C.-H., Relling, M.V., Janka-Schaub, G.E., Pieters, R. and Evans, W.E. Gene-expression patterns in drug-
resistant acute lymphoblastic leukemia cells and response to treatment N. Engl. J. Med. 351:533-542, 2004
143. Haferlach, T., Kohlmann, A., Schnittger, S., Dugas, M., Hiddemann, W., Kern, W. and Schoch, C. Global
approach to the diagnosis of leukemia using gene expression profiling Blood 106:1189-1198, 2005
144. Bhojwani, D., Kang, H., Moskowitz, N.P., Min, D.-J., Lee, H., Potter, J.W., Davidson, G., Willman, C.L., Borowitz,
M.J., Belitskaya-Levy, I., Hunger, S.P., Raetz, E.A. and Carroll, W.L. Biologic pathways associated with relapse
in childhood acute lymphoblastic leukemia: a Children's Oncology Group study Blood 108:711-717, 2006
145. Zuna, J., Burjanivova, T., Mejstrikova, E., Zemanova, Z., Muzikova, K., Meyer, C., Horsley, S.W., Kearney, L.,
Colman, S., Ptoszkova, H., Marschalek, R., Hrusak, O., Stary, J., Greaves, M. and Trka, J. Covert preleukemia
driven by MLL gene fusion Genes Chromosomes Cancer 48:98-107, 2009
146. Rossetti, S., Hoogeveen, A.T., Liang, P., Stanciu, C., van der Spek, P. and Sacchi, N. A distinct epigenetic
signature at targets of a leukemia protein BMC Genomics 8:38, 2007
147. Silveira, V.S., Scrideli, C.A., Moreno, D.A., Yunes, J.A., Brandalise, S.R., Toledo, S., Lee, M.L.M., Petrili, A.S.,
Odoni-Filho, V., Bendit, I. and Tone, L.G. Expression profile analysis of genes related to resistance/sensibility
to prednisolone, daunorubicin, L-asparaginase and vincristine in childhood acute lymphoblastic leukemia
Abstract #3463 Blood 110, 2007
148. Slovak, M.L., Bedell, V., Bobadilla, D., Nowak, N.J., Delioukina, M.L., Weiss, L.M., Smith, D. and Forman, S.J.
Genomic alterations in Hodgkin's and Reed/Sternberg (HRS) cells at disease onset reveals distinct
signatures for chemosensitive and primary refractory Hodgkin's lymphoma Blood 112:1451, 2008
149. Ding, L.-H., Xie, Y., Park, S., Xiao, G. and Story, M.D. Enhanced identification and biological validation of
differential gene expression via Illumina whole-genome expression arrays through the use of the model-
based background correction methodology Nucleic Acids Res. 36:e58, 2008
150. Roepman, P., de Koning, E., van Leenen, D., de Weger, R.A., Kummer, J.A., Slootweg, P.J. and Holstege, F.C.P.
Dissection of a metastatic gene expression signature into distinct components Genome Biol. 7:R117, 2006
151. Levina, V., Marrangoni, A.M., DeMarco, R., Gorelik, E. and Lokshin, A.E. Drug-selected human lung cancer
stem cells: Cytokine network, tumorigenic and metastatic properties PLoS ONE 3:e3077, 2008
152. Waddell, N., Haaf, A.T., Marsh, A., Johnson, J., Walker, L.C., kConFab Investigators, Gongora, M., Brown, M.,
Grover, P., Girolami, M., Grimmond, S., Chenevix-Trench, G. and Spurdle, A.B. BRCA1 and BRCA2 missense
variants of high and low clinical significance influence lymphoblastoid cell line post-irradiation gene expression
PLoS Genetics 4:e1000080, 2008
153. Modena, P., Lualdi, E., Facchinetti, F., Veltman, J., Reid, J.F., Minardi, S., Janssen, I., Giangaspero, F., Forni,
M., Finocchiaro, G., Genitori, L., Giordano, F., Riccardi, R., Schoenmakers, E.F.P.M., Massimino, M. and Sozzi, G.
Identification of tumor-specific molecular signatures in intracranial ependymoma and association with clinical
characteristics J. Clin. Oncol. 24:5223-5233, 2006
154. Staege, M.S., Hutter, C., Neumann, I., Foja, S., Hattenhorst, U.E., Hansen, G., Afar, D. and Burdach, S.E.G.
DNA microarrays reveal relationship of Ewing family tumors to both endothelial and fetal neural crest-
derived cells and define novel targets Cancer Res. 64:8213-8221, 2004
155. Ishikawa, K., Koyama-Saegusa, K., Otsuka, Y., Ishikawa, A., Kawai, S., Yasuda, K., Suga, T., Michikawa, Y.,
Suzuki, M., Iwakawa, M. and Imai, T. Gene expression profile changes correlating with radioresistance in
human cell lines Int. J. Radiat. Oncol. Biol. Physics 65:234-245, 2006
156. Montor, W.R. Use of proteomics and functional genomics to unravel the molecular mechanisms of retinoic
acid as an anti-tumor agent Universidade de SÃo Paulo, Instituto de QuÍmica Data da Defesa 09/03/
2005; Data de PublicaÇÃo 13/04/2007
157. Jimeno, A., Rubio-Viqueira, B., Amador, M.L., Grunwald, V., Maitra, A., Iacobuzio-Donahue, C. and Hidalgo,
M. Dual mitogen-activated protein kinase and epidermal growth factor receptor inhibition in biliary and
pancreatic cancer Mol. Cancer Ther. 6:1079-1088, 2007
158. Yao, R., Yi, Y., Grubbsy, C.J., Lubetz, R.A. and You, M. Gene expression profiling of chemically induced rat
bladder tumors Neoplasia 9:207-221, 2007
159. Taranger, C.K., Noer, A., Sorensen, A.L., HÅkelien, A.-M., Boquest, A.C. and Collas, P. Induction of
dedifferentiation, genomewide transcriptional programming, and epigenetic reprogramming by extracts of
carcinoma and embryonic stem cells Mol. Biol. Cell 16:5719-5735, 2005
160. Mbeunkui, F., Fodstad, O. and Pannell, L.K. Secretory protein enrichment and analysis: An optimized
approach applied on cancer cell lines using 2D LC-MS/MS J. Proteome Res. 5:899-906, 2006
161. Dimas, K., Tsimplouli, C., Anagnostopoulos, A.K., Mahaira, L., Iliopoulou, E., Perez, S., Vougas, K. and
Tsangaris, G.T. The proteome profile of two cell lines and their xenografts isolated from a patient with clear
cell sarcoma (soft tissue melanoma) Cancer Genomics Proteomics 5:175-238, 2008
162. Rappa, G., Fodstad, O. and Lorico, A. The stem cell-associated antigen CD133 (prominin-1) is a molecular
therapeutic target for metastatic melanoma Stem Cells 26:3008-3017, 2008
163. Schmidt, W.M., Kalipciyan, M., Dornstauder, E., Rizovski, B., Steger, G.G., Sedivy, R., Mueller, M.W. and Mader,
R.M. Dissecting progressive stages of 5-fluorouracil resistance in vitro using RNA expression profiling Int. J.
Cancer 112:200-212, 2004
164. Antonescu, C.R., Viale, A., Sarran, L., Tschernyavsky, S.J., Gonen, M., Segal, N.H., Maki, R.G., Socci, N.D.,
DeMatteo, R.P. and Besmer, P. Gene expression in gastrointestinal stromal tumors is distinguished by KIT
genotype and anatomic site Clin. Cancer Res. 10:3282-3290, 2004
165. Galamb, O., Sipos, F., Dinya, E., Spisak, S., Tulassay, Z. and Molnar, B. mRNA expression, functional profiling
and multivariate classification of colon biopsy specimen by cDNA overall glass microarray World J.
Gastroenterol. 12:6998-7006, 2006
166. Jazag, A., Ijichi, H., Kanai, F., Imamura, T., Guleng, B., Ohta, M., Imamura, J., Tanaka, Y., Tateishi, K., Ikenoue,
T., Kawakami, T., Arakawa, Y., Miyagishi, M., Taira, K., Kawabe, T. and Omata, M. Smad4 silencing in pancreatic
cancer cell lines using stable RNA interference and gene expression profiles induced by transforming growth
factor-beta Oncogene 24:662-671, 2005
167. Gashaw, I., Dushaj, O., Behr, R., Biermann, K., Brehm, R., Rubben, H., Grobholz, R., Schmid, K.W., Bergmann,
M. and Winterhager, E. Novel germ cell markers characterize testicular seminoma and fetal testis Mol. Hum.
Reprod. 13:721-727, 2007
168. Gal, H., Amariglio, N., Trakhtenbrot, L., Jacob-Hirsh, J., Margalit, O., Avigdor, A., Nagler, A., Tavor, S., Ein-Dor,
L., Lapidot, T., Domany, E., Rechavi, G. and Givol, D. Gene expression profiles of AML derived stem cells;
similarity to hematopoietic stem cells Leukemia 20:2147-2154, 2006
169. Yocum, A.K., Busch, C.M., Felix, C.A. and Blair, I.A. Proteomics-based strategy to identify biomarkers and
pharmacological targets in leukemias with t(4;11) translocations J. Proteome Res. 5:2743-2753, 2006
170. Nilsson, L., EdÉn, P., Olsson, E., MÅnsson, R.,Åstrand-GrundstrÖm, I., StrÖmbeck, B., Theilgaard-
"Önch, K., Anderson, K., Hast, R., HellstrÖm-Lindberg, E., Samuelsson, J., Bergh, G., Nerlov, C., Johansson,
B., Sigvardsson, M., Borg,Å. and Jacobsen, S.E.W. The molecular signature of MDS stem cells supports a
stem-cell origin of 5q- myelodysplastic syndromes Blood 110:3005-3014, 2007
171. Piquemal, D., Commes, T., Manchon, L., Lejeune, M., Ferraz, C., Pugnere, D., Demaille, J., Elalouf, J.-M. and
Marti, J. Transcriptome analysis of monocytic leukemia cell differentiation Genomics 80:361-371, 2002
172. Liu, L.-R., Yue, J. and Wang, H.-H. Analysis of differential expression proteins of U937 infected with
isoniazid-resistant MTB by two-dimensional electrophoresis Chn. J. Biochem. Mol. Biol. 22:142-150, 2006
173. Bannwarth, S., Giordanengo, V., Josette Lesimple, J. and Lefebvre, J.-C.Molecular cloning of a new
secreted sulfated mucin-like protein with a C-type lectin domain that is expressed in lymphoblastic cells J.
Biol. Chem. 273:1911-1916, 1998
174. Yu, Y., Wang, L.-S., Shen, S.-M., Xia, L., Zhang, L., Zhu, Y.-S. and Chen, G.-Q. Subcellular proteome analysis
of camptothecin analogue NSC606985-treated acute myeloid leukemic cells J. Proteome Res. 6:3808-3818,
2007
175. Keller, C.C., Ouma, C., Ouma, Y., Awandare, G.A., Davenport, G.C., Were,T., Hittner, J.B., Vulule, J.M.,
Ong'echa, J.M. and Perkins, D.J. Suppressionof a novel hematopoietic mediator in children with severe
malarial anemia Infect. Immun. 77:3864-3871, 2009
176. Tsangaris, G.T., Botsonis, A., Politis, I. and Tzortzatou-Stathopoulou, F. Evaluation of cadmium-induced
transcriptome alterations by three color cDNA labeling microarray analysis on a T-cell line Toxicology 178:
135-160, 2002
177. Koyama, N., Zhang, J., Huqun, Miyazawa, H., Tanaka, T., Su, X. and Hagiwara, K. Identification of IGFBP-6 as
an effector of the tumor suppressor activity of SEMA3B Oncogene 27:6581-6589, 2008
178. Narayan, S., Head, S.R., Gilmartin, T.J., Brian Dean, B. and Thomas, E.A. Evidence for disruption of
sphingolipid metabolism in schizophrenia J. Neurosci. Res. 87:278-288, 2009
179. Tay, M.X., Nath, A., Tan, V. and Feng, Z.W. Nuclear factor kappa B transcription profiling of genes protect
against nitric oxide-induced neuronal apoptosis National Healthcare Group Annual Scientific Congress 2004
33 (Suppl):S64
180. Stenzel-Poore,M.P., Stevens, S.L., Xiong, Z., Lessov, N.S., Harrington, C.A., Mori, M., Meller, R., Rosenzweig,
H.L., Tobar, E., Shaw, T.E., Chu, X. and Simon, R.P. Effect of ischaemic preconditioning on genomic response
to cerebral ischaemia: similarity to neuroprotective strategies in hibernation and hypoxia-tolerant states
Lancet 362:1028-1037, 2003
181. SÄrkijÄrvi, S., Kuusisto, H., Paalavuo, R., Levula, M., Airla, N., LehtimÄki, T., Kaprio, J., Koskenvuo, M. and
Elovaara, I. Gene expression profiles in Finnish twins with multiple sclerosis BMC Med. Genet. 7:11, 2006
182. Martino, D.J., Tulic, M.K., Gordon, L., Hodder, M., Richman, T.R., Metcalfe, J., Prescott, S.L. and Saffery, R.
Evidence for age-related and individual-specific changes in DNA methylation profile of mononuclear cells
during early immune development in humans Epigenetics 6:1085-1094, 2011
183. Nishimura, Y., Martin, C.L., Vazquez-Lopez, A., Spence, S.J., Alvarez-Retuerto, A.I., Sigman, M., Steindler, C.,
Pellegrini, S., Schanen, N.C., Warren, S.T. and Geschwind, D.H. Genome-wide expression profiling of
lymphoblastoid cell lines distinguishes different forms of autism and reveals shared pathways Hum. Mol.
Genet. 16:1682-1698, 2007
184. Lee, K.S., Chung, J.H., Lee, K.H., Shin, H.-J., Oh, B.H. and Hong, C.H. Bioplex analysis of plasma cytokines in
Alzheimer's disease and mild cognitive impairment Immunol. Lett. 121:105-109, 2008
185. Biancotto, A., Feng, X., Langweiler, M., Young, N.S. and McCoy, J.P. Effect of anticoagulants on multiplexed
measurement of cytokine/chemokines in healthy subjects Cytokine 60:438-446, 2012
186. Nguyen-Ngoc, K.-V., Cheung, K.J., Brenot, A., Shamir, E.R., Gray, R.S., Hines, W.C., Yaswen, P., Werb, Z. and
Ewald, A.J. ECM microenvironment regulates collective migration and local dissemination in normal and
malignant mammary epithelium Proc. Natl. Acad. Sci. USA 109:E2595-E2604, 2012
187. Gouveia, R., Schaffer, L., Papp, S., Grammel, N., Kandzia, S., Head, S.R., Kleene, R., Schachner, M., Conradt,
H.S. and Costa, J. Expression of glycogenes in differentiating human NT2N neurons. Downregulation of
fucosyltransferase 9 leads to decreased Lewisxlevels and impaired neurite outgrowth Biochim. Biophys.
Acta 1820:2007-2019, 2012
188. Woelfle, U., Cloos, J., Sauter, G., Riethdorf, L., Jaenicke, F., van Diest, P., Brakenhoff, R. and Pantel, K.
Molecular signature associated with bone marrow micrometastasis in human breast cancer Cancer Res. 63:
5679-5684, 2003
189. Provenzani, A., Fronza, R., Loreni, F., Pascale, A., Amadio, M. and Quattrone, A. Global alterations in mRNA
polysomal recruitment in a cell model of colorectal cancer progression to metastasis Carcinogenesis 27:1323-
1333, 2006
190. Loo, L.W.M., Ton, C., Wang, Y.-W., Grove, D.I., Bouzek, H., Vartanian, N., Lin, M.-G., Yuan, X., Lawton, T.L.,
Daling, J.R., Malone, K.E., Li, C.I., Hsu, L. and Porter, P.L. Differential patterns of allelic loss in estrogen
receptor-positive infiltrating lobular and ductal breast cancer Genes Chromosomes Cancer 47:1049-1066,
2008
191. Thirunavukkarasu, M., Addya, S., Juhasz, B., Pant, R., Zhan, L., Surrey, S., Maulik, G., Menon, V.P. and Maulik,
N. Heterozygous disruption of Flk-1 receptor leads to myocardial ischaemia reperfusion injury in mice:
application of affymetrix gene chip analysis J. Cell. Mol. Med. 12:1284-1302, 2008
192. Schirmer, S.H., van Royen, N., Moerland, P.D., Fledderus, J.O., Henriques, J.P., van der Schaaf, R.J., Vis, M.
M., Baan, J., Jr, Koch, K.T., Horrevoets, A.J.G., Hoefer, I.E. & Piek, J.J. Local cytokine concentrations and
oxygen pressure are related to maturation of the collateral circulation in humans J. Am. Coll. Cardiol. 53:
2141-2147, 2009
193. Nakagome, Y., Ueno, Y., Kogure, T., Fukushima, K., Moritoki, Y., Ridgway, W.M., Gershwin, M.E. and
Shimosegawa, T. Autoimmune cholangitis in NOD.c3c4 mice is associated with cholangiocyte-specific Fas
antigen deficiency J. Autoimmun. 29:20-29, 2007
194. Moto, M., Okamura, M., Muto, T., Kashida, Y., Machida, N. and Mistumori, K. Molecular pathological analysis
on the mechanism of liver carcinogenesis in dicyclanil-treated mice Toxicology 207:419-436, 2005
195. Jung, M., Sabat, R., Kratzschmar, J., Seidel, H., Wolk, K., Schonbein, C., Schutt,S., Friedrich, M., Docke, W.-D.,
Asadullah, K., Volk, H.-D. and Grutz, G. Expression profiling of IL-10-regulated genes in human monocytes
and peripheral blood mononuclear cells from psoriatic patients during IL-10 therapy Eur. J. Immunol. 34:481-
493, 2004
196. Tykodi, S.S., Warren, E.H., Thompson, J.A., Riddell, S.R., Childs, R.W., Otterud, B.E., Leppert, M.F., Storb, R.
and Sandmaier, B.M. Allogeneic hematopoietic cell transplantation for metastatic renal cell carcinoma after
nonmyeloablative conditioning: toxicity, clinical response, and immunological response to minor
histocompatibility antigens Clin. Cancer Res. 10:7799-7811, 2004
197. Gajduskova, P., Snijders, A.M., Kwek, S., Roydasgupta, R., Fridlyand, J., Tokuyasu, T., Pinkel, D. and
Albertson, D.G. Genome position and gene amplification Genome Biol. 8:R120, 2007
198. Elshatory, Y., Brooks, A.I., Chattopadhyay, S., Curran, T.M., Gupta, P., Ramalingam, V., Hofmann, S.L. and
Pearce, D.A. Early changes in gene expression in two models of Batten disease FEBS Lett. 538:207-212, 2003
199. Skubitz, K.M. and Skubitz, A.P.N. Gene expression in aggressive fibromatosis J. Lab. Clin. Med. 143:89-98,
2004
200. Ma, X.-H., Hu, S.-J., Ni, H., Zhao, Y.-C., Tian, Z., Liu, J.-L., Ren, G., Liang, X.-H., Yu, H., Wan, P. & Yang, Z.-M.
Serial analysis of gene expression in mouse uterus at the implantation site J. Biol. Chem. 281:9351-9360,
2006
201. Way, K.J., Dinh, H., Keene, M.R., White, K.E., Clanchy, F.I.L., Lusby, P., Roiniotis, J., Cook, A.D., Cassady, A.I.,
Curtis, D.J. & Hamilton, J.A. The generation and properties of human macrophage populations from
hemopoietic stem cells J. Leukoc. Biol. 85:766-778, 2009
202. Sohn, S.-H., Ko, E., Jeon, S.-B., Lee, B.-J., Kim, S.-H., Dong, M.-S., Lee, D.-U., Kwak, J.-H., Kim, Y., Shin, M.,
Hong, M. & Bae, H. The genome-wide expression profile of Scrophularia ningpoensis-treated thapsigargin-
stimulated U-87MG cells NeuroToxicology 30:368-376, 2009
203. Lan, C.-C.E., Ko, Y.-C., Tu, H.-P., Wu, C.-S., Lee, C.-H., Wu, C.-S. & Yu, H.-S. Association study between
keratinocyte-derived growth factor gene polymorphisms and susceptibility to vitiligo vulgaris in a Taiwanese
population: potential involvement of stem cell factor Br. J. Dermatol. 160:1180-1187, 2009
204. Gundacker, N.C., Haudek, V.J., Wimmer, H., Slany, A., Griss, J., Bochkov, V., Zielinski, C., Wagner, O.,
StÖckl, J. and Gerner, C. Cytoplasmic proteome and secretome profiles of differently stimulated human
dendritic cells J. Proteome Res. 8:2799-2811, 2009
205. Ermonval, M., Petit, D., Le Duc, A., Odile Kellermann, O. and Gallet, P.-F. Glycosylation-related genes are
variably expressed depending on the differentiation state of a bioaminergic neuronal cell line: implication for
the cellular prion protein Glycoconj. J. 26:477-493, 2009
206. Drach, J., Slany, A., Mohr, T., Griss, J., Zielinski, C.C. and Gerner, C. Secretome analyses of primary bone
marrow fibroblasts isolated from MGUS and multiple myeloma show a stepwise occurrence of alterations
Poster Board I-827Blood (ASH Annual Meeting Abstracts) 114:1801, 2009
207. Langer, C., Marcucci, G., Holland, K.B., Radmacher, M.D., Maharry, K., Paschka, P., Whitman, S.P., MrÓzek,
K., Baldus, C.D., Vij, R., Powell, B.L., Carroll, A.J., Kolitz, J.E., Caligiuri, M.A., Larson, R.A. and Bloomfield, C.D.
Prognostic importance of MN1 transcript levels, and biologic insights from MN1-associated gene and
microRNA expression signatures in cytogenetically normal acute myeloid leukemia: A cancer and leukemia
group B study J. Clin. Oncol. 27:3198-3204, 2009
208. Gupta, P.B., Onder, T.T., Jiang, G., Tao, K., Kuperwasser, C., Weinberg, R.A. and Lander, E.S. Identification of
selective inhibitors of cancer stem cells by high-throughput screening Cell 138:645-659, 2009
209. Paic, F., Igwe, J.C., Nori, R., Kronenberg, M.S., Franceschetti, T., Harrington, P., Kuo, L., Shin, D.-G., Rowe, D.
W., Harris, S.E. and Kalajzic, I. Identificationof differentially expressed genes between osteoblasts and
osteocytes Bone 45:682-692, 2009
210. Meade, M.L., Shiyanov, P. and Schlager, J.J. Enhanced detection method for corneal protein identification
using shotgun proteomics Proteome Sci. 7:23, 2009
211. Rush, C., Nyara, M., Moxon, J.V., Trollope, A., Cullen, B. and Golledge, J. Whole genome expression analysis
within the angiotensin II-apolipoprotein E deficient mouse model of abdominal aortic aneurysm BMC
Genomics 10:298, 2009
212. Scotton, C.J., Krupiczojc, M.A., KÖnigshoff, M., Mercer, P.F., Lee, Y.C.G., Kaminski, N., Morser, J., Post, J.M.,
Maher, T.M., Nicholson, A.G., Moffatt, J.D., Laurent, G.J., Derian, C.K., Eickelberg, O. and Chambers, R.C.
Increased local expression of coagulation factor X contributes to the fibrotic response in human and murine
lung injury J. Clin. Invest. 119:2550-2563, 2009
213. Cellai, C., Laurenzana, A., Bianchi, E., Sdelci, S., Manfredini, R., Vannucchi, A.M., Caporale, R., Balliu, M.,
Mannelli, F., Ferrari, S., Bosi, A., Miniati, D., Cocco, P.L., Veronneau, S., Stankova, J. and Paoletti, F.
Mechanistic insight into WEB-2170-induced apoptosis in human acute myelogenous leukemia cells: The
crucial role of PTEN Exp. Hematol. 37:1176-1185, 2009
214. Lee, K.S., Chung, J.H., Lee, K.H., Shin, M.-J., Oh, B.H., Lee, S.H. and Hong, C.H. Simultaneous measurement
of 23 plasma cytokines in late-life depression Neurol. Sci. 30:435-438, 2009
215. Gnana-Prakasam, J.P., Thangaraju, M., Liu, K., Ha, Y., Martin, P.M., Smith, S.B. and Ganapathy, V. Absence
of iron-regulatory protein Hfe results in hyperproliferation of retinal pigment epithelium: role of cystine/
glutamate exchanger Biochem. J. 424:243-252, 2009
216. Janot, M., Audfray, A., Loriol, C., Germot, A., Maftah, A. and Dupuy, F. Glycogenome expression dynamics
during mouse C2C12 myoblast differentiation suggests a sequential reorganization of membrane
glycoconjugates BMC Genomics 10:483, 2009
217. Annicotte, J.-S., Blanchet, E., Chavey, C., Iankova, I., Costes, S., Assou, S., Teyssier, J., Dalle, S., Sardet, C.
and Fajas, L. The CDK4-pRB-E2F1 pathway controls insulin secretion Nat. Cell Biol. 11:1017-1023, 2009
218. Thiollier, C., Lopez, C.K., Gerby, B., Ignacimouttou, C., Poglio, S., Duffourd, Y., GuÉgan, J., Rivera-Munoz, P.,
Bluteau, O., Mabialah, V., Diop, M., Wen, Q., Petit, A., Bauchet, A.-L., Reinhardt, D., Bornhauser, B., Gautheret,
D., Lecluse, Y., Landman-Parker, J., Radford, I., Vainchenker, W., Dastugue, N., de Botton, S., Dessen, P.,
Bourquin, J.-P., Crispino, J.D., Ballerini, P., Bernard, O.A., Pflumio, F. and Mercher, T. Characterization of
novel genomic alterations and therapeutic approaches using acute megakaryoblastic leukemia xenograft
models J. Exp. Med. 209:2017-2031, 2012
219. Van Loo, P., Aerts, S.,Thienpont, B., De Moor, B., Moreau, Y. and Marynen, P. ModuleMiner-improved
computational detection of cis-regulatory modules: are there different modes of gene regulation in
embryonic development and adult tissues? Genome Biol. 9:R66, 2008
220. Bridges, R.S., Kass, D., Loh, K., Glackin, C., Borczuk, A.C. and Greenberg, S. Gene expression profiling of
pulmonary fibrosis identifies Twist1 as an antiapoptotic molecular "rectifier" of growth factor signaling Am. J.
Pathol. 175:2351-2361, 2009
221. Ouma, C., Keller, C.C., Davenport, G.C., Were, T., Konah, S., Otieno, M.F., Hittner, J.B., Vulule, J.M., Martinson,
J., Ong'echa, J.M., Ferrell, R.E. and Perkins, D.J. A novel functional variant in the stem cell growth factor
promoter protects against severe malarial anemia Infect. Immun. 78:453-460, 2010
222. Rice, K.L., Hormaeche, I., Doulatov, S., Flatow, J.M., Grimwade, D., Mills, K.I., Leiva, M., Ablain, J., Ambardekar,
C., McConnell, M.J., Dick, J.E. and Licht, J.D. Comprehensive genomic screens identify a rolefor PLZF-RARΑ
as a positive regulator of cell proliferation via direct regulation of c-MYC Blood 114:5499-5511, 2009
223. Ostroff, R., Foreman, T., Keeney, T.R., Stratford, S., Walker, J.J. and Zichi, D. The stability of the circulating
human proteome to variations in sample collection and handling procedures measured with an aptamer-
based proteomics array J. Proteomics 73:649-666, 2010
224. Kamath, M.B., Houston, I.B., Janovski, A.J., Zhu, X., Gowrisankar, S., Jegga, A.G. and DeKoter, R.P. Dose-
dependent repression of T-cell and natural killer cell genes by PU.1 enforces myeloid and B-cell identity
Leukemia 22:1214-1225, 2008
225. Park, S.-H., Cheung, L.W.T., Wong, A.S.T. and Leung, P.C.K. Estrogen regulates Snail and Slug in the down-
regulation of E-cadherin and induces metastatic potential of ovarian cancer cells through estrogen receptor
ΑMol. Endocrinol. 22:2085-2098, 2008
226. Idaghdour, Y., Czika, W., Shianna, K.V., Lee, S.H., Visscher, P.M., Martin, H.C., Miclaus, K., Jadallah, S.J.,
Goldstein, D.B., Wolfinger, R.D. and Gibson, G. Geographical genomics of human leukocyte gene expression
variation in southern Morocco Nat. Genet. 42:62-67, 2010
227. BÄr, A., Dorfman, S.E., Fischer, P., Hilfiker-Kleiner, D., Cebotari, S., Tudorache, I., Suprunov, M., Haverich, A.
and Hilfiker, A. The pro-angiogenic factor CCN1 enhances the re-endothelialization of biological vascularized
matricesin vitroCardiovasc. Res. 85:806-813, 2010
228. Fernandes, H., Dechering, K., Van Someren, E., Steeghs, I., Apotheker, M., Leusink, A., Bank, R., Janeczek, K.,
Van Blitterswijk, C. and de Boer, J. The role of collagen crosslinking in differentiation of human mesenchymal
stem cells and MC3T3-E1 cells Tissue Eng. Pt. A 15:3857-3867, 2009
229. Stevens, A.L., Wishnok, J.S., White, F.M., Grodzinsky, A.J. and Tannenbaum, S.R. Mechanical injury and
cytokines cause lossof cartilage integrity and upregulate proteins associated with catabolism, immunity,
inflammation, and repair Mol. Cell. Proteomics 8:1475-1489, 2009
230. Verhaak, R.G.W., Wouters, B.J., Erpelinck, C.A.J., Abbas, S., Beverloo, H.B., Lugthart, S., LÖwenberg, B.,
Delwel, R. and Valk, P.J.M. Prediction of molecular subtypes in acute myeloid leukemia based on gene
expression profiling Haematologica 94:131-134, 2009
231. Kopetz, S., Hoff, P.M., Morris, J.S., Wolff, R.A., Eng, C., Glover, K.Y., Adinin, R., Overman, M.J., Valero, V., Wen,
S., Lieu, C., Yan, S., Tran, H.T., Ellis, L.M., Abbruzzese, J.L. and Heymach, J.V. Phase II trial of infusional
fluorouracil, irinotecan, and bevacizumab for metastatic colorectal cancer: Efficacy and circulating
angiogenic biomarkers associated with therapeutic resistance J. Clin. Oncol. 28:453-459, 2010
232. Sagaert, X., Tousseyn, T., Vanhentenrijk, V., Van Loo, P., Baens, M., Marynen, P., DeHertogh, G., Geboes, K.
and De Wolf-Peeters, C. Comparative expressed sequence hybridization studies of t(11;18)(q21;q21)-positive
and -negative gastric MALT lymphomas reveal both unique and overlapping gene programs Modern Pathol.
23:458-469, 2010
233. Han, J., Yuan, P., Yang, H., Zhang, J., Soh, B.S., Li, P., Lim, S.L., Cao, S., Tay, J., Orlov, Y.L., Lufkin, T., Ng, H.-
H., Tam, W.-L. and Lim, B. Tbx3 improves the germ-line competency of induced pluripotent stem cells Nature
463:1096-1100, 2010
234. Charest-Marcotte, A., Dufour, C.R., Wilson, B.J., Tremblay, A.M., Eichner, L.J., Arlow, D.H., Mootha, V.K. and
GiguÈre, V. The homeobox protein Prox1 is a negative modulator of ERRΑ/PGC-1Αbioenergetic functions
Genes Dev. 24(6):537-542, 2010
235. Franco, H.L., Lee, K.Y., Broaddus, R.R., White, L.D., Lanske, B., Lydon, J.P., Jeong, J.-W. and DeMayo, F.J.
Ablation of indian hedgehog in the murine uterus results in decreased cell cycle progression, aberrant
epidermal growth factor signaling, and increased estrogen signaling Biol. Reprod. 82:783-790, 2010
236. Nikolinakos, P.G., Altorki, N., Yankelevitz, D., Tran, H.T., Yan, S., Rajagopalan, D., Bordogna, W., Ottesen, L.H.
and Heymach, J.V. Plasma cytokine and angiogenic factor profiling identifies markers associated with tumor
shrinkage in early-stage non-small cell lung cancer patients treated with pazopanib Cancer Res. 70:2171-
2179, 2010
237. Lottaz, C., Beier, D., Meyer, K., Kumar, P., Hermann, A., Schwarz, J., Junker, M., Oefner, P.J., Bogdahn, U.,
Wischhusen, J., Spang, R., Storch, A. and Beier, C.P. Transcriptional profiles of CD133+and CD133-
glioblastoma-derived cancer stem cell lines suggest different cells of origin Cancer Res. 70:2030-2040, 2010
238. Berger, M.F., Levin, J.Z., Vijayendran, K., Sivachenko, A., Adiconis, X., Maguire, J., Johnson, L.A., Robinson, J.,
Verhaak, R.G., Sougnez, C., Onofrio, R.C., Ziaugra, L., Cibulskis, K., Laine, E., Barretina, J., Winckler, W., Fisher,
D.E., Getz, G., Meyerson, M., Jaffe, D.B., Gabriel, S.B., Lander, E.S., Dummer, R., Gnirke, A., Nusbaum, C. and
Garraway, L.A. Integrative analysis of the melanoma transcriptome Genome Res. 20:413-427, 2010
239. Pitteri, S.J., Faca, V.M., Kelly-Spratt, K.S., Kasarda, A.E., Wang, H., Zhang, Q., Newcomb, L., Krasnoselsky, A.,
Paczesny, S., Choi, G., Fitzgibbon, M., McIntosh, M.W., Kemp, C.J. and Hanash, S.M. Plasma proteome profiling
of a mouse model of breast cancer identifies a set of up-regulated proteins in common with human breast
cancer cells J. Proteome Res. 7:1481-1489, 2008
240. Paun, A.., Lemay, A.-M. and Haston, C.K. Gene expression profiling distinguishes radiation-induced fibrosing
alveolitis from alveolitis in mice Radiat. Res. 173:512-521, 2010
241. Mutsuga, N., Shahar, T., Verbalis, J.G., Brownstein, M.J., Xiang, C.C., Bonner, R.F. and Gainer, H. Selective
gene expression in magnocellular neurons in rat supraoptic nucleus J. Neurosci. 24:7174-7185, 2004
242. Poplawski, A.B., Jankowski, M., Erickson, S.W., de StÅhl, T.D., Partridge, E.C., Crasto, C., Guo, J., Gibson, J.,
Menzel, U., Bruder, C.E.G., Kaczmarczyk, A., Benetkiewicz, M., Andersson, R., Sandgren, J., Zegarska, B., Bala,
D., Srutek, E., Allison, D.B., Piotrowski, A., Zegarski, W. and Dumanski, J.P. Frequent genetic differences
between matched primary and metastatic breast cancer provide an approach to identification of biomarkers
for disease progression Eur. J. Human Genet. 18:560-568, 2010
243. Miettinen, J.J., Matikainen, S. and Nyman, T.A. Global secretome characterization of herpes simplex virus 1-
infected human primary macrophages J. Virol. 86:12770-12778, 2012
244. Penolazzi, L., Tavanti, E., Vecchiatini, R., Lambertini, E., Vesce, F., Gambari, R., Mazzitelli, S., Mancuso, F.,
Luca, G., Nastruzzi, C. and Piva, R. Encapsulation of mesenchymal stem cells from Wharton's jelly in alginate
microbeads Tissue Eng. Pt. C 16:141-155, 2010
245. Gu, L., Dagvadorj, A., Lutz, J., Leiby, B., Bonuccelli, G., Lisanti, M.P., Addya, S., Fortina, P., Dasgupta, A.,
Hyslop, T., Bubendorf, L. and Nevalainen, M.T. Transcription factor stat3 stimulates metastatic behavior of
human prostate cancer cells in vivo, whereas stat5b has a preferential role in the promotion of prostate
cancer cell viability and tumor growth Am. J. Pathol. 176:1959-1972, 2010
246. Matteucci, C., Minutolo, A., Sinibaldi-Vallebona, P., Palamara, A.T., Rasi, G., Mastino, A. and Garaci, E.
Transcription profile of human lymphocytes following in vitro treatment with thymosin alpha-1 Ann. N. Y.
Acad. Sci. 1194:6-19, 2010
247. Fortier, J.M., Payton, J.E., Cahan, P., Ley, T.J., Walter, M.J. and Graubert, T.A. POU4F1 is associated with
t(8;21) acute myeloid leukemia and contributes directly to its unique transcriptional signature Leukemia 24:
950-957, 2010
248. Sims-Lucas, S., Young, R.J., Martinez, G., Taylor, D., Grimmond, S.M.,Teasdale, R., Little, M.H., Bertram, J.F.
and Caruana, G. Redirection of renal mesenchyme to stromal and chondrocytic fates in the presence of TGF
"Β2 Differentiation 79:272-284, 2010
249. Aryee, D.N.T., Niedan, S., Kauer, M., Schwentner, R., Bennani-Baiti, I.M., Ban, J., Muehlbacher, K., Kreppel, M.,
Walker, R.L., Meltzer, P., Poremba, C., Kofler, R. and Kovar, H. Hypoxia modulates EWS-FLI1 transcriptional
signature and enhances the malignant properties of Ewing's sarcoma cells in vitro Cancer Res. 70:4015-4023,
2010
250. Kawazu, M., Yamamoto, G., Yoshimi, M., Yamamoto, K., Asai, T., Ichikawa, M., Seo, S., Nakagawa, M., Chiba, S.,
Kurokawa, M. and Ogawa, S. Expression profiling of immature thymocytes revealed a novel homeobox gene
that regulates double-negative thymocyte development J. Immunol. 179:5335-5345, 2007
251. LÓpez-Boado, Y.S., Li, J.U., Clayton, C.L., Wright, J.L. and Churg, A. Modification of the rat airway explant
transcriptome by cigarette smoke Inhalat. Toxicol. 22:234-244, 2010
252. Choi, Y.-A., Lim, J., Kim, K.M., Acharya, B., Cho, J.-Y., Bae, Y.-C., Shin, H.-I., Kim, S.-Y. and Park, E.K.
Secretome analysis of human BMSCs and identification of SMOC1 as an important ECM protein in
osteoblast differentiation J. Proteome Res. 9:2946-2956, 2010
253. He, K., Zhao, H., Wang, Q. and Pan, Y. A comparative genome analysis of gene expression reveals different
regulatory mechanisms between mouse and human embryo pre-implantation development Reprod. Biol.
Endocrinol. 8:41, 2010
254. Asselin-Labat, M.-L., Vaillant, F., Sheridan, J.M., Pal, B., Wu, D., Simpson, E.R., Yasuda, H., Smyth, G.K.,
Martin, T.J., Lindeman, G.J. and Visvader, J.E. Control of mammary stem cell function by steroid hormone
signalling Nautre 465:798-802, 2010
255. Wu, C.-C., Hsu, C.-W., Chen, C.-D., Yu, C.-J., Chang, K.-P., Tai, D.-I., Liu, H.-P., Su, W.-H., Chang, Y.-S. and
Yu, J.-S. Candidate serological biomarkers for cancer identified from the secretomes of 23 cancer cell lines
and the human protein atlas Mol. Cell. Proteomics 9:1100-1117, 2010
256. Cheung, I., Shulha, H.P., Jianga, Y., Matevossian, A., Wang, J., Weng, Z. and Akbarian, S Developmental
regulation and individual differences of neuronal H3K4me3 epigenomes in the prefrontal cortex Proc. Natl.
Acad. Sci. USA 107:8824-8829, 2010
257. Xia, M., Chen, Y., Wang, L.-C., Zandi, E., Yang, H., Bemanian, S., MartÍnez-Chantar, M.L., Mato, J.M. and Lu,
S.C. Novel function and intracellular localization of methionine adenosyltransferase 2Βsplicing variants J.
Biol. Chem. 285:20015-20021, 2010
258. Sainaghi, P.P., Collimedaglia, L., Alciato, F., Leone, M.A., Naldi, P., Molinari, R., Monaco, F. and Avanzi, G.C.
The expression pattern of inflammatory mediators in cerebrospinal fluid differentiates Guillain-BarrÉ
syndrome from chronic inflammatory demyelinating polyneuropathy Cytokine 51:138-143, 2010
259. Carolan, B.J., Harvey, B.-G., De, B.P., Vanni, H. and Crystal, R.G. Decreased expression of intelectin 1 in the
human airway epithelium of smokers compared to nonsmokers J. Immunol. 181:5760-5767, 2008
260. Capulli, M., Rufo, A., Teti, A. and Rucci, N. Global transcriptome analysis in mouse calvarial osteoblasts
highlights sets of genes regulated by modeled microgravity and identifies a "mechanoresponsive osteoblast
gene signature" J. Cell. Biochem. 107:240-252, 2009
261. Caron, C., Lestrat, C., Marsal, S., Escoffier, E., Curtet, S., Virolle, V., Barbry, P., Debernardi, A., Brambilla, C.,
Brambilla, E., Rousseaux, S. and Khochbin, S. Functional characterization of ATAD2 as a new cancer/testis
factor and a predictor of poor prognosis in breast and lung cancers Oncogene 29:5171-5181, 2010
262. LÓpez-Huertas, M.R., Callejas, S., Abia, D., Mateos, E., Dopazo, A., AlcamÍ, J. and Coiras, M. Modifications
in host cell cytoskeleton structure and function mediated by intracellular HIV-1 Tat protein are greatly
dependent on the second coding exon Nucleic Acids Res. 38:3287-3307, 2010
263. Mehra, S., Pahar, B., Dutta, N.K., Conerly, C.N., Philippi-Falkenstein, K., Alvarez, X. and Kausha, D.
Transcriptional reprogramming in nonhuman primate (rhesus macaque) tuberculosis granulomas PLoS ONE 5:
e12266, 2010
264. Tauber, S., Jais, A., Jeitler, M., Haider, S., Husa, J., Lindroos, J., KnÖfler, M., Mayerhofer, M., Pehamberger,
H., Wagner, O. and Bilban, M. Transcriptome analysis of human cancer reveals a functional role of heme
oxygenase-1 in tumor cell adhesion Mol. Cancer 9:200, 2010
265. Sordi, V., Melzi, R., Mercalli, A., Formicola, R., Doglioni, C., Tiboni, F., Ferrari, G., Nano, R., Chwalek, K.,
Lammert, E., Bonfacio, E. and Piemonti, L. Mesenchymal cells appearing in pancreatic tissue culture are bone
marrow-derived stem cells with the capacity to improve transplanted islet function Stem Cells 28:140-151,
2010
266. Van der Auwera, I., Yu, W., Suo, L., van Neste, L., van Dam, P., van Marck, E.A., Pauwels, P., Vermeulen, P.B.,
Dirix, L.Y. and van Laere, S.J. Array-based DNA methylation profiling for breast cancer subtype
discrimination PLoS ONE 5:e12616, 2010
267. Parker, A.M., Shang, H., Khurgel, M. and Katz, A.J. Low serum and serum-free culture of multipotential
human adipose stem cells Cytotherapy 9:637-646, 2007
268. Amos, P.J., Kapur, S.K., Stapor, P.C., Shang, H., Bekiranov, S., Khurgel, M., Rodeheaver, G.T., Peirce, S.M.
and Katz, A.J. Human adipose-derived stromal cells accelerate diabetic wound healing: Impact of cell
