Alex Bateman

发表

Pfam 10 years on: 10 000 families and still growing

Robert D. Finn, Stephen John Sammut, Alex Bateman, 2008, Briefings Bioinform..

Filling out the structural map of the NTF2-like superfamily

Alex Bateman, Alexey G. Murzin, Ruth Y. Eberhardt, 2013, BMC Bioinformatics.

LUD, a new protein domain associated with lactate utilization

Neil D. Rawlings, Alex Bateman, Marco Punta, 2013, BMC Bioinformatics.

MEROPS: the database of proteolytic enzymes, their substrates and inhibitors

Alex Bateman, Neil D Rawlings, Alan J Barrett, 2011, Nucleic Acids Res..

Rfam 12.0: updates to the RNA families database

Robert D. Finn, Sean R. Eddy, Alex Bateman, 2014, Nucleic Acids Res..

The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database

Neil D. Rawlings, Alan J. Barrett, Robert D. Finn, 2017, Nucleic Acids Res..

Rfam: updates to the RNA families database

Robert D. Finn, Sean R. Eddy, Alex Bateman, 2008, Nucleic Acids Res..

The SGS3 protein involved in PTGS finds a family

Alex Bateman, A. Bateman, 2002, BMC Bioinformatics.

Crowdsourcing Protein Family Database Curation

Alex Bateman, Maria Liakata, Matt Jeffryes, 2016, ICBO/BioCreative.

Reuse of structural domain–domain interactions in protein networks

Alex Bateman, Benjamin Schuster-Böckler, 2007, BMC Bioinformatics.

Rfam: Wikipedia, clans and the “decimal” release

Robert D. Finn, Sean R. Eddy, Alex Bateman, 2010, Nucleic Acids Res..

Rapid identification of novel protein families using similarity searches

Alex Bateman, Matt Jeffryes, A. Bateman, 2018, F1000Research.

Software patents in Bioinformatics

Alfonso Valencia, Alex Bateman, 2006, Bioinform..

The challenge of increasing Pfam coverage of the human proteome

Robert D. Finn, Alex Bateman, Marco Punta, 2013, Database J. Biol. Databases Curation.

The Pfam protein families database

Robert D. Finn, Sean R. Eddy, Stephen John Sammut, 2007, Nucleic Acids Res..

Making your database available through Wikipedia: the pros and cons

Robert D. Finn, Alex Bateman, Paul P. Gardner, 2011, Nucleic Acids Res..

InterPro : An integrated documentation resource for protein families , domains and functional sites The InterPro Consortium :

Alex Bateman, Rolf Apweiler, Beate Marx, 2005 .

Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila

Robert D. Finn, Alex Bateman, Alexey G. Murzin, 2013, BMC Bioinformatics.

Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families

Robert D. Finn, Elena Rivas, Sean R. Eddy, 2017, Nucleic Acids Res..

Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins

Robert D. Finn, Sean R. Eddy, Alex Bateman, 1999, Nucleic Acids Res..

Example domain architectures of PPC-containing proteins

Alex Bateman, Stephen D. Bentley, Corin Yeats, 2011 .

HOMSTRAD: adding sequence information to structure-based alignments of homologous protein families

Jiye Shi, Alex Bateman, Kenji Mizuguchi, 2001, Bioinform..

Modelling structural rearrangements in proteins using Euclidean distance matrices

Alex Bateman, Aleix Lafita, A. Bateman, 2020 .

Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors

Robert D. Finn, Alex Bateman, Johannes Söding, 2008, Bioinform..

TreeFam v9: a new website, more species and orthology-on-the-fly

Alex Bateman, Miguel Pignatelli, Matthieu Muffato, 2013, Nucleic Acids Res..

Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat

Neil D. Rawlings, Robert D. Finn, Alex Bateman, 2015, Database J. Biol. Databases Curation.

HMM-based databases in InterPro

Alex Bateman, Daniel H. Haft, A. Bateman, 2002, Briefings Bioinform..

