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List of works by Alex Bateman

A comparison of Pfam and MEROPS: two databases, one comprehensive, and one specialised ⬇️

scientific article published on May 9, 2003

A member of the immunoglobulin superfamily in bacteriophage T4

scientific article published in 1997

A structural biology community assessment of AlphaFold2 applications

scientific article published in 2022

A subgroup of light-driven sodium pumps with an additional Schiff base counterion

scientific article published in 2024

Acetylation of Surface Carbohydrates in Bacterial Pathogens Requires Coordinated Action of a Two-Domain Membrane-Bound Acyltransferase

scientific article published on 25 August 2020

Alternative splicing of intrinsically disordered regions and rewiring of protein interactions

scientific article published on 22 May 2013

An introduction to hidden Markov models

scientific article published on June 2007

An update from the Bioinformatics Editors

scientific article published on 6 December 2005

AntiFam: a tool to help identify spurious ORFs in protein annotation

scientific article published on 20 March 2012

Asparagine peptide lyases: a seventh catalytic type of proteolytic enzymes

scientific article

Bacterial Pleckstrin Homology Domains: A Prokaryotic Origin for the PH Domain

scientific article

Bacterial retrons encode phage-defending tripartite toxin–antitoxin systems

scientific article published on 18 July 2022

Biocurators and biocuration: surveying the 21st century challenges

scientific article

Bioimage informatics: a new category in Bioinformatics ⬇️

scientific article

Bioinformatics for next generation sequencing.

scientific article

Bioinformatics--The new home for protein sequence motifs

scientific article published in January 2006

CASP2 knowledge-based approach to distant homology recognition and fold prediction in CASP4.

scientific article

Caenorhabditis elegans AF4/FMR2 Family Homolog affl-2 Regulates Heat Shock Induced Gene Expression

scientific article published on 09 June 2020

Cloud computing

scientific article published on 12 May 2009

Comparative analysis of the polycystic kidney disease 1 (PKD1) gene reveals an integral membrane glycoprotein with multiple evolutionary conserved domains

scientific article

Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2) ⬇️

scientific article (publication date: 9 May 2002)

Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research

scientific article published on 23 May 2020

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

scientific article published on 04 November 2020

Corticostatic peptides ⬇️

scientific article published on January 1, 1991

Corticostatic peptides cause nifedipine-sensitive volume reduction in jejunal villus enterocytes ⬇️

scientific article published on January 15, 1991

Corticostatins/defensins inhibit in vitro NK activity and cytokine production by human peripheral blood mononuclear cells

scientific article published in April 1996

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

scientific article

Cryo-EM structures of human RNA polymerase III in its unbound and transcribing states

scientific article

Curators of the world unite: the International Society of Biocuration

scientific article

DATABASE, The Journal of Biological Databases and Curation, is now the official journal of the International Society for Biocuration.

scientific article published on 6 December 2013

DUFs: families in search of function

scientific article

Database Commons: A Catalog of Worldwide Biological Databases

scientific article published on 23 December 2022

Databases, data tombs and dust in the wind

scientific article published on October 2008

Defining the remarkable structural malleability of a bacterial surface protein Rib domain implicated in infection ⬇️

scientific article published on 09 December 2019

Discovery of fibrillar adhesins across bacterial species

scientific article published on 18 July 2021

Distant homology recognition using structural classification of proteins

scientific article

Distant homology recognition using structural classification of proteins

scientific article published in 1997

Domain atrophy creates rare cases of functional partial protein domains

scientific article

Domain shuffling of a highly mutable ligand‐binding fold drives adhesin generation across the bacterial kingdom

scientific article published on 20 March 2023

Domains in gene silencing and cell differentiation proteins: the novel PAZ domain and redefinition of the Piwi domain

scientific article (publication date: October 2000)

Dosage sensitivity shapes the evolution of copy-number varied regions.

scientific article

EDITORIAL

scientific article (publication date: 2006)

EDITORIAL

scientific article published on 15 January 2007

Editorial

scientific article (published 2004-12-17)

Editorial

scientific article published on 23 December 2007

Enhanced protein domain discovery by using language modeling techniques from speech recognition.

scientific article

Enhanced protein domain discovery using taxonomy

scientific article

Eros is a novel transmembrane protein that controls the phagocyte respiratory burst and is essential for innate immunity

scientific article published on 28 March 2017

Expanding the repertoire of human tandem repeat RNA-binding proteins

scientific article published on 20 September 2023

Exploring Non-Coding RNAs in RNAcentral

scientific article published on 01 September 2020

Fibronectin type III domains in yeast detected by a hidden Markov model

scientific article published on 01 December 1996

Filling out the structural map of the NTF2-like superfamily

scientific article

GREENER principles for environmentally sustainable computational science

Gene Families

scientific article published on 23 September 2005

Gene Ontology Consortium: going forward

scientific article (publication date: 2015)

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

scientific article published in 2018

Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling

scientific article

Granulins, a novel class of peptide from leukocytes

scientific article

HMM-based databases in InterPro

scientific article published in January 2002

HMMER web server: 2015 update

scientific article published on 5 May 2015

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

scientific article published in August 2001

Highly accurate protein structure prediction for the human proteome

How to use the MEROPS database and website to help understand peptidase specificity

scientific article published on 13 September 2020

INCREASING THE IMPACT OF BIOINFORMATICS

scientific article published in January 2005

ISCB computational biology Wikipedia competition

scientific article published in 2013

Identifying Protein Domains with the Pfam Database

scientific article published in September 2008

Identifying protein domains with the Pfam database

scientific article

Initial sequencing and analysis of the human genome

scientific article published on 15 February 2001

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

scientific article

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

scientific article published on 19 May 2012

InterPro in 2017-beyond protein family and domain annotations

scientific article

InterPro, progress and status in 2005

scientific article

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

scientific article (publication date: December 2000)

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

scientific article

InterPro: the integrative protein signature database

scientific article

Isolation and Characterization of Three Forms of Joining Peptide from Adult Human Pituitaries: Lack of Adrenal Androgen-Stimulating Activity* ⬇️

scientific article published on August 1, 1991

Isolation and biological activity of corticostatic peptides (anti-ACTH).

scientific article

Isolation and sequence of the granulin precursor cDNA from human bone marrow reveals tandem cysteine-rich granulin domains ⬇️

scientific article published on March 1, 1992

Key challenges for the creation and maintenance of specialist protein resources

scientific article

LUD, a new protein domain associated with lactate utilization

scientific article

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

scientific article

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

scientific article

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

scientific article (publication date: 2014)

MEROPS: the peptidase database

scientific article

Making your database available through Wikipedia: the pros and cons ⬇️

scientific article published on December 5, 2011

Members of the immunoglobulin superfamily in bacteria

scientific article

Membrane-bound progesterone receptors contain a cytochrome b5-like ligand-binding domain

scientific article

Metazoan Scc4 homologs link sister chromatid cohesion to cell and axon migration guidance

scientific article

Mining the draft human genome

scientific article

Modelling structural rearrangements in proteins using Euclidean distance matrices

scientific article published in 2020

New Leadership for Bioinformatics

scientific article published on 10 August 2004

New developments in the InterPro database

scientific article

New knowledge from old: in silico discovery of novel protein domains in Streptomyces coelicolor

scientific article

Non-Coding RNA Analysis Using the Rfam Database

article

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

scientific article published on 13 July 2017

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

scientific article published on 14 December 2016

Origins of peptidases

scientific article published on 01 August 2019

Outline structure of the human L1 cell adhesion molecule and the sites where mutations cause neurological disorders

scientific article

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

scientific article

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

scientific article

Pepsin homologues in bacteria

scientific article (publication date: 16 September 2009)

Perspectives on tracking data reuse across biodata resources

Pfam 10 years on: 10,000 families and still growing

scientific article

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

scientific article

Pfam: The protein families database in 2021

scientific article published on 30 October 2020

Pfam: clans, web tools and services

scientific article

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

scientific article published in January 1998

Pfam: the protein families database

scientific article (publication date: 2014)

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

scientific article

Post-translational modification of bovine pro-opiomelanocortin. Tyrosine sulfation and pyroglutamate formation, a mass spectrometric study

scientific article published on 01 December 1990

Predicting active site residue annotations in the Pfam database

scientific article

Protein interactions in human genetic diseases.

scientific article

Purification of cationic cystine-rich peptides from rat bone marrow. Primary structures and biological activity of the rat corticostatin family of peptides

scientific article published on July 2, 1992

Quantifying the mechanisms of domain gain in animal proteins

scientific article

QuickTree: building huge Neighbour-Joining trees of protein sequences

scientific article published in November 2002

RK-2: a novel rabbit kidney defensin and its implications for renal host defense

scientific article published on January 1998

RNAcentral: A vision for an international database of RNA sequences

scientific article (publication date: November 2011)

RNAcentral: a comprehensive database of non-coding RNA sequences

scientific article (publication date: 4 January 2017)

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

scientific article published on 5 November 2018

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

scholarly article published in Nucleic Acids Research

RNAcentral: an international database of ncRNA sequences

scientific article

RNIE: genome-wide prediction of bacterial intrinsic terminators

scientific article published on 7 April 2011

Rapid identification of novel protein families using similarity searches

scientific article published on 24 December 2018

Recent advances in biocuration: meeting report from the Fifth International Biocuration Conference

scientific article (publication date: 2012)

Reuse of structural domain-domain interactions in protein networks

scientific article

Rfam 11.0: 10 years of RNA families

scientific article

Rfam 12.0: updates to the RNA families database

scientific article

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

scientific article published on 3 November 2017

Rfam 14: expanded coverage of metagenomic, viral and microRNA families

scientific article published on 19 November 2020

Rfam 15: RNA families database in 2025

scientific article published on 24 September 2024

Rfam: Wikipedia, clans and the "decimal" release

scientific article

Rfam: an RNA family database

scientific article

Rfam: annotating non-coding RNAs in complete genomes

scientific article

Rfam: updates to the RNA families database

scientific article

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

scientific article published on 3 February 2007

Searching databases to find protein domain organization

scientific article

SnoPatrol: how many snoRNA genes are there?

scientific article

Software patents in Bioinformatics

scientific article published on 9 June 2006

Solution structure of human myeloid-derived growth factor suggests a conserved function in the endoplasmic reticulum

scientific article published on 09 December 2019

Structural and functional analysis of a promoter of the human granulin/epithelin gene

scientific article

Structural genomics meets computational biology.

scientific article

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

scientific article

Structure and distribution of pentapeptide repeats in bacteria ⬇️

scientific article published on June 1, 1998

Structure of a novel human granulocyte peptide with anti-ACTH activity

scientific article

Structure of the Escherichia coli ProQ RNA-binding protein

scientific article published on 13 February 2017

TADOSS: computational estimation of tandem domain swap stability

scientific article published on 01 July 2019

TOWARDS COORDINATED INTERNATIONAL SUPPORT OF CORE DATA RESOURCES FOR THE LIFE SCIENCES

scientific article (publication date: 23 February 2017)

Tandem domain swapping: determinants of multidomain protein misfolding

scientific article published on 28 June 2019

Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases

scientific article published on 01 December 2019

Ten simple rules for chairing a scientific session

scientific article (publication date: September 2009)

Ten simple rules for editing Wikipedia ⬇️

scientific article

Ten simple rules to make your computing more environmentally sustainable

scientific article

The BON domain: a putative membrane-binding domain

scientific article published in July 2003

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

scientific article

The COMBREX project: design, methodology, and initial results

scientific article

The DUTT1 gene, a novel NCAM family member is expressed in developing murine neural tissues and has an unusually broad pattern of expression

scientific article

The ENTH domain

scientific article (publication date: 20 February 2002)

The European Bioinformatics Institute (EMBL-EBI) in 2021

scientific article published on 25 November 2021

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

scientific article published on 14 December 2004

The Gene Ontology knowledgebase in 2023

scientific article published in 2023

The HMMER Web Server for Protein Sequence Similarity Search

scientific article published on 8 December 2017

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

scientific article

The Human RNA-Binding Proteome and Its Dynamics During Arsenite-Induced Translational Arrest

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

scientific article published on 06 December 2018

The Importance of Biological Databases in Biological Discovery

scientific article published on 19 June 2015

The InterPro database, 2003 brings increased coverage and new features

scientific article (publication date: 2003)

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

scientific article (publication date: 2001)

The InterPro protein families and domains database: 20 years on

scientific article published on 06 November 2020

The InterPro protein families database: the classification resource after 15 years

scientific article

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

scientific article published on 14 November 2017

The PA domain: a protease-associated domain

scientific article published on October 2000

The PASTA domain: a beta-lactam-binding domain

scientific article

The PepSY domain: a regulator of peptidase activity in the microbial environment?

scientific article

The Pfam protein families database

scientific article (publication date: 2004)

