A distinct abundant group of microbial rhodopsins discovered using functional metagenomics

Asgard archaea illuminate the origin of eukaryotic cellular complexity

(2017) Katarzyna Zaremba-Niedzwiedzka et al.   NATURE

Functional metagenomic screen reveals new and diverse microbial rhodopsins

(2016) Alina Pushkarev et al.   ISME Journal

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

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

The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis

(2016) Vikram Alva et al.   NUCLEIC ACIDS RESEARCH

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

(2016) Karthik Anantharaman et al.   Nature Communications

Unusual biology across a group comprising more than 15% of domain Bacteria

(2015) Christopher T. Brown et al.   NATURE

Structural basis for Na+ transport mechanism by a light-driven Na+ pump

(2015) Hideaki E. Kato et al.   NATURE

The Phyre2 web portal for protein modeling, prediction and analysis

(2015) Lawrence A Kelley et al.   Nature Protocols

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Patterns and ecological drivers of ocean viral communities

(2015) J. R. Brum et al.   SCIENCE

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

Spectroscopic Study of a Light-Driven Chloride Ion Pump from Marine Bacteria

(2014) Keiichi Inoue et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Microbial and Animal Rhodopsins: Structures, Functions, and Molecular Mechanisms

(2013) Oliver P. Ernst et al.   CHEMICAL REVIEWS

Bacterial, archaeal and viral-like rhodopsins from the Red Sea

(2013) Alon Philosof et al.   Environmental Microbiology Reports

A light-driven sodium ion pump in marine bacteria

(2013) Keiichi Inoue et al.   Nature Communications

Global abundance of microbial rhodopsins

(2012) Omri M Finkel et al.   ISME Journal

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Proteorhodopsin-Bearing Bacteria in Antarctic Sea Ice

(2010) E. Y. Koh et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Chemical synthesis of the mouse mitochondrial genome

(2010) Daniel G Gibson et al.   NATURE METHODS

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Actinorhodopsin genes discovered in diverse freshwater habitats and among cultivated freshwater Actinobacteria

(2009) Adrian K Sharma et al.   ISME Journal

Enzymatic assembly of DNA molecules up to several hundred kilobases

(2009) Daniel G Gibson et al.   NATURE METHODS

SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology

(2008) Håkan Viklund et al.   BIOINFORMATICS

Widespread distribution of proteorhodopsins in freshwater and brackish ecosystems

(2008) Nof Atamna-Ismaeel et al.   ISME Journal

Phylogeny.fr: robust phylogenetic analysis for the non-specialist

(2008) A. Dereeper et al.   NUCLEIC ACIDS RESEARCH

Transmembrane Topology and Signal Peptide Prediction Using Dynamic Bayesian Networks

(2008) Sheila M. Reynolds et al.   PLoS Computational Biology