Insights from the Metagenome of an Acid Salt Lake: The Role of Biology in an Extreme Depositional Environment

Model Organisms Retain an “Ecological Memory” of Complex Ecologically Relevant Environmental Variation

(2014) Karlyn D. Beer et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

From Metagenomics to Pure Culture: Isolation and Characterization of the Moderately Halophilic Bacterium Spiribacter salinus gen. nov., sp. nov.

(2014) María José León et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Whole-genome sequencing reveals novel insights into sulfur oxidation in the extremophile Acidithiobacillus thiooxidans

(2014) Huaqun Yin et al.   BMC MICROBIOLOGY

Desulfosporosinus acididurans sp. nov.: an acidophilic sulfate-reducing bacterium isolated from acidic sediments

(2014) Irene Sánchez-Andrea et al.   EXTREMOPHILES

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Defining the Functional Potential and Active Community Members of a Sediment Microbial Community in a High-Arctic Hypersaline Subzero Spring

(2013) Chih-Ying Lay et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Extreme sulfur-cycling in acid brine lake environments of Western Australia

(2013) Kathleen Counter Benison et al.   CHEMICAL GEOLOGY

Role of Central Metabolism in the Osmoadaptation of the Halophilic BacteriumChromohalobacter salexigens

(2013) José M. Pastor et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Complete genome sequence of Halorhodospira halophila SL1

(2013) Jean F. Challacombe et al.   Standards in Genomic Sciences

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline

(2013) Todd J Treangen et al.   GENOME BIOLOGY

Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data

(2012) Yongchao Liu et al.   BIOINFORMATICS

The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools

(2012) Andreas Wilke et al.   BMC BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Structural and Functional Insights from the Metagenome of an Acidic Hot Spring Microbial Planktonic Community in the Colombian Andes

(2012) Diego Javier Jiménez et al.   PLoS One

Ancient Impact and Aqueous Processes at Endeavour Crater, Mars

(2012) S. W. Squyres et al.   SCIENCE

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Bambus 2: scaffolding metagenomes

(2011) Sergey Koren et al.   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Interactive metagenomic visualization in a Web browser

(2011) Brian D Ondov et al.   BMC BIOINFORMATICS

Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences

(2011) Bo Liu et al.   BMC GENOMICS

Acidiferrobacter thiooxydans, gen. nov. sp. nov.; an acidophilic, thermo-tolerant, facultatively anaerobic iron- and sulfur-oxidizer of the family Ectothiorhodospiraceae

(2011) Kevin B. Hallberg et al.   EXTREMOPHILES

KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases

(2011) Chen Xie et al.   NUCLEIC ACIDS RESEARCH

Selective removal of transition metals from acidic mine waters by novel consortia of acidophilic sulfidogenic bacteria

(2011) Ivan Ňancucheo et al.   Microbial Biotechnology

Manipulation of FASTQ data with Galaxy

(2010) D. Blankenberg et al.   BIOINFORMATICS

Jarosite formation by an AMD sulphide-oxidizing environmental enrichment: Implications for biomarkers on Mars

(2010) Kelsey L.I. Norlund et al.   CHEMICAL GEOLOGY

Bacterial Diversity in the Haloalkaline Lake Elmenteita, Kenya

(2010) R. Mwirichia et al.   CURRENT MICROBIOLOGY

FragGeneScan: predicting genes in short and error-prone reads

(2010) Mina Rho et al.   NUCLEIC ACIDS RESEARCH

Molecular Analysis of the Microbial Communities of Mars Analog Lakes in Western Australia

(2009) Melanie R. Mormile et al.   ASTROBIOLOGY

A Novel Heuristic for Local Multiple Alignment of Interspersed DNA Repeats

(2009) T.J. Treangen et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Halarchaeum acidiphilum gen. nov., sp. nov., a moderately acidophilic haloarchaeon isolated from commercial solar salt

(2009) H. Minegishi et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Comparative community genomics in the Dead Sea: an increasingly extreme environment

(2009) Idan Bodaker et al.   ISME Journal

Albidoferax, a new genus of Comamonadaceae and reclassification of Rhodoferax ferrireducens (Finneran et al., 2003) as Albidoferax ferrireducens comb. nov.

(2009) Chintalapati Venkata Ramana et al.   JOURNAL OF GENERAL AND APPLIED MICROBIOLOGY

eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations

(2009) J. Muller et al.   NUCLEIC ACIDS RESEARCH

Complete genome sequence of Halomicrobium mukohataei type strain (arg-2T)

(2009) Brian J. Tindall et al.   Standards in Genomic Sciences

Geochemical characteristics of naturally acid and alkaline saline lakes in southern Western Australia

(2008) Brenda Beitler Bowen et al.   APPLIED GEOCHEMISTRY

“Hairy Blobs:” Microbial Suspects Preserved in Modern and Ancient Extremely Acid Lake Evaporites

(2008) Kathleen C. Benison et al.   ASTROBIOLOGY

Life And Death Around Acid-Saline Lakes

(2008) K. C. Benison   PALAIOS