Recent '''Wold Lab Publications'''
Publication lists for individual lab members can be seen on their [[people | 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
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.Title: [[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html | 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.
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.Title: [[http://www.nature.com/nmeth/journal/v6/n11s/abs/nmeth.1371.html | 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.
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.Title: [[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2492748/?tool=pubmed | 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.
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.Title: [[http://genome.cshlp.org/content/18/12/1955.long | 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.
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.Title: [[ http://www.nature.com/nmeth/journal/v5/n7/abs/nmeth.1226.html | 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.
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.Title: [[ http://www.nature.com/nmeth/journal/v5/n1/full/nmeth1157.html | 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.
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.Title: [[ http://www.sciencemag.org/cgi/content/abstract/316/5830/1497 | 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.
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.Title: [[ http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pcbi.0020169 | 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.
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.Title: [[ http://aem.asm.org/cgi/content/full/72/11/7324?view=long&pmid=16936048 | 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.
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.Title: [[http://www.genome.org/cgi/content/full/16/10/1208 | 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.
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.Title: [[http://woldlab.caltech.edu/publications/pca-bmc-2005 | 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.
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.Title: [[ http://nar.oupjournals.org/cgi/content/full/33/8/2580 | 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.
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.Title: [[http://bioinformatics.oupjournals.org/cgi/reprint/19/5/677 | 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
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.Title: [[http://www.pnas.org/cgi/content/full/99/20/12975 | 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.
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.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
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.Title: [[http://woldlab.caltech.edu/publications/Cornelison_etal00.pdf | 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
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.Title: [[http://woldlab.caltech.edu/publications/publications/Yoon_etal00.pdf | 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
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.Title: [[http://woldlab.caltech.edu/publications/Mjolsness_etal99b.pdf | 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
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.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
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.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
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.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
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.Title: [[http://woldlab.caltech.edu/publications/publications/Cornelison_Wold97.pdf | 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
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