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

Comparative RNA-Seq Analysis of Early-Infected Peach Leaves by the Invasive Phytopathogen Xanthomonas arboricola pv. pruni

(2013) Didier Socquet-Juglard et al.   PLoS One

Genome Analysis Coupled with Physiological Studies Reveals a Diverse Nitrogen Metabolism in Methylocystis sp. Strain SC2

(2013) Bomba Dam et al.   PLoS One

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

Complete Sequence Analysis of Two Methanotroph-SpecificrepABC-Containing Plasmids from Methylocystis sp. Strain SC2

(2012) Bomba Dam et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Complete Genome Sequence of Methylocystis sp. Strain SC2, an Aerobic Methanotroph with High-Affinity Methane Oxidation Potential

(2012) B. Dam et al.   JOURNAL OF BACTERIOLOGY

Need-based activation of ammonium uptake in Escherichia coli

(2012) Minsu Kim et al.   Molecular Systems Biology

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

(2012) Cole Trapnell et al.   Nature Protocols

Maize (Zea mays L.) Genome Diversity as Revealed by RNA-Sequencing

(2012) Candice N. Hansey et al.   PLoS One

The Pseudomonas aeruginosa Transcriptome in Planktonic Cultures and Static Biofilms Using RNA Sequencing

(2012) Andreas Dötsch et al.   PLoS One

mRNA-Seq Analysis of the Pseudoperonospora cubensis Transcriptome During Cucumber (Cucumis sativus L.) Infection

(2012) Elizabeth A. Savory et al.   PLoS One

Nitrifying and denitrifying pathways of methanotrophic bacteria

(2011) Lisa Y. Stein et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Identification and removal of ribosomal RNA sequences from metatranscriptomes

(2011) Robert Schmieder et al.   BIOINFORMATICS

Quantitative RNA-seq analysis of the Campylobacter jejuni transcriptome

(2011) R. R. Chaudhuri et al.   MICROBIOLOGY-SGM

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Effects of Ammonium and Nitrite on Growth and Competitive Fitness of Cultivated Methanotrophic Bacteria

(2010) G. Nyerges et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard et al.   BMC BIOINFORMATICS

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Ammonia cometabolism and product inhibition vary considerably among species of methanotrophic bacteria

(2009) Györgyi Nyerges et al.   FEMS MICROBIOLOGY LETTERS

Transcriptome Complexity in a Genome-Reduced Bacterium

(2009) M. Guell et al.   SCIENCE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

Transcription of nitrification genes by the methane-oxidizing bacterium, Methylococcus capsulatus strain Bath

(2008) Amisha T Poret-Peterson et al.   ISME Journal

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Two isozymes of particulate methane monooxygenase with different methane oxidation kinetics are found in Methylocystis sp. strain SC2

(2008) M. Baani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA