Michael A Beer

Michael A Beer

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Michael A Beer

Michael A Beer

Publications by authors named "Michael A Beer"

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Epigenetic activation and memory at a enhancer in systemic sclerosis.

Sci Transl Med 2019 Jun;11(497)

McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.1126/scitranslmed.aaw0790DOI Listing
June 2019

Parkinson-Associated SNCA Enhancer Variants Revealed by Open Chromatin in Mouse Dopamine Neurons.

Am J Hum Genet 2018 12 29;103(6):874-892. Epub 2018 Nov 29.

McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2018.10.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6288322PMC
December 2018

Local epigenomic state cannot discriminate interacting and non-interacting enhancer-promoter pairs with high accuracy.

PLoS Comput Biol 2018 12 18;14(12):e1006625. Epub 2018 Dec 18.

Department of Biomedical Engineering John Hopkins, Baltimore, MD, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1006625DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6298642PMC
December 2018

Predicting enhancer activity and variant impact using gkm-SVM.

Authors:
Michael A Beer

Hum Mutat 2017 09 15;38(9):1251-1258. Epub 2017 Mar 15.

McKusick-Nathans Institute of Genetic Medicine and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland.

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http://dx.doi.org/10.1002/humu.23185DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5526747PMC
September 2017

Embryonic loss of human females with partial trisomy 19 identifies region critical for the single active X.

PLoS One 2017 12;12(4):e0170403. Epub 2017 Apr 12.

McKusick Nathans Institute of Genetic Medicine, Baltimore, MD, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0170403PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5389809PMC
April 2017

gkmSVM: an R package for gapped-kmer SVM.

Bioinformatics 2016 07 19;32(14):2205-7. Epub 2016 Apr 19.

McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btw203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937197PMC
July 2016

Identification of Predictive Cis-Regulatory Elements Using a Discriminative Objective Function and a Dynamic Search Space.

PLoS One 2015 14;10(10):e0140557. Epub 2015 Oct 14.

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States of America; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0140557PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4605740PMC
June 2016

Epigenomic landscapes of retinal rods and cones.

Elife 2016 Mar 7;5:e11613. Epub 2016 Mar 7.

Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States.

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http://dx.doi.org/10.7554/eLife.11613DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4798964PMC
March 2016

A method to predict the impact of regulatory variants from DNA sequence.

Nat Genet 2015 Aug 15;47(8):955-61. Epub 2015 Jun 15.

1] McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA. [2] Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA.

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http://dx.doi.org/10.1038/ng.3331DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4520745PMC
August 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

Robust k-mer frequency estimation using gapped k-mers.

J Math Biol 2014 Aug 17;69(2):469-500. Epub 2013 Jul 17.

Department of Biomedical Engineering and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA,

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http://dx.doi.org/10.1007/s00285-013-0705-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3895138PMC
August 2014

Enhanced regulatory sequence prediction using gapped k-mer features.

PLoS Comput Biol 2014 Jul 17;10(7):e1003711. Epub 2014 Jul 17.

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1003711DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4102394PMC
July 2014

kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic data sets.

Nucleic Acids Res 2013 Jul 14;41(Web Server issue):W544-56. Epub 2013 Jun 14.

McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.1093/nar/gkt519DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3692045PMC
July 2013

Group normalization for genomic data.

PLoS One 2012 13;7(8):e38695. Epub 2012 Aug 13.

McKusick-Nathans Institute of Genetic Medicine and the Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0038695PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418286PMC
April 2013

Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes.

Genome Res 2012 Nov 27;22(11):2290-301. Epub 2012 Sep 27.

McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.1101/gr.139360.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3483558PMC
November 2012

Discriminative prediction of mammalian enhancers from DNA sequence.

Genome Res 2011 Dec 29;21(12):2167-80. Epub 2011 Aug 29.

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21205, USA.

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http://dx.doi.org/10.1101/gr.121905.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3227105PMC
December 2011

Lin-28B transactivation is necessary for Myc-mediated let-7 repression and proliferation.

Proc Natl Acad Sci U S A 2009 Mar 11;106(9):3384-9. Epub 2009 Feb 11.

McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.1073/pnas.0808300106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2651245PMC
March 2009

Identification of miR-21 targets in breast cancer cells using a quantitative proteomic approach.

Proteomics 2009 Mar;9(5):1374-84

McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.1002/pmic.200800551DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3030979PMC
March 2009

Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b.

Genome Res 2008 Feb 10;18(2):252-60. Epub 2007 Dec 10.

McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.

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http://dx.doi.org/10.1101/gr.6929408DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2203623PMC
February 2008

Functional characterization of a novel Ku70/80 pause site at the H19/Igf2 imprinting control region.

Mol Cell Biol 2005 May;25(10):3855-63

Department of Molecular Biology, One Nassau Hall, Princeton University, Princeton, NJ 08544-0015, USA.

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http://dx.doi.org/10.1128/MCB.25.10.3855-3863.2005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1087736PMC
May 2005

Predicting gene expression from sequence.

Cell 2004 Apr;117(2):185-98

Lewis-Sigler Institute for Integrative Genomics and Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1016/s0092-8674(04)00304-6DOI Listing
April 2004

Whole-genome discovery of transcription factor binding sites by network-level conservation.

Genome Res 2004 Jan 12;14(1):99-108. Epub 2003 Dec 12.

Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA.

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http://dx.doi.org/10.1101/gr.1739204DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC314286PMC
January 2004