Publications by authors named "Adam Siepel"

83Publications

Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph.

PLoS Genet 2020 08 6;16(8):e1008895. Epub 2020 Aug 6.

Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1008895DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7410169PMC
August 2020

Phylogenetic Modeling of Regulatory Element Turnover Based on Epigenomic Data.

Mol Biol Evol 2020 07;37(7):2137-2152

Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.

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http://dx.doi.org/10.1093/molbev/msaa073DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7306682PMC
July 2020

An inferred fitness consequence map of the rice genome.

Nat Plants 2020 02 10;6(2):119-130. Epub 2020 Feb 10.

Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA.

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http://dx.doi.org/10.1038/s41477-019-0589-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7446671PMC
February 2020

Inference of Ancestral Recombination Graphs Using ARGweaver.

Methods Mol Biol 2020 ;2090:231-266

Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.

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http://dx.doi.org/10.1007/978-1-0716-0199-0_10DOI Listing
January 2020

From Summary Statistics to Gene Trees: Methods for Inferring Positive Selection.

Trends Genet 2020 04 15;36(4):243-258. Epub 2020 Jan 15.

Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.

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http://dx.doi.org/10.1016/j.tig.2019.12.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7177178PMC
April 2020

Challenges in funding and developing genomic software: roots and remedies.

Authors:
Adam Siepel

Genome Biol 2019 07 29;20(1):147. Epub 2019 Jul 29.

Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.

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http://dx.doi.org/10.1186/s13059-019-1763-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6664559PMC
July 2019

Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease.

Genome Res 2019 08 27;29(8):1310-1321. Epub 2019 Jun 27.

Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.

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http://dx.doi.org/10.1101/gr.245522.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6673719PMC
August 2019

Publisher Correction: An evolutionary framework for measuring epigenomic information and estimating cell-type-specific fitness consequences.

Nat Genet 2019 03;51(3):577

Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.

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http://dx.doi.org/10.1038/s41588-019-0369-zDOI Listing
March 2019

An evolutionary framework for measuring epigenomic information and estimating cell-type-specific fitness consequences.

Nat Genet 2019 02 17;51(2):335-342. Epub 2018 Dec 17.

Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.

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http://dx.doi.org/10.1038/s41588-018-0300-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6544027PMC
February 2019

Dynamic evolution of regulatory element ensembles in primate CD4 T cells.

Nat Ecol Evol 2018 03 29;2(3):537-548. Epub 2018 Jan 29.

Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.

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http://dx.doi.org/10.1038/s41559-017-0447-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5957490PMC
March 2018

Scikit-ribo Enables Accurate Estimation and Robust Modeling of Translation Dynamics at Codon Resolution.

Cell Syst 2018 Feb 17;6(2):180-191.e4. Epub 2018 Jan 17.

Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD 21211, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2017.12.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5832574PMC
February 2018

Deep experimental profiling of microRNA diversity, deployment, and evolution across the genus.

Genome Res 2018 01 12;28(1):52-65. Epub 2017 Dec 12.

Tri-Institutional Training Program in Computational Biology and Medicine, New York, New York 10021, USA.

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http://dx.doi.org/10.1101/gr.226068.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5749182PMC
January 2018

Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol.

Genome Res 2017 11 12;27(11):1816-1829. Epub 2017 Oct 12.

Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.

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http://dx.doi.org/10.1101/gr.222935.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5668940PMC
November 2017

Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data.

Nat Genet 2017 Apr 13;49(4):618-624. Epub 2017 Mar 13.

Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.

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http://dx.doi.org/10.1038/ng.3810DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5395419PMC
April 2017

Is a super-enhancer greater than the sum of its parts?

Nat Genet 2016 12;49(1):2-3

Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.

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http://dx.doi.org/10.1038/ng.3759DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5379849PMC
December 2016

Distinguishing noise from signal in patterns of genomic divergence in a highly polymorphic avian radiation.

Mol Ecol 2015 Aug 3;24(16):4238-51. Epub 2015 Aug 3.

Fuller Evolutionary Biology Program, Cornell Laboratory of Ornithology, 159 Sapsucker Woods Road, Ithaca, NY, 14850, USA.

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http://dx.doi.org/10.1111/mec.13314DOI Listing
August 2015

GAGA factor maintains nucleosome-free regions and has a role in RNA polymerase II recruitment to promoters.

PLoS Genet 2015 Mar 27;11(3):e1005108. Epub 2015 Mar 27.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1005108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4376892PMC
March 2015

Identification of active transcriptional regulatory elements from GRO-seq data.

Nat Methods 2015 May 23;12(5):433-8. Epub 2015 Mar 23.

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA.

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http://dx.doi.org/10.1038/nmeth.3329DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4507281PMC
May 2015

A method for calculating probabilities of fitness consequences for point mutations across the human genome.

Nat Genet 2015 Mar 19;47(3):276-83. Epub 2015 Jan 19.

1] Graduate Field of Computer Science, Cornell University, Ithaca, New York, USA. [2] Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA.

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http://dx.doi.org/10.1038/ng.3196DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4342276PMC
March 2015

Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers.

Nat Genet 2014 Dec 10;46(12):1311-20. Epub 2014 Nov 10.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA.

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http://dx.doi.org/10.1038/ng.3142DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4254663PMC
December 2014

Diverse modes of evolutionary emergence and flux of conserved microRNA clusters.

RNA 2014 Dec 20;20(12):1850-63. Epub 2014 Oct 20.

Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA

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http://dx.doi.org/10.1261/rna.046805.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4238352PMC
December 2014

Enabling large-scale next-generation sequence assembly with Blacklight.

Concurr Comput 2014 Sep;26(13):2157-2166

Pittsburgh Supercomputing Center, Carnegie Mellon University, 300 S. Craig St. Pittsburgh, PA, 15213 USA.

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http://doi.wiley.com/10.1002/cpe.3231
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http://dx.doi.org/10.1002/cpe.3231DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4185199PMC
September 2014

Cis-regulatory elements and human evolution.

Curr Opin Genet Dev 2014 Dec 16;29:81-9. Epub 2014 Sep 16.

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

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http://dx.doi.org/10.1016/j.gde.2014.08.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4258466PMC
December 2014

Adaptive evolution of testis-specific, recently evolved, clustered miRNAs in Drosophila.

RNA 2014 Aug 18;20(8):1195-209. Epub 2014 Jun 18.

Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA.

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http://dx.doi.org/10.1261/rna.044644.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4105746PMC
August 2014

Contrasting X-linked and autosomal diversity across 14 human populations.

Am J Hum Genet 2014 Jun 15;94(6):827-44. Epub 2014 May 15.

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

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http://dx.doi.org/10.1016/j.ajhg.2014.04.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4121480PMC
June 2014

Genome-wide inference of ancestral recombination graphs.

PLoS Genet 2014 15;10(5):e1004342. Epub 2014 May 15.

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs, United Kingdom.

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http://dx.doi.org/10.1371/journal.pgen.1004342DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4022496PMC
December 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://dx.doi.org/10.1371/journal.pgen.1003684DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3744432PMC
March 2014

The impact of age, biogenesis, and genomic clustering on Drosophila microRNA evolution.

RNA 2013 Sep 23;19(9):1295-308. Epub 2013 Jul 23.

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

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http://dx.doi.org/10.1261/rna.039248.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753935PMC
September 2013

Genome-wide inference of natural selection on human transcription factor binding sites.

Nat Genet 2013 Jul 9;45(7):723-9. Epub 2013 Jun 9.

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

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http://dx.doi.org/10.1038/ng.2658DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3932982PMC
July 2013

Gene regulation by CcpA and catabolite repression explored by RNA-Seq in Streptococcus mutans.

PLoS One 2013 28;8(3):e60465. Epub 2013 Mar 28.

Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0060465PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3610829PMC
September 2013

Inference of natural selection from interspersed genomic elements based on polymorphism and divergence.

Mol Biol Evol 2013 May 5;30(5):1159-71. Epub 2013 Feb 5.

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

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http://dx.doi.org/10.1093/molbev/mst019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3697874PMC
May 2013

Replacing and additive horizontal gene transfer in Streptococcus.

Mol Biol Evol 2012 Nov 21;29(11):3309-20. Epub 2012 May 21.

Department of Biological Statistics and Computational Biology, Cornell University.

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http://dx.doi.org/10.1093/molbev/mss138DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3472495PMC
November 2012

Accurate prediction of inducible transcription factor binding intensities in vivo.

PLoS Genet 2012 29;8(3):e1002610. Epub 2012 Mar 29.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1002610DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3315474PMC
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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https://academic.oup.com/mbe/article-lookup/doi/10.1093/molb
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http://dx.doi.org/10.1093/molbev/msr279DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3278478PMC
March 2012

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

Bayesian inference of ancient human demography from individual genome sequences.

Nat Genet 2011 Sep 18;43(10):1031-4. Epub 2011 Sep 18.

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA.

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http://dx.doi.org/10.1038/ng.937DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245873PMC
September 2011

Three periods of regulatory innovation during vertebrate evolution.

Science 2011 Aug;333(6045):1019-24

Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1126/science.1202702DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3511857PMC
August 2011

Analyses of X-linked and autosomal genetic variation in population-scale whole genome sequencing.

Nat Genet 2011 Jul 24;43(8):741-3. Epub 2011 Jul 24.

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA.

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http://dx.doi.org/10.1038/ng.877DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3145052PMC
July 2011

A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells.

Cell 2011 May 5;145(4):622-34. Epub 2011 May 5.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.

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http://dx.doi.org/10.1016/j.cell.2011.03.042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3099127PMC
May 2011

Error and error mitigation in low-coverage genome assemblies.

PLoS One 2011 Feb 14;6(2):e17034. Epub 2011 Feb 14.

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0017034PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3038916PMC
February 2011

Comparative genomic analysis of the Streptococcus dysgalactiae species group: gene content, molecular adaptation, and promoter evolution.

Genome Biol Evol 2011 31;3:168-85. Epub 2011 Jan 31.

Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York.

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http://dx.doi.org/10.1093/gbe/evr006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3056289PMC
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

Comparative and demographic analysis of orang-utan genomes.

Authors:
Devin P Locke LaDeana W Hillier Wesley C Warren Kim C Worley Lynne V Nazareth Donna M Muzny Shiaw-Pyng Yang Zhengyuan Wang Asif T Chinwalla Pat Minx Makedonka Mitreva Lisa Cook Kim D Delehaunty Catrina Fronick Heather Schmidt Lucinda A Fulton Robert S Fulton Joanne O Nelson Vincent Magrini Craig Pohl Tina A Graves Chris Markovic Andy Cree Huyen H Dinh Jennifer Hume Christie L Kovar Gerald R Fowler Gerton Lunter Stephen Meader Andreas Heger Chris P Ponting Tomas Marques-Bonet Can Alkan Lin Chen Ze Cheng Jeffrey M Kidd Evan E Eichler Simon White Stephen Searle Albert J Vilella Yuan Chen Paul Flicek Jian Ma Brian Raney Bernard Suh Richard Burhans Javier Herrero David Haussler Rui Faria Olga Fernando Fleur Darré Domènec Farré Elodie Gazave Meritxell Oliva Arcadi Navarro Roberta Roberto Oronzo Capozzi Nicoletta Archidiacono Giuliano Della Valle Stefania Purgato Mariano Rocchi Miriam K Konkel Jerilyn A Walker Brygg Ullmer Mark A Batzer Arian F A Smit Robert Hubley Claudio Casola Daniel R Schrider Matthew W Hahn Victor Quesada Xose S Puente Gonzalo R Ordoñez Carlos López-Otín Tomas Vinar Brona Brejova Aakrosh Ratan Robert S Harris Webb Miller Carolin Kosiol Heather A Lawson Vikas Taliwal André L Martins Adam Siepel Arindam Roychoudhury Xin Ma Jeremiah Degenhardt Carlos D Bustamante Ryan N Gutenkunst Thomas Mailund Julien Y Dutheil Asger Hobolth Mikkel H Schierup Oliver A Ryder Yuko Yoshinaga Pieter J de Jong George M Weinstock Jeffrey Rogers Elaine R Mardis Richard A Gibbs Richard K Wilson

Nature 2011 Jan;469(7331):529-33

The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nature09687DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3060778PMC
January 2011

Reconstructing histories of complex gene clusters on a phylogeny.

J Comput Biol 2010 Sep;17(9):1267-79

Faculty of Mathematics, Physics and Informatics, Comenius University , Bratislava, Slovakia.

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http://dx.doi.org/10.1089/cmb.2010.0090DOI Listing
September 2010

Positive selection on apoptosis related genes.

FEBS Lett 2010 Feb 22;584(3):469-76. Epub 2009 Dec 22.

Department of Integrative Biology, UC-Berkeley, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1016/j.febslet.2009.12.022DOI Listing
February 2010

Detection of nonneutral substitution rates on mammalian phylogenies.

Genome Res 2010 Jan 26;20(1):110-21. Epub 2009 Oct 26.

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

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http://dx.doi.org/10.1101/gr.097857.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2798823PMC
January 2010

Phylogenomics of primates and their ancestral populations.

Authors:
Adam Siepel

Genome Res 2009 Nov 3;19(11):1929-41. Epub 2009 Oct 3.

Department of Biological Statistics and Computational Biology, Cornell Center for Comparative and Population Genomics, Cornell University, Ithaca, New York 14853, USA.

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http://dx.doi.org/10.1101/gr.084228.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2775601PMC
November 2009

Darwinian alchemy: Human genes from noncoding DNA.

Authors:
Adam Siepel

Genome Res 2009 Oct;19(10):1693-5

Department of Biological Statistics and Computational Biology, Cornell Center for Comparative and Population Genomics, Cornell University, Ithaca, New York 14853, USA.

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http://dx.doi.org/10.1101/gr.098376.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2765273PMC
October 2009

The completion of the Mammalian Gene Collection (MGC).

Authors:
Gary Temple Daniela S Gerhard Rebekah Rasooly Elise A Feingold Peter J Good Cristen Robinson Allison Mandich Jeffrey G Derge Jeanne Lewis Debonny Shoaf Francis S Collins Wonhee Jang Lukas Wagner Carolyn M Shenmen Leonie Misquitta Carl F Schaefer Kenneth H Buetow Tom I Bonner Linda Yankie Ming Ward Lon Phan Alex Astashyn Garth Brown Catherine Farrell Jennifer Hart Melissa Landrum Bonnie L Maidak Michael Murphy Terence Murphy Bhanu Rajput Lillian Riddick David Webb Janet Weber Wendy Wu Kim D Pruitt Donna Maglott Adam Siepel Brona Brejova Mark Diekhans Rachel Harte Robert Baertsch Jim Kent David Haussler Michael Brent Laura Langton Charles L G Comstock Michael Stevens Chaochun Wei Marijke J van Baren Kourosh Salehi-Ashtiani Ryan R Murray Lila Ghamsari Elizabeth Mello Chenwei Lin Christa Pennacchio Kirsten Schreiber Nicole Shapiro Amber Marsh Elizabeth Pardes Troy Moore Anita Lebeau Mike Muratet Blake Simmons David Kloske Stephanie Sieja James Hudson Praveen Sethupathy Michael Brownstein Narayan Bhat Joseph Lazar Howard Jacob Chris E Gruber Mark R Smith John McPherson Angela M Garcia Preethi H Gunaratne Jiaqian Wu Donna Muzny Richard A Gibbs Alice C Young Gerard G Bouffard Robert W Blakesley Jim Mullikin Eric D Green Mark C Dickson Alex C Rodriguez Jane Grimwood Jeremy Schmutz Richard M Myers Martin Hirst Thomas Zeng Kane Tse Michelle Moksa Merinda Deng Kevin Ma Diana Mah Johnson Pang Greg Taylor Eric Chuah Athena Deng Keith Fichter Anne Go Stephanie Lee Jing Wang Malachi Griffith Ryan Morin Richard A Moore Michael Mayo Sarah Munro Susan Wagner Steven J M Jones Robert A Holt Marco A Marra Sun Lu Shuwei Yang James Hartigan Marcus Graf Ralf Wagner Stanley Letovksy Jacqueline C Pulido Keith Robison Dominic Esposito James Hartley Vanessa E Wall Ralph F Hopkins Osamu Ohara Stefan Wiemann

