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List of works by Robert D. Finn

3DPatch: fast 3D structure visualization with residue conservation

scientific article published on 01 January 2019

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

scientific article published on 30 December 2021

A human gut bacterial genome and culture collection for improved metagenomic analyses

scientific article published on 04 February 2019

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

scientific article published in 2022

A new genomic blueprint of the human gut microbiota

scientific article published on 11 February 2019

A unified catalog of 204,938 reference genomes from the human gut microbiome

scientific article published on 20 July 2020

A vaccinology Approach to the Identification and Characterization of Dermanyssus Gallinae Candidate Protective Antigens for the Control of Poultry Red Mite Infestations

scientific article published on 20 November 2019

An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities

scientific article published on 19 May 2021

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

scientific article

Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments.

scientific article

COVID-19 pandemic reveals the peril of ignoring metadata standards

scientific article published on 19 June 2020

Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes

scientific article

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

scientific article

Clustered coding variants in the glutamate receptor complexes of individuals with schizophrenia and bipolar disorder

scientific article

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

Conformational changes of Escherichia coli sigma54-RNA-polymerase upon closed-promoter complex formation

scientific article published on 5 October 2005

Consent insufficient for data release-Response

scientific article published on 01 May 2019

DASMI: exchanging, annotating and assessing molecular interaction data

scientific article (publication date: 15 May 2009)

DUFs: families in search of function

scientific article

Determination of Escherichia coli RNA polymerase structure by single particle cryoelectron microscopy.

scientific article

Determination of the redox potentials and electron transfer properties of the FAD- and FMN-binding domains of the human oxidoreductase NR1

scientific article

Dfam: a database of repetitive DNA based on profile hidden Markov models

scientific article (publication date: 2013)

EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies.

scientific article published on 23 October 2017

EBI metagenomics in 2016--an expanding and evolving resource for the analysis and archiving of metagenomic data

scientific article

ELIXIR pilot action: Marine metagenomics - towards a domain specific set of sustainable services

scientific article published on 23 January 2017

Eleven quick tips to build a usable REST API for life sciences

scientific article published on 13 December 2018

Ensembl 2023

scientific article published in November 2022

Ensembl 2024

scientific article published on 11 November 2023

Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species.

scientific article published on 30 October 2017

Escherichia coli RNA polymerase core and holoenzyme structures

scientific article

Establishing the ELIXIR Microbiome Community

scientific article published on 8 January 2024

Experience using web services for biological sequence analysis.

scientific article published on 11 July 2008

GO annotation in InterPro: why stability does not indicate accuracy in a sea of changing annotations

scientific article published on 19 March 2016

Gene Ontology Consortium: going forward

scientific article (publication date: 2015)

Genome properties in 2019: a new companion database to InterPro for the inference of complete functional attributes

scientific article published on 01 January 2019

Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation

scientific article published on 01 January 2020

HMMER web server: 2015 update

scientific article published on 5 May 2015

HMMER web server: 2018 update.

scientific article published in July 2018

HMMER web server: interactive sequence similarity searching ⬇️

scientific article published on May 18, 2011

HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes

scientific article published on 17 November 2015

Identification of a functionally impaired allele of human novel oxidoreductase 1 (NDOR1), NDOR1*1

scientific article

Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies

scientific article published on 04 January 2019

Identifying protein domains with the Pfam database

scientific article

Integrating biological data--the Distributed Annotation System

scientific article

Integrating sequence and structural biology with DAS

scientific article

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 in 2019: improving coverage, classification and access to protein sequence annotations

article by Alex Mitchell et al published 6 November 2018 in Nucleic Acids Research

InterPro: the integrative protein signature database

scientific article

Key challenges for the creation and maintenance of specialist protein resources

scientific article

MGnify: the microbiome analysis resource in 2020

scientific article published on 01 January 2020

MGnify: the microbiome sequence data analysis resource in 2023

scientific article published in 2022

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

scientific article published on December 5, 2011

Metaproteomics characterization of the alphaproteobacteria microbiome in different developmental and feeding stages of the poultry red mite Dermanyssus gallinae (De Geer, 1778)

scientific article published on 02 August 2019

Microbial abundance, activity and population genomic profiling with mOTUs2

scientific article published on 4 March 2019

Microbial community drivers of PK/NRP gene diversity in selected global soils

article

Microbial composition of Kombucha determined using amplicon sequencing and shotgun metagenomics

scientific article published on 20 January 2020

Modifier effects between regulatory and protein-coding variation

scientific article

New developments in the InterPro database

scientific article

Non-Coding RNA Analysis Using the Rfam Database

article

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

scientific article

Pfam: a domain-centric method for analyzing proteins and proteomes

scientific article

Pfam: clans, web tools and services

scientific article

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

Predicting active site residue annotations in the Pfam database

scientific article

ProServer: a simple, extensible Perl DAS server

scientific article

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

scientific article published on 09 June 2021

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

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

scientific article (publication date: 2012)

Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation.

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: Wikipedia, clans and the "decimal" release

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

Single-particle electron cryo-microscopy: towards atomic resolution.

scientific article

Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models

scientific article (publication date: 13 January 2014)

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

The C-Terminal 12 Amino Acids of ςN Are Required for Structure and Function

scientific article published in 1999

The Dfam database of repetitive DNA families

scientific article

The EMBL-EBI search and sequence analysis tools APIs in 2019

scientific article published on 01 July 2019

The European Bioinformatics Institute in 2016: Data growth and integration

scientific article

The HMMER Web Server for Protein Sequence Similarity Search

scientific article published on 8 December 2017

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 PASTA domain: a beta-lactam-binding domain

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 in 2019

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

The challenge of increasing Pfam coverage of the human proteome

scientific article

The complexity, challenges and benefits of comparing two transporter classification systems in TCDB and Pfam

scientific article

The crystal structure of a bacterial Sufu-like protein defines a novel group of bacterial proteins that are similar to the N-terminal domain of human Sufu

scientific article

The first structure in a family of peptidase inhibitors reveals an unusual Ig-like fold

scientific article

The genome of the simian and human malaria parasite Plasmodium knowlesi

scientific article

The metagenomic data life-cycle: standards and best practices.

scientific article

The second paradigm for activation of transcription.

scientific article

The structure of BVU2987 from Bacteroides vulgatus reveals a superfamily of bacterial periplasmic proteins with possible inhibitory function

scientific article

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

scientific article

Toward unrestricted use of public genomic data:

scientific article

TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations

article

Twenty years of the MEROPS database of proteolytic enzymes, their substrates and inhibitors.

scientific article

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

scientific article

Unifying the known and unknown microbial coding sequence space

scientific article published on 31 March 2022

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

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