formulation and delivery Tissue Eng. Pt A 16:1595-1606, 2010
269. Assaad, A.M., Kawut, S.M., Arcasoy, S.M., Rosenzweig, E.B., Wilt, J.S., Sonett, J.R. and Borczuk, A.C.
Platelet-derived growth factor is increased in pulmonary capillary hemangiomatosis Chest 131:850-855,
2007
270. Nishino, K., Toyoda, M., Yamazaki-Inoue, M., Makino, H., Fukawatase, Y., Chikazawa, E., Takahashi, Y.,
Miyagawa, Y., Okita, H., Kiyokawa, N., Akutsu, H. and Umezawa, A. Defining hypo-methylated regions of stem
cell-specific promoters in human iPS cells derived from extra-embryonic amnions and lung fibroblasts PLoS
ONE 5:e13017, 2010
271. Eyster, K.M., Hansen, K.A., Winterton, E., Klinkova, O., Drappeau, D. and Mark-Kappeler, C.J. Reciprocal
communication between endometrial stromal cells and macrophages Reprod. Sci. 17:809-822, 2010
272. Wauquier, N., Becquart, P., Padilla, C., Baize, S. and Leroy, E.M. Human fatal Zaire ebola virus infection is
associated with an aberrant innate immunity and with massive lymphocyte apoptosis PLoS Negl. Trop. Dis. 4:
e837, 2010
273. Smura, T., Ylipaasto, P., Klemola, P., Kaijalainen, S., Kyllonen, L., Sordi, V., Piemonti, L. and Roivainen, M.
Cellular tropism of human enterovirus D species serotypes EV-94, EV-70, and EV-68 in vitro: Implications
for pathogenesis J. Med. Virol. 82:1940-1949, 2010
274. Kim, J., Woo, A.J., Chu, J., Snow, J.W., Fujiwara, Y., Kim, C.G., Cantor, A.B. and Orkin, S.H. A myc network
accounts for similarities between embryonic stem and cancer cell transcription programs Cell 143:313-324,
2010
275. Chittur, S.V., Sangster-Guity, N. and McCormick, P.J. Histone deacetylase inhibitors: A new mode for
inhibition of cholesterol metabolism BMC Genomics 9:507, 2008
276. Korf-Klingebiel, M., Kempf, T., Sauer, T., Brinkmann, E., Fischer, P., Meyer, G.P., Ganser, A., Drexler, H. and
Wollert, K.C. Bone marrow cells are a rich source of growth factors and cytokines: Implications for cell
therapy trials after myocardial infarction Eur. Heart J. 29:2851-2858, 2008
277. SØrensen, A.L., Jacobsen, B.M., Reiner, A.H., Andersen, I.S. and Collas, P. Promoter DNA methylation
patterns of differentiated cells are largely programmed at the progenitor stage Mol. Biol. Cell 21:2066-2077,
2010
278. Boeva, V., Surdez, D., Guillon, N., Tirode, F., Fejes, A.P., Delattre, O. and Barillot, E. De novo motif
identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data
analysis Nucleic Acids Res. 38:e126, 2010
279. Yixuan, Y., Kiat, L.S., Yee, C.L., Huiyin, L., Yunhao, C., Kuan, C.P., Hassan, A., Ting, W.T., Manuel, S.-T., Guan,
Y.K. and Pin, L.Y. Cathepsin S mediates gastric cancer cell migration and invasion via a putative network of
metastasis-associated proteins J. Proteome Res. 9:4767-4778, 2010
280. Sen, G.L., Reuter, J.A., Webster, D.E., Zhu, L.Z. and Khavari, P.A. DNMT1 maintains progenitor function in self
-renewing somatic tissue Nature 463:563-567, 2010
281. Bienvenu, F., Jirawatnotai, S., Elias, J.E., Meyer, C.A., Mizeracka, K., Marson, A., Frampton, G.M., Cole, M.F.,
Odom, D.T., Odajima, J., Geng, Y., Zagozdzon, A., Jecrois, M., Young, R.A., Liu, X.S., Cepko, C.L., Gygi, S.P. and
Sicinski, P. Transcriptional role of cyclin D1 in development revealed by a genetic-proteomic screen Nature
463:374-378, 2010
282. Bousette, N., Chugh, S., Fong, V., Isserlin, R., Kim, K.-H., Volchuk, A., Backx, P.H., Liu, P., Kislinger, T.,
MacLennan, D.H., Emili, A. and Gramolini, A.O. Constitutively active calcineurin induces cardiac endoplasmic
reticulum stress and protects against apoptosis that is mediated byΑ-crystallin-B Proc. Natl. Acad. Sci.
USA 107:18481-18486, 2010
283. Marshall, G.M., Gherardi, S., Xu, N., Neiron, Z., Trahair, T., Scarlett, C.J., Chang, D.K., Liu, P.Y., Jankowski, K.,
Iraci, N., Haber, M., Norris, M.D., Keating, J., Sekyere, E., Jonquieres, G., Stossi, F., Katzenellenbogen, B.S.,
Biankin,A.V., Perini, G. and Liu, T. Transcriptional upregulation of histone deacetylase 2 promotes Myc-
induced oncogenic effects Oncogene 29:5957-5968, 2010
284. Ji, H., Ehrlich, L.I.R., Seita, J., Murakami, P., Doi, A., Lindau, P., Lee, H., Aryee, M.J., Irizarry, R.A., Kim, K.,
Rossi, D.J., Inlay, M.A., Serwold, T., Karsunky, H., Ho, L., Daley, G.Q., Weissman, I.L. and Feinberg, A.P.
Comprehensive methylome map of lineage commitment from haematopoietic progenitors Nature 467:338-342,
2010
285. Chia, N.-Y., Chan, Y.-S., Feng, B., Lu, X., Orlov,Y.L., Moreau, D., Kumar, P., Yang, L., Jiang, J., Lau, M.-S.,
Huss, M., Soh, B.-S., Kraus, P., Li, P., Lufkin, T., Lim, B., Clarke, N.D., Bard, F. and Ng, H.-H. A genome-wide
RNAi screen reveals determinants of human embryonic stem cell identity Nature 468:316-320, 2010
286. Alachkar, N., Ugarte, R., Huang, E., Womer, K.L., Montgomery, R., Kraus, E. and Rabb, H. Stem cell factor,
interleukin-16, and interleukin-2 receptor alpha are predictive biomarkers for delayed and slow graft function
Transplant. Proc. 42:3399-3405, 2010
287. Kim, H., Watkinson, J., Varadan, V. and Anastassiou, D. Multi-cancer computational analysis reveals invasion-
associated variant of desmoplastic reaction involving INHBA, THBS2 and COL11A1 BMC Med. Genomics 3:
51, 2010
288. Lu, X., Baudouin, S.V., Gillespie, J.I., Anderson, J.J. and Dickinson, A.M. A comparison of CFU-GM, BFU-E
and endothelial progenitor cells using ex vivoexpansion of selected cord blood CD133+and CD34+cells
Cytotherapy 9:292-300, 2007
289. Yin, H., Li, J., Xiong, K., Wang, L., Wang, T., Tan, Q., Fu, J., Ren, X. and Zeng, H. Novel mechanism of ethaselen
in poorly differentiated colorectal RKO cell growth inhibition: Simultaneous regulation of TrxR transcription,
expression and enzyme activity Differentiation 81:49-56, 2011
290. Fei, T., Xia, K., Li, Z., Zhou, B., Zhu, S., Chen, H., Zhang, J., Chen, Z., Xiao, H., Han, J.-D.J. and Chen, Y.-G.
Genome-wide mapping of SMAD target genes reveals the role of BMP signaling in embryonic stem cell fate
determination Genome Res. 20:36-44, 2010
291. Fei, T., Zhu, S., Xia, K., Zhang, J., Li, Z., Han, J.-D.J. and Chen, Y.-G. Smad2 mediates Activin/Nodal signaling
in mesendoderm differentiation of mouse embryonic stem cells Cell Res. 20:1306-1318, 2010
292. Renthal, N.E., Chen, C.-C., Williams, K.C., Gerard, R.D., Prange-Kiel, J. and Mendelson, C.R. miR-200 family
and targets, ZEB1 and ZEB2, modulate uterine quiescence and contractility during pregnancy and labor
Proc. Natl. Acad. Sci. USA 107:20828-20833, 2010
293. Carlini, F., Ridolfi, B., Molinari, A., Parisi, C., Bozzuto, G., Toccacieli, L., Formisano, G., De Orsi, D., Paradisi, S.,
Grober, O.M.V., Ravo, M., Weisz, A., Arcieri, R., Vella, S. and Gaudi, S. The reverse transcription inhibitor
abacavir shows anticancer activity in prostate cancer cell lines PLoS ONE 5:e14221, 2010
294. Shimizu, T., Krebs, S., Bauersachs, S., Blum, H., Wolf, E. and Miyamoto, A. Actions and interactions of
progesterone and estrogen on transcriptome profiles of the bovine endometrium Physiol. Genomics 42A:290-
300, 2010
295. Becquart, P., Wauquier, N., Nkoghe, D., Ndjoyi-Mbiguino, A., Padilla, C., Souris, M. and Leroy, E.M. Acute
dengue virus 2 infection in Gabonese patients is associated with an early innate immune response, including
strong interferon alpha production BMC Infect. Dis. 10:356, 2010
296. Agirre, X., JimÉnez-Velasco, A., JosÉ-EnÉriz, E.S., Garate, L., BandrÉs, E., Cordeu, L., Aparicio, O., Saez,
B., Navarro, G., Vilas-Zornoza, A., PÉrez-Roger, I., GarcÍa-Foncillas, J., Torres, A., Heiniger, A., Calasanz, M.
J., Fortes, P., RomÁn-GÓmez, J. and PrÓsper, F. Down-regulation of hsa-miR-10a in chronic myeloid
leukemia CD34+cells increases USF2-mediated cell growth Mol. Cancer Res. 6:1830-1840, 2008
297. Barsotti, M.C., Magera, A., Armani, C., Chiellini, F., Felice, F., Dinucci, D., Piras, A.M., Minnocci, A., Solaro, R.,
Soldani, G., Balbarini, A. and Di Stefano, R. Fibrin acts as biomimetic niche inducing both differentiation and
stem cell marker expression of early human endothelial progenitor cells Cell Prolif. 44:33-48, 2011
298. Toischer, K., Rokita, A.G., UnsÖld, B., Zhu, W., Kararigas, G., Sossalla, S., Reuter, S.P., Becker, A., Teucher,
N., Seidler, T., Grebe, C., Preuß, L., Gupta, S.N., Schmidt, K., Lehnart, S.E., KrÜger, M., Linke, W.A., Backs, J.,
Regitz-Zagrosek, V., SchÄfer, K., Field, L.J., Maier, L.S. and Hasenfuss, G. Differential cardiac remodeling in
preload versus afterload Circulation 122:993-1003, 2010
299. Barreiro, L.B., Marioni, J.C., Blekhman, R., Stephens, M. and Gilad, Y. Functional comparison of innate
immune signaling pathways in primates PLoS Genet. 6:e1001249, 2010
300. Zhang, B., Chen, B., Wu, T., Tan, Y., Qiu, S., Xuan, Z., Zhu, X. and Chen, R. Estimating the quality of
reprogrammed cells using ES cell differentiation expression patterns PLoS ONE 6:e15336, 2011
301. Wei, P., Milbauer, L.C., Enenstein, J., Nguyen, J., Pan, W. and Hebbel, R.P. Differential endothelial cell gene
expression by African Americans versus Caucasian Americans: a possible contribution to health disparity in
vascular disease and cancer BMC Med. 9:2, 2011
302. Enquobahrie, D.A., Qiu, C., Muhie, S.Y. and Williams, M.A. Maternal peripheral blood gene expression in early
pregnancy and preeclampsia Int. J. Mol. Epidemiol. Genet. 2:78-94, 2011
303. Birlea, S.A., Jin, Y., Bennett, D.C., Herbstman, D.M., Wallace, M.R., McCormack, W.T., Kemp, E.H., Gawkrodger,
D.J., Weetman, A.P., Picardo, M., Leone, G., TaÏeb, A., Jouary, T., Ezzedine, K., van Geel, N., Lambert, J.,
Overbeck, A., Fain, P.R. and Spritz, R.A. Comprehensive association analysis of candidate genes for
generalized vitiligo supports XBP1, FOXP3, and TSLP J. Invest. Dermatol. 131:371-381, 2011
304. Hess, C., Wiegmann, B., Maurer, A.N., Fischer, P., MÖller, L., Martin, U., Hilfiker, A., Haverich, A. and Fischer,
S. Reduced thrombocyte adhesion to endothelialized poly 4-methyl-1-pentene gas exchange membranes-A
first step toward bioartificial lung development Tissue Eng. Pt. A 16:3043-3053, 2010
305. Sugano, G., Bernard-Pierrot, I., LaÉ, M., Battail, C., Allory, Y., Stransky, N., Krumeich, S., Lepage, M.-L.,
Maille, P., Donnadieu, M.-H., Abbou, C.C., Benhamou, S., Lebret, T., Sastre-Garau, X., Amigorena, S.,
Radvanyi, F. and ThÉry, C. Milk fat globule-epidermal growth factor-factor VIII (MFGE8)/lactadherin
promotes bladder tumor development Oncogene 30:642-653, 2011
306. Marques, F., Sousa, J.C., Coppola, G., Gao, F., Puga, R., Brentani, H., Geschwind, D.H., Sousa, N., Correia-
Neves, M. and Palha, J.A. Transcriptome signature of the adult mouse choroid plexus Fluids Barriers CNS 8:
10, 2011
307. Gatta, V., Drago, D., Fincati, K., Valenti, M.T., Carbonare, L.D., Sensi, S.L. and Zatta, P. Microarray analysis
on human neuroblastoma cells exposed to aluminum, Β1-42-amyloid or the Β1-42-amyloid aluminum
complex PLoS ONE 6:e15965, 2011
308. Schutzer, S.E., Angel, T.E., Liu, T., Schepmoes, A.A., Clauss, T.R., Adkins, J.N., Camp II, D.G., Holland, B.K.,
Bergquist, J., Coyle, P.K., Smith, R.D., Fallon, B.A. and Natelson, B.H. Distinct cerebrospinal fluid proteomes
differentiate post-treatment Lyme disease from chronic fatigue syndrome PLoS ONE 6:e17287, 2011
309. Heemers, H.V., Schmidt, L.J., Sun, Z., Regan, K.M., Anderson, S.K., Duncan, K., Wang, D., Liu, S., Ballman, K.V.
and Tindall, D.J. Identification of a clinically relevant androgen-dependent gene signature in prostate cancer
Cancer Res. 71:1978-1988, 2011
310. Patil, S.P., Wisnivesky, J.P., Busse, P.J., Halm, E.A. and Li, X.M. Detection of immunological biomarkers
correlated with asthma control and quality of life measurements in sera from chronic asthmatic patients.
Ann. Allergy Asthma Immunol. 106:205-213, 2011
311. Gilpin, S.E., Sato, M., Cypel, M., Keshavjee, S. and Waddell, T.K. Lung progenitor cell profiles in bronchiolitis
obliterans syndrome are mediated by circulating inflammatory and stem cell-specific factors J. Heart Lung
Transplant. 30, Suppl. 1:S82, 2011
312. Moreaux, J., Klein, B., Bataille, R., Descamps, G., MaÏga, S., Hose, D., Goldschmidt, H., Jauch, A., RÈme, T.,
Jourdan, M., Amiot, M. and Pellat-Deceunynck, C. A high-risk signature for patients with multiple myeloma
established from the molecular classification of human myeloma cell lines Haematologica 96:574-582, 2011
313. Thampi, N., Bitnun, A., Banner, D., Rowe, T., Kelvin, D.J., Richardson, S.E., Parkin, P. and Tran, D. Influenza-
associated encephalopathy with elevated antibody titers to pandemic (H1N1) 2009 influenza J. Child Neurol.
26:501-506, 2011
314. Meijer, K., de Vries, M., Al-Lahham, S., Bruinenberg, M., Weening, D., Dijkstra, M., Kloosterhuis, N., van der
Leij, R.J., van der Want, H., Kroesen, B.-J., Vonk, R. and Rezaee, F. Human primary adipocytes exhibit
immune cell function: Adipocytes prime inflammation independent of macrophages PLoS ONE 6:e17154,
2011
315. Lee, H.M., Zhang, H., Schulz, V., Tuck, D.P. and Forget, B.G. Downstream targets of HOXB4 in a cell line
model of primitive hematopoietic progenitor cells Blood 116:720-730, 2010
316. Armstrong, S.A., Staunton, J.E., Silverman, L.B., Pieters, R., den Boer, M.L., Minden, M.D., Sallan, S.E.,
Lander, E.S., Golub, T.R. and Korsmeyer, S.J. MLL translocations specify a distinct gene expression profile
that distinguishes a unique leukemia Nat. Genet. 30:41-47, 2001
317. Tothill, R.W., Tinker, A.V., George, J., Brown, R., Fox, S.B., Lade, S., Johnson, D.S., Trivett, M.K.,
Etemadmoghadam, D., Locandro, B., Traficante, N., Fereday, S., Hung, J.A., Chiew, Y.E., Haviv, I., Australian
Ovarian Cancer Study Group, Gertig, D., DeFazio, A. and Bowtell, D.D. Novel molecular subtypes of serous
and endometrioid ovarian cancer linked to clinical outcome Clin. Cancer Res. 14:5198-5208, 2008
318. Pastrana, E., Moreno-Flores, M.T., Gurzov, E.N., Avila, J., Wandosell, F. and az-Nido, J. Genes associated
with adult axon regeneration promoted by olfactory ensheathing cells: a new role for matrix
metalloproteinase 2 J. Neurosci. 26:5347-5359, 2006
319. Guerout, N., Derambure, C., Drouot, L., Bon-Mardion, N., Duclos, C., Boyer, O. and Marie, J.P. Comparative
gene expression profiling of olfactory ensheathing cells from olfactory bulb and olfactory mucosa Glia 58:1570
-1580, 2010
320. Franssen, E.H., de Bree, F.M., Essing, A.H., Ramon-Cueto, A. and Verhaagen, J. Comparative gene
expression profiling of olfactory ensheathing glia and Schwann cells indicates distinct tissue repair
characteristics of olfactory ensheathing glia Glia 56:1285-1298, 2008
321. Tamez, P.A., Liu, H., Wickrema, A. and Haldar, K.P. falciparum modulates erythroblast cell gene expression
in signaling and erythrocyte production pathways PLoS ONE 6:e19307, 2011
322. Sakabe, S., Iwatsuki-Horimoto, K., Takano, R., Nidom, C.A., Le, M.Q., Nagamura-Inoue, T., Horimoto, T.,
Yamashita, N. and Kawaoka, Y. Cytokine production by primary human macrophages infected with highly
pathogenic H5N1 or pandemic H1N1 2009 influenza viruses J. Gen. Virol. 92:1428-1434, 2011
323.Slovak, M.L., Bedell, V., Hsu, Y.-H., Estrine, D.B., Nowak, N.J., Delioukina, M.L., Weiss, L.M., Smith, D.D. and
Forman, S.J. Molecular karyotypes of Hodgkin and Reed-Sternberg cells at disease onset reveal distinct
copy number alterations in chemosensitive versus refractory Hodgkin lymphoma Clin. Cancer Res. 17:3443-
3454, 2011
324. Chun, S.Y., Lee, H.J., Choi, Y.A., Kim, K.M., Baek, S.H., Park, H.S., Kim, J.-Y., Ahn, J.-M., Cho, J.-Y., Cho, D.-
W., Shin, H.-I. and Park, E.K. Analysis of the soluble human tooth proteome and its ability to induce dentin/
tooth regeneration Tissue Eng. Pt. A 17:181-191, 2011
325.Wauquier, N., Becquart, P., Nkoghe, D., Padilla, C., Ndjoyi-Mbiguino, A. and Leroy, E.M. The acute phase of
Chikungunya virus infection in humans is associated with strong innate immunity and T CD8 cell activation J.
Infect. Dis. 204:115-123, 2011
326. Yang, J.D., Sun, Z., Hu, C., Lai, J., Dove, R., Nakamura, I., Lee, J.-S., Thorgeirsson, S.S., Kang, K.J., Chu, I.-S.
and Roberts, L.R. Sulfatase 1 and sulfatase 2 in hepatocellular carcinoma: Associated signaling pathways,
tumor phenotypes, and survival Genes Chromosomes Cancer 50:122-135, 2011
327. Liu, H.-C., Shih, L.-Y., Chen, M.-J.M., Wang, C.-C., Yeh, T.-C., Lin, T.-H., Chen, C.-Y., Lin, C.-J. and Liang,
D.-C. Expression of HOXB genes is significantly different in acute myeloid leukemia with a partial tandem
duplication of MLL vs. a MLL translocation: a cross-laboratory study Cancer Genet. 204:252-259, 2011
328. Camp, J.T., Elloumi, F., Roman-Perez, E., Rein, J., Stewart, D.A., Harrell, J.C., Perou, C.M. and Troester, M.A.
Interactions with fibroblasts are distinct in basal-like and luminal breast cancers Mol.Cancer Res. 9:3-13,
2011
329.Maubach, G., Lim, M.C.C., Chen, J., Yang, H. and Zhuo, L. miRNA studies in in vitro and in vivo activated
hepatic stellate cells World J. Gastroenterol. 17:2748-2773, 2011
330. Lehmann, B.D., Bauer, J.A., Chen, X., Sanders, M.E., Chakravarthy, A.B., Shyr, Y. and Pietenpol, J.A.
Identification of human triple-negative breast cancer subtypes and preclinical models for selection of
targeted therapies J. Clin. Invest. 121:2750-2767, 2011
331. Hwang, K.-A., Park, S.-H., Yi, B.-R. and Choi, K.-C. Gene alterations of ovarian cancer cells expressing
estrogen receptors by estrogen and bisphenol A using microarray analysis Lab. Anim. Res. 27:99-107, 2011
332. Felkin, L.E., Narita, T., Germack, R., Shintani, Y., Takahashi, K., Sarathchandra, P., Lopez-Olaneta, M.M.,
Gomez-Salinero, J.M., Suzuki, K., Barton, P.J.R., Rosenthal, N. and Lara-Pezzi, E. Calcineurin splicing variant
calcineurin AΒ1 improves cardiac function after myocardial infarction without inducing hypertrophy
Circulation 123:2838-2847, 2011
333. Bonetto, A., Aydogdu, T., Kunzevitzky, N., Guttridge, D.C., Khuri, S., Koniaris, L.G. and Zimmers,T.A. STAT3
activation in skeletal muscle links muscle wasting and the acute phase response in cancer cachexia PLoS
ONE 6:e22538, 2011
334. De Groot, J.F., Piao, Y., Tran, H., Gilbert, M., Wu, H.-K., Liu, J., Bekele, B.N., Cloughesy, T., Mehta, M., Robins,
H.I., Lassman, A., DeAngelis, L., Camphausen, K., Chen, A., Yung, W.K.A., Prados, M., Wen, P.Y. and Heymach, J.