Evolutionary history reconstruction for Mammalian complex gene clusters.

J Comput Biol 2009 Aug;16(8):1051-70

Center for Comparative Genomics and Bioinformatics, Penn State University , University Park, PA 16802, USA.

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http://dx.doi.org/10.1089/cmb.2009.0040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2879273PMC
August 2009

Sequencing and comparative analysis of a conserved syntenic segment in the Solanaceae.

Genetics 2008 Sep 24;180(1):391-408. Epub 2008 Aug 24.

Department of Plant Breeding and Genetics, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, People's Republic of China.

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http://dx.doi.org/10.1534/genetics.108.087981DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2535690PMC
September 2008

Patterns of positive selection in six Mammalian genomes.

PLoS Genet 2008 Aug 1;4(8):e1000144. Epub 2008 Aug 1.

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1000144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2483296PMC
August 2008

Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster.

Genome Res 2008 Oct 26;18(10):1592-601. Epub 2008 Jun 26.

Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, California 95691, USA.

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http://dx.doi.org/10.1101/gr.077131.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2556263PMC
October 2008

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:
Ewan Birney John A Stamatoyannopoulos Anindya Dutta Roderic Guigó Thomas R Gingeras Elliott H Margulies Zhiping Weng Michael Snyder Emmanouil T Dermitzakis Robert E Thurman Michael S Kuehn Christopher M Taylor Shane Neph Christoph M Koch Saurabh Asthana Ankit Malhotra Ivan Adzhubei Jason A Greenbaum Robert M Andrews Paul Flicek Patrick J Boyle Hua Cao Nigel P Carter Gayle K Clelland Sean Davis Nathan Day Pawandeep Dhami Shane C Dillon Michael O Dorschner Heike Fiegler Paul G Giresi Jeff Goldy Michael Hawrylycz Andrew Haydock Richard Humbert Keith D James Brett E Johnson Ericka M Johnson Tristan T Frum Elizabeth R Rosenzweig Neerja Karnani Kirsten Lee Gregory C Lefebvre Patrick A Navas Fidencio Neri Stephen C J Parker Peter J Sabo Richard Sandstrom Anthony Shafer David Vetrie Molly Weaver Sarah Wilcox Man Yu Francis S Collins Job Dekker Jason D Lieb Thomas D Tullius Gregory E Crawford Shamil Sunyaev William S Noble Ian Dunham France Denoeud Alexandre Reymond Philipp Kapranov Joel Rozowsky Deyou Zheng Robert Castelo Adam Frankish Jennifer Harrow Srinka Ghosh Albin Sandelin Ivo L Hofacker Robert Baertsch Damian Keefe Sujit Dike Jill Cheng Heather A Hirsch Edward A Sekinger Julien Lagarde Josep F Abril Atif Shahab Christoph Flamm Claudia Fried Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Missal Andrea Tanzer Stefan Washietl Jan Korbel Olof Emanuelsson Jakob S Pedersen Nancy Holroyd Ruth Taylor David Swarbreck Nicholas Matthews Mark C Dickson Daryl J Thomas Matthew T Weirauch James Gilbert Jorg Drenkow Ian Bell XiaoDong Zhao K G Srinivasan Wing-Kin Sung