Steven E Brenner

Steven E Brenner

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Steven E Brenner

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Precision Medicine: Addressing the Challenges of Sharing, Analysis, and Privacy at Scale.

Pac Symp Biocomput 2020 ;25:547-550

University of California, Berkeley, USA.

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January 2020

Navigating ethical quandaries with the privacy dilemma of biomedical datasets.

Pac Symp Biocomput 2020 ;25:736-738

Yale University, New Haven, CT, 06511, USA,

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January 2020

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.

Authors:
Naihui Zhou Yuxiang Jiang Timothy R Bergquist Alexandra J Lee Balint Z Kacsoh Alex W Crocker Kimberley A Lewis George Georghiou Huy N Nguyen Md Nafiz Hamid Larry Davis Tunca Dogan Volkan Atalay Ahmet S Rifaioglu Alperen Dalkıran Rengul Cetin Atalay Chengxin Zhang Rebecca L Hurto Peter L Freddolino Yang Zhang Prajwal Bhat Fran Supek José M Fernández Branislava Gemovic Vladimir R Perovic Radoslav S Davidović Neven Sumonja Nevena Veljkovic Ehsaneddin Asgari Mohammad R K Mofrad Giuseppe Profiti Castrense Savojardo Pier Luigi Martelli Rita Casadio Florian Boecker Heiko Schoof Indika Kahanda Natalie Thurlby Alice C McHardy Alexandre Renaux Rabie Saidi Julian Gough Alex A Freitas Magdalena Antczak Fabio Fabris Mark N Wass Jie Hou Jianlin Cheng Zheng Wang Alfonso E Romero Alberto Paccanaro Haixuan Yang Tatyana Goldberg Chenguang Zhao Liisa Holm Petri Törönen Alan J Medlar Elaine Zosa Itamar Borukhov Ilya Novikov Angela Wilkins Olivier Lichtarge Po-Han Chi Wei-Cheng Tseng Michal Linial Peter W Rose Christophe Dessimoz Vedrana Vidulin Saso Dzeroski Ian Sillitoe Sayoni Das Jonathan Gill Lees David T Jones Cen Wan Domenico Cozzetto Rui Fa Mateo Torres Alex Warwick Vesztrocy Jose Manuel Rodriguez Michael L Tress Marco Frasca Marco Notaro Giuliano Grossi Alessandro Petrini Matteo Re Giorgio Valentini Marco Mesiti Daniel B Roche Jonas Reeb David W Ritchie Sabeur Aridhi Seyed Ziaeddin Alborzi Marie-Dominique Devignes Da Chen Emily Koo Richard Bonneau Vladimir Gligorijević Meet Barot Hai Fang Stefano Toppo Enrico Lavezzo Marco Falda Michele Berselli Silvio C E Tosatto Marco Carraro Damiano Piovesan Hafeez Ur Rehman Qizhong Mao Shanshan Zhang Slobodan Vucetic Gage S Black Dane Jo Erica Suh Jonathan B Dayton Dallas J Larsen Ashton R Omdahl Liam J McGuffin Danielle A Brackenridge Patricia C Babbitt Jeffrey M Yunes Paolo Fontana Feng Zhang Shanfeng Zhu Ronghui You Zihan Zhang Suyang Dai Shuwei Yao Weidong Tian Renzhi Cao Caleb Chandler Miguel Amezola Devon Johnson Jia-Ming Chang Wen-Hung Liao Yi-Wei Liu Stefano Pascarelli Yotam Frank Robert Hoehndorf Maxat Kulmanov Imane Boudellioua Gianfranco Politano Stefano Di Carlo Alfredo Benso Kai Hakala Filip Ginter Farrokh Mehryary Suwisa Kaewphan Jari Björne Hans Moen Martti E E Tolvanen Tapio Salakoski Daisuke Kihara Aashish Jain Tomislav Šmuc Adrian Altenhoff Asa Ben-Hur Burkhard Rost Steven E Brenner Christine A Orengo Constance J Jeffery Giovanni Bosco Deborah A Hogan Maria J Martin Claire O'Donovan Sean D Mooney Casey S Greene Predrag Radivojac Iddo Friedberg

Genome Biol 2019 11 19;20(1):244. Epub 2019 Nov 19.

Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA.

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http://dx.doi.org/10.1186/s13059-019-1835-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6864930PMC
November 2019

VIPdb, a genetic Variant Impact Predictor Database.

Hum Mutat 2019 09 17;40(9):1202-1214. Epub 2019 Aug 17.

Department of Plant and Microbial Biology, University of California, Berkeley, California.

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http://dx.doi.org/10.1002/humu.23858DOI Listing
September 2019

Reports from the fifth edition of CAGI: The Critical Assessment of Genome Interpretation.

Hum Mutat 2019 09 26;40(9):1197-1201. Epub 2019 Aug 26.

Department of Plant and Microbial Biology, University of California, Berkeley, California.

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http://dx.doi.org/10.1002/humu.23876DOI Listing
September 2019

SCOPe: classification of large macromolecular structures in the structural classification of proteins-extended database.

Nucleic Acids Res 2019 Jan;47(D1):D475-D481

Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1093/nar/gky1134DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323910PMC
January 2019

Precision Medicine: Improving health through high-resolution analysis of personal data.

Pac Symp Biocomput 2019 ;24:220-223

University of California, Berkeley, USA†Supported by U41 HG007346 and U19 HD077627.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6526370PMC
January 2019

When Biology Gets Personal: Hidden Challenges of Privacy and Ethics in Biological Big Data.

Pac Symp Biocomput 2019 ;24:386-390

Computational Biology and Bioinformatics Program, Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06511, USA*This work is partially supported by NIH grant U01EB023686.,

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January 2019

Putting benchmarks in their rightful place: The heart of computational biology.

PLoS Comput Biol 2018 11 8;14(11):e1006494. Epub 2018 Nov 8.

Department of Biological Sciences, University of Maryland, College Park, Maryland, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1006494DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6224028PMC
November 2018

PRECISION MEDICINE: FROM DIPLOTYPES TO DISPARITIES TOWARDS IMPROVED HEALTH AND THERAPIES.

Pac Symp Biocomput 2018 ;23:389-399

Population and Quantitative Health Sciences, Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, 44106, USA,

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6182117PMC
August 2018

KBase: The United States Department of Energy Systems Biology Knowledgebase.

Nat Biotechnol 2018 07;36(7):566-569

Computer Science and Math, Computer Science Initiative, Brookhaven National Laboratory, Upton, New York, USA.

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http://dx.doi.org/10.1038/nbt.4163DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6870991PMC
July 2018

PRECISION MEDICINE: DATA AND DISCOVERY FOR IMPROVED HEALTH AND THERAPY.

Pac Symp Biocomput 2016 ;21:243-8

Stanford University School of Medicine & Khosla Ventures, Stanford, CA, USA,

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5180448PMC
February 2018

A novel pathogenic variant in a family with paroxysmal kinesigenic dyskinesia and benign familial infantile seizures.

Cold Spring Harb Mol Case Stud 2018 02 1;4(1). Epub 2018 Feb 1.

Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94143, USA.

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http://dx.doi.org/10.1101/mcs.a002287DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5793775PMC
February 2018

Reports from CAGI: The Critical Assessment of Genome Interpretation.

Hum Mutat 2017 09;38(9):1039-1041

Department of Plant and Microbial Biology, University of California, Berkeley, California.

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http://dx.doi.org/10.1002/humu.23290DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5606199PMC
September 2017

The evolution of function within the Nudix homology clan.

Proteins 2017 05 16;85(5):775-811. Epub 2017 Mar 16.

Plant and Microbial Biology Department, University of California, Berkeley, California, 94720.

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http://doi.wiley.com/10.1002/prot.25223
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http://dx.doi.org/10.1002/prot.25223DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5389931PMC
May 2017

Non-Coding Variation: The 2016 Annual Scientific Meeting of the Human Genome Variation Society.

Hum Mutat 2017 04 14;38(4):460-463. Epub 2017 Feb 14.

Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.

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http://dx.doi.org/10.1002/humu.23169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6546288PMC
April 2017

SCOPe: Manual Curation and Artifact Removal in the Structural Classification of Proteins - extended Database.

J Mol Biol 2017 02 30;429(3):348-355. Epub 2016 Nov 30.

Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S00222836163051
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http://dx.doi.org/10.1016/j.jmb.2016.11.023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5272801PMC
February 2017

Substrate specificity characterization for eight putative nudix hydrolases. Evaluation of criteria for substrate identification within the Nudix family.

Proteins 2016 12 1;84(12):1810-1822. Epub 2016 Oct 1.

Molecular and Cell Biology Department, University of California, Berkeley, California, 94720.

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http://dx.doi.org/10.1002/prot.25163DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5158307PMC
December 2016

Multisystem Anomalies in Severe Combined Immunodeficiency with Mutant BCL11B.

N Engl J Med 2016 12;375(22):2165-2176

From the Department of Pediatrics, University of California, San Francisco (UCSF), School of Medicine and UCSF Benioff Children's Hospital (D.P., J.Y., M.J.C., A.K., B.A.M., J.M.P.), and the Cardiovascular Research Institute, UCSF (C.O.L.), San Francisco, and the Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley (A.N.A., S.E.B.) - all in California; the Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia (Y.Z., S.P.F., D.L.W.); and Innovation Labs, Tata Consultancy Services, Telangana, India (S.R., A.C., R.S.).

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http://dx.doi.org/10.1056/NEJMoa1509164DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5215776PMC
December 2016

USE OF GENOME DATA IN NEWBORNS AS A STARTING POINT FOR LIFE-LONG PRECISION MEDICINE.

Pac Symp Biocomput 2016 ;21:568-75

Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA,

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October 2016

An expanded evaluation of protein function prediction methods shows an improvement in accuracy.

Authors:
Yuxiang Jiang Tal Ronnen Oron Wyatt T Clark Asma R Bankapur Daniel D'Andrea Rosalba Lepore Christopher S Funk Indika Kahanda Karin M Verspoor Asa Ben-Hur Da Chen Emily Koo Duncan Penfold-Brown Dennis Shasha Noah Youngs Richard Bonneau Alexandra Lin Sayed M E Sahraeian Pier Luigi Martelli Giuseppe Profiti Rita Casadio Renzhi Cao Zhaolong Zhong Jianlin Cheng Adrian Altenhoff Nives Skunca Christophe Dessimoz Tunca Dogan Kai Hakala Suwisa Kaewphan Farrokh Mehryary Tapio Salakoski Filip Ginter Hai Fang Ben Smithers Matt Oates Julian Gough Petri Törönen Patrik Koskinen Liisa Holm Ching-Tai Chen Wen-Lian Hsu Kevin Bryson Domenico Cozzetto Federico Minneci David T Jones Samuel Chapman Dukka Bkc Ishita K Khan Daisuke Kihara Dan Ofer Nadav Rappoport Amos Stern Elena Cibrian-Uhalte Paul Denny Rebecca E Foulger Reija Hieta Duncan Legge Ruth C Lovering Michele Magrane Anna N Melidoni Prudence Mutowo-Meullenet Klemens Pichler Aleksandra Shypitsyna Biao Li Pooya Zakeri Sarah ElShal Léon-Charles Tranchevent Sayoni Das Natalie L Dawson David Lee Jonathan G Lees Ian Sillitoe Prajwal Bhat Tamás Nepusz Alfonso E Romero Rajkumar Sasidharan Haixuan Yang Alberto Paccanaro Jesse Gillis Adriana E Sedeño-Cortés Paul Pavlidis Shou Feng Juan M Cejuela Tatyana Goldberg Tobias Hamp Lothar Richter Asaf Salamov Toni Gabaldon Marina Marcet-Houben Fran Supek Qingtian Gong Wei Ning Yuanpeng Zhou Weidong Tian Marco Falda Paolo Fontana Enrico Lavezzo Stefano Toppo Carlo Ferrari Manuel Giollo Damiano Piovesan Silvio C E Tosatto Angela Del Pozo José M Fernández Paolo Maietta Alfonso Valencia Michael L Tress Alfredo Benso Stefano Di Carlo Gianfranco Politano Alessandro Savino Hafeez Ur Rehman Matteo Re Marco Mesiti Giorgio Valentini Joachim W Bargsten Aalt D J van Dijk Branislava Gemovic Sanja Glisic Vladmir Perovic Veljko Veljkovic Nevena Veljkovic Danillo C Almeida-E-Silva Ricardo Z N Vencio Malvika Sharan Jörg Vogel Lakesh Kansakar Shanshan Zhang Slobodan Vucetic Zheng Wang Michael J E Sternberg Mark N Wass Rachael P Huntley Maria J Martin Claire O'Donovan Peter N Robinson Yves Moreau Anna Tramontano Patricia C Babbitt Steven E Brenner Michal Linial Christine A Orengo Burkhard Rost Casey S Greene Sean D Mooney Iddo Friedberg Predrag Radivojac

Genome Biol 2016 09 7;17(1):184. Epub 2016 Sep 7.

Department of Computer Science and Informatics, Indiana University, Bloomington, IN, USA.

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http://dx.doi.org/10.1186/s13059-016-1037-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5015320PMC
September 2016

Personalized medicine: from genotypes, molecular phenotypes and the quantified self, towards improved medicine.

Pac Symp Biocomput 2015 :342-6

Icahn School of Medicine at Mount Sinai, 1425 Madison Ave., New York, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5893135PMC
April 2016

Multiple breast cancer risk variants are associated with differential transcript isoform expression in tumors.

Hum Mol Genet 2015 Dec 15;24(25):7421-31. Epub 2015 Oct 15.

Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center and.

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http://dx.doi.org/10.1093/hmg/ddv432DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4664170PMC
December 2015

Regulation of alternative splicing in Drosophila by 56 RNA binding proteins.

Genome Res 2015 Nov 20;25(11):1771-80. Epub 2015 Aug 20.

Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA; Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1101/gr.192518.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4617972PMC
November 2015

The value of protein structure classification information-Surveying the scientific literature.

Proteins 2015 Nov 19;83(11):2025-38. Epub 2015 Sep 19.

Lawrence Berkeley National Laboratory, Physical Biosciences Division, Berkeley, California, 94720.

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http://doi.wiley.com/10.1002/prot.24915
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http://dx.doi.org/10.1002/prot.24915DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4609302PMC
November 2015

SIFTER search: a web server for accurate phylogeny-based protein function prediction.

Nucleic Acids Res 2015 Jul 15;43(W1):W141-7. Epub 2015 May 15.

Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA

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http://dx.doi.org/10.1093/nar/gkv461DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489292PMC
July 2015

Ten Years of PLoS Computational Biology: A Decade of Appreciation and Innovation.

PLoS Comput Biol 2015 Jun 24;11(6):e1004317. Epub 2015 Jun 24.

Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America.

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https://dx.plos.org/10.1371/journal.pcbi.1004317
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http://dx.doi.org/10.1371/journal.pcbi.1004317DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4479580PMC
June 2015

Regulation of splicing factors by alternative splicing and NMD is conserved between kingdoms yet evolutionarily flexible.

Mol Biol Evol 2015 Apr 8;32(4):1072-9. Epub 2015 Jan 8.

Departments of Molecular and Cell Biology and Plant and Microbial Biology, University of California, Berkeley

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http://dx.doi.org/10.1093/molbev/msv002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4379411PMC
April 2015

Combined immunodeficiency due to MALT1 mutations, treated by hematopoietic cell transplantation.

J Clin Immunol 2015 Feb 28;35(2):135-46. Epub 2015 Jan 28.

Department of Pediatrics, University of California San Francisco School of Medicine, and UCSF Benioff Children's Hospital, Box 0519, 513 Parnassus Avenue, HSE-301A, San Francisco, CA, 94143-0519, USA.

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http://dx.doi.org/10.1007/s10875-014-0125-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4352191PMC
February 2015

Nijmegen breakage syndrome detected by newborn screening for T cell receptor excision circles (TRECs).

J Clin Immunol 2015 Feb 13;35(2):227-33. Epub 2015 Feb 13.

Division of General Pediatrics, Children's Hospital of Los Angeles, Los Angeles, CA, USA,

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http://dx.doi.org/10.1007/s10875-015-0136-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4352190PMC
February 2015

Comparative analysis of the transcriptome across distant species.

Nature 2014 Aug;512(7515):445-8

1] Department of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA [2].

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http://dx.doi.org/10.1038/nature13424DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4155737PMC
August 2014

Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs.

J Struct Biol 2014 Jul 30;187(1):66-75. Epub 2014 Mar 30.

Life Sciences Division, Lawrence Berkeley National Laboratory, CA 94720, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S10478477140007
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http://dx.doi.org/10.1016/j.jsb.2014.03.017DOI Listing
July 2014

Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data.

Genome Res 2014 Jul;24(7):1086-101

Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA.

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http://genome.cshlp.org/cgi/doi/10.1101/gr.170100.113
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http://dx.doi.org/10.1101/gr.170100.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4079965PMC
July 2014

SCOPe: Structural Classification of Proteins--extended, integrating SCOP and ASTRAL data and classification of new structures.

