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Employment (8)

European Molecular Biology Laboratory: Heidelberg, DE

2023-07-01 to present | Senior Scientist (EMBL-European Bioinformatics Institute [EMBL-EBI])
Employment
Source: Self-asserted source
Robert D. Finn

European Molecular Biology Laboratory: Heidelberg, DE

2022 to present | Co-Chair, Microbial Ecosystems Transversal Theme (EMBL-European Bioinformatics Institute [EMBL-EBI])
Employment
Source: Self-asserted source
Robert D. Finn

European Bioinformatics Institute: Hinxton, Cambridgeshire, GB

2020-10-09 to present | Section Head (Genome Assembly and Annotation)
Employment
Source: Self-asserted source
Robert D. Finn

European Bioinformatics Institute: Hinxton, Cambridgeshire, GB

2020-07-01 to present | Team Leader, Microbiome Informatics (Genome Assembly and Annotation)
Employment
Source: Self-asserted source
Robert D. Finn

European Bioinformatics Institute: Hinxton, Cambridgeshire, GB

2014-01-01 to 2020-06-30 | Team Leader, Sequence Families (Proteins and Protein Families)
Employment
Source: Self-asserted source
Robert D. Finn

Howard Hughes Medical Institute Janelia Farm Research Campus: Ashburn, VA, US

2012-12-01 to 2013-12-01 | Manager, Computational Genomics (Scientific Computing)
Employment
Source: Self-asserted source
Robert D. Finn

Howard Hughes Medical Institute Janelia Farm Research Campus: Ashburn, VA, US

2010-07-15 to 2012-11-31 | HMMER Project Leader (Scientific Computing)
Employment
Source: Self-asserted source
Robert D. Finn

Wellcome Trust Sanger Institute: Cambridge, Cambridgeshire, GB

2004-09-01 to 2010-07-01 | Project leader (Informatics)
Employment
Source: Self-asserted source
Robert D. Finn

Education and qualifications (2)

Imperial College London: London, Westminster, GB

2001 | PhD (Biochemistry Department)
Education
Source: Self-asserted source
Robert D. Finn

Imperial College London: London, Westminster, GB

1998 | BSc (Biology Department)
Education
Source: Self-asserted source
Robert D. Finn

Professional activities (37)

Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement: Paris, FR

2024-05-10 to present | Scientific Advisory Board Member for the EU Horizon Europe funded grant "DOMINO - Harnessing the microbial potential of fermented foods for healthy and sustainable food systems"
Service
Source: Self-asserted source
Robert D. Finn

European Molecular Biology Laboratory: Heidelberg, DE

2024-02-22 to present | Member of the Committee to Advance Environmental Research at EMBL (CAERE)
Service
Source: Self-asserted source
Robert D. Finn

SeqCode: Athens, US

2023-09-29 to present | Standards Working Group Member (Standards Working Group)
Service
Source: Self-asserted source
Robert D. Finn

United Nations Framework Convention on Climate Change: Bonn, Nordrhein-Westfalen, DE

2022 to present | Member of the Resilience Frontiers Technology Advisory Group
Service
Source: Self-asserted source
Robert D. Finn

UK Research and Innovation: Swindon, Swindon, GB

2022 to present | Panel Member, Innovation and Knowledge Centre (IKC) – National Biofilms Innovation Centre (NBIC) Phase 1 review and Phase 2 strategic assessment
Service
Source: Self-asserted source
Robert D. Finn

National Research Data Infrastructure Germany (NFDI): Karlsruhe, DE

2022 to present | Member, NFDI4Microbiota Consortium Scientific Advisory Board
Service
Source: Self-asserted source
Robert D. Finn

European Molecular Biology Laboratory: Heidelberg, DE

2022 to present | Co-Chair, Microbial Ecosystems Transversal Theme (European Bioinformatics Institute (EMBL-EBI))
Service
Source: Self-asserted source
Robert D. Finn

European Bioinformatics Institute: Hinxton, GB

2022 to present | Senior IT Stakeholder Committee (SITSC)
Service
Source: Self-asserted source
Robert D. Finn

Rothamsted Research: Harpenden, Hertfordshire, GB

2020-09-08 to present | Member, UK Crop Microbiome CryoBank Scientific Advisory Board
Service
Source: Self-asserted source
Robert D. Finn

UK Research and Innovation: Swindon, Swindon, GB

2020-09-01 to present | Member, KTN Microbiome Innovation Network
Service
Source: Self-asserted source
Robert D. Finn

European Science Foundation: Strasbourg, Alsace, FR

2020-04-15 to present | Member, College of Expert Reviewers
Service
Source: Self-asserted source
Robert D. Finn

Genome Standards Consortium: Bethesda, US

2019-05-01 to present | Board Member
Service
Source: Self-asserted source
Robert D. Finn

National Microbiome Data Collaborative: Berkeley , US

2019 to present | Member, Scientific Advisory Board
Service
Source: Self-asserted source
Robert D. Finn

Health Data Research UK: London, GB

2018 to present | Associated Researcher
Service
Source: Self-asserted source
Robert D. Finn

BioMed Central Ltd: London, London, GB

2018 to present | Associate Editor, Microbiome Journal
Service
Source: Self-asserted source
Robert D. Finn

Common Workflow Language : Berlin, DE

2017 to present | Member, Advisory Committee
Service
Source: Self-asserted source
Robert D. Finn

Genomic Standards Consortium: Bethesda, US

2016 to present | Co-Lead, Metagenomics Analysis Standard
Service
Source: Self-asserted source
Robert D. Finn

