Related references
Note: Only part of the references are listed.Combining a robust thermophilic methanogen and packing material with high liquid hold-up to optimize biological methanation in trickle-bed reactors
Anja Kaul et al.
BIORESOURCE TECHNOLOGY (2022)
Multiscale models quantifying yeast physiology: towards a whole-cell model
Hongzhong Lu et al.
TRENDS IN BIOTECHNOLOGY (2022)
A Nanobody-Based Toolset to Monitor and Modify the Mitochondrial GTPase Miro1
Funmilayo O. Fagbadebo et al.
FRONTIERS IN MOLECULAR BIOSCIENCES (2022)
Gas detection of hydrogen/natural gas blends in the gas industry
J. E. Hall et al.
INTERNATIONAL JOURNAL OF HYDROGEN ENERGY (2021)
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes
Samuel M. D. Seaver et al.
NUCLEIC ACIDS RESEARCH (2021)
Database resources of the National Center for Biotechnology Information
Eric W. Sayers et al.
NUCLEIC ACIDS RESEARCH (2021)
Archaea Biotechnology
Kevin Pfeifer et al.
BIOTECHNOLOGY ADVANCES (2021)
Recent advances in constraint and machine learning-based metabolic modeling by leveraging stoichiometric balances, thermodynamic feasibility and kinetic law formalisms
Patrick F. Suthers et al.
METABOLIC ENGINEERING (2021)
multiTFA: a Python package for multi-variate thermodynamics-based flux analysis
Vishnuvardhan Mahamkali et al.
BIOINFORMATICS (2021)
A Shuttle-Vector System Allows Heterologous Gene Expression in the Thermophilic Methanogen Methanothermobacter thermautotrophicus ΔH
Christian Fink et al.
MBIO (2021)
Twelve years of SAMtools and BCFtools
Petr Danecek et al.
GIGASCIENCE (2021)
High-Quality Genome-Scale Reconstruction of Corynebacterium glutamicum ATCC 13032
Martina Feierabend et al.
FRONTIERS IN MICROBIOLOGY (2021)
Optimized biological CO2-methanation with a pure culture of thermophilic methanogenic archaea in a trickle-bed reactor
Martin Thema et al.
BIORESOURCE TECHNOLOGY (2021)
Three-megadalton complex of methanogenic electron-bifurcating and CO2-fixing enzymes
Tomohiro Watanabe et al.
SCIENCE (2021)
A standardized archaeal taxonomy for the Genome Taxonomy Database
Christian Rinke et al.
NATURE MICROBIOLOGY (2021)
COG database update: focus on microbial diversity, model organisms, and widespread pathogens
Michael Y. Galperin et al.
NUCLEIC ACIDS RESEARCH (2021)
MultiMotifMaker: A Multi-Thread Tool for Identifying DNA Methylation Motifs from Pacbio Reads
Tao Li et al.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2020)
The MetaCyc database of metabolic pathways and enzymes - a 2019 update
Ron Caspi et al.
NUCLEIC ACIDS RESEARCH (2020)
MEMOTE for standardized genome-scale metabolic model testing
Christian Lieven et al.
NATURE BIOTECHNOLOGY (2020)
Assessment of the combustion performance of a room furnace operating on pipeline natural gas mixed with simulated biogas or hydrogen
Yan Zhao et al.
INTERNATIONAL JOURNAL OF HYDROGEN ENERGY (2020)
SBML Level 3: an extensible format for the exchange and reuse of biological models
Sarah M. Keating et al.
MOLECULAR SYSTEMS BIOLOGY (2020)
Community standards to facilitate development and address challenges in metabolic modeling
Maureen A. Carey et al.
MOLECULAR SYSTEMS BIOLOGY (2020)
Reconstructing organisms in silico: genome-scale models and their emerging applications
Xin Fang et al.
NATURE REVIEWS MICROBIOLOGY (2020)
Rapid Peptides Generator: fast and efficient in silico protein digestion
Maillet Nicolas
NAR GENOMICS AND BIOINFORMATICS (2020)
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0
Laurent Heirendt et al.
NATURE PROTOCOLS (2019)
A hydrogen supply chain with spatial resolution: Comparative analysis of infrastructure technologies in Germany
Markus Reuss et al.
APPLIED ENERGY (2019)
Energy metabolism controls phenotypes by protein efficiency and allocation
Yu Chen et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)
Comparative proteomic analysis of Methanothermobacter thermautotrophicus reveals methane formation from H2 and CO2 under different temperature conditions
Cong Liu et al.
MICROBIOLOGYOPEN (2019)
A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism
Hongzhong Lu et al.
NATURE COMMUNICATIONS (2019)
UniProt: a worldwide hub of protein knowledge
Alex Bateman et al.
NUCLEIC ACIDS RESEARCH (2019)
BRENDA in 2019: a European ELIXIR core data resource
Lisa Jeske et al.
NUCLEIC ACIDS RESEARCH (2019)
The PRIDE database and related tools and resources in 2019: improving support for quantification data
Yasset Perez-Riverol et al.
NUCLEIC ACIDS RESEARCH (2019)
consensusDE: an R package for assessing consensus of multiple RNA-seq algorithms with RUV correction
Ashley J. Waardenberg et al.
PEERJ (2019)
The BioCyc collection of microbial genomes and metabolic pathways
Peter D. Karp et al.
BRIEFINGS IN BIOINFORMATICS (2019)
Current status and applications of genome-scale metabolic models
Changdai Gu et al.
GENOME BIOLOGY (2019)
A systematic assessment of current genome-scale metabolic reconstruction tools
Sebastian N. Mendoza et al.
GENOME BIOLOGY (2019)
Biological hydrogen methanation systems ? an overview of design and efficiency
Davis Rusmanis et al.
BIOENGINEERED (2019)
BioModels: expanding horizons to include more modelling approaches and formats
Mihai Glont et al.
NUCLEIC ACIDS RESEARCH (2018)
H-2 drives metabolic rearrangements in gas-fermenting Clostridium autoethanogenum
Kaspar Valgepea et al.
BIOTECHNOLOGY FOR BIOFUELS (2018)
Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation
Sergey Koren et al.
GENOME RESEARCH (2017)
Arginine deiminase pathway provides ATP and boosts growth of the gas-fermenting acetogen Clostridium autoethanogenum
Kaspar Valgepea et al.
METABOLIC ENGINEERING (2017)
Salmon provides fast and bias-aware quantification of transcript expression
Rob Patro et al.
NATURE METHODS (2017)
Characteristics of adapted hydrogenotrophic community during biomethanation
Lydia Rachbauer et al.
SCIENCE OF THE TOTAL ENVIRONMENT (2017)
Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function
ShengShee Thor et al.
ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL (2017)
Metabolic Models of Protein Allocation Call for the Kinetome
Avlant Nilsson et al.
CELL SYSTEMS (2017)
The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism
Garrett W. Birkel et al.
BMC BIOINFORMATICS (2017)
Genome-wide gene expression and RNA half-life measurements allow predictions of regulation and metabolic behavior in Methanosarcina acetivorans
Joseph R. Peterson et al.
BMC GENOMICS (2016)
Process analysis of biological Sabatier reaction for bio-methane production
Grazia Leonzio
CHEMICAL ENGINEERING JOURNAL (2016)
The formate bio-economy
Oren Yishai et al.
CURRENT OPINION IN CHEMICAL BIOLOGY (2016)
Pan-proteomics, a concept for unifying quantitative proteome measurements when comparing closely-related bacterial strains
James A. Broadbent et al.
EXPERT REVIEW OF PROTEOMICS (2016)
Low carbon fuels and commodity chemicals from waste gases - systematic approach to understand energy metabolism in a model acetogen
Esteban Marcellin et al.
