Alex Bateman
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Explore the profile of Alex Bateman including associated specialties, affiliations and a list of published articles.
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181
Citations
41715
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Recent Articles
1.
Green A, Ribas C, Ontiveros-Palacios N, Griffiths-Jones S, Petrov A, Bateman A, et al.
Database (Oxford)
. 2025 Feb;
2025.
PMID: 39908113
Curation of literature in life sciences is a growing challenge. The continued increase in the rate of publication, coupled with the relatively fixed number of curators worldwide, presents a major...
2.
Costa F, Blum M, Bateman A
Bioinform Adv
. 2024 Dec;
4(1):vbae188.
PMID: 39659588
Motivation: High confidence structure prediction models have become available for nearly all protein sequences. More than 200 million AlphaFold2 models are now publicly available. We observe that there can be...
3.
Blum M, Andreeva A, Florentino L, Chuguransky S, Grego T, Hobbs E, et al.
Nucleic Acids Res
. 2024 Nov;
53(D1):D444-D456.
PMID: 39565202
InterPro (https://www.ebi.ac.uk/interpro) is a freely accessible resource for the classification of protein sequences into families. It integrates predictive models, known as signatures, from multiple member databases to classify sequences into...
4.
Schaeffer R, Medvedev K, Andreeva A, Chuguransky S, Pinto B, Zhang J, et al.
Nucleic Acids Res
. 2024 Nov;
53(D1):D411-D418.
PMID: 39565196
The evolutionary classification of protein domains (ECOD) classifies protein domains using a combination of sequence and structural data (http://prodata.swmed.edu/ecod). Here we present the culmination of our previous efforts at classifying...
5.
Paysan-Lafosse T, Andreeva A, Blum M, Chuguransky S, Grego T, Pinto B, et al.
Nucleic Acids Res
. 2024 Nov;
53(D1):D523-D534.
PMID: 39540428
The Pfam protein families database is a comprehensive collection of protein domains and families used for genome annotation and protein structure and function analysis (https://www.ebi.ac.uk/interpro/). This update describes major developments...
6.
Ontiveros-Palacios N, Cooke E, Nawrocki E, Triebel S, Marz M, Rivas E, et al.
Nucleic Acids Res
. 2024 Nov;
53(D1):D258-D267.
PMID: 39526405
The Rfam database, a widely used repository of non-coding RNA families, has undergone significant updates in release 15.0. This paper introduces major improvements, including the expansion of Rfamseq to 26 ...
7.
Ponamareva I, Andreeva A, Bileschi M, Colwell L, Bateman A
Bioinform Adv
. 2024 Oct;
4(1):vbae132.
PMID: 39399373
Motivation: In this article, we propose a method for finding similarities between Pfam families based on the pre-trained neural network ProtENN2. We use the model ProtENN2 per-residue embeddings to produce...
8.
Ontiveros N, Cooke E, Nawrocki E, Triebel S, Marz M, Rivas E, et al.
bioRxiv
. 2024 Oct;
PMID: 39372780
The Rfam database, a widely-used repository of non-coding RNA (ncRNA) families, has undergone significant updates in release 15.0. This paper introduces major improvements, including the expansion of Rfamseq to 26,106...
9.
Pei J, Andreeva A, Chuguransky S, Pinto B, Paysan-Lafosse T, Schaeffer R, et al.
J Mol Biol
. 2024 Aug;
436(22):168764.
PMID: 39197652
Classification of protein domains based on homology and structural similarity serves as a fundamental tool to gain biological insights into protein function. Recent advancements in protein structure prediction, exemplified by...
10.
Ross K, Bastian F, Buys M, Cook C, DEustachio P, Harrison M, et al.
Bioinform Adv
. 2024 May;
4(1):vbae057.
PMID: 38721398
Motivation: Data reuse is a common and vital practice in molecular biology and enables the knowledge gathered over recent decades to drive discovery and innovation in the life sciences. Much...