Katherine S Pollard

Katherine S Pollard

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Katherine S Pollard

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phylogenize: correcting for phylogeny reveals genes associated with microbial distributions.

Bioinformatics 2019 Oct 7. Epub 2019 Oct 7.

Gladstone Institute of Data Science and Biotechnology, San Francisco, CA USA.

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http://dx.doi.org/10.1093/bioinformatics/btz722DOI Listing
October 2019

Global ecotypes in the ubiquitous marine clade SAR86.

ISME J 2019 Oct 14. Epub 2019 Oct 14.

Gladstone Institutes, San Francisco, CA, USA.

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http://dx.doi.org/10.1038/s41396-019-0516-7DOI Listing
October 2019

Principles of meiotic chromosome assembly revealed in S. cerevisiae.

Nat Commun 2019 Oct 22;10(1):4795. Epub 2019 Oct 22.

Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK.

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http://dx.doi.org/10.1038/s41467-019-12629-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6805904PMC
October 2019

Reply to 'Inflated performance measures in enhancer-promoter interaction-prediction methods'.

Nat Genet 2019 Aug;51(8):1198-1200

Gladstone Institutes, San Francisco, CA, USA.

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http://dx.doi.org/10.1038/s41588-019-0473-0DOI Listing
August 2019

Context-Specific Transcription Factor Functions Regulate Epigenomic and Transcriptional Dynamics during Cardiac Reprogramming.

Cell Stem Cell 2019 Jul;25(1):87-102.e9

Gladstone Institutes, San Francisco, CA 94158, USA; Departments of Pediatrics and Biochemistry & Biophysics, University of California, San Francisco, CA 94143, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2019.06.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6632093PMC
July 2019

Empowering statistical methods for cellular and molecular biologists.

Mol Biol Cell 2019 06;30(12):1359-1368

Gladstone Institutes, Chan-Zuckerberg Biohub, and University of California, San Francisco, San Francisco, CA 94158.

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http://dx.doi.org/10.1091/mbc.E15-02-0076DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6724699PMC
June 2019

A Metagenomic Meta-analysis Reveals Functional Signatures of Health and Disease in the Human Gut Microbiome.

mSystems 2019 Jul-Aug;4(4). Epub 2019 May 14.

Department of Microbiology, Oregon State University, Corvallis, Oregon, USA.

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http://dx.doi.org/10.1128/mSystems.00332-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6517693PMC
May 2019

Evolution of Mechanisms that Control Mating in Drosophila Males.

Cell Rep 2019 May;27(9):2527-2536.e4

Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Department of Neurobiology, Stanford University, Stanford, CA 94305, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S22111247193058
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http://dx.doi.org/10.1016/j.celrep.2019.04.104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6646047PMC
May 2019

New insights from uncultivated genomes of the global human gut microbiome.

Nature 2019 04 13;568(7753):505-510. Epub 2019 Mar 13.

United States Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.

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http://www.nature.com/articles/s41586-019-1058-x
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http://dx.doi.org/10.1038/s41586-019-1058-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6784871PMC
April 2019

Most chromatin interactions are not in linkage disequilibrium.

Genome Res 2019 03 7;29(3):334-343. Epub 2019 Jan 7.

Gladstone Institutes, San Francisco, California 94158, USA.

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http://genome.cshlp.org/lookup/doi/10.1101/gr.238022.118
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http://dx.doi.org/10.1101/gr.238022.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6396425PMC
March 2019

Chromatin features constrain structural variation across evolutionary timescales.

Proc Natl Acad Sci U S A 2019 02 18;116(6):2175-2180. Epub 2019 Jan 18.

Gladstone Institute of Data Science and Biotechnology, San Francisco, CA 94158;

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http://dx.doi.org/10.1073/pnas.1808631116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6369792PMC
February 2019

A De Novo Shape Motif Discovery Algorithm Reveals Preferences of Transcription Factors for DNA Shape Beyond Sequence Motifs.

Cell Syst 2019 01 16;8(1):27-42.e6. Epub 2019 Jan 16.

Gladstone Institutes, San Francisco, CA 94158, USA; Department of Epidemiology & Biostatistics, Institute for Human Genetics, Quantitative Biology Institute, and Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2018.12.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6368855PMC
January 2019

Evolutionary dynamics of bacteria in the gut microbiome within and across hosts.

PLoS Biol 2019 01 23;17(1):e3000102. Epub 2019 Jan 23.

Gladstone Institutes, San Francisco, California, United States of America.

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http://dx.plos.org/10.1371/journal.pbio.3000102
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http://dx.doi.org/10.1371/journal.pbio.3000102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6361464PMC
January 2019

Existing Climate Change Will Lead to Pronounced Shifts in the Diversity of Soil Prokaryotes.

mSystems 2018 Sep-Oct;3(5). Epub 2018 Oct 23.

State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.

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http://msystems.asm.org/lookup/doi/10.1128/mSystems.00167-18
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http://dx.doi.org/10.1128/mSystems.00167-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6199470PMC
October 2018

Phylogeny-corrected identification of microbial gene families relevant to human gut colonization.

PLoS Comput Biol 2018 08 9;14(8):e1006242. Epub 2018 Aug 9.

Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.

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http://dx.doi.org/10.1371/journal.pcbi.1006242DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6084841PMC
August 2018

The Epstein-Barr Virus Episome Maneuvers between Nuclear Chromatin Compartments during Reactivation.

J Virol 2018 02 17;92(3). Epub 2018 Jan 17.

Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA

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http://dx.doi.org/10.1128/JVI.01413-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5774889PMC
February 2018

Human evolution: the non-coding revolution.

BMC Biol 2017 10 2;15(1):89. Epub 2017 Oct 2.

Gladstone Institutes, San Francisco, CA, 94158, USA.

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http://dx.doi.org/10.1186/s12915-017-0428-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5625771PMC
October 2017

Genomic analyses identify hundreds of variants associated with age at menarche and support a role for puberty timing in cancer risk.

Authors:
Felix R Day Deborah J Thompson Hannes Helgason Daniel I Chasman Hilary Finucane Patrick Sulem Katherine S Ruth Sean Whalen Abhishek K Sarkar Eva Albrecht Elisabeth Altmaier Marzyeh Amini Caterina M Barbieri Thibaud Boutin Archie Campbell Ellen Demerath Ayush Giri Chunyan He Jouke J Hottenga Robert Karlsson Ivana Kolcic Po-Ru Loh Kathryn L Lunetta Massimo Mangino Brumat Marco George McMahon Sarah E Medland Ilja M Nolte Raymond Noordam Teresa Nutile Lavinia Paternoster Natalia Perjakova Eleonora Porcu Lynda M Rose Katharina E Schraut Ayellet V Segrè Albert V Smith Lisette Stolk Alexander Teumer Irene L Andrulis Stefania Bandinelli Matthias W Beckmann Javier Benitez Sven Bergmann Murielle Bochud Eric Boerwinkle Stig E Bojesen Manjeet K Bolla Judith S Brand Hiltrud Brauch Hermann Brenner Linda Broer Thomas Brüning Julie E Buring Harry Campbell Eulalia Catamo Stephen Chanock Georgia Chenevix-Trench Tanguy Corre Fergus J Couch Diana L Cousminer Angela Cox Laura Crisponi Kamila Czene George Davey Smith Eco J C N de Geus Renée de Mutsert Immaculata De Vivo Joe Dennis Peter Devilee Isabel Dos-Santos-Silva Alison M Dunning Johan G Eriksson Peter A Fasching Lindsay Fernández-Rhodes Luigi Ferrucci Dieter Flesch-Janys Lude Franke Marike Gabrielson Ilaria Gandin Graham G Giles Harald Grallert Daniel F Gudbjartsson Pascal Guénel Per Hall Emily Hallberg Ute Hamann Tamara B Harris Catharina A Hartman Gerardo Heiss Maartje J Hooning John L Hopper Frank Hu David J Hunter M Arfan Ikram Hae Kyung Im Marjo-Riitta Järvelin Peter K Joshi David Karasik Manolis Kellis Zoltan Kutalik Genevieve LaChance Diether Lambrechts Claudia Langenberg Lenore J Launer Joop S E Laven Stefania Lenarduzzi Jingmei Li Penelope A Lind Sara Lindstrom YongMei Liu Jian'an Luan Reedik Mägi Arto Mannermaa Hamdi Mbarek Mark I McCarthy Christa Meisinger Thomas Meitinger Cristina Menni Andres Metspalu Kyriaki Michailidou Lili Milani Roger L Milne Grant W Montgomery Anna M Mulligan Mike A Nalls Pau Navarro Heli Nevanlinna Dale R Nyholt Albertine J Oldehinkel Tracy A O'Mara Sandosh Padmanabhan Aarno Palotie Nancy Pedersen Annette Peters Julian Peto Paul D P Pharoah Anneli Pouta Paolo Radice Iffat Rahman Susan M Ring Antonietta Robino Frits R Rosendaal Igor Rudan Rico Rueedi Daniela Ruggiero Cinzia F Sala Marjanka K Schmidt Robert A Scott Mitul Shah Rossella Sorice Melissa C Southey Ulla Sovio Meir Stampfer Maristella Steri Konstantin Strauch Toshiko Tanaka Emmi Tikkanen Nicholas J Timpson Michela Traglia Thérèse Truong Jonathan P Tyrer André G Uitterlinden Digna R Velez Edwards Veronique Vitart Uwe Völker Peter Vollenweider Qin Wang Elisabeth Widen Ko Willems van Dijk Gonneke Willemsen Robert Winqvist Bruce H R Wolffenbuttel Jing Hua Zhao Magdalena Zoledziewska Marek Zygmunt Behrooz Z Alizadeh Dorret I Boomsma Marina Ciullo Francesco Cucca Tõnu Esko Nora Franceschini Christian Gieger Vilmundur Gudnason Caroline Hayward Peter Kraft Debbie A Lawlor Patrik K E Magnusson Nicholas G Martin Dennis O Mook-Kanamori Ellen A Nohr Ozren Polasek David Porteous Alkes L Price Paul M Ridker Harold Snieder Tim D Spector Doris Stöckl Daniela Toniolo Sheila Ulivi Jenny A Visser Henry Völzke Nicholas J Wareham James F Wilson Amanda B Spurdle Unnur Thorsteindottir Katherine S Pollard Douglas F Easton Joyce Y Tung Jenny Chang-Claude David Hinds Anna Murray Joanne M Murabito Kari Stefansson Ken K Ong John R B Perry

