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Items: 1 to 50 of 65

1.

Reconstructing a metazoan genetic pathway with transcriptome-wide epistasis measurements.

Angeles-Albores D, Puckett Robinson C, Williams BA, Wold BJ, Sternberg PW.

Proc Natl Acad Sci U S A. 2018 Mar 27;115(13):E2930-E2939. doi: 10.1073/pnas.1712387115. Epub 2018 Mar 12.

2.

Pitfalls of mapping high-throughput sequencing data to repetitive sequences: Piwi's genomic targets still not identified.

Marinov GK, Wang J, Handler D, Wold BJ, Weng Z, Hannon GJ, Aravin AA, Zamore PD, Brennecke J, Toth KF.

Dev Cell. 2015 Mar 23;32(6):765-71. doi: 10.1016/j.devcel.2015.01.013.

3.

Single-cell transcriptome analysis reveals dynamic changes in lncRNA expression during reprogramming.

Kim DH, Marinov GK, Pepke S, Singer ZS, He P, Williams B, Schroth GP, Elowitz MB, Wold BJ.

Cell Stem Cell. 2015 Jan 8;16(1):88-101. doi: 10.1016/j.stem.2014.11.005.

4.

A ratiometric-based measure of gene co-expression.

Abelin AC, Marinov GK, Williams BA, McCue K, Wold BJ.

BMC Bioinformatics. 2014 Nov 20;15:331. doi: 10.1186/1471-2105-15-331.

5.

Fully automated high-throughput chromatin immunoprecipitation for ChIP-seq: identifying ChIP-quality p300 monoclonal antibodies.

Gasper WC, Marinov GK, Pauli-Behn F, Scott MT, Newberry K, DeSalvo G, Ou S, Myers RM, Vielmetter J, Wold BJ.

Sci Rep. 2014 Jun 12;4:5152. doi: 10.1038/srep05152.

6.

Evidence for site-specific occupancy of the mitochondrial genome by nuclear transcription factors.

Marinov GK, Wang YE, Chan D, Wold BJ.

PLoS One. 2014 Jan 20;9(1):e84713. doi: 10.1371/journal.pone.0084713. eCollection 2014.

7.

Large-scale quality analysis of published ChIP-seq data.

Marinov GK, Kundaje A, Park PJ, Wold BJ.

G3 (Bethesda). 2014 Feb 19;4(2):209-23. doi: 10.1534/g3.113.008680.

8.

From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing.

Marinov GK, Williams BA, McCue K, Schroth GP, Gertz J, Myers RM, Wold BJ.

Genome Res. 2014 Mar;24(3):496-510. doi: 10.1101/gr.161034.113. Epub 2013 Dec 3.

9.

Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps.

Mortazavi A, Pepke S, Jansen C, Marinov GK, Ernst J, Kellis M, Hardison RC, Myers RM, Wold BJ.

Genome Res. 2013 Dec;23(12):2136-48. doi: 10.1101/gr.158261.113. Epub 2013 Oct 29.

10.

Genome-wide analysis reveals coating of the mitochondrial genome by TFAM.

Wang YE, Marinov GK, Wold BJ, Chan DC.

PLoS One. 2013 Aug 26;8(8):e74513. doi: 10.1371/journal.pone.0074513. eCollection 2013.

11.

Transcriptional regulation by nicotine in dopaminergic neurons.

Henley BM, Williams BA, Srinivasan R, Cohen BN, Xiao C, Mackey ED, Wold BJ, Lester HA.

Biochem Pharmacol. 2013 Oct 15;86(8):1074-83. doi: 10.1016/j.bcp.2013.07.031. Epub 2013 Aug 9.

12.

Dynamic DNA methylation across diverse human cell lines and tissues.

Varley KE, Gertz J, Bowling KM, Parker SL, Reddy TE, Pauli-Behn F, Cross MK, Williams BA, Stamatoyannopoulos JA, Crawford GE, Absher DM, Wold BJ, Myers RM.

Genome Res. 2013 Mar;23(3):555-67. doi: 10.1101/gr.147942.112. Epub 2013 Jan 16.

13.

Using patient-provided information to refine sexually transmitted infection screening criteria among women presenting in the emergency department.

Jenkins WD, Kovach R, Wold BJ, Zahnd WE.

Sex Transm Dis. 2012 Dec;39(12):965-7. doi: 10.1097/OLQ.0b013e31826e882f.

PMID:
23191951
14.

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M.

Genome Res. 2012 Sep;22(9):1813-31. doi: 10.1101/gr.136184.111.

15.

RNA editing in the human ENCODE RNA-seq data.

Park E, Williams B, Wold BJ, Mortazavi A.

Genome Res. 2012 Sep;22(9):1626-33. doi: 10.1101/gr.134957.111.

16.

An encyclopedia of mouse DNA elements (Mouse ENCODE).