European Bioinformatics Institute: Cambridge, GB

2016 to present | Member, Equality and Diversity Committee
Service
Source: Self-asserted source
Robert D. Finn

ELIXIR: Hinxton, GB

2015 to present | Co-Lead, Microbiome Community
Service
Source: Self-asserted source
Robert D. Finn

Latvian Biomedical Research and Study Centre: Riga, LV

2023 to 2028 | Member of the LBMC Scientific Advisory Board
Service
Source: Self-asserted source
Robert D. Finn

UK Research and Innovation: Swindon, Swindon, GB

2022 to 2023 | Member, BBSRC Pool of Experts
Service
Source: Self-asserted source
Robert D. Finn

Biotechnology and Biological Sciences Research Council: Swindon, Wiltshire, GB

2022 to 2022 | Panel Member, Canada International Partnering Award Plus review committee
Service
Source: Self-asserted source
Robert D. Finn

Biotechnology and Biological Sciences Research Council: Swindon, Wiltshire, GB

2022 to 2022 | Panel Member, sLOLA 2022, first-stage review committee
Service
Source: Self-asserted source
Robert D. Finn

Coordination and Support Action Microbiome Support: Tulln, AT

2018 to 2022 | Member, Advisory Group
Service
Source: Self-asserted source
Robert D. Finn

Earlham Institute: Norwich, England, GB

2021 to 2021 | Panel Member, Tenure Track review
Service
Source: Self-asserted source
Robert D. Finn

European Bioinformatics Institute: Cambridge, GB

2018 to 2021 | Member, Tools Committee
Service
Source: Self-asserted source
Robert D. Finn

Czech Academy of Sciences: Prague, CZ

2020-04-01 to 2020-06-30 | Member, Biological Sciences B Panel
Service
Source: Self-asserted source
Robert D. Finn

UK Biobank: Stockport, Stockport, GB

2018 to 2020 | Member, Gut Microbiome Expert Working Group
Service
Source: Self-asserted source
Robert D. Finn

European Bioinformatics Institute: Cambridge, GB

2017 to 2020 | Panel Member, External Training Advisory Group
Service
Source: Self-asserted source
Robert D. Finn

Genome Canada: Ottawa, Ontario, CA

2018 to 2018 | Member, GAPP review Committee
Service
Source: Self-asserted source
Robert D. Finn

Genome Canada: Ottawa, Ontario, CA

2018 to 2018 | Member, B/CB Multi-sector review Committee
Service
Source: Self-asserted source
Robert D. Finn

FPS Public Health: Brussels, BE

2018 to 2018 | Reviewer, Euphresco network for phytosanitary research
Service
Source: Self-asserted source
Robert D. Finn

Biotechnology and Biological Sciences Research Council: Swindon, GB

2018 to 2018 | Panel Member, Biofilms - Information Knowledge Centre review committee
Service
Source: Self-asserted source
Robert D. Finn

Biotechnology and Biological Sciences Research Council: Swindon, GB

2018 to 2018 | Panel Member, Quadram Institutional review committee
Service
Source: Self-asserted source
Robert D. Finn

BioMed Central Ltd: London, London, GB

2018 to 2018 | Editor, Biology Direct Journal
Service
Source: Self-asserted source
Robert D. Finn

Microbiology Society: London, London, GB

2017 to 2017 | Member, Microbiome Expert Working Group
Service
Source: Self-asserted source
Robert D. Finn

Biotechnology and Biological Sciences Research Council: Swindon, GB

2016 to 2016 | Member, Microbiome Executive Working Group
Service
Source: Self-asserted source
Robert D. Finn

Funding (45)

Infectome - Infective competence of the human microbiome in health and disease

2024-03 to 2027-02 | Grant
Fonds National de la Recherche (Luxembourg, LU)
Part of GRANT_NUMBER:

C23/BM/18091896
Source: Self-asserted source
Robert D. Finn

EUREMAP - European Research Infrastructure for Marine Bioprospecting

2024-01 to 2026-12 | Grant
European Commission (Brussels, BE)
Part of GRANT_NUMBER:

101131663
Source: Self-asserted source
Robert D. Finn

Annotation of microbiome dark matter

2023-10 to 2024-03 | Grant
NIHR Cambridge Biomedical Research Centre (Cambridge, GB)
GRANT_NUMBER:

RHAG/414 BRC
Source: Self-asserted source
Robert D. Finn

Novel Plastizymes: discovery and improvement of plastic-degrading enzymes by integrated cycles of computational and experimental approaches

2023-04 to 2028-03 | Grant
Biotechnology and Biological Sciences Research Council (Swindon, Wiltshire, GB)
Part of GRANT_NUMBER:

BB/X00306X/1
Source: Self-asserted source
Robert D. Finn

DTO-BioFlow - Integration of biodiversity monitoring data into the Digital Twin Ocean

2023-04 to 2026-09 | Grant
European Commission (Brussels, BE)
Part of GRANT_NUMBER:

101112823
Source: Self-asserted source
Robert D. Finn

MICROBE - Microbiome Biobanking (RI) Enabler

2023-02 to 2027-01 | Grant
European Commission (Brussels, BE)
Part of GRANT_NUMBER:

101094353
Source: Self-asserted source
Robert D. Finn

PDBe-KB - enhancing impact of structural knowledgebase in basic and translational research with focus on Pathogenic Mutations

2023-01 to 2028-12 | Grant
Wellcome Trust (London, GB)
GRANT_NUMBER:

