David Haussler

David Haussler

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David Haussler

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Blockchain-Authenticated Sharing of Genomic and Clinical Outcomes Data of Patients With Cancer: A Prospective Cohort Study.

J Med Internet Res 2020 03 20;22(3):e16810. Epub 2020 Mar 20.

Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, CA, United States.

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http://dx.doi.org/10.2196/16810DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7125440PMC
March 2020

Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design.

Cell Rep 2019 11;29(6):1675-1689.e9

Division of Oncology, Children's Hospital of Philadelphia, and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104-4318, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2019.09.071DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6880934PMC
November 2019

Data sharing for clinical utility.

Cold Spring Harb Mol Case Stud 2019 10 23;5(5). Epub 2019 Oct 23.

University of California Santa Cruz Genomics Institute, Santa Cruz, California 95064, USA.

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http://dx.doi.org/10.1101/mcs.a004689DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6824251PMC
October 2019

Data sharing for pediatric cancers.

Science 2019 03;363(6432):1125

David Haussler is a Distinguished Professor in the Genomics Institute, in the Department of Biomolecular Engineering, and in the Howard Hughes Medical Institute at the University of California, Santa Cruz, Santa Cruz, CA, USA.

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http://dx.doi.org/10.1126/science.aax2739DOI Listing
March 2019

Structurally Conserved Primate LncRNAs Are Transiently Expressed during Human Cortical Differentiation and Influence Cell-Type-Specific Genes.

Stem Cell Reports 2019 02 10;12(2):245-257. Epub 2019 Jan 10.

Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA; Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1016/j.stemcr.2018.12.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6372947PMC
February 2019

Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution.

Cell 2019 02;176(4):743-756.e17

Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.01.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6544371PMC
February 2019

Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation.

Genome Res 2018 07 8;28(7):1029-1038. Epub 2018 Jun 8.

Genomics Institute, University of California Santa Cruz and Howard Hughes Medical Institute, Santa Cruz, California 95064, USA.

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http://dx.doi.org/10.1101/gr.233460.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6028123PMC
July 2018

Linear assembly of a human centromere on the Y chromosome.

Nat Biotechnol 2018 04 19;36(4):321-323. Epub 2018 Mar 19.

UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California, USA.

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http://dx.doi.org/10.1038/nbt.4109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5886786PMC
April 2018

Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs.

BMC Bioinformatics 2016 Sep 29;17(1):400. Epub 2016 Sep 29.

Center for Biomolecular Sciences and Engineering, CBSE/ITI, UC Santa Cruz, 1156 High St, Santa Cruz, 95064, CA, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5043639PMC
http://dx.doi.org/10.1186/s12859-016-1258-4DOI Listing
September 2016

Long-read sequence assembly of the gorilla genome.

Science 2016 Apr;352(6281):aae0344

Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1126/science.aae0344DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4920363PMC
April 2016

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage.

Genome Res 2016 Mar 4;26(3):342-50. Epub 2016 Feb 4.

Dovetail Genomics LLC, Santa Cruz, California 95060, USA; Department of Biomolecular Engineering, University of California, Santa Cruz, California 95066, USA;

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http://dx.doi.org/10.1101/gr.193474.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4772016PMC
March 2016

Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma.

Authors:
W Marston Linehan Paul T Spellman Christopher J Ricketts Chad J Creighton Suzanne S Fei Caleb Davis David A Wheeler Bradley A Murray Laura Schmidt Cathy D Vocke Myron Peto Abu Amar M Al Mamun Eve Shinbrot Anurag Sethi Samira Brooks W Kimryn Rathmell Angela N Brooks Katherine A Hoadley A Gordon Robertson Denise Brooks Reanne Bowlby Sara Sadeghi Hui Shen Daniel J Weisenberger Moiz Bootwalla Stephen B Baylin Peter W Laird Andrew D Cherniack Gordon Saksena Scott Haake Jun Li Han Liang Yiling Lu Gordon B Mills Rehan Akbani Mark D M Leiserson Benjamin J Raphael Pavana Anur Donald Bottaro Laurence Albiges Nandita Barnabas Toni K Choueiri Bogdan Czerniak Andrew K Godwin A Ari Hakimi Thai H Ho James Hsieh Michael Ittmann William Y Kim Bhavani Krishnan Maria J Merino Kenna R Mills Shaw Victor E Reuter Ed Reznik Carl S Shelley Brian Shuch Sabina Signoretti Ramaprasad Srinivasan Pheroze Tamboli George Thomas Satish Tickoo Kenneth Burnett Daniel Crain Johanna Gardner Kevin Lau David Mallery Scott Morris Joseph D Paulauskis Robert J Penny Candace Shelton W Troy Shelton Mark Sherman Eric Thompson Peggy Yena Melissa T Avedon Jay Bowen Julie M Gastier-Foster Mark Gerken Kristen M Leraas Tara M Lichtenberg Nilsa C Ramirez Tracie Santos Lisa Wise Erik Zmuda John A Demchok Ina Felau Carolyn M Hutter Margi Sheth Heidi J Sofia Roy Tarnuzzer Zhining Wang Liming Yang Jean C Zenklusen Jiashan Zhang Brenda Ayala Julien Baboud Sudha Chudamani Jia Liu Laxmi Lolla Rashi Naresh Todd Pihl Qiang Sun Yunhu Wan Ye Wu Adrian Ally Miruna Balasundaram Saianand Balu Rameen Beroukhim Tom Bodenheimer Christian Buhay Yaron S N Butterfield Rebecca Carlsen Scott L Carter Hsu Chao Eric Chuah Amanda Clarke Kyle R Covington Mahmoud Dahdouli Ninad Dewal Noreen Dhalla Harsha V Doddapaneni Jennifer A Drummond Stacey B Gabriel Richard A Gibbs Ranabir Guin Walker Hale Alicia Hawes D Neil Hayes Robert A Holt Alan P Hoyle Stuart R Jefferys Steven J M Jones Corbin D Jones Divya Kalra Christie Kovar Lora Lewis Jie Li Yussanne Ma Marco A Marra Michael Mayo Shaowu Meng Matthew Meyerson Piotr A Mieczkowski Richard A Moore Donna Morton Lisle E Mose Andrew J Mungall Donna Muzny Joel S Parker Charles M Perou Jeffrey Roach Jacqueline E Schein Steven E Schumacher Yan Shi Janae V Simons Payal Sipahimalani Tara Skelly Matthew G Soloway Carrie Sougnez Angela Tam Donghui Tan Nina Thiessen Umadevi Veluvolu Min Wang Matthew D Wilkerson Tina Wong Junyuan Wu Liu Xi Jane Zhou Jason Bedford Fengju Chen Yao Fu Mark Gerstein David Haussler Katayoon Kasaian Phillip Lai Shiyun Ling Amie Radenbaugh David Van Den Berg John N Weinstein Jingchun Zhu Monique Albert Iakovina Alexopoulou Jeremiah J Andersen J Todd Auman John Bartlett Sheldon Bastacky Julie Bergsten Michael L Blute Lori Boice Roni J Bollag Jeff Boyd Erik Castle Ying-Bei Chen John C Cheville Erin Curley Benjamin Davies April DeVolk Rajiv Dhir Laura Dike John Eckman Jay Engel Jodi Harr Ronald Hrebinko Mei Huang Lori Huelsenbeck-Dill Mary Iacocca Bruce Jacobs Michael Lobis Jodi K Maranchie Scott McMeekin Jerome Myers Joel Nelson Jeremy Parfitt Anil Parwani Nicholas Petrelli Brenda Rabeno Somak Roy Andrew L Salner Joel Slaton Melissa Stanton R Houston Thompson Leigh Thorne Kelinda Tucker Paul M Weinberger Cynthia Winemiller Leigh Anne Zach Rosemary Zuna

Canonical, stable, general mapping using context schemes.

