Heliorhodopsins are absent in diderm (Gram-negative) bacteria: Some thoughts and possible implications for activity

Solar-panel and parasol strategies shape the proteorhodopsin distribution pattern in marine Flavobacteriia

(2018) Yohei Kumagai et al.   ISME Journal

Bacterial outer membrane constriction

(2018) Alexander J. F. Egan   MOLECULAR MICROBIOLOGY

GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes

(2018) Joel A Boyd et al.   NUCLEIC ACIDS RESEARCH

HMMER web server: 2018 update

(2018) Simon C Potter et al.   NUCLEIC ACIDS RESEARCH

A distinct abundant group of microbial rhodopsins discovered using functional metagenomics

(2018) Alina Pushkarev et al.   NATURE

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

(2017) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

Marine Bacterial and Archaeal Ion-Pumping Rhodopsins: Genetic Diversity, Physiology, and Ecology

(2016) Jarone Pinhassi et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

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

Molecular mechanisms of antibiotic resistance

(2014) Jessica M. A. Blair et al.   NATURE REVIEWS MICROBIOLOGY

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

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

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The Chimeric Genome of Sphaerochaeta: Nonspiral Spirochetes That Break with the Prevalent Dogma in Spirochete Biology

(2012) A. Caro-Quintero et al.   mBio

Origin of diderm (Gram-negative) bacteria: antibiotic selection pressure rather than endosymbiosis likely led to the evolution of bacterial cells with two membranes

(2011) Radhey S. Gupta   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

The Light-Driven Proton Pump Proteorhodopsin Enhances Bacterial Survival during Tough Times

(2010) Edward F. DeLong et al.   PLOS BIOLOGY