223739/Z/21/Z
Source: Self-asserted source
Robert D. Finn

Blue-Cloud 2026 - A federated European FAIR and Open Research Ecosystem for oceans, seas, coastal and inland waters

2023-01 to 2026-06 | Grant
European Commission (Brussels, BE)
Part of GRANT_NUMBER:

101094227
Source: Self-asserted source
Robert D. Finn

BIOcean5D - Marine Biodiversity Assessment And Prediction Across Space, Time And Human Scales

2022-12 to 2026-11 | Grant
European Commission (Brussels, BE)
Part of GRANT_NUMBER:

101059915
Source: Self-asserted source
Robert D. Finn

BlueRemediomics: Harnessing the marine microbiome for novel sustainable biogenics and ecosystem services

2022-12 to 2026-11 | Grant
European Commission (Brussels, BE)
GRANT_NUMBER:

101082304
Source: Self-asserted source
Robert D. Finn

Leverhulme Research Centre for The Holobiont

2022-10 to 2032-09 | Grant
Leverhulme Trust (London, GB)
Part of GRANT_NUMBER:

RC-2021-058
Source: Self-asserted source
Robert D. Finn

National Mouse Genetics Network: Mouse genetic models of barrier immunity dysfunction: Role of the microbiome in modifying disease phenotype

2022-04 to 2025-03 | Grant
Medical Research Council (Swindon, GB)
Part of GRANT_NUMBER:

MR/W022532/1
Source: Self-asserted source
Robert D. Finn

Enriching MGnify Genomes to capture the full spectrum of the microbiota and bolster taxonomic classifications

2022-03 to 2025-02 | Grant
Biotechnology and Biological Sciences Research Council (Swindon, GB)
GRANT_NUMBER:

BB/V01868X/1
Source: Self-asserted source
Robert D. Finn

REDEFINE - Development of efficient, large-scale metagenomics sequence comparison algorithms to facilitate novel genomic insights

2022-01 to 2024-12 | Grant
Biotechnology and Biological Sciences Research Council (Swindon, GB)
GRANT_NUMBER:

BB/W002965/1
Source: Self-asserted source
Robert D. Finn

Ensembl V - Ensembl: A Comprehensive Reference Resource for Genomics

2021-10 to 2026-09 | Grant
Wellcome (London, GB)
GRANT_NUMBER:

222155/Z/20/Z
Source: Self-asserted source
Robert D. Finn

InterPro and Pfam: Protein domains and families for biomedical research

2021-04 to 2026-03 | Grant
Wellcome Trust (London, GB)
Part of GRANT_NUMBER:

221320/Z/20/Z
Source: Self-asserted source
Robert D. Finn

FindingPheno - Unified computational solutions to disentangle biological interactions in multi-omics data

2021-03 to 2025-02 | Grant
European Commission (Brussels, BE)
Part of GRANT_NUMBER:

952914
Source: Self-asserted source
Robert D. Finn

SymbNET - Genomics and Metabolomics in a Host-Microbe Symbiosis Network

2021-01 to 2023-12 | Grant
European Commission (Brussels, BE)
Part of GRANT_NUMBER:

952537
Source: Self-asserted source
Robert D. Finn

Atlantic ECOsystems assessment, forecasting & sustainability

2020-09 to 2025-08 | Grant
European Commission (Brussels, BE)
Part of GRANT_NUMBER:

862923
Source: Self-asserted source
Robert D. Finn

SENSE - Screening of ENvironmental SEquences to discover novel protein functions, using informatics target selection and high-throughput validation

2020-06 to 2023-04 | Grant
Biotechnology and Biological Sciences Research Council (Swindon, GB)
Part of GRANT_NUMBER:

BB/T000902/1
Source: Self-asserted source
Robert D. Finn

The dark metaproteome: identifying proteins of unknown function in the human gut microbiome

2020-04 to 2022-09 | Grant
Fonds National de la Recherche Luxembourg (Luxembourg, LU)
Part of GRANT_NUMBER:

EMBL-FNR-CORE 2019
Source: Self-asserted source
Robert D. Finn

Scaling the next generation of protein sequence searches to enable rapid discovery of novel actives

2019-10 to 2023-09 | Grant
Biotechnology and Biological Sciences Research Council (Swindon, GB)
Part of GRANT_NUMBER:

BB/T508391/1
Source: Self-asserted source
Robert D. Finn

Development of a comprehensive (meta-)genome informatics platform for gut microbiome research

2019-08 to 2021-12 | Grant
European Molecular Biology Laboratory (Heidelberg, DE)
Part of GRANT_NUMBER:

N/A
Source: Self-asserted source
Robert D. Finn

EMERALD - Enriching MEtagenomics Results using Artificial intelligence and Literature Data

2019-04 to 2022-08 | Grant
Biotechnology and Biological Sciences Research Council (Swindon, GB)
GRANT_NUMBER:

BB/S009043/1
Source: Self-asserted source
Robert D. Finn

EOSC-Life: Providing an open collaborative space for digital biology in Europe

2019-03 to 2023-08 | Grant
European Commission (Brussels, BE)
Part of GRANT_NUMBER:

824087
Source: Self-asserted source
Robert D. Finn

REFRACT - Repeat protein Function Refinement, Annotation and Classification of Topologies

2019-01 to 2023-09 | Grant
European Commission (Brussles, BE)
Part of GRANT_NUMBER:

823886
Source: Self-asserted source
Robert D. Finn

Holofood - Holistic solution to improve animal food production through deconstructing the biomolecular interactions between feed, gut microorganisms and animals in relation to performance parameters