Bioinformatics 2015 Nov 27;31(22):3569-76. Epub 2015 Jul 27.

UC Santa Cruz Genomics Institute, 1156 High Street, Santa Cruz, CA 95064 and.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btv435DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4757953PMC
November 2015

RADIA: RNA and DNA integrated analysis for somatic mutation detection.

PLoS One 2014 18;9(11):e111516. Epub 2014 Nov 18.

University of California Santa Cruz Genomics Institute, Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America; Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0111516PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4236012PMC
July 2015

Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection.

Nat Methods 2015 Jul 18;12(7):623-30. Epub 2015 May 18.

1] Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada. [2] Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada. [3] Department of Pharmacology &Toxicology, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1038/nmeth.3407DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4856034PMC
July 2015

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.

Authors:
Daniel J Brat Roel G W Verhaak Kenneth D Aldape W K Alfred Yung Sofie R Salama Lee A D Cooper Esther Rheinbay C Ryan Miller Mark Vitucci Olena Morozova A Gordon Robertson Houtan Noushmehr Peter W Laird Andrew D Cherniack Rehan Akbani Jason T Huse Giovanni Ciriello Laila M Poisson Jill S Barnholtz-Sloan Mitchel S Berger Cameron Brennan Rivka R Colen Howard Colman Adam E Flanders Caterina Giannini Mia Grifford Antonio Iavarone Rajan Jain Isaac Joseph Jaegil Kim Katayoon Kasaian Tom Mikkelsen Bradley A Murray Brian Patrick O'Neill Lior Pachter Donald W Parsons Carrie Sougnez Erik P Sulman Scott R Vandenberg Erwin G Van Meir Andreas von Deimling Hailei Zhang Daniel Crain Kevin Lau David Mallery Scott Morris Joseph Paulauskis Robert Penny Troy Shelton Mark Sherman Peggy Yena Aaron Black Jay Bowen Katie Dicostanzo Julie Gastier-Foster Kristen M Leraas Tara M Lichtenberg Christopher R Pierson Nilsa C Ramirez Cynthia Taylor Stephanie Weaver Lisa Wise Erik Zmuda Tanja Davidsen John A Demchok Greg Eley Martin L Ferguson Carolyn M Hutter Kenna R Mills Shaw Bradley A Ozenberger Margi Sheth Heidi J Sofia Roy Tarnuzzer Zhining Wang Liming Yang Jean Claude Zenklusen Brenda Ayala Julien Baboud Sudha Chudamani Mark A Jensen Jia Liu Todd Pihl Rohini Raman Yunhu Wan Ye Wu Adrian Ally J Todd Auman Miruna Balasundaram Saianand Balu Stephen B Baylin Rameen Beroukhim Moiz S Bootwalla Reanne Bowlby Christopher A Bristow Denise Brooks Yaron Butterfield Rebecca Carlsen Scott Carter Lynda Chin Andy Chu Eric Chuah Kristian Cibulskis Amanda Clarke Simon G Coetzee Noreen Dhalla Tim Fennell Sheila Fisher Stacey Gabriel Gad Getz Richard Gibbs Ranabir Guin Angela Hadjipanayis D Neil Hayes Toshinori Hinoue Katherine Hoadley Robert A Holt Alan P Hoyle Stuart R Jefferys Steven Jones Corbin D Jones Raju Kucherlapati Phillip H Lai Eric Lander Semin Lee Lee Lichtenstein Yussanne Ma Dennis T Maglinte Harshad S Mahadeshwar Marco A Marra Michael Mayo Shaowu Meng Matthew L Meyerson Piotr A Mieczkowski Richard A Moore Lisle E Mose Andrew J Mungall Angeliki Pantazi Michael Parfenov Peter J Park Joel S Parker Charles M Perou Alexei Protopopov Xiaojia Ren Jeffrey Roach Thaís S Sabedot Jacqueline Schein Steven E Schumacher Jonathan G Seidman Sahil Seth Hui Shen Janae V Simons Payal Sipahimalani Matthew G Soloway Xingzhi Song Huandong Sun Barbara Tabak Angela Tam Donghui Tan Jiabin Tang Nina Thiessen Timothy Triche David J Van Den Berg Umadevi Veluvolu Scot Waring Daniel J Weisenberger Matthew D Wilkerson Tina Wong Junyuan Wu Liu Xi Andrew W Xu Lixing Yang Travis I Zack Jianhua Zhang B Arman Aksoy Harindra Arachchi Chris Benz Brady Bernard Daniel Carlin Juok Cho Daniel DiCara Scott Frazer Gregory N Fuller JianJiong Gao Nils Gehlenborg David Haussler David I Heiman Lisa Iype Anders Jacobsen Zhenlin Ju Sol Katzman Hoon Kim Theo Knijnenburg Richard Bailey Kreisberg Michael S Lawrence William Lee Kalle Leinonen Pei Lin Shiyun Ling Wenbin Liu Yingchun Liu Yuexin Liu Yiling Lu Gordon Mills Sam Ng Michael S Noble Evan Paull Arvind Rao Sheila Reynolds Gordon Saksena Zack Sanborn Chris Sander Nikolaus Schultz Yasin Senbabaoglu Ronglai Shen Ilya Shmulevich Rileen Sinha Josh Stuart S Onur Sumer Yichao Sun Natalie Tasman Barry S Taylor Doug Voet Nils Weinhold John N Weinstein Da Yang Kosuke Yoshihara Siyuan Zheng Wei Zhang Lihua Zou Ty Abel Sara Sadeghi Mark L Cohen Jenny Eschbacher Eyas M Hattab Aditya Raghunathan Matthew J Schniederjan Dina Aziz Gene Barnett Wendi Barrett Darell D Bigner Lori Boice Cathy Brewer Chiara Calatozzolo Benito Campos Carlos Gilberto Carlotti Timothy A Chan Lucia Cuppini Erin Curley Stefania Cuzzubbo Karen Devine Francesco DiMeco Rebecca Duell J Bradley Elder Ashley Fehrenbach Gaetano Finocchiaro William Friedman Jordonna Fulop Johanna Gardner Beth Hermes Christel Herold-Mende Christine Jungk Ady Kendler Norman L Lehman Eric Lipp Ouida Liu Randy Mandt Mary McGraw Roger Mclendon Christopher McPherson Luciano Neder Phuong Nguyen Ardene Noss Raffaele Nunziata Quinn T Ostrom Cheryl Palmer Alessandro Perin Bianca Pollo Alexander Potapov Olga Potapova W Kimryn Rathmell Daniil Rotin Lisa Scarpace Cathy Schilero Kelly Senecal Kristen Shimmel Vsevolod Shurkhay Suzanne Sifri Rosy Singh Andrew E Sloan Kathy Smolenski Susan M Staugaitis Ruth Steele Leigh Thorne Daniela P C Tirapelli Andreas Unterberg Mahitha Vallurupalli Yun Wang Ronald Warnick Felicia Williams Yingli Wolinsky Sue Bell Mara Rosenberg Chip Stewart Franklin Huang Jonna L Grimsby Amie J Radenbaugh Jianan Zhang
June 2015

Building a pan-genome reference for a population.

J Comput Biol 2015 May 7;22(5):387-401. Epub 2015 Jan 7.

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

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http://dx.doi.org/10.1089/cmb.2014.0146DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4424974PMC
May 2015

Navigating protected genomics data with UCSC Genome Browser in a Box.

Bioinformatics 2015 Mar 27;31(5):764-6. Epub 2014 Oct 27.

Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA and Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu712DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4341066PMC
March 2015

The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data.

Database (Oxford) 2014 29;2014. Epub 2014 Sep 29.

Biomolecular Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA, USA, Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Annai Systems Inc., 2100 Palomar Airport Road, Suite 210 Carlsbad, California 92011, USA, Cardinal Peak, LLC, 1380 Forest Park Circle, Suite 202 Lafayette, CO 80026, USA and Information Technology Services, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA.

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https://academic.oup.com/database/article-lookup/doi/10.1093
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http://dx.doi.org/10.1093/database/bau093DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4178372PMC
February 2015

The birds of Genome10K.

Gigascience 2014 11;3(1):32. Epub 2014 Dec 11.

San Diego Zoo Institute for Conservation Research, Escondido, CA 92027 USA.

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http://dx.doi.org/10.1186/2047-217X-3-32DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4326320PMC
February 2015

Integrative analysis of 111 reference human epigenomes.

Nature 2015 Feb;518(7539):317-30

1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1038/nature14248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4530010PMC
February 2015

The UCSC Cancer Genomics Browser: update 2015.

Nucleic Acids Res 2015 Jan 11;43(Database issue):D812-7. Epub 2014 Nov 11.

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

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http://dx.doi.org/10.1093/nar/gku1073DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383911PMC
January 2015

Feather development genes and associated regulatory innovation predate the origin of Dinosauria.

Mol Biol Evol 2015 Jan 18;32(1):23-8. Epub 2014 Nov 18.

Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA

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http://dx.doi.org/10.1093/molbev/msu309DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4271537PMC
January 2015

Comparative assembly hubs: web-accessible browsers for comparative genomics.

Bioinformatics 2014 Dec 18;30(23):3293-301. Epub 2014 Aug 18.

Center for Biomolecular Sciences and Engineering, CBSE/ITI, UC Santa Cruz, 1156 High St, Santa Cruz, CA 95064, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu534DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4296145PMC
December 2014

Alignathon: a competitive assessment of whole-genome alignment methods.

Genome Res 2014 Dec 1;24(12):2077-89. Epub 2014 Oct 1.

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

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http://dx.doi.org/10.1101/gr.174920.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4248324PMC
December 2014

An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons.

Nature 2014 Dec 28;516(7530):242-5. Epub 2014 Sep 28.

1] Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA [2] Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, California 95064, USA.

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http://dx.doi.org/10.1038/nature13760DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4268317PMC
December 2014

Comparative genomics reveals insights into avian genome evolution and adaptation.

Science 2014 Dec 11;346(6215):1311-20. Epub 2014 Dec 11.

China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. Macau University of Science and Technology, Avenida Wai long, Taipa, Macau 999078, China. Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark. Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia. Department of Medicine, University of Hong Kong, Hong Kong.

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http://jarvislab.net/wp-content/uploads/2014/12/Science-2014
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http://www.sciencemag.org/cgi/doi/10.1126/science.1251385
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http://dx.doi.org/10.1126/science.1251385DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4390078PMC
December 2014

Whole-genome analyses resolve early branches in the tree of life of modern birds.

Authors:
Erich D Jarvis Siavash Mirarab Andre J Aberer Bo Li Peter Houde Cai Li Simon Y W Ho Brant C Faircloth Benoit Nabholz Jason T Howard Alexander Suh Claudia C Weber Rute R da Fonseca Jianwen Li Fang Zhang Hui Li Long Zhou Nitish Narula Liang Liu Ganesh Ganapathy Bastien Boussau Md Shamsuzzoha Bayzid Volodymyr Zavidovych Sankar Subramanian Toni Gabaldón Salvador Capella-Gutiérrez Jaime Huerta-Cepas Bhanu Rekepalli Kasper Munch Mikkel Schierup Bent Lindow Wesley C Warren David Ray Richard E Green Michael W Bruford Xiangjiang Zhan Andrew Dixon Shengbin Li Ning Li Yinhua Huang Elizabeth P Derryberry Mads Frost Bertelsen Frederick H Sheldon Robb T Brumfield Claudio V Mello Peter V Lovell Morgan Wirthlin Maria Paula Cruz Schneider Francisco Prosdocimi José Alfredo Samaniego Amhed Missael Vargas Velazquez Alonzo Alfaro-Núñez Paula F Campos Bent Petersen Thomas Sicheritz-Ponten An Pas Tom Bailey Paul Scofield Michael Bunce David M Lambert Qi Zhou Polina Perelman Amy C Driskell Beth Shapiro Zijun Xiong Yongli Zeng Shiping Liu Zhenyu Li Binghang Liu Kui Wu Jin Xiao Xiong Yinqi Qiuemei Zheng Yong Zhang Huanming Yang Jian Wang Linnea Smeds Frank E Rheindt Michael Braun Jon Fjeldsa Ludovic Orlando F Keith Barker Knud Andreas Jønsson Warren Johnson Klaus-Peter Koepfli Stephen O'Brien David Haussler Oliver A Ryder Carsten Rahbek Eske Willerslev Gary R Graves Travis C Glenn John McCormack Dave Burt Hans Ellegren Per Alström Scott V Edwards Alexandros Stamatakis David P Mindell Joel Cracraft Edward L Braun Tandy Warnow Wang Jun M Thomas P Gilbert Guojie Zhang

Science 2014 Dec;346(6215):1320-31

China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark.

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http://dx.doi.org/10.1126/science.1253451DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405904PMC
December 2014

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.

Science 2014 Dec 11;346(6215):1254449. Epub 2014 Dec 11.

Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA.

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http://jarvislab.net/wp-content/uploads/2012/02/Green-et-al-
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http://www.sciencemag.org/cgi/doi/10.1126/science.1254449
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http://dx.doi.org/10.1126/science.1254449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4386873PMC
December 2014

A unifying model of genome evolution under parsimony.

BMC Bioinformatics 2014 Jun 19;15:206. Epub 2014 Jun 19.

University of California, Santa Cruz, 1156 High St, 95064 Santa Cruz, USA.

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http://dx.doi.org/10.1186/1471-2105-15-206DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4082375PMC
June 2014

Current status and new features of the Consensus Coding Sequence database.

Nucleic Acids Res 2014 Jan 11;42(Database issue):D865-72. Epub 2013 Nov 11.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA, Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK and Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/nar/gkt1059DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965069PMC
January 2014

The UCSC Genome Browser database: 2014 update.

Nucleic Acids Res 2014 Jan 21;42(Database issue):D764-70. Epub 2013 Nov 21.

Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, Santa Cruz, CA 95064, USA, Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA, Department of Genetics, Stanford University School of Medicine, 3165 Porter Drive, Stanford, CA 94305, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/nar/gkt1168DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964947PMC
January 2014

Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE).

Bioinformatics 2013 Nov 27;29(21):2757-64. Epub 2013 Aug 27.

Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, Department of Systems Biology, HMS LINCS Center, Harvard Medical School, Boston, MA 02115 and Howard Hughes Medical Institute, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt471DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3799471PMC
November 2013

Double minute chromosomes in glioblastoma multiforme are revealed by precise reconstruction of oncogenic amplicons.

Cancer Res 2013 Oct 12;73(19):6036-45. Epub 2013 Aug 12.

Authors' Affiliations: Five3 Genomics, LLC; Center for Biomolecular Science and Engineering, University of California; Howard Hughes Medical Institute, Santa Cruz, California; Human Oncology & Pathogenesis Program and Department of Neurosurgery; Cytogenetics Laboratory, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York; Departments of Neurology & Neurosurgery, Henry Ford Hospital, Detroit, Michigan; and Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas.

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http://dx.doi.org/10.1158/0008-5472.CAN-13-0186DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3800429PMC
October 2013

Exploring TCGA Pan-Cancer data at the UCSC Cancer Genomics Browser.

Sci Rep 2013 Oct 2;3:2652. Epub 2013 Oct 2.

