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

The nutritional status ofMethanosarcina acetivoransregulates glycogen metabolism and gluconeogenesis and glycolysis fluxes

(2016) Michel Geovanni Santiago-Martínez et al.   FEBS Journal

Acis-prenyltransferase fromMethanosarcina acetivoranscatalyzes both head-to-tail and nonhead-to-tail prenyl condensation

(2016) Takuya Ogawa et al.   FEBS Journal

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

A phytoene desaturase homolog gene from the methanogenic archaeon Methanosarcina acetivorans is responsible for hydroxyarchaeol biosynthesis

(2015) Takeshi Mori et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

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

Genome-wide investigation of mRNA lifetime determinants in Escherichia coli cells cultured at different growth rates

(2015) Thomas Esquerré et al.   BMC GENOMICS

Genomic and phenotypic differentiation among Methanosarcina mazei populations from Columbia River sediment

(2015) Nicholas D Youngblut et al.   ISME Journal

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

Effects of DNA replication on mRNA noise

(2015) Joseph R. Peterson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Determination of in vivo target search kinetics of regulatory noncoding RNA

(2015) J. Fei et al.   SCIENCE

Global mapping transcriptional start sites revealed both transcriptional and post-transcriptional regulation of cold adaptation in the methanogenic archaeon Methanolobus psychrophilus

(2015) Jie Li et al.   Scientific Reports

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

(2015) Zachary A. King et al.   PLoS Computational Biology

Air-Adapted Methanosarcina acetivorans Shows High Methane Production and Develops Resistance against Oxygen Stress

(2015) Ricardo Jasso-Chávez et al.   PLoS One

Role of a putative tungsten-dependent formylmethanofuran dehydrogenase in Methanosarcina acetivorans

(2014) Nicole Matschiavelli et al.   ARCHIVES OF MICROBIOLOGY

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

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

(2014) Matthew N Benedict et al.   BMC GENOMICS

Global Analysis of mRNA Isoform Half-Lives Reveals Stabilizing and Destabilizing Elements in Yeast

(2014) Joseph V. Geisberg et al.   CELL

Expanded microbial genome coverage and improved protein family annotation in the COG database

(2014) Michael Y. Galperin et al.   NUCLEIC ACIDS RESEARCH

Methanogenic burst in the end-Permian carbon cycle

(2014) D. H. Rothman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Towards a Computational Model of a Methane Producing Archaeum

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

Mechanism for Stabilizing mRNAs Involved in Methanol-Dependent Methanogenesis of Cold-Adaptive Methanosarcina mazei zm-15

(2013) Yi Cao et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen

(2013) Sung Ho Yoon et al.   GENOME RESEARCH

Geranylgeranyl Reductase and Ferredoxin from Methanosarcina acetivorans Are Required for the Synthesis of Fully Reduced Archaeal Membrane Lipid in Escherichia coli Cells

(2013) K. Isobe et al.   JOURNAL OF BACTERIOLOGY

Dual role of transcription and transcript stability in the regulation of gene expression in Escherichia coli cells cultured on glucose at different growth rates

(2013) Thomas Esquerré et al.   NUCLEIC ACIDS RESEARCH

DOOR 2.0: presenting operons and their functions through dynamic and integrated views

(2013) Xizeng Mao et al.   NUCLEIC ACIDS RESEARCH

Computational analysis of bacterial RNA-Seq data

(2013) Ryan McClure et al.   NUCLEIC ACIDS RESEARCH

Role of mRNA Stability during Bacterial Adaptation

(2013) Clémentine Dressaire et al.   PLoS One

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

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

Global analysis of mRNA stability in Mycobacterium tuberculosis

(2012) Tige R. Rustad et al.   NUCLEIC ACIDS RESEARCH

An archaeal sRNA targeting cis - and trans -encoded mRNAs via two distinct domains

(2012) Dominik Jäger et al.   NUCLEIC ACIDS RESEARCH

GenBank

(2012) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

(2012) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

Changes in mRNA Stability Associated with Cold Stress in Arabidopsis Cells

(2012) Yukako Chiba et al.   PLANT AND CELL PHYSIOLOGY

MreA Functions in the Global Regulation of Methanogenic Pathways in Methanosarcina acetivorans

(2012) M. J. Reichlen et al.   mBio

Global mRNA decay analysis at single nucleotide resolution reveals segmental and positional degradation patterns in a Gram-positive bacterium

(2012) Simen M Kristoffersen et al.   GENOME BIOLOGY

Integration of expression data in genome-scale metabolic network reconstructions

(2012) Anna S. Blazier et al.   Frontiers in Physiology

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

Normalization, testing, and false discovery rate estimation for RNA-sequencing data

(2011) J. Li et al.   BIOSTATISTICS

Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans

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

Python for Scientists and Engineers

(2011) K. Jarrod Millman et al.   COMPUTING IN SCIENCE & ENGINEERING

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

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

Dynamic profiling of mRNA turnover reveals gene-specific and system-wide regulation of mRNA decay

(2011) Sarah E. Munchel et al.   MOLECULAR BIOLOGY OF THE CELL

ProOpDB: Prokaryotic Operon DataBase

(2011) B. Taboada et al.   NUCLEIC ACIDS RESEARCH

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

Carbon-dependent control of electron transfer and central carbon pathway genes for methane biosynthesis in the Archaean, Methanosarcina acetivorans strain C2A

(2010) Lars Rohlin et al.   BMC MICROBIOLOGY

Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics

(2010) Frank J Stewart et al.   ISME Journal

Functional Analysis of the Three TATA Binding Protein Homologs in Methanosarcina acetivorans

(2010) M. J. Reichlen et al.   JOURNAL OF BACTERIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Regulation of Translation Initiation in Eukaryotes: Mechanisms and Biological Targets

(2009) Nahum Sonenberg et al.   CELL

Transcriptional Profiling of Methyltransferase Genes during Growth of Methanosarcina mazei on Trimethylamine

(2009) C. Kratzer et al.   JOURNAL OF BACTERIOLOGY

A 5' Leader Sequence Regulates Expression of Methanosarcinal CO Dehydrogenase/Acetyl Coenzyme A Synthase

(2009) K. L. Anderson et al.   JOURNAL OF BACTERIOLOGY

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

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

Distinct regulators control the expression of methanol methyltransferase isozymes inMethanosarcina acetivoransC2A

(2009) Arpita Bose et al.   MOLECULAR MICROBIOLOGY

Regulation of putative methyl-sulphide methyltransferases inMethanosarcina acetivoransC2A

(2009) Arpita Bose et al.   MOLECULAR MICROBIOLOGY

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

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

Regulation of Translation in Haloarchaea: 5′- and 3′-UTRs Are Essential and Have to Functionally Interact In Vivo

(2009) Mariam Brenneis et al.   PLoS One

Toolbox model of evolution of prokaryotic metabolic networks and their regulation

(2009) S. Maslov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deep sequencing analysis of the Methanosarcina mazei Go1 transcriptome in response to nitrogen availability

(2009) D. Jager et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Messenger RNA processing in Methanocaldococcus (Methanococcus) jannaschii

(2009) J. Zhang et al.   RNA

New methods for tightly regulated gene expression and highly efficient chromosomal integration of cloned genes forMethanosarcinaspecies

(2009) Adam M. Guss et al.   ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL

Methanogenic archaea: ecologically relevant differences in energy conservation

(2008) Rudolf K. Thauer et al.   NATURE REVIEWS MICROBIOLOGY