Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems

Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids

(2017) Sean P. Jungbluth et al.   Scientific Data

Variations in microbial carbon sources and cycling in the deep continental subsurface

(2016) Danielle N. Simkus et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Novel microbial assemblages inhabiting crustal fluids within mid-ocean ridge flank subsurface basalt

(2016) Sean P Jungbluth et al.   ISME Journal

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4)

(2016) Marcel Huntemann et al.   Standards in Genomic Sciences

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

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

A metagenomic window into carbon metabolism at 3 km depth in Precambrian continental crust

(2015) Cara Magnabosco et al.   ISME Journal

ProDeGe: a computational protocol for fully automated decontamination of genomes

(2015) Kristin Tennessen 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

Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population

(2015) Jessica M. Labonté et al.   Frontiers in Microbiology

Activity and phylogenetic diversity of sulfate-reducing microorganisms in low-temperature subsurface fluids within the upper oceanic crust

(2015) Alberto Robador et al.   Frontiers in Microbiology

Dissolved hydrogen and methane in the oceanic basaltic biosphere

(2014) Huei-Ting Lin et al.   EARTH AND PLANETARY SCIENCE LETTERS

Phylogeny and phylogeography of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships

(2014) Maggie C. Y. Lau et al.   Frontiers in Microbiology

Phylogenetic diversity of microorganisms in subseafloor crustal fluids from Holes 1025C and 1026B along the Juan de Fuca Ridge flank

(2014) Sean P. Jungbluth et al.   Frontiers in Microbiology

Comparisons of the composition and biogeographic distribution of the bacterial communities occupying South African thermal springs with those inhabiting deep subsurface fracture water

(2014) Cara Magnabosco et al.   Frontiers in Microbiology

PhyloSift: phylogenetic analysis of genomes and metagenomes

(2014) Aaron E. Darling et al.   PeerJ

MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm

(2014) Yu-Wei Wu et al.   Microbiome

Thermal effects on microbial composition and microbiologically induced corrosion and mineral precipitation affecting operation of a geothermal plant in a deep saline aquifer

(2013) Stephanie Lerm et al.   EXTREMOPHILES

IMG/M 4 version of the integrated metagenome comparative analysis system

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

Systematic Identification of Gene Families for Use as “Markers” for Phylogenetic and Phylogeny-Driven Ecological Studies of Bacteria and Archaea and Their Major Subgroups

(2013) Dongying Wu et al.   PLoS One

Gene and translation initiation site prediction in metagenomic sequences

(2012) Doug Hyatt et al.   BIOINFORMATICS

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

Microbial and functional diversity of a subterrestrial high pH groundwater associated to serpentinization

(2012) Igor Tiago et al.   ENVIRONMENTAL MICROBIOLOGY

Inorganic chemistry, gas compositions and dissolved organic carbon in fluids from sedimented young basaltic crust on the Juan de Fuca Ridge flanks

(2012) Huei-Ting Lin et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Microbial diversity within basement fluids of the sediment-buried Juan de Fuca Ridge flank

(2012) Sean P Jungbluth et al.   ISME Journal

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

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

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes

(2011) Beifang Niu et al.   BIOINFORMATICS

Easyfig: a genome comparison visualizer

(2011) M. J. Sullivan et al.   BIOINFORMATICS

Advanced instrument system for real-time and time-series microbial geochemical sampling of the deep (basaltic) crustal biosphere

(2011) James P. Cowen et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Characterization of bacterial diversity to a depth of 1500 m in the Outokumpu deep borehole, Fennoscandian Shield

(2011) Merja Itävaara et al.   FEMS MICROBIOLOGY ECOLOGY

IMG: the integrated microbial genomes database and comparative analysis system

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

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data

(2011) Christopher S Miller et al.   GENOME BIOLOGY

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

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Reverse dissimilatory sulfite reductase as phylogenetic marker for a subgroup of sulfur-oxidizing prokaryotes

(2008) Alexander Loy et al.   ENVIRONMENTAL MICROBIOLOGY

Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth

(2008) D. Chivian et al.   SCIENCE

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY