Serafim Batzoglou

Serafim Batzoglou

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Serafim Batzoglou

Publications by authors named "Serafim Batzoglou"

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88Publications

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Meltos: Multi-Sample Tumor Phylogeny Reconstruction for Structural Variants.

Bioinformatics 2019 Oct 4. Epub 2019 Oct 4.

Institute for Computational Biomedicine, Englander Institute for Precision Medicine, The Meyer Cancer Center, Department of Physiology and Biophysics, Weill Cornell Medicine of Cornell University, NY, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz737DOI Listing
October 2019

A machine-compiled database of genome-wide association studies.

Nat Commun 2019 Jul 26;10(1):3341. Epub 2019 Jul 26.

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

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http://dx.doi.org/10.1038/s41467-019-11026-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6659642PMC
July 2019

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

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

Network enhancement as a general method to denoise weighted biological networks.

Nat Commun 2018 08 6;9(1):3108. Epub 2018 Aug 6.

Department of Computer Science, Stanford University, 353 Serra Mall, Stanford, 94305, CA, USA.

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http://dx.doi.org/10.1038/s41467-018-05469-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6078978PMC
August 2018

Fast Metagenomic Binning via Hashing and Bayesian Clustering.

J Comput Biol 2018 07 16;25(7):677-688. Epub 2018 Apr 16.

1 Department of Computer Science, Stanford University , Stanford, California.

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http://dx.doi.org/10.1089/cmb.2017.0250DOI Listing
July 2018

Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer.

Cell 2018 07 19;174(3):758-769.e9. Epub 2018 Jul 19.

Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, CA, USA; Division of Hematology and Oncology, Department of Medicine, UCSF, San Francisco, CA, USA; Department of Radiation Oncology, UCSF, San Francisco, CA, USA; Department of Urology, UCSF, San Francisco, CA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2018.06.039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6425931PMC
July 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

SIMLR: A Tool for Large-Scale Genomic Analyses by Multi-Kernel Learning.

Proteomics 2018 01;18(2)

Department of Computer Science, Stanford University, Stanford, CA, USA.

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http://dx.doi.org/10.1002/pmic.201700232DOI Listing
January 2018

Vicus: Exploiting local structures to improve network-based analysis of biological data.

PLoS Comput Biol 2017 Oct 12;13(10):e1005621. Epub 2017 Oct 12.

SickKids Research Institute, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1371/journal.pcbi.1005621DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5638230PMC
October 2017

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

A hybrid cloud read aligner based on MinHash and kmer voting that preserves privacy.

Nat Commun 2017 05 16;8:15311. Epub 2017 May 16.

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

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http://dx.doi.org/10.1038/ncomms15311DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5440850PMC
May 2017

Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning.

Nat Methods 2017 Apr 6;14(4):414-416. Epub 2017 Mar 6.

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

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http://dx.doi.org/10.1038/nmeth.4207DOI Listing
April 2017

Reveel: large-scale population genotyping using low-coverage sequencing data.

Bioinformatics 2016 06 9;32(11):1686-96. Epub 2015 Sep 9.

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

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http://dx.doi.org/10.1093/bioinformatics/btv530DOI Listing
June 2016

Genome assembly from synthetic long read clouds.

Bioinformatics 2016 06;32(12):i216-i224

Department of Computer Science, Stanford University.

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http://dx.doi.org/10.1093/bioinformatics/btw267DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4908351PMC
June 2016

Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome.

Nat Biotechnol 2016 Jan 14;34(1):64-9. Epub 2015 Dec 14.

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

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http://dx.doi.org/10.1038/nbt.3416DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4884093PMC
January 2016

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

Fast and scalable inference of multi-sample cancer lineages.

Genome Biol 2015 May 6;16:91. Epub 2015 May 6.

Department of Computer Science, Stanford University, Stanford, CA, USA.

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http://dx.doi.org/10.1186/s13059-015-0647-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4501097PMC
May 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

Parente2: a fast and accurate method for detecting identity by descent.

Genome Res 2015 Feb 1;25(2):280-9. Epub 2014 Oct 1.

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

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http://genome.cshlp.org/lookup/doi/10.1101/gr.173641.114
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http://dx.doi.org/10.1101/gr.173641.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4315301PMC
February 2015

An effective filter for IBD detection in large data sets.

PLoS One 2014 25;9(3):e92713. Epub 2014 Mar 25.

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

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0092713PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965454PMC
December 2014

Computational biology and bioinformatics.

Bioinformatics 2014 Jun;30(12):i1-2

Computer Science Department, Stanford University and Department of Biological Sciences and Lane Center for Computational Biology, Carnegie Mellon University.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btu304DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058912PMC
June 2014

Short read alignment with populations of genomes.

Bioinformatics 2013 Jul;29(13):i361-70

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

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http://dx.doi.org/10.1093/bioinformatics/btt215DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694645PMC
July 2013

Ancestry inference in complex admixtures via variable-length Markov chain linkage models.

J Comput Biol 2013 Mar 19;20(3):199-211. Epub 2013 Feb 19.

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

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http://dx.doi.org/10.1089/cmb.2012.0088DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3590892PMC
March 2013

Linking disease associations with regulatory information in the human genome.

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

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

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

The Human OligoGenome Resource: a database of oligonucleotide capture probes for resequencing target regions across the human genome.

Nucleic Acids Res 2012 Jan 18;40(Database issue):D1137-43. Epub 2011 Nov 18.

Biomedical Informatics Training Program, Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, Stanford Genome Technology Center, Stanford University, Palo Alto and Department of Computer Science, Stanford University, Stanford, CA 94304, USA.

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http://dx.doi.org/10.1093/nar/gkr973DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245143PMC
January 2012

Reconstruction of genealogical relationships with applications to Phase III of HapMap.

Bioinformatics 2011 Jul;27(13):i333-41

Department of Computer Science, Biomedical Informatics Training Program, Stanford University School of Medicine, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr243DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3117348PMC
July 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

RECOMB Main Conference 2009.

J Comput Biol 2010 Mar;17(3):201

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http://dx.doi.org/10.1089/cmb.2010.Pr01DOI Listing
March 2010

Autoimmune disease classification by inverse association with SNP alleles.

PLoS Genet 2009 Dec 24;5(12):e1000792. Epub 2009 Dec 24.

Stanford Center for Biomedical Informatics Research, Stanford University School of Medicine, Stanford, California, USA.

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http://dx.doi.org/10.1371/journal.pgen.1000792DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2791168PMC
December 2009

Automatic parameter learning for multiple local network alignment.

J Comput Biol 2009 Aug;16(8):1001-22

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

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http://dx.doi.org/10.1089/cmb.2009.0099DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3154456PMC
August 2009

A Classifier-based approach to identify genetic similarities between diseases.

Bioinformatics 2009 Jun;25(12):i21-9

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

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http://dx.doi.org/10.1093/bioinformatics/btp226DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2687980PMC
June 2009

A serial founder effect model for human settlement out of Africa.

Proc Biol Sci 2009 Jan;276(1655):291-300

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

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http://www.royalsocietypublishing.org/doi/10.1098/rspb.2008.
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http://dx.doi.org/10.1098/rspb.2008.0750DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2674957PMC
January 2009

Genetic and computational identification of a conserved bacterial metabolic module.

PLoS Genet 2008 Dec 19;4(12):e1000310. Epub 2008 Dec 19.

Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.

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http://dx.doi.org/10.1371/journal.pgen.1000310DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2597717PMC
December 2008

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

What is the expectation maximization algorithm?

Nat Biotechnol 2008 Aug;26(8):897-9

Computer Science Department, Stanford University, 318 Campus Drive, Stanford, California 94305-5428, USA.

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http://dx.doi.org/10.1038/nbt1406DOI Listing
August 2008

A max-margin model for efficient simultaneous alignment and folding of RNA sequences.

Bioinformatics 2008 Jul;24(13):i68-76

Computer Science Department, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn177DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2718655PMC
July 2008

Effect of genetic divergence in identifying ancestral origin using HAPAA.

Genome Res 2008 Apr 18;18(4):676-82. Epub 2008 Mar 18.

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

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http://dx.doi.org/10.1101/gr.072850.107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2279255PMC
April 2008

Evolution of genes and genomes on the Drosophila phylogeny.

Authors:
Andrew G Clark Michael B Eisen Douglas R Smith Casey M Bergman Brian Oliver Therese A Markow Thomas C Kaufman Manolis Kellis William Gelbart Venky N Iyer Daniel A Pollard Timothy B Sackton Amanda M Larracuente Nadia D Singh Jose P Abad Dawn N Abt Boris Adryan Montserrat Aguade Hiroshi Akashi Wyatt W Anderson Charles F Aquadro David H Ardell Roman Arguello Carlo G Artieri Daniel A Barbash Daniel Barker Paolo Barsanti Phil Batterham Serafim Batzoglou Dave Begun Arjun Bhutkar Enrico Blanco Stephanie A Bosak Robert K Bradley Adrianne D Brand Michael R Brent Angela N Brooks Randall H Brown Roger K Butlin Corrado Caggese Brian R Calvi A Bernardo de Carvalho Anat Caspi Sergio Castrezana Susan E Celniker Jean L Chang Charles Chapple Sourav Chatterji Asif Chinwalla Alberto Civetta Sandra W Clifton Josep M Comeron James C Costello Jerry A Coyne Jennifer Daub Robert G David Arthur L Delcher Kim Delehaunty Chuong B Do Heather Ebling Kevin Edwards Thomas Eickbush Jay D Evans Alan Filipski Sven Findeiss Eva Freyhult Lucinda Fulton Robert Fulton Ana C L Garcia Anastasia Gardiner David A Garfield Barry E Garvin Greg Gibson Don Gilbert Sante Gnerre Jennifer Godfrey Robert Good Valer Gotea Brenton Gravely Anthony J Greenberg Sam Griffiths-Jones Samuel Gross Roderic Guigo Erik A Gustafson Wilfried Haerty Matthew W Hahn Daniel L Halligan Aaron L Halpern Gillian M Halter Mira V Han Andreas Heger LaDeana Hillier Angie S Hinrichs Ian Holmes Roger A Hoskins Melissa J Hubisz Dan Hultmark Melanie A Huntley David B Jaffe Santosh Jagadeeshan William R Jeck Justin Johnson Corbin D Jones William C Jordan Gary H Karpen Eiko Kataoka Peter D Keightley Pouya Kheradpour Ewen F Kirkness Leonardo B Koerich Karsten Kristiansen Dave Kudrna Rob J Kulathinal Sudhir Kumar Roberta Kwok Eric Lander Charles H Langley Richard Lapoint Brian P Lazzaro So-Jeong Lee Lisa Levesque Ruiqiang Li Chiao-Feng Lin Michael F Lin Kerstin Lindblad-Toh Ana Llopart Manyuan Long Lloyd Low Elena Lozovsky Jian Lu Meizhong Luo Carlos A Machado Wojciech Makalowski Mar Marzo Muneo Matsuda Luciano Matzkin Bryant McAllister Carolyn S McBride Brendan McKernan Kevin McKernan Maria Mendez-Lago Patrick Minx Michael U Mollenhauer Kristi Montooth Stephen M Mount Xu Mu Eugene Myers Barbara Negre Stuart Newfeld Rasmus Nielsen Mohamed A F Noor Patrick O'Grady Lior Pachter Montserrat Papaceit Matthew J Parisi Michael Parisi Leopold Parts Jakob S Pedersen Graziano Pesole Adam M Phillippy Chris P Ponting Mihai Pop Damiano Porcelli Jeffrey R Powell Sonja Prohaska Kim Pruitt Marta Puig Hadi Quesneville Kristipati Ravi Ram David Rand Matthew D Rasmussen Laura K Reed Robert Reenan Amy Reily Karin A Remington Tania T Rieger Michael G Ritchie Charles Robin Yu-Hui Rogers Claudia Rohde Julio Rozas Marc J Rubenfield Alfredo Ruiz Susan Russo Steven L Salzberg Alejandro Sanchez-Gracia David J Saranga Hajime Sato Stephen W Schaeffer Michael C Schatz Todd Schlenke Russell Schwartz Carmen Segarra Rama S Singh Laura Sirot Marina Sirota Nicholas B Sisneros Chris D Smith Temple F Smith John Spieth Deborah E Stage Alexander Stark