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Sequence analysis

A Method for Studying Protistan Diversity Using Massively Parallel Sequencing of V9 Hypervariable Regions of Small-Subunit Ribosomal RNA Genes

Linda A. Amaral-Zettler, Elizabeth A. McCliment, Hugh W. Ducklow, Susan M. Huse

Simultaneous Assessment of Soil Microbial Community Structure and Function through Analysis of the Meta-Transcriptome

Tim Urich, Anders Lanzén, [ ... ], Stephan C. Schuster

Comparative Analysis of Human Gut Microbiota by Barcoded Pyrosequencing

Anders F. Andersson, Mathilda Lindberg, [ ... ], Lars Engstrand

Taxonomic Classification of Bacterial 16S rRNA Genes Using Short Sequencing Reads: Evaluation of Effective Study Designs

Orna Mizrahi-Man, Emily R. Davenport, Yoav Gilad

A Species-Level Phylogeny of Extant Snakes with Description of a New Colubrid Subfamily and Genus

Alex Figueroa, Alexander D. McKelvy, [ ... ], Simon P. Lailvaux

In Silico Approach for Predicting Toxicity of Peptides and Proteins

Sudheer Gupta, Pallavi Kapoor, [ ... ], Gajendra P. S. Raghava

A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq

Lin Wang, Yaqing Si, [ ... ], Thomas P. Brutnell

Identification and Classification of Hubs in Brain Networks

Olaf Sporns, Christopher J. Honey, Rolf Kötter

Absence of Ancient DNA in Sub-Fossil Insect Inclusions Preserved in ‘Anthropocene’ Colombian Copal

David Penney, Caroline Wadsworth, [ ... ], Terence A. Brown

Designer Self-Assembling Peptide Nanofiber Scaffolds for Adult Mouse Neural Stem Cell 3-Dimensional Cultures

Fabrizio Gelain, Daniele Bottai, Angleo Vescovi, Shuguang Zhang

Using Sequence Similarity Networks for Visualization of Relationships Across Diverse Protein Superfamilies

Holly J. Atkinson, John H. Morris, Thomas E. Ferrin, Patricia C. Babbitt

MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

Vincent Ranwez, Sébastien Harispe, Frédéric Delsuc, Emmanuel J. P. Douzery

Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices

Jenna Morgan Lang, Aaron E. Darling, Jonathan A. Eisen

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