Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function

Genome-wide gene expression and RNA half-life measurements allow predictions of regulation and metabolic behavior in Methanosarcina acetivorans

(2016) Joseph R. Peterson et al.   BMC GENOMICS

Assessing methanotrophy and carbon fixation for biofuel production by Methanosarcina acetivorans

(2016) Hadi Nazem-Bokaee et al.   Microbial Cell Factories

Rerouting Cellular Electron Flux To Increase the Rate of Biological Methane Production

(2015) Jennie L. Catlett et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Mechanism of the Enzymatic Synthesis of 4-(Hydroxymethyl)-2-furancarboxaldehyde-phosphate (4-HFC-P) from Glyceraldehyde-3-phosphate Catalyzed by 4-HFC-P Synthase

(2015) Yu Wang et al.   BIOCHEMISTRY

Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology

(2015) Peter D. Karp et al.   BRIEFINGS IN BIOINFORMATICS

Identification of the Final Two Genes Functioning in Methanofuran Biosynthesis in Methanocaldococcus jannaschii

(2015) Yu Wang et al.   JOURNAL OF BACTERIOLOGY

Genetic Basis for Metabolism of Methylated Sulfur Compounds in Methanosarcina Species

(2015) He Fu et al.   JOURNAL OF BACTERIOLOGY

Reconstructing genome-scale metabolic models with merlin

(2015) Oscar Dias et al.   NUCLEIC ACIDS RESEARCH

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Designing overall stoichiometric conversions and intervening metabolic reactions

(2015) Anupam Chowdhury et al.   Scientific Reports

Untapped Resources: Biotechnological Potential of Peptides and Secondary Metabolites in Archaea

(2015) James C. Charlesworth et al.   ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL

Thermodynamics and H2 Transfer in a Methanogenic, Syntrophic Community

(2015) Joshua J. Hamilton et al.   PLoS Computational Biology

Biosynthesis of the 5-(Aminomethyl)-3-furanmethanol Moiety of Methanofuran

(2014) Danielle Miller et al.   BIOCHEMISTRY

Identification and Characterization of a Tyramine–Glutamate Ligase (MfnD) Involved in Methanofuran Biosynthesis

(2014) Yu Wang et al.   BIOCHEMISTRY

Efficient searching and annotation of metabolic networks using chemical similarity

(2014) Dante A. Pertusi et al.   BIOINFORMATICS

ITEP: An integrated toolkit for exploration of microbial pan-genomes

(2014) Matthew N Benedict et al.   BMC GENOMICS

Rooting the Domain Archaea by Phylogenomic Analysis Supports the Foundation of the New Kingdom Proteoarchaeota

(2014) Céline Petitjean et al.   Genome Biology and Evolution

Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path

(2014) Miguel A. Campodonico et al.   METABOLIC ENGINEERING

A genome-scale metabolic model of Methanococcus maripaludis S2 for CO2capture and conversion to methane

(2014) Nishu Goyal et al.   Molecular BioSystems

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

How Do Haloarchaea Synthesize Aromatic Amino Acids?

(2014) Miriam Kolog Gulko et al.   PLoS One

Towards a Computational Model of a Methane Producing Archaeum

(2014) Joseph R. Peterson et al.   ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL

Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species

(2014) Esa Pitkänen et al.   PLoS Computational Biology

Toward quantitative understanding on microbial community structure and functioning: a modeling-centered approach using degradation of marine oil spills as example

(2014) Wilfred F. M. Röling et al.   Frontiers in Microbiology

Genomically and biochemically accurate metabolic reconstruction ofMethanosarcina barkeriFusaro, iMG746

(2013) Matthew C. Gonnerman et al.   Biotechnology Journal

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

The legacy of Carl Woese and Wolfram Zillig: from phylogeny to landmark discoveries

(2013) Sonja-Verena Albers et al.   NATURE REVIEWS MICROBIOLOGY

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Community Flux Balance Analysis for Microbial Consortia at Balanced Growth

(2013) Ruchir A. Khandelwal et al.   PLoS One

Understanding the interactions between bacteria in the human gut through metabolic modeling

(2013) Saeed Shoaie et al.   Scientific Reports

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

(2013) Rasmus Agren et al.   PLoS Computational Biology

MicrobesFlux: a web platform for drafting metabolic models from the KEGG database