Wolfgang Stephan Robert L Strausberg Sebastian Strempel David Sturgill Granger Sutton Granger G Sutton Wei Tao Sarah Teichmann Yoshiko N Tobari Yoshihiko Tomimura Jason M Tsolas Vera L S Valente Eli Venter J Craig Venter Saverio Vicario Filipe G Vieira Albert J Vilella Alfredo Villasante Brian Walenz Jun Wang Marvin Wasserman Thomas Watts Derek Wilson Richard K Wilson Rod A Wing Mariana F Wolfner Alex Wong Gane Ka-Shu Wong Chung-I Wu Gabriel Wu Daisuke Yamamoto Hsiao-Pei Yang Shiaw-Pyng Yang James A Yorke Kiyohito Yoshida Evgeny Zdobnov Peili Zhang Yu Zhang Aleksey V Zimin Jennifer Baldwin Amr Abdouelleil Jamal Abdulkadir Adal Abebe Brikti Abera Justin Abreu St Christophe Acer Lynne Aftuck Allen Alexander Peter An Erica Anderson Scott Anderson Harindra Arachi Marc Azer Pasang Bachantsang Andrew Barry Tashi Bayul Aaron Berlin Daniel Bessette Toby Bloom Jason Blye Leonid Boguslavskiy Claude Bonnet Boris Boukhgalter Imane Bourzgui Adam Brown Patrick Cahill Sheridon Channer Yama Cheshatsang Lisa Chuda Mieke Citroen Alville Collymore Patrick Cooke Maura Costello Katie D'Aco Riza Daza Georgius De Haan Stuart DeGray Christina DeMaso Norbu Dhargay Kimberly Dooley Erin Dooley Missole Doricent Passang Dorje Kunsang Dorjee Alan Dupes Richard Elong Jill Falk Abderrahim Farina Susan Faro Diallo Ferguson Sheila Fisher Chelsea D Foley Alicia Franke Dennis Friedrich Loryn Gadbois Gary Gearin Christina R Gearin Georgia Giannoukos Tina Goode Joseph Graham Edward Grandbois Sharleen Grewal Kunsang Gyaltsen Nabil Hafez Birhane Hagos Jennifer Hall Charlotte Henson Andrew Hollinger Tracey Honan Monika D Huard Leanne Hughes Brian Hurhula M Erii Husby Asha Kamat Ben Kanga Seva Kashin Dmitry Khazanovich Peter Kisner Krista Lance Marcia Lara William Lee Niall Lennon Frances Letendre Rosie LeVine Alex Lipovsky Xiaohong Liu Jinlei Liu Shangtao Liu Tashi Lokyitsang Yeshi Lokyitsang Rakela Lubonja Annie Lui Pen MacDonald Vasilia Magnisalis Kebede Maru Charles Matthews William McCusker Susan McDonough Teena Mehta James Meldrim Louis Meneus Oana Mihai Atanas Mihalev Tanya Mihova Rachel Mittelman Valentine Mlenga Anna Montmayeur Leonidas Mulrain Adam Navidi Jerome Naylor Tamrat Negash Thu Nguyen Nga Nguyen Robert Nicol Choe Norbu Nyima Norbu Nathaniel Novod Barry O'Neill Sahal Osman Eva Markiewicz Otero L Oyono Christopher Patti Pema Phunkhang Fritz Pierre Margaret Priest Sujaa Raghuraman Filip Rege Rebecca Reyes Cecil Rise Peter Rogov Keenan Ross Elizabeth Ryan Sampath Settipalli Terry Shea Ngawang Sherpa Lu Shi Diana Shih Todd Sparrow Jessica Spaulding John Stalker Nicole Stange-Thomann Sharon Stavropoulos Catherine Stone Christopher Strader Senait Tesfaye Talene Thomson Yama Thoulutsang Dawa Thoulutsang Kerri Topham Ira Topping Tsamla Tsamla Helen Vassiliev Andy Vo Tsering Wangchuk Tsering Wangdi Michael Weiand Jane Wilkinson Adam Wilson Shailendra Yadav Geneva Young Qing Yu Lisa Zembek Danni Zhong Andrew Zimmer Zac Zwirko David B Jaffe Pablo Alvarez Will Brockman Jonathan Butler CheeWhye Chin Sante Gnerre Manfred Grabherr Michael Kleber Evan Mauceli Iain MacCallum

