Genomic and Transcriptomic Analyses of the Facultative Methanotroph Methylocystis sp. Strain SB2 Grown on Methane or Ethanol

Ammonium induces differential expression of methane and nitrogen metabolism-related genes inMethylocystissp. strain SC2

(2013) Bomba Dam et al.   ENVIRONMENTAL MICROBIOLOGY

Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage

(2013) Mohamed F. Haroon et al.   NATURE

Global Molecular Analyses of Methane Metabolism in Methanotrophic Alphaproteobacterium, Methylosinus trichosporium OB3b. Part I: Transcriptomic Study

(2013) Janet B. Matsen et al.   Frontiers in Microbiology

Distribution and Properties of the Genes Encoding the Biosynthesis of the Bacterial Cofactor, Pyrroloquinoline Quinone

(2012) Yao-Qing Shen et al.   BIOCHEMISTRY

How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?

(2012) Brian J Haas et al.   BMC GENOMICS

Draft Genome Sequence of the Volcano-Inhabiting Thermoacidophilic Methanotroph Methylacidiphilum fumariolicum Strain SolV

(2012) A. F. Khadem et al.   JOURNAL OF BACTERIOLOGY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data

(2012) David Vallenet et al.   NUCLEIC ACIDS RESEARCH

Assimilation of acetate by the putative atmospheric methane oxidizers belonging to the USCα clade

(2011) Jennifer Pratscher et al.   ENVIRONMENTAL MICROBIOLOGY

Facultative methanotrophy: false leads, true results, and suggestions for future research

(2011) Jeremy D. Semrau et al.   FEMS MICROBIOLOGY LETTERS

Expression patterns of mRNAs for methanotrophy and thiotrophy in symbionts of the hydrothermal vent mussel Bathymodiolus puteoserpentis

(2011) Annelie Wendeberg et al.   ISME Journal

Genome Sequence of the Methanotrophic Alphaproteobacterium Methylocystis sp. Strain Rockwell (ATCC 49242)

(2011) L. Y. Stein et al.   JOURNAL OF BACTERIOLOGY

Autotrophic Methanotrophy in Verrucomicrobia: Methylacidiphilum fumariolicumSolV Uses the Calvin-Benson-Bassham Cycle for Carbon Dioxide Fixation

(2011) A. F. Khadem et al.   JOURNAL OF BACTERIOLOGY

The Ethylmalonyl-CoA Pathway Is Used in Place of the Glyoxylate Cycle byMethylobacterium extorquensAM1 during Growth on Acetate

(2011) Kathrin Schneider et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

IMG: the integrated microbial genomes database and comparative analysis system

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

Interaction of PqqE and PqqD in the pyrroloquinoline quinone (PQQ) biosynthetic pathway links PqqD to the radical SAM superfamily

(2010) Stephen R. Wecksler et al.   CHEMICAL COMMUNICATIONS

Nitrite-driven anaerobic methane oxidation by oxygenic bacteria

(2010) Katharina F. Ettwig et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Constitutive expression of pMMO by Methylocystis strain SB2 when grown on multi-carbon substrates: implications for biodegradation of chlorinated ethenes

(2010) Sukhwan Yoon et al.   Environmental Microbiology Reports

Characterization of a novel facultative Methylocystis species capable of growth on methane, acetate and ethanol

(2010) Jeongdae Im et al.   Environmental Microbiology Reports

A novel family of functional operons encoding methane/ammonia monooxygenase-related proteins in gammaproteobacterial methanotrophs

(2010) Patricia L. Tavormina et al.   Environmental Microbiology Reports

Anaerobic Oxidation of Methane: Progress with an Unknown Process

(2009) Katrin Knittel et al.   Annual Review of Microbiology

Chemotrophic Microbial Mats and Their Potential for Preservation in the Rock Record

(2009) Jake V. Bailey et al.   ASTROBIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Pebble and Rock Band: Heuristic Resolution of Repeats and Scaffolding in the Velvet Short-Read de Novo Assembler

(2009) Daniel R. Zerbino et al.   PLoS One

Manganese- and Iron-Dependent Marine Methane Oxidation

(2009) E. J. Beal et al.   SCIENCE

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Formate as the Main Branch Point for Methylotrophic Metabolism in Methylobacterium extorquens AM1

(2008) G. J. Crowther et al.   JOURNAL OF BACTERIOLOGY

Methane oxidation at 55 C and pH 2 by a thermoacidophilic bacterium belonging to the Verrucomicrobia phylum

(2008) T. Islam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA