Robert L. Hettich

Publications

• Towards Engineering Ectomycorrhization into Switchgrass Bioenergy Crops Via a Lectin Receptor-like Kinase
  Plant Biotechnology Journal. Jul, 2021  |   Pubmed ID: 34272801
• Genetic and Behavioral Adaptation of Candida Parapsilosis to the Microbiome of Hospitalized Infants Revealed by in Situ Genomics, Transcriptomics, and Proteomics
  Microbiome. 06, 2021  |   Pubmed ID: 34154658
• Genomic Reconstruction of Fossil and Living Microorganisms in Ancient Siberian Permafrost
  Microbiome. 05, 2021  |   Pubmed ID: 34001281
• Formation, Characterization and Modeling of Emergent Synthetic Microbial Communities
  Computational and Structural Biotechnology Journal. 2021  |   Pubmed ID: 33995895
• Identification and Characterization of Proteins of Unknown Function (PUFs) in Clostridium Thermocellum DSM 1313 Strains As Potential Genetic Engineering Targets
  Biotechnology for Biofuels. May, 2021  |   Pubmed ID: 33971924
• Anaerobic Microbial Metabolism of Dichloroacetate
  MBio. 04, 2021  |   Pubmed ID: 33906923
• Stepping on the Gas to a Circular Economy: Accelerating Development of Carbon-Negative Chemical Production from Gas Fermentation
  Annual Review of Chemical and Biomolecular Engineering. 06, 2021  |   Pubmed ID: 33872517
• Metabolism of Syringyl Lignin-derived Compounds in Pseudomonas Putida Enables Convergent Production of 2-pyrone-4,6-dicarboxylic Acid
  Metabolic Engineering. 05, 2021  |   Pubmed ID: 33741529
• Microbiota Functional Activity Biosensors for Characterizing Nutrient Metabolism in Vivo
  ELife. Mar, 2021  |   Pubmed ID: 33684031
• Respiratory Vinyl Chloride Reductive Dechlorination to Ethene in TceA-Expressing
  Environmental Science & Technology. 04, 2021  |   Pubmed ID: 33683880
• Five Key Aspects of Metaproteomics As a Tool to Understand Functional Interactions in Host-associated Microbiomes
  PLoS Pathogens. 02, 2021  |   Pubmed ID: 33630960
• The Core Chemotaxis Proteins CheA1 and CheA4 Link Chemotaxis Signaling with Nitrogen Metabolism
  MSystems. Feb, 2021  |   Pubmed ID: 33594007
• A Lysate Proteome Engineering Strategy for Enhancing Cell-free Metabolite Production
  Metabolic Engineering Communications. Jun, 2021  |   Pubmed ID: 33552897
• Coculture with Hemicellulose-fermenting Microbes Reverses Inhibition of Corn Fiber Solubilization by Clostridium Thermocellum at Elevated Solids Loadings
  Biotechnology for Biofuels. Jan, 2021  |   Pubmed ID: 33461608
• Targeted Growth Medium Dropouts Promote Aromatic Compound Synthesis in Crude Cell-Free Systems
  ACS Synthetic Biology. 11, 2020  |   Pubmed ID: 33044063
• Structural and Proteomic Studies of the Virus Demonstrate a Global Distribution of Virus-Encoded Carbohydrate Processing
  Frontiers in Microbiology. 2020  |   Pubmed ID: 33013751
• A Carotenoid-deficient Mutant of the Plant-associated Microbe Pantoea Sp. YR343 Displays an Altered Membrane Proteome
  Scientific Reports. 09, 2020  |   Pubmed ID: 32917935
• A Nitrogenase-like Enzyme System Catalyzes Methionine, Ethylene, and Methane Biogenesis
  Science (New York, N.Y.). 08, 2020  |   Pubmed ID: 32855335
• Molecular Remodeling in Populus PdKOR RNAi Roots Profiled Using LC-MS/MS Proteomics
  Proteomics. 12, 2020  |   Pubmed ID: 32846035
• Characterizing Intracellular Proteomes for Microbes: An Experimental Approach Using Label-Free Protein Quantitation
  Methods in Molecular Biology (Clifton, N.J.). 2020  |   Pubmed ID: 32720148
• Biogeography of Microbial Bile Acid Transformations Along the Murine Gut
  Journal of Lipid Research. 11, 2020  |   Pubmed ID: 32661017
• A Viable New Strategy for the Discovery of Peptide Proteolytic Cleavage Products in Plant-Microbe Interactions
  Molecular Plant-microbe Interactions : MPMI. Oct, 2020  |   Pubmed ID: 32597696
• Impact of Fatty-Acid Labeling of Membranes on the Cellular Lipidome and Proteome
  Frontiers in Microbiology. 2020  |   Pubmed ID: 32499768
• Outer Membrane Vesicles Catabolize Lignin-derived Aromatic Compounds in KT2440
  Proceedings of the National Academy of Sciences of the United States of America. 04, 2020  |   Pubmed ID: 32245809
• Gene Targets for Engineering Osmotolerance in
