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Items: 1 to 20 of 37

1.

Learning global models of transcriptional regulatory networks from data.

Madar A, Bonneau R.

Methods Mol Biol. 2009;541:181. doi: 10.1007/978-1-59745-243-4_9. Review.

PMID:
19381524
2.

An integrated software system for analyzing ChIP-chip and ChIP-seq data.

Ji H, Jiang H, Ma W, Johnson DS, Myers RM, Wong WH.

Nat Biotechnol. 2008 Nov;26(11):1293-300. doi: 10.1038/nbt.1505. Epub 2008 Nov 2.

3.

Extracting sequence features to predict protein-DNA interactions: a comparative study.

Zhou Q, Liu JS.

Nucleic Acids Res. 2008 Jul;36(12):4137-48. doi: 10.1093/nar/gkn361. Epub 2008 Jun 13.

4.

Integration of external signaling pathways with the core transcriptional network in embryonic stem cells.

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.

Cell. 2008 Jun 13;133(6):1106-17. doi: 10.1016/j.cell.2008.04.043.

5.

Stem cell transcriptome profiling via massive-scale mRNA sequencing.

Cloonan N, Forrest AR, Kolle G, Gardiner BB, Faulkner GJ, Brown MK, Taylor DF, Steptoe AL, Wani S, Bethel G, Robertson AJ, Perkins AC, Bruce SJ, Lee CC, Ranade SS, Peckham HE, Manning JM, McKernan KJ, Grimmond SM.

Nat Methods. 2008 Jul;5(7):613-9. doi: 10.1038/nmeth.1223. Epub 2008 May 30.

PMID:
18516046
6.

Mapping and quantifying mammalian transcriptomes by RNA-Seq.

Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B.

Nat Methods. 2008 Jul;5(7):621-8. doi: 10.1038/nmeth.1226. Epub 2008 May 30.

PMID:
18516045
7.

Nanog and Oct4 associate with unique transcriptional repression complexes in embryonic stem cells.

Liang J, Wan M, Zhang Y, Gu P, Xin H, Jung SY, Qin J, Wong J, Cooney AJ, Liu D, Songyang Z.

Nat Cell Biol. 2008 Jun;10(6):731-9. doi: 10.1038/ncb1736. Epub 2008 May 4.

PMID:
18454139
8.

An extended transcriptional network for pluripotency of embryonic stem cells.

Kim J, Chu J, Shen X, Wang J, Orkin SH.

Cell. 2008 Mar 21;132(6):1049-61. doi: 10.1016/j.cell.2008.02.039. Erratum in: Cell. 2008 Jun 27;133(7):1290.

9.

Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm.

Li XY, MacArthur S, Bourgon R, Nix D, Pollard DA, Iyer VN, Hechmer A, Simirenko L, Stapleton M, Luengo Hendriks CL, Chu HC, Ogawa N, Inwood W, Sementchenko V, Beaton A, Weiszmann R, Celniker SE, Knowles DW, Gingeras T, Speed TP, Eisen MB, Biggin MD.

PLoS Biol. 2008 Feb;6(2):e27. doi: 10.1371/journal.pbio.0060027.

10.

A gene regulatory network in mouse embryonic stem cells.

Zhou Q, Chipperfield H, Melton DA, Wong WH.

Proc Natl Acad Sci U S A. 2007 Oct 16;104(42):16438-43. Epub 2007 Oct 10.

11.

Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions.

Zhang ZD, Paccanaro A, Fu Y, Weissman S, Weng Z, Chang J, Snyder M, Gerstein MB.

Genome Res. 2007 Jun;17(6):787-97.

12.

Genome-wide mapping of in vivo protein-DNA interactions.

Johnson DS, Mortazavi A, Myers RM, Wold B.

Science. 2007 Jun 8;316(5830):1497-502. Epub 2007 May 31.

13.

A protein interaction network for pluripotency of embryonic stem cells.

Wang J, Rao S, Chu J, Shen X, Levasseur DN, Theunissen TW, Orkin SH.

Nature. 2006 Nov 16;444(7117):364-8. Epub 2006 Nov 8.

PMID:
17093407
14.

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements.

