Publications by authors named "Michael L Tress"

40Publications

An analysis of tissue-specific alternative splicing at the protein level.

PLoS Comput Biol 2020 Oct 5;16(10):e1008287. Epub 2020 Oct 5.

Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez, Madrid, Spain.

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http://dx.doi.org/10.1371/journal.pcbi.1008287DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7561204PMC
October 2020

Few SINEs of life: Alu elements have little evidence for biological relevance despite elevated translation.

NAR Genom Bioinform 2020 Mar 19;2(1):lqz023. Epub 2019 Dec 19.

Bioinformatics Unit, Spanish National Cancer Research Centre, 28029 Madrid, Spain.

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http://dx.doi.org/10.1093/nargab/lqz023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6924539PMC
March 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

APPRIS 2017: principal isoforms for multiple gene sets.

Nucleic Acids Res 2018 01;46(D1):D213-D217

Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain.

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http://dx.doi.org/10.1093/nar/gkx997DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753224PMC
January 2018

Most Alternative Isoforms Are Not Functionally Important.

Trends Biochem Sci 2017 06 5;42(6):408-410. Epub 2017 May 5.

Current address: Life Sciences Department, Barcelona Supercomputing Center (BSC-CNS), 08034 Barcelona, Spain.

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http://dx.doi.org/10.1016/j.tibs.2017.04.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6449685PMC
June 2017

Alternative Splicing May Not Be the Key to Proteome Complexity.

Trends Biochem Sci 2017 02 3;42(2):98-110. Epub 2016 Oct 3.

Structural Biology and Bioinformatics Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, 28029 Madrid, Spain; National Bioinformatics Institute (INB), Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, 28029 Madrid, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.tibs.2016.08.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6526280PMC
February 2017

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

The potential clinical impact of the release of two drafts of the human proteome.

Expert Rev Proteomics 2015 23;12(6):579-93. Epub 2015 Oct 23.

d Structural Biology and Bioinformatics Programme , Spanish National Cancer Research Centre (CNIO) , Madrid , Spain.

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http://dx.doi.org/10.1586/14789450.2015.1103186DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4732427PMC
April 2017

APPRIS WebServer and WebServices.

Nucleic Acids Res 2015 Jul 18;43(W1):W455-9. Epub 2015 May 18.

Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain

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http://dx.doi.org/10.1093/nar/gkv512DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489225PMC
July 2015

The evolutionary fate of alternatively spliced homologous exons after gene duplication.

Genome Biol Evol 2015 Apr 29;7(6):1392-403. Epub 2015 Apr 29.

Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.

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https://academic.oup.com/gbe/article-lookup/doi/10.1093/gbe/
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http://dx.doi.org/10.1093/gbe/evv076DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4494069PMC
April 2015

Alternative splicing and co-option of transposable elements: the case of TMPO/LAP2α and ZNF451 in mammals.

Bioinformatics 2015 Jul 2;31(14):2257-61. Epub 2015 Mar 2.

Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre, Madrid 28029, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btv132DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4495291PMC
July 2015

Most highly expressed protein-coding genes have a single dominant isoform.

J Proteome Res 2015 Apr 11;14(4):1880-7. Epub 2015 Mar 11.

†Unidad de Proteómica and ‡Laboratorio de Proteómica Cardiovascular, Centro Nacional de Investigaciones Cardiovasculares, 28029 Madrid, Spain.

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http://pubs.acs.org/doi/10.1021/pr501286b
Publisher Site
http://dx.doi.org/10.1021/pr501286bDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4768900PMC
April 2015

FireDB: a compendium of biological and pharmacologically relevant ligands.

Nucleic Acids Res 2014 Jan 15;42(Database issue):D267-72. Epub 2013 Nov 15.

Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre, Madrid, 28029, Spain and Spanish National Bioinformatics Institute (INB-ISCIII).

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkt1127DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965074PMC
January 2014

APPRIS: annotation of principal and alternative splice isoforms.

Nucleic Acids Res 2013 Jan 17;41(Database issue):D110-7. Epub 2012 Nov 17.

Spanish National Bioinformatics Institute (INB), Madrid 28029, Spain.

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http://dx.doi.org/10.1093/nar/gks1058DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531113PMC
January 2013

Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function.

Mol Biol Evol 2012 Sep 22;29(9):2265-83. Epub 2012 Mar 22.

Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre, Madrid, Spain.

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http://dx.doi.org/10.1093/molbev/mss100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3424414PMC
September 2012

Protein structural domains: definition and prediction.

Curr Protoc Protein Sci 2011 Nov;Chapter 2:Unit2.14

Spanish National Cancer Research Centre (CNIO)-Structural Biology and Biocomputing Programme, Madrid, Spain.

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http://dx.doi.org/10.1002/0471140864.ps0214s66DOI Listing
November 2011

firestar--advances in the prediction of functionally important residues.

Nucleic Acids Res 2011 Jul 14;39(Web Server issue):W235-41. Epub 2011 Jun 14.

Structural Computational Biology Group, Spanish National Cancer Research Centre (CNIO), c. Melchor Fernandez Almagro, 3, 28029 Madrid, Spain.

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http://dx.doi.org/10.1093/nar/gkr437DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125799PMC
July 2011

Predicted residue-residue contacts can help the scoring of 3D models.

Proteins 2010 Jun;78(8):1980-91

Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.

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http://dx.doi.org/10.1002/prot.22714DOI Listing
June 2010

Assessment of ligand binding residue predictions in CASP8.

Proteins 2009 ;77 Suppl 9:138-46

Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.

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http://dx.doi.org/10.1002/prot.22557DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204792PMC
January 2010

Assessment of domain boundary predictions and the prediction of intramolecular contacts in CASP8.

Proteins 2009 ;77 Suppl 9:196-209

Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.

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http://dx.doi.org/10.1002/prot.22554DOI Listing
January 2010

Target domain definition and classification in CASP8.

Proteins 2009 ;77 Suppl 9:10-7

Structural and Computational Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.

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http://dx.doi.org/10.1002/prot.22497DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2805415PMC
January 2010

Progress and challenges in predicting protein-protein interaction sites.

Brief Bioinform 2009 May 3;10(3):233-46. Epub 2009 Apr 3.

Centro Nacional de Biotechnolgia, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.

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http://bib.oxfordjournals.org/content/10/3/233.full.pdf
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http://bib.oxfordjournals.org/cgi/doi/10.1093/bib/bbp021
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http://dx.doi.org/10.1093/bib/bbp021DOI Listing
May 2009

Sequence-based feature prediction and annotation of proteins.

Genome Biol 2009 Feb 2;10(2):206. Epub 2009 Feb 2.

Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark.

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http://dx.doi.org/10.1186/gb-2009-10-2-206DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2688272PMC
February 2009

Proteomics studies confirm the presence of alternative protein isoforms on a large scale.

Genome Biol 2008 18;9(11):R162. Epub 2008 Nov 18.

Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), C, Melchor Fernandez Almagro, Madrid 28029, Spain.

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http://dx.doi.org/10.1186/gb-2008-9-11-r162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2614494PMC
February 2009

Determination and validation of principal gene products.

Bioinformatics 2008 Jan 15;24(1):11-7. Epub 2007 Nov 15.

Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre, Madrid, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btm547DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734078PMC
January 2008

Assessment of intramolecular contact predictions for CASP7.

Proteins 2007 ;69 Suppl 8:152-8

Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre, 3E-28029 Madrid, Spain.

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http://dx.doi.org/10.1002/prot.21637DOI Listing
January 2008

firestar--prediction of functionally important residues using structural templates and alignment reliability.

Nucleic Acids Res 2007 Jul 21;35(Web Server issue):W573-7. Epub 2007 Jun 21.

Structural Biology and Biocomputing Program, Spanish National Cancer Research Centre (CNIO) Melchor Fernández Almagro, 3, E-28029, Madrid, Spain.

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http://dx.doi.org/10.1093/nar/gkm297DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933227PMC
July 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

An analysis of the Sargasso Sea resource and the consequences for database composition.

BMC Bioinformatics 2006 Apr 19;7:213. Epub 2006 Apr 19.

Protein Design Group, CNB-CSIC, Calle Darwin, Cantoblanco 28049 Madrid, Spain.

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http://dx.doi.org/10.1186/1471-2105-7-213DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1513258PMC
April 2006

CASP6 assessment of contact prediction.

Proteins 2005 ;61 Suppl 7:214-24

Protein Design Group, Centro Nacional de Biotecnologia (CNB-CSIC), C/Darwin 3, Cantoblanco, Madrid, Spain.

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http://dx.doi.org/10.1002/prot.20739DOI Listing
May 2006

SQUARE--determining reliable regions in sequence alignments.

Bioinformatics 2004 Apr 5;20(6):974-5. Epub 2004 Feb 5.

CNB-CSIC, Calle Darwin, Cantoblanco, 28049 Madrid, Spain.

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http://dx.doi.org/10.1093/bioinformatics/bth032DOI Listing
April 2004

Predicting reliable regions in protein alignments from sequence profiles.

J Mol Biol 2003 Jul;330(4):705-18

Protein Design Group, Centro Nacional de Biotechnologia, CNB-CSIC, Cantoblanco, 28049 Madrid, Spain.

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http://dx.doi.org/10.1016/s0022-2836(03)00622-3DOI Listing
July 2003