  Biotechnology for Biofuels. 2020  |   Pubmed ID: 32190115
• Active Sulfur Cycling in the Terrestrial Deep Subsurface
  The ISME Journal. 05, 2020  |   Pubmed ID: 32047278
• Genome-Resolved Proteomic Stable Isotope Probing of Soil Microbial Communities Using CO and C-Methanol
  Frontiers in Microbiology. 2019  |   Pubmed ID: 31866955
• Integrated Proteomics and Lipidomics Reveal That the Swarming Motility of Is Characterized by Phospholipid Modification, Surfactant Deployment, and Flagellar Specialization Relative to Swimming Motility
  Frontiers in Microbiology. 2019  |   Pubmed ID: 31798553
• Comparing DNA, RNA and Protein Levels for Measuring Microbial Dynamics in Soil Microcosms Amended with Nitrogen Fertilizer
  Scientific Reports. 11, 2019  |   Pubmed ID: 31772206
• Impact of Fixed Nitrogen Availability on Reductive Dechlorination Activity
  Environmental Science & Technology. 12, 2019  |   Pubmed ID: 31693350
• Bioremediation of a Common Product of Food Processing by a Human Gut Bacterium
  Cell Host & Microbe. 10, 2019  |   Pubmed ID: 31585844
• Interspecies Competition Impacts Targeted Manipulation of Human Gut Bacteria by Fiber-Derived Glycans
  Cell. 09, 2019  |   Pubmed ID: 31539500
• Surface Water Microbial Community Response to the Biocide 2,2-Dibromo-3-Nitrilopropionamide, Used in Unconventional Oil and Gas Extraction
  Applied and Environmental Microbiology. 11, 2019  |   Pubmed ID: 31444200
• Targeted Detection of Dehalococcoides Mccartyi Microbial Protein Biomarkers As Indicators of Reductive Dechlorination Activity in Contaminated Groundwater
  Scientific Reports. 07, 2019  |   Pubmed ID: 31332202
• Effects of Microbiota-directed Foods in Gnotobiotic Animals and Undernourished Children
  Science (New York, N.Y.). 07, 2019  |   Pubmed ID: 31296738
• One-time Nitrogen Fertilization Shifts Switchgrass Soil Microbiomes Within a Context of Larger Spatial and Temporal Variation
  PloS One. 2019  |   Pubmed ID: 31211785
• Exploiting the Dynamic Relationship Between Peptide Separation Quality and Peptide Coisolation in a Multiple-Peptide Matches-per-Spectrum Approach Offers a Strategy To Optimize Bottom-Up Proteomics Throughput and Depth
  Analytical Chemistry. 06, 2019  |   Pubmed ID: 31075198
• Correction To: Diel Rewiring and Positive Selection of Ancient Plant Proteins Enabled Evolution of CAM Photosynthesis in Agave
  BMC Genomics. 04, 2019  |   Pubmed ID: 30971209
• Scavenging Organic Nitrogen and Remodelling Lipid Metabolism Are Key Survival Strategies Adopted by the Endophytic Fungi, Serendipita Vermifera and Serendipita Bescii to Alleviate Nitrogen and Phosphorous Starvation in Vitro
  Environmental Microbiology Reports. 08, 2019  |   Pubmed ID: 30970176
• Evaluation of an Untargeted Nano-liquid Chromatography-mass Spectrometry Approach to Expand Coverage of Low Molecular Weight Dissolved Organic Matter in Arctic Soil
  Scientific Reports. 04, 2019  |   Pubmed ID: 30967565
• Metaproteomics Reveals Persistent and Phylum-redundant Metabolic Functional Stability in Adult Human Gut Microbiomes of Crohn's Remission Patients Despite Temporal Variations in Microbial Taxa, Genomes, and Proteomes
  Microbiome. 02, 2019  |   Pubmed ID: 30744677
• Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing
  Journal of Proteome Research. 04, 2019  |   Pubmed ID: 30702898
• Proteogenomics Reveals Novel Reductive Dehalogenases and Methyltransferases Expressed During Anaerobic Dichloromethane Metabolism
  Applied and Environmental Microbiology. 03, 2019  |   Pubmed ID: 30658979
• Comparative Genomics and Proteomic Analysis of Assimilatory Sulfate Reduction Pathways in Anaerobic Methanotrophic Archaea
  Frontiers in Microbiology. 2018  |   Pubmed ID: 30559729
• Quantifying Codon Usage in Signal Peptides: Gene Expression and Amino Acid Usage Explain Apparent Selection for Inefficient Codons
  Biochimica Et Biophysica Acta. Biomembranes. 12, 2018  |   Pubmed ID: 30279149
• Utilization of a Detergent-Based Method for Direct Microbial Cellular Lysis/Proteome Extraction from Soil Samples for Metaproteomics Studies
  Methods in Molecular Biology (Clifton, N.J.). 2018  |   Pubmed ID: 30259494
• Biogeochemical Cycling by a Low-Diversity Microbial Community in Deep Groundwater
  Frontiers in Microbiology. 2018  |   Pubmed ID: 30245678
• Transcriptomic and Proteomic Changes from Medium Supplementation and Strain Evolution in High-yielding Clostridium Thermocellum Strains
  Journal of Industrial Microbiology & Biotechnology. Nov, 2018  |   Pubmed ID: 30187243
• Diel Rewiring and Positive Selection of Ancient Plant Proteins Enabled Evolution of CAM Photosynthesis in Agave
  BMC Genomics. Aug, 2018  |   Pubmed ID: 30081833
• Author Correction: Maternal Consumption of Fish Oil Programs Reduced Adiposity in Broiler Chicks
  Scientific Reports. Jul, 2018  |   Pubmed ID: 30054506
• Quantitative Proteomic Analysis of Biological Processes and Responses of the Bacterium Desulfovibrio Desulfuricans ND132 Upon Deletion of Its Mercury Methylation Genes
  Proteomics. 09, 2018  |   Pubmed ID: 30009483
• Hospitalized Premature Infants Are Colonized by Related Bacterial Strains with Distinct Proteomic Profiles
  MBio. 04, 2018  |   Pubmed ID: 29636439
• The Diversity and Specificity of the Extracellular Proteome in the Cellulolytic Bacterium is Driven by the Nature of the Cellulosic Growth Substrate
  Biotechnology for Biofuels. 2018  |   Pubmed ID: 29588665
• Quantitative Proteome Profile of Water Deficit Stress Responses in Eastern Cottonwood (Populus Deltoides) Leaves
  PloS One. 2018  |   Pubmed ID: 29447168
• Identification of Peptide-binding Sites Within BSA Using Rapid, Laser-induced Covalent Cross-linking Combined with High-performance Mass Spectrometry
  Journal of Molecular Recognition : JMR. 02, 2018  |   Pubmed ID: 28994207
• Phosphorylation of Ribosomal Protein RPS6 Integrates Light Signals and Circadian Clock Signals
  Frontiers in Plant Science. 2017  |   Pubmed ID: 29403507
• Deletion of the Gene Increases Ethanol Production in and Several Other Thermophilic Anaerobic Bacteria
  Biotechnology for Biofuels. 2017  |   Pubmed ID: 29213322
• The Kalanchoë Genome Provides Insights into Convergent Evolution and Building Blocks of Crassulacean Acid Metabolism
  Nature Communications. 12, 2017  |   Pubmed ID: 29196618
• Eliminating a Global Regulator of Carbon Catabolite Repression Enhances the Conversion of Aromatic Lignin Monomers to Muconate in KT2440
  Metabolic Engineering Communications. Dec, 2017  |   Pubmed ID: 29188181
• Maternal Consumption of Fish Oil Programs Reduced Adiposity in Broiler Chicks
  Scientific Reports. 10, 2017  |   Pubmed ID: 29030616
• Functional Analysis of the Glucan Degradation Locus in Caldicellulosiruptor Bescii Reveals Essential Roles of Component Glycoside Hydrolases in Plant Biomass Deconstruction
  Applied and Environmental Microbiology. 12, 2017  |   Pubmed ID: 28986379
• Erratum for Skennerton Et Al., "Methane-Fueled Syntrophy Through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved Within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea"
  MBio. 10, 2017  |   Pubmed ID: 28974619
• Mechanisms of Subzero Growth in the Cryophile Planococcus Halocryophilus Determined Through Proteomic Analysis
  Environmental Microbiology. 11, 2017  |   Pubmed ID: 28834033
• Grape Pomace Compost Harbors Organohalide-respiring Dehalogenimonas Species with Novel Reductive Dehalogenase Genes
  The ISME Journal. 12, 2017  |   Pubmed ID: 28809851
• Phylogenetically Conserved Resource Partitioning in the Coastal Microbial Loop
  The ISME Journal. 12, 2017  |   Pubmed ID: 28800138
• Methane-Fueled Syntrophy Through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved Within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea
  MBio. 08, 2017  |   Pubmed ID: 28765215
• Genome-resolved Metaproteomic Characterization of Preterm Infant Gut Microbiota Development Reveals Species-specific Metabolic Shifts and Variabilities During Early Life
  Microbiome. 07, 2017  |   Pubmed ID: 28693612
• Multi-omics Analysis Provides Insight to the Ignicoccus Hospitalis-Nanoarchaeum Equitans Association
  Biochimica Et Biophysica Acta. General Subjects. Sep, 2017  |   Pubmed ID: 28591626
• Optimized Extraction Method To Remove Humic Acid Interferences from Soil Samples Prior to Microbial Proteome Measurements
  Journal of Proteome Research. 07, 2017  |   Pubmed ID: 28537741
• The Effects of Micronutrient Deficiencies on Bacterial Species from the Human Gut Microbiota
  Science Translational Medicine. 05, 2017  |   Pubmed ID: 28515336
• Specialized Activities and Expression Differences for Clostridium Thermocellum Biofilm and Planktonic Cells
  Scientific Reports. 02, 2017  |   Pubmed ID: 28240279
• Pentose Sugars Inhibit Metabolism and Increase Expression of an AgrD-type Cyclic Pentapeptide in Clostridium Thermocellum
  Scientific Reports. 02, 2017  |   Pubmed ID: 28230109
• Genome-Resolved Meta-Omics Ties Microbial Dynamics to Process Performance in Biotechnology for Thiocyanate Degradation
  Environmental Science & Technology. 03, 2017  |   Pubmed ID: 28139919
• The Protein and Neutral Lipid Composition of Lipid Droplets Isolated from the Fission Yeast, Schizosaccharomyces Pombe
  Journal of Microbiology (Seoul, Korea). Feb, 2017  |   Pubmed ID: 28120187
• Impacts of Chemical Gradients on Microbial Community Structure
  The ISME Journal. 04, 2017  |   Pubmed ID: 28094795
• Improved Growth Rate in Hydrogenase Mutant Via Perturbed Sulfur Metabolism
  Biotechnology for Biofuels. 2017  |   Pubmed ID: 28053665
• Development of a Plasmid-based Expression System in and Its Use to Screen Heterologous Expression of Bifunctional Alcohol Dehydrogenases (s)
  Metabolic Engineering Communications. Dec, 2016  |   Pubmed ID: 29142822
• Transcriptomic and Proteomic Insights into Innate Immunity and Adaptations to a Symbiotic Lifestyle in the Gutless Marine Worm Olavius Algarvensis
  BMC Genomics. 11, 2016  |   Pubmed ID: 27871231
• Transcript, Protein and Metabolite Temporal Dynamics in the CAM Plant Agave
  Nature Plants. 11, 2016  |   Pubmed ID: 27869799
• Proteogenomic Analyses Indicate Bacterial Methylotrophy and Archaeal Heterotrophy Are Prevalent Below the Grass Root Zone
  PeerJ. 2016  |   Pubmed ID: 27843720
• Proteomic Stable Isotope Probing Reveals Taxonomically Distinct Patterns in Amino Acid Assimilation by Coastal Marine Bacterioplankton
  MSystems. Mar-Apr, 2016  |   Pubmed ID: 27822523
• Reconstructing a Hydrogen-driven Microbial Metabolic Network in Opalinus Clay Rock
  Nature Communications. 10, 2016  |   Pubmed ID: 27739431
• Global Proteome Response to Deletion of Genes Related to Mercury Methylation and Dissimilatory Metal Reduction Reveals Changes in Respiratory Metabolism in Geobacter Sulfurreducens PCA
  Journal of Proteome Research. 10, 2016  |   Pubmed ID: 27463218
• Metabolic Regulation As a Consequence of Anaerobic 5-Methylthioadenosine Recycling in Rhodospirillum Rubrum
  MBio. 07, 2016  |   Pubmed ID: 27406564
• Genomics-informed Isolation and Characterization of a Symbiotic Nanoarchaeota System from a Terrestrial Geothermal Environment
  Nature Communications. 07, 2016  |   Pubmed ID: 27378076
• Simultaneous Achievement of High Ethanol Yield and Titer in Clostridium Thermocellum
  Biotechnology for Biofuels. 2016  |   Pubmed ID: 27257435
• Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities
  Frontiers in Microbiology. 2016  |   Pubmed ID: 27199908
• Dramatic Performance of Clostridium Thermocellum Explained by Its Wide Range of Cellulase Modalities
  Science Advances. Feb, 2016  |   Pubmed ID: 26989779
• Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage
  Frontiers in Microbiology. 2016  |   Pubmed ID: 26973616
• Draft Genome Sequence of Streptomyces Vitaminophilus ATCC 31673, a Producer of Pyrrolomycin Antibiotics, Some of Which Contain a Nitro Group
  Genome Announcements. Jan, 2016  |   Pubmed ID: 26798098
• Critical Biogeochemical Functions in the Subsurface Are Associated with Bacteria from New Phyla and Little Studied Lineages
  Environmental Microbiology. Jan, 2016  |   Pubmed ID: 26033198
• Characterization of Fatty Acids in Crenarchaeota by GC-MS and NMR
  Archaea (Vancouver, B.C.). 2015  |   Pubmed ID: 26880868
• Integrating MRNA and Protein Sequencing Enables the Detection and Quantitative Profiling of Natural Protein Sequence Variants of Populus Trichocarpa
