Lawrence Berkeley National Laboratory Recent Work Title Fungi contribute critical but spatially varying roles in nitrogen and carbon cycling in acid mine drainage

[1]  M. Romero-González,et al.  Characterization of extracellular polymeric substances (EPS) different carbon concentration , 2016 .

[2]  José A. Dianes,et al.  2016 update of the PRIDE database and its related tools , 2016, Nucleic Acids Res..

[3]  T. Sharpton,et al.  Metagenome sequence of Elaphomyces granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and a Proteobacteria-rich microbiome. , 2015, Environmental microbiology.

[4]  Annika C. Mosier,et al.  Elevated temperature alters proteomic responses of individual organisms within a biofilm community , 2014, The ISME Journal.

[5]  J. Banfield,et al.  Comparison of environmental and isolate Sulfobacillus genomes reveals diverse carbon, sulfur, nitrogen, and hydrogen metabolisms , 2014, BMC Genomics.

[6]  B. Henrissat CARBOHYDRATE-ACTIVE ENZYMES IN MICROBIOMES , 2014 .

[7]  J. W. Taylor,et al.  Metatranscriptomic analysis of ectomycorrhizal roots reveals genes associated with Piloderma-Pinus symbiosis: improved methodologies for assessing gene expression in situ. , 2014, Environmental microbiology.

[8]  T. Anderson,et al.  Dual isotope and isotopomer signatures of nitrous oxide from fungal denitrification--a pure culture study. , 2014, Rapid communications in mass spectrometry : RCM.

[9]  T. Anderson,et al.  Fungal oxygen exchange between denitrification intermediates and water. , 2014, Rapid communications in mass spectrometry : RCM.

[10]  C. Schadt,et al.  Watershed-Scale Fungal Community Characterization along a pH Gradient in a Subsurface Environment Cocontaminated with Uranium and Nitrate , 2014, Applied and Environmental Microbiology.

[11]  Inna Dubchak,et al.  MycoCosm portal: gearing up for 1000 fungal genomes , 2013, Nucleic Acids Res..

[12]  Pedro M. Coutinho,et al.  The carbohydrate-active enzymes database (CAZy) in 2013 , 2013, Nucleic Acids Res..

[13]  Inna Dubchak,et al.  The genome portal of the Department of Energy Joint Genome Institute: 2014 updates , 2013, Nucleic Acids Res..

[14]  Itai Sharon,et al.  Genomes from Metagenomics , 2013, Science.

[15]  Brian C. Thomas,et al.  Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla , 2013, mBio.

[16]  Kenneth H. Williams,et al.  Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment , 2013, Nature Communications.

[17]  Brian C. Thomas,et al.  The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria , 2013, eLife.

[18]  Zhou Li,et al.  Sipros/ProRata: a versatile informatics system for quantitative community proteomics , 2013, Bioinform..

[19]  P. Hugenholtz,et al.  Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes , 2013, Nature Biotechnology.

[20]  J. Banfield,et al.  New Group in the Leptospirillum Clade: Cultivation-Independent Community Genomics, Proteomics, and Transcriptomics of the New Species “Leptospirillum Group IV UBA BS” , 2013, Applied and Environmental Microbiology.

[21]  Brian C. Thomas,et al.  Metabolites Associated with Adaptation of Microorganisms to an Acidophilic, Metal-Rich Environment Identified by Stable-Isotope-Enabled Metabolomics , 2013, mBio.

[22]  K. Katoh,et al.  MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.

[23]  Brian C. Thomas,et al.  Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization , 2013, Genome research.

[24]  M. Pagni,et al.  De Novo Assembly of the Pneumocystis jirovecii Genome from a Single Bronchoalveolar Lavage Fluid Specimen from a Patient , 2012, mBio.

[25]  A. Salamov,et al.  Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi , 2012, PLoS pathogens.

[26]  Brian C. Thomas,et al.  Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla , 2012, Science.

[27]  Christine L. Sun,et al.  Heterotrophic Archaea Contribute to Carbon Cycling in Low-pH, Suboxic Biofilm Communities , 2012, Applied and Environmental Microbiology.

[28]  Doug Hyatt,et al.  Exhaustive database searching for amino acid mutations in proteomes , 2012, Bioinform..

[29]  J. Poulain,et al.  Metagenomes of the Picoalga Bathycoccus from the Chile Coastal Upwelling , 2012, PloS one.

[30]  S. Fushinobu,et al.  Fungal denitrification and nitric oxide reductase cytochrome P450nor , 2012, Philosophical Transactions of the Royal Society B: Biological Sciences.

[31]  John L. Spouge,et al.  Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi , 2012, Proceedings of the National Academy of Sciences.

[32]  R. Morris,et al.  Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota , 2012, Science.

[33]  G. Weinstock,et al.  Phosphate transporters in marine phytoplankton and their viruses: cross-domain commonalities in viral-host gene exchanges , 2012, Environmental microbiology.

[34]  Acidiella bohemica gen. et sp. nov. and Acidomyces spp. (Teratosphaeriaceae), the indigenous inhabitants of extremely acidic soils in Europe , 2012, Fungal Diversity.

[35]  R. Graham,et al.  Quantitative proteomic analysis of the heat stress response in Clostridium difficile strain 630. , 2011, Journal of proteome research.

[36]  J. Jurka,et al.  Next Generation Sequencing Provides Rapid Access to the Genome of Puccinia striiformis f. sp. tritici, the Causal Agent of Wheat Stripe Rust , 2011, PloS one.

[37]  Vincent J. Denef,et al.  Quantitative proteomic analyses of the response of acidophilic microbial communities to different pH conditions , 2011, The ISME Journal.

[38]  R. Stepanauskas,et al.  Single-Cell Genomics Reveals Organismal Interactions in Uncultivated Marine Protists , 2011, Science.

[39]  Sixue Chen,et al.  Exoproteome of Staphylococcus aureus reveals putative determinants of nasal carriage. , 2011, Journal of proteome research.

[40]  M. Bogo,et al.  Arsenic toxicity in mammals and aquatic animals: a comparative biochemical approach. , 2011, Ecotoxicology and environmental safety.

[41]  K. Park,et al.  Detection of differential proteomes associated with the development of type 2 diabetes in the Zucker rat model using the iTRAQ technique. , 2011, Journal of proteome research.

[42]  Jillian F. Banfield,et al.  Quantitative Tracking of Isotope Flows in Proteomes of Microbial Communities , 2011, Molecular & Cellular Proteomics.

[43]  J. Banfield,et al.  Micron-scale Fe2+/Fe3+, intermediate sulfur species and O2 gradients across the biofilm–solution–sediment interface control biofilm organization , 2010 .

[44]  Eoin L. Brodie,et al.  Direct cellular lysis/protein extraction protocol for soil metaproteomics. , 2010, Journal of proteome research.

[45]  J. Griffiths,et al.  Proteomic analysis reveals a novel mechanism induced by the leukemic oncogene Tel/PDGFRβ in stem cells: activation of the interferon response pathways. , 2010, Stem cell research.

[46]  Annika C. Mosier,et al.  Denitrifier abundance and activity across the San Francisco Bay estuary. , 2010, Environmental microbiology reports.

[47]  S. Tringe,et al.  Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton , 2010, Proceedings of the National Academy of Sciences.

[48]  A new acidophilic fungus Teratosphaeria acidotherma (Capnodiales, Ascomycota) from a hot spring , 2010 .

[49]  Vincent J. Denef,et al.  Ecological distribution and population physiology defined by proteomics in a natural microbial community , 2010, Molecular systems biology.

[50]  Vincent J. Denef,et al.  AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature , 2010, The ISME Journal.

[51]  Wendy S. Schackwitz,et al.  One Bacterial Cell, One Complete Genome , 2010, PloS one.

[52]  Korin E. Wheeler,et al.  Characterization of Extracellular Polymeric Substances from Acidophilic Microbial Biofilms , 2010, Applied and Environmental Microbiology.

[53]  S. Assmann,et al.  ABA-regulated G protein signaling in Arabidopsis guard cells: a proteomic perspective. , 2010, Journal of proteome research.

[54]  Paramvir S. Dehal,et al.  FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.

[55]  N. Soares,et al.  Associating growth-phase-related changes in the proteome of Acinetobacter baumannii with increased resistance to oxidative stress. , 2010, Journal of proteome research.

[56]  L. Holm,et al.  The Pfam protein families database , 2005, Nucleic Acids Res..

[57]  M. Kolařík,et al.  Diversity of fungal communities in saline and acidic soils in the Soos National Natural Reserve, Czech Republic , 2010, Mycological Progress.

[58]  Sean R Eddy,et al.  A new generation of homology search tools based on probabilistic inference. , 2009, Genome informatics. International Conference on Genome Informatics.

[59]  Brian C. Thomas,et al.  Community-wide analysis of microbial genome sequence signatures , 2009, Genome Biology.

[60]  Christine L. Sun,et al.  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, Applied and Environmental Microbiology.

[61]  M. Mann,et al.  Universal sample preparation method for proteome analysis , 2009, Nature Methods.

[62]  P. Shi,et al.  A novel highly acidic β-mannanase from the acidophilic fungus Bispora sp. MEY-1: gene cloning and overexpression in Pichia pastoris , 2009, Applied Microbiology and Biotechnology.

[63]  J. Banfield,et al.  Insights into the Diversity of Eukaryotes in Acid Mine Drainage Biofilm Communities , 2009, Applied and Environmental Microbiology.

[64]  Keith Bradnam,et al.  Assessing the gene space in draft genomes , 2008, Nucleic acids research.

[65]  Robert D. Finn,et al.  InterPro: the integrative protein signature database , 2008, Nucleic Acids Res..

[66]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[67]  E. Birney,et al.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

[68]  Crispin Miller,et al.  Quantitative Proteomics Analysis Demonstrates Post-transcriptional Regulation of Embryonic Stem Cell Differentiation to Hematopoiesis*S , 2008, Molecular & Cellular Proteomics.

[69]  Yoshihiro Yamanishi,et al.  KEGG for linking genomes to life and the environment , 2007, Nucleic Acids Res..

[70]  L. Selbmann,et al.  UvA-DARE (Digital Academic Repository) Drought meets acid: Three new genera in a dothidealean clade of extremotolerant , 2008 .

[71]  Gerard Talavera,et al.  Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. , 2007, Systematic biology.

[72]  J A Harrison,et al.  Denitrification across landscapes and waterscapes: a synthesis. , 2006, Ecological applications : a publication of the Ecological Society of America.

[73]  N. Samatova,et al.  ProRata: A quantitative proteomics program for accurate protein abundance ratio estimation with confidence interval evaluation. , 2006, Analytical chemistry.

[74]  P. L. Bond,et al.  Design and performance of rRNA targeted oligonucleotide probes for in situ detection and phylogenetic identification of microorganisms inhabiting acid mine drainage environments , 2006, Microbial Ecology.

[75]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[76]  A. Hernández,et al.  Interactions of sodium selenite, glutathione, arsenic species, and omega class human glutathione transferase. , 2005, Chemical research in toxicology.

[77]  A. Brauman,et al.  Quantification of denitrifying bacteria in soils by nirK gene targeted real-time PCR. , 2004, Journal of microbiological methods.

[78]  J. Banfield,et al.  Metabolically Active Eukaryotic Communities in Extremely Acidic Mine Drainage , 2004, Applied and Environmental Microbiology.

[79]  Rainer Breitling,et al.  Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments , 2004, FEBS letters.

[80]  J. Banfield,et al.  Acid mine drainage biogeochemistry at Iron Mountain, California , 2004, Geochemical transactions.

[81]  J. G. Kuenen,et al.  Aerobic denitrification: a controversy revived , 2004, Archives of Microbiology.

[82]  Jodie J. Yin,et al.  A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes , 2004, Genome Biology.

[83]  Darren A. Natale,et al.  The COG database: an updated version includes eukaryotes , 2003, BMC Bioinformatics.

[84]  Jillian F Banfield,et al.  Microbial communities in acid mine drainage. , 2003, FEMS microbiology ecology.

[85]  A I Saeed,et al.  TM4: a free, open-source system for microarray data management and analysis. , 2003, BioTechniques.

[86]  Joakim Nivre AN EFFICIENT ALGORITHM , 2003 .

[87]  J. Tiedje,et al.  Diversity of Nitrite Reductase (nirK and nirS) Gene Fragments in Forested Upland and Wetland Soils , 2002, Applied and Environmental Microbiology.

[88]  Anton J. Enright,et al.  An efficient algorithm for large-scale detection of protein families. , 2002, Nucleic acids research.

[89]  Zhemin Zhou,et al.  Ammonia Fermentation, a Novel Anoxic Metabolism of Nitrate by Fungi* , 2002, Journal of Biological Chemistry.

[90]  J. Yates,et al.  Large-scale analysis of the yeast proteome by multidimensional protein identification technology , 2001, Nature Biotechnology.

[91]  Zhemin Zhou,et al.  Oxygen requirement for denitrification by the fungus Fusarium oxysporum , 2000, Archives of Microbiology.

[92]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[93]  D. Lipman,et al.  A genomic perspective on protein families. , 1997, Science.

[94]  K. Schleifer,et al.  Phylogenetic identification and in situ detection of individual microbial cells without cultivation. , 1995, Microbiological reviews.

[95]  H. Shoun,et al.  Diauxic Growth of Fusarium oxysporum during Aerobic Culture in the Presence of Nitrate/Nitrite , 1992 .

[96]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[97]  L. Sigler,et al.  A new acidophilic Scytalidium. , 1974, Canadian journal of microbiology.

[98]  J. Raymund Hoffert,et al.  Acid Mine Drainage , 1947 .