Publications by authors named "Arend Sidow"

66Publications

Assessment of human diploid genome assembly with 10x Linked-Reads data.

Gigascience 2019 11;8(11)

Department of Pathology, 300 Pasteur Dr, Stanford University, Stanford, CA 94305 USA.

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http://dx.doi.org/10.1093/gigascience/giz141DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6879002PMC
November 2019

Comprehensive genomic characterization of breast tumors with BRCA1 and BRCA2 mutations.

BMC Med Genomics 2019 06 10;12(1):84. Epub 2019 Jun 10.

Department of Pathology, Stanford University, Stanford, CA, 94305, USA.

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http://dx.doi.org/10.1186/s12920-019-0545-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6558765PMC
June 2019

Multi-omic tumor data reveal diversity of molecular mechanisms that correlate with survival.

Nat Commun 2018 10 26;9(1):4453. Epub 2018 Oct 26.

Department of Pathology, Stanford University, Stanford, CA, 94305, USA.

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http://www.nature.com/articles/s41467-018-06921-8
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http://dx.doi.org/10.1038/s41467-018-06921-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6203719PMC
October 2018

High-quality genome sequences of uncultured microbes by assembly of read clouds.

Nat Biotechnol 2018 Oct 15. Epub 2018 Oct 15.

Department of Medicine (Hematology, Blood and Marrow Transplantation) and Department of Genetics, Stanford University, Stanford, California, USA.

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http://www.nature.com/doifinder/10.1038/nbt.4266
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http://dx.doi.org/10.1038/nbt.4266DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6465186PMC
October 2018

HAPDeNovo: a haplotype-based approach for filtering and phasing de novo mutations in linked read sequencing data.

BMC Genomics 2018 Jun 18;19(1):467. Epub 2018 Jun 18.

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

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https://bmcgenomics.biomedcentral.com/articles/10.1186/s1286
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http://dx.doi.org/10.1186/s12864-018-4867-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6006847PMC
June 2018

Genome-wide reconstruction of complex structural variants using read clouds.

Nat Methods 2017 Sep 17;14(9):915-920. Epub 2017 Jul 17.

Joint Initiative for Metrology in Biology, Stanford, California, USA.

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http://dx.doi.org/10.1038/nmeth.4366DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5578891PMC
September 2017

Lineage-specific enhancers activate self-renewal genes in macrophages and embryonic stem cells.

Science 2016 Feb 21;351(6274):aad5510. Epub 2016 Jan 21.

Centre d'Immunologie de Marseille-Luminy, Université Aix-Marseille, UM2, Campus de Luminy, Case 906, 13288 Marseille Cedex 09, France. INSERM, U1104, Marseille, France. CNRS, UMR 7280, Marseille, France. Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtz-Gemeinschaft, 10 Robert-Rössle-Strasse, 13125 Berlin, Germany.

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http://dx.doi.org/10.1126/science.aad5510DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4811353PMC
February 2016

svviz: a read viewer for validating structural variants.

Bioinformatics 2015 Dec 18;31(24):3994-6. Epub 2015 Aug 18.

Department of Genetics, Stanford University, Department of Pathology, Stanford University.

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http://dx.doi.org/10.1093/bioinformatics/btv478DOI Listing
December 2015

Read clouds uncover variation in complex regions of the human genome.

Genome Res 2015 Oct 18;25(10):1570-80. Epub 2015 Aug 18.

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

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http://dx.doi.org/10.1101/gr.191189.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4579342PMC
October 2015

Constraint and divergence of global gene expression in the mammalian embryo.

Elife 2015 Apr 14;4:e05538. Epub 2015 Apr 14.

Department of Pathology, Stanford University School of Medicine, Stanford, United States.

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http://dx.doi.org/10.7554/eLife.05538DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4417935PMC
April 2015

Concepts in solid tumor evolution.

Trends Genet 2015 Apr 27;31(4):208-14. Epub 2015 Feb 27.

Departments of Pathology and of Genetics, Stanford University, Stanford, CA 94305, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S01689525150001
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http://dx.doi.org/10.1016/j.tig.2015.02.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4380537PMC
April 2015

Maternal bias and escape from X chromosome imprinting in the midgestation mouse placenta.

Dev Biol 2014 Jun 2;390(1):80-92. Epub 2014 Mar 2.

Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, United States. Electronic address:

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http://dx.doi.org/10.1016/j.ydbio.2014.02.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4045483PMC
June 2014

Discovery of recurrent structural variants in nasopharyngeal carcinoma.

Genome Res 2014 Feb 8;24(2):300-9. Epub 2013 Nov 8.

Division of Bioinformatics, Department of Preventive Medicine, University of Southern California Keck School of Medicine, Los Angeles, California 90087, USA;

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http://dx.doi.org/10.1101/gr.156224.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3912420PMC
February 2014

Transcription-factor occupancy at HOT regions quantitatively predicts RNA polymerase recruitment in five human cell lines.

BMC Genomics 2013 Oct 20;14:720. Epub 2013 Oct 20.

Department of Genetics, Stanford University, 300 Pasteur Drive, Stanford, California 94305, USA.

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http://dx.doi.org/10.1186/1471-2164-14-720DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3826616PMC
October 2013

Global genomic profiling reveals an extensive p53-regulated autophagy program contributing to key p53 responses.

Genes Dev 2013 May;27(9):1016-31

Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California 94305, USA.

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http://dx.doi.org/10.1101/gad.212282.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3656320PMC
May 2013

A cell cycle phosphoproteome of the yeast centrosome.

Science 2011 Jun;332(6037):1557-61

Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA.

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http://dx.doi.org/10.1126/science.1205193DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3825980PMC
June 2011

Determinants of nucleosome organization in primary human cells.

Nature 2011 May 22;474(7352):516-20. Epub 2011 May 22.

Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, USA.

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http://dx.doi.org/10.1038/nature10002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3212987PMC
May 2011

Identifying a high fraction of the human genome to be under selective constraint using GERP++.

PLoS Comput Biol 2010 Dec 2;6(12):e1001025. Epub 2010 Dec 2.

Department of Computer Science, Stanford University, Stanford, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1001025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2996323PMC
December 2010

An in vitro-identified high-affinity nucleosome-positioning signal is capable of transiently positioning a nucleosome in vivo.

Epigenetics Chromatin 2010 Jul 1;3(1):13. Epub 2010 Jul 1.

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

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http://dx.doi.org/10.1186/1756-8935-3-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2915997PMC
July 2010

Functional analyses of variants reveal a significant role for dominant negative and common alleles in oligogenic Bardet-Biedl syndrome.

Proc Natl Acad Sci U S A 2010 Jun 24;107(23):10602-7. Epub 2010 May 24.

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

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http://dx.doi.org/10.1073/pnas.1000219107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2890780PMC
June 2010

Jarid2/Jumonji coordinates control of PRC2 enzymatic activity and target gene occupancy in pluripotent cells.

Cell 2009 Dec;139(7):1290-302

Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1016/j.cell.2009.12.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2911953PMC
December 2009

ProPhylER: a curated online resource for protein function and structure based on evolutionary constraint analyses.

Genome Res 2010 Jan 21;20(1):142-54. Epub 2009 Oct 21.

Stanford University School of Medicine, Departments of Pathology and Genetics, Stanford, California 94305, USA.

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http://genome.cshlp.org/cgi/doi/10.1101/gr.097121.109
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http://dx.doi.org/10.1101/gr.097121.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2798826PMC
January 2010

SHRiMP: accurate mapping of short color-space reads.

PLoS Comput Biol 2009 May 22;5(5):e1000386. Epub 2009 May 22.

Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1371/journal.pcbi.1000386DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2678294PMC
May 2009

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data.

Nat Methods 2008 Sep;5(9):829-34

Department of Pathology, Stanford University Medical Center, 300 Pasteur Drive, Stanford, California 94305, USA.

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http://dx.doi.org/10.1038/nmeth.1246DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2917543PMC
September 2008

Identification of the Otopetrin Domain, a conserved domain in vertebrate otopetrins and invertebrate otopetrin-like family members.

BMC Evol Biol 2008 Feb 6;8:41. Epub 2008 Feb 6.

Department of Developmental Biology, Washington University School of Medicine, St, Louis, MO 63110, USA.

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http://dx.doi.org/10.1186/1471-2148-8-41DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2268672PMC
February 2008

Fruit fly family fun.

Cell 2007 Dec;131(7):1222-3

Department of Pathology and Department of Genetics, SUMC L235, Stanford CA 94305-5324, USA.

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http://dx.doi.org/10.1016/j.cell.2007.12.003DOI Listing
December 2007

Functional architecture and evolution of transcriptional elements that drive gene coexpression.

Science 2007 Sep;317(5844):1557-60

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

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http://dx.doi.org/10.1126/science.1145893DOI Listing
September 2007

Mammalian comparative sequence analysis of the Agrp locus.

PLoS One 2007 Aug 8;2(8):e702. Epub 2007 Aug 8.

Department of Genetics, Stanford University, Stanford, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0000702PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1931611PMC
August 2007

Constructing a meaningful evolutionary average at the phylogenetic center of mass.

BMC Bioinformatics 2007 Jun 26;8:222. Epub 2007 Jun 26.

Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695-7566, USA.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-8-222DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1919398PMC
June 2007

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://mendel.stanford.edu/sidowlab/pdfs/2007EncodeGR.pdf
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http://www.genome.org/cgi/doi/10.1101/gr.6034307
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http://dx.doi.org/10.1101/gr.6034307DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891336PMC
June 2007

A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome.

Genome Biol 2007 ;8(3):R41

Department of Pathology, Stanford University Medical Center, Stanford, California 94305-5324, USA.

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http://dx.doi.org/10.1186/gb-2007-8-3-r41DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1868934PMC
June 2007

Extreme genomic variation in a natural population.

Proc Natl Acad Sci U S A 2007 Mar 19;104(13):5698-703. Epub 2007 Mar 19.

Departments of Genetics and Pathology, Stanford University Medical Center, Stanford, CA 94305-5324, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0700890104
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http://dx.doi.org/10.1073/pnas.0700890104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1838466PMC
March 2007

Structural and molecular evolutionary analysis of Agouti and Agouti-related proteins.

Chem Biol 2006 Dec;13(12):1297-305

Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA.

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http://dx.doi.org/10.1016/j.chembiol.2006.10.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2907901PMC
December 2006

De novo discovery of a tissue-specific gene regulatory module in a chordate.

Genome Res 2005 Oct 16;15(10):1315-24. Epub 2005 Sep 16.

Department of Pathology, Stanford University Medical Center, Stanford, California 94305-5324, USA.

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http://dx.doi.org/10.1101/gr.4062605DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240073PMC
October 2005

Trade-offs in detecting evolutionarily constrained sequence by comparative genomics.

Annu Rev Genomics Hum Genet 2005 ;6:143-64

Department of Statistics, Stanford University, Stanford, California 94305, USA.

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http://www.annualreviews.org/doi/10.1146/annurev.genom.6.080
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http://dx.doi.org/10.1146/annurev.genom.6.080604.162146DOI Listing
December 2005

Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity.

Genome Res 2005 Jul 17;15(7):978-86. Epub 2005 Jun 17.

Department of Statistics, Stanford University, Stanford, California 94305-5324, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.3804205
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http://dx.doi.org/10.1101/gr.3804205DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1172042PMC
July 2005

Distribution and intensity of constraint in mammalian genomic sequence.

Genome Res 2005 Jul 17;15(7):901-13. Epub 2005 Jun 17.

Department of Genetics, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1101/gr.3577405DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1172034PMC
July 2005

Phenotype-genotype correlation in Hirschsprung disease is illuminated by comparative analysis of the RET protein sequence.

Proc Natl Acad Sci U S A 2005 Jun 13;102(25):8949-54. Epub 2005 Jun 13.

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

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http://dx.doi.org/10.1073/pnas.0503259102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1157046PMC
June 2005

ABC: software for interactive browsing of genomic multiple sequence alignment data.

BMC Bioinformatics 2004 Dec 8;5:192. Epub 2004 Dec 8.

Department of Genetics, Stanford University, Stanford, CA 94305-9010, USA.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-5-192DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC539296PMC
December 2004

Characterization of evolutionary rates and constraints in three Mammalian genomes.

Genome Res 2004 Apr;14(4):539-48

Department of Genetics, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1101/gr.2034704DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC383297PMC
April 2004

Genome sequence of the Brown Norway rat yields insights into mammalian evolution.

Authors:
Richard A Gibbs George M Weinstock Michael L Metzker Donna M Muzny Erica J Sodergren Steven Scherer Graham Scott David Steffen Kim C Worley Paula E Burch Geoffrey Okwuonu Sandra Hines Lora Lewis Christine DeRamo Oliver Delgado Shannon Dugan-Rocha George Miner Margaret Morgan Alicia Hawes Rachel Gill Celera Robert A Holt Mark D Adams Peter G Amanatides Holly Baden-Tillson Mary Barnstead Soo Chin Cheryl A Evans Steve Ferriera Carl Fosler Anna Glodek Zhiping Gu Don Jennings Cheryl L Kraft Trixie Nguyen Cynthia M Pfannkoch Cynthia Sitter Granger G Sutton J Craig Venter Trevor Woodage Douglas Smith Hong-Mei Lee Erik Gustafson Patrick Cahill Arnold Kana Lynn Doucette-Stamm Keith Weinstock Kim Fechtel Robert B Weiss Diane M Dunn Eric D Green Robert W Blakesley Gerard G Bouffard Pieter J De Jong Kazutoyo Osoegawa Baoli Zhu Marco Marra Jacqueline Schein Ian Bosdet Chris Fjell Steven Jones Martin Krzywinski Carrie Mathewson Asim Siddiqui Natasja Wye John McPherson Shaying Zhao Claire M Fraser Jyoti Shetty Sofiya Shatsman Keita Geer Yixin Chen Sofyia Abramzon William C Nierman Paul H Havlak Rui Chen K James Durbin Amy Egan Yanru Ren Xing-Zhi Song Bingshan Li Yue Liu Xiang Qin Simon Cawley Kim C Worley A J Cooney Lisa M D'Souza Kirt Martin Jia Qian Wu Manuel L Gonzalez-Garay Andrew R Jackson Kenneth J Kalafus Michael P McLeod Aleksandar Milosavljevic Davinder Virk Andrei Volkov David A Wheeler Zhengdong Zhang Jeffrey A Bailey Evan E Eichler Eray Tuzun Ewan Birney Emmanuel Mongin Abel Ureta-Vidal Cara Woodwark Evgeny Zdobnov Peer Bork Mikita Suyama David Torrents Marina Alexandersson Barbara J Trask Janet M Young Hui Huang Huajun Wang Heming Xing Sue Daniels Darryl Gietzen Jeanette Schmidt Kristian Stevens Ursula Vitt Jim Wingrove Francisco Camara M Mar Albà Josep F Abril Roderic Guigo Arian Smit Inna Dubchak Edward M Rubin Olivier Couronne Alexander Poliakov Norbert Hübner Detlev Ganten Claudia Goesele Oliver Hummel Thomas Kreitler Young-Ae Lee Jan Monti Herbert Schulz Heike Zimdahl Heinz Himmelbauer Hans Lehrach Howard J Jacob Susan Bromberg Jo Gullings-Handley Michael I Jensen-Seaman Anne E Kwitek Jozef Lazar Dean Pasko Peter J Tonellato Simon Twigger Chris P Ponting Jose M Duarte Stephen Rice Leo Goodstadt Scott A Beatson Richard D Emes Eitan E Winter Caleb Webber Petra Brandt Gerald Nyakatura Margaret Adetobi Francesca Chiaromonte Laura Elnitski Pallavi Eswara Ross C Hardison Minmei Hou Diana Kolbe Kateryna Makova Webb Miller Anton Nekrutenko Cathy Riemer Scott Schwartz James Taylor Shan Yang Yi Zhang Klaus Lindpaintner T Dan Andrews Mario Caccamo Michele Clamp Laura Clarke Valerie Curwen Richard Durbin Eduardo Eyras Stephen M Searle Gregory M Cooper Serafim Batzoglou Michael Brudno Arend Sidow Eric A Stone J Craig Venter Bret A Payseur Guillaume Bourque Carlos López-Otín Xose S Puente Kushal Chakrabarti Sourav Chatterji Colin Dewey Lior Pachter Nicolas Bray Von Bing Yap Anat Caspi Glenn Tesler Pavel A Pevzner David Haussler Krishna M Roskin Robert Baertsch Hiram Clawson Terrence S Furey Angie S Hinrichs Donna Karolchik William J Kent Kate R Rosenbloom Heather Trumbower Matt Weirauch David N Cooper Peter D Stenson Bin Ma Michael Brent Manimozhiyan Arumugam David Shteynberg Richard R Copley Martin S Taylor Harold Riethman Uma Mudunuri Jane Peterson Mark Guyer Adam Felsenfeld Susan Old Stephen Mockrin Francis Collins