Nat Genet 2017 Jun 24;49(6):834-841. Epub 2017 Apr 24.

MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK.

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http://dx.doi.org/10.1038/ng.3841DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5841952PMC
June 2017

Proteobacteria explain significant functional variability in the human gut microbiome.

Microbiome 2017 03 23;5(1):36. Epub 2017 Mar 23.

Gladstone Institutes, San Francisco, CA, USA.

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http://dx.doi.org/10.1186/s40168-017-0244-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5363007PMC
March 2017

Unboxing cluster heatmaps.

BMC Bioinformatics 2017 Feb 15;18(Suppl 2):63. Epub 2017 Feb 15.

Gladstone Institutes, San Francisco, 94158, CA, USA.

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http://dx.doi.org/10.1186/s12859-016-1442-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5333167PMC
February 2017

Discovery of Reactive Microbiota-Derived Metabolites that Inhibit Host Proteases.

Cell 2017 01 19;168(3):517-526.e18. Epub 2017 Jan 19.

Department of Bioengineering and Therapeutic Sciences and California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2016.12.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5302092PMC
January 2017

Modulation of a Circulating Uremic Solute via Rational Genetic Manipulation of the Gut Microbiota.

Cell Host Microbe 2016 Dec 1;20(6):709-715. Epub 2016 Dec 1.

Department of Bioengineering and Therapeutic Sciences and California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94143, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S19313128163044
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http://dx.doi.org/10.1016/j.chom.2016.10.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5159218PMC
December 2016

Urban greenness influences airborne bacterial community composition.

Sci Total Environ 2016 Nov 11;571:680-7. Epub 2016 Jul 11.

Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States.

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http://dx.doi.org/10.1016/j.scitotenv.2016.07.037DOI Listing
November 2016

An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography.

Genome Res 2016 11 18;26(11):1612-1625. Epub 2016 Oct 18.

Integrative Program in Quantitative Biology, University of California, San Francisco, San Francisco, California 94158, USA.

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http://dx.doi.org/10.1101/gr.201863.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5088602PMC
November 2016

Toward Accurate and Quantitative Comparative Metagenomics.

Cell 2016 Aug;166(5):1103-1116

Gladstone Institutes, San Francisco, CA 94158, USA; Division of Biostatistics, Institute for Human Genetics, and Institute for Computational Health Sciences, University of California, San Francisco, CA 94158, USA. Electronic address:

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5080976PMC
http://dx.doi.org/10.1016/j.cell.2016.08.007DOI Listing
August 2016

Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin.

