Publications by authors named "Peter Woolf"

33Publications

Tissue-specific profiling reveals transcriptome alterations in Arabidopsis mutants lacking morphological phenotypes.

Authors:
Marissa Simon Angela Bruex Raghunandan M Kainkaryam Xiaohua Zheng Ling Huang Peter J Woolf John Schiefelbein

Plant Cell 2013 Sep 6;25(9):3175-85. Epub 2013 Sep 6.

Department of Molecular, Cellular, and Developmental Biology, University of Michigan, An Arbor, Michigan 48109.

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September 2013

Smart pooling of mRNA samples for efficient transcript profiling.

Authors:
Raghunandan M Kainkaryam Angela Bruex Peter J Woolf John Schiefelbein

Methods Mol Biol 2012 ;876:189-94

Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA.

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September 2012

A gene regulatory network for root epidermis cell differentiation in Arabidopsis.

Authors:
Angela Bruex Raghunandan M Kainkaryam Yana Wieckowski Yeon Hee Kang Christine Bernhardt Yang Xia Xiaohua Zheng Jean Y Wang Myeong Min Lee Philip Benfey Peter J Woolf John Schiefelbein

PLoS Genet 2012 Jan 12;8(1):e1002446. Epub 2012 Jan 12.

Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.

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January 2012

Temporal dynamics of host molecular responses differentiate symptomatic and asymptomatic influenza a infection.

Authors:
Yongsheng Huang Aimee K Zaas Arvind Rao Nicolas Dobigeon Peter J Woolf Timothy Veldman N Christine Øien Micah T McClain Jay B Varkey Bradley Nicholson Lawrence Carin Stephen Kingsmore Christopher W Woods Geoffrey S Ginsburg Alfred O Hero

PLoS Genet 2011 Aug 25;7(8):e1002234. Epub 2011 Aug 25.

Center for Computational Biology and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America.

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August 2011

The transcription factor osterix (SP7) regulates BMP6-induced human osteoblast differentiation.

Authors:
Fengchang Zhu Michael S Friedman Weijun Luo Peter Woolf Kurt D Hankenson

J Cell Physiol 2012 Jun;227(6):2677-85

Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.

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June 2012

RegNetB: predicting relevant regulator-gene relationships in localized prostate tumor samples.

Authors:
Angel Alvarez Peter J Woolf

BMC Bioinformatics 2011 Jun 17;12:243. Epub 2011 Jun 17.

Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.

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June 2011

Partially observed bipartite network analysis to identify predictive connections in transcriptional regulatory networks.

Authors:
Angel Alvarez Peter J Woolf

BMC Syst Biol 2011 May 27;5:86. Epub 2011 May 27.

Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.

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May 2011

Time series gene expression profiling and temporal regulatory pathway analysis of BMP6 induced osteoblast differentiation and mineralization.

Authors:
Weijun Luo Michael S Friedman Kurt D Hankenson Peter J Woolf

BMC Syst Biol 2011 May 23;5:82. Epub 2011 May 23.

Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.

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May 2011

vProtein: identifying optimal amino acid complements from plant-based foods.

Authors:
Peter J Woolf Leeann L Fu Avik Basu

PLoS One 2011 Apr 22;6(4):e18836. Epub 2011 Apr 22.

Foodwiki, Ann Arbor, Michigan, United States of America.

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April 2011

BN+1 Bayesian network expansion for identifying molecular pathway elements.

Authors:
Andrew P Hodges Peter Woolf Yongqun He

Commun Integr Biol 2010 Nov 1;3(6):549-54. Epub 2010 Nov 1.

Center for Computational Medicine and Bioinformatics; University of Michigan Medical School; University of Michigan; Michigan USA.

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November 2010

Reconstructing transcriptional regulatory networks using three-way mutual information and Bayesian networks.

Authors:
Weijun Luo Peter J Woolf

Methods Mol Biol 2010 ;674:401-18

Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.

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December 2010

A mechanistic model of PCR for accurate quantification of quantitative PCR data.

Authors:
Gregory J Boggy Peter J Woolf

PLoS One 2010 Aug 30;5(8):e12355. Epub 2010 Aug 30.

Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America.

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August 2010

poolMC: smart pooling of mRNA samples in microarray experiments.

Authors:
Raghunandan M Kainkaryam Angela Bruex Anna C Gilbert John Schiefelbein Peter J Woolf

BMC Bioinformatics 2010 Jun 2;11:299. Epub 2010 Jun 2.

Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.

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June 2010

Bayesian network expansion identifies new ROS and biofilm regulators.

Authors:
Andrew P Hodges Dongjuan Dai Zuoshuang Xiang Peter Woolf Chuanwu Xi Yongqun He

PLoS One 2010 Mar 3;5(3):e9513. Epub 2010 Mar 3.

Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America.

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March 2010

Python Environment for Bayesian Learning: Inferring the Structure of Bayesian Networks from Knowledge and Data.

Authors:
Abhik Shah Peter Woolf

J Mach Learn Res 2009 Jun;10:159-162

Department of Chemical Engineering, 3320 G.G. Brown, Ann Arbor, MI 48103, USA.

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June 2009

Using mechanistic Bayesian networks to identify downstream targets of the sonic hedgehog pathway.

Authors:
Abhik Shah Toyoaki Tenzen Andrew P McMahon Peter J Woolf

BMC Bioinformatics 2009 Dec 18;10:433. Epub 2009 Dec 18.

Bioinformatics Program, University of Michigan, Ann Arbor, MI 48109, USA.

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December 2009

A computational approach to inferring cellular protein-binding affinities from quantitative fluorescence resonance energy transfer imaging.

Authors:
Khamir Mehta Adam D Hoppe Raghunandan Kainkaryam Peter J Woolf Jennifer J Linderman

Proteomics 2009 Dec;9(23):5371-83

Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109-2136, USA.

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December 2009

GAGE: generally applicable gene set enrichment for pathway analysis.

Authors:
Weijun Luo Michael S Friedman Kerby Shedden Kurt D Hankenson Peter J Woolf

BMC Bioinformatics 2009 May 27;10:161. Epub 2009 May 27.

Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.

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May 2009

Pooling in high-throughput drug screening.

Authors:
Raghunandan M Kainkaryam Peter J Woolf

Curr Opin Drug Discov Devel 2009 May;12(3):339-50

Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.

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May 2009

Learning transcriptional regulatory networks from high throughput gene expression data using continuous three-way mutual information.

Authors:
Weijun Luo Kurt D Hankenson Peter J Woolf

BMC Bioinformatics 2008 Nov 3;9:467. Epub 2008 Nov 3.

Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.

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November 2008