Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage

Metagenome sequence ofElaphomyces granulatusfrom sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and aProteobacteria-rich microbiome

(2015) C. Alisha Quandt et al.   ENVIRONMENTAL MICROBIOLOGY

2016 update of the PRIDE database and its related tools

(2015) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Comparison of environmental and isolate Sulfobacillus genomes reveals diverse carbon, sulfur, nitrogen, and hydrogen metabolisms

(2015) Nicholas B Justice et al.   BMC GENOMICS

Watershed-Scale Fungal Community Characterization along a pH Gradient in a Subsurface Environment Cocontaminated with Uranium and Nitrate

(2014) Puja Jasrotia et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metatranscriptomic analysis of ectomycorrhizal roots reveals genes associated withPiloderma-Pinussymbiosis: improved methodologies for assessing gene expressionin situ

(2014) H.-L. Liao et al.   ENVIRONMENTAL MICROBIOLOGY

Elevated temperature alters proteomic responses of individual organisms within a biofilm community

(2014) Annika C Mosier et al.   ISME Journal

Dual isotope and isotopomer signatures of nitrous oxide from fungal denitrification - a pure culture study

(2014) Lena Rohe et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

New Group in the Leptospirillum Clade: Cultivation-Independent Community Genomics, Proteomics, and Transcriptomics of the New Species “Leptospirillum Group IV UBA BS”

(2013) Daniela S. Aliaga Goltsman et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Sipros/ProRata: a versatile informatics system for quantitative community proteomics

(2013) Yingfeng Wang et al.   BIOINFORMATICS

Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea

(2013) Alexis P Yelton et al.   BMC GENOMICS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

MycoCosm portal: gearing up for 1000 fungal genomes

(2013) Igor V. Grigoriev et al.   NUCLEIC ACIDS RESEARCH

Fungal oxygen exchange between denitrification intermediates and water

(2013) Lena Rohe et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

Genomes from Metagenomics

(2013) I. Sharon et al.   SCIENCE

Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla

(2013) R. S. Kantor et al.   mBio

Metabolites Associated with Adaptation of Microorganisms to an Acidophilic, Metal-Rich Environment Identified by Stable-Isotope-Enabled Metabolomics

(2013) A. C. Mosier et al.   mBio

Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment

(2013) Cindy J. Castelle et al.   Nature Communications

The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria

(2013) Sara C Di Rienzi et al.   eLife

Heterotrophic Archaea Contribute to Carbon Cycling in Low-pH, Suboxic Biofilm Communities

(2012) Nicholas B. Justice et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Exhaustive database searching for amino acid mutations in proteomes

(2012) Doug Hyatt et al.   BIOINFORMATICS

Acidiella bohemica gen. et sp. nov. and Acidomyces spp. (Teratosphaeriaceae), the indigenous inhabitants of extremely acidic soils in Europe

(2012) Martina Hujslová et al.   FUNGAL DIVERSITY

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

(2012) I. Sharon et al.   GENOME RESEARCH

Fungal denitrification and nitric oxide reductase cytochrome P450nor

(2012) H. Shoun et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Metagenomes of the Picoalga Bathycoccus from the Chile Coastal Upwelling

(2012) Daniel Vaulot et al.   PLoS One

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

(2012) C. L. Schoch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla

(2012) K. C. Wrighton et al.   SCIENCE

Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota

(2012) V. Iverson et al.   SCIENCE

De Novo Assembly of the Pneumocystis jirovecii Genome from a Single Bronchoalveolar Lavage Fluid Specimen from a Patient

(2012) O. H. Cisse et al.   mBio

Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi

(2012) Robin A. Ohm et al.   PLoS Pathogens

Phosphate transporters in marine phytoplankton and their viruses: cross-domain commonalities in viral-host gene exchanges

(2011) Adam Monier et al.   ENVIRONMENTAL MICROBIOLOGY

Micron-scale Fe2+/Fe3+, intermediate sulfur species and O2 gradients across the biofilm–solution–sediment interface control biofilm organization

(2011) Shufen Ma et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Quantitative proteomic analyses of the response of acidophilic microbial communities to different pH conditions

(2011) Christopher P Belnap et al.   ISME Journal

Quantitative Proteomic Analysis of the Heat Stress Response inClostridium difficileStrain 630