2019-01 to 2023-04 | Grant
European Commission (Brussels, BE)
Part of GRANT_NUMBER:

817729
Source: Self-asserted source
Robert D. Finn

Creation of error tolerant profile HMMs by EMBl-EBI and putting them into production

2018-10 to 2022-12 | Grant
Oxford Nanopore Technologies (Oxford, GB)
GRANT_NUMBER:

N/A
Source: Self-asserted source
Robert D. Finn
grade
Preferred source (of 4)‎

EBI Metagenomics - enabling the reconstruction of microbial populations

2018-09 to 2022-03 | Grant
Biotechnology and Biological Sciences Research Council (Swindon, GB)
GRANT_NUMBER:

BB/R015228/1
Source: Self-asserted source
Robert D. Finn

HGNC III - The Nomenclature of Human and Vertebrate Genes

2018-06 to 2023-04 | Grant
National Human Genome Research Institute (Md., Md., US)
Part of GRANT_NUMBER:

U24HG003345
Source: Self-asserted source
Robert D. Finn

HGNC III - The Nomenclature of Human and Vertebrate Genes

2017-09 to 2023-08 | Grant
Wellcome (London, GB)
Part of GRANT_NUMBER:

208349/Z/17/Z
Source: Self-asserted source
Robert D. Finn

A Metagenomics Exchange - enriching analysis by synergistic harmonisation of MG-RAST and the EBI Metagenomics Portal

2017-07 to 2021-03 | Grant
Biotechnology and Biological Sciences Research Council (Swindon, GB)
GRANT_NUMBER:

BB/N018354/1
Source: Self-asserted source
Robert D. Finn

Expanding Genome3D and disseminating the structural annotations via InterPro and PDBe

2016 to 2019 | Grant
Biotechnology and Biological Sciences Research Council (Swindon, Wiltshire, GB)
GRANT_NUMBER:

BB/N019172/1
Source: Self-asserted source
Robert D. Finn

MetXtra – An integrated High-Throughput Metagenomics Platform for Enzyme Discovery

2016 to 2018 | Grant
Innovate UK (Swindon, GB)
Part of GRANT_NUMBER:

2560
Source: Self-asserted source
Robert D. Finn

Unifam: an integrated protein families resource

2015-10 to 2021-03 | Grant
Wellcome Trust (London, GB)
GRANT_NUMBER:

108433/Z/15/Z
Source: Self-asserted source
Robert D. Finn

ELIXIR-EXCELERATE: Fast-track ELIXIR implementation and drive early user exploitation across the life-sciences

2015-09 to 2019-08 | Grant
European Commission (Brussels, BE)
Part of GRANT_NUMBER:

676559
Source: Self-asserted source
Robert D. Finn

Rfam: Towards a sustainable resource for understanding the genomic functional ncRNA repertoire

2015-01-21 to 2018-05-03 | Grant
Biotechnology and Biological Sciences Research Council (Swindon, GB)
GRANT_NUMBER: BB/M011690/1
GRANT_NUMBER: BB/M011690/1
Source: Self-asserted source
Robert D. Finn via DimensionsWizard

EBI Metagenomics Portal - Towards a better understanding of community metabolism

2015-01-21 to 2018-01-20 | Grant
Biotechnology and Biological Sciences Research Council (Swindon, GB)
GRANT_NUMBER: BB/M011755/1
GRANT_NUMBER: BB/M011755/1
Source: Self-asserted source
Robert D. Finn via DimensionsWizard

Towards detailed and consistent function prediction from protein family databases

2015 to 2018 | Grant
Biotechnology and Biological Sciences Research Council (Swindon, Wiltshire, GB)
GRANT_NUMBER:

BB/N00521X/1
Source: Self-asserted source
Robert D. Finn

Keeping pace with protein sequence annotation; consolidating and enhancing Pfam and InterPro's methodologies for functional prediction

2014-07-31 to 2017-07-30 | Grant
Biotechnology and Biological Sciences Research Council (Swindon, GB)
GRANT_NUMBER: BB/L024136/1
GRANT_NUMBER: BB/L024136/1
Source: Self-asserted source
Robert D. Finn via DimensionsWizard

Building a global metagenomics portal ('MGportal') to handle next generation sequencing data and associated metadata

2012-01-01 to 2014-12-31 | Grant
Biotechnology and Biological Sciences Research Council (Swindon, GB)
GRANT_NUMBER: BB/I02612X/1
GRANT_NUMBER: BB/I02612X/1
Source: Self-asserted source
Robert D. Finn via DimensionsWizard

Micro B3: Marine Microbial Biodiversity, Bioinformatics and Biotechnology

2012 to 2015 | Grant
European Commission (Brussels, BE)
Part of GRANT_NUMBER:

287589
Source: Self-asserted source
Robert D. Finn

IDA2GO: Improving Domain Annotation and Representation within InterPro

2012 to 2014 | Grant
Biotechnology and Biological Sciences Research Council (Swindon, Wiltshire, GB)
Part of GRANT_NUMBER:

BB/K004328/1
Source: Self-asserted source
Robert D. Finn

Integrated bioinformatics resources for fungal and oomycetes pathogens of pla

Grant
Biotechnology and Biological Sciences Research Council (Swindon, GB)
Part of GRANT_NUMBER:

BBSRC-BBR APP40209
Source: Self-asserted source
Robert D. Finn

MIMICC – Modelling microbiome dynamics in continuous culture

Grant
Biotechnology and Biological Sciences Research Council (Swindon, GB)
GRANT_NUMBER:

BB/Z516648/1
Source: Self-asserted source
Robert D. Finn

Works (50 of 192)

Items per page:
Page 1 of 4

A holo-omics analysis shows how sugar kelp can boost gut health in Atlantic salmon

Aquaculture.
2025-02 | Journal article
OTHER-ID:

IND608711958
Contributors: Rasmussen JA; Bernhard A; Lecaudey LA; Kale V; Baldi G; Myrmel LS; Hansen M; Brealey JC; Mak SST; Nielsen IB et al.
Source: Self-asserted source
Robert D. Finn via Europe PubMed Central

mettannotator: a comprehensive and scalable Nextflow annotation pipeline for prokaryotic assemblies

Bioinformatics
2025-02-04 | Journal article
DOI: 10.1093/bioinformatics/btaf037
Contributors: Tatiana A Gurbich; Martin Beracochea; Nishadi H De Silva; Robert D Finn; Xin Gao
Source: check_circle
Crossref

HoloFood Data Portal: holo-omic datasets for analysing host-microbiota interactions in animal production.

Database : the journal of biological databases and curation
2025-01 | Journal article
DOI: 10.1093/database/baae112
PMID: 39797569
Contributors: Rogers AB; Kale V; Baldi G; Alberdi A; Gilbert MTP; Gupta D; Limborg MT; Li S; Payne T; Petersen B et al.
Source: Self-asserted source
Robert D. Finn via Europe PubMed Central

EMBL’s European Bioinformatics Institute (EMBL-EBI) in 2024

Nucleic Acids Research
2025-01-06 | Journal article
DOI: 10.1093/nar/gkae1089
Contributors: Matthew Thakur; Catherine Brooksbank; Robert D Finn; Helen V Firth; Julia Foreman; Mallory Freeberg; Kim T Gurwitz; Melissa Harrison; David Hulcoop; Sarah E Hunt et al.
Source: check_circle
Crossref

The growing repertoire of phage anti-defence systems

Trends in Microbiology
2024-12 | Journal article
DOI: 10.1016/j.tim.2024.05.005
Contributors: Khalimat Murtazalieva; Andre Mu; Aleksandra Petrovskaya; Robert D. Finn
Source: check_circle
Crossref

Fungtion: A Server for Predicting and Visualizing Fungal Effector Proteins

Journal of Molecular Biology
2024-09 | Journal article
DOI: 10.1016/j.jmb.2024.168613
Part of ISSN: 0022-2836
Contributors: Jiahui Li; Jinzheng Ren; WEI DAI; Christopher Stubenrauch; Robert D. Finn; Jiawei Wang
Source: Self-asserted source
Robert D. Finn

CELEBRIMBOR: core and accessory genes from metagenomes

Bioinformatics
2024-09-02 | Journal article
DOI: 10.1093/bioinformatics/btae542
Contributors: Joel Hellewell; Samuel T Horsfield; Johanna von Wachsmann; Tatiana A Gurbich; Robert D Finn; Zamin Iqbal; Leah W Roberts; John A Lees; Can Alkan
Source: check_circle
Crossref

Diversity and specificity of molecular functions in cyanobacterial symbionts

Scientific Reports
2024-08-12 | Journal article
DOI: 10.1038/s41598-024-69215-8
Contributors: Ellen S. Cameron; Santiago Sanchez; Nick Goldman; Mark L. Blaxter; Robert D. Finn
Source: check_circle
Crossref

Gut microbiome community structure correlates with different behavioral phenotypes in the Belyaev farm-fox experiment

2024-08-12 | Preprint
DOI: 10.21203/rs.3.rs-4697888/v1
Contributors: Lara C Puetz; Tom O. Delmont; Alex L. Mitchell; Robert Finn; Guojie Zhang; Darya V. Shepeleva; Anastasiya V. Kharlamova; Anna Kukekova; Lyudmila N. Trut; M Thomas P Gilbert
Source: check_circle
Crossref

CODARFE: Unlocking the prediction of continuous environmental variables based on microbiome

2024-07-19 | Preprint
DOI: 10.1101/2024.07.18.604052
Contributors: Murilo Caminotto Barbosa; João Fernando Marques da Silva; Leonardo Cardoso Alves; Robert D Finn; Alexandre Rossi Paschoal
Source: check_circle
Crossref

mettannotator: a comprehensive and scalable Nextflow annotation pipeline for prokaryotic assemblies

2024-07-11 | Preprint
DOI: 10.1101/2024.07.11.603040
Contributors: Tatiana A. Gurbich; Martin Beracochea; Nishadi H. De Silva; Robert D. Finn
Source: check_circle
Crossref

CELEBRIMBOR: Pangenomes from metagenomes

2024-04-09 | Preprint
DOI: 10.1101/2024.04.05.588231
Contributors: Joel Hellewell; Samuel T. Horsfield; Johanna von Wachsmann; Tatiana Gurbich; Robert D. Finn; Zamin Iqbal; Leah W. Roberts; John A. Lees
Source: check_circle
Crossref

Specialization in Molecular Functions and Secondary Metabolite Production Potential in Cyanobacterial Symbionts

2024-03-23 | Preprint
DOI: 10.1101/2024.03.22.586251
Contributors: Ellen S Cameron; Santiago Sanchez; Nick Goldman; Mark Blaxter; Robert D. Finn
Source: check_circle
Crossref

Establishing the ELIXIR Microbiome Community [version 1; peer review: 1 approved, 1 approved with reservations]

2024-01-08 | Journal article
DOI: 10.12688/f1000research.144515.1
Part of ISSN: 2046-1402
Funded by GRANT_NUMBER:

1286824N

Funded by GRANT_NUMBER: BB/V01868X/1
Funded by GRANT_NUMBER:

C19/BM/13684739

Funded by GRANT_NUMBER:

IR0000010

Funded by GRANT_NUMBER:

PIR01_00017

Funded by GRANT_NUMBER: UIDB/04326/2020, UIDP/04326/2020, LA/P/0101/2020
Contributors: Robert D. Finn; Bachir Balech; Josephine Burgin; Physilia Chua; Erwan Corre; Cymon J. Cox; Claudio Donati; Vitor Martins dos Santos; Bruno Fosso; John Hancock et al.
Source: check_circle
F1000
grade
Preferred source (of 2)‎

Ensembl 2024.

