Computational Biology

Biotechnology
In Silico Identification of Gene Amplification Targets for Improvement of Lycopene Production
Hyung Seok Choi, Sang Yup Lee, Tae Yong Kim, Han Min Woo
Methods
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
Patrick D. Schloss, Sarah L. Westcott, Thomas Ryabin, Justine R. Hall, Martin Hartmann, Emily B. Hollister, Ryan A. Lesniewski, Brian B. Oakley, Donovan H. Parks, Courtney J. Robinson, Jason W. Sahl, Blaz Stres, Gerhard G. Thallinger, David J. Van Horn, Carolyn F. Weber
Environmental Microbiology
Assessment of Microbial Communities by Graph Partitioning in a Study of Soil Fungi in Two Alpine Meadows
L. Zinger, E. Coissac, P. Choler, R. A. Geremia
Microbial Ecology
Defining DNA-Based Operational Taxonomic Units for Microbial-Eukaryote Ecology
David A. Caron, Peter D. Countway, Pratik Savai, Rebecca J. Gast, Astrid Schnetzer, Stefanie D. Moorthi, Mark R. Dennett, Dawn M. Moran, Adriane C. Jones
Genetics and Molecular Biology
Identification of a Novel Two-Peptide Lantibiotic, Lichenicidin, following Rational Genome Mining for LanM Proteins
Máire Begley, Paul D. Cotter, Colin Hill, R. Paul Ross
Evolutionary and Genomic Microbiology
Genome-Derived Criteria for Assigning Environmental narG and nosZ Sequences to Operational Taxonomic Units of Nitrate Reducers
Katharina Palmer, Harold L. Drake, Marcus A. Horn
PHYSIOLOGY AND BIOTECHNOLOGY
Bioinformatic and Expression Analyses of Genes Mediating Zinc Homeostasis in Nostoc punctiforme
Lee Hudek, L. C. Rai, David Freestone, Agnes Michalczyk, Maria Gibson, Y. F. Song, M. Leigh Ackland
PHYSIOLOGY AND BIOTECHNOLOGY
In Silico Geobacter sulfurreducens Metabolism and Its Representation in Reactive Transport Models
E. L. King, K. Tuncay, P. Ortoleva, C. Meile
Methods
TRiFLe, a Program for In Silico Terminal Restriction Fragment Length Polymorphism Analysis with User-Defined Sequence Sets
Pilar Junier, Thomas Junier, Karl-Paul Witzel
Evolutionary and Genomic Microbiology
Metagenomics: Read Length Matters
K. Eric Wommack, Jaysheel Bhavsar, Jacques Ravel

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