Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill

The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs

(2012) Ryan A Lesniewski et al.   ISME Journal

Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill

(2012) Olivia U Mason et al.   ISME Journal

Isolation of Two Novel Marine Ethylene-Assimilating Bacteria, Haliea Species ETY-M and ETY-NAG, Containing Particulate Methane Monooxygenase-like Genes

(2012) Toshihiro Suzuki et al.   MICROBES AND ENVIRONMENTS

Chemical data quantify Deepwater Horizon hydrocarbon flow rate and environmental distribution

(2012) T. B. Ryerson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Co-Occurrence Patterns of Plants and Soil Bacteria in the High-Alpine Subnival Zone Track Environmental Harshness

(2012) Andrew J. King et al.   Frontiers in Microbiology

Methane flux to the atmosphere from the Deepwater Horizon oil disaster

(2011) Shari A. Yvon-Lewis et al.   GEOPHYSICAL RESEARCH LETTERS

Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume

(2011) Zhenmei Lu et al.   ISME Journal

Draft Genome Sequence of the Chemolithoheterotrophic, Halophilic Methylotroph Methylophaga thiooxydans DMS010

(2011) R. Boden et al.   JOURNAL OF BACTERIOLOGY

Genome Sequence of the Arctic Methanotroph Methylobacter tundripaludum SV96

(2011) Mette M. Svenning et al.   JOURNAL OF BACTERIOLOGY

Magnitude and oxidation potential of hydrocarbon gases released from the BP oil well blowout

(2011) Samantha B. Joye et al.   Nature Geoscience

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2011) R. Caspi et al.   NUCLEIC ACIDS RESEARCH

Composition and fate of gas and oil released to the water column during the Deepwater Horizon oil spill

(2011) C. M. Reddy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Natural gas and temperature structured a microbial community response to the Deepwater Horizon oil spill

(2011) M. C. Redmond et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Persistent Oxygen Anomaly Reveals the Fate of Spilled Methane in the Deep Gulf of Mexico

(2011) J. D. Kessler et al.   SCIENCE

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Identification of Novel Methane-, Ethane-, and Propane-Oxidizing Bacteria at Marine Hydrocarbon Seeps by Stable Isotope Probing

(2010) M. C. Redmond et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

SeqTrim: a high-throughput pipeline for preprocessing any type of sequence reads

(2010) Juan Falgueras et al.   BMC BIOINFORMATICS

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS

Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads

(2010) Jeffrey Martin et al.   BMC GENOMICS

UniFrac: an effective distance metric for microbial community comparison

(2010) Catherine Lozupone et al.   ISME Journal

Distributions of putative aerobic methanotrophs in diverse pelagic marine environments

(2010) Patricia L Tavormina et al.   ISME Journal

Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics

(2010) Frank J Stewart et al.   ISME Journal

Quantitative analysis of a deeply sequenced marine microbial metatranscriptome

(2010) Scott M Gifford et al.   ISME Journal

Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions

(2010) Jens Reeder et al.   NATURE METHODS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Ab initio gene identification in metagenomic sequences

(2010) Wenhan Zhu et al.   NUCLEIC ACIDS RESEARCH

Unlocking Short Read Sequencing for Metagenomics

(2010) Sébastien Rodrigue et al.   PLoS One

Tracking Hydrocarbon Plume Transport and Biodegradation at Deepwater Horizon

(2010) Richard Camilli et al.   SCIENCE

Deep-Sea Oil Plume Enriches Indigenous Oil-Degrading Bacteria

(2010) Terry C. Hazen et al.   SCIENCE

Propane Respiration Jump-Starts Microbial Response to a Deep Oil Spill

(2010) David L. Valentine et al.   SCIENCE

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

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

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

phyloXML: XML for evolutionary biology and comparative genomics

(2009) Mira V Han et al.   BMC BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Phylogenetic mixture models for proteins

(2008) S. Q. Le et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES