Ivanova NB, Dimos JT, Schaniel C, Hackney JA, Moore KA, Lemischka IR: A stem cell molecular signature. Science. 2002, 298: 601-604. 10.1126/science.1073823
Article
CAS
PubMed
Google Scholar
Ramalho-Santos M, Yoon S, Matsuzaki Y, Mulligan RC, Melton DA: "Stemness": transcriptional profiling of embryonic and adult stem cells. Science. 2002, 298: 597-600. 10.1126/science.1072530
Article
CAS
PubMed
Google Scholar
Bhattacharya B, Miura T, Brandenberger R, Mejido J, Luo Y, Yang AX, Joshi BH, Ginis I, Thies RS, Amit M, Lyons I, Condie BG, Itskovitz-Eldor J, Rao MS, Puri RK: Gene expression in human embryonic stem cell lines: unique molecular signature. Blood. 2004, 103: 2956-2964. 10.1182/blood-2003-09-3314
Article
CAS
PubMed
Google Scholar
Pavlidis P, Weston J, Cai J, Noble WS: Learning gene functional classifications from multiple data types. J Comput Biol. 2002, 9: 401-411. 10.1089/10665270252935539
Article
CAS
PubMed
Google Scholar
Jaakkola T, Diekhans M, Haussler D: Using the Fisher kernel method to detect remote protein homologies. Proc Int Conf Intell Syst Mol Biol. 1999, 149-158.
Google Scholar
Moler EJ, Chow ML, Mian IS: Analysis of molecular profile data using generative and discriminative methods. Physiol Genomics. 2000, 4: 109-126.
CAS
PubMed
Google Scholar
Brown MP, Grundy WN, Lin D, Cristianini N, Sugnet CW, Furey TS, Ares M, Haussler D: Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc Natl Acad Sci USA. 2000, 97: 262-267. 10.1073/pnas.97.1.262
Article
PubMed Central
CAS
PubMed
Google Scholar
Furey TS, Cristianini N, Duffy N, Bednarski DW, Schummer M, Haussler D: Support vector machine classification and validation of cancer tissue samples using microarray expression data. Bioinformatics. 2000, 16: 906-914. 10.1093/bioinformatics/16.10.906
Article
CAS
PubMed
Google Scholar
Zhu Y, Shen X, Pan W: Network-based support vector machine for classification of microarray samples. BMC Bioinformatics. 2009, 10 (Suppl 1): S21.-
Article
PubMed Central
PubMed
Google Scholar
Guan Y, Myers CL, Hess DC, Barutcuoglu Z, Caudy AA, Troyanskaya OG: Predicting gene function in a hierarchical context with an ensemble of classifiers. Genome Biol. 2008, 9 (Suppl 1): S3.- 10.1186/gb-2008-9-s1-s3
Article
PubMed Central
PubMed
Google Scholar
Vapnik V: Statistical Learning Theory. 1998, New York: Wiley
Google Scholar
Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Edgar R: NCBI GEO: mining tens of millions of expression profiles--database and tools update. Nucleic Acids Res. 2007, 35: D760-765. 10.1093/nar/gkl887
Article
PubMed Central
CAS
PubMed
Google Scholar
Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, Wong E, Orlov YL, Zhang W, Jiang J, Loh YH, Yeo HC, Yeo ZX, Narang V, Govindarajan KR, Leong B, Shahab A, Ruan Y, Bourque G, Sung WK, Clarke ND, Wei CL, Ng HH: Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell. 2008, 133: 1106-1117. 10.1016/j.cell.2008.04.043
Article
CAS
PubMed
Google Scholar
Nishiyama A, Xin L, Sharov AA, Thomas M, Mowrer G, Meyers E, Piao Y, Mehta S, Yee S, Nakatake Y, Stagg C, Sharova L, Correa-Cerro LS, Bassey U, Hoang H, Kim E, Tapnio R, Qian Y, Dudekula D, Zalzman M, Li M, Falco G, Yang HT, Lee SL, Monti M, Stanghellini I, Islam MN, Nagaraja R, Goldberg I, Wang W, et al.: Uncovering early response of gene regulatory networks in ESCs by systematic induction of transcription factors. Cell Stem Cell. 2009, 5: 420-433. 10.1016/j.stem.2009.07.012
Article
PubMed Central
CAS
PubMed
Google Scholar
Ouyang Z, Zhou Q, Wong WH: ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells. Proc Natl Acad Sci USA. 2009, 106: 21521-6. 10.1073/pnas.0904863106
Article
PubMed Central
CAS
PubMed
Google Scholar
Jiang J, Chan YS, Loh YH, Cai J, Tong GQ, Lim CA, Robson P, Zhong S: Ng A core Klf circuitry regulates self-renewal of embryonic stem cells. Nat Cell Biol. 2008, 10: 353-360. 10.1038/ncb1698
Article
PubMed
Google Scholar
Xu H, Schaniel C, Lemischka IR, Ma'ayan A: Toward a complete in silico, multi-layered embryonic stem cell regulatory network. Wiley Interdiscip Rev Syst Biol Med. 2010, 2: 708-733.
Article
PubMed Central
CAS
PubMed
Google Scholar
Guyon I, Weston J, Barnhill S, Vapnik V: Gene selection for cancer classification using support vector machines. Machine Learning. 2002, 46: 389-422. 10.1023/A:1012487302797.
Article
Google Scholar
Cristianini N, SHawe-Taylor J: An introduciton to Support Vector. Machines. 2000, Cambridge: Cambridge University Press
Google Scholar
Bishop CM: Pattern Recognition and Machine Learning. 2006, New York: Springer Science + Business Media
Google Scholar
Quinlan JR: Induction of Decision Trees. Machine Learning. 1986, 1: 81-106.
Google Scholar
Hu G, Kim J, Xu Q, Leng Y, Orkin SH, Elledge SJ: A genome-wide RNAi screen identifies a new transcriptional module required for self-renewal. Genes Dev. 2009, 23: 837-848. 10.1101/gad.1769609
Article
PubMed Central
CAS
PubMed
Google Scholar
Tu Z, Argmann C, Wong KK, Mitnaul LJ, Edwards S, Sach IC, Zhu J, Schadt EE: Integrating siRNA and protein-protein interaction data to identify an expanded insulin signaling network. Genome Res. 2009, 19: 1057-1067. 10.1101/gr.087890.108
Article
PubMed Central
CAS
PubMed
Google Scholar
Ding L, Paszkowski-Rogacz M, Nitzsche A, Slabicki MM, Heninger AK, de Vries I, Kittler R, Junqueira M, Shevchenko A, Schulz H, Hubner N, Doss MX, Sachinidis A, Hescheler J, Lacone R, Anastassiadis K, Stewart AF, Pisabarro MT, Caldarelli A, Poser I, Theis M, Buchholz F: A genome-scale RNAi screen for Oct4 modulators defines a role of the Paf1 complex for embryonic stem cell identity. Cell Stem Cell. 2009, 4: 403-415. 10.1016/j.stem.2009.03.009
Article
CAS
PubMed
Google Scholar
Pirity MK, Locker J, Schreiber-Agus N: Rybp/DEDAF is required for early postimplantation and for central nervous system development. Mol Cell Biol. 2005, 25: 7193-7202. 10.1128/MCB.25.16.7193-7202.2005
Article
PubMed Central
CAS
PubMed
Google Scholar
Aksoy I, Sakabedoyan C, Bourillot PY, Malashicheva AB, Mancip J, Knoblauch K, Afanassieff M, Savatier P: Self-renewal of murine embryonic stem cells is supported by the serine/threonine kinases Pim-1 and Pim-3. Stem Cells. 2007, 25: 2996-3004. 10.1634/stemcells.2007-0066
Article
CAS
PubMed
Google Scholar
Howlin J, Rosenkvist J, Andersson T: TNK2 preserves epidermal growth factor receptor expression on the cell surface and enhances migration and invasion of human breast cancer cells. Breast Cancer Res. 2008, 10: R36- 10.1186/bcr2087
Article
PubMed Central
PubMed
Google Scholar
Brill LM, Xiong W, Lee KB, Ficarro SB, Crain A, Xu Y, Terskikh A, Snyder EY, Ding S: Phosphoproteomic analysis of human embryonic stem cells. Cell Stem Cell. 2009, 5: 204-213. 10.1016/j.stem.2009.06.002
Article
PubMed Central
CAS
PubMed
Google Scholar
Van Hoof D, Munoz J, Braam SR, Pinkse MW, Linding R, Heck AJ, Mummery CL, Krijgsveld J: Phosphorylation dynamics during early differentiation of human embryonic stem cells. Cell Stem Cell. 2009, 5: 214-226. 10.1016/j.stem.2009.05.021
Article
CAS
PubMed
Google Scholar
Ivanova N, Dobrin R, Lu R, Kotenko I, Levorse J, DeCoste C, Schafer X, Lun Y, Lemischka IR: Dissecting self-renewal in stem cells with RNA interference. Nature. 2006, 442: 533-538. 10.1038/nature04915
Article
CAS
PubMed
Google Scholar
Hailesellasse Sene K, Porter CJ, Palidwor G, Perez-Iratxeta C, Muro EM, Campbell PA, Rudnicki MA, Andrade-Navarro MA: Gene function in early mouse embryonic stem cell differentiation. BMC Genomics. 2007, 8: 85- 10.1186/1471-2164-8-85
Article
PubMed
Google Scholar