Nucleic acids research
2023-11 | Journal article
DOI: 10.1093/nar/gkad1049
PMID: 37953337
Contributors: Harrison PW; Amode MR; Austine-Orimoloye O; Azov AG; Barba M; Barnes I; Becker A; Bennett R; Berry A; Bhai J et al.
Source: Self-asserted source
Robert D. Finn via Europe PubMed Central

plastiC: A pipeline for recovery and characterization of plastid genomes from metagenomic datasets

2023-10 | Preprint
DOI: 10.12688/wellcomeopenres.19589.1
PPR: PPR744059
Contributors: Cameron ES; Blaxter ML; Finn RD
Source: Self-asserted source
Robert D. Finn via Europe PubMed Central

SPIRE: a Searchable, Planetary-scale mIcrobiome REsource

2023-10-11 | Other
DOI: 10.1093/nar/gkad943
Contributors: Thomas S Schmidt; Pamela Ferretti; Hans Ruscheweyh; Yiqian Duan; Thea Van Rossum; Robert Finn; Michael Kuhn; Daniel R Mende; Askarbek Orakov; Luis Pedro Coelho et al.
Source: check_circle
Crossref

Challenges and opportunities in sharing microbiome data and analyses

Nature Microbiology
2023-10-02 | Journal article
DOI: 10.1038/s41564-023-01484-x
Contributors: Curtis Huttenhower; Robert D. Finn; Alice Carolyn McHardy
Source: check_circle
Crossref

VIRify: An integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models

PLOS Computational Biology
2023-08-28 | Journal article
DOI: 10.1371/journal.pcbi.1011422
Contributors: Guillermo Rangel-Pineros; Christos A. Ouzounis; Alexandre Almeida; Martin Beracochea; Ekaterina Sakharova; Manja Marz; Alejandro Reyes Muñoz; Martin Hölzer; Robert D. Finn
Source: check_circle
Crossref

Tanner Awards for the Most‐Cited Articles of 2020

Journal of Food Science
2023-06-20 | Journal article
DOI: 10.1111/1750-3841.16670
Part of ISSN: 0022-1147
Part of ISSN: 1750-3841
Source: Self-asserted source
Robert D. Finn

Expansion of novel biosynthetic gene clusters from diverse environments using SanntiS

2023-05-24 | Preprint
DOI: 10.1101/2023.05.23.540769
Contributors: Santiago Sanchez; Joel D. Rogers; Alexander B. Rogers; Maaly Nassar; Johanna McEntyre; Martin Welch; Florian Hollfelder; Robert D. Finn
Source: check_circle
Crossref

Staphylococcal diversity in atopic dermatitis from an individual to a global scale.

Cell host & microbe
2023-04 | Journal article
DOI: 10.1016/j.chom.2023.03.010
PMID: 37054678
Contributors: Saheb Kashaf S; Harkins CP; Deming C; Joglekar P; Conlan S; Holmes CJ; NISC Comparative Sequencing Program; Almeida A; Finn RD; Segre JA et al.
Source: Self-asserted source
Robert D. Finn via Europe PubMed Central

Exploring microbial functional biodiversity at the protein family level-From metagenomic sequence reads to annotated protein clusters.

Frontiers in bioinformatics
2023-03 | Journal article
DOI: 10.3389/fbinf.2023.1157956
PMID: 36959975
PMC: PMC10029925
Contributors: Baltoumas FA; Karatzas E; Paez-Espino D; Venetsianou NK; Aplakidou E; Oulas A; Finn RD; Ovchinnikov S; Pafilis E; Kyrpides NC et al.
Source: Self-asserted source
Robert D. Finn via Europe PubMed Central

Evidence for a core set of microbial lichen symbionts from a global survey of metagenomes

2023-02 | Preprint
DOI: 10.1101/2023.02.02.524463
PPR: PPR611879
Contributors: Tagirdzhanova G; Saary P; Cameron ES; Garber AI; Díaz Escandón D; Goyette S; Nogerius VT; Passo A; Mayrhofer H; Holien H et al.
Source: Self-asserted source
Robert D. Finn via Europe PubMed Central

MGnify Genomes: a resource for biome-specific microbial genome catalogues.

Journal of molecular biology
2023-02 | Journal article
DOI: 10.1016/j.jmb.2023.168016
PMID: 36806692
Contributors: Gurbich TA; Almeida A; Beracochea M; Burdett T; Burgin J; Cochrane G; Raj S; Richardson L; Rogers AB; Sakharova E et al.
Source: Self-asserted source
Robert D. Finn via Europe PubMed Central

Ensembl 2023.