  Journal of Proteome Research. Dec, 2015  |   Pubmed ID: 26483142
• Untargeted Metabolomics Studies Employing NMR and LC-MS Reveal Metabolic Coupling Between and Its Archaeal Host
  Metabolomics : Official Journal of the Metabolomic Society. Aug, 2015  |   Pubmed ID: 26273237
• Strain-resolved Microbial Community Proteomics Reveals Simultaneous Aerobic and Anaerobic Function During Gastrointestinal Tract Colonization of a Preterm Infant
  Frontiers in Microbiology. 2015  |   Pubmed ID: 26191049
• A Roadmap for Research on Crassulacean Acid Metabolism (CAM) to Enhance Sustainable Food and Bioenergy Production in a Hotter, Drier World
  The New Phytologist. Aug, 2015  |   Pubmed ID: 26153373
• Rescuing Those Left Behind: Recovering and Characterizing Underdigested Membrane and Hydrophobic Proteins To Enhance Proteome Measurement Depth
  Analytical Chemistry. Aug, 2015  |   Pubmed ID: 26110888
• Metaproteomics Reveals Functional Shifts in Microbial and Human Proteins During a Preterm Infant Gut Colonization Case
  Proteomics. Oct, 2015  |   Pubmed ID: 26077811
• Metagenome Sequencing of a Coastal Marine Microbial Community from Monterey Bay, California
  Genome Announcements. Apr, 2015  |   Pubmed ID: 25931598
• Microbial Metaproteomics for Characterizing the Range of Metabolic Functions and Activities of Human Gut Microbiota
  Proteomics. Oct, 2015  |   Pubmed ID: 25914197
• Discrete and Structurally Unique Proteins (tāpirins) Mediate Attachment of Extremely Thermophilic Caldicellulosiruptor Species to Cellulose
  The Journal of Biological Chemistry. Apr, 2015  |   Pubmed ID: 25720489
• Development of an Enhanced Metaproteomic Approach for Deepening the Microbiome Characterization of the Human Infant Gut
  Journal of Proteome Research. Jan, 2015  |   Pubmed ID: 25350865
• Elevated Temperature Alters Proteomic Responses of Individual Organisms Within a Biofilm Community
  The ISME Journal. Jan, 2015  |   Pubmed ID: 25050524
• Life on the Edge: Functional Genomic Response of Ignicoccus Hospitalis to the Presence of Nanoarchaeum Equitans
  The ISME Journal. Jan, 2015  |   Pubmed ID: 25012904
• A Comparative Multidimensional LC-MS Proteomic Analysis Reveals Mechanisms for Furan Aldehyde Detoxification in Thermoanaerobacter Pseudethanolicus 39E
  Biotechnology for Biofuels. 2014  |   Pubmed ID: 25506391
• Nitrogen Cycling. The Environmental Controls That Govern the End Product of Bacterial Nitrate Respiration
  Science (New York, N.Y.). Aug, 2014  |   Pubmed ID: 25104387
• Diverse and Divergent Protein Post-translational Modifications in Two Growth Stages of a Natural Microbial Community
  Nature Communications. Jul, 2014  |   Pubmed ID: 25059763
• Metaproteomics: Extracting and Mining Proteome Information to Characterize Metabolic Activities in Microbial Communities
  Current Protocols in Bioinformatics. Jun, 2014  |   Pubmed ID: 24939130
• Recoding of the Stop Codon UGA to Glycine by a BD1-5/SN-2 Bacterium and Niche Partitioning Between Alpha- and Gammaproteobacteria in a Tidal Sediment Microbial Community Naturally Selected in a Laboratory Chemostat
  Frontiers in Microbiology. 2014  |   Pubmed ID: 24904545
• Development of a Multipoint Quantitation Method to Simultaneously Measure Enzymatic and Structural Components of the Clostridium Thermocellum Cellulosome Protein Complex
  Journal of Proteome Research. Feb, 2014  |   Pubmed ID: 24274857
• Identification and Environmental Distribution of DcpA, Which Encodes the Reductive Dehalogenase Catalyzing the Dichloroelimination of 1,2-dichloropropane to Propene in Organohalide-respiring Chloroflexi
  Applied and Environmental Microbiology. Feb, 2014  |   Pubmed ID: 24242248
• Effects of Diet on Resource Utilization by a Model Human Gut Microbiota Containing Bacteroides Cellulosilyticus WH2, a Symbiont with an Extensive Glycobiome
  PLoS Biology. 2013  |   Pubmed ID: 23976882
• Environmental Proteomics Reveals Early Microbial Community Responses to Biostimulation at a Uranium- and Nitrate-contaminated Site
  Proteomics. Oct, 2013  |   Pubmed ID: 23894087
• Isolation and Chemical Analysis of Nanoparticles from English Ivy (Hedera Helix L.)
  Journal of the Royal Society, Interface / the Royal Society. Oct, 2013  |   Pubmed ID: 23883948
• Comparative Informatics Analysis to Evaluate Site-specific Protein Oxidation in Multidimensional LC-MS/MS Data
  Journal of Proteome Research. Jul, 2013  |   Pubmed ID: 23827042
• Insights into the Structure and Metabolic Function of Microbes That Shape Pelagic Iron-rich Aggregates ("iron Snow")
  Applied and Environmental Microbiology. Jul, 2013  |   Pubmed ID: 23645202
• New Group in the Leptospirillum Clade: Cultivation-independent Community Genomics, Proteomics, and Transcriptomics of the New Species "Leptospirillum Group IV UBA BS"
  Applied and Environmental Microbiology. Sep, 2013  |   Pubmed ID: 23645189
• Metaproteomics: Harnessing the Power of High Performance Mass Spectrometry to Identify the Suite of Proteins That Control Metabolic Activities in Microbial Communities
  Analytical Chemistry. May, 2013  |   Pubmed ID: 23469896
• Characterizing the Range of Extracellular Protein Post-translational Modifications in a Cellulose-degrading Bacteria Using a Multiple Proteolyic Digestion/peptide Fragmentation Approach
  Analytical Chemistry. Mar, 2013  |   Pubmed ID: 23406086
• Experimental Approach to Controllably Vary Protein Oxidation While Minimizing Electrode Adsorption for Boron-doped Diamond Electrochemical Surface Mapping Applications
  Analytical Chemistry. Jan, 2013  |   Pubmed ID: 23210708
• Role of the CipA Scaffoldin Protein in Cellulose Solubilization, As Determined by Targeted Gene Deletion and Complementation in Clostridium Thermocellum
  Journal of Bacteriology. Feb, 2013  |   Pubmed ID: 23204466
• Putting the Pieces Together: High-performance LC-MS/MS Provides Network-, Pathway-, and Protein-level Perspectives in Populus
  Molecular & Cellular Proteomics : MCP. Jan, 2013  |   Pubmed ID: 23073815
• Integrated Metagenomics/metaproteomics Reveals Human Host-microbiota Signatures of Crohn's Disease
  PloS One. 2012  |   Pubmed ID: 23209564
• Biostimulation Induces Syntrophic Interactions That Impact C, S and N Cycling in a Sediment Microbial Community
  The ISME Journal. Nov, 2012  |   Pubmed ID: 23190730
• Clostridium Thermocellum ATCC27405 Transcriptomic, Metabolomic and Proteomic Profiles After Ethanol Stress
  BMC Genomics. Jul, 2012  |   Pubmed ID: 22823947
• Phage-induced Expression of CRISPR-associated Proteins is Revealed by Shotgun Proteomics in Streptococcus Thermophilus
  PloS One. 2012  |   Pubmed ID: 22666452
• Caldicellulosiruptor Core and Pangenomes Reveal Determinants for Noncellulosomal Thermophilic Deconstruction of Plant Biomass
  Journal of Bacteriology. Aug, 2012  |   Pubmed ID: 22636774
• Microbial Metaproteomics: Identifying the Repertoire of Proteins That Microorganisms Use to Compete and Cooperate in Complex Environmental Communities
  Current Opinion in Microbiology. Jun, 2012  |   Pubmed ID: 22632760
• Systematic Comparison of Label-free, Metabolic Labeling, and Isobaric Chemical Labeling for Quantitative Proteomics on LTQ Orbitrap Velos
  Journal of Proteome Research. Mar, 2012  |   Pubmed ID: 22188275
• Microbes in Thawing Permafrost: the Unknown Variable in the Climate Change Equation
  The ISME Journal. Apr, 2012  |   Pubmed ID: 22094350
• Defining the Boundaries and Characterizing the Landscape of Functional Genome Expression in Vascular Tissues of Populus Using Shotgun Proteomics
  Journal of Proteome Research. Jan, 2012  |   Pubmed ID: 22003893
• Strategies for Metagenomic-guided Whole-community Proteomics of Complex Microbial Environments
  PloS One. 2011  |   Pubmed ID: 22132090
• Comparative Shotgun Proteomic Analysis of Clostridium Acetobutylicum from Butanol Fermentation Using Glucose and Xylose
  Proteome Science. Oct, 2011  |   Pubmed ID: 22008648
• Label-free Quantitative Proteomics for the Extremely Thermophilic Bacterium Caldicellulosiruptor Obsidiansis Reveal Distinct Abundance Patterns Upon Growth on Cellobiose, Crystalline Cellulose, and Switchgrass
  Journal of Proteome Research. Dec, 2011  |   Pubmed ID: 21988591
• Proteomic Characterization of Cellular and Molecular Processes That Enable the Nanoarchaeum Equitans--Ignicoccus Hospitalis Relationship
  PloS One. 2011  |   Pubmed ID: 21826220
• Identification of Biofilm Matrix-associated Proteins from an Acid Mine Drainage Microbial Community
