• publications

Recent Wold Lab Publications Publication lists for individual lab members can be seen on their personal web pages.

• Title: Scaffolding a Caenorhabditis nematode genome with RNA-seq
• Authors: Mortazavi A, Schwarz EM, Williams B, Schaeffer L, Antoshechkin I, Wold BJ, Sternberg PW
• Published: Genome Res. in press

  
  

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

• Authors: Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L.
• Published: Nat Biotechnol. 2010 May;28(5):511-5. Epub 2010 May 2.

  
  

• Title: Computation for ChIP-seq and RNA-seq studies.

• Authors: Pepke S, Wold B, Mortazavi A.
• Published: Nat Methods. 2009 Nov;6(11 Suppl):S22-32. Review.

  
  

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

• Authors: Berghella L, De Angelis L, De Buysscher T, Mortazavi A, Biressi S, Forcales SV, Sirabella D, Cossu G, Wold BJ.
• Published: Genes Dev. 2008 Aug 1;22(15):2125-38.

  
  

• Title: Multigenome DNA sequence conservation identifies Hox cis-regulatory elements.

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

• Published: Genome Res. 2008 Dec;18(12):1955-68. Epub 2008 Nov 3.

  
  

• Title: Mapping and quantifying mammalian transcriptomes by RNA-seq.

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

• Published: Nature Methods, 2008 Jul;5(7):621-8. Epub 2008 May 30.

  
  

• Title: Sequence census methods for functional genomics.

• Authors: Wold B, Myers RM.
• Published: Nature Methods. 2008 Jan;5(1):19-21. Epub 2007 Dec 19. Review.

  
  

• Title: Genome-wide mapping of in vivo protein-DNA interactions.

• Authors: Johnson DS, Mortazavi A, Myers RM, Wold B.
• Published: Science, 2007 Jun 8;316(5830):1497-502. Epub 2007 May 31.

  
  

• Title: Connectivity in the Yeast Cell Cycle Transcription Network: Inferences from Neural Networks.

• Authors: Hart CE, Mjolsness E, Wold BJ
• Published: PLoS Comput Biol. 2006 Dec 22;2(12):e169.

  
  

• Title: Spatiometabolic stratificiation of Shewanella oneidensis biofilms.

• Authors: Teal TK, Lies DP, Wold BJ, Newman DK
• Published: Appl Environ Microbiol, 2006 Nov;72(11):7324-30.

  
  

• Title: Comparative genomics modeling of the NRSF/REST repressor network: from single conserved sites to genome-wide repertoire.

• Authors: Mortazavi A, Thompson EC, Garcia ST, Myers RM, Wold B.
• Published: Genome Research, 2006 Oct;16(10):1208-21. Epub 2006 Sep 8.

  
  

• Title: Mining gene expression data by interpreting principal components.

• Authors: Roden, JC, King, B, Trout D, Mortazavi, A, Wold, BJ, Hart CE
• Published: BMC Bioinformatics, 2006 Apr 7;7:194.

  
  

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

• Authors: Hart CE, Sharenbroich L, Bornstein BJ, Trout D, King B, Mjolsness E, Wold BJ
• Published: Nucleic Acids Res. 2005 May 10;33(8):2580-94.

  
  

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

• Authors: Shapiro BE, Levchenko A, Meyerowitz EM, Wold BJ, Mjolsness ED
• Published: Bioinformatics. 2003 Mar 22;19(5):677-8

  
  

• Title: Significance and statistical errors in the analysis of DNA microarray data

• Authors: Brody JP, Williams BA, Wold BJ, Quake SR
• Published: Proc Natl Acad Sci U S A. 2002 Oct 1;99(20):12975-8.

  
  

• Title: The bHLH regulator pMesogenin1 is required for maturation and segmentation of paraxial mesoderm
• Authors: Yoon, JK and Wold, BW
• Published: Genes and Development 14 (24): 3204-3214 Dec 15 2000

  
  

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

• Authors: D. D. Cornelison, B. B. Olwin, M. A. Rudnicki and B. J. Wold
• Published: Dev Biol 224 (2): 122-37 Aug 2000

  
  

• Title: The bHLH class protein pMesogenin1 can specify paraxial mesoderm phenotypes

• Authors: Yoon JK, Moon RT, Wold B
• Published: Dev Biol 222 (2): 376-391 Jun 15 2000

  
  

• Title: Coexpression to Coregulation: An Approach to Inferring Transcriptional Regulation among Gene Classes from Large-Scale Expression Data

• Authors: E. Mjolsness, T. Mann, R. Castano and B. Wold
• Published: Technical Report JPL-ICTR-99-4 1999

  
  

• Title: p27Kip1 is expressed transiently in developing myotomes and enhances myogenesis
• Authors: S. D. Zabludoff, M. Csete, R. Wagner, X. Yu and B. J. Wold
• Published: Cell Growth Differ 9 (1): 1-11 Jan 1998

  
  

• Title: Different MRF4 knockout alleles differentially disrupt Myf-5 expression: cis-regulatory interactions at the MRF4/Myf-5 locus
• Authors: J. K. Yoon, E. N. Olson, H. H. Arnold and B. J. Wold
• Published: Dev Biol 188 (2): 349-62 Aug 1997

  
  

• Title: Single-cell analysis of regulatory gene expression in quiescent and activated mouse skeletal muscle satellite
• Authors: D. D. Cornelison and B. J. Wold
• Published: Dev Biol 191 (2): 270-283 Nov 1997

  
  

• Title: Skeletal muscle determination and differentiation: story of a core regulatory network and its context

• Authors: K. Yun and B. Wold
• Published: Curr Opin Cell Biol 8 (6): 877-79 Dec 1996