Barbara Wold

Barbara Wold

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Barbara Wold

Barbara Wold

Publications by authors named "Barbara Wold"

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Single-Cell Analysis Reveals Regulatory Gene Expression Dynamics Leading to Lineage Commitment in Early T Cell Development.

Cell Syst 2019 Oct 16;9(4):321-337.e9. Epub 2019 Oct 16.

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2019.09.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6932747PMC
October 2019

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

Proc Natl Acad Sci U S A 2018 03 12;115(13):E2930-E2939. Epub 2018 Mar 12.

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125;

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http://dx.doi.org/10.1073/pnas.1712387115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5879656PMC
March 2018

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

Cell Stem Cell 2015 Jan;16(1):88-101

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2014.11.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4291542PMC
January 2015

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

PLoS One 2014 20;9(1):e84713. Epub 2014 Jan 20.

Division of Biology, California Institute of Technology, Pasadena, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0084713PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3896368PMC
December 2014

A comparative encyclopedia of DNA elements in the mouse genome.

Authors:
Feng Yue Yong Cheng Alessandra Breschi Jeff Vierstra Weisheng Wu Tyrone Ryba Richard Sandstrom Zhihai Ma Carrie Davis Benjamin D Pope Yin Shen Dmitri D Pervouchine Sarah Djebali Robert E Thurman Rajinder Kaul Eric Rynes Anthony Kirilusha Georgi K Marinov Brian A Williams Diane Trout Henry Amrhein Katherine Fisher-Aylor Igor Antoshechkin Gilberto DeSalvo Lei-Hoon See Meagan Fastuca Jorg Drenkow Chris Zaleski Alex Dobin Pablo Prieto Julien Lagarde Giovanni Bussotti Andrea Tanzer Olgert Denas Kanwei Li M A Bender Miaohua Zhang Rachel Byron Mark T Groudine David McCleary Long Pham Zhen Ye Samantha Kuan Lee Edsall Yi-Chieh Wu Matthew D Rasmussen Mukul S Bansal Manolis Kellis Cheryl A Keller Christapher S Morrissey Tejaswini Mishra Deepti Jain Nergiz Dogan Robert S Harris Philip Cayting Trupti Kawli Alan P Boyle Ghia Euskirchen Anshul Kundaje Shin Lin Yiing Lin Camden Jansen Venkat S Malladi Melissa S Cline Drew T Erickson Vanessa M Kirkup Katrina Learned Cricket A Sloan Kate R Rosenbloom Beatriz Lacerda de Sousa Kathryn Beal Miguel Pignatelli Paul Flicek Jin Lian Tamer Kahveci Dongwon Lee W James Kent Miguel Ramalho Santos Javier Herrero Cedric Notredame Audra Johnson Shinny Vong Kristen Lee Daniel Bates Fidencio Neri Morgan Diegel Theresa Canfield Peter J Sabo Matthew S Wilken Thomas A Reh Erika Giste Anthony Shafer Tanya Kutyavin Eric Haugen Douglas Dunn Alex P Reynolds Shane Neph Richard Humbert R Scott Hansen Marella De Bruijn Licia Selleri Alexander Rudensky Steven Josefowicz Robert Samstein Evan E Eichler Stuart H Orkin Dana Levasseur Thalia Papayannopoulou Kai-Hsin Chang Arthur Skoultchi Srikanta Gosh Christine Disteche Piper Treuting Yanli Wang Mitchell J Weiss Gerd A Blobel Xiaoyi Cao Sheng Zhong Ting Wang Peter J Good Rebecca F Lowdon Leslie B Adams Xiao-Qiao Zhou Michael J Pazin Elise A Feingold Barbara Wold James Taylor Ali Mortazavi Sherman M Weissman John A Stamatoyannopoulos Michael P Snyder Roderic Guigo Thomas R Gingeras David M Gilbert Ross C Hardison Michael A Beer Bing Ren

Nature 2014 Nov;515(7527):355-64

Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1038/nature13992DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4266106PMC
November 2014

A ratiometric-based measure of gene co-expression.