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

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http://dx.doi.org/10.1038/srep02652DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3788369PMC
October 2013

The somatic genomic landscape of glioblastoma.

Cell 2013 Oct;155(2):462-77

Human Oncology and Pathogenesis Program, Brain Tumor Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Department of Neurosurgery, Memorial Sloan-Kettering Cancer Center, Department of Neurological Surgery, Weill Cornell Medical Center, New York, NY 10065, USA. Electronic address:

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https://www.genome.gov/Multimedia/Slides/TCGA2/27_Verhaak.pd
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http://linkinghub.elsevier.com/retrieve/pii/S009286741301208
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http://dx.doi.org/10.1016/j.cell.2013.09.034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3910500PMC
October 2013

The UCSC Interaction Browser: multidimensional data views in pathway context.

Nucleic Acids Res 2013 Jul 8;41(Web Server issue):W218-24. Epub 2013 Jun 8.

Biomolecular Engineering Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/nar/gkt473DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3692096PMC
July 2013

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.

Gigascience 2013 Jul 22;2(1):10. Epub 2013 Jul 22.

Genome Center, UC, Davis, CA 95616, USA.

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http://dx.doi.org/10.1186/2047-217X-2-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3844414PMC
July 2013

HAL: a hierarchical format for storing and analyzing multiple genome alignments.

Bioinformatics 2013 May 16;29(10):1341-2. Epub 2013 Mar 16.

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

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http://dx.doi.org/10.1093/bioinformatics/btt128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3654707PMC
May 2013

Gene isoform specificity through enhancer-associated antisense transcription.

PLoS One 2012 24;7(8):e43511. Epub 2012 Aug 24.

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

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0043511PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427357PMC
April 2013

The UCSC genome browser and associated tools.

Brief Bioinform 2013 Mar 20;14(2):144-61. Epub 2012 Aug 20.

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

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http://dx.doi.org/10.1093/bib/bbs038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3603215PMC
March 2013

29 mammalian genomes reveal novel exaptations of mobile elements for likely regulatory functions in the human genome.

PLoS One 2012 27;7(8):e43128. Epub 2012 Aug 27.

Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0043128PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3428314PMC
February 2013

The UCSC Cancer Genomics Browser: update 2013.

Nucleic Acids Res 2013 Jan 29;41(Database issue):D949-54. Epub 2012 Oct 29.

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

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http://dx.doi.org/10.1093/nar/gks1008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531186PMC
January 2013

ENCODE data in the UCSC Genome Browser: year 5 update.

Nucleic Acids Res 2013 Jan 27;41(Database issue):D56-63. Epub 2012 Nov 27.

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

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http://dx.doi.org/10.1093/nar/gks1172DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531152PMC
January 2013

The fishes of Genome 10K.

Mar Genomics 2012 Sep 24;7:3-6. Epub 2012 Mar 24.

Department of Ecology and Evolutionary Biology, University of California Santa Cruz, CA, USA.

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http://dx.doi.org/10.1016/j.margen.2012.02.002DOI Listing
September 2012

PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis.

Bioinformatics 2012 Sep;28(18):i640-i646

Department of Biomolecular Engineering and CBSE, University of California Santa Cruz, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts402DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3436829PMC
September 2012

Human tRNA genes function as chromatin insulators.

EMBO J 2012 Jan 15;31(2):330-50. Epub 2011 Nov 15.

Department of MCD Biology, University of California, Santa Cruz, CA, USA.

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http://dx.doi.org/10.1038/emboj.2011.406DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3261562PMC
January 2012

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

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

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

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https://academic.oup.com/gbe/article/doi/10.1093/gbe/evr058/
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http://dx.doi.org/10.1093/gbe/evr058DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3157837PMC
December 2011

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

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

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

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

Cactus: Algorithms for genome multiple sequence alignment.

Genome Res 2011 Sep 10;21(9):1512-28. Epub 2011 Jun 10.

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

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http://dx.doi.org/10.1101/gr.123356.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166836PMC
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