GREEN CHEMISTRY (2016)
Exploring Hydrogenotrophic Methanogenesis: a Genome Scale Metabolic Reconstruction of Methanococcus maripaludis
Matthew A. Richards et al.
JOURNAL OF BACTERIOLOGY (2016)
Assessing methanotrophy and carbon fixation for biofuel production by Methanosarcina acetivorans
Hadi Nazem-Bokaee et al.
MICROBIAL CELL FACTORIES (2016)
Proteomic Analysis of the Hydrogen and Carbon Monoxide Metabolism of Methanothermobacter marburgensis
Martijn Diender et al.
FRONTIERS IN MICROBIOLOGY (2016)
A Ferredoxin Disulfide Reductase Delivers Electrons to the Methanosarcina barkeri Class III Ribonucleotide-Reductase
Yifeng Wei et al.
BIOCHEMISTRY (2015)
Power to gas: Technological overview, systems analysis and economic assessment for a case study in Germany
Sebastian Schiebahn et al.
INTERNATIONAL JOURNAL OF HYDROGEN ENERGY (2015)
Thermodynamics and H2 Transfer in a Methanogenic, Syntrophic Community
Joshua J. Hamilton et al.
PLOS COMPUTATIONAL BIOLOGY (2015)
Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways
Zachary A. King et al.
PLOS COMPUTATIONAL BIOLOGY (2015)
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
Yang Liao et al.
BIOINFORMATICS (2014)
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project
Frank T. Bergmann et al.
BMC BIOINFORMATICS (2014)
A genome-scale metabolic model of Methanococcus maripaludis S2 for CO2 capture and conversion to methane
Nishu Goyal et al.
MOLECULAR BIOSYSTEMS (2014)
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Michael I. Love et al.
GENOME BIOLOGY (2014)
Genetic Techniques for the Archaea
Joel A. Farkas et al.
ANNUAL REVIEW OF GENETICS, VOL 47 (2013)
Genomically and biochemically accurate metabolic reconstruction of Methanosarcina barkeri Fusaro, iMG746
Matthew C. Gonnerman et al.
BIOTECHNOLOGY JOURNAL (2013)
COBRApy: COnstraints-Based Reconstruction and Analysis for Python
Ali Ebrahim et al.
BMC SYSTEMS BIOLOGY (2013)
Sabatier-based CO2-methanation by catalytic conversion
K. Mueller et al.
ENVIRONMENTAL EARTH SCIENCES (2013)
Direct and Reversible Hydrogenation of CO2 to Formate by a Bacterial Carbon Dioxide Reductase
K. Schuchmann et al.
SCIENCE (2013)
Understanding the interactions between bacteria in the human gut through metabolic modeling
Saeed Shoaie et al.
SCIENTIFIC REPORTS (2013)
A Single-Culture Bioprocess of Methanothermobacter thermautotrophicus to Upgrade Digester Biogas by CO2-to-CH4 Conversion with H-2
Matthew R. Martin et al.
ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL (2013)
Genome-Scale Metabolic Reconstruction and Hypothesis Testing in the Methanogenic Archaeon Methanosarcina acetivorans C2A
Matthew N. Benedict et al.
JOURNAL OF BACTERIOLOGY (2012)
Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation
Aarash Bordbar et al.
MOLECULAR SYSTEMS BIOLOGY (2012)
Identifiers.org and MIRIAM Registry: community resources to provide persistent identification
Nick Juty et al.
NUCLEIC ACIDS RESEARCH (2012)
The Wolfe cycle comes full circle
Rudolf K. Thauer
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)
Purine biosynthesis in archaea: variations on a theme
Anne M. Brown et al.
BIOLOGY DIRECT (2011)
Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans
Vinay Satish Kumar et al.
BMC SYSTEMS BIOLOGY (2011)
The evolution of metabolic networks of E. coli
David J. Baumler et al.