BMC Bioinformatics 2014 Nov 20;15:331. Epub 2014 Nov 20.

Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Blvd, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1186/1471-2105-15-331DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289233PMC
November 2014

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

PLoS One 2013 26;8(8):e74513. Epub 2013 Aug 26.

Division of Biology, California Institute of Technology, Pasadena, California, USA.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0074513PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753274PMC
June 2014

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

Genome Res 2014 Mar 3;24(3):496-510. Epub 2013 Dec 3.

Division of Biology, California Institute of Technology, Pasadena, California 91125, USA;

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http://genome.cshlp.org/cgi/doi/10.1101/gr.161034.113
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http://dx.doi.org/10.1101/gr.161034.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3941114PMC
March 2014

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

G3 (Bethesda) 2014 Feb 19;4(2):209-23. Epub 2014 Feb 19.

Division of Biology, California Institute of Technology, Pasadena, California 91125.

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http://dx.doi.org/10.1534/g3.113.008680DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3931556PMC
February 2014

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

Genome Res 2013 Dec 29;23(12):2136-48. Epub 2013 Oct 29.

Department of Developmental and Cell Biology, University of California, Irvine, California 92697, USA;

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http://dx.doi.org/10.1101/gr.158261.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3847782PMC
December 2013

Microglia in the cerebral cortex in autism.

J Autism Dev Disord 2012 Dec;42(12):2569-84

Division of Biology, California Institute of Technology, 1200 East California Blvd, MC216-76, Pasadena, CA 91125, USA.

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http://www.allmanlab.caltech.edu/pdfs/Tetreault2012.pdf
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http://www.springerlink.com/index/12153u176422pk58.pdf
Web Search
http://link.springer.com/10.1007/s10803-012-1513-0
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http://dx.doi.org/10.1007/s10803-012-1513-0DOI Listing
December 2012

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

Genome Res 2012 Oct 22;22(10):1907-19. Epub 2012 Jun 22.

Division of Biology, California Institute of Technology, Pasadena, California 91125, USA.

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http://dx.doi.org/10.1101/gr.133306.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3460186PMC
October 2012

Gene expression changes in a tumor xenograft by a pyrrole-imidazole polyamide.

Proc Natl Acad Sci U S A 2012 Oct 17;109(40):16041-5. Epub 2012 Sep 17.

Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1073/pnas.1214267109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3479560PMC
October 2012

Landscape of transcription in human cells.

Nature 2012 Sep;489(7414):101-8

Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain.

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http://dx.doi.org/10.1038/nature11233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3684276PMC
September 2012

RNA editing in the human ENCODE RNA-seq data.

Genome Res 2012 Sep;22(9):1626-33

Department of Developmental and Cell Biology, University of California Irvine, Irvine, California 92697, USA.

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http://genome.cshlp.org/cgi/doi/10.1101/gr.134957.111
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http://dx.doi.org/10.1101/gr.134957.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431480PMC
September 2012

An encyclopedia of mouse DNA elements (Mouse ENCODE).

August 2012

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

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

California Institute of Technology, Pasadena, CA USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3127164PMC
http://dx.doi.org/10.4161/cc.10.10.15643DOI Listing
May 2011

Scaffolding a Caenorhabditis nematode genome with RNA-seq.

Genome Res 2010 Dec 27;20(12):1740-7. Epub 2010 Oct 27.

Division of Biology, California Institute of Technology, Pasadena, California 91125, USA.

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http://dx.doi.org/10.1101/gr.111021.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2990000PMC
December 2010

Computation for ChIP-seq and RNA-seq studies.

Nat Methods 2009 Nov;6(11 Suppl):S22-32

Center for Advanced Computing Research, California Institute of Technology, Pasadena, California, USA.

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http://dx.doi.org/10.1038/nmeth.1371DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4121056PMC
November 2009

Multigenome DNA sequence conservation identifies Hox cis-regulatory elements.

