Search Results - "Finn RD"

From "synthetic" to defined microbial communities for clearer terminology.

Authors: Koch H Clavel T Mayr C et al.

Source: Nature communications [Nat Commun] 2026 Jun 08; Vol. 17 (1). Date of Electronic Publication: 2026 Jun 08.

Publication Type: Journal Article

Journal Info: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE; In Process

HoloFoodR: a statistical programming framework for holo-omics data integration workflows.

Authors: Borman T Sannikov A Finn RD et al.

Source: Bioinformatics (Oxford, England) [Bioinformatics] 2025 Nov 01; Vol. 41 (11).

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE

An Approach to Integrate Metagenomics, Metatranscriptomics and Metaproteomics Data in Public Data Resources.

Authors: Wang S Kaur S Kunath BJ et al.

Source: Proteomics [Proteomics] 2025 Sep; Vol. 25 (17-18), pp. 33-42. Date of Electronic Publication: 2025 Apr 28.

Publication Type: Journal Article

Journal Info: Publisher: Wiley-VCH Country of Publication: Germany NLM ID: 101092707 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1615-9861 (Electronic) Linking ISSN: 16159853 NLM ISO Abbreviation: Proteomics Subsets: MEDLINE

HMMER web server: 2026 update.

Authors: Rajković A Beracochea M Rogers AB et al.

Source: Nucleic acids research [Nucleic Acids Res] 2026 Apr 27. Date of Electronic Publication: 2026 Apr 27.

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE

Functional gut microbiota dynamics of generalist and specialist bacteria in association with chicken growth.

Authors: Marcos S Odriozola I Aizpurua O et al.

Source: ISME communications [ISME Commun] 2026 Apr 10; Vol. 6 (1), pp. ycag091. Date of Electronic Publication: 2026 Apr 10 (Print Publication: 2026).

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 9918205372406676 Publication Model: eCollection Cited Medium: Internet ISSN: 2730-6151 (Electronic) Linking ISSN: 27306151 NLM ISO Abbreviation: ISME Commun Subsets: PubMed not MEDLINE

Gut microbiome community structure correlates with different behavioral phenotypes in the Belyaev Farm-Fox Experiment.

Authors: Puetz LC O Delmont T Mitchell AL et al.

Source: Communications biology [Commun Biol] 2026 Mar 27; Vol. 9 (1). Date of Electronic Publication: 2026 Mar 27.

Publication Type: Journal Article

Journal Info: Publisher: Nature Publishing Group UK Country of Publication: England NLM ID: 101719179 Publication Model: Electronic Cited Medium: Internet ISSN: 2399-3642 (Electronic) Linking ISSN: 23993642 NLM ISO Abbreviation: Commun Biol Subsets: MEDLINE

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

Authors: Gurbich TA Beracochea M De Silva NH et al.

Source: Bioinformatics (Oxford, England) [Bioinformatics] 2025 Feb 04; Vol. 41 (2).

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE

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

Authors: Rogers AB Kale V Baldi G et al.

Source: Database : the journal of biological databases and curation [Database (Oxford)] 2025 Jan 11; Vol. 2025.

Publication Type: Journal Article; Dataset; Research Support, Non-U.S. Gov't

Journal Info: Publisher: Oxford Journals Country of Publication: England NLM ID: 101517697 Publication Model: Print Cited Medium: Internet ISSN: 1758-0463 (Electronic) Linking ISSN: 17580463 NLM ISO Abbreviation: Database (Oxford) Subsets: MEDLINE

GENCODE 2025: reference gene annotation for human and mouse.

Authors: Mudge JM Carbonell-Sala S Diekhans M et al.

Source: Nucleic acids research [Nucleic Acids Res] 2025 Jan 06; Vol. 53 (D1), pp. D966-D975.

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE

Ensembl 2025.

Authors: Dyer SC Austine-Orimoloye O Azov AG et al.

Source: Nucleic acids research [Nucleic Acids Res] 2025 Jan 06; Vol. 53 (D1), pp. D948-D957.

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE

EMBL's European Bioinformatics Institute (EMBL-EBI) in 2024.

Authors: Thakur M Brooksbank C Finn RD et al.