Nat Genet 2016 05 4;48(5):488-96. Epub 2016 Apr 4.

Gladstone Institutes, San Francisco, California, USA.

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http://dx.doi.org/10.1038/ng.3539DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4910881PMC
May 2016

Toward a Predictive Understanding of Earth's Microbiomes to Address 21st Century Challenges.

MBio 2016 05 13;7(3). Epub 2016 May 13.

Earth and Environmental Sciences, Lawrence Berkeley National Lab, Berkeley, California, USA Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA

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http://dx.doi.org/10.1128/mBio.00714-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4895116PMC
May 2016

Accelerated Evolution of Enhancer Hotspots in the Mammal Ancestor.

Mol Biol Evol 2016 Apr 29;33(4):1008-18. Epub 2015 Dec 29.

Gladstone Institute of Cardiovascular Disease, San Francisco, CA Department of Epidemiology and Biostatistics, University of California, San Francisco, CA Institute for Human Genetics, University of California, San Francisco, CA

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http://dx.doi.org/10.1093/molbev/msv344DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4776709PMC
April 2016

Bat Accelerated Regions Identify a Bat Forelimb Specific Enhancer in the HoxD Locus.

PLoS Genet 2016 Mar 28;12(3):e1005738. Epub 2016 Mar 28.

Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1005738DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4809552PMC
March 2016

Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis.

Cell 2016 Feb 11;164(5):999-1014. Epub 2016 Feb 11.

Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA; Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94143, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2016.01.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4769693PMC
February 2016

Marked seasonal variation in the wild mouse gut microbiota.

ISME J 2015 Nov 29;9(11):2423-34. Epub 2015 May 29.

FAS Center for Systems Biology, Harvard University, Cambridge, MA, USA.

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http://dx.doi.org/10.1038/ismej.2015.53DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4611506PMC
November 2015

MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome.

Bioinformatics 2015 Oct 22;31(20):3368-70. Epub 2015 Jun 22.

Integrative Program in Quantitative Biology, Gladstone Institutes, and Division of Biostatistics, University of California San Francisco and.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btv382DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4595903PMC
October 2015

Can a few non-coding mutations make a human brain?

Bioessays 2015 Oct 25;37(10):1054-61. Epub 2015 Aug 25.

Gladstone Institutes, San Francisco, CA, USA.

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http://dx.doi.org/10.1002/bies.201500049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5054932PMC
October 2015

Genomic approaches to studying human-specific developmental traits.

Development 2015 Sep;142(18):3100-12

Gladstone Institutes, San Francisco, CA 94158, USA Institute for Human Genetics, Department of Epidemiology & Biostatistics, University of California, San Francisco, CA 94158, USA

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http://dx.doi.org/10.1242/dev.120048DOI Listing
September 2015

Coevolutionary analyses require phylogenetically deep alignments and better null models to accurately detect inter-protein contacts within and between species.

BMC Bioinformatics 2015 Aug 25;16:268. Epub 2015 Aug 25.

Bioinformatics Graduate Program, University of California, San Francisco, USA.

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http://dx.doi.org/10.1186/s12859-015-0677-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4549020PMC
August 2015

Signatures of accelerated somatic evolution in gene promoters in multiple cancer types.

Nucleic Acids Res 2015 Jun 1;43(11):5307-17. Epub 2015 May 1.

Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA Computational Biosciences Program, University of Colorado-Denver, Aurora, CO, USA University of Colorado Cancer Center, Aurora, CO, USA Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO, USA

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http://dx.doi.org/10.1093/nar/gkv419DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4477653PMC
June 2015

Profile hidden Markov models for the detection of viruses within metagenomic sequence data.

PLoS One 2014 20;9(8):e105067. Epub 2014 Aug 20.

Departments of Medicine, Biochemistry and Biophysics, and Microbiology, University of California San Francisco, San Francisco, California, United States of America; Howard Hughes Medical Institute, Bethesda, Maryland, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0105067PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4139300PMC
May 2015

Genomic and network patterns of schizophrenia genetic variation in human evolutionary accelerated regions.

Mol Biol Evol 2015 May 12;32(5):1148-60. Epub 2015 Feb 12.

Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY

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http://dx.doi.org/10.1093/molbev/msv031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4408416PMC
May 2015

Continental-scale distributions of dust-associated bacteria and fungi.

Proc Natl Acad Sci U S A 2015 May 20;112(18):5756-61. Epub 2015 Apr 20.

Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309; Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309;

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http://dx.doi.org/10.1073/pnas.1420815112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4426398PMC
May 2015

Human disease modeling reveals integrated transcriptional and epigenetic mechanisms of NOTCH1 haploinsufficiency.

Cell 2015 Mar;160(6):1072-86

Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA; Program in Developmental and Stem Cell Biology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.02.035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4359747PMC
March 2015

Evolution of lysine acetylation in the RNA polymerase II C-terminal domain.

BMC Evol Biol 2015 Mar 10;15:35. Epub 2015 Mar 10.

Center for Human Genetics Research, Vanderbilt University, Nashville, TN, 37232, USA.

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http://dx.doi.org/10.1186/s12862-015-0327-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4362643PMC
March 2015

motifDiverge: a model for assessing the statistical significance of gene regulatory motif divergence between two DNA sequences.

Stat Interface 2015;8(4):463-476

Gladstone Institutes, Institute for Human Genetics, Division of Biostatistics, University of California, 1650 Owens Street, San Francisco, CA 94158, USA.

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http://www.intlpress.com/site/pub/pages/journals/items/sii/c
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http://dx.doi.org/10.4310/SII.2015.v8.n4.a6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4689439PMC
January 2015

Exploring the genesis and functions of Human Accelerated Regions sheds light on their role in human evolution.

Curr Opin Genet Dev 2014 Dec 23;29:15-21. Epub 2014 Aug 23.

Gladstone Institutes, Division of Biostatistics & Institute for Human Genetics, University of California, 1650 Owens Street, San Francisco, CA 94158, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S0959437X140007
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http://dx.doi.org/10.1016/j.gde.2014.07.005DOI Listing
December 2014

A taxonomic signature of obesity in the microbiome? Getting to the guts of the matter.

PLoS One 2014 8;9(1):e84689. Epub 2014 Jan 8.

The J. David Gladstone Institutes, San Francisco, California, United States of America ; Institute for Human Genetics and Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0084689PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3885756PMC
September 2014

Gibbon genome and the fast karyotype evolution of small apes.

Nature 2014 Sep;513(7517):195-201

Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1038/nature13679DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4249732PMC
September 2014

Liquefaction of semen generates and later degrades a conserved semenogelin peptide that enhances HIV infection.

J Virol 2014 Jul 16;88(13):7221-34. Epub 2014 Apr 16.

Gladstone Institute of Virology and Immunology, University of California, San Francisco, California, USA Departments of Medicine and Microbiology and Immunology, University of California, San Francisco, California, USA.

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http://dx.doi.org/10.1128/JVI.00269-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4054457PMC
July 2014

Integrating diverse datasets improves developmental enhancer prediction.

PLoS Comput Biol 2014 Jun 26;10(6):e1003677. Epub 2014 Jun 26.

Center for Human Genetics Research and Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1003677DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4072507PMC
June 2014

A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes.

PLoS Genet 2013 15;9(8):e1003684. Epub 2013 Aug 15.

Gladstone Institutes, University of California, San Francisco, California, United States of America.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3744432PMC
March 2014

Many human accelerated regions are developmental enhancers.

Philos Trans R Soc Lond B Biol Sci 2013 Dec 11;368(1632):20130025. Epub 2013 Nov 11.

Gladstone Institutes, University of California, , San Francisco, CA 94158, USA.

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December 2013

How old is my gene?

Trends Genet 2013 Nov 1;29(11):659-68. Epub 2013 Aug 1.

Center for Human Genetics Research and Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37232, USA.

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http://dx.doi.org/10.1016/j.tig.2013.07.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3812327PMC
November 2013

Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States.

Science 2013 Nov;342(6158):621-4

Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA.

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http://dx.doi.org/10.1126/science.1243768DOI Listing
November 2013

Global marine bacterial diversity peaks at high latitudes in winter.

ISME J 2013 Sep 21;7(9):1669-77. Epub 2013 Mar 21.

The Gladstone Institutes, University of California, San Francisco, CA 94158, USA.

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http://dx.doi.org/10.1038/ismej.2013.37DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3749493PMC
September 2013

Beyond classification: gene-family phylogenies from shotgun metagenomic reads enable accurate community analysis.

BMC Genomics 2013 Jun 22;14:419. Epub 2013 Jun 22.

Gladstone Institute of Cardiovascular Disease, University of California, San Francisco, CA 94158, USA.