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

Division of Biology, California Institute of Technology, Pasadena, California 91125, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.085472.108
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http://dx.doi.org/10.1101/gr.085472.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2593573PMC
December 2008

Mapping and quantifying mammalian transcriptomes by RNA-Seq.

Nat Methods 2008 Jul 30;5(7):621-8. Epub 2008 May 30.

Division of Biology, MC 156-29, California Institute of Technology, Pasadena, California 91125, USA.

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http://dx.doi.org/10.1038/nmeth.1226DOI Listing
July 2008

Sequence census methods for functional genomics.

Nat Methods 2008 Jan 19;5(1):19-21. Epub 2007 Dec 19.

Division of Biology, California Institute of Technology, Pasadena, California 91125, USA.

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http://www.nature.com/articles/nmeth1157
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http://dx.doi.org/10.1038/nmeth1157DOI Listing
January 2008

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

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

Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305-5120, USA.

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http://dx.doi.org/10.1126/science.1141319DOI Listing
June 2007

Genomic DNA as a general cohybridization standard for ratiometric microarrays.

Methods Enzymol 2006 ;410:237-79

Biology Division 156-29, Caltech, Pasadena, California, USA.

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http://dx.doi.org/10.1016/S0076-6879(06)10012-9DOI Listing
December 2006

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

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

Division of Biology, California Institute of Technology, Pasadena, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.0020169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1761652PMC
December 2006

Spatiometabolic stratification of Shewanella oneidensis biofilms.

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

Division of Biological Sciences, California Institute of Technology, Pasadena, California 91125, USA.

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http://dx.doi.org/10.1128/AEM.01163-06DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1636161PMC
November 2006

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

Genome Res 2006 Oct 8;16(10):1208-21. Epub 2006 Sep 8.

Division of Biology, California Institute of Technology, Pasadena, California 91125, USA.

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http://dx.doi.org/10.1101/gr.4997306DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1581430PMC
October 2006

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

Angew Chem Int Ed Engl 2006 May;45(22):3618-23

California Institute of Technology, Pasadena, CA 94305, USA.

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http://doi.wiley.com/10.1002/anie.200503830
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http://dx.doi.org/10.1002/anie.200503830DOI Listing
May 2006

Mining gene expression data by interpreting principal components.

BMC Bioinformatics 2006 Apr 7;7:194. Epub 2006 Apr 7.

Jet Propulsion Laboratory, California Institute of Technology, Pasadena, USA.

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http://dx.doi.org/10.1186/1471-2105-7-194DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1501050PMC
April 2006

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

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

Division of Hematology and Bone Marrow Transplantation, City of Hope National Medical Center, 1500 East Duarte Rd., Duarte, CA 91010, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867503PMC
http://dx.doi.org/10.1016/S1525-1578(10)60008-6DOI Listing
February 2005

Genomic DNA as a cohybridization standard for mammalian microarray measurements.

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

Division of Biology, MC 156-29, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1093/nar/gnh078DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC434457PMC
June 2004

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

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

Department of Biology, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1074/mcp.M300099-MCP200DOI Listing
March 2004

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

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

Department of Biomedical Engineering, University of California, CA 92697-2715, USA.

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http://www.nature.com/articles/1206325
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http://dx.doi.org/10.1038/sj.onc.1206325DOI Listing
April 2003

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

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

Jet Propulsion Laboratory, California Institute of Technology, Mail Stop 126-347, 4800 Oak Grove Drive, Pasadena, CA 91109, USA.

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http://dx.doi.org/10.1093/bioinformatics/btg042DOI Listing
March 2003

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

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

Departments of Applied Physics and Biology, California Institute of Technology, Pasadena, CA 91125, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.162468199
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http://dx.doi.org/10.1073/pnas.162468199DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC130571PMC
October 2002

Identification and confirmation of a module of coexpressed genes.

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

Department of Biomedical Engineering, University of California Irvine, Irvine, California 92697, USA.

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http://dx.doi.org/10.1101/gr.418402DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC187523PMC
October 2002