  Applied and Environmental Microbiology. Aug, 2011  |   Pubmed ID: 21685158
• Use of Label-free Quantitative Proteomics to Distinguish the Secreted Cellulolytic Systems of Caldicellulosiruptor Bescii and Caldicellulosiruptor Obsidiansis
  Applied and Environmental Microbiology. Jun, 2011  |   Pubmed ID: 21498747
• Discovery and Annotation of Small Proteins Using Genomics, Proteomics, and Computational Approaches
  Genome Research. Apr, 2011  |   Pubmed ID: 21367939
• Quantitative Tracking of Isotope Flows in Proteomes of Microbial Communities
  Molecular & Cellular Proteomics : MCP. Apr, 2011  |   Pubmed ID: 21285414
• Quantitative Proteomic Analyses of the Response of Acidophilic Microbial Communities to Different PH Conditions
  The ISME Journal. Jul, 2011  |   Pubmed ID: 21228889
• Metabolome-proteome Differentiation Coupled to Microbial Divergence
  MBio. Oct, 2010  |   Pubmed ID: 20978538
• Direct Cellular Lysis/protein Extraction Protocol for Soil Metaproteomics
  Journal of Proteome Research. Dec, 2010  |   Pubmed ID: 20954746
• Ecological Distribution and Population Physiology Defined by Proteomics in a Natural Microbial Community
  Molecular Systems Biology. Jun, 2010  |   Pubmed ID: 20531404
• Proteomics Reveals a Core Molecular Response of Pseudomonas Putida F1 to Acute Chromate Challenge
  BMC Genomics. 2010  |   Pubmed ID: 20482812
• Enigmatic, Ultrasmall, Uncultivated Archaea
  Proceedings of the National Academy of Sciences of the United States of America. May, 2010  |   Pubmed ID: 20421484
• A High-throughput De Novo Sequencing Approach for Shotgun Proteomics Using High-resolution Tandem Mass Spectrometry
  BMC Bioinformatics. Mar, 2010  |   Pubmed ID: 20205730
• PTMSearchPlus: Software Tool for Automated Protein Identification and Post-translational Modification Characterization by Integrating Accurate Intact Protein Mass and Bottom-up Mass Spectrometric Data Searches
  Analytical Chemistry. Oct, 2009  |   Pubmed ID: 19775152
• Proteogenomic Monitoring of Geobacter Physiology During Stimulated Uranium Bioremediation
  Applied and Environmental Microbiology. Oct, 2009  |   Pubmed ID: 19717633
• Community Genomic and Proteomic Analyses of Chemoautotrophic Iron-oxidizing "Leptospirillum Rubarum" (Group II) and "Leptospirillum Ferrodiazotrophum" (Group III) Bacteria in Acid Mine Drainage Biofilms
  Applied and Environmental Microbiology. Jul, 2009  |   Pubmed ID: 19429552
• Differential Accumulation of Form I RubisCO in Rhodopseudomonas Palustris CGA010 Under Photoheterotrophic Growth Conditions with Reduced Carbon Sources
  Journal of Bacteriology. Jul, 2009  |   Pubmed ID: 19376869
• Characterizing a Model Human Gut Microbiota Composed of Members of Its Two Dominant Bacterial Phyla
  Proceedings of the National Academy of Sciences of the United States of America. Apr, 2009  |   Pubmed ID: 19321416
• Phenotype Fingerprinting Suggests the Involvement of Single-genotype Consortia in Degradation of Aromatic Compounds by Rhodopseudomonas Palustris
  PloS One. 2009  |   Pubmed ID: 19242537
• Systems Biology: Functional Analysis of Natural Microbial Consortia Using Community Proteomics
  Nature Reviews. Microbiology. Mar, 2009  |   Pubmed ID: 19219053
• Comparative Temporal Proteomics of a Response Regulator (SO2426)-deficient Strain and Wild-type Shewanella Oneidensis MR-1 During Chromate Transformation
  Journal of Proteome Research. Jan, 2009  |   Pubmed ID: 19118451
• Shotgun Metaproteomics of the Human Distal Gut Microbiota
  The ISME Journal. Feb, 2009  |   Pubmed ID: 18971961
• Experimental Approach for Deep Proteome Measurements from Small-scale Microbial Biomass Samples
  Analytical Chemistry. Dec, 2008  |   Pubmed ID: 19072265
• Characterization of Cytochrome 579, an Unusual Cytochrome Isolated from an Iron-oxidizing Microbial Community
  Applied and Environmental Microbiology. Jul, 2008  |   Pubmed ID: 18469132
• Development of an Electrochemical Oxidation Method for Probing Higher Order Protein Structure with Mass Spectrometry
  Analytical Chemistry. May, 2008  |   Pubmed ID: 18351783
• Systematic Assessment of the Benefits and Caveats in Mining Microbial Post-translational Modifications from Shotgun Proteomic Data: the Response of Shewanella Oneidensis to Chromate Exposure
  Journal of Proteome Research. Feb, 2008  |   Pubmed ID: 18171020