Nature 2004 Apr;428(6982):493-521

Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA. http://www.hgsc.bcm.tmc.edu

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http://dx.doi.org/10.1038/nature02426DOI Listing
April 2004

Genomic regulatory regions: insights from comparative sequence analysis.

Curr Opin Genet Dev 2003 Dec;13(6):604-10

Department of Genetics, Stanford University, Stanford, CA 94305-9010, USA.

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http://dx.doi.org/10.1016/j.gde.2003.10.001DOI Listing
December 2003

Functional evolution in the ancestral lineage of vertebrates or when genomic complexity was wagging its morphological tail.

J Struct Funct Genomics 2003 ;3(1-4):45-52

Department of Pathology, Stanford University Medical Center, Room 248B, 300 Pasteur Drive, Stanford, CA 94305-5324, USA.

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July 2003

Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes.

Genome Res 2003 May;13(5):813-20

Department of Genetics, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1101/gr.1064503DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC430923PMC
May 2003

LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA.

Genome Res 2003 Apr 12;13(4):721-31. Epub 2003 Mar 12.

Department of Computer Science, Stanford University, Stanford, California 94305-9010, USA.

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http://dx.doi.org/10.1101/gr.926603DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC430158PMC
April 2003

The integrity of a cholesterol-binding pocket in Niemann-Pick C2 protein is necessary to control lysosome cholesterol levels.

Proc Natl Acad Sci U S A 2003 Mar 18;100(5):2518-25. Epub 2003 Feb 18.

Department of Developmental Biology, Beckman Center B300, 279 Campus Drive, Stanford University School of Medicine, Stanford, CA 94305-5329, USA.

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http://dx.doi.org/10.1073/pnas.0530027100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC151373PMC
March 2003

Sequence first. Ask questions later.

Authors:
Arend Sidow

Cell 2002 Oct;111(1):13-6

Department of Pathology, SUMC R248B, 300 Pasteur Drive, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1016/s0092-8674(02)01003-6DOI Listing
October 2002

Inference of functional regions in proteins by quantification of evolutionary constraints.

Proc Natl Acad Sci U S A 2002 Mar;99(5):2912-7

Program in Cancer Biology and Department of Pathology, Stanford University Medical School, Stanford, CA 94305-5324, USA.

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http://dx.doi.org/10.1073/pnas.042692299DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC122447PMC
March 2002