Sharan R, Ulitsky I, Shamir R: Network-based prediction of protein function. Mol Syst Biol. 2007, 3: 88-
Article
PubMed Central
PubMed
Google Scholar
Lee I, Lehner B, Crombie C, Wong W, Fraser AG, Marcotte EM: A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans. Nat Genet. 2008, 40 (2): 181-188. 10.1038/ng.2007.70
Article
CAS
PubMed
Google Scholar
Lee I, Lehner B, Vavouri T, Shin J, Fraser AG, Marcotte EM: Predicting genetic modifier loci using functional gene networks. Genome Res. 2010, 20 (8): 1143-1153. 10.1101/gr.102749.109
Article
PubMed Central
CAS
PubMed
Google Scholar
Barabasi AL, Gulbahce N, Loscalzo J: Network medicine: a network-based approach to human disease. Nat Rev Genet. 2011, 12 (1): 56-68. 10.1038/nrg2918
Article
PubMed Central
CAS
PubMed
Google Scholar
Pattin KA, Moore JH: Role for protein-protein interaction databases in human genetics. Expert Rev Proteomics. 2009, 6 (6): 647-659. 10.1586/epr.09.86
Article
PubMed Central
CAS
PubMed
Google Scholar
Emily M, Mailund T, Hein J, Schauser L, Schierup MH: Using biological networks to search for interacting loci in genome-wide association studies. Eur J Hum Genet. 2009, 17 (10): 1231-1240. 10.1038/ejhg.2009.15
Article
PubMed Central
CAS
PubMed
Google Scholar
Kumar D, Nath L, Kamal MA, Varshney A, Jain A, Singh S, Rao KV: Genome-wide analysis of the host intracellular network that regulates survival of Mycobacterium tuberculosis. Cell. 2010, 140 (5): 731-743. 10.1016/j.cell.2010.02.012
Article
CAS
PubMed
Google Scholar
Navratil V, de Chassey B, Combe CR, Lotteau V: When the human viral infectome and diseasome networks collide: towards a systems biology platform for the aetiology of human diseases. BMC Syst Biol. 2011, 5: 13- 10.1186/1752-0509-5-13
Article
PubMed Central
PubMed
Google Scholar
Ideker T, Ozier O, Schwikowski B, Siegel AF: Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics. 2002, 18 (Suppl 1): S233-240. 10.1093/bioinformatics/18.suppl_1.S233
Article
PubMed
Google Scholar
Ulitsky I, Shamir R: Identification of functional modules using network topology and high-throughput data. BMC Syst Biol. 2007, 1: 8- 10.1186/1752-0509-1-8
Article
PubMed Central
PubMed
Google Scholar
Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, et al.: Integration of biological networks and gene expression data using Cytoscape. Nat Protoc. 2007, 2 (10): 2366-2382. 10.1038/nprot.2007.324
Article
PubMed Central
CAS
PubMed
Google Scholar
Lin CC, Hsiang JT, Wu CY, Oyang YJ, Juan HF, Huang HC: Dynamic functional modules in co-expressed protein interaction networks of dilated cardiomyopathy. BMC Syst Biol. 2010, 4: 138- 10.1186/1752-0509-4-138
Article
PubMed Central
PubMed
Google Scholar
Carlson BM: Human embryology and developmental biology. 2004, St. Louis: Mosby, 3,
Google Scholar
Dobson AT, Raja R, Abeyta MJ, Taylor T, Shen S, Haqq C, Pera RA: The unique transcriptome through day 3 of human preimplantation development. Hum Mol Genet. 2004, 13 (14): 1461-1470. 10.1093/hmg/ddh157
Article
CAS
PubMed
Google Scholar
Li SS, Liu YH, Tseng CN, Singh S: Analysis of gene expression in single human oocytes and preimplantation embryos. Biochem Biophys Res Commun. 2006, 340 (1): 48-53. 10.1016/j.bbrc.2005.11.149
Article
CAS
PubMed
Google Scholar
Wells D, Patrizio P: Gene expression profiling of human oocytes at different maturational stages and after in vitro maturation. Am J Obstet Gynecol. 2008, 198 (4): e451-459. discussion 455 e459-411,
Article
Google Scholar
Zhang P, Zucchelli M, Bruce S, Hambiliki F, Stavreus-Evers A, Levkov L, Skottman H, Kerkela E, Kere J, Hovatta O: Transcriptome profiling of human pre-implantation development. PLoS One. 2009, 4 (11): e7844- 10.1371/journal.pone.0007844
Article
PubMed Central
PubMed
Google Scholar
Assou S, Boumela I, Haouzi D, Anahory T, Dechaud H, De Vos J, Hamamah S: Dynamic changes in gene expression during human early embryo development: from fundamental aspects to clinical applications. Hum Reprod Update. 2011, 17 (2): 272-290. 10.1093/humupd/dmq036
Article
CAS
PubMed
Google Scholar
Geng X, Oliver G: Elucidating the molecular characteristics of organogenesis in human embryos. Genome Biol. 2010, 11 (8): 130- 10.1186/gb-2010-11-8-130
Article
PubMed Central
PubMed
Google Scholar
Fang H, Yang Y, Li C, Fu S, Yang Z, Jin G, Wang K, Zhang J, Jin Y: Transcriptome analysis of early organogenesis in human embryos. Dev Cell. 2010, 19 (1): 174-184. 10.1016/j.devcel.2010.06.014
Article
CAS
PubMed
Google Scholar
Yi H, Xue L, Guo MX, Ma J, Zeng Y, Wang W, Cai JY, Hu HM, Shu HB, Shi YB, Li WX: Gene expression atlas for human embryogenesis. FASEB J. 2010, 24 (9): 3341-3350. 10.1096/fj.10-158782
Article
PubMed Central
CAS
PubMed
Google Scholar
Wang K, Fang H, Xiao D, Zhu X, He M, Pan X, Shi J, Zhang H, Jia X, Du Y, Zhang J: Converting redox signaling to apoptotic activities by stress-responsive regulators HSF1 and NRF2 in fenretinide treated cancer cells. PLoS One. 2009, 4 (10): e7538- 10.1371/journal.pone.0007538
Article
PubMed Central
PubMed
Google Scholar
Fang H, Wang K, Zhang J: Transcriptome and proteome analyses of drug interactions with natural products. Curr Drug Metab. 2008, 9 (10): 1038-1048. 10.2174/138920008786927802
Article
CAS
PubMed
Google Scholar
Fang H, Du Y, Xia L, Li J, Zhang J, Wang K: A Topology-Preserving Selection and Clustering Approach to Multidimensional Biological Data. OMICS. 2011, ,
Google Scholar
Mitiku N, Baker JC: Genomic analysis of gastrulation and organogenesis in the mouse. Dev Cell. 2007, 13 (6): 897-907. 10.1016/j.devcel.2007.10.004
Article
CAS
PubMed
Google Scholar
Boyer LA, Lee TI, Cole MF, Johnstone SE, Levine SS, Zucker JP, Guenther MG, Kumar RM, Murray HL, Jenner RG, Gifford DK, Melton DA, Jaenisch R, Young RA: Core transcriptional regulatory circuitry in human embryonic stem cells. Cell. 2005, 122 (6): 947-956. 10.1016/j.cell.2005.08.020
Article
PubMed Central
CAS
PubMed
Google Scholar
Assou S, Le Carrour T, Tondeur S, Strom S, Gabelle A, Marty S, Nadal L, Pantesco V, Reme T, Hugnot JP, Gasca S, Hovatta O, Hamamah S, Klein B, De Vos J: A meta-analysis of human embryonic stem cells transcriptome integrated into a web-based expression atlas. Stem Cells. 2007, 25 (4): 961-973. 10.1634/stemcells.2006-0352
Article
PubMed Central
CAS
PubMed
Google Scholar
Pan G, Tian S, Nie J, Yang C, Ruotti V, Wei H, Jonsdottir GA, Stewart R, Thomson JA: Whole-genome analysis of histone H3 lysine 4 and lysine 27 methylation in human embryonic stem cells. Cell Stem Cell. 2007, 1 (3): 299-312. 10.1016/j.stem.2007.08.003
Article
CAS
PubMed
Google Scholar
Bader GD, Donaldson I, Wolting C, Ouellette BF, Pawson T, Hogue CW: BIND--The Biomolecular Interaction Network Database. Nucleic Acids Res. 2001, 29 (1): 242-245. 10.1093/nar/29.1.242
Article
PubMed Central
CAS
PubMed
Google Scholar
Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D: The Database of Interacting Proteins: 2004 update. Nucleic Acids Res. 2004, D449-451. 32 Database,
Google Scholar
Kerrien S, Alam-Faruque Y, Aranda B, Bancarz I, Bridge A, Derow C, Dimmer E, Feuermann M, Friedrichsen A, Huntley R, Kohler C, Khadake J, Leroy C, Liban A, Lieftink C, Montecchi-Palazzi L, Orchard S, Risse J, Robbe K, Roechert B, Thorneycroft D, Zhang Y, Apweiler R, Hermjakob H: IntAct--open source resource for molecular interaction data. Nucleic Acids Res. 2007, D561-565. 35 Database,
Google Scholar
Mishra GR, Suresh M, Kumaran K, Kannabiran N, Suresh S, Bala P, Shivakumar K, Anuradha N, Reddy R, Raghavan TM, Menon S, Hanumanthu G, Gupta M, Upendran S, Gupta S, Mahesh M, Jacob B, Mathew P, Chatterjee P, Arun KS, Sharma S, Chandrika KN, Deshpande N, Palvankar K, Raghavnath R, Krishnakanth R, Karathia H, Rekha B, Nayak R, Vishnupriya G: Human protein reference database--2006 update. Nucleic Acids Res. 2006, D411-414. 34 Database,
Google Scholar
Joshi-Tope G, Gillespie M, Vastrik I, D'Eustachio P, Schmidt E, de Bono B, Jassal B, Gopinath GR, Wu GR, Matthews L, Lewis S, Birney E, Stein L: Reactome: a knowledgebase of biological pathways. Nucleic Acids Res. 2005, D428-432. 33 Database,
Google Scholar
von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, Kruger B, Snel B, Bork P: STRING 7--recent developments in the integration and prediction of protein interactions. Nucleic Acids Res. 2007, D358-362. 35 Database,
Google Scholar
Hood L, Heath JR, Phelps ME, Lin B: Systems biology and new technologies enable predictive and preventative medicine. Science. 2004, 306 (5696): 640-643. 10.1126/science.1104635
Article
CAS
PubMed
Google Scholar
Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Muertter RN, Edgar R: NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res. 2009, D885-890. 37 Database,
Google Scholar
Muller FJ, Laurent LC, Kostka D, Ulitsky I, Williams R, Lu C, Park IH, Rao MS, Shamir R, Schwartz PH, Schmidt NO, Loring JF: Regulatory networks define phenotypic classes of human stem cell lines. Nature. 2008, 455 (7211): 401-405. 10.1038/nature07213
Article
PubMed Central
PubMed
Google Scholar
Lu SJ, Hipp JA, Feng Q, Hipp JD, Lanza R, Atala A: GeneChip analysis of human embryonic stem cell differentiation into hemangioblasts: an in silico dissection of mixed phenotypes. Genome Biol. 2007, 8 (11): R240- 10.1186/gb-2007-8-11-r240
Article
PubMed Central
PubMed
Google Scholar
Sun BW, Yang AC, Feng Y, Sun YJ, Zhu Y, Zhang Y, Jiang H, Li CL, Gao FR, Zhang ZH, Wang WC, Kong XY, Jin G, Fu SJ, Jin Y: Temporal and parental-specific expression of imprinted genes in a newly derived Chinese human embryonic stem cell line and embryoid bodies. Hum Mol Genet. 2006, 15 (1): 65-75.
Article
PubMed
Google Scholar
Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP: Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA. 2005, 102 (43): 15545-15550. 10.1073/pnas.0506580102
Article
PubMed Central
CAS
PubMed
Google Scholar
Smyth GK: Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol. 2004, 3: Article 3-
Google Scholar
Subramanian A, Kuehn H, Gould J, Tamayo P, Mesirov JP: GSEA-P: a desktop application for Gene Set Enrichment Analysis. Bioinformatics. 2007, 23 (23): 3251-3253. 10.1093/bioinformatics/btm369
Article
CAS
PubMed
Google Scholar
Waddington CH: The strategy of the genes: a discussion of some aspects of theoretical biology. 1957, Allen, Unwin,
Google Scholar
Graf T, Enver T: Forcing cells to change lineages. Nature. 2009, 462 (7273): 587-594. 10.1038/nature08533
Article
CAS
PubMed
Google Scholar
Macarthur BD, Ma'ayan A, Lemischka IR: Systems biology of stem cell fate and cellular reprogramming. Nat Rev Mol Cell Biol. 2009, 10 (10): 672-681.
PubMed Central
CAS
PubMed
Google Scholar
Bhattacharya S, Zhang Q, Andersen ME: A deterministic map of Waddington's epigenetic landscape for cell fate specification. BMC Syst Biol. 2011, 5: 85- 10.1186/1752-0509-5-85
Article
PubMed Central
PubMed
Google Scholar
Wang J, Zhang K, Xu L, Wang E: Quantifying the Waddington landscape and biological paths for development and differentiation. Proc Natl Acad Sci USA. 2011, 108 (20): 8257-8262. 10.1073/pnas.1017017108
Article
PubMed Central
CAS
PubMed
Google Scholar
Thomson JA, Itskovitz-Eldor J, Shapiro SS, Waknitz MA, Swiergiel JJ, Marshall VS, Jones JM: Embryonic stem cell lines derived from human blastocysts. Science. 1998, 282 (5391): 1145-1147.
Article
CAS
PubMed
Google Scholar
Pera MF, Cooper S, Mills J, Parrington JM: Isolation and characterization of a multipotent clone of human embryonal carcinoma cells. Differentiation. 1989, 42 (1): 10-23. 10.1111/j.1432-0436.1989.tb00602.x
Article
CAS
PubMed
Google Scholar
Takahashi K, Yamanaka S: Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell. 2006, 126 (4): 663-676. 10.1016/j.cell.2006.07.024
Article
CAS
PubMed
Google Scholar
Takahashi K, Tanabe K, Ohnuki M, Narita M, Ichisaka T, Tomoda K, Yamanaka S: Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell. 2007, 131 (5): 861-872. 10.1016/j.cell.2007.11.019
Article
CAS
PubMed
Google Scholar
Yu J, Vodyanik MA, Smuga-Otto K, Antosiewicz-Bourget J, Frane JL, Tian S, Nie J, Jonsdottir GA, Ruotti V, Stewart R, Thomson JA: Induced pluripotent stem cell lines derived from human somatic cells. Science. 2007, 318 (5858): 1917-1920. 10.1126/science.1151526
Article
CAS
PubMed
Google Scholar
Park IH, Zhao R, West JA, Yabuuchi A, Huo H, Ince TA, Lerou PH, Lensch MW, Daley GQ: Reprogramming of human somatic cells to pluripotency with defined factors. Nature. 2008, 451 (7175): 141-146. 10.1038/nature06534
Article
CAS
PubMed
Google Scholar
Chin MH, Mason MJ, Xie W, Volinia S, Singer M, Peterson C, Ambartsumyan G, Aimiuwu O, Richter L, Zhang J, Khvorostov I, Ott V, Grunstein M, Lavon N, Benvenisty N, Croce CM, Clark AT, Baxter T, Pyle AD, Teitell MA, Pelegrini M, Plath K, Lowry WE: Induced pluripotent stem cells and embryonic stem cells are distinguished by gene expression signatures. Cell Stem Cell. 2009, 5 (1): 111-123. 10.1016/j.stem.2009.06.008
Article
PubMed Central
CAS
PubMed
Google Scholar
Doi A, Park IH, Wen B, Murakami P, Aryee MJ, Irizarry R, Herb B, Ladd-Acosta C, Rho J, Loewer S, Miller J, Schlaeger T, Daley GQ, Feinberg AP: Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nat Genet. 2009, 41 (12): 1350-1353. 10.1038/ng.471
Article
PubMed Central
CAS
PubMed
Google Scholar
Poirier F, Chan CT, Timmons PM, Robertson EJ, Evans MJ, Rigby PW: The murine H19 gene is activated during embryonic stem cell differentiation in vitro and at the time of implantation in the developing embryo. Development. 1991, 113 (4): 1105-1114.
CAS
PubMed
Google Scholar
Doetschman TC, Eistetter H, Katz M, Schmidt W, Kemler R: The in vitro development of blastocyst-derived embryonic stem cell lines: formation of visceral yolk sac, blood islands and myocardium. J Embryol Exp Morphol. 1985, 87: 27-45.
CAS
PubMed
Google Scholar
Xiao L, Wang K, Teng Y, Zhang J: Component plane presentation integrated self-organizing map for microarray data analysis. FEBS Lett. 2003, 538 (1-3): 117-124. 10.1016/S0014-5793(03)00156-X
Article
CAS
PubMed
Google Scholar
Fang H: Topology-Preserving Selection and Clustering (TPSC). http://www.cs.bris.ac.uk/~hfang/TPSC/index.html
Gene Set Enrichment Analysis (GSEA). http://www.broadinstitute.org/gsea/index.jsp
Benjamini Y, Hochberg Y: Controlling the False Discovery Rate - a Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society Series B-Methodological. 1995, 57 (1): 289-300.
Google Scholar