Virus-associated organosulfur metabolism in human and environmental systems

Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages

(2021) Kristopher Kieft et al.   Nature Communications

Lytic archaeal viruses infect abundant primary producers in Earth’s crust

(2021) Janina Rahlff et al.   Nature Communications

Phage-specific metabolic reprogramming of virocells

(2020) Cristina Howard-Varona et al.   ISME Journal

VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences

(2020) Kristopher Kieft et al.   Microbiome

Advantages and Limits of Metagenomic Assembly and Binning of a Giant Virus

(2020) Frederik Schulz et al.   mSystems

Large freshwater phages with the potential to augment aerobic methane oxidation

(2020) Lin-Xing Chen et al.   Nature Microbiology

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

(2019) Edoardo Pasolli et al.   CELL

Megaphages infect Prevotella and variants are widespread in gut microbiomes

(2019) Audra E. Devoto et al.   Nature Microbiology

Novel insights from uncultivated genomes of the global human gut microbiome

(2019) Stephen Nayfach et al.   NATURE

A new genomic blueprint of the human gut microbiota

(2019) Alexandre Almeida et al.   NATURE

Time-series metatranscriptomes reveal conserved patterns between phototrophic and heterotrophic microbes in diverse freshwater systems

(2019) Alexandra M. Linz et al.   LIMNOLOGY AND OCEANOGRAPHY

Sulfur metabolites in the pelagic ocean

(2019) Mary Ann Moran et al.   NATURE REVIEWS MICROBIOLOGY

Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle

(2018) Karthik Anantharaman et al.   ISME Journal

Hydrogen sulfide in physiology and pathogenesis of bacteria and viruses

(2018) Virender Kumar Pal et al.   IUBMB LIFE

UniProt: the universal protein knowledgebase

(2018) The UniProt Consortium   NUCLEIC ACIDS RESEARCH

BigR is a sulfide sensor that regulates a sulfur transferase/dioxygenase required for aerobic respiration of plant bacteria under sulfide stress

(2018) Nayara Patricia Vieira de Lira et al.   Scientific Reports

Dynamics of metatranscription in the inflammatory bowel disease gut microbiome

(2018) Melanie Schirmer et al.   Nature Microbiology

Discovery of several novel, widespread, and ecologically distinct marine Thaumarchaeota viruses that encode amoC nitrification genes

(2018) Nathan A. Ahlgren et al.   ISME Journal

Role of APS reductase in biogeochemical sulfur isotope fractionation

(2018) Min Sub Sim et al.   Nature Communications

Freshwater carbon and nutrient cycles revealed through reconstructed population genomes

(2018) Alexandra M. Linz et al.   PeerJ

Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing

(2018) Gareth Trubl et al.   mSystems

Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates

(2017) Matthew R. Olm et al.   GENOME RESEARCH

The immune response to Prevotella bacteria in chronic inflammatory disease

(2017) Jeppe Madura Larsen   IMMUNOLOGY

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

(2017) Matthew R Olm et al.   ISME Journal

Sulfide production and oxidation by heterotrophic bacteria under aerobic conditions

(2017) Yongzhen Xia et al.   ISME Journal

Subspecies in the global human gut microbiome

(2017) Paul I Costea et al.   Molecular Systems Biology

Sulfide-responsive transcriptional repressor SqrR functions as a master regulator of sulfide-dependent photosynthesis

(2017) Takayuki Shimizu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Energetic cost of building a virus

(2017) Gita Mahmoudabadi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional Characterization of Novel Faecalibacterium prausnitzii Strains Isolated from Healthy Volunteers: A Step Forward in the Use of F. prausnitzii as a Next-Generation Probiotic

(2017) Rebeca Martín et al.   Frontiers in Microbiology

Connections between the human gut microbiome and gestational diabetes mellitus

(2017) Ya-Shu Kuang et al.   GigaScience

Sulfide Homeostasis and Nitroxyl Intersect via Formation of Reactive Sulfur Species in Staphylococcus aureus

(2017) Hui Peng et al.   mSphere

A fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomic

(2017) Orlane Patrascu et al.   Scientific Reports

DNA Backbone Sulfur-Modification Expands Microbial Growth Range under Multiple Stresses by its anti-oxidation function

(2017) Yan Yang et al.   Scientific Reports

Viral metabolic reprogramming in marine ecosystems

(2016) Bonnie L Hurwitz et al.   CURRENT OPINION IN MICROBIOLOGY

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

(2016) Simon Roux et al.   NATURE

Uncovering Earth’s virome

(2016) David Paez-Espino et al.   NATURE

Measurement of bacterial replication rates in microbial communities

(2016) Christopher T Brown et al.   NATURE BIOTECHNOLOGY

CDD/SPARCLE: functional classification of proteins via subfamily domain architectures

(2016) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

NCBI prokaryotic genome annotation pipeline

(2016) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

Emerging Roles of Hydrogen Sulfide in Inflammatory and Neoplastic Colonic Diseases

(2016) Fang-Fang Guo et al.   Frontiers in Physiology

Rethinking the Ancient Sulfur Cycle

(2015) David A. Fike et al.   Annual Review of Earth and Planetary Sciences

Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease

(2015) Jason M. Norman et al.   CELL

The Oxidative Stress Network of Mycobacterium tuberculosis Reveals Coordination between Radical Detoxification Systems

(2015) Subhalaxmi Nambi et al.   Cell Host & Microbe

tRNA thiolation links translation to stress responses in Saccharomyces cerevisiae

(2015) Jadyn R. Damon et al.   MOLECULAR BIOLOGY OF THE CELL

l-Cysteine metabolism and its nutritional implications

(2015) Jie Yin et al.   MOLECULAR NUTRITION & FOOD RESEARCH

GenBank

(2015) Karen Clark et al.   NUCLEIC ACIDS RESEARCH

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Crystal Structures of the Kinase Domain of the Sulfate-Activating Complex in Mycobacterium tuberculosis

(2015) Ömer Poyraz et al.   PLoS One

Dysbiosis gut microbiota associated with inflammation and impaired mucosal immune function in intestine of humans with non-alcoholic fatty liver disease

(2015) Weiwei Jiang et al.   Scientific Reports

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Engineering Modular Viral Scaffolds for Targeted Bacterial Population Editing

(2015) Hiroki Ando et al.   Cell Systems

Methanesulfonate (MSA) Catabolic Genes from Marine and Estuarine Bacteria

(2015) Ana C. Henriques et al.   PLoS One

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

The Gut Commensal Bacteroides thetaiotaomicron Exacerbates Enteric Infection through Modification of the Metabolic Landscape

(2014) Meredith M. Curtis et al.   Cell Host & Microbe

Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome

(2014) Bonnie L Hurwitz et al.   ISME Journal

The elemental composition of virus particles: implications for marine biogeochemical cycles

(2014) Luis F. Jover et al.   NATURE REVIEWS MICROBIOLOGY

NCBI Viral Genomes Resource

(2014) J. Rodney Brister et al.   NUCLEIC ACIDS RESEARCH

Sulfur Oxidation Genes in Diverse Deep-Sea Viruses

(2014) K. Anantharaman et al.   SCIENCE

A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes

(2014) Bas E. Dutilh et al.   Nature Communications

Changes of the human gut microbiome induced by a fermented milk product

(2014) Patrick Veiga et al.   Scientific Reports

Non-contiguous finished genome sequence and description of Alistipes ihumii sp. nov.

(2014) Anne Pfleiderer et al.   Standards in Genomic Sciences

Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics

(2014) Simon Roux et al.   eLife

Tail Tip Proteins Related to Bacteriophage λ gpL Coordinate an Iron-Sulfur Cluster

(2013) William Tam et al.   JOURNAL OF MOLECULAR BIOLOGY

A versatile, efficient strategy for assembly of multi-fragment expression vectors in Saccharomyces cerevisiae using 60 bp synthetic recombination sequences

(2013) Niels GA Kuijpers et al.   Microbial Cell Factories

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

IMG/M 4 version of the integrated metagenome comparative analysis system

(2013) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

High-resolution view of bacteriophage lambda gene expression by ribosome profiling

(2013) X. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Non contiguous-finished genome sequence and description of Alistipes obesi sp. nov

(2013) Perrine Hugon et al.   Standards in Genomic Sciences

Metabolic reprogramming by viruses in the sunlit and dark ocean

(2013) Bonnie L Hurwitz et al.   GENOME BIOLOGY

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

The Fe(II)/α-ketoglutarate-dependent taurine dioxygenases from Pseudomonas putida and Escherichia coli are tetramers

(2012) Stefan H. Knauer et al.   FEBS Journal

Butyricicoccus pullicaecorumin inflammatory bowel disease

(2012) Venessa Eeckhaut et al.   GUT

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A fully decompressed synthetic bacteriophage øX174 genome assembled and archived in yeast

(2012) Paul R. Jaschke et al.   VIROLOGY

Microbial pathways in colonic sulfur metabolism and links with health and disease

(2012) Franck Carbonero et al.   Frontiers in Physiology

Easyfig: a genome comparison visualizer

(2011) M. J. Sullivan et al.   BIOINFORMATICS

Microfossils of sulphur-metabolizing cells in 3.4-billion-year-old rocks of Western Australia

(2011) David Wacey et al.   Nature Geoscience

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2011) R. Caspi et al.   NUCLEIC ACIDS RESEARCH

Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism

(2011) L. R. Thompson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CD-HIT Suite: a web server for clustering and comparing biological sequences

(2010) Ying Huang et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Microbial production of recalcitrant dissolved organic matter: long-term carbon storage in the global ocean

(2010) Nianzhi Jiao et al.   NATURE REVIEWS MICROBIOLOGY

New function and application of the cysteine synthase from archaea

(2009) Kazuhiko Ishikawa et al.   BIOCHEMICAL ENGINEERING JOURNAL

H2S Biogenesis by Human Cystathionine γ-Lyase Leads to the Novel Sulfur Metabolites Lanthionine and Homolanthionine and Is Responsive to the Grade of Hyperhomocysteinemia

(2009) Taurai Chiku et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

An Iron-Sulfur Cluster Is Essential for the Binding of Broken DNA by AddAB-type Helicase-Nucleases

(2009) Joseph T. P. Yeeles et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

P087, a lactococcal phage with a morphogenesis module similar to an Enterococcus faecalis prophage

(2009) Manuela Villion et al.   VIROLOGY

Identification of replication origins in prokaryotic genomes

(2008) Natalia V. Sernova et al.   BRIEFINGS IN BIOINFORMATICS

The Complete Genome Sequence of Escherichia coli DH10B: Insights into the Biology of a Laboratory Workhorse

(2008) T. Durfee et al.   JOURNAL OF BACTERIOLOGY

Modeling the Fitness Consequences of a Cyanophage-Encoded Photosynthesis Gene

(2008) Jason G. Bragg et al.   PLoS One