Metagenomics-guided analysis of microbial chemolithoautotrophic phosphite oxidation yields evidence of a seventh natural CO2fixation pathway

Reinforcing carbon fixation: CO 2 reduction replacing and supporting carboxylation

(2018) Charles AR Cotton et al.   CURRENT OPINION IN BIOTECHNOLOGY

Characterization of an anaerobic marine microbial community exposed to combined fluxes of perchlorate and salinity

(2016) Charlotte I. Carlström et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Formate Assimilation: The Metabolic Architecture of Natural and Synthetic Pathways

(2016) Arren Bar-Even   BIOCHEMISTRY

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices

(2016) Dinghua Li et al.   METHODS

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

(2015) Dinghua Li et al.   BIOINFORMATICS

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)

(2015) Marcel Huntemann et al.   Standards in Genomic Sciences

Determination of phosphite in a full-scale municipal wastewater treatment plant

(2015) Xiaolong Yu et al.   Environmental Science-Processes & Impacts

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

Genome-Guided Analysis of Physiological Capacities of Tepidanaerobacter acetatoxydans Provides Insights into Environmental Adaptations and Syntrophic Acetate Oxidation

(2015) Bettina Müller et al.   PLoS One

PRISE2: Software for designing sequence-selective PCR primers and probes

(2014) Yu-Ting Huang et al.   BMC BIOINFORMATICS

Molybdenum and tungsten-dependent formate dehydrogenases

(2014) Luisa B. Maia et al.   JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY

Redox chemistry in the phosphorus biogeochemical cycle

(2014) M. A. Pasek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A bioassay for the detection of benzimidazoles reveals their presence in a range of environmental samples

(2014) Terence S. Crofts et al.   Frontiers in Microbiology

Life based on phosphite: a genome-guided analysis of Desulfotignum phosphitoxidans

(2013) Anja Poehlein et al.   BMC GENOMICS

Phosphite in Sedimentary Interstitial Water of Lake Taihu, a Large Eutrophic Shallow Lake in China

(2013) Chao Han et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Energy conservation via electron bifurcating ferredoxin reduction and proton/Na+ translocating ferredoxin oxidation

(2012) Wolfgang Buckel et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Design and analysis of metabolic pathways supporting formatotrophic growth for electricity-dependent cultivation of microbes

(2012) Arren Bar-Even et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

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

(2012) Y. Peng et al.   BIOINFORMATICS

The Bovine Ruminal Fluid Metabolome

(2012) Fozia Saleem et al.   Metabolomics

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

(2012) Anna Klindworth et al.   NUCLEIC ACIDS RESEARCH

Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks

(2012) Daniel H. Huson et al.   SYSTEMATIC BIOLOGY

The Emergence and Early Evolution of Biological Carbon-Fixation

(2012) Rogier Braakman et al.   PLoS Computational Biology

Phosphite utilization by the marine picocyanobacterium Prochlorococcus MIT9301

(2011) Asunción Martínez et al.   ENVIRONMENTAL MICROBIOLOGY

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

IMG: the integrated microbial genomes database and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Identification and Heterologous Expression of Genes Involved in Anaerobic Dissimilatory Phosphite Oxidation by Desulfotignum phosphitoxidans

(2010) D. D. Simeonova et al.   JOURNAL OF BACTERIOLOGY

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Detection of Geothermal Phosphite Using High-Performance Liquid Chromatography

(2009) Herbe Pech et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Lightning-induced reduction of phosphorus oxidation state

(2009) Matthew Pasek et al.   Nature Geoscience

Acetogenesis and the Wood–Ljungdahl pathway of CO2 fixation

(2008) Stephen W. Ragsdale et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Evolutionary primacy of sodium bioenergetics

(2008) Armen Y Mulkidjanian et al.   Biology Direct

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Rethinking early Earth phosphorus geochemistry

(2008) M. A. Pasek   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA