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Keywords

RNA bioinformatics, RNA 3D structure, RNAcentral, Rfam, RNA 3D Hub

Biography

I am a bioinformatician specialising in non-coding RNA. I worked at EMBL-EBI where I established RNAcentral and led a team responsible for the development of Rfam. During my PhD in the Leontis-Zirbel lab I developed RNA 3D Motif Atlas, an automatic classification of RNA 3D motifs, and contributed to several databases and web apps for RNA 3D structure analysis, including RNA 3D Hub, WebFR3D, JAR3D, and R3D Align.

Most recently I created R2DT, the first method for automatic visualisation of RNA secondary structure in standard, community-accepted layouts, and applied my skills to developing drugs targeting RNA at Ladder Therapeutics.

Activities

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Employment (2)

Riboscope Ltd: Cambridge, GB

2022-09-09 to present | Director
Employment
Source: Self-asserted source
Anton I Petrov

European Bioinformatics Institute: Cambridge, Cambridgeshire, GB

2013-06-01 to 2022-05-31
Employment
Source: Self-asserted source
Anton I Petrov

Education and qualifications (2)

Bowling Green State University: Bowling Green, OH, US

2007-08-06 to 2012-05-05 | PhD (Biology)
Education
Source: Self-asserted source
Anton I Petrov

Saint Petersburg State University: Saint Petersburg, RU

2003-09-01 to 2007-07-01 | Bachelor (Biology)
Education
Source: Self-asserted source
Anton I Petrov

Works (32)

LitSumm: large language models for literature summarization of noncoding RNAs

Database
2025-02-05 | Journal article
DOI: 10.1093/database/baaf006
Contributors: Andrew Green; Carlos Eduardo Ribas; Nancy Ontiveros-Palacios; Sam Griffiths-Jones; Anton I Petrov; Alex Bateman; Blake Sweeney
Source: check_circle
Crossref

Expansion of the tmRNA sequence database and new tools for search and visualization

NAR Genomics and Bioinformatics
2025-01-07 | Journal article
DOI: 10.1093/nargab/lqaf019
Contributors: Eric P Nawrocki; Anton I Petrov; Kelly P Williams
Source: check_circle
Crossref

Rfam 15: RNA families database in 2025

Nucleic Acids Research
2025-01-06 | Journal article
DOI: 10.1093/nar/gkae1023
Contributors: Nancy Ontiveros-Palacios; Emma Cooke; Eric P Nawrocki; Sandra Triebel; Manja Marz; Elena Rivas; Sam Griffiths-Jones; Anton I Petrov; Alex Bateman; Blake Sweeney
Source: check_circle
Crossref

Rfam 15: RNA families database in 2025

2024-09-24 | Preprint
DOI: 10.1101/2024.09.23.614430
Contributors: Nancy Ontiveros; Emma Cooke; Eric P. Nawrocki; Sandra Triebel; Manja Marz; Elena Rivas; Sam Griffiths-Jones; Anton I. Petrov; Alex Bateman; Blake Sweeney
Source: check_circle
Crossref

LitSumm: Large language models for literature summarisation of non-coding RNAs

2023 | Preprint
DOI: 10.48550/ARXIV.2311.03056
Contributors: Andrew Green; Carlos Ribas; Nancy Ontiveros-Palacios; Anton I. Petrov; Alex Bateman; Blake Sweeney
Source: Self-asserted source
Anton I Petrov

Comprehensive Survey of Conserved RNA Secondary Structures in Full-Genome Alignment of Hepatitis C Virus

2023-11-17 | Preprint
DOI: 10.1101/2023.11.15.567179
Contributors: Sandra Triebel; Kevin Lamkiewicz; Nancy Ontiveros; Blake Sweeney; Peter F. Stadler; Anton I. Petrov; Michael Niepmann; Manja Marz
Source: check_circle
Crossref

The European Bioinformatics Institute (EMBL-EBI) in 2021

Nucleic Acids Research
2022-01-07 | Journal article
DOI: 10.1093/nar/gkab1127
Contributors: Gaia Cantelli; Alex Bateman; Cath Brooksbank; Anton I Petrov; Rahuman S Malik-Sheriff; Michele Ide-Smith; Henning Hermjakob; Paul Flicek; Rolf Apweiler; Ewan Birney et al.
Source: check_circle
Crossref

R2DT is a framework for predicting and visualising RNA secondary structure using templates

Nature Communications
2021-12 | Journal article
DOI: 10.1038/s41467-021-23555-5
Part of ISSN: 2041-1723
Source: Self-asserted source
Anton I Petrov

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

Briefings in bioinformatics
2020-11 | Journal article
DOI: 10.1093/bib/bbaa232
PMID: 33147627
PMC: PMC7665365
Contributors: Hufsky F; Lamkiewicz K; Almeida A; Aouacheria A; Arighi C; Bateman A; Baumbach J; Beerenwinkel N; Brandt C; Cacciabue M et al.
Source: Self-asserted source
Anton I Petrov via Europe PubMed Central

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

Nucleic acids research
2020-11 | Journal article
DOI: 10.1093/nar/gkaa1047
PMID: 33211869
Contributors: Kalvari I; Nawrocki EP; Ontiveros-Palacios N; Argasinska J; Lamkiewicz K; Marz M; Griffiths-Jones S; Toffano-Nioche C; Gautheret D; Weinberg Z et al.
Source: Self-asserted source
Anton I Petrov via Europe PubMed Central

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

Nucleic acids research
2020-10-27 | Journal article
DOI: 10.1093/nar/gkaa921
PMID: 33106848
Source: Self-asserted source
Anton I Petrov

Exploring Non-Coding RNAs in RNAcentral.

Current protocols in bioinformatics
2020-09 | Journal article
DOI: 10.1002/cpbi.104
PMID: 32846052
Contributors: Sweeney BA; Tagmazian AA; Ribas CE; Finn RD; Bateman A; Petrov AI
Source: Self-asserted source
Anton I Petrov via Europe PubMed Central

R2DT: computational framework for template-based RNA secondary structure visualisation across non-coding RNA types

2020-09 | Other
DOI: 10.1101/2020.09.10.290924
OTHER-ID:

PPR212864
Contributors: Sweeney BA; Hoksza D; Nawrocki EP; Ribas CE; Madeira F; Cannone JJ; Gutell R; Maddala A; Meade C; Williams LD et al.
Source: Self-asserted source
Anton I Petrov via Europe PubMed Central

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

Nucleic Acids Research
2019-01-08 | Journal article
DOI: 10.1093/nar/gky1034
Contributors: Blake A Sweeney; Anton I Petrov; Boris Burkov; Robert D Finn; Alex Bateman; Maciej Szymanski; Wojciech M Karlowski; Jan Gorodkin; Stefan E Seemann; Jamie J Cannone et al.
Source: check_circle
Crossref

Non-Coding RNA Analysis Using the Rfam Database.

Current protocols in bioinformatics
2018-06 | Journal article
DOI: 10.1002/cpbi.51
PMID: 29927072
Contributors: Kalvari I; Nawrocki EP; Argasinska J; Quinones-Olvera N; Finn RD; Bateman A; Petrov AI
Source: Self-asserted source
Anton I Petrov via Europe PubMed Central

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

Nucleic Acids Research
2018-01-04 | Journal article
DOI: 10.1093/nar/gkx1038
Contributors: Ioanna Kalvari; Joanna Argasinska; Natalia Quinones-Olvera; Eric P Nawrocki; Elena Rivas; Sean R Eddy; Alex Bateman; Robert D Finn; Anton I Petrov
Source: check_circle
Crossref

RNAcentral: a comprehensive database of non-coding RNA sequences.

2016-10 | Journal article
PMID: 27794554
Contributors: The RNAcentral Consortium
Source: Self-asserted source
Anton I Petrov via Europe PubMed Central

JAR3D Webserver: Scoring and aligning RNA loop sequences to known 3D motifs

Nucleic Acids Research
2016-05-27 | Journal article
DOI: 10.1093/nar/gkw453
Contributors: James Roll; Craig L. Zirbel; Blake Sweeney; Anton I. Petrov; Neocles Leontis
Source: check_circle
Crossref

Identifying novel sequence variants of RNA 3D motifs

Nucleic Acids Research
2015-09-03 | Journal article
DOI: 10.1093/nar/gkv651
Source: check_circle
Crossref

R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server.

2015-07 | Journal article
DOI: 10.1093/nar/gkv543
PMID: 26048960
PMC: PMC4489222
Contributors: Cannone JJ; Sweeney BA; Petrov AI; Gutell RR; Zirbel CL; Leontis N
Source: Self-asserted source
Anton I Petrov via Europe PubMed Central
grade
Preferred source (of 2)‎

RNAcentral: an international database of ncRNA sequences.

2014-10 | Journal article
DOI: 10.1093/nar/gku991
PMID: 25352543
Contributors: The RNAcentral Consortium
Source: Self-asserted source
Anton I Petrov via Europe PubMed Central

Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas.

2013-10 | Journal article
DOI: 10.1261/rna.039438.113
PMID: 23970545
Contributors: Petrov AI; Zirbel CL; Leontis NB
Source: Self-asserted source
Anton I Petrov via Europe PubMed Central

The nucleic acid database: new features and capabilities.

2013-10 | Journal article
PMID: 24185695
Contributors: Coimbatore Narayanan B; Westbrook J; Ghosh S; Petrov AI; Sweeney B; Zirbel CL; Leontis NB; Berman HM
Source: Self-asserted source
Anton I Petrov via Europe PubMed Central

R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures.

2013-07 | Journal article
DOI: 10.1093/nar/gkt417
PMID: 23716643
PMC: PMC3692076
Contributors: Rahrig RR; Petrov AI; Leontis NB; Zirbel CL
Source: Self-asserted source
Anton I Petrov via Europe PubMed Central

RNA 3D Motifs: Identification, Clustering, and Analysis

2012 | Dissertation or Thesis
Source: Self-asserted source
Anton I Petrov

Comprehensive survey and geometric classification of base triples in RNA structures.

2012-02 | Journal article
DOI: 10.1093/nar/gkr810
PMID: 22053086
PMC: PMC3287178
Contributors: Abu Almakarem AS; Petrov AI; Stombaugh J; Zirbel CL; Leontis NB
Source: Self-asserted source
Anton I Petrov via Europe PubMed Central

WebFR3D--a server for finding, aligning and analyzing recurrent RNA 3D motifs.

2011-07 | Journal article
DOI: 10.1093/nar/gkr249
PMID: 21515634
PMC: PMC3125732
Contributors: Petrov AI; Zirbel CL; Leontis NB
Source: Self-asserted source
Anton I Petrov via Europe PubMed Central

A three-dimensional RNA motif in Potato spindle tuber viroid mediates trafficking from palisade mesophyll to spongy mesophyll in Nicotiana benthamiana.

2011-01 | Journal article
DOI: 10.1105/tpc.110.081414
PMID: 21258006
Contributors: Takeda R; Petrov AI; Leontis NB; Ding B
Source: Self-asserted source
Anton I Petrov via Europe PubMed Central

Quantum chemical studies of nucleic acids: can we construct a bridge to the RNA structural biology and bioinformatics communities?

2010-12 | Journal article
DOI: 10.1021/jp104361m
PMID: 21049899
Contributors: Šponer J; Šponer JE; Petrov AI; Leontis NB
Source: Self-asserted source
Anton I Petrov via Europe PubMed Central

Understanding Sequence Variability of RNA Motifs Using Geometric Search and IsoDiscrepancy Matrices

2009 | Conference paper
DOI: 10.1109/OCCBIO.2009.15
Source: Self-asserted source
Anton I Petrov

15. Analyzing, searching, and annotating recurrent RNA three-dimensional motifs
Source: Self-asserted source
Anton I Petrov via Crossref Metadata Search

Contributions to Rfam
Source: check_circle
APICURON

Peer review (135 reviews for 24 publications/grants)

Review activity for Bioinformatics (26)
Review activity for Bioinformatics advances. (2)
Review activity for BMC bioinformatics (1)
Review activity for Cancers. (4)
Review activity for Cell death and disease. (1)
Review activity for Database. (7)
Review activity for Diagnostics. (3)
Review activity for Frontiers in genetics. (1)
Review activity for Gene. (1)
Review activity for Genes. (3)
Review activity for Genome biology. (2)
Review activity for Genomics. (3)
Review activity for International journal of molecular sciences. (2)
Review activity for International journal of molecular sciences. (1)
Review activity for NAR genomics and bioinformatics. (4)
Review activity for Nature communications (6)
Review activity for Nucleic acids research. (48)
Review activity for PLoS computational biology. (2)
Review activity for PloS one. (6)
Review activity for Research square. (2)
Review activity for RNA biology. (3)
Review activity for RNA. (2)
Review activity for Scientific data. (4)
Review activity for Viruses. (1)
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