Nucleic Acids Res 2014 Jan 3;42(Database issue):D304-9. Epub 2013 Dec 3.

Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA and Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1093/nar/gkt1240DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965108PMC
January 2014

The future of genome-based medicine.

Pac Symp Biocomput 2013 :456-8

University of Toronto, Donnelly Centre, 160 College Street, Toronto, ON M5S 3E1, Canada.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5894348PMC
December 2013

Optimal and fast rotational alignment of volumes with missing data in Fourier space.

J Struct Biol 2013 Nov 28;184(2):345-7. Epub 2013 Aug 28.

Physical Biosciences Division, Lawrence Berkeley National Laboratory, CA 94720, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jsb.2013.08.006DOI Listing
November 2013

Association of gut microbiota with post-operative clinical course in Crohn's disease.

BMC Gastroenterol 2013 Aug 22;13:131. Epub 2013 Aug 22.

Department of Medicine, Division of Gastroenterology, University of California, San Francisco, 513 Parnassus Avenue, Room S-357, San Francisco, CA 94143-0538, USA.

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http://dx.doi.org/10.1186/1471-230X-13-131DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3848607PMC
August 2013

A continuous fluorescence assay for the characterization of Nudix hydrolases.

Anal Biochem 2013 Jun 7;437(2):178-84. Epub 2013 Mar 7.

Department of Comparative Biochemistry, University of California, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1016/j.ab.2013.02.023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3744803PMC
June 2013

Be prepared for the big genome leak.

Authors:
Steven E Brenner

Nature 2013 Jun;498(7453):139

University of California, Berkeley, USA.

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http://www.nature.com/doifinder/10.1038/498139a
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http://dx.doi.org/10.1038/498139aDOI Listing
June 2013

Newborn screening for SCID identifies patients with ataxia telangiectasia.

J Clin Immunol 2013 Apr 20;33(3):540-9. Epub 2012 Dec 20.

Department of Pediatrics, University of California San Francisco, San Francisco, CA 94143-0519, USA.

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http://dx.doi.org/10.1007/s10875-012-9846-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3591536PMC
April 2013

A large-scale evaluation of computational protein function prediction.

Authors:
Predrag Radivojac Wyatt T Clark Tal Ronnen Oron Alexandra M Schnoes Tobias Wittkop Artem Sokolov Kiley Graim Christopher Funk Karin Verspoor Asa Ben-Hur Gaurav Pandey Jeffrey M Yunes Ameet S Talwalkar Susanna Repo Michael L Souza Damiano Piovesan Rita Casadio Zheng Wang Jianlin Cheng Hai Fang Julian Gough Patrik Koskinen Petri Törönen Jussi Nokso-Koivisto Liisa Holm Domenico Cozzetto Daniel W A Buchan Kevin Bryson David T Jones Bhakti Limaye Harshal Inamdar Avik Datta Sunitha K Manjari Rajendra Joshi Meghana Chitale Daisuke Kihara Andreas M Lisewski Serkan Erdin Eric Venner Olivier Lichtarge Robert Rentzsch Haixuan Yang Alfonso E Romero Prajwal Bhat Alberto Paccanaro Tobias Hamp Rebecca Kaßner Stefan Seemayer Esmeralda Vicedo Christian Schaefer Dominik Achten Florian Auer Ariane Boehm Tatjana Braun Maximilian Hecht Mark Heron Peter Hönigschmid Thomas A Hopf Stefanie Kaufmann Michael Kiening Denis Krompass Cedric Landerer Yannick Mahlich Manfred Roos Jari Björne Tapio Salakoski Andrew Wong Hagit Shatkay Fanny Gatzmann Ingolf Sommer Mark N Wass Michael J E Sternberg Nives Škunca Fran Supek Matko Bošnjak Panče Panov Sašo Džeroski Tomislav Šmuc Yiannis A I Kourmpetis Aalt D J van Dijk Cajo J F ter Braak Yuanpeng Zhou Qingtian Gong Xinran Dong Weidong Tian Marco Falda Paolo Fontana Enrico Lavezzo Barbara Di Camillo Stefano Toppo Liang Lan Nemanja Djuric Yuhong Guo Slobodan Vucetic Amos Bairoch Michal Linial Patricia C Babbitt Steven E Brenner Christine Orengo Burkhard Rost Sean D Mooney Iddo Friedberg

Nat Methods 2013 Mar 27;10(3):221-7. Epub 2013 Jan 27.

School of Informatics and Computing, Indiana University, Bloomington, Indiana, USA.

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http://dx.doi.org/10.1038/nmeth.2340DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3584181PMC
March 2013

PERSONALIZED MEDICINE: FROM GENOTYPES AND MOLECULAR PHENOTYPES TOWARDS COMPUTED THERAPY.

Pac Symp Biocomput 2013 ;18:171-174

Max Planck Institutes Tübingen, 72076 Tübingen, Germany.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5894351PMC
January 2013

Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences.

ISME J 2012 Jul 12;6(7):1440-4. Epub 2012 Jan 12.

Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.

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http://dx.doi.org/10.1038/ismej.2011.208DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3379642PMC
July 2012

Genome-scale phylogenetic function annotation of large and diverse protein families.

Genome Res 2011 Nov 22;21(11):1969-80. Epub 2011 Jul 22.

Electrical Engineering and Computer Science Department, University of California, Berkeley, California 94720, USA.

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http://genome.cshlp.org/cgi/doi/10.1101/gr.104687.109
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http://dx.doi.org/10.1101/gr.104687.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3205580PMC
November 2011

An SF1 affinity model to identify branch point sequences in human introns.

Nucleic Acids Res 2011 Mar 10;39(6):2344-56. Epub 2010 Nov 10.

Department of Biochemistry and Biophysics, University of California, San Francisco, USA.

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http://dx.doi.org/10.1093/nar/gkq1046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3064769PMC
March 2011

Conservation of an RNA regulatory map between Drosophila and mammals.

Genome Res 2011 Feb 4;21(2):193-202. Epub 2010 Oct 4.

Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1101/gr.108662.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3032923PMC
February 2011

Identification of functional elements and regulatory circuits by Drosophila modENCODE.

Science 2010 Dec 22;330(6012):1787-97. Epub 2010 Dec 22.

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.

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http://www.sciencemag.org/cgi/doi/10.1126/science.1198374
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3192495PMC
December 2010

Biases in Illumina transcriptome sequencing caused by random hexamer priming.

Nucleic Acids Res 2010 Jul 14;38(12):e131. Epub 2010 Apr 14.

Division of Biostatistics, School of Public Health, UC Berkeley, 101 Haviland Hall, Berkeley, CA 94720-7358, USA.

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http://dx.doi.org/10.1093/nar/gkq224DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896536PMC
July 2010

Alignment-free local structural search by writhe decomposition.

Bioinformatics 2010 May 5;26(9):1176-84. Epub 2010 Apr 5.

Department of Plant and Microbial Biology, UC Berkeley and Physical Biosciences Division, LBNL, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1093/bioinformatics/btq127DOI Listing
May 2010

Automated multi-model reconstruction from single-particle electron microscopy data.

J Struct Biol 2010 Apr 18;170(1):98-108. Epub 2010 Jan 18.

Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1016/j.jsb.2010.01.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2841227PMC
April 2010

Survey of large protein complexes in D. vulgaris reveals great structural diversity.

Proc Natl Acad Sci U S A 2009 Sep 11;106(39):16580-5. Epub 2009 Sep 11.

Life Sciences, Genomics, Earth Sciences, and Physical Biosciences Divisions, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2742403PMC
September 2009

A method for the alignment of heterogeneous macromolecules from electron microscopy.

J Struct Biol 2009 Apr 30;166(1):67-78. Epub 2008 Dec 30.

Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2740748PMC
April 2009

Planning the human variome project: the Spain report.

