M. Serres

发表

Detection of transcriptional triggers in the dynamics of microbial growth: application to the respiratorily versatile bacterium Shewanella oneidensis

Niels Klitgord, C. Altafini, Sara B. Collins, 2012, Nucleic acids research.

Towards environmental systems biology of Shewanella

Grigoriy E. Pinchuk, T. Gardner, J. Reed, 2008, Nature Reviews Microbiology.

Escherichia coli K-12: a cooperatively developed annotation snapshot—2005

Monica Riley, Martha B. Arnaud, Jeremy D. Glasner, 2006, Nucleic acids research.

Develop the Knowledgebase, Computational Meth- Ods, and Capabilities to Advance Understanding and Prediction of Complex Biological Systems Computing Infrastructure, Bioinformatics, and Data Management 112 Center Blockinfor Blockincomputational Blockinbiology Blockinat Blockinthe Blockinuniversity Bl

Grigoriy E. Pinchuk, K. Nealson, M. Leuze, 2022 .

A functional update of the Escherichia coli K-12 genome

Monica Riley, Terry Gaasterland, Shuba Gopal, 2001, Genome Biology.

Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations.

Gordon A Anderson, John R Yates, Monica Riley, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Interim report on genomics of Escherichia coli.

M. Riley, M. Serres, M Riley, 2000, Annual review of microbiology.

Inference of interactions in cyanobacterial–heterotrophic co-cultures via transcriptome sequencing

Hans C. Bernstein, Grigoriy E. Pinchuk, A. Konopka, 2014, The ISME Journal.

Draft Genome Sequence of Desulfurobacterium sp. Strain AV08, a Thermophilic Chemolithoautotroph Isolated from a Deep-Sea Hydrothermal Vent

J. Huber, M. Serres, L. Zeigler Allen, 2021, Microbiology resource announcements.

Protein families reflect the metabolic diversity of organisms and provide support for functional prediction.

L. Nahum, M. Serres, S. Goswami, 2009, Physiological genomics.

Changes in translational efficiency is a dominant regulatory mechanism in the environmental response of bacteria.

Ronald C. Taylor, Lye Meng Markillie, Ronald C Taylor, 2013, Integrative biology : quantitative biosciences from nano to macro.

Conserved synteny at the protein family level reveals genes underlying Shewanella species’ cold tolerance and predicts their novel phenotypes

E. Uberbacher, K. Nealson, M. Land, 2009, Functional & Integrative Genomics.

Supplementary Text for " Detection of Transcriptional Triggers in the Dynamics of Microbial Growth: Application to the Respiratory-versatile Bacterium

Niels Klitgord, C. Altafini, Sara B. Collins, 2022 .

Genomics and Metabolism in Escherichia coli

M. Riley, M. Serres, 2006 .

Comparative systems biology across an evolutionary gradient within the Shewanella genus

K. Konstantinidis, J. Tiedje, K. Nealson, 2009, Proceedings of the National Academy of Sciences of the United States of America.

Evolution by leaps: gene duplication in bacteria

Monica Riley, M. Riley, Alastair R W Kerr, 2009, Biology Direct.

MultiFun, a multifunctional classification scheme for Escherichia coli K-12 gene products.

M. Riley, M. Serres, M Riley, 2000, Microbial & comparative genomics.

GenProtEC: an updated and improved analysis of functions of Escherichia coli K-12 proteins

Monica Riley, Margrethe H. Serres, Sulip Goswami, 2004, Nucleic Acids Res..

Comparisons of Shewanella strains based on genome annotations, modeling, and experiments

Wai Ong, Jennifer L. Reed, Trang T. Vu, 2014, BMC Systems Biology.

Large-Scale Comparative Phenotypic and Genomic Analyses Reveal Ecological Preferences of Shewanella Species and Identify Metabolic Pathways Conserved at the Genus Level

James M. Tiedje, Margrethe H. Serres, J. Tiedje, 2011, Applied and Environmental Microbiology.

Identification of diverse carbon utilization pathways in Shewanella oneidensis MR-1 via expression profiling.

Lee Anne McCue, T. Gardner, J. Fredrickson, 2007, Genome informatics. International Conference on Genome Informatics.

Genomic Analysis of Carbon Source Metabolism of Shewanella oneidensis MR-1: Predictions versus Experiments

M. Riley, M. Serres, 2006, Journal of Bacteriology.

Live cell chemical profiling of temporal redox dynamics in a photoautotrophic cyanobacterium.

Natalie C. Sadler, Richard D. Smith, A. Konopka, 2014, ACS chemical biology.

Shewanella knowledgebase: integration of the experimental data and computational predictions suggests a biological role for transcription of intergenic regions

Nagiza F. Samatova, Byung-Hoon Park, Edward C. Uberbacher, 2010, Database J. Biol. Databases Curation.

Structural domains, protein modules, and sequence similarities enrich our understanding of the Shewanella oneidensis MR-1 proteome.

Monica Riley, M. Riley, M. Serres, 2004, Omics : a journal of integrative biology.

Evolution by leaps: gene duplication in bacteria

M. Riley, Alastair R W Kerr, M. Serres, 2009 .

Gene fusions and gene duplications: relevance to genomic annotation and functional analysis

Monica Riley, M. Riley, M. Serres, 2005, BMC Genomics.

Escherichia coli K-12: a cooperatively developed annotation snapshot—2005

Martha B. Arnaud, J. Glasner, F. Blattner, 2006, Nucleic acids research.

Comparative systems biology across an evolutionary gradient within the Shewanella genus

K. Konstantinidis, J. Tiedje, K. Nealson, 2009, Proceedings of the National Academy of Sciences.

Microbial eukaryotic predation pressure and biomass at deep-sea hydrothermal vents

Sarah K. Hu, C. German, J. Huber, 2023, bioRxiv.