The Pfam protein families database

scientific article (publication date: 2012)

The Pfam protein families database

scientific article (published 2010-01-01)

The Pfam protein families database ⬇️

scientific article

The Pfam protein families database

scientific article (publication date: 2002)

The Pfam protein families database in 2019

scholarly article by Sara El-Gebali et al published 24 October 2018 in Nucleic Acids Research

The Pfam protein families database.

scientific article

The Pfam protein families database: towards a more sustainable future

scientific article

The RNA WikiProject: community annotation of RNA families ⬇️

scientific article

The SGS3 protein involved in PTGS finds a family

scientific article

The SHOCT domain: a widespread domain under-represented in model organisms

scientific article

The SIS domain: a phosphosugar-binding domain

scientific article published in March 1999

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

scientific article

The YARHG domain: an extracellular domain in search of a function

scientific article

The challenge of increasing Pfam coverage of the human proteome

scientific article

The challenge of increasing Pfam coverage of the human proteome

scientific article published in January 2013

The characterisation of three types of genes that overlie copy number variable regions

scientific article

The corticostatic (anti-ACTH) and cytotoxic activity of peptides isolated from fetal, adult and tumor-bearing lung

scientific article published on 01 January 1987

The effect of HP-1 and related neutrophil granule peptides on DNA synthesis in HL60 cells

scientific article published on August 1991

The evolution of protein domain families.

scientific article

The immune-hypothalamic-pituitary-adrenal axis

scientific article published on February 1989

The isolation and characterization of a novel corticostatin/defensin-like peptide from the kidney.

scientific article

The isolation and identification of multiple forms of the neutrophil granule peptides from human leukemic cells

scientific article

The levels and biologic action of the human neutrophil granule peptide HP-1 in lung tumors ⬇️

scientific article published on 01 January 1992

The rise and fall of supervised machine learning techniques

scientific article (publication date: 17 November 2011)

The structure of Jann_2411 (DUF1470) from Jannaschia sp. at 1.45 Å resolution reveals a new fold (the ABATE domain) and suggests its possible role as a transcription regulator

scientific article

The structure of a LysM domain from E. coli membrane-bound lytic murein transglycosylase D (MltD)

scientific article

The structure of a PKD domain from polycystin-1: implications for polycystic kidney disease

scientific article

The structure of a domain common to archaebacteria and the homocystinuria disease protein

scientific article

The structure of pyogenecin immunity protein, a novel bacteriocin-like immunity protein from Streptococcus pyogenes

scientific article

The systematic functional analysis of Plasmodium protein kinases identifies essential regulators of mosquito transmission

scientific article

The thrombospondin module 1 domain of the matricellular protein CCN3 shows an atypical disulfide pattern and incomplete CWR layers

scientific article published on 24 January 2020

The tify family previously known as ZIM.

scientific article

The use of structure information to increase alignment accuracy does not aid homologue detection with profile HMMs

scientific article published in September 2002

Time to underpin Wikipedia wisdom ⬇️

scientific article published on December 9, 2010

Tissue-specific rewiring of signalling pathways through alternatively spliced disordered segments

scientific article published in April 2010

Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks

scientific article published on June 2012

Towards BioDBcore: a community-defined information specification for biological databases

scientific article

Towards BioDBcore: a community-defined information specification for biological databases

scientific article (publication date: 2011)

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

scientific article (publication date: 2014)

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

scientific article

Uncovering new families and folds in the natural protein universe

scientific article published on 13 September 2023

UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB

scientific article published on 07 March 2016

Using the MEROPS Database for Proteolytic Enzymes and Their Inhibitors and Substrates

scientific article published on 12 December 2014

Visualizing profile-profile alignment: pairwise HMM logos

scientific article published on 12 April 2005

What is hidden in the darkness? Deep-learning assisted large-scale protein family curation uncovers novel protein families and folds

When will RNA get its AlphaFold moment?

scientific article published on 13 September 2023

Yeast non-coding RNA interaction network

scientific article published on 12 July 2017

[In vitro effects of peptides of the corticostatin/defensin family on production of mitogen-induced cytokines]

scientific article published on 01 April 1995

[The autocrine-paracrine modulation of natural killer activity in man by peptides of the corticostatin-defensin family]

scientific article published on 01 April 1993

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

scientific article (publication date: 2014)

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

scientific article

miRBase: microRNA sequences, targets and gene nomenclature

scientific article

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