Mouse ENCODE Consortium, Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, Canfield T, Giste E, Johnson A, Zhang M, Balasundaram G, Byron R, Roach V, Sabo PJ, Sandstrom R, Stehling AS, Thurman RE, Weissman SM, Cayting P, Hariharan M, Lian J, Cheng Y, Landt SG, Ma Z, Wold BJ, Dekker J, Crawford GE, Keller CA, Wu W, Morrissey C, Kumar SA, Mishra T, Jain D, Byrska-Bishop M, Blankenberg D, Lajoie BR, Jain G, Sanyal A, Chen KB, Denas O, Taylor J, Blobel GA, Weiss MJ, Pimkin M, Deng W, Marinov GK, Williams BA, Fisher-Aylor KI, Desalvo G, Kiralusha A, Trout D, Amrhein H, Mortazavi A, Edsall L, McCleary D, Kuan S, Shen Y, Yue F, Ye Z, Davis CA, Zaleski C, Jha S, Xue C, Dobin A, Lin W, Fastuca M, Wang H, Guigo R, Djebali S, Lagarde J, Ryba T, Sasaki T, Malladi VS, Cline MS, Kirkup VM, Learned K, Rosenbloom KR, Kent WJ, Feingold EA, Good PJ, Pazin M, Lowdon RF, Adams LB.

Genome Biol. 2012 Aug 13;13(8):418. doi: 10.1186/gb-2012-13-8-418.

17.

Transcription factor redundancy and tissue-specific regulation: evidence from functional and physical network connectivity.

Kuntz SG, Williams BA, Sternberg PW, Wold BJ.

Genome Res. 2012 Oct;22(10):1907-19. doi: 10.1101/gr.133306.111. Epub 2012 Jun 22.

18.

Systematic evaluation of factors influencing ChIP-seq fidelity.

Chen Y, Negre N, Li Q, Mieczkowska JO, Slattery M, Liu T, Zhang Y, Kim TK, He HH, Zieba J, Ruan Y, Bickel PJ, Myers RM, Wold BJ, White KP, Lieb JD, Liu XS.

Nat Methods. 2012 Jun;9(6):609-14. doi: 10.1038/nmeth.1985. Epub 2012 Apr 22.

19.

Dynamic transformations of genome-wide epigenetic marking and transcriptional control establish T cell identity.

Zhang JA, Mortazavi A, Williams BA, Wold BJ, Rothenberg EV.

Cell. 2012 Apr 13;149(2):467-82. doi: 10.1016/j.cell.2012.01.056.

20.

Microglia in the cerebral cortex in autism.

Tetreault NA, Hakeem AY, Jiang S, Williams BA, Allman E, Wold BJ, Allman JM.

J Autism Dev Disord. 2012 Dec;42(12):2569-84. doi: 10.1007/s10803-012-1513-0.

PMID:
22466688
21.

Differentiation and fiber type-specific activity of a muscle creatine kinase intronic enhancer.

Tai PW, Fisher-Aylor KI, Himeda CL, Smith CL, Mackenzie AP, Helterline DL, Angello JC, Welikson RE, Wold BJ, Hauschka SD.

Skelet Muscle. 2011 Jul 7;1:25. doi: 10.1186/2044-5040-1-25.

22.

Inviability of a DNA2 deletion mutant is due to the DNA damage checkpoint.

Budd ME, Antoshechkin IA, Reis C, Wold BJ, Campbell JL.

Cell Cycle. 2011 May 15;10(10):1690-8. Epub 2011 May 15.

23.

High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation.

Ozdemir A, Fisher-Aylor KI, Pepke S, Samanta M, Dunipace L, McCue K, Zeng L, Ogawa N, Wold BJ, Stathopoulos A.

Genome Res. 2011 Apr;21(4):566-77. doi: 10.1101/gr.104018.109. Epub 2011 Mar 7.

24.

Scaffolding a Caenorhabditis nematode genome with RNA-seq.

Mortazavi A, Schwarz EM, Williams B, Schaeffer L, Antoshechkin I, Wold BJ, Sternberg PW.

Genome Res. 2010 Dec;20(12):1740-7. doi: 10.1101/gr.111021.110. Epub 2010 Oct 27.

25.

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.

Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L.

Nat Biotechnol. 2010 May;28(5):511-5. doi: 10.1038/nbt.1621. Epub 2010 May 2.

26.

Multigenome DNA sequence conservation identifies Hox cis-regulatory elements.

Kuntz SG, Schwarz EM, DeModena JA, De Buysscher T, Trout D, Shizuya H, Sternberg PW, Wold BJ.

Genome Res. 2008 Dec;18(12):1955-68. doi: 10.1101/gr.085472.108. Epub 2008 Nov 3.

27.

A highly conserved molecular switch binds MSY-3 to regulate myogenin repression in postnatal muscle.

Berghella L, De Angelis L, De Buysscher T, Mortazavi A, Biressi S, Forcales SV, Sirabella D, Cossu G, Wold BJ.

Genes Dev. 2008 Aug 1;22(15):2125-38. doi: 10.1101/gad.468508.

28.

Connectivity in the yeast cell cycle transcription network: inferences from neural networks.

Hart CE, Mjolsness E, Wold BJ.

PLoS Comput Biol. 2006 Dec 22;2(12):e169. Epub 2006 Oct 30.

29.

Genomic DNA as a general cohybridization standard for ratiometric microarrays.

Williams BA, Gwirtz RM, Wold BJ.

Methods Enzymol. 2006;410:237-79. Review.

PMID:
16938555
30.

Spatiometabolic stratification of Shewanella oneidensis biofilms.

Teal TK, Lies DP, Wold BJ, Newman DK.

Appl Environ Microbiol. 2006 Nov;72(11):7324-30. Epub 2006 Aug 25.

31.

Enhanced signals and fast nucleic acid hybridization by microfluidic chaotic mixing.

Liu J, Williams BA, Gwirtz RM, Wold BJ, Quake S.

Angew Chem Int Ed Engl. 2006 May 26;45(22):3618-23. No abstract available.

PMID:
16639763
32.

Mining gene expression data by interpreting principal components.

Roden JC, King BW, Trout D, Mortazavi A, Wold BJ, Hart CE.

BMC Bioinformatics. 2006 Apr 7;7:194.

33.

A mathematical and computational framework for quantitative comparison and integration of large-scale gene expression data.

Hart CE, Sharenbroich L, Bornstein BJ, Trout D, King B, Mjolsness E, Wold BJ.

Nucleic Acids Res. 2005 May 10;33(8):2580-94. Print 2005.

34.

Reproducibility, fidelity, and discriminant validity of mRNA amplification for microarray analysis from primary hematopoietic cells.

Li L, Roden J, Shapiro BE, Wold BJ, Bhatia S, Forman SJ, Bhatia R.

J Mol Diagn. 2005 Feb;7(1):48-56.

35.

Genomic DNA as a cohybridization standard for mammalian microarray measurements.

Williams BA, Gwirtz RM, Wold BJ.

Nucleic Acids Res. 2004 Jun 9;32(10):e81.

36.

Applicability of tandem affinity purification MudPIT to pathway proteomics in yeast.

Graumann J, Dunipace LA, Seol JH, McDonald WH, Yates JR 3rd, Wold BJ, Deshaies RJ.

Mol Cell Proteomics. 2004 Mar;3(3):226-37. Epub 2003 Dec 5.

37.

p62 overexpression in breast tumors and regulation by prostate-derived Ets factor in breast cancer cells.

Thompson HG, Harris JW, Wold BJ, Lin F, Brody JP.

Oncogene. 2003 Apr 17;22(15):2322-33.

PMID:
12700667
38.

Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations.

Shapiro BE, Levchenko A, Meyerowitz EM, Wold BJ, Mjolsness ED.

Bioinformatics. 2003 Mar 22;19(5):677-8.

PMID:
12651737
39.

Identification and confirmation of a module of coexpressed genes.

Thompson HG, Harris JW, Wold BJ, Quake SR, Brody JP.

Genome Res. 2002 Oct;12(10):1517-22.

40.

Significance and statistical errors in the analysis of DNA microarray data.

Brody JP, Williams BA, Wold BJ, Quake SR.

Proc Natl Acad Sci U S A. 2002 Oct 1;99(20):12975-8. Epub 2002 Sep 16.

41.

New computational approaches for analysis of cis-regulatory networks.

Brown CT, Rust AG, Clarke PJ, Pan Z, Schilstra MJ, De Buysscher T, Griffin G, Wold BJ, Cameron RA, Davidson EH, Bolouri H.

Dev Biol. 2002 Jun 1;246(1):86-102.

42.

MyoD(-/-) satellite cells in single-fiber culture are differentiation defective and MRF4 deficient.

Cornelison DD, Olwin BB, Rudnicki MA, Wold BJ.

Dev Biol. 2000 Aug 15;224(2):122-37.

43.

p27Kip1 is expressed transiently in developing myotomes and enhances myogenesis.

Zabludoff SD, Csete M, Wagner R, Yu X, Wold BJ.

Cell Growth Differ. 1998 Jan;9(1):1-11.

44.
45.
46.

BRCA1 mRNA is expressed highly during meiosis and spermiogenesis but not during mitosis of male germ cells.

Zabludoff SD, Wright WW, Harshman K, Wold BJ.

Oncogene. 1996 Aug 1;13(3):649-53.

PMID:
8760307
47.

Know your neighbors: three phenotypes in null mutants of the myogenic bHLH gene MRF4.

Olson EN, Arnold HH, Rigby PW, Wold BJ.

Cell. 1996 Apr 5;85(1):1-4. Review. No abstract available.

48.

Evidence for developmentally programmed transdifferentiation in mouse esophageal muscle.

Patapoutian A, Wold BJ, Wagner RA.

Science. 1995 Dec 15;270(5243):1818-21.

PMID:
8525375
49.
50.

Phosphorothioate oligonucleotide-directed triple helix formation.

Hacia JG, Wold BJ, Dervan PB.

Biochemistry. 1994 May 10;33(18):5367-9.

PMID:
8180158

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