(2012) Xueyang Feng et al.   BMC Systems Biology

FAME, the Flux Analysis and Modeling Environment

(2012) Joost Boele et al.   BMC Systems Biology

Function and Regulation of Isoforms of Carbon Monoxide Dehydrogenase/Acetyl Coenzyme A Synthase in Methanosarcina acetivorans

(2012) N. Matschiavelli et al.   JOURNAL OF BACTERIOLOGY

Genome-Scale Reconstruction and Analysis of the Metabolic Network in the Hyperthermophilic Archaeon Sulfolobus Solfataricus

(2012) Thomas Ulas et al.   PLoS One

OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities

(2012) Ali R. Zomorrodi et al.   PLoS Computational Biology

Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans

(2011) Vinay Satish Kumar et al.   BMC Systems Biology

MEMOSys: Bioinformatics platform for genome-scale metabolic models

(2011) Stephan Pabinger et al.   BMC Systems Biology

Genome-Scale Metabolic Reconstruction and Hypothesis Testing in the Methanogenic Archaeon Methanosarcina acetivorans C2A

(2011) M. N. Benedict et al.   JOURNAL OF BACTERIOLOGY

A Computational Approach To Design and Evaluate Enzymatic Reaction Pathways: Application to 1-Butanol Production from Pyruvate

(2011) Di Wu et al.   Journal of Chemical Information and Modeling

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

(2011) Jan Schellenberger et al.   Nature Protocols

OptFlux: an open-source software platform for in silico metabolic engineering

(2010) Isabel Rocha et al.   BMC Systems Biology

Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments

(2010) Kai Zhuang et al.   ISME Journal

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

Importance of the methanogenic archaea populations in anaerobic wastewater treatments

(2010) Meisam Tabatabaei et al.   PROCESS BIOCHEMISTRY

An Engineered Methanogenic Pathway Derived from the Domains Bacteria and Archaea

(2010) D. J. Lessner et al.   mBio

Characterization of Growth and Metabolism of the Haloalkaliphile Natronomonas pharaonis

(2010) Orland Gonzalez et al.   PLoS Computational Biology

OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions

(2010) Sridhar Ranganathan et al.   PLoS Computational Biology

Influence of carbon monoxide on metabolite formation inMethanosarcina acetivorans

(2009) Ellen Oelgeschläger et al.   FEMS MICROBIOLOGY LETTERS

Physiology and Posttranscriptional Regulation of Methanol:Coenzyme M Methyltransferase Isozymes in Methanosarcina acetivorans C2A

(2009) R. B. Opulencia et al.   JOURNAL OF BACTERIOLOGY

Improved approach for transferring and cultivatingMethanosarcina acetivoransC2A (DSM 2834)

(2009) H. Summer   LETTERS IN APPLIED MICROBIOLOGY

Distinct regulators control the expression of methanol methyltransferase isozymes inMethanosarcina acetivoransC2A

(2009) Arpita Bose et al.   MOLECULAR MICROBIOLOGY

In vivorole of three fused corrinoid/methyl transfer proteins inMethanosarcina acetivorans

(2009) Ellen Oelgeschläger et al.   MOLECULAR MICROBIOLOGY

Methanogenesis byMethanosarcina acetivoransinvolves two structurally and functionally distinct classes of heterodisulfide reductase

(2009) Nicole R. Buan et al.   MOLECULAR MICROBIOLOGY

Systems Analysis of Bioenergetics and Growth of the Extreme Halophile Halobacterium salinarum

(2009) Orland Gonzalez et al.   PLoS Computational Biology

A Genome-Scale Metabolic Reconstruction of Mycoplasma genitalium, iPS189

(2009) Patrick F. Suthers et al.   PLoS Computational Biology

Genetic Analysis of the Methanol- and Methylamine-Specific Methyltransferase 2 Genes of Methanosarcina acetivorans C2A

(2008) A. Bose et al.   JOURNAL OF BACTERIOLOGY

Molecular signatures of ribosomal evolution

(2008) E. Roberts et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A korarchaeal genome reveals insights into the evolution of the Archaea

(2008) J. G. Elkins et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reconstruction, modeling & analysis of Halobacterium salinarum R-1 metabolism

(2007) Orland Gonzalez et al.   Molecular BioSystems