• Characterization of Anaerobic Catabolism of P-coumarate in Rhodopseudomonas Palustris by Integrating Transcriptomics and Quantitative Proteomics
  Molecular & Cellular Proteomics : MCP. May, 2008  |   Pubmed ID: 18156135
• Dosage-dependent Proteome Response of Shewanella Oneidensis MR-1 to Acute Chromate Challenge
  Journal of Proteome Research. May, 2007  |   Pubmed ID: 17385904
• Detecting Differential and Correlated Protein Expression in Label-free Shotgun Proteomics
  Journal of Proteome Research. Nov, 2006  |   Pubmed ID: 17081042
• ProRata: A Quantitative Proteomics Program for Accurate Protein Abundance Ratio Estimation with Confidence Interval Evaluation
  Analytical Chemistry. Oct, 2006  |   Pubmed ID: 17037911
• Robust Estimation of Peptide Abundance Ratios and Rigorous Scoring of Their Variability and Bias in Quantitative Shotgun Proteomics
  Analytical Chemistry. Oct, 2006  |   Pubmed ID: 17037910
• Global Molecular and Morphological Effects of 24-hour Chromium(VI) Exposure on Shewanella Oneidensis MR-1
  Applied and Environmental Microbiology. Sep, 2006  |   Pubmed ID: 16957260
• Characterization of PII Family (GlnK1, GlnK2, and GlnB) Protein Uridylylation in Response to Nitrogen Availability for Rhodopseudomonas Palustris
  Analytical Biochemistry. Oct, 2006  |   Pubmed ID: 16860774
• Determination of Peptide and Protein Ion Charge States by Fourier Transformation of Isotope-resolved Mass Spectra
  Journal of the American Society for Mass Spectrometry. Jul, 2006  |   Pubmed ID: 16713712
• Molecular Dynamics of the Shewanella Oneidensis Response to Chromate Stress
  Molecular & Cellular Proteomics : MCP. Jun, 2006  |   Pubmed ID: 16524964
• Determination and Comparison of the Baseline Proteomes of the Versatile Microbe Rhodopseudomonas Palustris Under Its Major Metabolic States
  Journal of Proteome Research. Feb, 2006  |   Pubmed ID: 16457594
• MASPIC: Intensity-based Tandem Mass Spectrometry Scoring Scheme That Improves Peptide Identification at High Confidence
  Analytical Chemistry. Dec, 2005  |   Pubmed ID: 16316165
• 53rd American Society for Mass Spectrometry Conference. 5-9 June, 2005, Henry B Gonzalez Conference Center, San Antonio, TX, USA
  Expert Review of Proteomics. Aug, 2005  |   Pubmed ID: 16097880
• Multipole-storage-assisted Dissociation for the Characterization of Large Proteins and Simple Protein Mixtures by ESI-FTICR-MS
  Analytical Chemistry. May, 2005  |   Pubmed ID: 15889895
• Photochemical Surface Mapping of C14S-Sml1p for Constrained Computational Modeling of Protein Structure
  Analytical Biochemistry. May, 2005  |   Pubmed ID: 15840492
• DBDigger: Reorganized Proteomic Database Identification That Improves Flexibility and Speed
  Analytical Chemistry. Apr, 2005  |   Pubmed ID: 15828782
• Transcriptomic and Proteomic Characterization of the Fur Modulon in the Metal-reducing Bacterium Shewanella Oneidensis
  Journal of Bacteriology. Dec, 2004  |   Pubmed ID: 15576789
• Characterization of the 70S Ribosome from Rhodopseudomonas Palustris Using an Integrated "top-down" and "bottom-up" Mass Spectrometric Approach
  Journal of Proteome Research. Sep-Oct, 2004  |   Pubmed ID: 15473684
• A Computational Method for Assessing Peptide- Identification Reliability in Tandem Mass Spectrometry Analysis with SEQUEST
  Proteomics. Apr, 2004  |   Pubmed ID: 15048978
• Analysis of Protein Solvent Accessible Surfaces by Photochemical Oxidation and Mass Spectrometry
  Analytical Chemistry. Feb, 2004  |   Pubmed ID: 14750862
• Protein Surface Mapping by Chemical Oxidation: Structural Analysis by Mass Spectrometry
  Analytical Biochemistry. Feb, 2003  |   Pubmed ID: 12605858
• Integrating 'top-down" and "bottom-up" Mass Spectrometric Approaches for Proteomic Analysis of Shewanella Oneidensis
  Journal of Proteome Research. May-Jun, 2002  |   Pubmed ID: 12645901
• Intact Protein Analysis for Site-directed Mutagenesis Overexpression Products: Plasmid-encoded R67 Dihydrofolate Reductase
  Analytical Biochemistry. Jun, 2002  |   Pubmed ID: 12018947
• Formation and Characterization of Iron-oligonucleotide Complexes with Matrix-assisted Laser Desorption/ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry
  Journal of the American Society for Mass Spectrometry. Oct, 1999  |   Pubmed ID: 10497807