Alan P Boyle

Alan P Boyle

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Alan P Boyle

Alan P Boyle

Publications by authors named "Alan P Boyle"

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TRACE: transcription factor footprinting using chromatin accessibility data and DNA sequence.

Genome Res 2020 Jul 6. Epub 2020 Jul 6.

University of Michigan

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http://dx.doi.org/10.1101/gr.258228.119DOI Listing
July 2020

Transposable elements contribute to cell and species-specific chromatin looping and gene regulation in mammalian genomes.

Nat Commun 2020 04 14;11(1):1796. Epub 2020 Apr 14.

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.

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http://dx.doi.org/10.1038/s41467-020-15520-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7156512PMC
April 2020

Poly-Enrich: count-based methods for gene set enrichment testing with genomic regions.

NAR Genom Bioinform 2020 Mar 6;2(1):lqaa006. Epub 2020 Feb 6.

Biostatistics Department, University of Michigan, Ann Arbor, MI 48109, USA.

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http://dx.doi.org/10.1093/nargab/lqaa006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7003681PMC
March 2020

Predicting the effects of SNPs on transcription factor binding affinity.

Bioinformatics 2020 01;36(2):364-372

Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz612DOI Listing
January 2020

Predicting functional variants in enhancer and promoter elements using RegulomeDB.

Hum Mutat 2019 09 22;40(9):1292-1298. Epub 2019 Jun 22.

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan.

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http://dx.doi.org/10.1002/humu.23791DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6744346PMC
September 2019

CGIMP: Real-time exploration and covariate projection for self-organizing map datasets.

J Open Source Softw 2019 10;4(39). Epub 2019 Jul 10.

Department of Computational Medicine and Bioinformatics, University of Michigan.

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http://dx.doi.org/10.21105/joss.01520DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7272009PMC
July 2019

The ENCODE Blacklist: Identification of Problematic Regions of the Genome.

Sci Rep 2019 06 27;9(1):9354. Epub 2019 Jun 27.

Graduate Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, USA.

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http://dx.doi.org/10.1038/s41598-019-45839-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6597582PMC
June 2019

Cell Specificity of Human Regulatory Annotations and Their Genetic Effects on Gene Expression.

Genetics 2019 02 28;211(2):549-562. Epub 2018 Dec 28.

Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109

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http://dx.doi.org/10.1534/genetics.118.301525DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6366912PMC
February 2019

Conserved and species-specific transcription factor co-binding patterns drive divergent gene regulation in human and mouse.

Nucleic Acids Res 2018 02;46(4):1878-1894

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.

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http://dx.doi.org/10.1093/nar/gky018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5829737PMC
February 2018

Genome-wide Study of Atrial Fibrillation Identifies Seven Risk Loci and Highlights Biological Pathways and Regulatory Elements Involved in Cardiac Development.

Am J Hum Genet 2018 01 28;102(1):103-115. Epub 2017 Dec 28.

Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA; Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA; K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health, Norwegian University of Science and Technology, Trondheim 7491, Norway; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2017.12.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5777936PMC
January 2018

A proximity-based graph clustering method for the identification and application of transcription factor clusters.

BMC Bioinformatics 2017 Nov 29;18(1):530. Epub 2017 Nov 29.

University of Michigan Department of Computational Medicine and Bioinformatics, 100 Washtenaw Avenue, Ann Arbor, 48109, USA.

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http://dx.doi.org/10.1186/s12859-017-1935-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5706350PMC
November 2017

Mining the Unknown: Assigning Function to Noncoding Single Nucleotide Polymorphisms.

Trends Genet 2017 01 6;33(1):34-45. Epub 2016 Dec 6.

Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA. Electronic address:

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http://dx.doi.org/10.1016/j.tig.2016.10.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5553318PMC
January 2017

Deciphering ENCODE.

Trends Genet 2016 Apr 5;32(4):238-249. Epub 2016 Mar 5.

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan, Ann Arbor MI 48109, USA. Electronic address:

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http://dx.doi.org/10.1016/j.tig.2016.02.002DOI Listing
April 2016

Pattern matching approach to pseudosymmetry problems in electron backscatter diffraction.

Ultramicroscopy 2016 Jan 23;160:146-154. Epub 2015 Oct 23.

Department of Earth, Ocean & Ecological Sciences, Herdman Building, 4 Brownlow Street, University of Liverpool, Liverpool L69 3GP, UK.

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http://dx.doi.org/10.1016/j.ultramic.2015.10.010DOI Listing
January 2016

Mango: a bias-correcting ChIA-PET analysis pipeline.

Bioinformatics 2015 Oct 1;31(19):3092-8. Epub 2015 Jun 1.

Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 and.

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http://dx.doi.org/10.1093/bioinformatics/btv336DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4592333PMC
October 2015

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

Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures.

Bioinformatics 2014 Oct 5;30(19):2808-10. Epub 2014 Jun 5.

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

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http://dx.doi.org/10.1093/bioinformatics/btu379DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4173017PMC
October 2014

Dynamic trans-acting factor colocalization in human cells.

Cell 2013 Oct 24;155(3):713-24. Epub 2013 Oct 24.

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

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http://dx.doi.org/10.1016/j.cell.2013.09.043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4079469PMC
October 2013

Linking disease associations with regulatory information in the human genome.

Genome Res 2012 Sep;22(9):1748-59

Department of Computer Science, Stanford University, Stanford, California 94305, USA.

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http://genome.cshlp.org/cgi/doi/10.1101/gr.136127.111
Publisher Site
http://dx.doi.org/10.1101/gr.136127.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431491PMC
September 2012

Evidence-ranked motif identification.

Genome Biol 2010 15;11(2):R19. Epub 2010 Feb 15.

Program for Computational Biology and Bioinformatics, Duke University, 102 North Building, Durham, NC 27708, USA.

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http://dx.doi.org/10.1186/gb-2010-11-2-r19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2872879PMC
August 2010

Heritable individual-specific and allele-specific chromatin signatures in humans.

Science 2010 Apr 18;328(5975):235-9. Epub 2010 Mar 18.

Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Section of Molecular Genetics and Microbiology, University of Texas, Austin, TX 78712, USA.

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http://dx.doi.org/10.1126/science.1184655DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2929018PMC
April 2010

Both noncoding and protein-coding RNAs contribute to gene expression evolution in the primate brain.

Genome Biol Evol 2010 Jan 18;2:67-79. Epub 2010 Jan 18.

Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina, USA.

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http://dx.doi.org/10.1093/gbe/evq002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2839352PMC
January 2010

DNaseI hypersensitivity at gene-poor, FSH dystrophy-linked 4q35.2.

Nucleic Acids Res 2009 Dec;37(22):7381-93

Human Genetics Program and Department of Biochemistry and Tulane Cancer Center, Tulane Medical School, New Orleans, LA 70112, USA.

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http://dx.doi.org/10.1093/nar/gkp833DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2794184PMC
December 2009

F-Seq: a feature density estimator for high-throughput sequence tags.

Bioinformatics 2008 Nov 10;24(21):2537-8. Epub 2008 Sep 10.

Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn480DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2732284PMC
November 2008