Julian Gough

Julian Gough

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Julian Gough

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The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures.

Nucleic Acids Res 2020 Jan;48(D1):D376-D382

MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.

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http://dx.doi.org/10.1093/nar/gkz1064DOI Listing
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

Molecular Interaction Networks to Select Factors for Cell Conversion.

Methods Mol Biol 2019 ;1975:333-361

Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore.

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http://dx.doi.org/10.1007/978-1-4939-9224-9_16DOI Listing
September 2019

'Why genes in pieces?'-revisited.

Nucleic Acids Res 2019 06;47(10):4970-4973

Department of Computer Science, University of Bristol, Bristol BS8 1UB, UK.

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http://dx.doi.org/10.1093/nar/gkz284DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6547436PMC
June 2019

The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver.

Nucleic Acids Res 2019 Jan;47(D1):D490-D494

MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.

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http://dx.doi.org/10.1093/nar/gky1130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6324026PMC
January 2019

Correction to: Molecular Interaction Networks to Select Factors for Cell Conversion.

Methods Mol Biol 2019 ;1975:C1

Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore.

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http://dx.doi.org/10.1007/978-1-4939-9224-9_20DOI Listing
January 2019

A Subset of Ubiquitin-Conjugating Enzymes Is Essential for Plant Immunity.

Plant Physiol 2017 02 1;173(2):1371-1390. Epub 2016 Dec 1.

Plant Science Innovation Center and Plant Pathology Department, University of Nebraska, Lincoln, Nebraska 68583 (B.Z., L.Z.);

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http://dx.doi.org/10.1104/pp.16.01190DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5291023PMC
February 2017

Computational methods for direct cell conversion.

Cell Cycle 2016 Dec 13;15(24):3343-3354. Epub 2016 Oct 13.

a Cardiovascular and Metabolic Disorders, Duke-NUS Medical School , Singapore.

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http://dx.doi.org/10.1080/15384101.2016.1238119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5224461PMC
December 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

Did Viruses Evolve As a Distinct Supergroup from Common Ancestors of Cells?

Genome Biol Evol 2016 08 27;8(8):2474-81. Epub 2016 Aug 27.

Microbial Ecology, Department of Biology, Lund University, Sweden.

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http://dx.doi.org/10.1093/gbe/evw175DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5010908PMC
August 2016

Evolution of the Calcium-Based Intracellular Signaling System.

Genome Biol Evol 2016 07 14;8(7):2118-32. Epub 2016 Jul 14.

Department of Computer Sciences, University of Bristol, United Kingdom.

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http://dx.doi.org/10.1093/gbe/evw139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987107PMC
July 2016

Three reasons protein disorder analysis makes more sense in the light of collagen.

Protein Sci 2016 May 19;25(5):1030-6. Epub 2016 Apr 19.

Department of Computer Science, University of Bristol, Bristol, BS8 1UB, United Kingdom.

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http://dx.doi.org/10.1002/pro.2913DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4838654PMC
May 2016

Function-selective domain architecture plasticity potentials in eukaryotic genome evolution.

Biochimie 2015 Dec 15;119:269-77. Epub 2015 May 15.

Computational Genomics Group, Department of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, UK; Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK. Electronic address:

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http://dx.doi.org/10.1016/j.biochi.2015.05.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4679076PMC
December 2015

The genome of Aiptasia, a sea anemone model for coral symbiosis.

Proc Natl Acad Sci U S A 2015 Sep 31;112(38):11893-8. Epub 2015 Aug 31.

Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia;

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http://dx.doi.org/10.1073/pnas.1513318112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4586855PMC
September 2015

An integrative approach to predicting the functional effects of non-coding and coding sequence variation.

Bioinformatics 2015 May 11;31(10):1536-43. Epub 2015 Jan 11.

MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol BS8 2BN, UK, Bristol Centre for Systems Biomedicine, University of Bristol, Bristol BS8 2BN, UK, Intelligent Systems Laboratory, University of Bristol, Bristol BS8 1UB, UK, Department of Computer Science, University of Bristol, Bristol BS8 1UB, UK and Institute of Medical Genetics, Cardiff University, Cardiff CF14 4XN, UK.

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http://dx.doi.org/10.1093/bioinformatics/btv009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4426838PMC
May 2015

Splice junctions are constrained by protein disorder.

Nucleic Acids Res 2015 May 30;43(10):4814-22. Epub 2015 Apr 30.

Department of Computer Science, University of Bristol, Bristol, BS8 1UB, UK.

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http://dx.doi.org/10.1093/nar/gkv407DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4446445PMC
May 2015

A proteome quality index.

Environ Microbiol 2015 Jan 22;17(1):4-9. Epub 2014 Oct 22.

Department of Computer Science, University of Bristol, Bristol, UK; Bristol Centre for Complexity Sciences, University of Bristol, Bristol, UK.

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http://dx.doi.org/10.1111/1462-2920.12622DOI Listing
January 2015

The SUPERFAMILY 1.75 database in 2014: a doubling of data.

Nucleic Acids Res 2015 Jan 20;43(Database issue):D227-33. Epub 2014 Nov 20.

Computer Science, University of Bristol, Bristol, BS8 1UB, UK.

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http://dx.doi.org/10.1093/nar/gku1041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383889PMC
January 2015

The 'dnet' approach promotes emerging research on cancer patient survival.

Genome Med 2014 26;6(8):64. Epub 2014 Aug 26.

Computational Genomics Group, Department of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol, BS8 1UB UK.

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http://dx.doi.org/10.1186/s13073-014-0064-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4160547PMC
September 2014

Structured and disordered facets of the GPCR fold.

Curr Opin Struct Biol 2014 Aug 3;27:129-37. Epub 2014 Sep 3.

MRC Laboratory of Molecular Biology, Cambridge, United Kingdom. Electronic address:

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http://dx.doi.org/10.1016/j.sbi.2014.08.002DOI Listing
August 2014

The evolution of human cells in terms of protein innovation.

Mol Biol Evol 2014 Jun 1;31(6):1364-74. Epub 2014 Apr 1.

Department of Computer Science, University of Bristol, Bristol, United KingdomMedical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London, United Kingdom

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http://dx.doi.org/10.1093/molbev/mst139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4032124PMC
June 2014

Ranking non-synonymous single nucleotide polymorphisms based on disease concepts.

Hum Genomics 2014 Jun 30;8:11. Epub 2014 Jun 30.

Bristol Centre for Systems Biomedicine and MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.

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http://dx.doi.org/10.1186/1479-7364-8-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4083756PMC
June 2014

A promoter-level mammalian expression atlas.

Authors:
Alistair R R Forrest Hideya Kawaji Michael Rehli J Kenneth Baillie Michiel J L de Hoon Vanja Haberle Timo Lassmann Ivan V Kulakovskiy Marina Lizio Masayoshi Itoh Robin Andersson Christopher J Mungall Terrence F Meehan Sebastian Schmeier Nicolas Bertin Mette Jørgensen Emmanuel Dimont Erik Arner Christian Schmidl Ulf Schaefer Yulia A Medvedeva Charles Plessy Morana Vitezic Jessica Severin Colin A Semple Yuri Ishizu Robert S Young Margherita Francescatto Intikhab Alam Davide Albanese Gabriel M Altschuler Takahiro Arakawa John A C Archer Peter Arner Magda Babina Sarah Rennie Piotr J Balwierz Anthony G Beckhouse Swati Pradhan-Bhatt Judith A Blake Antje Blumenthal Beatrice Bodega Alessandro Bonetti James Briggs Frank Brombacher A Maxwell Burroughs Andrea Califano Carlo V Cannistraci Daniel Carbajo Yun Chen Marco Chierici Yari Ciani Hans C Clevers Emiliano Dalla Carrie A Davis Michael Detmar Alexander D Diehl Taeko Dohi Finn Drabløs Albert S B Edge Matthias Edinger Karl Ekwall Mitsuhiro Endoh Hideki Enomoto Michela Fagiolini Lynsey Fairbairn Hai Fang Mary C Farach-Carson Geoffrey J Faulkner Alexander V Favorov Malcolm E Fisher Martin C Frith Rie Fujita Shiro Fukuda Cesare Furlanello Masaaki Furino Jun-ichi Furusawa Teunis B Geijtenbeek Andrew P Gibson Thomas Gingeras Daniel Goldowitz Julian Gough Sven Guhl Reto Guler Stefano Gustincich Thomas J Ha Masahide Hamaguchi Mitsuko Hara Matthias Harbers Jayson Harshbarger Akira Hasegawa Yuki Hasegawa Takehiro Hashimoto Meenhard Herlyn Kelly J Hitchens Shannan J Ho Sui Oliver M Hofmann Ilka Hoof Furni Hori Lukasz Huminiecki Kei Iida Tomokatsu Ikawa Boris R Jankovic Hui Jia Anagha Joshi Giuseppe Jurman Bogumil Kaczkowski Chieko Kai Kaoru Kaida Ai Kaiho Kazuhiro Kajiyama Mutsumi Kanamori-Katayama Artem S Kasianov Takeya Kasukawa Shintaro Katayama Sachi Kato Shuji Kawaguchi Hiroshi Kawamoto Yuki I Kawamura Tsugumi Kawashima Judith S Kempfle Tony J Kenna Juha Kere Levon M Khachigian Toshio Kitamura S Peter Klinken Alan J Knox Miki Kojima Soichi Kojima Naoto Kondo Haruhiko Koseki Shigeo Koyasu Sarah Krampitz Atsutaka Kubosaki Andrew T Kwon Jeroen F J Laros Weonju Lee Andreas Lennartsson Kang Li Berit Lilje Leonard Lipovich Alan Mackay-Sim Ri-ichiroh Manabe Jessica C Mar Benoit Marchand Anthony Mathelier Niklas Mejhert Alison Meynert Yosuke Mizuno David A de Lima Morais Hiromasa Morikawa Mitsuru Morimoto Kazuyo Moro Efthymios Motakis Hozumi Motohashi Christine L Mummery Mitsuyoshi Murata Sayaka Nagao-Sato Yutaka Nakachi Fumio Nakahara Toshiyuki Nakamura Yukio Nakamura Kenichi Nakazato Erik van Nimwegen Noriko Ninomiya Hiromi Nishiyori Shohei Noma Shohei Noma Tadasuke Noazaki Soichi Ogishima Naganari Ohkura Hiroko Ohimiya Hiroshi Ohno Mitsuhiro Ohshima Mariko Okada-Hatakeyama Yasushi Okazaki Valerio Orlando Dmitry A Ovchinnikov Arnab Pain Robert Passier Margaret Patrikakis Helena Persson Silvano Piazza James G D Prendergast Owen J L Rackham Jordan A Ramilowski Mamoon Rashid Timothy Ravasi Patrizia Rizzu Marco Roncador Sugata Roy Morten B Rye Eri Saijyo Antti Sajantila Akiko Saka Shimon Sakaguchi Mizuho Sakai Hiroki Sato Suzana Savvi Alka Saxena Claudio Schneider Erik A Schultes Gundula G Schulze-Tanzil Anita Schwegmann Thierry Sengstag Guojun Sheng Hisashi Shimoji Yishai Shimoni Jay W Shin Christophe Simon Daisuke Sugiyama Takaai Sugiyama Masanori Suzuki Naoko Suzuki Rolf K Swoboda Peter A C 't Hoen Michihira Tagami Naoko Takahashi Jun Takai Hiroshi Tanaka Hideki Tatsukawa Zuotian Tatum Mark Thompson Hiroo Toyodo Tetsuro Toyoda Elvind Valen Marc van de Wetering Linda M van den Berg Roberto Verado Dipti Vijayan Ilya E Vorontsov Wyeth W Wasserman Shoko Watanabe Christine A Wells Louise N Winteringham Ernst Wolvetang Emily J Wood Yoko Yamaguchi Masayuki Yamamoto Misako Yoneda Yohei Yonekura Shigehiro Yoshida Susan E Zabierowski Peter G Zhang Xiaobei Zhao Silvia Zucchelli Kim M Summers Harukazu Suzuki Carsten O Daub Jun Kawai Peter Heutink Winston Hide Tom C Freeman Boris Lenhard Vladimir B Bajic Martin S Taylor Vsevolod J Makeev Albin Sandelin David A Hume Piero Carninci Yoshihide Hayashizaki

Nature 2014 Mar;507(7493):462-70

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http://dx.doi.org/10.1038/nature13182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4529748PMC
March 2014

supraHex: an R/Bioconductor package for tabular omics data analysis using a supra-hexagonal map.

Biochem Biophys Res Commun 2014 Jan 2;443(1):285-9. Epub 2013 Dec 2.

Computational Genomics Group, Department of Computer Science, University of Bristol, Merchant Venturers Building, Bristol BS8 1UB, UK.

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http://dx.doi.org/10.1016/j.bbrc.2013.11.103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3905187PMC
January 2014

A disease-drug-phenotype matrix inferred by walking on a functional domain network.

Mol Biosyst 2013 Jul 5;9(7):1686-96. Epub 2013 Mar 5.

Department of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, UK.

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http://dx.doi.org/10.1039/c3mb25495jDOI Listing
July 2013

A domain-centric solution to functional genomics via dcGO Predictor.

BMC Bioinformatics 2013 28;14 Suppl 3:S9. Epub 2013 Feb 28.

Department of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, UK.

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http://dx.doi.org/10.1186/1471-2105-14-S3-S9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3584936PMC
July 2013

Predicting the functional consequences of cancer-associated amino acid substitutions.

Bioinformatics 2013 Jun 25;29(12):1504-10. Epub 2013 Apr 25.

Bristol Centre for Systems Biomedicine and MRC CAiTE Centre, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK.

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http://dx.doi.org/10.1093/bioinformatics/btt182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3673218PMC
June 2013

Sequences and topology: disorder, modularity, and post/pre translation modification.

Curr Opin Struct Biol 2013 Jun 28;23(3):417-9. Epub 2013 May 28.

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http://dx.doi.org/10.1016/j.sbi.2013.05.001DOI Listing
June 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

Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models.

Hum Mutat 2013 Jan 2;34(1):57-65. Epub 2012 Nov 2.

Bristol Centre for Systems Biomedicine and MRC CAiTE Centre, School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom.

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http://dx.doi.org/10.1002/humu.22225DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3558800PMC
January 2013

DcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more.

Nucleic Acids Res 2013 Jan 17;41(Database issue):D536-44. Epub 2012 Nov 17.

Department of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, UK.

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http://dx.doi.org/10.1093/nar/gks1080DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531119PMC
January 2013

D²P²: database of disordered protein predictions.

Nucleic Acids Res 2013 Jan 29;41(Database issue):D508-16. Epub 2012 Nov 29.

Department of Computer Science, University of Bristol, Bristol BS8 1UB, UK.

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http://dx.doi.org/10.1093/nar/gks1226DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531159PMC
January 2013

Evolutionarily consistent families in SCOP: sequence, structure and function.

BMC Struct Biol 2012 Oct 18;12:27. Epub 2012 Oct 18.

Department of Computer Science, University of Bristol, The Merchant Venturers Building, Room 3,16, Woodland Road, Bristol, UK.

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http://bmcstructbiol.biomedcentral.com/articles/10.1186/1472
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http://dx.doi.org/10.1186/1472-6807-12-27DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3495643PMC
October 2012

Are viruses a source of new protein folds for organisms? - Virosphere structure space and evolution.

Bioessays 2011 Aug 1;33(8):626-35. Epub 2011 Jun 1.

Estonian Biocentre, Tartu, Estonia.

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http://doi.wiley.com/10.1002/bies.201000126
Publisher Site
http://dx.doi.org/10.1002/bies.201000126DOI Listing
August 2011

Sequences and topology: intrinsic disorder in the evolving universe of protein structure.

Curr Opin Struct Biol 2011 Jun 29;21(3):379-81. Epub 2011 Apr 29.

Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.

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http://dx.doi.org/10.1016/j.sbi.2011.04.002DOI Listing
June 2011

SUPERFAMILY 1.75 including a domain-centric gene ontology method.

Nucleic Acids Res 2011 Jan 9;39(Database issue):D427-34. Epub 2010 Nov 9.

Department of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, UK.

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http://dx.doi.org/10.1093/nar/gkq1130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013712PMC
January 2011

The evolution and structure prediction of coiled coils across all genomes.

J Mol Biol 2010 Oct 9;403(3):480-93. Epub 2010 Sep 9.

Department of Computer Science, University of Bristol, Bristol BS8 1UB, UK.

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http://dx.doi.org/10.1016/j.jmb.2010.08.032DOI Listing
October 2010

Improving protein secondary structure prediction using a simple k-mer model.

Bioinformatics 2010 Mar 3;26(5):596-602. Epub 2010 Feb 3.

Department of Computer Science, University of Bristol, Woodland Road, Bristol BS8 1UB, UK.

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http://dx.doi.org/10.1093/bioinformatics/btq020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2828123PMC
March 2010

TreeVector: scalable, interactive, phylogenetic trees for the web.

PLoS One 2010 Jan 28;5(1):e8934. Epub 2010 Jan 28.

Computer Science Department, University of Bristol, Bristol, United Kingdom.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812488PMC
January 2010

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

Authors:
Harukazu Suzuki Alistair R R Forrest Erik van Nimwegen Carsten O Daub Piotr J Balwierz Katharine M Irvine Timo Lassmann Timothy Ravasi Yuki Hasegawa Michiel J L de Hoon Shintaro Katayama Kate Schroder Piero Carninci Yasuhiro Tomaru Mutsumi Kanamori-Katayama Atsutaka Kubosaki Altuna Akalin Yoshinari Ando Erik Arner Maki Asada Hiroshi Asahara Timothy Bailey Vladimir B Bajic Denis Bauer Anthony G Beckhouse Nicolas Bertin Johan Björkegren Frank Brombacher Erika Bulger Alistair M Chalk Joe Chiba Nicole Cloonan Adam Dawe Josee Dostie Pär G Engström Magbubah Essack Geoffrey J Faulkner J Lynn Fink David Fredman Ko Fujimori Masaaki Furuno Takashi Gojobori Julian Gough Sean M Grimmond Mika Gustafsson Megumi Hashimoto Takehiro Hashimoto Mariko Hatakeyama Susanne Heinzel Winston Hide Oliver Hofmann Michael Hörnquist Lukasz Huminiecki Kazuho Ikeo Naoko Imamoto Satoshi Inoue Yusuke Inoue Ryoko Ishihara Takao Iwayanagi Anders Jacobsen Mandeep Kaur Hideya Kawaji Markus C Kerr Ryuichiro Kimura Syuhei Kimura Yasumasa Kimura Hiroaki Kitano Hisashi Koga Toshio Kojima Shinji Kondo Takeshi Konno Anders Krogh Adele Kruger Ajit Kumar Boris Lenhard Andreas Lennartsson Morten Lindow Marina Lizio Cameron Macpherson Norihiro Maeda Christopher A Maher Monique Maqungo Jessica Mar Nicholas A Matigian Hideo Matsuda John S Mattick Stuart Meier Sei Miyamoto Etsuko Miyamoto-Sato Kazuhiko Nakabayashi Yutaka Nakachi Mika Nakano Sanne Nygaard Toshitsugu Okayama Yasushi Okazaki Haruka Okuda-Yabukami Valerio Orlando Jun Otomo Mikhail Pachkov Nikolai Petrovsky Charles Plessy John Quackenbush Aleksandar Radovanovic Michael Rehli Rintaro Saito Albin Sandelin Sebastian Schmeier Christian Schönbach Ariel S Schwartz Colin A Semple Miho Sera Jessica Severin Katsuhiko Shirahige Cas Simons George St Laurent Masanori Suzuki Takahiro Suzuki Matthew J Sweet Ryan J Taft Shizu Takeda Yoichi Takenaka Kai Tan Martin S Taylor Rohan D Teasdale Jesper Tegnér Sarah Teichmann Eivind Valen Claes Wahlestedt Kazunori Waki Andrew Waterhouse Christine A Wells Ole Winther Linda Wu Kazumi Yamaguchi Hiroshi Yanagawa Jun Yasuda Mihaela Zavolan David A Hume Takahiro Arakawa Shiro Fukuda Kengo Imamura Chikatoshi Kai Ai Kaiho Tsugumi Kawashima Chika Kawazu Yayoi Kitazume Miki Kojima Hisashi Miura Kayoko Murakami Mitsuyoshi Murata Noriko Ninomiya Hiromi Nishiyori Shohei Noma Chihiro Ogawa Takuma Sano Christophe Simon Michihira Tagami Yukari Takahashi Jun Kawai Yoshihide Hayashizaki

Nat Genet 2009 May 19;41(5):553-62. Epub 2009 Apr 19.

RIKEN Omics Science Center, RIKEN Yokohama Institute, Kanagawa, Japan.

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http://dx.doi.org/10.1038/ng.375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6711855PMC
May 2009

Genomic and structural aspects of protein evolution.

Biochem J 2009 Apr;419(1):15-28

MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.

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http://dx.doi.org/10.1042/BJ20090122DOI Listing
April 2009

SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny.

Nucleic Acids Res 2009 Jan 26;37(Database issue):D380-6. Epub 2008 Nov 26.

MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, Department of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, UK.

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http://dx.doi.org/10.1093/nar/gkn762DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686452PMC
January 2009

Expression and in silico structural analysis of a rice (Oryza sativa) hemoglobin 5.

Plant Physiol Biochem 2008 Oct 24;46(10):855-9. Epub 2008 May 24.

Laboratorio de Biofísica y Biología Molecular, Facultad de Ciencias, Universidad Autónoma del Estado de Morelos, Avenida Universidad 1001, Colonia Chamilpa, 62210 Cuernavaca, Morelos, México.

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http://dx.doi.org/10.1016/j.plaphy.2008.05.004DOI Listing
October 2008

Classification, expression pattern, and E3 ligase activity assay of rice U-box-containing proteins.

Mol Plant 2008 Sep;1(5):800-15

Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA.

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http://dx.doi.org/10.1093/mp/ssn044DOI Listing
September 2008

The SUPERFAMILY database in 2007: families and functions.

Nucleic Acids Res 2007 Jan 10;35(Database issue):D308-13. Epub 2006 Nov 10.

MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.

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http://dx.doi.org/10.1093/nar/gkl910DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1669749PMC
January 2007

Genomic scale sub-family assignment of protein domains.

Authors:
Julian Gough

Nucleic Acids Res 2006 28;34(13):3625-33. Epub 2006 Jul 28.

Unite de Bioinformatique Structurale, Institut Pasteur, 25-28 Rue du Docteur Roux, 75724 Paris Cedex 15, Paris, France.

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http://dx.doi.org/10.1093/nar/gkl484DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1540727PMC
August 2006

A database of bacterial lipoproteins (DOLOP) with functional assignments to predicted lipoproteins.

J Bacteriol 2006 Apr;188(8):2761-73

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.

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http://dx.doi.org/10.1128/JB.188.8.2761-2773.2006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1446993PMC
April 2006

A phylogenomic profile of globins.

BMC Evol Biol 2006 Apr 7;6:31. Epub 2006 Apr 7.

Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI 48201, USA.

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http://dx.doi.org/10.1186/1471-2148-6-31DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1457004PMC
April 2006

Distinguishing protein-coding from non-coding RNAs through support vector machines.

PLoS Genet 2006 Apr 28;2(4):e29. Epub 2006 Apr 28.

Columbia University Bioinformatics Center, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.0020029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449884PMC
April 2006

Three globin lineages belonging to two structural classes in genomes from the three kingdoms of life.

Proc Natl Acad Sci U S A 2005 Aug 1;102(32):11385-9. Epub 2005 Aug 1.

Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI 48201, USA.

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http://dx.doi.org/10.1073/pnas.0502103102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1183549PMC
August 2005

Convergent evolution of domain architectures (is rare).

Authors:
Julian Gough

Bioinformatics 2005 Apr 7;21(8):1464-71. Epub 2004 Dec 7.

RIKEN Genomic Sciences Centre, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.

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http://dx.doi.org/10.1093/bioinformatics/bti204DOI Listing
April 2005

The linked conservation of structure and function in a family of high diversity: the monomeric cupredoxins.

Structure 2004 Jun;12(6):917-25

RIKEN Genomic Sciences Centre, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.

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http://linkinghub.elsevier.com/retrieve/pii/S096921260400158
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http://dx.doi.org/10.1016/j.str.2004.03.029DOI Listing
June 2004

Supra-domains: evolutionary units larger than single protein domains.

J Mol Biol 2004 Feb;336(3):809-23

MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, UK.

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http://dx.doi.org/10.1016/j.jmb.2003.12.026DOI Listing
February 2004

The SUPERFAMILY database in 2004: additions and improvements.

Nucleic Acids Res 2004 Jan;32(Database issue):D235-9

MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.

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http://dx.doi.org/10.1093/nar/gkh117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC308851PMC
January 2004

Evolution of the protein repertoire.

Science 2003 Jun;300(5626):1701-3

Structural Studies Division, MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.

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http://dx.doi.org/10.1126/science.1085371DOI Listing
June 2003

Mouse proteome analysis.

Genome Res 2003 Jun;13(6B):1335-44

EMBL Outstation-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK.

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http://dx.doi.org/10.1101/gr.978703DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403658PMC
June 2003

Development and evaluation of an automated annotation pipeline and cDNA annotation system.

Genome Res 2003 Jun;13(6B):1542-51

Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

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http://dx.doi.org/10.1101/gr.992803DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403710PMC
June 2003

The SUPERFAMILY database in structural genomics.

Authors:
Julian Gough

Acta Crystallogr D Biol Crystallogr 2002 Nov 21;58(Pt 11):1897-900. Epub 2002 Oct 21.

MRC Laboratory of Molecular Biology, Hills Road, cambridge CB2 2QH, England.

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http://dx.doi.org/10.1107/s0907444902015160DOI Listing
November 2002

A comparison of profile hidden Markov model procedures for remote homology detection.

Nucleic Acids Res 2002 Oct;30(19):4321-8

MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC140544PMC
http://dx.doi.org/10.1093/nar/gkf544DOI Listing
October 2002

Proteins with class alpha/beta fold have high-level participation in fusion events.

J Mol Biol 2002 Jul;320(4):713-9

Institute of Bioinformatics, Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing 100084, People's Republic of China.

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http://dx.doi.org/10.1016/s0022-2836(02)00467-9DOI Listing
July 2002

Comparison of the small molecule metabolic enzymes of Escherichia coli and Saccharomyces cerevisiae.

Genome Res 2002 Jun;12(6):916-29

Department of Crystallography, Birkbeck College, London WC1E 7HX, United Kingdom.

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http://dx.doi.org/10.1101/gr.228002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC313875PMC
June 2002

SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments.

Nucleic Acids Res 2002 Jan;30(1):268-72

MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC99153PMC
http://dx.doi.org/10.1093/nar/30.1.268DOI Listing
January 2002