Short-chain alkanes fuel mussel and sponge Cycloclasticus symbionts from deep-sea gas and oil seeps

The Gulf of Mexico ecosystem, six years after the Macondo oil well blowout

(2016) Samantha B. Joye et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

Genome sequence of obligate marine polycyclic aromatic hydrocarbons-degrading bacterium Cycloclasticus sp. 78-ME, isolated from petroleum deposits of the sunken tanker Amoco Milford Haven , Mediterranean Sea

(2016) Enzo Messina et al.   Marine Genomics

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Reconstructing metabolic pathways of hydrocarbon-degrading bacteria from the Deepwater Horizon oil spill

(2016) Nina Dombrowski et al.   Nature Microbiology

Chemosynthetic symbionts of marine invertebrate animals are capable of nitrogen fixation

(2016) Jillian M. Petersen et al.   Nature Microbiology

Origins and Evolutionary Flexibility of Chemosynthetic Symbionts From Deep-Sea Animals

(2016) Jillian M. Petersen et al.   BIOLOGICAL BULLETIN

Bacterial reference genes for gene expression studies by RT-qPCR: survey and analysis

(2015) Danilo J. P. Rocha et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

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

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

Diverse, rare microbial taxa responded to the Deepwater Horizon deep-sea hydrocarbon plume

(2015) Sara Kleindienst et al.   ISME Journal

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

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

gbtools: Interactive Visualization of Metagenome Bins in R

(2015) Brandon K. B. Seah et al.   Frontiers in Microbiology

Marine microbes rapidly adapt to consume ethane, propane, and butane within the dissolved hydrocarbon plume of a natural seep

(2015) Stephanie D. Mendes et al.   JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS

Species Distribution and Population Connectivity of Deep-Sea Mussels at Hydrocarbon Seeps in the Gulf of Mexico

(2015) Baptiste Faure et al.   PLoS One

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

(2014) Alexey Vorobev et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

(2014) Juan A Vizcaíno et al.   NATURE BIOTECHNOLOGY

The polycyclic aromatic hydrocarbon degradation potential of Gulf of Mexico native coastal microbial communities after the Deepwater Horizon oil spill

(2014) Anthony D. Kappell et al.   Frontiers in Microbiology

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Novel hydrocarbon monooxygenase genes in the metatranscriptome of a natural deep-sea hydrocarbon plume

(2013) Meng Li et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2013) Adam R Rivers et al.   ISME Journal

Hydrocarbon-degrading bacteria enriched by the Deepwater Horizon oil spill identified by cultivation and DNA-SIP

(2013) Tony Gutierrez et al.   ISME Journal

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

IMG 4 version of the integrated microbial genomes comparative analysis system

(2013) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

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

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

(2012) Y. Peng et al.   BIOINFORMATICS

Bacterial symbionts ofBathymodiolusmussels andEscarpiatubeworms from Chapopote, an asphalt seep in the southern Gulf of Mexico

(2012) L. Raggi et al.   ENVIRONMENTAL MICROBIOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

Deep Sequencing of Myxilla (Ectyomyxilla) methanophila, an Epibiotic Sponge on Cold-Seep Tubeworms, Reveals Methylotrophic, Thiotrophic, and Putative Hydrocarbon-Degrading Microbial Associations

(2012) Shawn M. Arellano et al.   MICROBIAL ECOLOGY

Petroleum degradation and associated microbial signatures at the Chapopote asphalt volcano, Southern Gulf of Mexico

(2011) Florence Schubotz et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Hydrocarbon monooxygenase in Mycobacterium: recombinant expression of a member of the ammonia monooxygenase superfamily

(2011) Nicholas V Coleman et al.   ISME Journal

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

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

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

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

Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean

(2011) B. K. Swan et al.   SCIENCE

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

Interactive microbial genome visualization with GView

(2010) Aaron Petkau et al.   BIOINFORMATICS

High-throughput sequencing and analysis of the gill tissue transcriptome from the deep-sea hydrothermal vent mussel Bathymodiolus azoricus

(2010) Raul Bettencourt et al.   BMC GENOMICS

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

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Molecular and isotopic partitioning of low-molecular-weight hydrocarbons during migration and gas hydrate precipitation in deposits of a high-flux seepage site

(2009) Thomas Pape et al.   CHEMICAL GEOLOGY

Universal sample preparation method for proteome analysis

(2009) Jacek R Wiśniewski et al.   NATURE METHODS

Bacterial Degradation of Aromatic Compounds

(2009) Jong-Su Seo et al.   International Journal of Environmental Research and Public Health

Planktonic and Sediment-Associated Aerobic Methanotrophs in Two Seep Systems along the North American Margin

(2008) P. L. Tavormina et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

NCBI BLAST: a better web interface

(2008) M. Johnson et al.   NUCLEIC ACIDS RESEARCH