Hong Sain Ooi Kuo Ping Chiu Sylvain Foissac Tyler Alioto Michael Brent Lior Pachter Michael L Tress Alfonso Valencia Siew Woh Choo Chiou Yu Choo Catherine Ucla Caroline Manzano Carine Wyss Evelyn Cheung Taane G Clark James B Brown Madhavan Ganesh Sandeep Patel Hari Tammana Jacqueline Chrast Charlotte N Henrichsen Chikatoshi Kai Jun Kawai Ugrappa Nagalakshmi Jiaqian Wu Zheng Lian Jin Lian Peter Newburger Xueqing Zhang Peter Bickel John S Mattick Piero Carninci Yoshihide Hayashizaki Sherman Weissman Tim Hubbard Richard M Myers Jane Rogers Peter F Stadler Todd M Lowe Chia-Lin Wei Yijun Ruan Kevin Struhl Mark Gerstein Stylianos E Antonarakis Yutao Fu Eric D Green Ulaş Karaöz Adam Siepel James Taylor Laura A Liefer Kris A Wetterstrand Peter J Good Elise A Feingold Mark S Guyer Gregory M Cooper George Asimenos Colin N Dewey Minmei Hou Sergey Nikolaev Juan I Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham Haiyan Huang Nancy R Zhang Ian Holmes James C Mullikin Abel Ureta-Vidal Benedict Paten Michael Seringhaus Deanna Church Kate Rosenbloom W James Kent Eric A Stone Serafim Batzoglou Nick Goldman Ross C Hardison David Haussler Webb Miller Arend Sidow Nathan D Trinklein Zhengdong D Zhang Leah Barrera Rhona Stuart David C King Adam Ameur Stefan Enroth Mark C Bieda Jonghwan Kim Akshay A Bhinge Nan Jiang Jun Liu Fei Yao Vinsensius B Vega Charlie W H Lee Patrick Ng Atif Shahab Annie Yang Zarmik Moqtaderi Zhou Zhu Xiaoqin Xu Sharon Squazzo Matthew J Oberley David Inman Michael A Singer Todd A Richmond Kyle J Munn Alvaro Rada-Iglesias Ola Wallerman Jan Komorowski Joanna C Fowler Phillippe Couttet Alexander W Bruce Oliver M Dovey Peter D Ellis Cordelia F Langford David A Nix Ghia Euskirchen Stephen Hartman Alexander E Urban Peter Kraus Sara Van Calcar Nate Heintzman Tae Hoon Kim Kun Wang Chunxu Qu Gary Hon Rosa Luna Christopher K Glass M Geoff Rosenfeld Shelley Force Aldred Sara J Cooper Anason Halees Jane M Lin Hennady P Shulha Xiaoling Zhang Mousheng Xu Jaafar N S Haidar Yong Yu Yijun Ruan Vishwanath R Iyer Roland D Green Claes Wadelius Peggy J Farnham Bing Ren Rachel A Harte Angie S Hinrichs Heather Trumbower Hiram Clawson Jennifer Hillman-Jackson Ann S Zweig Kayla Smith Archana Thakkapallayil Galt Barber Robert M Kuhn Donna Karolchik Lluis Armengol Christine P Bird Paul I W de Bakker Andrew D Kern Nuria Lopez-Bigas Joel D Martin Barbara E Stranger Abigail Woodroffe Eugene Davydov Antigone Dimas Eduardo Eyras Ingileif B Hallgrímsdóttir Julian Huppert Michael C Zody Gonçalo R Abecasis Xavier Estivill Gerard G Bouffard Xiaobin Guan Nancy F Hansen Jacquelyn R Idol Valerie V B Maduro Baishali Maskeri Jennifer C McDowell Morgan Park Pamela J Thomas Alice C Young Robert W Blakesley Donna M Muzny Erica Sodergren David A Wheeler Kim C Worley Huaiyang Jiang George M Weinstock Richard A Gibbs Tina Graves Robert Fulton Elaine R Mardis Richard K Wilson Michele Clamp James Cuff Sante Gnerre David B Jaffe Jean L Chang Kerstin Lindblad-Toh Eric S Lander Maxim Koriabine Mikhail Nefedov Kazutoyo Osoegawa Yuko Yoshinaga Baoli Zhu Pieter J de Jong
June 2007

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.

Genome Res 2007 Jun;17(6):760-74

Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.6034307
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891336PMC
June 2007

Genomic analyses of transcription factor binding, histone acetylation, and gene expression reveal mechanistically distinct classes of estrogen-regulated promoters.

Mol Cell Biol 2007 Jul 21;27(14):5090-104. Epub 2007 May 21.

Department of Molecular Biology and Genetics, Cornell University, 465 Biotechnology Building, Ithaca, NY 14853, USA.

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http://dx.doi.org/10.1128/MCB.00083-07DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1951957PMC
July 2007

Evolutionary and biomedical insights from the rhesus macaque genome.

Authors:
Richard A Gibbs Jeffrey Rogers Michael G Katze Roger Bumgarner George M Weinstock Elaine R Mardis Karin A Remington Robert L Strausberg J Craig Venter Richard K Wilson Mark A Batzer Carlos D Bustamante Evan E Eichler Matthew W Hahn Ross C Hardison Kateryna D Makova Webb Miller Aleksandar Milosavljevic Robert E Palermo Adam Siepel James M Sikela Tony Attaway Stephanie Bell Kelly E Bernard Christian J Buhay Mimi N Chandrabose Marvin Dao Clay Davis Kimberly D Delehaunty Yan Ding Huyen H Dinh Shannon Dugan-Rocha Lucinda A Fulton Ramatu Ayiesha Gabisi Toni T Garner Jennifer Godfrey Alicia C Hawes Judith Hernandez Sandra Hines Michael Holder Jennifer Hume Shalini N Jhangiani Vandita Joshi Ziad Mohid Khan Ewen F Kirkness Andrew Cree R Gerald Fowler Sandra Lee Lora R Lewis Zhangwan Li Yih-Shin Liu Stephanie M Moore Donna Muzny Lynne V Nazareth Dinh Ngoc Ngo Geoffrey O Okwuonu Grace Pai David Parker Heidie A Paul Cynthia Pfannkoch Craig S Pohl Yu-Hui Rogers San Juana Ruiz Aniko Sabo Jireh Santibanez Brian W Schneider Scott M Smith Erica Sodergren Amanda F Svatek Teresa R Utterback Selina Vattathil Wesley Warren Courtney Sherell White Asif T Chinwalla Yucheng Feng Aaron L Halpern Ladeana W Hillier Xiaoqiu Huang Pat Minx Joanne O Nelson Kymberlie H Pepin Xiang Qin Granger G Sutton Eli Venter Brian P Walenz John W Wallis Kim C Worley Shiaw-Pyng Yang Steven M Jones Marco A Marra Mariano Rocchi Jacqueline E Schein Robert Baertsch Laura Clarke Miklós Csürös Jarret Glasscock R Alan Harris Paul Havlak Andrew R Jackson Huaiyang Jiang Yue Liu David N Messina Yufeng Shen Henry Xing-Zhi Song Todd Wylie Lan Zhang Ewan Birney Kyudong Han Miriam K Konkel Jungnam Lee Arian F A Smit Brygg Ullmer Hui Wang Jinchuan Xing Richard Burhans Ze Cheng John E Karro Jian Ma Brian Raney Xinwei She Michael J Cox Jeffery P Demuth Laura J Dumas Sang-Gook Han Janet Hopkins Anis Karimpour-Fard Young H Kim Jonathan R Pollack Tomas Vinar Charles Addo-Quaye Jeremiah Degenhardt Alexandra Denby Melissa J Hubisz Amit Indap Carolin Kosiol Bruce T Lahn Heather A Lawson Alison Marklein Rasmus Nielsen Eric J Vallender Andrew G Clark Betsy Ferguson Ryan D Hernandez Kashif Hirani Hildegard Kehrer-Sawatzki Jessica Kolb Shobha Patil Ling-Ling Pu Yanru Ren David Glenn Smith David A Wheeler Ian Schenck Edward V Ball Rui Chen David N Cooper Belinda Giardine Fan Hsu W James Kent Arthur Lesk David L Nelson William E O'brien Kay Prüfer Peter D Stenson James C Wallace Hui Ke Xiao-Ming Liu Peng Wang Andy Peng Xiang Fan Yang Galt P Barber David Haussler Donna Karolchik Andy D Kern Robert M Kuhn Kayla E Smith Ann S Zwieg

Science 2007 Apr;316(5822):222-34

Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.

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April 2007

Forces shaping the fastest evolving regions in the human genome.

PLoS Genet 2006 Oct 23;2(10):e168. Epub 2006 Aug 23.

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

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http://dx.doi.org/10.1371/journal.pgen.0020168DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1599772PMC
October 2006

An RNA gene expressed during cortical development evolved rapidly in humans.

Nature 2006 Sep 16;443(7108):167-72. Epub 2006 Aug 16.

Center for Biomolecular Science & Engineering, Department of Molecular, Cell & Developmental Biology, University of California, Santa Cruz, California 95064, USA.

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http://dx.doi.org/10.1038/nature05113DOI Listing
September 2006

Identification and classification of conserved RNA secondary structures in the human genome.

PLoS Comput Biol 2006 Apr 21;2(4):e33. Epub 2006 Apr 21.

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

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http://dx.doi.org/10.1371/journal.pcbi.0020033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1440920PMC
April 2006

A distal enhancer and an ultraconserved exon are derived from a novel retroposon.

Nature 2006 May 16;441(7089):87-90. Epub 2006 Apr 16.

Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA.

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http://dx.doi.org/10.1038/nature04696DOI Listing
May 2006

Computational screening of conserved genomic DNA in search of functional noncoding elements.

Nat Methods 2005 Jul;2(7):535-45

Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA.

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http://dx.doi.org/10.1038/nmeth0705-535DOI Listing
July 2005

Combining phylogenetic and hidden Markov models in biosequence analysis.

J Comput Biol 2004 ;11(2-3):413-28

Center for Biomolecular Science and Engineering, University of California, 1156 High Street, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1089/1066527041410472DOI Listing
August 2004

Efficient approximations for learning phylogenetic HMM models from data.

Bioinformatics 2004 Aug;20 Suppl 1:i161-8

Microsoft Research, Redmond, WA 98052, USA.

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http://dx.doi.org/10.1093/bioinformatics/bth917DOI Listing
August 2004

Phylogenetic estimation of context-dependent substitution rates by maximum likelihood.

Mol Biol Evol 2004 Mar 5;21(3):468-88. Epub 2003 Dec 5.

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

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http://dx.doi.org/10.1093/molbev/msh039DOI Listing
March 2004

An algorithm to enumerate sorting reversals for signed permutations.

Authors:
Adam C Siepel

J Comput Biol 2003 ;10(3-4):575-97

Department of Computer Science, University of New Mexico, Albuquerque, NM 87131, USA.

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March 2004