V. Myeloid biomarkers associated with glioblastoma response to anti-VEGF therapy with aflibercept Clin.
Cancer Res. 17:4872-4881, 2011
335. Hertenstein, A., Schumacher, T., Litzenburger, U., Opitz, C.A., Falk, C.S., Serafini, T., Wick, W. and Platten, M.
Suppression of human CD4+ T cell activation by 3,4-dimethoxycinnamonyl-anthranilic acid (tranilast) is
mediated by CXCL9 and CXCL10 Biochem. Pharmacol. 82:632-641, 2011
336. Wong, K.L., Tai, J.J.-Y., Wong, W.-C., Han, H., Sem, X., Yeap, W.-H., Kourilsky, P. and Wong, S.-C. Gene
expression profiling reveals the defining features of the classical, intermediate, and nonclassical human
monocyte subsets Blood 118:e16-e31, 2011
337. Chaturvedi, A.K., Kemp, T.J., Pfeiffer, R.M., Biancotto, A., Williams, M., Munuo, S., Purdue, M.P., Hsing, A.W.,
Pinto, L., McCoy, J.P. and Hildesheim, A. Evaluation of multiplexed cytokine and inflammation marker
measurements: a methodologic study Cancer Epidemiol. Biomarkers Prev. 20:1902-1911, 2011
338. Suzuki, K., Matsuzaki, H., Iwata, K., Kameno, Y., Shimmura, C., Kawai, S., Yoshihara, Y., Wakuda, T.,
Takebayashi, K., Takagai, S., Matsumoto, K., Tsuchiya, K.J., Iwata, Y., Nakamura, K., Tsujii, M., Sugiyama, T.
and Mori, N. Plasma cytokine profiles in subjects with high-functioning autism spectrum disorders PLoS ONE
6:e20470, 2011
339. Da Riva, L., Bozzi, F., Mondellini, P., Micciche, F., Fumagalli, E., Vaghi, E., Tarantino, E., Huber, V., Gronchi, A.,
Tamborini, E., Pierotti, M.A.., Pilotti, S. and Bongarzone, I. Proteomic detection of a large amount of
SCGFalpha in the stroma of GISTs after imatinib therapy J.Transl. Med. 9:158, 2011
340. Miclea, R.L., Siebelt, M., Finos, L., Goeman, J.J., Lowik, C.W.G.M., Oostdijk, W., Weinans, H., Wit, J.M., Robanus-
Maandag, E.C. and Karperien, M. Inhibition of Gsk3Βin cartilage induces osteoarthritic features through
activation of the canonical Wnt signaling pathway Osteoarthritis Cartilage 19:1363-1372, 2011
341. Liu, P., Barb, J., Woodhouse, K.,Taylor, VI, J.G., Munson, P.J. and Raghavachari, N. Transcriptome profiling
and sequencing of differentiated human hematopoietic stem cells reveal lineage-specific expression and
alternative splicing of genes Physiol. Genomics 43:1117-1134, 2011
342. Kanamori-Katayama, M., Kaiho, A., Ishizu, Y., Okamura-Oho, Y., Hino, O., Abe, M., Kishimoto, T., Sekihara, H.,
Nakamura, Y., Suzuki, H., Forrest, A.R.R. and Hayashizaki, Y. LRRN4 and UPK3B are markers of primary
mesothelial cells PLoS ONE 6:e25391, 2011
343. Lai., Y., Asthana., A., Cheng, K. and Kisaalita, W.S. Neural cell 3D microtissue formation is marked by
cytokines' up-regulation PLoS ONE 6:e26821, 2011
344. Hogan, L.E., Meyer, J.A., Yang, J., Wang, J., Wong, N., Yang, W., Condos, G., Hunger, S.P., Raetz, E., Saffery,
R., Relling, M.V., Bhojwani, D., Morrison, D.J. and Carroll, W.L. Integrated genomic analysis of relapsed
childhood acute lymphoblastic leukemia reveals therapeutic strategies Blood 118:5218-5226, 2011
345.Beltran, A.S., Rivenbark, A.G., Richardson, B.T., Yuan, X., Quian, H., Hunt, J.P., Zimmerman, E., Graves, L.M.
and Blancafort, P. Generation of tumor-initiating cells by exogenous delivery of OCT4 transcription factor
Breast Cancer Res. 13:R94, 2011
346.Baron, D., Magot, A., Ramstein, G., Steenman, M., Fayet, G., Chevalier, C., Jourdon, P., Houlgatte, R.,
Savagner, F. and Pereon, Y. Immune response and mitochondrial metabolism are commonly deregulated in
DMD and aging skeletal muscle PLoS ONE 6:e26952, 2011
347. Acharya, A., Hans, C.P., Koenig, S.N., Nichols, H.A., Galindo, C.L., Garner, H.R., Merrill, W.H., Hinton, R.B. and
Garg, V. Inhibitory role of notch1 in calcific aortic valve disease PLoS ONE 6:e27743, 2011
348.Yung, S., Ledran, M., Moreno-Gimeno, I., Conesa, A., Montaner, D., Dopazo, J., Dimmick, I., Slater, N.J.,
Marenah, L., Real, P.J., Paraskevopoulou, I., Bisbal, V., Burks, D., Santibanez-Koref, M., Moreno, R., Mountford,
J., Menendez, P., Armstrong, L. and Lako, M. Large-scale transcriptional profiling and functional assays
reveal important roles for Rho-GTPase signalling and SCL during haematopoietic differentiation of human
embryonic stem cells Hum. Mol. Genet. 20:4932-4946, 2011
349. Agnelli, L., Forcato, M., Ferrari, F., Tuana, G., Todoerti, K., Walker, B.A., Morgan, G.J., Lombardi, L., Bicciato,
S. and Neri, A. The reconstruction of transcriptional networks reveals critical genes with implications for
clinical outcome of multiple myeloma Clin. Cancer Res. 17:7402-7412, 2011
350. Lee, J.-H., Gao, C., Peng, G., Greer, C., Ren, S., Wang, Y. and Xiao, X. Analysis of transcriptome complexity
through RNA sequencing in normal and failing murine hearts Circ. Res. 109:1332-1341, 2011
351.Wong, V.W., Paterno, J., Sorkin, M., Glotzbach, J.P., Levi, K., Januszyk, M.J., Rustad, K.C., Longaker, M.T. and
Gurtner, G.C. Mechanical force prolongs acute inflammation via T-cell-dependent pathways during scar
formation FASEB J. 25:4498-4510, 2011
352.Janich, P., Pascual, G., Merlos-SuÁrez, A., Batlle, E., Ripperger, J., Albrecht, U., Cheng, H.-Y.M., Obrietan, K.,
Di Croce, L. and Benitah, S.A.The circadian molecular clock creates epidermal stem cell heterogeneity
Nature 480:209-214, 2011
353. Nascimento, E.M., Cox, C.L., MacArthur, S., Hussain, S., Trotter, M., Blanco, S., Suraj, M., Nichols, J., KÜbler,
B., Benitah, S.A., Hendrich, B., Odom, D.T. and Frye, M. The opposing transcriptional functions of Sin3a and c-
Myc are required to maintain tissue homeostasis Nat. Cell Biol. 13:1395-1405, 2011
354. Zurita, A.J., Jonasch, E., Wang, X., Khajavi, M., Yan, S., Du, D.Z., Xu, L., Herynk, M.H., McKee, K.S., Tran, H.T.,
Logothetis, C.J.,Tannir, N.M. and Heymach, J.V. A cytokine and angiogenic factor (CAF) analysis in plasma
for selection of sorafenib therapy in patients with metastatic renal cell carcinoma Ann. Oncol. 23:46-52, 2012
355.de Jonge, H.J.M., Woolthuis, C.M., Vos, A.Z., Mulder, A., van den Berg, E., Kluin, P.M., van der Weide, K., de
Bont, E.S.J.M., Huls, G., Vellenga, E. and Schuringa, J.J. Gene expression profiling in the leukemic stem cell-
enriched CD34+fraction identifies target genes that predict prognosis in normal karyotype AML Leukemia 25:
1825-1833, 2011
356. Baird, G.S., Nelson, S.K., Keeney, T.R., Stewart, A., Williams, S., Kraemer, S., Peskind, E.R. and Montine, T.J.
Age-dependent changes in the cerebrospinal fluid proteome by slow off-rate modified aptamer array Am. J.
Pathol. 180:446-456, 2012
357. Kim, Y., Sharov, A.A., McDole, K., Cheng, M., Hao, H., Fan, C.-M., Gaiano, N., Ko, M.S.H. and Zheng, Y. Mouse
B-type lamins are required for proper organogenesis but not by embryonic stem cells Science 334:1706-
1710, 2011
358. Lu, Y., Wang, L., Liu, P., Yang, P. and You, M. Gene-expression signature predicts postoperative recurrence
in stage I non-small cell lung cancer patients PLoS ONE 7:e30880, 2012
359. Miller, W.R., Larionov, A., Anderson, T.J., Evans, D.B. and Dixon, J.M. Sequential changes in gene expression
profiles in breast cancers during treatment with the aromatase inhibitor, letrozole Pharmacogenomics J. 12:
10-21, 2012
360. Sohn, D.H., Sokolove, J., Sharpe, O., Erhart, J.C., Chandra, P.E., Lahey, L.J., Lindstrom, T.M., Hwang, I.,
Boyer, K.A., Andriacchi, T.P.and Robinson, W.H. Plasma proteins present in osteoarthritic synovial fluid can
stimulate cytokine production via Toll-like receptor 4 Arthritis Res. Ther. 14:R7, 2012
361.Ichii, M., Frank, M.B., Iozzo, R.V. and Kincade, P.W. The canonical Wnt pathway shapes niches supportive of
hematopoietic stem/progenitor cells Blood 119:1683-1692, 2012
362. Swain, S.D., Meissner, N.N., Siemsen, D.W., McInnerney, K. and Harmsen, A.G. Pneumocystis elicits a STAT6-
dependent, strain-specific innate immune response and airway hyperresponsiveness Am. J. Respir. Cell Mol.
Biol. 46:290-298, 2012
363.Manikkam, M., Guerrero-Bosagna, C., Tracey, R., Haque, M.M. and Skinner, M.K. Transgenerational actions of
environmental compounds on reproductive disease and identification of epigenetic biomarkers of ancestral
exposures PLoS ONE 7:e31901, 2012
364. Benhamed, M., Herbig, U., Ye, T., Dejean, A. and Bischof, O. Senescence is an endogenous trigger for
microRNA-directed transcriptional gene silencing in human cells Nat. Cell Biol. 14:266-275, 2012
365.Kassambara, A., Hose, D., Moreaux, J., Walker, B.A., Protopopov, A., Reme, T., Pellestor, F., Pantesco, V.,
Jauch, A., Morgan, G., Goldschmidt, H. and Klein, B. Genes with a spike expression are clustered in
chromosome (sub)bands and spike (sub)bands have a powerful prognostic value in patients with multiple
myeloma Haematologica 97:622-630, 2012
366. Uboldi, S., Calura, E., Beltrame, L., Nerini, I.F., Marchini, S., Cavalieri, D., Erba, E., Chiorino, G., Ostano, P.,
D'Angelo, D., D'Incalci, M. and Romualdi, C. A systems biology approach to characterize the regulatory
networks leading to trabectedin resistance in an in vitro model of myxoid liposarcoma PLoS ONE 7:e35423,
2012
367.Chernikova, S.B., Razorenova, O.V., Higgins, J.P., Sishc, B.J., Nicolau, M., Dorth, J.A., Chernikova, D.A., Kwok,
S., Brooks, J.D., Bailey, S.M., Game, J.C. and Brown, J.M. Deficiency in mammalian histone H2B ubiquitin
ligase Bre1 (Rnf20/Rnf40) leads to replication stress and chromosomal instability Cancer Res. 72:2111-2119,
2012
368. Sato, D., Lionel, A.C., Leblond, C.S., Prasad, A., Pinto, D., Walker, S., O'Connor, I., Russell, C., Drmic, I.E.,
Hamdan, F.F., Michaud, J.L., Endris, V., Roeth, R., Delorme, R., Huguet, G., Leboyer, M., Rastam, M., Gillberg,
C., Lathrop, M., Stavropoulos, D.J., Anagnostou, E., Weksberg, R., Fombonne, E., Zwaigenbaum, L., Fernandez,
B.A., Roberts, W., Rappold, G.A., Marshall, C.R., Bourgeron, T., Szatmari, P. and Scherer, S.W. SHANK1
deletions in males with autism spectrum disorder Am. J. Hum. Genet. 90:879-887, 2012
369. Kapur, S.K., Wang, X., Shang, H., Yun, S., Li, X., Feng, G., Khurgel, M. and Katz, A.J. Human adipose stem cells
maintain proliferative, synthetic and multipotential properties when suspension cultured as self-assembling
spheroids Biofabrication 4:025004, 2012
370. Laranjeira, A.B.A., de Vasconcellos, J.F., Sodek, L., Spago, M.C., Fornazim, M.C., Tone, L.G., Brandalise, S.R.,
Nowill, A.E. and Yunes, J.A. IGFBP7 participates in the reciprocal interaction between acute lymphoblastic
leukemia and BM stromal cells and in leukemia resistance to asparaginase Leukemia 26:1001-1011, 2012
371.Pereira, B.P., Tan, B.L., Han, H.C., Zou, Y., Aung, K.Z. and Leong, D.T. Intramuscular nerve damage in
lacerated skeletal muscles may direct the inflammatory cytokine response during recovery J. Cell. Biochem.
113:2330-2345, 2012
372. Maertzdorf, J., Weiner, 3rd, J., Mollenkopf, H.-J., TBornotTB Network, Bauer, T., Prasse, A., MÜller-
Quernheim, J. and Kaufmann, S.H.E. Common patterns and disease-related signatures in tuberculosis and
sarcoidosis Proc. Natl. Acad. Sci. USA 109:7853-7858, 2012
373. Melenhorst, J.J., Tian, X., Xu, D., Sandler, N.G., Scheinberg, P., Biancotto, A., Scheinberg, P., McCoy, Jr, J.P.,
Hensel, N.F., McIver, Z., Douek, D.C. and Barrett, A.J. Cytopenia and leukocyte recovery shape cytokine
fluctuations after myeloablative allogeneic hematopoietic stem cell transplantation Haematologica 97:867-
873, 2012
374. Kadirvel, R., Ding, Y.H., Dai, D., Lewis, D.A. and Kallmes, D.F. Proteomic analysis of aneurysm healing
mechanism after coil embolization: Comparison of dense packing with loose packing Am. J. Neuroradiol. 33:
1177-1181, 2012
375.Koolen, D.A., Kramer, J.M., Neveling, K., Nillesen, W.M., Moore-Barton, H.L., Elmslie, F.V., Toutain, A., Amiel, J.,
Malan, V., Tsai, A.C.-H., Cheung, S.W., Gilissen, C., Verwiel, E.T.P., Martens, S., Feuth, T., Bongers, E.M.H.F., de
Vries, P., Scheffer, H., Vissers, L.E.L.M., deBrouwer, A.P.M., Brunner, H.G., Veltman, J.A., Schenck, A., Yntema,
H.G. and deVries, B.B.A. Mutations in the chromatin modifier gene KANSL1 cause the 17q21.31 microdeletion
syndrome Nat. Genet. 44:639-641, 2012
376. Capone, F., Costantini, S., Guerriero, E., Calemma, R., Napolitano, M., Scala, S., Izzo, F. and Castello, G.
Serum cytokine levels in patients with hepatocellular carcinoma Eur. Cytokine Netw. 21:99-104, 2010
377.Banerji, S., Cibulskis, K., Rangel-Escareno, C., Brown, K.K., Carter, S.L., Frederick, A.M., Lawrence, M.S.,
Sivachenko, A.Y., Sougnez, C., Zou, L., Cortes, M.L., Fernandez-Lopez, J.C., Peng, S., Ardlie, K.G., Auclair, D.,
Bautista-PiÑa, V., Duke, F., Francis, J., Jung, J., Maffuz-Aziz, A., Onofrio, R.C., Parkin, M., Pho, N.H., Quintanar
-Jurado, V., Ramos, A.H., Rebollar-Vega, R., Rodriguez-Cuevas, S., Romero-Cordoba, S.L., Schumacher, S.E.,
Stransky, N.,Thompson, K.M., Uribe-Figueroa, L., Baselga, J., Beroukhim, R., Polyak, K., Sgroi, D.C., Richardson,
A.L., Jimenez-Sanchez, G., Lander, E.S., Gabriel, S.B., Garraway, L.A., Golub, T.R., Melendez-Zajgla, J., Toker,
A., Getz, G., Hidalgo-Miranda A. and Meyerson, M. Sequence analysis of mutations and translocations across
breast cancer subtypes Nature 486:405-409, 2012
378. Ezra, D.G., Krell, J., Rose, G.E., Bailly, M., Stebbing, J. and Castellano, L. Transcriptome-level microarray
expression profiling implicates IGF-1 and Wnt signalling dysregulation in the pathogenesis of thyroid-
associated orbitopathy J. Clin. Pathol. 65:608-613, 2012
379.Sun, Y. and Zhan, M. Comparative transcriptomics for global functional profiling of embryonic stem cells
Stemcells: From mechanisms to technologies (Stachowiak, M.K. and Tzanakakis, E.S., eds., World Scientific
Publishing Co. Pte. Ltd.) Chapter 3 pp. 63-86, 2012
380. Lee, L.S., Banks, P.A., Bellizzi, A.M., Sainani, N.I., Kadiyala, V., Suleiman, S., Conwell, D.L. and Paulo, J.A.
Inflammatory protein profiling of pancreatic cyst fluid using EUS-FNA in tandem with cytokine microarray
differentiates between branch duct IPMN and inflammatory cysts J. Immunol. Methods 382:142-149, 2012
381.Lokk, K., Vooder, T., Kolde, R., VÄlk, K., VÕsa, U., Roosipuu, R., Milani, L., Fischer, K., Koltsina, M., Urgard, E.,
Annilo, T., Metspalu, A. and TÕnisson, N. Methylation markers of early-stage non-small cell lung cancer
PLoS ONE 7:e39813, 2012
382. StÜnkel, W., Pan, H., Chew, S.B., Tng, E.,Tan, J.H., Chen, L., Joseph, R., Cheong, C.Y., Ong, M.-L., Lee, Y.S.,
Chong, Y.-S., Saw, S.M., Meaney, M.J., Kwek, K., Sheppard, A.M., Gluckman, P.D., GUSTO Study Group and
Holbrook, J.D. Transcriptome changes affecting hedgehog and cytokine signalling in the umbilical cord:
Implications for disease risk PLoS ONE 7:e39744, 2012
383. Huang, C.-L., Lamb, J., Chindelevitch, L., Kostrowicki, J., Guinney, J., DeLisi, C. and Ziemek, D. Correlation
set analysis: detecting active regulators in disease populations using prior causal knowledge BMC
Bioinformatics 13:46, 2012
384. Khan, A. Detection and quantitation of forty eight cytokines, chemokines, growth factors and nine acute
phase proteins in healthy human plasma, saliva and urine J. Proteomics 75:4802-4819, 2012
385. Chauncey, K.M., Lopez, M.C., Sidhu, G., Szarowicz, S.E., Baker, H.V., Quinn, C.and Southwick, F.S.Bacillus
anthracis' lethal toxin induces broad transcriptional responses in human peripheral monocytes BMC Immunol.
13:33, 2012
386. Wladis, E.J., Iglesias, B.V., Adam, A.P. and Gosselin, E.J. Molecular biologic assessment of cutaneous
specimens of ocular rosacea Ophthal. Plast. Reconstr. Surg. 28:246-250, 2012
387. Fouraschen, S.M.G., Pan, Q., de Ruiter, P.E., Farid, W.R.R., Kazemier, G., Kwekkeboom, J., Ijzermans, J.N.M.,
Metselaar, H.J., Tilanus, H.W., de Jonge, J. and van der Laan, L.J.W. Secreted factors of human liver-derived
mesenchymal stem cells promote liver regeneration early after partial hepatectomy Stem Cells Dev. 21:2410
-2419, 2012
388. JÁgr, M., Eckhardt, A., Pataridis, S. and MiksÍk, I. Comprehensive proteomic analysis of human dentin Eur.
J. Oral Sci. 120:259-268, 2012
389. Fischer, U., Ruckert, C., Hubner, B., Eckermann, O., Binder, V., Bakchoul, T., Schuster, F.R., Merk, S., Klein,
H.-U., Fuhrer, M., Dugas, M. and Borkhardt, A. CD34+gene expression profiling of individual children with very
severe aplastic anemia indicates a pathogenic role of integrin receptors and the proapoptotic death ligand
TRAIL Haematologica 97:1304-1311, 2012
390. Wallace, D.L., Han, M.-H., Graham, D.L., Green, T.A., Vialou, V., IÑiguez, S.D., Cao, J.-L., Kirk, A.,
Chakravarty, S., Kumar, A., Krishnan, V., Neve, R.L., Cooper, D.C., BolaÑos, C.A., Barrot, M., McClung, C.A.
and Nestler, E.J. CREB regulation of nucleus accumbens excitability mediates social isolation-induced
behavioral deficits Nat. Neurosci. 12:200-209, 2009
391. Beshiri, M.L., Holmes, K.B., Richter, W.F., Hess, S., Islam, A.B.M.M.K., Yan, Q., Plante, L., Litovchick, L., GÉvry,
N., Lopez-Bigas, N., Kaelin, Jr., W.G. and Benevolenskaya, E.V. Coordinated repression of cell cycle genes by
KDM5A and E2F4 during differentiation Proc. Natl. Acad. Sci. USA 109:18499-18504, 2012
392. Kulis, M., Heath, S., Bibikova, M., QueirÓs, A.C., Navarro, A., Clot, G., MartÍnez-Trillos, A., Castellano, G.,
Brun-Heath, I., Pinyol, M., BarberÁn-Soler, S., Papasaikas, P., Jares, P., BeÁ, S., Rico, D., Ecker, S., Rubio,
M., Royo, R., Ho, V., Klotzle, B., HernÁndez, L., Conde, L., LÓpez-Guerra, M., Colomer, D., Villamor, N.,
Aymerich, M., Rozman, M., Bayes, M., Gut, M., GelpÍ, J.L., Orozco, M., Fan, J.-B., Quesada, V., Puente, X.S.,
Pisano, D.G., Valencia, A., LÓpez-Guillermo, A., Gut, I., LÓpez-OtÍn, C., Campo, E. and MartÍn-Subero, J.I.
Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia
Nat. Genet. 44:1236-1242, 2012
393. Martinez, E.E., Anderson, P.D., Logan, M. and Abdulkadir, S.A. Antioxidant treatment promotes prostate
epithelial proliferation in Nkx3.1 mutant mice PLoS ONE 7:e46792, 2012
394. Radillo, O., Norcio, A., Addobbati, R. and Zauli, G. Presence of CTAK/CCL27, MCP-3/CCL7 and LIF in
human colostrum and breast milk Cytokine 61:26-28, 2013
395. Ley, S., Weigert, A., HÉrichÉ, J.-K., Mille-Baker, B., Janssen, R.A.J. and BrÜne, B. RNAi screen in
apoptotic cancer cell-stimulated human macrophages reveals co-regulation of IL-6/IL-10 expression
Immunobiology 218:40-51, 2013
396. Roy, S., Javed, S., Jain, S.K., Majumdar, S.S. and Mukhopadhyay, A. Donor hematopoietic stem cells confer
long-term marrow reconstitution by self-renewal divisions exceeding to that of host cells PLoS ONE 7:
e50693, 2012
397. Capua, I., Mercalli, A., Pizzuto, M.S., Romero-Tejeda, A., Kasloff, S., De Battisti, C., Bonfante, F., Patrono, L.
V., Vicenzi, E., Zappulli, V., Lampasona, V., Stefani, A., Doglioni, C., Terregino, C., Cattoli, G. and Piemonti, L.
Influenza A viruses grow in human pancreatic cells and cause pancreatitis and diabetes in an animal model J.
Virol. 87:597-610, 2013
398. Kordes, C., Sawitza, I., GÖtze, S. and HÄussinger, D. Stellate cells from rat pancreas are stem cells and
can contribute to liver regeneration PLoS ONE 7:e51878, 2012
399. Brenner, M.and Gulko, P.S. The arthritis severity locus Cia5a regulates the expression of inflammatory
mediators including Syk pathway genes and proteases in pristane-induced arthritis BMC Genomics 13:710,
2012
400. Wasserman, E., Webster, D., Kuhn, G., Attar-Namdar, M., MÜller, R. and Bab, I. Differential load-regulated
global gene expression in mouse trabecular osteocytes Bone 53:14-23, 2013
401. Harman, A.N., Bye, C.R., Nasr, N., Sandgren, K.J., Kim, M., Mercier, S.K., Botting, R.A., Lewin, S.R.,
Cunningham, A.L. and Cameron, P.U. Identification of lineage relationships and novel markers of blood and
skin human dendritic cells J. Immunol. 190:66-79, 2013
402. Silveira, V.S., Scrideli, C.A., Moreno, D.A., Yunes, J.A., Queiroz, R.G.P., Toledo, S.C., Lee, M.L.M., Petrilli, A.S.,
Brandalise, S.R. and Tone, L.G. Gene expression pattern contributing to prognostic factors in childhood acute
lymphoblastic leukemia Leuk. Lymphoma 54:310-314, 2013
403. Lundberg, K., Albrekt, A.-S., Nelissen, I., Santegoets, S., de Gruijl, T.D., Gibbs, S. and Lindstedt, M.
Transcriptional profiling of human dendritic cell populations and models-Unique profiles of in vitro dendritic
cells and implications on functionality and applicability PLoS ONE 8:e52875, 2013
404. Sandoval, J., Heyn, H., MÉndez-GonzÁlez, J., Gomez, A., Moran, S., Baiget, M., Melo, M., Badell, I., NomdedÉu,
J.F. and Esteller, M. Genome-wide DNA methylation profiling predicts relapse in childhood B-cell acute
lymphoblastic leukaemia Br. J. Haematol. 160:406-409, 2013
405. Cieri, N., Camisa, B., Cocchiarella, F., Forcato, M., Oliveira, G., Provasi, E., Bondanza, A., Bordignon, C.,
Peccatori, J., Ciceri, F., Lupo-Stanghellini, M.T., Mavilio, F., Mondino, A., Bicciato, S., Recchia, A. and Bonini, C.
IL-7 and IL-15 instruct the generation of human memory stem T cells from naive precursors Blood 121:573-
584, 2013
406. Zama, A.M. and Uzumcu, M. Targeted genome-wide methylation and gene expression analyses reveal
signaling pathways involved in ovarian dysfunction after developmental EDC exposure in rats Biol. Reprod. 88:
52, 1-13, 2013
407. Heuck, C.J., Mehta, J., Bhagat, T., Gundabolu, K., Yu, Y., Khan, S., Chrysofakis, G., Schinke, C., Tariman, J.,
Vickrey, E., Pulliam, N., Nischal, S., Zhou, L., Bhattacharyya, S., Meagher, R., Hu, C., Maqbool, S., Suzuki, M.,
Parekh, S., Reu, F., Steidl, U., Greally, J., Verma, A. and Singhal, S.B. Myeloma is characterized by stage-
specific alterations in DNA methylation that occur early during myelomagenesis J. Immunol. 190:2966-2975,
2013
408. Wang, Y., Khan, A., Heringer-Walther, S., Schultheiss, H.-P., Moreira, M.C.V. and Walther, T. Prognostic value
of circulating levels of stem cell growth factor beta (SCGF beta) in patients with Chagas' disease and
idiopathic dilated cardiomyopathy Cytokine 61:728-731, 2013
409. Kleiner, G., Marcuzzi, A., Zanin, V., Monasta, L. and Zauli, G. Cytokine levels in the serum of healthy subjects
Mediators Inflamm. 434010, 2013
410. Wladis, E.J., Falk, N.S., Iglesias, B.V., Beer, P.M. and Gosselin, E.J. Analysis of the molecular biologic milieu of
the vitreous in proliferative vitreoretinopathy Retina 33:807-811, 2013
411. Klauke, K., Radulovic, V., Broekhuis, M., Weersing, E., Zwart, E., Olthof, S., Ritsema, M., Bruggeman, S., Wu, X.,
Helin, K., Bystrykh, L. and de Haan, G. Polycomb Cbx family members mediate the balance between
haematopoietic stem cell self-renewal and differentiation Nat.Cell Biol. 15:353-362, 2013
412. He, J., Shen, L., Wan, M., Taranova, O., Wu, H. and Zhang, Y. Kdm2b maintains murine embryonic stem cell
status by recruiting PRC1 complex to CpG islands of developmental genes Nat. Cell Biol. 15:373-384, 2013
413. Yin, X., Bern, M., Xing, Q., Ho, J., Viner, R. and Mayr, M. Glycoproteomic analysis of the secretome of human
endothelial cells Mol. Cell. Proteomics 12:956-978, 2013
414. Echchgadda, I., Roth, C.C., Cerna, C.Z. and Wilmink, G.J. Temporal gene expression kinetics for human
keratinocytes exposed to hyperthermic stress Cells 2:224-243, 2013
415. Schroeder, D.I., Blair, J.D., Lott, P., Yu, H.O.K., Hong, D., Crary, F., Ashwood, P., Walker, C., Korf, I., Robinson,
W.P. and LaSalle, J.M. The human placenta methylome Proc. Natl. Acad. Sci. USA 110:6037-6042, 2013
416. Hikichi, T., Matoba, R., Ikeda, T., Watanabe, A., Yamamoto, T., Yoshitake, S., Tamura-Nakano, M., Kimura, T.,
Kamon, M., Shimura, M., Kawakami, K., Okuda, A., Okochi, H., Inoue, T., Suzuki, A. and Masui, S. Transcription
factors interfering with dedifferentiation induce cell type-specific transcriptional profiles Proc. Natl. Acad.
Sci. USA 110:6412-6417, 2013
417. Lai, R.C., Tan, S.S., Teh, B.J., Sze, S.K., Arslan, F., de Kleijn, D.P., Choo, A. and Lim, S.K. Proteolytic potential
of the MSC exosome proteome: Implications for an exosome-mediated delivery of therapeutic proteasome
Int. J. Proteomics 971907, 2012
418. Zhang, X., Cruz, F.D., Terry, M., Remotti, F. and Matushansky, I. Terminal differentiation and loss of
tumorigenicity of human cancers via pluripotency-based reprogramming Oncogene 32:2249-2260, 2013
419. Burkhart, J.M., Vaudel, M., Gambaryan, S., Radau, S., Walter, U., Martens, L., Geiger, J., Sickmann, A. and
Zahedi, R.P. The first comprehensive and quantitative analysis of human platelet protein composition allows
the comparative analysis of structural and functional pathways. Blood 120:e73-e82, 2012
420. Karlsson, C., Baudet, A., Miharada, N., Soneji, S., Gupta, R., Magnusson, M., Enver, T., Karlsson, G. and
Larsson, J. Identification of the chemokine CCL28 as a growth and survival factor for human hematopoietic
stem and progenitor cells Blood 121:3838-3842, 2013
421. KÜttner, V., Mack, C., Rigbolt, K.T.G., Kern, J.S., Schilling, O., Busch, H., Bruckner-Tuderman, L. and Dengjel,
J. Global remodelling of cellular microenvironment due to loss of collagen VII Mol. Syst. Biol. 9:657, 2013
422. Corcoran, A.T., Yoshimura, N., Tyagi, V., Jacobs, B., Leng, W. and Tyagi, P. Mapping the cytokine profile of
painful bladder syndrome/interstitial cystitis in human bladder and urine specimens World J. Urol. 31:241-
246, 2013
423. Sarchielli, P., Nardi., K., Chiasserini, D., Eusebi, P., Tantucci, M., Di Piero, V., Altieri, M., Marini, C., Russo, T.,
Silvestrini, M., Paolino, I., Calabresi, P. and Parnetti, L. Immunological profile of silent brain infarction and
lacunar stroke PLoS ONE 8:e68428, 2013
424. Stein, A., Panjwani, A., Sison, C., Rosen, L., Chugh, R., Metz, C., Bank, M. and Bloom, O. Pilot study: elevated
circulating levels of the proinflammatory cytokine macrophage migration inhibitory factor in patients with
chronic spinal cord injury Arch. Phys. Med. Rehabil. 94:1498-1507, 2013
425. Gilpin, S.E., Lung, K., de Couto, G.T., Cypel, M., Sato, M., Singer, L.G., Keshavjee, S. and Waddell, T.K. Bone
marrow-derived progenitor cells in end-stage lung disease patients BMC Pulm. Med. 13:48, 2013
426. Daino, K., Imaoka, T., Morioka, T., Tani, S., Iizuka, D., Nishimura, M. and Shimada, Y. Loss of the BRCA1-
interacting helicase BRIP1 results in abnormal mammary acinar morphogenesis PLoS ONE 8:e74013, 2013
427. Mercalli, A., Calavita, I., Dugnani, E., Citro, A., Cantarelli, E., Nano, R., Melzi, R., Maffi, P., Secchi, A., Sordi, V.
and Piemonti, L. Rapamycin unbalances the polarization of human macrophages to M1 Immunology 140:179-
190, 2013
428. Kehrmann, A., Truong, H., Repenning, A., Boger, R., Klein-Hitpass, L., Pascheberg, U., Beckmann, A., Opalka,
B. and Kleine-Lowinski, K. Complementation of non-tumorigenicity of HPV18-positive cervical carcinoma
cells involves differential mRNA expression of cellular genes including potential tumor suppressor genes on
chromosome 11q13 Cancer Genet. 206:279-292, 2013
429. GÖrlich, A., Antolin-Fontes, B., Ables, J.L., Frahm, S., Slimak, M.A., Dougherty, J.D. and IbaÑez-Tallon, I.
Reexposure to nicotine during withdrawal increases the pacemaking activity of cholinergic habenular neurons
Proc. Natl. Acad. Sci. USA 110:17077-17082, 2013
430. Rosenow, A., Noben, J.-P., Bouwman, F.G., Mariman, E.C.M. and Renes, J. Hypoxia-mimetic effects in the
secretome of human preadipocytes and adipocytes Biochim. Biophys. Acta Proteins Proteomics 1834:2761-
2771, 2013
431. Roepman, P., Schlicker, A., Tabernero, J., Majewski, I., Tian, S., Moreno, V., Snel, M.H., Chresta, C.M.,
Rosenberg, R., Nitsche, U., Macarulla, T., Capella, G., Salazar, R., Orphanides, G., Wessels, L.F.A., Bernards, R.
and Simon, I.M. Colorectal cancer intrinsic subtypes predict chemotherapy benefit, deficient mismatch repair
and epithelial-to-mesenchymal transition Int. J. Cancer 134:552-562, 2014
432. Malhotra, N., Srivastava, A., Rana, H., Bahadur, A., Sengupta, J. and Ghosh, D. Comparative multiplex
analysis of cytokines, chemokines and growth factors in follicular fluid of normoresponder women undergoing
ovum donation with gonadotropin-releasing hormone agonist versus gonadotropin-releasing hormone
antagonist protocols J. Hum. Reprod. Sci. 6:205-212, 2013
433.Steentoft, C., Vakhrushev, S.Y., Joshi, H.J., Kong, Y., Vester-Christensen, M.B., Schjoldager, K.T., Lavrsen, K.,
Dabelsteen, S., Pedersen, N.B., Marcos-Silva, L., Gupta, R., Bennett, E.P., Mandel, U., Brunak, S., Wandall, H.H.,
Levery, S.B. and Clausen, H. Precision mapping of the human O-GalNAc glycoproteome through SimpleCell
technology EMBO J. 32:1478-1488, 2013
434. Wagner, S.A., Beli, P., Weinert, B.T., Nielsen, M.L., Cox, J., Mann, M. and Choudhary, C.A. A proteome-wide,
quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles Mol. Cell. Proteomics
10:M111.013284, 2011
435. Udeshi, N.D., Svinkina, T., Mertins, P., Kuhn, E., Mani, D.R., Qiao, J.W. and Carr, S.A. Refined preparation and
use of anti-diglycine remnant (K-Ε-GG) antibody enables routine quantification of 10,000s of ubiquitination
sites in single proteomics experiments Mol. Cell. Proteomics 12:825-831, 2013
436. Mertins, P., Qiao, J.W., Patel, J., Udeshi, N.D., Clauser, K.R., Mani, D.R., Burgess, M.W., Gillette, M.A., Jaffe, J.
D. and Carr, S.A. Integrated proteomic analysis of post-translational modifications by serial enrichment Nat.
Methods 10:634-637, 2013
437.Woolthuis, C.M., Brouwers-Vos, A.Z., Huls, G., de Wolf, J.T.M., Schuringa, J.J. and Vellenga, E. Loss of
quiescence and impaired function of CD34+/CD38lowcells one year following autologous stem cell
transplantation Haematologica 98:1964-1971, 2013
438.Srivastava, A., Sengupta, J., Kriplani, A., Roy, K.K. and Ghosh, D. Profiles of cytokines secreted by isolated
human endometrial cells under the influence of chorionic gonadotropin during the window of embryo
implantation Reprod. Biol. Endocrinol. 11:116, 2013
439. Slany, A., Haudek-Prinz, V., Zwick, H., StÄttner, S., Grasl-Kraupp, B. and Gerner, C. Myofibroblasts are
important contributors to human hepatocellular carcinoma: Evidence for tumor promotion by proteome
profiling Electrophoresis 34:3315-3325, 2013
440.Papait, R., Cattaneo, P., Kunderfranco, P., Greco, C., Carullo, P., Guffanti, A., ViganÒ, V., Stirparo, G.G.,
Latronico, M.V.G., Hasenfuss, G., Chen, J. and Condorelli, G. Genome-wide analysis of histone marks
identifying an epigenetic signature of promoters and enhancers underlying cardiac hypertrophy Proc. Natl.
Acad. Sci. USA 110:20164-20169, 2013
441. Zhao, S., Fung-Leung, W.-P., Bittner, A., Ngo, K. and Liu, X. Comparison of RNA-seq and microarray in
transcriptome profiling of activated T cells PLoS ONE 9:e78644, 2014
442. Biros, E., Moran, C.S., Rush, C.M., Gabel, G., Schreurs, C., Lindeman, J.H.N., Walker, P.J., Nataatmadja, M.,
West, M., Holdt, L.M., Hinterseher, I., Pilarsky, C. and Golledge, J. Differential gene expression in the proximal
neck of human abdominal aortic aneurysm Atherosclerosis 233:211-218, 2014
443. Italiani, P., Mazza, E.M.C., Lucchesi, D., Cifola, I., Gemelli, C., Grande, A., Battaglia, C., Bicciato, S. and
Boraschi, D. Transcriptomic profiling of the development of the inflammatory response in human monocytes
in vitro PLoS ONE 9:e87680, 2014
444.van de Garde, M.D.B., Martinez, F.O., Melgert, B.N., Hylkema, M.N., Jonkers, R.E. and Hamann, J. Chronic
exposure to glucocorticoids shapes gene expression and modulates innate and adaptive activation pathways
in macrophages with distinct changes in leukocyte attraction J. Immunol. 192:1196-1208, 2014
445.Cao, Q., Wang, X., Zhao, M., Yang, R., Malik, R., Qiao, Y., Poliakov, A., Yocum, A.K., Li, Y., Chen, W., Cao, X.,
Jiang, X., Dahiya, A., Harris, C., Feng, F.Y., Kalantry, S., Qin, Z.S., Dhanasekaran, S.M. and Chinnaiyan, A.M.
The central role of EED in the orchestration of polycomb group complexes Nat. Commun. 5:3127, 2014
446. Kim, S., Chaudhry, A., Lee, I. and Frank, J.A. Effects of long-term hypoxia and pro-survival cocktail in bone
marrow-derived stromal cell survival Stem Cells Dev. 23:530-540, 2014
447. Germanguz, I., Shtrichman, R., Osenberg, S., Ziskind, A., Novak, A., Domev, H., Laevsky, I., Jacob-Hirsch, J.,
Feiler, Y., Rechavi, G. and Itskovitz-Eldor, J. ADAR1 is involved in the regulation of reprogramming human
fibroblasts to induced pluripotent stem cells Stem Cells Dev. 23:443-456, 2014
448. Rager, J.E., Moeller, B.C., Miller, S.K., Kracko, D., Doyle-Eisele, M., Swenberg, J.A. and Fry, R.C. Formaldehyde
-associated changes in microRNAs: Tissue and temporal specificity in the rat nose, white blood cells, and
bone marrow Toxicol. Sci. 138:36-46, 2014
449. Kimura, T., Shiraishi, K., Furusho, A., Ito, S., Hirakata, S., Nishida, N., Yoshimura, K., Imanaka-Yoshida, K.,
Yoshida, T., Ikeda, Y., Miyamoto, T., Ueno, T., Hamano, K., Hiroe, H., Aonuma, K., Matsuzaki, M., Imaizumi, T. and
Aokia, H. Tenascin C protects aorta from acute dissection in mice Sci Rep. 11:4051, 2014
450. Malaud, E., Merle, D., Piquer, D., Molina, L., Salvetat, N., Rubrecht, L., Dupaty, E., Galea, P., Cobo, S., Blanc,
A., Saussine, M., Marty-AnÉ, C., Albat, B., Meilhac, O., Rieunier, F., Pouzet, A., Molina, F., Laune, D. and
Fareh, J. Local carotid atherosclerotic plaque proteins for the identification of circulating biomarkers in
coronary patients Atherosclerosis 233:551-558, 2014
451. Garaffo, G., Provero, P., Molineris, I., Pinciroli, P., Peano, C., Battaglia, C., Tomaiuolo, D., Etzion, T., Gothilf, Y.,
Santoro, M. and Merlo, G.R. Profiling, bioinformatic, and functional data on the developing olfactory/GnRH
system reveal cellular and molecular pathways essential for this process and potentially relevant for the
Kallmann syndrome Front. Endocrinol. 4:203, 2013
452. Lundberg, P., Karow, A., Nienhold, R., Looser, R., Hao-Shen, H., Nissen, I., Girsberger, S., Lehmann, T.,
Passweg, J., Stern, M., Beisel, C., Kralovics, R. and Skoda, R.C. Clonal evolution and clinical correlates of
somatic mutations in myeloproliferative neoplasms Blood 123:2220-2228, 2014
453. Gough, S.M., Lee, F., Yang, F., Walker, R.L., Zhu, Y.J., Pineda, M., Onozawa, M., Chung, Y.J., Bilke, S., Wagner,
E.K., Denu, J.M., Ning, Y., Xu, B., Wang, G.G., Meltzer, P.S. and Aplan, P.D. NUP98-PHF23 is a chromatin-
modifying oncoprotein that causes a wide array of leukemias sensitive to inhibition of PHD histone reader
function Cancer Discov. 4:564-577, 2014
454. Arredouani, M.S., Bhasin, M.K., Sage, D.R., Dunn, L.K., Gill, M.B., Agnani, D., Libermann, T.A. and Fingeroth, J.
D. Analysis of host gene expression changes reveals distinct roles for the cytoplasmic domain of the Epstein-
Barr virus receptor/CD21 in B-cell maturation, activation, and initiation of virus infection J. Virol. 88:5559-
5577, 2014
455. Breunig, C., Mueller, B.J., Umansky, L., Wahl, K., Hoffmann, K., Lehner, F., Manns, M.P., Bantel, H. and Falk, C.
S. BRaf and MEK inhibitors differentially regulate cell fate and microenvironment in human hepatocellular
carcinoma Clin. Cancer Res. 20:2410-2423, 2014
456. Cizkova, D., LeMarrec-Croq, F., Franck, J., Slovinska, L., Grulova, I., Devaux, S., Lefebvre, C., Fournier, I. and
Salzet, M. Alterations of protein composition along the rostro-caudal axis after spinal cord injury: proteomic,
in vitro and in vivo analyses Front. Cell. Neurosci. 8:1-15, 2014
457.Nieminen, A., Maksimow, M., Mentula, P., KyhÄlÄ, L., KylÄnpÄÄ, L., Puolakkainen, P., Kemppainen, E.,
Repo, H. and Salmi, M. Circulating cytokines in predicting development of severe acute pancreatitis Crit.
Care 18:R104, 2014
458.Suraokar, M.B., Nunez, M.I., Diao, L., Chow, C.W., Kim, D., Behrens, C., Lin, H., Lee, S., Raso, G., Moran, C.,
Rice, D., Mehran, R., Lee, J.J., Pass, H.I., Wang, J., Momin, A.A., James, B.P., Corvalan, A., Coombes, K., Tsao,
V. and Wistuba, V. Expression profiling stratifies mesothelioma tumors and signifies deregulation of spindle
checkpoint pathway and microtubule network with therapeutic implications Ann. Oncol. 25:1184-1192, 2014
459. Treutlein, B., Brownfield, D.G., Wu, A.R., Neff, N.F., Mantalas, G.L., Espinoza, F.H., Desai, T.J., Krasnow, M.A.
and Quake, S.R. Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq
Nature 509:371-375, 2014
460.Wilhelm, M., Schlegl, J., Hahne, H., Gholami, A.M., Lieberenz, M., Savitski, M.M., Ziegler, E., Butzmann, L.,
Gessulat, S., Marx, H., Mathieson, T., Lemeer, S., Schnatbaum, K., Reimer, U., Wenschuh, H., Mollenhauer, M.,
Slotta-Huspenina, J., Boese, J.-H., Bantscheff, M., Gerstmair, A., Faerber, F. and Kuster, B. Mass-
spectrometry-based draft of the human proteome Nature 509:582-587, 2014
461. Yu, Y., Chen, Y., Kim, B., Wang, H., Zhao, C., He, X., Liu, L., Liu, W., Wu, L.M.N., Mao, M., Chan, J.R., Wu, J. and
Lu, Q.R. Olig2 targets chromatin remodelers to enhancers to initiate oligodendrocyte differentiation Cell 152:
248-261, 2013
462. Pesce, M., Felaco, P., Franceschelli, S., Speranza, L., Grilli, A., De Lutiis, M.A., Ferrone, A., Sirolli, V.,
Bonomini, M., Felaco, M. and Patruno, A. Effect of erythropoietin on primed leucocyte expression profile
Open Biol. 4:140026, 2014
463. Nolen, B.M., Breen, E.C., Bream, J.H., Jenkins, F.J., Kingsley, L.A., Rinaldo, C.R. and Lokshin, A.E. Circulating
mediators of inflammation and immune activation in AIDS-related non-Hodgkin lymphoma PLoS ONE 9:
e99144, 2014
464. Yin, G.N., Choi, M.J., Kim, W.J., Kwon, M.-H., Song, K.-M., Park, J.-M., Das, N.D., Kwon, K.-D., Batbold, D., Oh,
G.T., Koh, G.Y., Kim, K.-W., Ryu, J.-K. and Suh, J.-K. Inhibition of Ninjurin 1 restores erectile function through
dual angiogenic and neurotrophic effects in the diabetic mouse Proc. Natl. Acad. Sci. USA 111:E2731-E2740,
2014
465. Risinger, J.I., Custer, M., Feigenbaum, L., Simpson, R.M., Hoover, S.B., Webster, J.D., Chandramouli, G.V.R.,
Tessarollo, L. and Barrett, J.C. Normal viability of Kai1/Cd82 deficient mice Mol. Carcinog. 53:610-624, 2014
466. Naba, A., Clauser, K.R., Whittaker, C.A., Carr, S.A., Tanabe, K.K. and Hynes, R.O. Extracellular matrix
signatures of human primary metastatic colon cancers and their metastases to liver BMC Cancer 14:518,
2014
467. van de Leemput, J., Boles, N.C., Kiehl, T.R., Corneo, B., Lederman, P., Menon, V., Lee, C., Martinez, R.A., Levi,
B.P., Thompson, C.L., Yao, S., Kaykas, A., Temple, S. and Fasano, C.A. CORTECON: A temporal transcriptome
analysis of in vitro human cerebral cortex development from human embryonic stem cells Neuron 83:51-68,
2014
468. Kopesky, P., Tiedemann, K., Alkekhia, D., Zechner, C., Millard, B., Schoeberl, B. and Komarova, S.V. Autocrine
signaling is a key regulatory element during osteoclastogenesis Biol. Open 3:767-776, 2014
469. Comar, M., Zanotta, N., Bonotti, A., Tognon, M., Negro, C., Cristaudo, A. and Bovenzi, M. Increased levels of C
-C chemokine RANTES in asbestos exposed workers and in malignant mesothelioma patients from an
hyperendemic area PLoS ONE 9:e104848, 2014
470. Yun, H., Damm, F., Yap, D., Schwarzer, A., Chaturvedi, A., Jyotsana, N., Lubbert, M., Bullinger, L., Dohner, K.,
Geffers, R., Aparicio, S., Humphries, R.K., Ganser, A. and Heuser, M. Impact of MLL5 expression on decitabine
efficacy and DNA methylation in acute myeloid leukemia Haematologica 99:1456-1464, 2014
471. Challen, G.A., Sun, D., Mayle, A., Jeong, M., Luo, M., Rodriguez, B., Mallaney, C., Celik, H., Yang, L., Xia, Z.,
Cullen, S., Berg, J., Zheng, Y., Darlington, G.J., Li, W. and Goodell, M.A. Dnmt3a and Dnmt3b have overlapping
and distinct functions in hematopoietic stem cells Cell Stem Cell 15:350-364, 2014
472. Uechi, G., Sun, Z., Schreiber, E.M., Halfter, W. and Balasubramani, M. Proteomic view of basement
membranes from human retinal blood vessels, inner limiting membranes, and lens capsules J. Proteome Res.
13:3693-3705, 2014
473. Salomon, C., Yee, S., Scholz-Romero, K., Kobayashi, M., Vaswani, K., Kvaskoff, D., Illanes, S.E., Mitchell, M.D.
and Rice, G.E. Extravillous trophoblast cells-derived exosomes promote vascular smooth muscle cell
migration Front. Pharmacol. 5:175, 2014
474. Foronjy, R.F., Dabo, A.J., Cummins, N. and Geraghty, P. Leukemia inhibitory factor protects the lung during
respiratory syncytial viral infection BMC Immunol. 15:41, 2014
475. Genz, B., Thomas, M., PÜtzer, B.M., Siatkowski, M., Fuellen, G., Vollmar, B. and Abshagen, K. Adenoviral
overexpression of Lhx2 attenuates cell viability but does not preserve the stem cell like phenotype of
hepatic stellate cells Exp. Cell Res. 328:429-443, 2014
476. Fergusson, J.R., Smith, K.E., Fleming, V.M., Rajoriya, N., Newell, E.W., Simmons, R., Marchi, E., BjÖrkander, S.,
Kang, Y.-H., Swadling, L., Kurioka, A., Sahgal, N., Lockstone, H., Baban, D., Freeman, G.J., Sverremark-
EkstrÖm, E., Davis, M.M., Davenport, M.P., Venturi, V., Ussher, J.E., Willberg, C.B. and Klenerman, P.
CD161 defines a transcriptional and functional phenotype across distinct human T cell lineages Cell Rep. 9:
1075-1088, 2014
477. Dietrich, P.A., Yang, C., Leung, H.H.L., Lynch, J.R., Gonzales, E., Liu, B., Haber, M., Norris, M.D., Wang, J. and
Wang, J.Y. GPR84 sustains aberrantΒ-catenin signaling in leukemic stem cells for maintenance of MLL
leukemogenesis Blood 124:3284-3294, 2014
478. Li, J., Hale, J., Bhagia, P., Xue, F., Chen, L., Jaffray, J., Yan, H., Lane, J., Gallagher, P.G., Mohandas, N., Liu, J.
and An, X. Isolation and transcriptome analyses of human erythroid progenitors: BFU-E and CFU-E Blood
124:3636-3645, 2014
479. Slany, A., Meshcheryakova, A., Beer, A., Ankersmit, H.J., Paulitschke, V. and Gerner, C. Plasticity of
fibroblasts demonstrated by tissue-specific and function-related proteome profiling Clin. Proteomics 11:41,
2014
480. Lunardi, S., Jamieson, N.B., Lim, S.Y., Griffiths, K.L., Carvalho-Gaspar, M., Al-Assar, O., Yameen, S., Carter, R.
C., McKay, C.J., Spoletini, G., D'Ugo, S., Silva, M.A., Sansom, O.J., Janssen, K.-P., Muschel, R.J. and Brunner, T.
B. IP-10/CXCL10 induction in human pancreatic cancer stroma influences lymphocytes recruitment and
correlates with poor survival Oncotarget 5:11064-11080, 2014
481. Cizkova, D., Devaux, S., Le Marrec-Croq, F., Franck, J., Slovinska, L., Blasko, J., Rosocha, J., Spakova, T.,
Lefebvre, C., Fournier, I. and Salzet, M. Modulation properties of factors released by bone marrow stromal
cells on activated microglia: an in vitro study Sci. Rep. 4:7514, 2014
482. Fujita, Y., Ito, M., Kojima, T., Yatsuga, S., Koga, Y. and Tanaka, M. GDF15 is a novel biomarker to evaluate
efficacy of pyruvate therapy for mitochondrial diseases Mitochondrion 20:34-42, 2015
483. Beppu, M., Sawai, S., Misawa, S., Sogawa, K., Mori, M., Ishige, T., Satoh, M., Nomura, F. and Kuwabara, S.
Serum cytokine and chemokine profiles in patients with chronic inflammatory demyelinating polyneuropathy
J. Neuroimmunol. 279:7-10, 2015
484. Machuca, T.N., Cypel, M., Yeung, J.C., Bonato, R., Zamel, R., Chen, M., Azad, S., Hsin, M.K., Saito, T., Guan, Z.,
Waddell, T.K., Liu, M. and Keshavjee, S. Protein expression profiling predicts graft performance in clinical ex
vivo lung perfusion Ann. Surg. 261:591-597, 2015
485. Walmsley, G.G., Rinkevich, Y., Hu, M.S., Montoro, D.T., Lo, D.D., McArdle, A., Maan, Z.N., Morrison, S.D.,
Duscher, D., Whittam, A.J., Wong, V.W., Weissman, I.L., Gurtner, G.C., and Longaker, M.T. Live fibroblast
harvest reveals surface marker shift in vitro Tissue Eng. Pt. C 21:314-321, 2015
486. Carayon, K., Chaoui, K., Ronzier, E., Lazar, I., Bertrand-Michel, J., Roques, V., Balor, S., Terce, F., Lopez, A.,
SalomÉ, L. and Joly, E. Proteolipidic composition of exosomes changes during reticulocyte maturation. J.
Biol. Chem. 286:34426-34439, 2011
487. Authier, A., Farrand, K.J., Broadley, K.W.R., Ancelet, L.R., Hunn, M.K., Stone, S., McConnell, M.J. and
Hermans, I.F. Enhanced immunosuppression by therapy-exposed glioblastoma multiforme tumor cells Int. J.
Cancer 136:2566-2578, 2015
488. Chen, Z.-Y., Raghav, K., Lieu, C.H., Jiang, Z.-Q., Eng, C., Vauthey, J.-N., Chang, G.J., Qiao, W., Morris, J.,
Hong, D., Hoff, P., Tran, H., Menter, D.G., Heymach, J., Overman, M. and Kopetz, S. Cytokine profile and
prognostic significance of high neutrophil-lymphocyte ratio in colorectal cancer Br. J. Cancer 112:1088-
1097, 2015
489. HollmÉn, M., Roudnicky, F., Karaman, S. and Detmar, M. Characterization of macrophage - cancer cell
crosstalk in estrogen receptor positive and triple-negative breast cancer Sci. Rep. 5:9188, 2015
490. Bank, M., Stein, A., Sison, C., Glazer, A., Jassal, N., McCarthy, D., Shatzer, M., Hahn, B., Chugh, R., Davies, P.
and Bloom, O. Elevated circulating levels of the pro-inflammatory cytokine macrophage migration inhibitory
factor in individuals with acute spinal cord injury Arch. Phys. Med. Rehabil. 96:633-644, 2015
491. Calon, A., Lonardo, E., Berenguer-Llergo, A., Espinet, E., Hernando-Momblona, X., Iglesias, M., Sevillano, M.,
Palomo-Ponce, S., Tauriello, D.V.F., Byrom, D., Cortina, C., Morral, C., Barcelo, C., Tosi, S., Riera, A., Stephan-
Otto Attolini, C., Rossell, D., Sancho, E. and Batlle, E. Stromal gene expression defines poor-prognosis
subtypes in colorectal cancer Nat. Genet. 47:320-329, 2015
492. Kim, E.S., Moon, J., Herbst, R.S., Redman, M.W., Dakhil, S.R., Velasco, M.R. Jr, Hirsch, F.R., Mack, P.C., Kelly,
K., Heymach, J.V., and Gandara, D.R. Phase II trial of carboplatin, paclitaxel, cetuximab, and bevacizumab
followed by cetuximab and bevacizumab in advanced nonsquamous non-small-cell lung cancer SWOG S0536
J. Thorac. Oncol. 8:1519-1528, 2013
493. Stefanantoni, K., Sciarra, I., Vasile, M., Badagliacca, R., Poscia, R., Pendolino, M., Alessandri, C., Vizza, C.D.,
Valesini, G. and Riccieri, V. Elevated serum levels of macrophage migration inhibitory factor and stem cell
growth factorΒin patients with idiopathic and systemic sclerosis associated pulmonary arterial
hypertension Reumatismo 66:270-276, 2015
494. Wu, Z., Wang, L., Guo, Z., Wang, K., Zhang, Y., Tian, K., Zhang, J., Sun, W. and Yu, C. Experimental study on
differences in clivus chordoma bone invasion: An iTRAQ-based quantitative proteomic analysis PLoS ONE 10:
e0119523, 2015
495. Cheng, J.M., Akkerhuis, M., Malaud, E., Piquer, D., Merle, D., Meilhac, O., van Geuns, R.-J., Boersma, E.,
Kardys, I. and Fareh, J. Evaluation of 42 cytokines, chemokines and growth factors for prediction of
cardiovascular outcome in patients with coronary artery disease Int. J. Cardiol. 184:724-727, 2015
496. Khaiboullina, S.F., Gumerova, A.R., Khafizova, I.F., Martynova, E.V., Lombardi, V.C., Bellusci, S. and Rizvanov,
A.A. CCL27: Novel cytokine with potential role in pathogenesis of multiple sclerosis BioMed Res. Int. 189638,
2015
497. Miyanaga, A., Masuda, M., Tsuta, K., Kawasaki, K., Nakamura, Y., Sakuma, T., Asamura, H., Gemma, A. and
Yamada, T. Hippo pathway gene mutations in malignant mesothelioma: Revealed by RNA and targeted exon
sequencing J. Thorac. Oncol. 10:844-851, 2015
498. Kleiner, G., Zanin, V., Monasta, L., Crovella, S., Caruso, L., Milani, D. and Marcuzzi, A. Pediatric patients with
inflammatory bowel disease exhibit increased serum levels of proinflammatory cytokines and chemokines, but
decreased circulating levels of macrophage inhibitory protein-1Β, interleukin-2 and interleukin-17 Exp. Ther.
Med. 9:2047-2052, 2015
499. Obenauf, A.C., Zou, Y., Ji, A.L., Vanharanta, S., Shu, W., Shi, H., Kong, X., Bosenberg, M.C., Wiesner, T., Rosen,
N., Lo, R.S. and Massague, J. Therapy-induced tumour secretomes promote resistance and tumour
progression Nature 520:368-372, 2015
500. Xu-Monette, Z.Y., Tu, M., Jabbar, K.J., Cao, X., Tzankov, A., Visco, C., Cai, Q., Montes-Moreno, S., An, Y.,
Dybkaer, K., Chiu, A., Orazi, A., Zu, Y., Bhagat, G., Richards, K.L., Hsi, E.D., Choi, W.W.L., van Krieken, J.H., Huh,
J., Ponzoni, M., Ferreri, A.J.M., Zhao, X., MØller, M.B., Farnen, J.P., Winter, J.N., Piris, M.A., Miranda, R.N.,
Medeiros, L.J. and Young, K.H. Clinical and biological significance of de novo CD5+ diffuse large B-cell
lymphoma in Western countries Oncotarget 6:5615-5633, 2015
501. Sekyere, S.O., Suneetha, P.V., Hardtke, S., Falk, C.S., Hengst, J., Manns, M.P., Cornberg, M., Wedemeyer, H.
and Schlaphoff, V. Type I interferon elevates co-regulatory receptor expression on CMV- andEBV-specific
CD8 T cells in chronic hepatitis C Front. Immunol. 6:270, 2015
502. Guo, J., Huang, F., Liu, J., Chen, Y., Wang, W., Cao, B., Zou, Z., Liu, S., Pan, J., Bao, C., Zeng, M., Xiao, H., Gao,
H., Yang, S., Zhao, Y., Liu, Q., Zhou, H., Zhu, J., Liu, X., Liang, W., Yang, Y., Zheng, S., Yang, J., Diao, H., Su, K.,
Shao, L., Cao, H., Wu, Y., Zhao, M., Tan, S., Li, H., Xu, X., Wang, C., Zhang, J., Wang, L., Wang, J., Xu, J., Li, D.,
Zhong, N., Cao, X., Gao, G.F., Li, L. and Jiang, C. The serum profile of hypercytokinemia factors identified in
H7N9-infected patients can predict fatal outcomes Sci. Rep. 5:10942, 2015
503. Reyes-Gibby, C.C., Yuan, C., Wang, J., Yeung, S.-C.J. and Shete, S. Gene network analysis shows immune-
signaling and ERK1/2 as novel genetic markers for multiple addiction phenotypes: alcohol, smoking and opioid
addiction BMC Syst. Biol. 9:25, 2015
504. Zhao, T., Zhao, W., Meng, W., Liu, C., Chen, Y., Gerling, I.C., Weber, K.T., Bhattacharya, S.K., Kumar, R. and
Sun, Y. VEGF-C/VEGFR-3 pathway promotes myocyte hypertrophy and survival in the infarcted
myocardium Am. J. Transl. Res. 7:697-709, 2015
505. Fan, E.W., Li, C.-C., Wu, W.-J., Huang, C.-N., Li, W.-M., Ke, H.-L., Yeh, H.-C., Wu, T.-F., Liang, P.-I., Ma, L.-J.
and Li, C.-F. FGF7 overexpression is an independent prognosticator in patients with urothelial carcinoma of
the upper urinary tract and bladder J. Urol. 194:223-229, 2015
506. Potter, A.S. and Potter, S.S. Molecular anatomy of palate development PLoS ONE 10:e0132662, 2015
507. Niu, P., Smagul, A., Wang, L., Sadvakas, A., Sha, Y., PÉrez, L.M., Nussupbekova, A., Amirbekov, A., Akanov, A.
A., GÁlvez, B.G., Jordan, I.K. and Lunyak, V.V. Transcriptional profiling of interleukin-2-primed human
adipose derived mesenchymal stem cells revealed dramatic changes in stem cells response imposed by
replicative senescence Oncotarget 6:17938-17957, 2015
508. Hjorth, M., Norheim, F., Meen, A.J., Pourteymour, S., Lee, S., Holen, T., Jensen, J., Birkeland, K.I., Martinov, V.
N., Langleite, T.M., Eckardt, K., Drevon, C.A. and Kolset, S.O. The effect of acute and long-term physical
activity on extracellular matrix and serglycin in human skeletal muscle Physiol. Rep. 3:e12473, 2015
509. Shah, M.S., Fogelman, D.R., Raghav, K.P.S., Heymach, J.V., Tran, H.T., Jiang, Z.-Q., Kopetz, S. and Daniel, C.
R. Joint prognostic effect of obesity and chronic systemic inflammation in patients with metastatic
colorectal cancer Cancer 121:2968-2975, 2015
510. Sebastian, A., Hum, N.R., Hudson, B.D. and Loots, G.G. Cancer-osteoblast interaction reduces Sost
expression in osteoblasts and up-regulates lncRNA MALAT1 in prostate cancer Microarrays 4:503-519,
2015
511. Schiro, A., Wilkinson, F.L., Weston, R., Smyth, J.V., Serracino-Inglott, F. and Alexander, M.Y. Elevated levels
of endothelial-derived microparticles, and serum CXCL9 and SCGF-Βare associated with unstable
asymptomatic carotid plaques Sci. Rep. 5:16658, 2015
512. Tachida, Y., Sakurai, H., Okutsu, J., Suda, K., Sugita, R., Yaginuma, Y., Ogura, Y., Shimada, K., Isono, F.,
Kubota, K. and Kobayashi, H. Proteomic comparison of the secreted factors of mesenchymal stem cells from
bone marrow, adipose tissue and dental pulp J. Proteomics Bioinform. 8:266-273, 2015
513. Weber, K.T., Satoh, S., Alipui, D.O., Virojanapa, J., Levine, M., Sison, C., Quraishi, S., Bloom, O. and Chahine,
N.O. Exploratory study for identifying systemic biomarkers that correlate with pain response in patients with
intervertebral disc disorders Immunol. Res. 63:170-180, 2015
514. Nijaguna, M.B., Patil, V., Urbach, S., Shwetha, S.D., Sravani, K., Hegde, A.S., Chandramouli, B.A., Arivazhagan,
A., Marin, P., Santosh, V. and Somasundaram, K. Glioblastoma-derived macrophage colony-stimulating factor
(MCSF) induces microglial release of insulin-like growth factor-binding protein 1 (IGFBP1) to promote
angiogenesis J. Biol. Chem. 290:23401-23415, 2015
515. Kisiel, J.B., Raimondo, M., Taylor, W.R., Yab, T.C., Mahoney, D.W., Sun, Z., Middha, S., Baheti, S., Zou, H.,
Smyrk, T.C., Boardman, L.A., Petersen, G.M. and Ahlquist, D.A. New DNA methylation markers for pancreatic
cancer: Discovery, tissue validation, and pilot testing in pancreatic juice Clin. Cancer Res. 21:4473-4481, 2015
516. Fagone, P., Nicoletti, F., Salvatorelli, L., Musumeci, G.and Magro, G. Cyclin D1 and Ewing's sarcoma/PNET: A
microarray analysis Acta Histochem. 117:824-828, 2015
517. Antonis, V., Ritsa, B., Despina, M., Georgina, M., Maria, P., Vasiliki, D., George, P., Peter, D., Dimitris, L. and
Kiessling, A.A. Microarray analyses reveal marked differences in growth factor and receptor expression
between 8-cell human embryos and pluripotent stem cells Stem Cells Dev. 25:160-177, 2016
518. Solano-Aguilar, G., Molokin, A., Botelho, C., Fiorino, A.-N., Vinyard, B., Li, R., Chen, C., Urban Jr., J., Dawson,
H., Andreyeva, I., Haverkamp, M. and Hibberd, P.L. Transcriptomic profile of whole blood cells from elderly
subjects fed probiotic bacteria Lactobacillus rhamnosus GG ATCC 53103 (LGG) in a phase I open label
study PLoS ONE 11:e0147426, 2016
519. Mego,M., Cholujova, D., Minarik, G., Sedlackova, T., Gronesova, P., Karaba, M., Benca, J., Cingelova, S.,
Cierna, Z., Manasova, D., Pindak, D., Sufliarsky, J., Cristofanilli, M., Reuben, J.M. and Mardiak, J. CXCR4-SDF-
1 interaction potentially mediates trafficking of circulating tumor cells in primary breast cancer BMC Cancer
16(1):127, 2016
520. Comar, M., Zanotta, N., Zanconati, F., Cortale, M., Bonotti, A., Cristaudo, A. and Bovenzi, M. Chemokines
involved in the early inflammatory response and in pro-tumoral activity in asbestos-exposed workers from
an Italian coastal area with territorial clusters of pleural malignant mesothelioma Lung Cancer 94:61-67, 2016
521. Fujita, T., Soontrapa, K., Ito, Y., Iwaisako, K., Moniaga, C.S., Asagiri, M., Majima, M. and Narumiya, S. Hepatic
stellate cells relay inflammation signaling from sinusoids to parenchyma in mouse models of immune-
mediated hepatitis Hepatology 63:1325-1339, 2016
522. Bailey, P., Chang, D.K., Nones, K., Johns, A.L., Patch, A.-N., Gingras, M.-C., Miller, D.K., et al. Genomic
analyses identify molecular subtypes of pancreatic cancer Nature 531:47-52, 2016
523. Pan, Q., O'Connor, M.I., Coutts, R.D., Hyzy, S.L., Olivares-Navarrete, R., Schwartz, Z. and Boyan, B.D.
Characterization of osteoarthritic human knees indicates potential sex differences Biol. Sex Differ. 7:27, 2016
524. Momcilovic, O., Sivapatham, R., Oron, T.R., Meyer, M., Mooney, S., Rao, M.S., and Zeng, X. Derivation,
characterization, and neural differentiation of integration-free induced pluripotent stem cell lines from
Parkinson's disease patients carrying SNCA, LRRK2, PARK2, and GBA mutations PLoS ONE 11:e0154890,
2016
525. Toivonen, R., Kong, L., Rasool, O., Lund, R.J., Lahesmaa, R. and HÄnninen, A. Activation of plasmacytoid
dendritic cells in colon-draining lymph nodes during Ctrobacter rodentium infection involves pathogen-
sensing and inflammatory pathways distinct from conventional dendritic cells J. Immunol. 196:4750-4759,
2016
526. Yildiz-Arslan, S., Coon, J.S., Hope, T.J. and Kim, J.J. Transcriptional profiling of human endocervical tissues
reveals distinct gene expression in the follicular and luteal phases of the menstrual cycle Biol. Reprod. 94:
138, 1-13, 2016
527. Matter, M.S., Marquardt, J.U., Andersen, J.B., Quintavalle, C., Korokhov, N., Stauffer, J.K., Kaji, K., Decaens,
T., Quagliata, L., Elloumi, F., Hoang, T., Molinolo, A., Conner, E.A., Weber, A., Heikenwalder, M., Factor, V.M. and
Thorgeirsson, S.S. Oncogenic driver genes and the inflammatory microenvironment dictate liver tumor
phenotype Hepatology 63:1888-1899, 2016
528. Gilchrist, J.J., Heath, J.N., Msefula, C.L., Naranbhai, V., Mandala, W., MacLennan, J.M., Molyneux E.M.,
Graham, S.M., Drayson, M.T., Molyneux, M.E. and MacLennan, C.A. Cytokine profiles during invasive
nontyphoidal Salmonella disease predict outcome in African children Clin. Vaccine Immunol. 23:601-609, 2016
529. Andriani, G.A., Almeida, V.P., Faggioli, F., Mauro, M., Tsai, W.L., Santambrogio, L., Maslov, A., Gadina, M.,
Campisi, J., Vijg, J. and Montagna, C. Whole chromosome instability induces senescence and promotes SASP
Sci. Rep. 6:35218, 2016
530. Meynier, S., Undurraga, M., Tille, J.C., Petignat, P. and Cohen, M. In ovo progression of borderline ovarian
tumors J. Oncol. Transl. Res. 2:109, 2016
531. Ngo, D., Sinha, S., Shen, D., Kuhn, E.W., Keyes, M.J., Shi, X., Benson, M.D., O'Sullivan, J.F., Keshishian, H.,
Farrell, L.A., Fifer, M.A., Vasan, R.S., Sabatine, M.S., Larson, M.G., Carr, S.A., Wang, T.J. and Gerszten, R.E.
Aptamer-based proteomic profiling reveals novel candidate biomarkers and pathways in cardiovascular
disease Circulation 134:270-285, 2016
532. Molinari, E., Bar, H., Pyle, A.M. and Patrizio, P. Transcriptome analysis of human cumulus cells reveals
hypoxia as the main determinant of follicular senescence Mol. Hum. Reprod. 22:866-876, 2016
533. Schrier, S.B., Hill, A.S., Plana, D. and Lauffenburger, D.A. Synergistic communication between CD4+ T cells
and monocytes impacts the cytokine environment Sci. Rep. 6:34942, 2016
534. Koh, Y.Q., Peiris, H.N., Vaswani, K., Reed, S., Rice, G.E., Salomon, C. and Mitchell, M.D. Characterization of
exosomal release in bovine endometrial intercaruncular stromal cells Reprod. Biol. Endocrinol. 14:78, 2016
535. Houshdaran, S., Nezhat, C.R., Vo, K.C., Zelenko, Z., Irwin, J.C. and Giudice, L.C. Aberrant endometrial DNA
methylome and associated gene expression in women with endometriosis Biol. Reprod. 95:1-16, 2016
536. LaganÀ, A., Perumal, D., Melnekoff, D., Readhead, B., Kidd, B.A., Leshchenko, V., Kuo, P.-Y., Keats, J.,
DeRome, M., Yesil, J., Auclair, D., Lonial, S., Chari, A., Cho, H.J., Barlogie, B., Jagannath, S., Dudley, J.T. and
Parekh, S. Integrative network analysis identifies novel drivers of pathogenesis and progression in newly
diagnosed multiple myeloma Leukemia 32:120-130, 2018
537. Yue, R., Shen, B. and Morrison, S.J. Clec11a/osteolectin is an osteogenic growth factor that promotes the
maintenance of the adult skeleton eLife 5:e18782, 2016
538. Sordi, V., Ferri, A., Ceserani, V., Ciusani, E., Dugnani, E., Pellegrini, S., Nano, R., Pecciarini, L., Pessina, A.,
Pascucci, L., Piemonti, L. and Alessandri, G. Establishment, characterization and long-term culture of human
endocrine pancreas-derived microvascular endothelial cells Cytotherapy 19:141-152, 2017
539. Nagy, A., Pongor, L.S., SzabÓ, A., Santarpia, M. and GyÖrffy, B. KRAS driven expression signature has
prognostic power superior to mutation status in non-small cell lung cancer Int. J. Cancer 140:930-937, 2017
540. Hueso, M., De Ramon, L., Navarro, E., Ripoll, E., Cruzado, J.M., Grinyo, J.M. and Torras, J. Silencing of CD40
in vivo reduces progression of experimental atherogenesis through an NF-ΚB/miR-125b axis and reveals
new potential mediators in the pathogenesis of atherosclerosis Atherosclerosis 255:80-89, 2016
541. Preciados, M., Yoo, C. and Roy, D. Estrogenic endocrine disrupting chemicals influencing NRF1 regulated
gene networks in the development of complex human brain diseases Int. J. Mol. Sci. 17:2086, 2016
542. Ahola-Olli, A.V., WÜrtz, P., Havulinna, A.S., Aalto, K., PitkÄnen, N., LehtimÄki, T., KÄhÖnen, M.,
LyytikÄinen, L.-P., Raitoharju, E., SeppÄlÄ, I., Sarin, A.-P., Ripatti, S., Palotie, A., Perola, M., Viikari, J.S.,
Jalkanen, S., Maksimow, M., Salomaa, V., Salmi, M., Kettunen, J. and Raitakari, O.T. Genome-wide association
study identifies 27 loci influencing concentrations of circulating cytokines and growth factors Am. J. Hum.
Genet. 100:40-50, 2017
543. Jalili, M., Salehzadeh-Yazdi, A., Mohammadi, S., Yaghmaie, M., Ghavamzadeh, A. and Alimoghaddam, K. Meta-
analysis of gene expression profiles in acute promyelocytic leukemia reveals involved pathways Int. J.
Hematol. Oncol. Stem Cell Res. 11:1-12, 2017
544. Xie, L., Mao, M., Zhou, L., Zhang, L. and Jiang, B. Signal factors secreted by 2D and spheroid mesenchymal
stem cells and by cocultures of mesenchymal stem cells derived microvesicles and retinal photoreceptor
neurons Stem Cells Int. 2017:2730472, 2017
545. Peacock, Z.S., Schwab, J.H., Faquin, W.C., Hornicek, F.J., Benita, Y., Ebb, D.H. and Kaban, L.B. Genetic
analysis of giant cell lesions of the maxillofacial and axial/appendicular skeletons J. Oral Maxillofac. Surg. 75:
298-308, 2017
546. Rea, M., Eckstein, M., Eleazer, R., Smith, C. and Fondufe-Mittendorf, Y.N. Genome-wide DNA methylation
reprogramming in response to inorganic arsenic links inhibition of CTCF binding, DNMT expression and cellular
transformation Sci.Rep. 7: 41474, 2017
547. Yin, X., Yu, H., Jin, X., Li, J., Guo, H., Shi, Q., Yin, Z., Xu, Y., Wang, X., Liu, R., Wang, S. and Zhang, L. Human
blood CD1c+ dendritic cells encompass CD5high and CD5low subsets that differ significantly in phenotype,
gene expression, and functions J. Immunol. 198:1553-1564, 2017
548. Chung, B., Esmaeili, A.A., Gopalakrishna-Pillai, S., Murad, J.P., Andersen, E.S., Reddy, N.K., Srinivasan, G.,
Armstrong, B., Chu, C., Kim, Y., Tong, T., Waisman, J., Yim, J.H., Badie, B. and Lee, P.P. Human brain
metastatic stroma attracts breast cancer cells via chemokines CXCL16 and CXCL12 npj Breast Cancer 3:
6, 2017
549. de Sa Rodrigues, L.C., Holmes, K.E., Thompson, V., Newton, M.A. and Stein, T.J. Tumourigenic canine
osteosarcoma cell lines associated with frizzled-6 up-regulation and enhanced side population cell frequency
Vet. Comp. Oncol. 15:78-93, 2017
550. Pourteymour, S., Eckardt, K., Holen, T., Langleite, T., Lee, S., Jensen, J., Birkeland, K.I., Drevon, C.A. and
Hjorth, M. Global mRNA sequencing of human skeletal muscle: Search for novel exercise-regulated myokines
Mol. Metabolism 6:352-365, 2017
551. Le Bihana, M.-C., Bigot, A., Jensen, S.S., Dennis, J.L., Rogowska-Wrzesinska, A., LainÉ, J., Gache, V., Furling,
D., Jensen, O.N., Voit, T., Mouly, V., Coulton, G.R. and Butler-Browne, G. In-depth analysis of the secretome
identifies three major independent secretory pathways in differentiating human myoblasts J. Proteomics 77:
344-356, 2012
552. Hartwig, S., Raschke, S., Knebel, B., Scheler, M., Irmler, M., Passlack, W., Muller, S., Hanisch, F.-G., Franz, T.,
Li, X., Dicken, H.-D., Eckardt, K., Beckers, J., de Angelis, M.H., Weigert, C., HÄring, H.-U., Al-Hasani, H.,
Ouwens, D.M., Eckel, J., Kotzka, J. and Lehr, S. Secretome profiling of primary human skeletal muscle cells
Biochim. Biophys. Acta 1844:1011-1017, 2014
553. Luga, V., Zhang, L., Viloria-Petit, A.M., Ogunjimi, A.A., Inanlou, M.R., Chiu, E., Buchanan, M., Hosein, A.N.,
Basik, M. and Wrana, J.L. Exosomes mediate stromal mobilization of autocrine Wnt-PCP signaling in breast
cancer cell migration Cell 151:1542-1556, 2012
554. Kharaziha, P., Chioureas, D., Rutishauser, D., Baltatzis, G., Lennartsson, L., Fonseca, P., Azimi, A., Hultenby,
K., Zubarev, R., UllÉn, A., Yachnin, J., Nilsson, S. and Panaretakis, T. Molecular profiling of prostate cancer
derived exosomes may reveal a predictive signature for response to docetaxel Oncotarget 6:21740-21754,
2015
555. Potter, E.A., Dolgova, E.V., Proskurina, A.S., Efremov, Y.R., Minkevich, A.M., Rozanov, A.S., Peltek, S.E.,
Nikolin, V.P., Popova, N.A., Seledtsov, I.A., Molodtsov, V.V., Zavyalov, E.L., Taranov, O.S., Baiborodin, S.I.,
Ostanin, A.A., Chernykh, E.R., Kolchanov, N.A. and Bogachev, S.S. Gene expression profiling of tumor-
initiating stem cells from mouse Krebs-2 carcinoma using a novel marker of poorly differentiated cells
Oncotarget 8:9425-9441, 2017
556. Li, H., Wang, W., Zhang, L., Lan, Q., Wang, J., Cao, Y. and Zhao, J. Identification of a long noncoding RNA-
associated competing endogenous RNA network in intracranial aneurysm World Neurosurg. 97:684-692, 2017
557. Bae, H.-S., Yoon, W.-J., Cho, Y.-D., Islam, R., Shin, H.-R., Kim, B.-S., Lim, J.-M., Seo, M.-S., Cho, S.-A., Choi,
K.-Y., Baek, S.-H., Kim, H.-G., Woo, K.-M., Baek, J.-H., Lee, Y.-S. and Ryoo, H.-M. An HDAC inhibitor,
Entinostat/MS-275, partially prevents delayed cranial suture closure in heterozygous Runx2 null mice J.
Bone Miner. Res. 32:951-961, 2017
558. JØrgensen, H., Hill, A.S., Beste, M.T., Kumar, M.P., Chiswick, E., Fedorcsak, P., Isaacson, K.B., Lauffenburger,
D.A., Griffith, L.G. and Qvigstad, E. Peritoneal fluid cytokines related to endometriosis in patients evaluated
for infertility Fertil. Steril. 107:1191-1199.e2, 2017
559. Svetlovska, D., Miskovska, V., Cholujova, D., Gronesova, P., Cingelova, S., Chovanec, M., Sycova-Mila, Z.,
Obertova, J., Palacka, P., Rajec, J., Kalavska, K., Usakova, V., Luha, J., Ondrus, D., Spanik, S., Mardiak, J. and
Mego, M. Plasma cytokines correlated with disease characteristics, progression-free survival, and overall
survival in testicular germ-cell tumor patients Clin. Genitourin. Cancer 15:411-416, 2017
560. Rinaldi, L., Avgustinova, A., Martin, M., Datta, D., Solanas, G., Prats, N. and Benitah, S.A. Loss of Dnmt3a and
Dnmt3b does not affect epidermal homeostasis but promotes squamous transformation through PPAR-Γ
eLife 6:e21697, 2017
561. Ran, S., Sun, N., Liu, Y., Zhang, W., Li, Y., Wei, L., Wang, J. and Liu, B. Fluoride resistance capacity in
mammalian cells involves complex global gene expression changes FEBS Open Bio. 7:968-980, 2017
562. Uhlen, M., Zhang, C., Lee, S., Sjostedt, E., Fagerberg, L., Bidkhori, G., Benfeitas, R., Arif, M., Liu, Z., Edfors, F.,
Sanli, K., von Feilitzen, K., Oksvold, P., Lundberg, E., Hober, S., Nilsson, P., Mattsson, J., Schwenk, J.M.,
Brunnstrom, H., Glimelius, B., Sjoblom, T., Edqvist, P.-H., Djureinovic, D., Micke, P., Lindskog, C., Mardinoglu, A.
and Ponten, F. A pathology atlas of the human cancer transcriptome Science 357:660, 2017
563. Jiang, J., Ye, F., Yang, X., Zong, C., Gao, L., Yang, Y., Zhao, Q., Han, Z. and Wei, L. Peri-tumor associated
fibroblasts promote intrahepatic metastasis of hepatocellular carcinoma by recruiting cancer stem cells
Cancer Lett. 404:19-28, 2017
564. Wu, S., Hivert, M.-F., Cardenas, A., Zhong, J., Rifas-Shiman, S.L., Agha, G., Colicino, E., Just, A.C.,
Amarasiriwardena, C., Lin, X., Litonjua, A.A., DeMeo, D.L., Gillman, M.W., Wright, R.O., Oken, E. and Baccarelli,
A.A. Exposure to low levels of lead in utero and umbilical cord blood DNA methylation in project viva: An
epigenome-wide association study Environ. Health Perspect. 125:EHP1246, 2017
565. CoccÈ, V., Farronato, D., Brini, A.T., Masia, C., GiannÌ, A.B., Piovani, G., Sisto, F., Alessandri, G., Angiero, F.
and Pessina, A. Drug loaded gingival mesenchymal stromal cells (GinPa-MSCs) inhibit in vitro proliferation of
oral squamous cell carcinoma Sci. Rep. 7:9376, 2017
566. Khaiboullina, S.F., Mendelevich, E.G., Shigapova, L.H., Shagimardanova, E., Gazizova, G., Nikitin, A.,
Martynova, E., Davidyuk, Y.N., Bogdanov, E.I., Gusev, O., van den Maagdenberg, A.M.J.M., Giniatullin, R.A. and
Rizvanov, A.A. Cerebellar atrophy and changes in cytokines associated with theCACNA1AR583Q mutation
in a Russian familial hemiplegic migraine type 1 family Front. Cell. Neurosci. 11:263, 2017
567. Soekmadji, C., Riches, J.D., Russell, P.J., Ruelcke, J.E., McPherson, S., Wang, C., Hovens, C.M., Corcoran, N.
M., The Australian Prostate Cancer Collaboration BioResource, Hill, M.M. and Nelson, C.C. Modulation of
paracrine signaling by CD9 positive small extracellular vesicles mediates cellular growth of androgen deprived
prostate cancer Oncotarget 8:52237-52255, 2017
568. Emene, C.C., Kravchenko, I.E., Aibatova, G.I. and Rizvanov, A.A. Analysis of serum cytokines and single-
nucleotide polymorphisms of SOD1, SOD2, and CAT in erysipelas patients J. Immunol. Res. 2017:2157247,
2017
569. Pasztoi, M., Pezoldt, J., Beckstette, M., Lipps, C., Wirth, D., Rohde, M., Paloczi, K., Buzas, E.I. and Huehn, J.
Mesenteric lymph node stromal cell-derived extracellular vesicles contribute to peripheral de novo induction
of Foxp3+ regulatory T cells Eur. J. Immunol. 47:2142-2152, 2017
570. Abe, Y., Kimura, N., Takahashi, R., Gotou, M., Mizukami, K., Uchida, H. and Matsubara, E. Relationship between
cytokine levels in the cerebrospinal fluid and 11C-Pittsburgh compound B retention in patients with mild
cognitive impairment Geriatr. Gerontol. Int. 17:1907-1913, 2017
571. Lau, D., Elezagic, D., Hermes, G., Morgelin, M., Wohl, A.P., Koch, M., Hartmann, U., Hollriegl, S., Wagener, R.,
Paulsson, M., Streichert, T. and Klatt, A.R. The cartilage-specific lectin C-type lectin domain family 3
member A (CLEC3A) enhances tissue plasminogen activator-mediated plasminogen activation J. Biol. Chem.
293:203-214, 2018
572. Xu, X., Yoshizaki, H., Ishigaki, Y., Kubo, E., Minato, H. and Kiyokawa, E. Upregulation of multiple signaling
pathways by Dock5 deletion in epithelial cells Mol. Vis. 23:1081-1092, 2017
573. Bonin, S., Zanotta, N., Sartori, A., Bratina, A., Manganotti, P., Trevisan, G. and Comar, M. Cerebrospinal fluid
cytokine expression profile in multiple sclerosis and chronic inflammatory demyelinating polyneuropathy
Immunol. Invest. 47:135-145, 2018
574. LÉvesque, J.-P., Zannettino, A.C.W., Pudney, M., Niutta, S., Haylock, D.N., Snapp, K.R., Kansas, G.S., Berndt,
M.C. and Simmons, P.J. PSGL-1-mediated adhesion of human hematopoietic progenitors to P-selectin
results in suppression of hematopoiesis Immunity 11:369-378, 1999
575. Sun, Y., Wang, Y., Zhou, L., Zou, Y., Huang, G., Gao, G., Ting, S., Lei, X. and Ding, X. Spheroid-cultured human
umbilical cord-derived mesenchymal stem cells attenuate hepatic ischemia-reperfusion injury in rats Sci.
Rep. 8:2518, 2018
576. Karsten, E., Breen, E. and Herbert, B.R. Red blood cells are dynamic reservoirs of cytokines Sci. Rep. 8:
3101, 2018
577. Goncalves, M.D., Hwang, S.-K., Pauli, C., Murphy, C.J., Cheng, Z., Hopkins, B.D., Wu, D., Loughran, R.M.,
Emerling, B.M., Zhang, G., Fearon, D.T. and Cantley, L.C. Fenofibrate prevents skeletal muscle loss in mice
with lung cancer Proc. Natl. Acad. Sci. USA 115:E743-E752, 2018
578. Hu, Q., Luni, C. and Elvassore, N. Microfluidics for secretome analysis under enhanced endogenous signaling
Biochem. Biophys. Res. Commun. 497:480-484, 2018
579. Ohno, T., Aoki, H., Ohno, S., Nishihara, M., Furusho, A., Hiromatsu, S., Akashi, H., Fukumoto, Y. and Tanaka, H.
Cytokine profile of human abdominal aortic aneurysm: Involvement of JAK/STAT pathway Ann. Vasc. Dis. 11:
84-90, 2018
580. Ando, W., Yokomori, H., Tsutsui, N., Yamanouchi, E., Suzuki, Y., Oda, M., Inagaki, Y., Otori, K. and Okazaki, I.
Serum matrix metalloproteinase-1 level represents disease activity as opposed to fibrosis in patients with
histologically proven nonalcoholic steatohepatitis Clin. Mol. Hepatol. 24:61-76, 2018
581. Kozawa, S., Ueda, R., Urayama, K., Sagawa, F., Endo, S., Shiizaki, K., Kurosu, H., de Almeida, G.M., Hasan, S.
M., Nakazato, K., Ozaki, S., Yamashita, Y., Kuro-o, M. and Sato, T.N. The body-wide transcriptome landscape
of disease models iScience 2:238-268, 2018
582. Rai, M.F., Tycksen , E.D., Sandell , L.J. and Brophy, R.H. Advantages of RNA-seq compared to RNA
microarrays for transcriptome profiling of anterior cruciate ligament tears J. Orthop. Res. 36:484-497, 2018
583. Lai, K.P., Li, J.W., Chan, T.F., Chen, A., Lee, C.Y.L., Yeung, W.S.B. and Wong, C.K.C. Transcriptomic and
methylomic analysis reveal the toxicological effect of 2,3,7,8-Tetrachlorodibenzodioxin on human embryonic
stem cell Chemosphere 206:663-673, 2018
584. Ruzafa, N., Pereiro, X., Lepper, M.F., Hauck, S.M. and Vecino, E. A proteomics approach to identify candidate
proteins secreted by MÜller glia that protect ganglion cells in the retina Proteomics 18:1700321, 2018
585. Schmidt, L., Taiyab, A., Melvin, V.S., Jones, K.L. and Williams, T. Increased FGF8 signaling promotes
chondrogenic rather than osteogenic development in the embryonic skull Dis. Models Mech. 11:dmm031526,
2018
586. Zhao, X., Li, Y. and Wu, H. A novel scoring system for acute myeloid leukemia risk assessment based on the
expression levels of six genes Int. J. Mol. Med. 42:1495-1507, 2018
587. Sukowati, C.H.C., Patti, R., Pascut, D., Ladju, R.B., Tarchi, P., Zanotta, N., Comar, M., Tiribelli, C. and CrocÈ,
L.S. Serum stem cell growth factor beta for the prediction of therapy response in hepatocellular carcinoma
BioMed Res. Int. 2018:6435482, 2018
588. Geyh, S., RodrÍguez-Paredes, M., JÄger, P., Koch, A., Bormann, F., Gutekunst, J., Zilkens, C., Germing, U.,
Kobbe, G., Lyko, F., Haas, R. and Schroeder, T. Transforming growth factorΒ1-mediated functional inhibition
of mesenchymal stromal cells in myelodysplastic syndromes and acute myeloid leukemia Haematologica 103:
1462-1471, 2018
589. Tasena, H., Faiz, A., Timens, W., Noordhoek, J., Hylkema, M.N., Gosens, R., Hiemstra, P.S., Spira, A., Postma,
D.S., Tew, G.W., Grimbaldeston, M.A., van den Berge, M., Heijink, I.H. and Brandsma, C.-A. microRNA-mRNA
regulatory networks underlying chronic mucus hypersecretion in COPD Eur. Respir. J. 52:1701556, 2018
590. GÓmez, C.M.A., Woodcock, R.M., Smith, J.J., Voss, R.S. and Delgado, J.P. Using transcriptomics to enable a
plethodontid salamander (Bolitoglossa ramosi) for limb regeneration research BMC Genomics 19:704, 2018
591. Kodama, T., Yi, J., Newberg, J.Y., Tien, J.C., Wu, H., Finegold, M.J., Kodama, M., Wei, Z., Tamura, T., Takehara,
T., Johnson, R.L., Jenkins, N.A. and Copeland, N.G. Molecular profiling of nonalcoholic fatty liver disease-
associated hepatocellular carcinoma using SB transposon mutagenesis Proc. Natl. Acad. Sci. USA 115:E10417
-E10426, 2018
592. Wang, P., Liu, Z., Zhang, X., Li, J., Sun, L., Ju, Z., Li, J., Chan, P., Liu, G.-H., Zhang, W., Song, M. and Qu, J.
CRISPR/Cas9-mediated gene knockout reveals a guardian role of NF-ΚB/RelA in maintaining the
homeostasis of human vascular cells Protein Cell 9:945-965, 2018
593. Anderson, B.W., Suh, Y.-S., Choi, B., Lee, H.-J., Yab, T.C., Taylor, W.R., Dukek, B.A., Berger, C.K., Cao, X.,
Foote, P.H., Devens, M.E., Boardman, L.A., Kisiel, J.B., Mahoney, D.W., Slettedahl, S.W., Allawi, H.T., Lidgard, G.
P., Smyrk, T.C., Yang, H.-K., and Ahlquist, D.A. Detection of gastric cancer with novel methylated DNA
markers: Discovery, tissue validation, and pilot testing in plasma Clin. Cancer Res. 24:5724-5734, 2018
594. Shen, B., Vardy, K., Hughes, P., Tasdogan, A., Zhao, Z., Yue, R., Crane, G. and Morrison, S.J. Integrin alpha11
is an osteolectin receptor and is required for the maintenance of adult skeletal bone mass eLife 8:e42274,
2019
595. Nava, S., Sordi, V., Pascucci, L., Tremolada, C., Ciusani, E., Zeira, O., Cadei, M., Soldati, G., Pessina, A.,
Parati, E., Slevin, M. and Alessandri, G. Long-lasting anti-inflammatory activity of human microfragmented
adipose tissue Stem Cells Int. 2019:5901479, 2019
596. Kisiel, J.B., Dukek, B.A., Kanipakam, R.V.S.R, Ghoz, H.M., Yab, T.C., Berger, C.K., Taylor, W.R., Foote, P.H.,
Giama, N.H., Onyirioha, K., Abdallah, M.A., Burger, K.N., Slettedahl, S.W., Mahoney, D.W., Smyrk, T.C., Lewis, J.
T., Giakoumopoulos, M., Allawi, H.T., Lidgard, G.P., Roberts, L.R. and Ahlquist, D.A. Hepatocellular carcinoma
detection by plasma methylated DNA: Discovery, phase I pilot, and phase II clinical validation Hepatology 69:
1180-1192, 2019
597. Assi, S.A., Imperato, M.R., Coleman, D.J.L., Pickin, A., Potluri, S., Ptasinska, A., Chin, P.S., Blair, H., Cauchy,
P., James, S.R., Zacarias-Cabeza, J., Gilding, L.N., Beggs, A., Clokie, S., Loke, J.C., Jenkin, P., Uddin, A., Delwel,
R., Richards, S.J., Raghavan, M., Griffiths, M.J., Heidenreich, O., Cockerill, P.N. and Bonifer, C. Subtype-
specific regulatory network rewiring in acute myeloid leukemia Nat. Genet. 51:151-162, 2019
598. Jalkanen, J., Hollmen, M., Maksimow, M., Jalkanen, S. and Hakovirta, H. Serum cytokine levels differ
according to major cardiovascular risk factors in patients with lower limb atherosclerosis Cytokine 114:74-
80, 2019
599. Lu, Y., Monaco, G., Camous, X., Andiappan, A.K., Rotzschke, O., Ng, T.P. and Larbi, A. Biomarker signatures
predicting 10-year all-cause and disease-specific mortality J. Gerontol. A 74:469-479, 2019
600. Romanov, Y.A., Volgina, N.E., Vtorushina, V.V., Romanov, A.Y., Dugina, T.N., Kabaeva, N.V. and Sukhikh, G.T.
Comparative analysis of secretome of human umbilical cord- and bone marrow-derived multipotent
mesenchymal stromal cells Bull. Exp. Biol. Med. 166:535-540, 2019
601. Dabee, S., Barnabas, S.L., Lennard, K.S., Jaumdally, S.Z., Gamieldien, H., Balle, C., Happel, A.-U., Murugan, B.
D., Williamson, A.-L., Mkhize, N., Dietrich, J., Lewis, D.A., Chiodi, F., Hope, T.J., Shattock, R., Gray, G., Bekker,
L.-G., Jaspan, H.B. and Passmore, J.-A.S. Defining characteristics of genital health in South African adolescent
girls and young women at high risk for HIV infection PLoS ONE 14:e0213975, 2019
602. Merrick, D., Sakers, A., Irgebay, Z., Okada, C., Calvert, C., Morley, M.P., Percec, I. and Seale, P. Identification
of a mesenchymal progenitor cell hierarchy in adipose tissue Science 364:2501, 2019
603. Altuna, M., Urdanoz-Casado, A., deGordoa, J.S.-R., Zelaya, M.V., Labarga, A., Lepesant, J.M.J., Roldan, M.,
Blanco-Luquin, I., Perdones, A., Larumbe, R., Jerico, I., Echavarri, C., Mendez-Lopez, I., Di Stefano, L. and
Mendioroz, M. DNA methylation signature of human hippocampus in Alzheimer's disease is linked to
neurogenesis Clin. Epigenet. 11:91, 2019
604. Bai , M., Han , Y., Wu, Y., Liao, J., Li, L., Wang, L., Li, Q., Xing, W., Chen, L., Zou, W. and Li, J. Targeted genetic
screening in mice through haploid embryonic stem cells identifies critical genes in bone development PLoS
Biol. 17:e3000350, 2019
605. Nees, T.A., Rosshirt, N., Zhang, J.A., Reiner, T., Sorbi, R., Tripel, E., Walker, T., Schiltenwolf, M., Hagmann, S.
and Moradi, B. Synovial cytokines significantly correlate with osteoarthritis-related knee pain and disability:
Inflammatory mediators of potential clinical relevance J. Clin. Med.8:1343, 2019
606. Magistroni, V., Mauri, M., D'Aliberti, D., Mezzatesta, C., Crespiatico, I., Nava, M., Fontana, D., Sharma, N.,
Parker, W., Schreiber, A., Yeung, D., Pirola, A., Readelli, S., Massimino, L., Wang, P., Khandelwal, P., Citterio, S.,
Viltadi, M., Bombelli, S., Rigolio, R., Perego, R., Boultwood, J., Morotti, A., Saglio, G., Kim, D.-W., Branford, S.,
Gambacorti-Passerini, C. and Piazza, R. De novo UBE2A mutations are recurrently acquired during chronic
myeloid leukemia progression and interfere with myeloid differentiation pathways Haematologica 104:1789-
1797, 2019
607. Huang, W., Wang, C., Xie, L., Wang,X., Zhang, L., Chen, C. and Jiang, B. Traditional two-dimensional
mesenchymal stem cells (MSCs) are better than spheroid MSCs on promoting retinal ganglion cells survival
and axon regeneration Exp. Eye Res. 185:107699, 2019
608. Tikhonova, A.N., Dolgalev, I., Hu, H., Sivaraj, K.K., Hoxha, E., Cuesta-Dominguez, A., Pinho, S., Akhmetzyanova,
I., Gao, J., Witkowski, M., Guillamot, M., Gutkin, M.C., Zhang, Y., Christian Marier, C., Diefenbach, C., Kousteni,
S., Heguy, A., Zhong, H., Fooksman, D.R., Butler, J.M., Economides, A.,Frenette, P.S., Adams, R.H., Satija, R.,
Tsirigos, A. and Aifantis, I. The bone marrow microenvironment at single-cell resolution Nature 569:222-228,
2019
609. Shi, R., Hu, J., Li, W., Wang, Z., Pan, Y., Bai, M., Mao, W., Wang, X., Zhong, M., Yuan, Y., Lau, J., Sun, Z. and
Zhao, S. Protective effects of Clec11a in islets against lipotoxicity via modulation of proliferation and lipid
metabolismin mice Exp. Cell Res. 384:111613, 2019
610. Kallioinen, M., Scheinin, A., Maksimow, M., Langsjo, J., Kaisti, K., Takala, R., Vahlberg, T., Valli, K., Salmi, M.,
Scheinin, H. and Maksimow, A. The influence of dexmedetomidine and propofol on circulating cytokine levels
in healthy subjects BMC Anesthesiol. 19:222, 2019
611. Kulcenty, K., Piotrowski, I., Wroblewska, J.P., Wasiewicz, J. and Suchorska, W.M. The composition of surgical
wound fluids from breast cancer patients is affected by intraoperative radiotherapy treatment and depends
on the molecular subtype of breast cancer Cancers 12:11, 2020
612. Yawata, N., Awate, S., Liu, Y.-C., Yuan, S., Woon, K., Siak, J., Kawano, Y., Sonoda, K., Mehta, J.S. and Yawata,
M. Kinetics of tear fluid proteins after endothelial keratoplasty and predictive factors for recovery from
corneal haze J. Clin. Med. 9:63, 2020
613. Zhang, Q., Thakur, C., Fu, Y., Bi, Z., Wadgaonkar, P., Xu, L., Liu, Z., Liu, W., Wang, J., Kidder, B.L. and Chen, F.
Mdig promotes oncogenic gene expression through antagonizing repressive histone methylation markers
Theranostics 10:602-614, 2020
614. Matsushita, Y., Nagata, M., Kozloff, K.M., Welch, J.D., Mizuhashi, K., Tokavanich, N., Hallett, S.A., Link, D.C.,
Nagasawa, T., Ono, W. and Ono, N. A Wnt-mediated transformation of the bone marrow stromal cell identity
orchestrates skeletal regeneration Nat. Commun. 11:332, 2020
615. Hu, Y., Zhang, Y., Ni, C.-Y., Chen, C.-Y., Rao, S.-S., Yin, H., Huang, J., Tan, Y.-J., Wang, Z.-X., Cao, J., Liu,Z.-
Z., Xie, P.-L., Wu, B., Luo, J. and Xie, H. Human umbilical cord mesenchymal stromal cells-derived
extracellular vesicles exert potent bone protective effects by CLEC11A-mediated regulation of bone
metabolism Theranostics 10:2293-2308, 2020
616. Ramalingam, P., Poulos, M.G., Lazzari, E., Gutkin, M.C., Lopez, D., Kloss, C.C., Crowley, M.J., Katsnelson, L.,
Freire, A.G., Greenblatt, M.B., Park, C.Y. and Butler, J.M. Chronic activation of endothelial MAPK disrupts
hematopoiesis via NFKB dependent inflammatory stress reversible by SCGF Nat. Commun. 11: 666, 2020
617. Sanchez, R. and Mackenzie, S.A. Integrative network analysis of differentially methylated and expressed genes
for biomarker identification in leukemia Sci. Rep. 10:2123, 2020
618. Tan, G.-K., Pryce, B.A., Stabio, A., Brigande, J.V., Wang, C., Xia, Z., Tufa, S.F., Keene, D.R. and Schweitzer, R.
TGFβsignaling is critical for maintenance of the tendon cell fate eLife9:e52695, 2020
619. Karsten, E., Breen, E., McCracken, S.A., Clarke, S. and Herbert, B.R. Red blood cells exposed to cancer cells in
culture have altered cytokine profiles and immune function Sci. Rep.10:7727, 2020
620. Chen, W.-F., Liu, Z.-Q., Pu, Z.-N., Xu, J.-Q., Yao, L., Wu, X.-Y., Xu, X.-Y., Xu, J.-X., Zhu, Y., Wang, Y., Cheng,J.,
Zhu, L., Zhou, P.-H. and Li, Q.-L. Multiplex immunoassays reveal increased serum cytokines and chemokines
associated with the subtypes of achalasia Neurogastroenterol. Motil. 32:e13832, 2020
621. Zhou, J., Chern, B.S.M., Barton-Smith, P., Phoon, J.W.L., Tan, T.Y., Viardot-Foucault, V., Ku, C.W., Tan, H.H.,
Chan, J.K.Y. and Lee, Y.H. Peritoneal fluid cytokines reveal new insights of endometriosis subphenotypes Int. J.
Mol. Sci. 21:3515, 2020
622. Diaz-Payno, P.J., Browe, D.C., Cunniffe, G.M. and Kelly, D.J. The identification of articular cartilage and growth
plate extracellular matrix-specific proteins supportive of either osteogenesis or stable chondrogenesis of stem
cells Biochem. Biophys. Res. Commun. 528:285-291, 2020
623. Tarantino, G., Citro, V., Balsano, C. and Capone, D. Could SCGF-beta levels be associated with inflammation
markers and insulin resistance in male patients suffering from obesity-related NAFLD? Diagnostics 10:395, 2020
624. Liu, L., Broszczak, D.A., Broadbent, J.A., Singh, D.P., Steck, R., Parker, T.J. and Peake, J.M. Comparative label-
free mass spectrometric analysis of temporal changes in the skeletal muscle proteome after impact trauma in
rats Am. J. Physiol. Endocrinol. Metab. 318:E1022-E1037, 2020
625. Rostam, H.M., Fisher, L.E., Hook,A.L., Burroughs, L., Luckett, J.C., Figueredo, G.P., Mbadugha, C., Teo, A.C.K.,
Latif, A., Kammerling, L., Day, M., Lawler, K., Barrett, D., Elsheikh, S., Ilyas, M., Winkler, D.A., Alexander, M.R. and
Ghaemmaghami, A.M. Immune-instructive polymers control macrophage phenotype and modulate the foreign
body response in vivo Matter 2:1564-1581, 2020
626. Balogh, A., Milibak, T., Szabo, V., Nagy, Z.Z. and Resch, M.D. Position of macula lutea and presence of
proliferative vitreoretinopathy affect vitreous cytokine expression in rhegmatogenous retinal detachment PLoS
ONE 15:e0234525, 2020
627. Molatlhegi, R.P., Liebenberg, L.J., Leslie, A., Noel-Romas, L., Mabhula, A., Mchunu, N., Perner, M., Birse, K.,
Ngcapu, S., Adamson, J.H., Govender, K., Garrett, N.J., Samsunder, N., Burgener, A.D., Karim, S.S.A., Karim,
Q.A., Passmore, J.-A.S., and McKinnon, L.R. Plasma concentration of injectable contraceptive correlates with
reduced cervicovaginal growth factor expression in South African women Mucosal Immunol. 13:449-459, 2020
628. Shanbhag, S., Mohamed-Ahmed, S., Lunde, T.H.F., Suliman, S., Bolstad, A.I., Hervig, T. and Mustafa, K. Influence
of platelet storage time on human platelet lysates and platelet lysate-expanded mesenchymal stromal cells for
bone tissue engineering Stem Cell Res. Ther. 11:351, 2020
629. Hosnijeh, F.S., van der Straten, L., Kater, A.P., van Oers, M.H.J., Posthuma, W.F.M., Chamuleau, M.E.D., Bellido,
M., Doorduijn, J.K., van Gelder, M., Hoogendoorn, M., de Boer, F., te Raam, D.D., Kerst, J.M., Marijt, E.W.A.,
Raymakers, R.A.P., Koene, H.R., Schaafsma, M.R., Dobber, J.A., Tonino, S.H., Kersting, S.S., Langerak, A.W. and
Levin, M.-D. Proteomic markers with prognostic impact on outcome of chronic lymphocytic leukemia patients
under chemo-immunotherapy: results from the HOVON 109 study Exp. Hematol. 89:55-60, 2020
630. Wei, H., Xu, Y., Wang, Y., Xu, L., Mo, C., Li, L., Shen, B., Sun, Y., Cheng, P., Yang, L., Pang, Y., Qin, A., Cao, Y.,
Morrison, S.J. and Yue, R. Identification of fibroblast activation protein as an osteogenic suppressor and anti-
osteoporosis drug target Cell Rep. 33:108252, 2020
1 2