Authors:
Jim Kaput Richard G H Cotton Lauren Hardman Michael Watson Aida I Al Aqeel Jumana Y Al-Aama Fahd Al-Mulla Santos Alonso Stefan Aretz Arleen D Auerbach Bharati Bapat Inge T Bernstein Jong Bhak Stacey L Bleoo Helmut Blöcker Steven E Brenner John Burn Mariona Bustamante Rita Calzone Anne Cambon-Thomsen Michele Cargill Paola Carrera Lawrence Cavedon Yoon Shin Cho Yeun-Jun Chung Mireille Claustres Garry Cutting Raymond Dalgleish Johan T den Dunnen Carlos Díaz Steven Dobrowolski M Rosário N dos Santos Rosemary Ekong Simon B Flanagan Paul Flicek Yoichi Furukawa Maurizio Genuardi Ho Ghang Maria V Golubenko Marc S Greenblatt Ada Hamosh John M Hancock Ross Hardison Terence M Harrison Robert Hoffmann Rania Horaitis Heather J Howard Carol Isaacson Barash Neskuts Izagirre Jongsun Jung Toshio Kojima Sandrine Laradi Yeon-Su Lee Jong-Young Lee Vera L Gil-da-Silva-Lopes Finlay A Macrae Donna Maglott Makia J Marafie Steven G E Marsh Yoichi Matsubara Ludwine M Messiaen Gabriela Möslein Mihai G Netea Melissa L Norton Peter J Oefner William S Oetting James C O'Leary Ana Maria Oller de Ramirez Mark H Paalman Jillian Parboosingh George P Patrinos Giuditta Perozzi Ian R Phillips Sue Povey Suyash Prasad Ming Qi David J Quin Rajkumar S Ramesar C Sue Richards Judith Savige Dagmar G Scheible Rodney J Scott Daniela Seminara Elizabeth A Shephard Rolf H Sijmons Timothy D Smith María-Jesús Sobrido Toshihiro Tanaka Sean V Tavtigian Graham R Taylor Jon Teague Thoralf Töpel Mollie Ullman-Cullere Joji Utsunomiya Henk J van Kranen Mauno Vihinen Elizabeth Webb Thomas K Weber Meredith Yeager Young I Yeom Seon-Hee Yim Hyang-Sook Yoo

Hum Mutat 2009 Apr;30(4):496-510

Division of Personalised Nutrition and Medicine, FDA/National Center for Toxicological Research, Jefferson, Arkansas 72079, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5879779PMC
April 2009

Phylogenetic molecular function annotation.

J Phys Conf Ser 2009 ;180(1):12024

EECS Department, University of California, Berkeley, CA, USA.

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http://dx.doi.org/10.1088/1742-6596/180/1/012024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2909777PMC
January 2009

The coupling of alternative splicing and nonsense-mediated mRNA decay.

Adv Exp Med Biol 2007 ;623:190-211

Department of Molecular and Cell Biology, University of California, Berkeley, USA.

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April 2008

Data growth and its impact on the SCOP database: new developments.

Nucleic Acids Res 2008 Jan 13;36(Database issue):D419-25. Epub 2007 Nov 13.

MRC Centre for Protein Engineering, Hills Road, Cambridge CB2 0QH, UK.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238974PMC
January 2008

Common sense for our genomes.

Authors:
Steven E Brenner

Nature 2007 Oct;449(7164):783-4

Department of Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, California 94720, USA.

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October 2007

Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements.

Nature 2007 Apr 14;446(7138):926-9. Epub 2007 Mar 14.

Department of Molecular and Cell Biology and, University of California, Berkeley, California 94720, USA.

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April 2007

ANDY: a general, fault-tolerant tool for database searching on computer clusters.

Bioinformatics 2006 Mar 5;22(5):618-20. Epub 2006 Jan 5.

Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA.

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March 2006

Target selection and deselection at the Berkeley Structural Genomics Center.

Proteins 2006 Feb;62(2):356-70

Berkeley Structural Genomics Center, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.

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February 2006

MeRNA: a database of metal ion binding sites in RNA structures.

Nucleic Acids Res 2006 Jan;34(Database issue):D131-4

Department of Structural Biology, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347421PMC
January 2006

The impact of structural genomics: expectations and outcomes.

Science 2006 Jan;311(5759):347-51

Berkeley Structural Genomics Center, Physical Biosciences Division, Lawrence Berkeley National Laboratory, and Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.

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January 2006

Pairwise alignment incorporating dipeptide covariation.

Bioinformatics 2005 Oct 25;21(19):3704-10. Epub 2005 Aug 25.

Department of Plant and Microbial Biology 111 Koshland Hall #3102 University of California, Berkeley, CA 94720-3102, USA.

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October 2005

Protein molecular function prediction by Bayesian phylogenomics.

PLoS Comput Biol 2005 Oct 7;1(5):e45. Epub 2005 Oct 7.

Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.0010045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1246806PMC
October 2005

RNA structural motifs: building blocks of a modular biomolecule.

Q Rev Biophys 2005 Aug 3;38(3):221-43. Epub 2006 Jul 3.

Department of Plant & Microbial Biology, University of California, Berkeley, CA, USA.

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August 2005