BMC SYSTEMS BIOLOGY (2011)
Global quantification of mammalian gene expression control
Bjoern Schwanhaeusser et al.
NATURE (2011)
More Than 200 Genes Required for Methane Formation from H2and CO2and Energy Conservation Are Present inMethanothermobacter marburgensisandMethanothermobacter thermautotrophicus
Anne-Kristin Kaster et al.
ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL (2011)
iMAT: an integrative metabolic analysis tool
Hadas Zur et al.
BIOINFORMATICS (2010)
Complete Genome Sequence of Methanothermobacter marburgensis, a Methanoarchaeon Model Organism
Heiko Liesegang et al.
JOURNAL OF BACTERIOLOGY (2010)
High-throughput generation, optimization and analysis of genome-scale metabolic models
Christopher S. Henry et al.
NATURE BIOTECHNOLOGY (2010)
A protocol for generating a high-quality genome-scale metabolic reconstruction
Ines Thiele et al.
NATURE PROTOCOLS (2010)
The Sequence Alignment/Map format and SAMtools
Heng Li et al.
BIOINFORMATICS (2009)
Biopython: freely available Python tools for computational molecular biology and bioinformatics
Peter J. A. Cock et al.
BIOINFORMATICS (2009)
BLAST plus : architecture and applications
Christiam Camacho et al.
BMC BIOINFORMATICS (2009)
Comparative transcriptome analysis of responses of Methanothermobacter thermautotrophicus to different environmental stimuli
Souichiro Kato et al.
ENVIRONMENTAL MICROBIOLOGY (2008)
Network-based prediction of human tissue-specific metabolism
Tomer Shlomi et al.
NATURE BIOTECHNOLOGY (2008)
Methanogenic archaea: ecologically relevant differences in energy conservation
Rudolf K. Thauer et al.
NATURE REVIEWS MICROBIOLOGY (2008)
Context-specific metabolic networks are consistent with experiments
Scott A. Becker et al.
PLOS COMPUTATIONAL BIOLOGY (2008)
Coupling of Methanothennobacter thermautotrophicus methane formation and growth in fed-batch and continuous cultures under different H2 gassing regimens
Linda M. I. De Poorter et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2007)
Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri
Adam M. Feist et al.
MOLECULAR SYSTEMS BIOLOGY (2006)
Tetrahydrofolate-specific enzymes in Methanosarcina barkeri and growth dependence of this methanogenic archaeon on folic acid or p-aminobenzoic acid
B Buchenau et al.
ARCHIVES OF MICROBIOLOGY (2004)
Bioenergetics of the formyl-methanofuran dehydrogenase and heterodisulfide reductase reactions in Methanothermobacter thermautotrophicus
LMI de Poorter et al.
EUROPEAN JOURNAL OF BIOCHEMISTRY (2003)
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
R Edgar et al.
NUCLEIC ACIDS RESEARCH (2002)
Approach to steady state in completely mixed flow reactors
JN Jensen
JOURNAL OF ENVIRONMENTAL ENGINEERING-ASCE (2001)
Regulation of the synthesis of H2-forming methylenetetrahydromethanopterin dehydrogenase (Hmd) and of HmdII and HmdIII in Methanothermobacter marburgensis
C Afting et al.
ARCHIVES OF MICROBIOLOGY (2000)
KEGG: Kyoto Encyclopedia of Genes and Genomes
M Kanehisa et al.
NUCLEIC ACIDS RESEARCH (2000)
Phylogenetic analysis of 18 thermophilic Methanobacterium isolates supports the proposals to create a new genus, Methanothermobacter gen. nov., and to reclassify several isolates in three species, Methanothermobacter thermautotrophicus comb. nov., methanothermobacter wolfeii comb. nov., and Methanothermobacter marburgensis sp nov.
A Wasserfallen et al.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2000)