InterPro: the integrative protein signature database

Robert D. Finn, Cathy H. Wu, Alex Bateman, 2008, Nucleic Acids Res..

A comparison of Pfam and MEROPS: Two databases, one comprehensive, and one specialised.

Neil D. Rawlings, Alan J. Barrett, Alex Bateman, 2003, BMC Bioinformatics.

The HMMER Web Server for Protein Sequence Similarity Search

Alex Bateman, Matt Jeffryes, Ananth Prakash, 2017, Current protocols in bioinformatics.

InterPro, progress and status in 2005

Cathy H. Wu, Alex Bateman, Rolf Apweiler, 2004, Nucleic Acids Res..

New developments in the InterPro database

Robert D. Finn, Robert Petryszak, Cathy H. Wu, 2007, Nucleic Acids Res..

iPfam: visualization of protein?Cprotein interactions in PDB at domain and amino acid resolutions

Robert D. Finn, Alex Bateman, Mhairi Marshall, 2005, Bioinform..

MEROPS: the peptidase database

Neil D. Rawlings, Alan J. Barrett, Alex Bateman, 2009, Nucleic Acids Res..

MEROPS: the database of proteolytic enzymes, their substrates and inhibitors

Neil D. Rawlings, Alan J. Barrett, Alex Bateman, 2013, Nucleic Acids Res..

RNAcentral: an international database of ncRNA sequences

Hsien-Da Huang, Alex Bateman, Janusz M Bujnicki, 2014, Nucleic Acids Res..

iPfam: a database of protein family and domain interactions found in the Protein Data Bank

Robert D. Finn, Alex Bateman, Jody Clements, 2013, Nucleic Acids Res..

QuickTree: building huge Neighbour-Joining trees of protein sequences

Alex Bateman, Richard Durbin, Kevin L. Howe, 2002, Bioinform..

Bioinformatics - The new home for protein sequence motifs

Alex Bateman, 2006, Bioinform..

Bioimage informatics: a new category in Bioinformatics

Alfonso Valencia, Alex Bateman, Hanchuan Peng, 2012, Bioinform..

The Hotdog fold: wrapping up a superfamily of thioesterases and dehydratases

Alex Bateman, Shane C. Dillon, A. Bateman, 2004, BMC Bioinformatics.

The Pfam protein families database in 2019

Silvio C. E. Tosatto, Robert D. Finn, Sean R. Eddy, 2018, Nucleic Acids Res..

HMMER web server: 2015 update

Robert D. Finn, Sean R. Eddy, Alex Bateman, 2015, Nucleic Acids Res..

Bioinformatics for next generation sequencing.

Alex Bateman, John Quackenbush, John Quackenbush, 2009, Bioinformatics.

The rise and fall of supervised machine learning techniques

Alex Bateman, Lars Juhl Jensen, L. Jensen, 2011, Bioinform..

Ten Simple Rules for Editing Wikipedia

Alex Bateman, Paul P. Gardner, Magnus Manske, 2010, PLoS Comput. Biol..

Databases, data tombs and dust in the wind

Alex Bateman, Jonathan D. Wren, A. Bateman, 2008, Bioinform..

Predicting active site residue annotations in the Pfam database

Robert D. Finn, Alex Bateman, Jaina Mistry, 2007, BMC Bioinformatics.

Enhanced protein domain discovery using taxonomy

Alex Bateman, Lachlan James M. Coin, Richard Durbin, 2004, BMC Bioinformatics.

Structure and computational analysis of a novel protein with metallopeptidase-like and circularly permuted winged-helix-turn-helix domains reveals a possible role in modified polysaccharide biosynthesis

Neil D. Rawlings, Robert D. Finn, Alex Bateman, 2014, BMC Bioinformatics.

Ten Simple Rules for Chairing a Scientific Session

Philip E. Bourne, Alex Bateman, A. Bateman, 2009, PLoS Comput. Biol..

The G5 domain: a potential N-acetylglucosamine recognition domain involved in biofilm formation

Alex Bateman, Corin Yeats, Matthew T. G. Holden, 2005, Bioinform..

New Leadership for Bioinformatics

Alfonso Valencia, Alex Bateman, A. Valencia, 2004, Bioinform..

Curators of the world unite: the International Society of Biocuration

Alex Bateman, A. Bateman, 2010, Bioinform..

Non‐Coding RNA Analysis Using the Rfam Database

Alex Bateman, Eric P. Nawrocki, Anton I. Petrov, 2018, Current protocols in bioinformatics.

Rfam: annotating non-coding RNAs in complete genomes

Sean R. Eddy, Alex Bateman, Sam Griffiths-Jones, 2004, Nucleic Acids Res..

The TROVE module: A common element in Telomerase, Ro and Vault ribonucleoproteins

Alex Bateman, Valerie A. Kickhoefer, V. Kickhoefer, 2003, BMC Bioinformatics.

Pfam: clans, web tools and services

Robert D. Finn, Sean R. Eddy, Alex Bateman, 2005, Nucleic Acids Res..

InterPro: An Integrated Documentation Resource for Protein Families, Domains and Functional Sites

Alex Bateman, Rolf Apweiler, Henning Hermjakob, 2002, Briefings Bioinform..

Computer Tools and Algorithms for Origami Tessellation Design

Alex Bateman, 2002 .

SCOOP: a simple method for identification of novel protein superfamily relationships

Robert D. Finn, Alex Bateman, R. Finn, 2007, Bioinform..

Exploring Non‐Coding RNAs in RNAcentral

Alex Bateman, Anton I. Petrov, Robert D Finn, 2020, Current protocols in bioinformatics.

Pfam: multiple sequence alignments and HMM-profiles of protein domains

Sean R. Eddy, Alex Bateman, Ewan Birney, 1998, Nucleic Acids Res..

Increasing the Impact of Bioinformatics

Alfonso Valencia, Alex Bateman, A. Valencia, 2005, Bioinform..

Gene Unprediction with Spurio: A tool to identify spurious protein sequences

Alex Bateman, Matt Jeffryes, Wolfram Höps, 2018, F1000Research.

Cloud computing

Alex Bateman, Matt Wood, 2009, Bioinform..

ISCB Computational Biology Wikipedia Competition

Burkhard Rost, Alex Bateman, Predrag Radivojac, 2013, PLoS Comput. Biol..

TADOSS: computational estimation of tandem domain swap stability

Alex Bateman, Robert B Best, Aleix Lafita, 2018, Bioinform..

The InterPro database, an integrated documentation resource for protein families, domains and functional sites

Alex Bateman, Rolf Apweiler, Beate Marx, 2001, Nucleic Acids Res..

The InterPro Database, 2003 brings increased coverage and new features

Alex Bateman, Rolf Apweiler, Nicola J. Mulder, 2003, Nucleic Acids Res..

InterPro in 2011: new developments in the family and domain prediction database

Robert D. Finn, Matthew Fraser, Cathy H. Wu, 2011, Nucleic acids research.

An update from the Bioinformatics Editors

Alfonso Valencia, Alex Bateman, A. Valencia, 2005, Bioinform..

Rfam 11.0: 10 years of RNA families

Sean R. Eddy, Alex Bateman, Ruth Y. Eberhardt, 2012, Nucleic Acids Res..

UniProt: the universal protein knowledgebase in 2021

Peter B. McGarvey, Cathy H. Wu, Alex Bateman, 2020, Nucleic Acids Res..

RNAcentral 2021: secondary structure integration, improved sequence search and new member databases

Robert D. Finn, Alex Bateman, Artemis G. Hatzigeorgiou, 2020, Nucleic Acids Res..

