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Items: 1 to 20 of 267

1.

Lists2Networks: integrated analysis of gene/protein lists.

Lachmann A, Ma'ayan A.

BMC Bioinformatics. 2010 Feb 12;11:87. doi: 10.1186/1471-2105-11-87.

PMID:
20152038
2.

Systems-level dynamic analyses of fate change in murine embryonic stem cells.

Lu R, Markowetz F, Unwin RD, Leek JT, Airoldi EM, MacArthur BD, Lachmann A, Rozov R, Ma'ayan A, Boyer LA, Troyanskaya OG, Whetton AD, Lemischka IR.

Nature. 2009 Nov 19;462(7271):358-62. doi: 10.1038/nature08575.

PMID:
19924215
3.

Smarcc1/Baf155 couples self-renewal gene repression with changes in chromatin structure in mouse embryonic stem cells.

Schaniel C, Ang YS, Ratnakumar K, Cormier C, James T, Bernstein E, Lemischka IR, Paddison PJ.

Stem Cells. 2009 Dec;27(12):2979-91. doi: 10.1002/stem.223.

PMID:
19785031
4.

Genome-wide identification of post-translational modulators of transcription factor activity in human B cells.

Wang K, Saito M, Bisikirska BC, Alvarez MJ, Lim WK, Rajbhandari P, Shen Q, Nemenman I, Basso K, Margolin AA, Klein U, Dalla-Favera R, Califano A.

Nat Biotechnol. 2009 Sep;27(9):829-39. doi: 10.1038/nbt.1563. Epub 2009 Sep 9.

PMID:
19741643
5.

Systems biology of stem cell fate and cellular reprogramming.

Macarthur BD, Ma'ayan A, Lemischka IR.

Nat Rev Mol Cell Biol. 2009 Oct;10(10):672-81. doi: 10.1038/nrm2766. Epub 2009 Sep 9. Review.

PMID:
19738627
6.

Highly dynamic and sex-specific expression of microRNAs during early ES cell differentiation.

Ciaudo C, Servant N, Cognat V, Sarazin A, Kieffer E, Viville S, Colot V, Barillot E, Heard E, Voinnet O.

PLoS Genet. 2009 Aug;5(8):e1000620. doi: 10.1371/journal.pgen.1000620. Epub 2009 Aug 28. Erratum in: PLoS Genet. 2015 Mar;11(3):e1005077.

PMID:
19714213
7.

Phosphorylation dynamics during early differentiation of human embryonic stem cells.

Van Hoof D, Muñoz J, Braam SR, Pinkse MW, Linding R, Heck AJ, Mummery CL, Krijgsveld J.

Cell Stem Cell. 2009 Aug 7;5(2):214-26. doi: 10.1016/j.stem.2009.05.021.

PMID:
19664995
8.

Phosphoproteomic analysis of human embryonic stem cells.

Brill LM, Xiong W, Lee KB, Ficarro SB, Crain A, Xu Y, Terskikh A, Snyder EY, Ding S.

Cell Stem Cell. 2009 Aug 7;5(2):204-13. doi: 10.1016/j.stem.2009.06.002.

PMID:
19664994
9.

Bioinformatics and microarray analysis of microRNA expression profiles of murine embryonic stem cells, neural stem cells induced from ESCs and isolated from E8.5 mouse neural tube.

Chen H, Qian K, Tang ZP, Xing B, Chen H, Liu N, Huang X, Zhang S.

Neurol Res. 2010 Jul;32(6):603-13. doi: 10.1179/174313209X455691. Epub 2009 Aug 5.

PMID:
19660235
10.

Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells.

Mason MJ, Fan G, Plath K, Zhou Q, Horvath S.

BMC Genomics. 2009 Jul 20;10:327. doi: 10.1186/1471-2164-10-327.

PMID:
19619308
11.

In silico identification of a core regulatory network of OCT4 in human embryonic stem cells using an integrated approach.

Chavez L, Bais AS, Vingron M, Lehrach H, Adjaye J, Herwig R.

BMC Genomics. 2009 Jul 15;10:314. doi: 10.1186/1471-2164-10-314.

PMID:
19604364
12.

Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps.

Chi SW, Zang JB, Mele A, Darnell RB.

Nature. 2009 Jul 23;460(7254):479-86. doi: 10.1038/nature08170. Epub 2009 Jun 17.

PMID:
19536157
13.

Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes.

Zambelli F, Pesole G, Pavesi G.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W247-52. doi: 10.1093/nar/gkp464. Epub 2009 May 31.

PMID:
19487240
14.

A review of gene expression profiling of human embryonic stem cell lines and their differentiated progeny.

Bhattacharya B, Puri S, Puri RK.

Curr Stem Cell Res Ther. 2009 May;4(2):98-106. Review.

PMID:
19442194
15.

DIANA-mirPath: Integrating human and mouse microRNAs in pathways.

Papadopoulos GL, Alexiou P, Maragkakis M, Reczko M, Hatzigeorgiou AG.

Bioinformatics. 2009 Aug 1;25(15):1991-3. doi: 10.1093/bioinformatics/btp299. Epub 2009 May 12.

PMID:
19435746
16.

MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression.

Nam S, Li M, Choi K, Balch C, Kim S, Nephew KP.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W356-62. doi: 10.1093/nar/gkp294. Epub 2009 May 6.

PMID:
19420067
17.

GeneSet2miRNA: finding the signature of cooperative miRNA activities in the gene lists.

Antonov AV, Dietmann S, Wong P, Lutter D, Mewes HW.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W323-8. doi: 10.1093/nar/gkp313. Epub 2009 May 6.

PMID:
19420064
18.

MicroRNA-145 regulates OCT4, SOX2, and KLF4 and represses pluripotency in human embryonic stem cells.

Xu N, Papagiannakopoulos T, Pan G, Thomson JA, Kosik KS.

Cell. 2009 May 15;137(4):647-58. doi: 10.1016/j.cell.2009.02.038. Epub 2009 Apr 30.

PMID:
19409607
19.

SysPTM: a systematic resource for proteomic research on post-translational modifications.

Li H, Xing X, Ding G, Li Q, Wang C, Xie L, Zeng R, Li Y.

Mol Cell Proteomics. 2009 Aug;8(8):1839-49. doi: 10.1074/mcp.M900030-MCP200. Epub 2009 Apr 14.

PMID:
19366988
20.

Characterization of the phosphoinositide 3-kinase-dependent transcriptome in murine embryonic stem cells: identification of novel regulators of pluripotency.

Storm MP, Kumpfmueller B, Thompson B, Kolde R, Vilo J, Hummel O, Schulz H, Welham MJ.

Stem Cells. 2009 Apr;27(4):764-75. doi: 10.1002/stem.3.

PMID:
19350676

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