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http://dx.doi.org/10.1186/1471-2164-14-419DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3701559PMC
June 2013

Novel bacterial taxa in the human microbiome.

PLoS One 2012 13;7(6):e35294. Epub 2012 Jun 13.

The Genome Institute, Washington University School of Medicine, St Louis, Missouri, United States of America.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3374617PMC
December 2012

ProteinHistorian: tools for the comparative analysis of eukaryote protein origin.

PLoS Comput Biol 2012 28;8(6):e1002567. Epub 2012 Jun 28.

J. David Gladstone Institutes, University of California, San Francisco, California, United States of America.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3386163PMC
October 2012

Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource.

BMC Bioinformatics 2012 Oct 13;13:264. Epub 2012 Oct 13.

The J. David Gladstone Institutes, University of California San Francisco, San Francisco, CA 94158, USA.

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http://dx.doi.org/10.1186/1471-2105-13-264DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3481395PMC
October 2012

G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes.

BMC Bioinformatics 2012 Sep 28;13:253. Epub 2012 Sep 28.

Genome Center, University of California Davis, 451 Health Science Dr, Davis, CA, 95616, United States of America.

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http://dx.doi.org/10.1186/1471-2105-13-253DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3575404PMC
September 2012

The role of GC-biased gene conversion in shaping the fastest evolving regions of the human genome.

Mol Biol Evol 2012 Mar 10;29(3):1047-57. Epub 2011 Nov 10.

Gladstone Institute of Cardiovascular Disease, University of California, San Francisco, USA.

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March 2012

Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hot spots.

Genome Biol Evol 2011 21;3:614-26. Epub 2011 Jun 21.

Center for Biomolecular Science and Engineering, University of California, Santa Cruz, USA.

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December 2011

The phylogenetic diversity of metagenomes.

PLoS One 2011 31;6(8):e23214. Epub 2011 Aug 31.

Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166145PMC
December 2011

Substitution patterns are GC-biased in divergent sequences across the metazoans.

Genome Biol Evol 2011 13;3:516-27. Epub 2011 Jun 13.

Gladstone Institutes, University of California, San Francisco, USA.

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http://dx.doi.org/10.1093/gbe/evr051DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3138425PMC
November 2011

A high-resolution map of human evolutionary constraint using 29 mammals.

Nature 2011 Oct 12;478(7370):476-82. Epub 2011 Oct 12.

Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1038/nature10530DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3207357PMC
October 2011

Novel genes exhibit distinct patterns of function acquisition and network integration.

Genome Biol 2010 27;11(12):R127. Epub 2010 Dec 27.

Gladstone Institutes, University of California, San Francisco, 1650 Owens St, San Francisco, CA 94158, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3046487PMC
June 2011

SIRT1 and SIRT3 deacetylate homologous substrates: AceCS1,2 and HMGCS1,2.

Aging (Albany NY) 2011 Jun;3(6):635-42

Gladstone Institute of Virology and Immunology, University of California, San Francisco, CA 94158, USA.

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http://dx.doi.org/10.18632/aging.100339DOI Listing
June 2011

PHAST and RPHAST: phylogenetic analysis with space/time models.

Brief Bioinform 2011 Jan 21;12(1):41-51. Epub 2010 Dec 21.

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA.

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http://dx.doi.org/10.1093/bib/bbq072DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3030812PMC
January 2011

PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data.

PLoS Comput Biol 2011 Jan 20;7(1):e1001061. Epub 2011 Jan 20.

The J. David Gladstone Institutes, University of California San Francisco, San Francisco, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1001061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3024254PMC
January 2011

Noncoding sequences near duplicated genes evolve rapidly.

Genome Biol Evol 2010 29;2:518-33. Epub 2010 Jun 29.

Gladstone Institute for Cardiovascular Disease, Gladstone Institutes, University of California-San Francisco, San Francisco, CA, USA.

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December 2010

The importance of being cis: evolution of orthologous fish and mammalian enhancer activity.

Mol Biol Evol 2010 Oct 21;27(10):2322-32. Epub 2010 May 21.

Department of Biology, Boston College, Chestnut Hill, Massachusetts, USA.

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http://dx.doi.org/10.1093/molbev/msq128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3107594PMC
October 2010

GC-biased evolution near human accelerated regions.

PLoS Genet 2010 May 20;6(5):e1000960. Epub 2010 May 20.

Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2873926PMC
May 2010