(2011) Shailesh Jain et al.   JOURNAL OF PROTEOME RESEARCH

Exoproteome ofStaphylococcus aureusReveals Putative Determinants of Nasal Carriage

(2011) Gowrishankar Muthukrishnan et al.   JOURNAL OF PROTEOME RESEARCH

Quantitative Tracking of Isotope Flows in Proteomes of Microbial Communities

(2011) Chongle Pan et al.   MOLECULAR & CELLULAR PROTEOMICS

The Genome Portal of the Department of Energy Joint Genome Institute

(2011) I. V. Grigoriev et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Next Generation Sequencing Provides Rapid Access to the Genome of Puccinia striiformis f. sp. tritici, the Causal Agent of Wheat Stripe Rust

(2011) Dario Cantu et al.   PLoS One

Single-Cell Genomics Reveals Organismal Interactions in Uncultivated Marine Protists

(2011) H. S. Yoon et al.   SCIENCE

Characterization of Extracellular Polymeric Substances from Acidophilic Microbial Biofilms

(2010) Y. Jiao et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Arsenic toxicity in mammals and aquatic animals: A comparative biochemical approach

(2010) Juliane Ventura-Lima et al.   ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY

AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature

(2010) Vincent J Denef et al.   ISME Journal

ABA-Regulated G Protein Signaling inArabidopsisGuard Cells: A Proteomic Perspective

(2010) Zhixin Zhao et al.   JOURNAL OF PROTEOME RESEARCH

Associating Growth-Phase-Related Changes in the Proteome ofAcinetobacter baumanniiwith Increased Resistance to Oxidative Stress

(2010) Nelson C. Soares et al.   JOURNAL OF PROTEOME RESEARCH

Direct Cellular Lysis/Protein Extraction Protocol for Soil Metaproteomics

(2010) Karuna Chourey et al.   JOURNAL OF PROTEOME RESEARCH

Detection of Differential Proteomes Associated with the Development of Type 2 Diabetes in the Zucker Rat Model Using the iTRAQ Technique

(2010) Dohyun Han et al.   JOURNAL OF PROTEOME RESEARCH

Ecological distribution and population physiology defined by proteomics in a natural microbial community

(2010) Ryan S Mueller et al.   Molecular Systems Biology

A new acidophilic fungus Teratosphaeria acidotherma (Capnodiales, Ascomycota) from a hot spring

(2010) Atsushi Yamazaki et al.   MYCOSCIENCE

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

One Bacterial Cell, One Complete Genome

(2010) Tanja Woyke et al.   PLoS One

Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton

(2010) M. L. Cuvelier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Proteomic analysis reveals a novel mechanism induced by the leukemic oncogene Tel/PDGFRβ in stem cells: Activation of the interferon response pathways

(2010) E. Dobbin et al.   Stem Cell Research

Drought meets acid: three new genera in a dothidealean clade of extremotolerant fungi

(2010) L. Selbmann et al.   STUDIES IN MYCOLOGY

Denitrifier abundance and activity across the San Francisco Bay estuary

(2010) Annika C. Mosier et al.   Environmental Microbiology Reports

Community Genomic and Proteomic Analyses of Chemoautotrophic Iron-Oxidizing "Leptospirillum rubarum" (Group II) and "Leptospirillum ferrodiazotrophum" (Group III) Bacteria in Acid Mine Drainage Biofilms

(2009) D. S. A. Goltsman et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Insights into the Diversity of Eukaryotes in Acid Mine Drainage Biofilm Communities

(2009) B. J. Baker et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Diversity of fungal communities in saline and acidic soils in the Soos National Natural Reserve, Czech Republic

(2009) Martina Hujslová et al.   MYCOLOGICAL PROGRESS

Universal sample preparation method for proteome analysis

(2009) Jacek R Wiśniewski et al.   NATURE METHODS

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

A novel highly acidic β-mannanase from the acidophilic fungus Bispora sp. MEY-1: gene cloning and overexpression in Pichia pastoris

(2008) Huiying Luo et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Assessing the gene space in draft genomes

(2008) Genis Parra et al.   NUCLEIC ACIDS RESEARCH

InterPro: the integrative protein signature database

(2008) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

(2008) B. L. Cantarel et al.   NUCLEIC ACIDS RESEARCH