Nature 2007 Nov;450(7167):203-18

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

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http://dx.doi.org/10.1038/nature06341DOI Listing
November 2007

Current progress in network research: toward reference networks for key model organisms.

Brief Bioinform 2007 Sep 29;8(5):318-32. Epub 2007 Aug 29.

318 Campus Drive, Clark Center S251, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1093/bib/bbm038DOI Listing
September 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
Web Search
http://www.genome.org/cgi/doi/10.1101/gr.6034307
Publisher Site
http://dx.doi.org/10.1101/gr.6034307DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891336PMC
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

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Proc IEEE Comput Syst Bioinform Conf 2005 :111-9

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

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May 2007

Evidence for intelligent (algorithm) design.

Genome Biol 2006 ;7(7):322

Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1186/gb-2006-7-7-322DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1779572PMC
May 2007

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PLoS One 2007 May 30;2(5):e484. Epub 2007 May 30.

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

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0000484PLOS
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May 2007

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Nucleic Acids Res 2006 13;34(20):5730-9. Epub 2006 Oct 13.

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

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http://dx.doi.org/10.1093/nar/gkl585DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635261PMC
December 2006

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Nucleic Acids Res 2006 26;34(20):5932-42. Epub 2006 Oct 26.

Department of Computer Science, Posts & Telecommunications Institute of Technology, Hanoi, Vietnam.

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December 2006

Graemlin: general and robust alignment of multiple large interaction networks.

Genome Res 2006 Sep 9;16(9):1169-81. Epub 2006 Aug 9.

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

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1557769PMC
September 2006

MotifCut: regulatory motifs finding with maximum density subgraphs.

Bioinformatics 2006 Jul;22(14):e150-7

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

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http://dx.doi.org/10.1093/bioinformatics/btl243DOI Listing
July 2006

CONTRAfold: RNA secondary structure prediction without physics-based models.

Bioinformatics 2006 Jul;22(14):e90-8

Computer Science Department, Stanford University, Stanford, CA 94305, USA.

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July 2006

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Curr Opin Struct Biol 2006 Jun 5;16(3):368-73. Epub 2006 May 5.

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June 2006

Using multiple alignments to improve seeded local alignment algorithms.

Nucleic Acids Res 2005 12;33(14):4563-77. Epub 2005 Aug 12.

Department of Computer Science, Stanford University, Stanford, CA 94304, USA.

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http://dx.doi.org/10.1093/nar/gki767DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1185574PMC
August 2005

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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

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Brief Bioinform 2005 Mar;6(1):6-22

Department of Computer Science, Stanford University, James H. Clark Center, 318 Campus Drive, RM S-266, Stanford, CA 94305-5428, USA.

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http://dx.doi.org/10.1093/bib/6.1.6DOI Listing
March 2005

ProbCons: Probabilistic consistency-based multiple sequence alignment.

Genome Res 2005 Feb;15(2):330-40

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

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http://www.genome.org/cgi/doi/10.1101/gr.2821705
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http://dx.doi.org/10.1101/gr.2821705DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC546535PMC
February 2005

Glocal alignment: finding rearrangements during alignment.

Bioinformatics 2003 ;19 Suppl 1:i54-62

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

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http://dx.doi.org/10.1093/bioinformatics/btg1005DOI Listing
October 2004

A suite of web-based programs to search for transcriptional regulatory motifs.

Nucleic Acids Res 2004 Jul;32(Web Server issue):W204-7

Stanford Medical Informatics, 251 Campus Drive X215, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1093/nar/gkh461DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC441599PMC
July 2004

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

Authors:
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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

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

Application of independent component analysis to microarrays.

Genome Biol 2003 24;4(11):R76. Epub 2003 Oct 24.

Department of Computer Science, Stanford University, Stanford, CA94305-9010, USA.

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http://dx.doi.org/10.1186/gb-2003-4-11-r76DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC329130PMC
March 2004

Eukaryotic regulatory element conservation analysis and identification using comparative genomics.

Genome Res 2004 Mar;14(3):451-8

Stanford Medical Informatics, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1101/gr.1327604DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC353232PMC
March 2004

Phylo-VISTA: interactive visualization of multiple DNA sequence alignments.

Bioinformatics 2004 Mar 22;20(5):636-43. Epub 2004 Jan 22.

Center for Image Processing and Integrated Computing, Department of Computer Science, One Shields Avenue, University of California, Davis, CA 95616-8562, USA.

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http://dx.doi.org/10.1093/bioinformatics/btg459DOI Listing
March 2004

Fast and sensitive multiple alignment of large genomic sequences.

BMC Bioinformatics 2003 Dec 23;4:66. Epub 2003 Dec 23.

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

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-4-66DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC521198PMC
December 2003

AGenDA: homology-based gene prediction.

Bioinformatics 2003 Aug;19(12):1575-7

International Graduate School for Bioinformatics and Genome Research University of Bielefeld, Postfach 10 01 31, 33501 Bielefeld, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btg181DOI Listing
August 2003

Identification of promoter regions in the human genome by using a retroviral plasmid library-based functional reporter gene assay.

Genome Res 2003 Jul 12;13(7):1765-74. Epub 2003 Jun 12.

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

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http://dx.doi.org/10.1101/gr.529803DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403750PMC
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://www.ncbi.nlm.nih.gov/pmc/articles/PMC430158PMC
April 2003

ARACHNE: a whole-genome shotgun assembler.

Genome Res 2002 Jan;12(1):177-89

Laboratory for Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1101/gr.208902DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC155255PMC
January 2002