Source: Nucleic acids research [Nucleic Acids Res] 2025 Jan 06; Vol. 53 (D1), pp. D10-D19.

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE

nf-core/proteinfamilies: a scalable pipeline for the generation of protein families.

Authors: Karatzas E Beracochea M Baltoumas FA et al.

Corporate Authors: Karatzas E Beracochea M Baltoumas FA et al.

Source: GigaScience [Gigascience] 2026 Jan 21; Vol. 15.

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: United States NLM ID: 101596872 Publication Model: Print Cited Medium: Internet ISSN: 2047-217X (Electronic) Linking ISSN: 2047217X NLM ISO Abbreviation: Gigascience Subsets: MEDLINE

Ensembl 2026.

Authors: Yates AD Austine-Orimoloye O Azov AG et al.

Source: Nucleic acids research [Nucleic Acids Res] 2026 Jan 06; Vol. 54 (D1), pp. D1053-D1060.

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE

CELEBRIMBOR: core and accessory genes from metagenomes.

Authors: Hellewell J Horsfield ST von Wachsmann J et al.

Source: Bioinformatics (Oxford, England) [Bioinformatics] 2024 Sep 02; Vol. 40 (9).

Publication Type: Journal Article; Research Support, Non-U.S. Gov't

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE

Establishing the ELIXIR Microbiome Community.

Authors: Finn RD Balech B Burgin J et al.

Source: F1000Research [F1000Res] 2025 Sep 08; Vol. 13. Date of Electronic Publication: 2025 Sep 08 (Print Publication: 2024).

Publication Type: Journal Article

Journal Info: Publisher: F1000 Research Ltd Country of Publication: England NLM ID: 101594320 Publication Model: eCollection Cited Medium: Internet ISSN: 2046-1402 (Electronic) Linking ISSN: 20461402 NLM ISO Abbreviation: F1000Res Subsets: MEDLINE

A bacterial and viral genome catalogue from Atlantic salmon highlights diverse gut microbiome compositions at pre- and post-smolt life stages.

Authors: Kale V Baldi G Beracochea M et al.

Source: Animal microbiome [Anim Microbiome] 2025 Aug 11; Vol. 7 (1), pp. 85. Date of Electronic Publication: 2025 Aug 11.

Publication Type: Journal Article

Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 101759457 Publication Model: Electronic Cited Medium: Internet ISSN: 2524-4671 (Electronic) Linking ISSN: 25244671 NLM ISO Abbreviation: Anim Microbiome Subsets: PubMed not MEDLINE

SPIRE: a Searchable, Planetary-scale mIcrobiome REsource.

Authors: Schmidt TSB Fullam A Ferretti P et al.

Source: Nucleic acids research [Nucleic Acids Res] 2024 Jan 05; Vol. 52 (D1), pp. D777-D783.

Publication Type: Journal Article; Research Support, Non-U.S. Gov't

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE

Ensembl 2024.

Authors: Harrison PW Amode MR Austine-Orimoloye O et al.

Source: Nucleic acids research [Nucleic Acids Res] 2024 Jan 05; Vol. 52 (D1), pp. D891-D899.

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE

Assessing the safety of microbiome perturbations.

Authors: Metris A Walker AW Showering A et al.

Source: Microbial genomics [Microb Genom] 2025 May; Vol. 11 (5).

Publication Type: Journal Article; Review

Journal Info: Publisher: Microbiology Society Country of Publication: England NLM ID: 101671820 Publication Model: Print Cited Medium: Internet ISSN: 2057-5858 (Electronic) Linking ISSN: 20575858 NLM ISO Abbreviation: Microb Genom Subsets: MEDLINE

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

Authors: Rangel-Pineros G Almeida A Beracochea M et al.

Source: PLoS computational biology [PLoS Comput Biol] 2023 Aug 28; Vol. 19 (8), pp. e1011422. Date of Electronic Publication: 2023 Aug 28 (Print Publication: 2023).

Publication Type: Journal Article; Research Support, Non-U.S. Gov't

Journal Info: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet ISSN: 1553-7358 (Electronic) Linking ISSN: 1553734X NLM ISO Abbreviation: PLoS Comput Biol Subsets: MEDLINE