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Bioinformatics

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

Systematic Comparison of Three Methods for Fragmentation of Long-Range PCR Products for Next Generation Sequencing

Ellen Knierim, Barbara Lucke, [ ... ], Dominik Seelow

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

BFAST: An Alignment Tool for Large Scale Genome Resequencing

Nils Homer, Barry Merriman, Stanley F. Nelson

Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

Robert Schmieder, Robert Edwards

A Large-Scale, Higher-Level, Molecular Phylogenetic Study of the Insect Order Lepidoptera (Moths and Butterflies)

Jerome C. Regier, Charles Mitter, [ ... ], Kim T. Mitter

Optimal classifier for imbalanced data using Matthews Correlation Coefficient metric

Sabri Boughorbel, Fethi Jarray, Mohammed El-Anbari

Pathogen Webs in Collapsing Honey Bee Colonies

R. Scott Cornman, David R. Tarpy, [ ... ], Jay D. Evans

A Three-Stage Colonization Model for the Peopling of the Americas

Andrew Kitchen, Michael M. Miyamoto, Connie J. Mulligan

A workflow with R: Phylogenetic analyses and visualizations using mitochondrial cytochrome b gene sequences

Emine Toparslan, Kemal Karabag, Ugur Bilge

High-Throughput Sequencing of Arabidopsis microRNAs: Evidence for Frequent Birth and Death of MIRNA Genes

Noah Fahlgren, Miya D. Howell, [ ... ], James C. Carrington

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