Nucleic acids research
2023-01 | Journal article
DOI: 10.1093/nar/gkac958
PMID: 36318249
PMC: PMC9825606
Contributors: Martin FJ; Amode MR; Aneja A; Austine-Orimoloye O; Azov AG; Barnes I; Becker A; Bennett R; Berry A; Bhai J et al.
Source: Self-asserted source
Robert D. Finn via Europe PubMed Central

MGnify: the microbiome sequence data analysis resource in 2023.

Nucleic acids research
2023-01 | Journal article
DOI: 10.1093/nar/gkac1080
PMID: 36477304
PMC: PMC9825492
Contributors: Richardson L; Allen B; Baldi G; Beracochea M; Bileschi ML; Burdett T; Burgin J; Caballero-Pérez J; Cochrane G; Colwell LJ et al.
Source: Self-asserted source
Robert D. Finn via Europe PubMed Central

metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data.

GigaScience
2022-12 | Journal article
DOI: 10.1093/gigascience/giad078
PMID: 37850871
PMC: PMC10583283
Contributors: Zafeiropoulos H; Beracochea M; Ninidakis S; Exter K; Potirakis A; De Moro G; Richardson L; Corre E; Machado J; Pafilis E et al.
Source: Self-asserted source
Robert D. Finn via Europe PubMed Central

SymbNET: From metagenomics to metabolic interactions: course materials

2022-12 | Other
DOI: 10.6019/tol.symbnetmaterials-t.2022.00001.1
OTHER-ID:

C8150
Contributors: Rodrigues Araujo D; Finn R; Zimmerman M
Source: Self-asserted source
Robert D. Finn via Europe PubMed Central

plastiC: A pipeline for recovery and characterization of plastid genomes from metagenomic datasets

2022-12-23 | Preprint
DOI: 10.1101/2022.12.23.521586
Contributors: Ellen S. Cameron; Mark L. Blaxter; Robert D. Finn
Source: check_circle
Crossref

Screening of global microbiomes implies ecological boundaries impacting the distribution and dissemination of clinically relevant antimicrobial resistance genes

Communications Biology
2022-11-18 | Journal article
DOI: 10.1038/s42003-022-04187-x
Contributors: Qiang Lin; Basil Britto Xavier; Blaise T. F. Alako; Alex L. Mitchell; Sahaya Glingston Rajakani; Youri Glupczynski; Robert D. Finn; Guy Cochrane; Surbhi Malhotra-Kumar
Source: check_circle
Crossref

MetaGT: A pipeline for <i>de novo</i> assembly of metatranscriptomes with the aid of metagenomic data.

Frontiers in microbiology
2022-10 | Journal article
DOI: 10.3389/fmicb.2022.981458
PMID: 36386613
Contributors: Shafranskaya D; Kale V; Finn R; Lapidus AL; Korobeynikov A; Prjibelski AD
Source: Self-asserted source
Robert D. Finn via Europe PubMed Central

Novel strategies to improve chicken performance and welfare by unveiling host-microbiota interactions through hologenomics.

Frontiers in physiology
2022-09 | Journal article
DOI: 10.3389/fphys.2022.884925
PMID: 36148301
PMC: PMC9485813
Contributors: Tous N; Marcos S; Goodarzi Boroojeni F; Pérez de Rozas A; Zentek J; Estonba A; Sandvang D; Gilbert MTP; Esteve-Garcia E; Finn R et al.
Source: Self-asserted source
Robert D. Finn via Europe PubMed Central

VIRify: an integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models

2022-08-22 | Preprint
DOI: 10.1101/2022.08.22.504484
Contributors: Guillermo Rangel-Pineros; Alexandre Almeida; Martin Beracochea; Ekaterina Sakharova; Manja Marz; Alejandro Reyes Muñoz; Martin Hölzer; Robert D. Finn
Source: check_circle
Crossref

A machine learning framework for discovery and enrichment of metagenomics metadata from open access publications

GigaScience
2022-08-11 | Journal article
DOI: 10.1093/gigascience/giac077
Contributors: Maaly Nassar; Alexander B Rogers; Francesco Talo'; Santiago Sanchez; Zunaira Shafique; Robert D Finn; Johanna McEntyre
Source: check_circle
Crossref

Priorities for ocean microbiome research.

Nature microbiology
2022-06 | Journal article
DOI: 10.1038/s41564-022-01145-5
PMID: 35773399
Contributors: Tara Ocean Foundation; Tara Oceans; European Molecular Biology Laboratory (EMBL); European Marine Biological Resource Centre - European Research Infrastructure Consortium (EMBRC-ERIC)
Source: Self-asserted source
Robert D. Finn via Europe PubMed Central

A mouse model of occult intestinal colonization demonstrating antibiotic-induced outgrowth of carbapenem-resistant Enterobacteriaceae.

Microbiome
2022-03 | Journal article
DOI: 10.1186/s40168-021-01207-6
PMID: 35272717
Contributors: Sim CK; Kashaf SS; Stacy A; Proctor DM; Almeida A; Bouladoux N; Chen M; NISC Comparative Sequencing Program; Finn RD; Belkaid Y et al.
Source: Self-asserted source
Robert D. Finn via Europe PubMed Central

Unifying the known and unknown microbial coding sequence space.

eLife
2022-03 | Journal article
DOI: 10.7554/elife.67667
PMID: 35356891
PMC: PMC9132574
Contributors: Vanni C; Schechter MS; Acinas SG; Barberán A; Buttigieg PL; Casamayor EO; Delmont TO; Duarte CM; Eren AM; Finn RD et al.
Source: Self-asserted source
Robert D. Finn via Europe PubMed Central

Large-scale analysis reveals the distribution of novel cellular microbes across multiple biomes and kingdoms

2022-03-17 | Preprint
DOI: 10.21203/rs.3.rs-1441815/v1
Contributors: Paul Saary; Varsha Kale; Robert Finn
Source: check_circle
Crossref

A machine learning framework for discovery and enrichment of metagenomics metadata from open access publications

2022-02-25 | Preprint
DOI: 10.21203/rs.3.rs-1396476/v1
Contributors: Maaly Nassar; Alexander B. Rogers; Francesco Talo'; Santiago Sanchez; Zunaira Shafique; Robert D. Finn; Johanna McEntyre
Source: check_circle
Crossref

Ensembl Genomes 2022: an expanding genome resource for non-vertebrates.

Nucleic acids research
2022-01 | Journal article
DOI: 10.1093/nar/gkab1007
PMID: 34791415
PMC: PMC8728113
Contributors: Yates AD; Allen J; Amode RM; Azov AG; Barba M; Becerra A; Bhai J; Campbell LI; Carbajo Martinez M; Chakiachvili M et al.
Source: Self-asserted source
Robert D. Finn via Europe PubMed Central

The Ensembl COVID-19 resource: ongoing integration of public SARS-CoV-2 data.

Nucleic acids research
2022-01 | Journal article
DOI: 10.1093/nar/gkab889
PMID: 34634797
PMC: PMC8524594
Contributors: De Silva NH; Bhai J; Chakiachvili M; Contreras-Moreira B; Cummins C; Frankish A; Gall A; Genez T; Howe KL; Hunt SE et al.
Source: Self-asserted source
Robert D. Finn via Europe PubMed Central

Publisher Correction: A catalogue of 1,167 genomes from the human gut archaeome

Nature Microbiology
2022-01-10 | Journal article
DOI: 10.1038/s41564-022-01061-8
Contributors: Cynthia Maria Chibani; Alexander Mahnert; Guillaume Borrel; Alexandre Almeida; Almut Werner; Jean-François Brugère; Simonetta Gribaldo; Robert D. Finn; Ruth A. Schmitz; Christine Moissl-Eichinger
Source: check_circle
Crossref

Navigating bacterial taxonomy in a world of unchartered microbial organisms.

Trends in the systematics of bacteria and fungi
2021 | Book chapter
DOI: 10.1079/9781789244984.0179
Part of ISBN: 9781789244984
Source: Self-asserted source
Robert D. Finn
grade
Preferred source (of 2)‎

Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions.

Nature microbiology
2021-12 | Journal article
DOI: 10.1038/s41564-021-01011-w
PMID: 34952941
Contributors: Saheb Kashaf S; Proctor DM; Deming C; Saary P; Hölzer M; NISC Comparative Sequencing Program; Taylor ME; Kong HH; Segre JA; Almeida A et al.
Source: Self-asserted source
Robert D. Finn via Europe PubMed Central

A catalogue of 1,167 genomes from the human gut archaeome

Nature Microbiology
2021-12-30 | Journal article
DOI: 10.1038/s41564-021-01020-9
Contributors: Cynthia Maria Chibani; Alexander Mahnert; Guillaume Borrel; Alexandre Almeida; Almut Werner; Jean-François Brugère; Simonetta Gribaldo; Robert D. Finn; Ruth A. Schmitz; Christine Moissl-Eichinger
Source: check_circle
Crossref

Metagenomics approach for Polymyxa betae genome assembly enables comparative analysis towards deciphering the intracellular parasitic lifestyle of the plasmodiophorids.

Genomics
2021-11 | Journal article
DOI: 10.1016/j.ygeno.2021.11.018
PMID: 34798282
Contributors: Decroës A; Li JM; Richardson L; Mutasa-Gottgens E; Lima-Mendez G; Mahillon M; Bragard C; Finn RD; Legrève A
Source: Self-asserted source
Robert D. Finn via Europe PubMed Central

Reporting guidelines for human microbiome research: the STORMS checklist.

Nature medicine
2021-11 | Journal article
DOI: 10.1038/s41591-021-01552-x
PMID: 34789871
PMC: PMC9105086
Contributors: Mirzayi C; Renson A; Genomic Standards Consortium; Massive Analysis and Quality Control Society; Zohra F; Elsafoury S; Geistlinger L; Kasselman LJ; Waldron L
Source: Self-asserted source
Robert D. Finn via Europe PubMed Central

COP26: Meet the scientists behind the crucial climate summit

Nature News Q&A
2021-11-16 | Journal issue or edition
DOI: 10.1038/d41586-021-03029-w
Source: Self-asserted source
Robert D. Finn

Erratum to: Predicted Input of Uncultured Fungal Symbionts to a Lichen Symbiosis from Metagenome-Assembled Genomes.

Genome biology and evolution
2021-06 | Journal article
DOI: 10.1093/gbe/evab129
PMID: 34196707
PMC: PMC8247553
Contributors: Tagirdzhanova G; Saary P; Tingley JP; Díaz-Escandón D; Abbott DW; Finn RD; Spribille T
Source: Self-asserted source
Robert D. Finn via Europe PubMed Central
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Peer review (33 reviews for 11 publications/grants)

Review activity for Acta crystallographica. (1)
Review activity for Bioinformatics (11)
Review activity for Cell reports. (1)
Review activity for F1000Research. (1)
Review activity for Genome biology. (2)
Review activity for GigaScience. (4)
Review activity for Journal of molecular biology. (1)
Review activity for Nature biotechnology. (3)
Review activity for Nature methods. (1)
Review activity for Nucleic acids research. (7)
Review activity for Protein science. (1)
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