MAQC Consortium, Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, Baker SC, Collins PJ, de Longueville F, Kawasaki ES, Lee KY, Luo Y, Sun YA, Willey JC, Setterquist RA, Fischer GM, Tong W, Dragan YP, Dix DJ, Frueh FW, Goodsaid FM, Herman D, Jensen RV, Johnson CD, Lobenhofer EK, Puri RK, Schrf U, Thierry-Mieg J, Wang C, Wilson M, Wolber PK, Zhang L, Amur S, Bao W, Barbacioru CC, Lucas AB, Bertholet V, Boysen C, Bromley B, Brown D, Brunner A, Canales R, Cao XM, Cebula TA, Chen JJ, Cheng J, Chu TM, Chudin E, Corson J, Corton JC, Croner LJ, Davies C, Davison TS, Delenstarr G, Deng X, Dorris D, Eklund AC, Fan XH, Fang H, Fulmer-Smentek S, Fuscoe JC, Gallagher K, Ge W, Guo L, Guo X, Hager J, Haje PK, Han J, Han T, Harbottle HC, Harris SC, Hatchwell E, Hauser CA, Hester S, Hong H, Hurban P, Jackson SA, Ji H, Knight CR, Kuo WP, LeClerc JE, Levy S, Li QZ, Liu C, Liu Y, Lombardi MJ, Ma Y, Magnuson SR, Maqsodi B, McDaniel T, Mei N, Myklebost O, Ning B, Novoradovskaya N, Orr MS, Osborn TW, Papallo A, Patterson TA, Perkins RG, Peters EH, Peterson R, Philips KL, Pine PS, Pusztai L, Qian F, Ren H, Rosen M, Rosenzweig BA, Samaha RR, Schena M, Schroth GP, Shchegrova S, Smith DD, Staedtler F, Su Z, Sun H, Szallasi Z, Tezak Z, Thierry-Mieg D, Thompson KL, Tikhonova I, Turpaz Y, Vallanat B, Van C, Walker SJ, Wang SJ, Wang Y, Wolfinger R, Wong A, Wu J, Xiao C, Xie Q, Xu J, Yang W, Zhang L, Zhong S, Zong Y, Slikker W Jr.

Nat Biotechnol. 2006 Sep;24(9):1151-61.

15.

Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster.

Moorman C, Sun LV, Wang J, de Wit E, Talhout W, Ward LD, Greil F, Lu XJ, White KP, Bussemaker HJ, van Steensel B.

Proc Natl Acad Sci U S A. 2006 Aug 8;103(32):12027-32. Epub 2006 Jul 31.

16.

A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies.

Kuo WP, Liu F, Trimarchi J, Punzo C, Lombardi M, Sarang J, Whipple ME, Maysuria M, Serikawa K, Lee SY, McCrann D, Kang J, Shearstone JR, Burke J, Park DJ, Wang X, Rector TL, Ricciardi-Castagnoli P, Perrin S, Choi S, Bumgarner R, Kim JH, Short GF 3rd, Freeman MW, Seed B, Jensen R, Church GM, Hovig E, Cepko CL, Park P, Ohno-Machado L, Jenssen TK.

Nat Biotechnol. 2006 Jul;24(7):832-40. Epub 2006 Jul 2.

PMID:
16823376
17.

Dissecting self-renewal in stem cells with RNA interference.

Ivanova N, Dobrin R, Lu R, Kotenko I, Levorse J, DeCoste C, Schafer X, Lun Y, Lemischka IR.

Nature. 2006 Aug 3;442(7102):533-8. Epub 2006 Jun 11.

PMID:
16767105
18.

Myc-binding-site recognition in the human genome is determined by chromatin context.

Guccione E, Martinato F, Finocchiaro G, Luzi L, Tizzoni L, Dall' Olio V, Zardo G, Nervi C, Bernard L, Amati B.

Nat Cell Biol. 2006 Jul;8(7):764-70. Epub 2006 Jun 11.

PMID:
16767079
19.

Adaptively inferring human transcriptional subnetworks.

Das D, Nahlé Z, Zhang MQ.

Mol Syst Biol. 2006;2:2006.0029. Epub 2006 Jun 6.

20.

Deciphering principles of transcription regulation in eukaryotic genomes.

Nguyen DH, D'haeseleer P.

Mol Syst Biol. 2006;2:2006.0012. Epub 2006 Apr 18.

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