The Gene Ontology resource: enriching a GOld mine

Anushya Muruganujan, Cathy H. Wu, Alex Bateman, 2020, Nucleic Acids Res..

Outline structures for the extracellular domains of the fibroblast growth factor receptors

Alex Bateman, Cyrus Chothia, C. Chothia, 1995, Nature Structural Biology.

RNAcentral: a hub of information for non-coding RNA sequences

Alex Bateman, Guy Cochrane, Janusz M Bujnicki, 2018, Nucleic Acids Res..

The yeast noncoding RNA interaction network

Alex Bateman, Sandra Orchard, Simona Panni, 2017, RNA.

Alternative splicing of intrinsically disordered regions and rewiring of protein interactions.

A Keith Dunker, Alex Bateman, Monika Fuxreiter, 2013, Current opinion in structural biology.

A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium

Alex Bateman, Paul P. Gardner, Lars Barquist, 2013, Nucleic acids research.

The ENTH domain

Alex Bateman, Ezequiel Panepucci, Axel T Brunger, 2002, FEBS letters.

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research

Robert D. Finn, Alex Bateman, Niko Beerenwinkel, 2020, Briefings Bioinform..

Corrigendum: ''RNAcentral : a hub of information for non-coding RNA sequences'' [Nucleic acids research, 47 (2019) D1, p. D221-D229]

Robert D. Finn, James R. Cole, Alex Bateman, 2019 .

On expert curation and sustainability: UniProtKB/Swiss-Prot as a case study

Zhiyong Lu, Alex Bateman, Cecilia N. Arighi, 2016, bioRxiv.

Creating a specialist protein resource network

Neil D. Rawlings, Alex Bateman, Bernard Henrissat, 2015 .

Quantifying the mechanisms of domain gain in animal proteins

Alex Bateman, Adam Frankish, Marija Buljan, 2010, Genome Biology.

Large-scale screening for novel low-affinity extracellular protein interactions.

Alex Bateman, A. Bateman, Gavin J. Wright, 2008, Genome research.

Tissue-Specific Splicing of Disordered Segments that Embed Binding Motifs Rewires Protein Interaction Networks

Alex Bateman, M. Madan Babu, Monika Fuxreiter, 2012, Molecular cell.

The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest

Jeroen Krijgsveld, Alex Bateman, Matthias W. Hentze, 2019, Cell.

The PASTA domain: a β-lactam-binding domain

Robert D. Finn, Alex Bateman, Corin Yeats, 2002 .

New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor

Alex Bateman, Corin Yeats, A. Bateman, 2003, BMC Microbiology.

The PASTA domain: a beta-lactam-binding domain.

Alex Bateman, Corin Yeats, Robert D Finn, 2002, Trends in biochemical sciences.

RNAcentral: a comprehensive database of non-coding RNA sequences

Alex Bateman, Eva Huala, Guy Cochrane, 2016, Nucleic acids research.

SnoPatrol: how many snoRNA genes are there?

Alex Bateman, Paul P Gardner, A. Bateman, 2010, Journal of biology.

Patterns of database citation in articles and patents indicate long-term scientific and industry value of biological data resources

George Papadatos, Alex Bateman, Sameer Velankar, 2016, F1000Research.

DUFs: families in search of function

Robert D. Finn, Alex Bateman, Penny Coggill, 2010, Acta crystallographica. Section F, Structural biology and crystallization communications.

RNIE: genome-wide prediction of bacterial intrinsic terminators

Alex Bateman, Zasha Weinberg, Paul P. Gardner, 2011, Nucleic acids research.

The Systematic Functional Analysis of Plasmodium Protein Kinases Identifies Essential Regulators of Mosquito Transmission

Alex Bateman, Ulrike Böhme, Oliver Billker, 2010, Cell host & microbe.

The CHAP domain: a large family of amidases including GSP amidase and peptidoglycan hydrolases.

Alex Bateman, Neil D Rawlings, A. Bateman, 2003, Trends in biochemical sciences.