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Computational techniques

Alignment-Free Design of Highly Discriminatory Diagnostic Primer Sets for Escherichia coli O104:H4 Outbreak Strains

Leighton Pritchard, Nicola J. Holden, Martina Bielaszewska, Helge Karch, Ian K. Toth

published 05 Apr 2012

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Skip the Alignment: Degenerate, Multiplex Primer and Probe Design Using K-mer Matching Instead of Alignments

David A. Hysom, Pejman Naraghi-Arani, Maher Elsheikh, A. Celena Carrillo, Peter L. Williams, Shea N. Gardner

published 02 Apr 2012

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Treelength Optimization for Phylogeny Estimation

Kevin Liu, Tandy Warnow

published 19 Mar 2012

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Phylo: A Citizen Science Approach for Improving Multiple Sequence Alignment

Alexander Kawrykow, Gary Roumanis, Alfred Kam, Daniel Kwak, Clarence Leung, Chu Wu, Eleyine Zarour, Phylo players , Luis Sarmenta, Mathieu Blanchette, Jérôme Waldispühl

published 07 Mar 2012

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Optimization of Time-Course Experiments for Kinetic Model Discrimination

Nuno F. Lages, Carlos Cordeiro, Marta Sousa Silva, Ana Ponces Freire, António E. N. Ferreira

published 05 Mar 2012

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Detecting Remote Sequence Homology in Disordered Proteins: Discovery of Conserved Motifs in the N-Termini of Mononegavirales phosphoproteins

David Karlin, Robert Belshaw

published 05 Mar 2012

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Diversity Measures in Environmental Sequences Are Highly Dependent on Alignment Quality—Data from ITS and New LSU Primers Targeting Basidiomycetes

Dirk Krüger, Danuta Kapturska, Christiane Fischer, Rolf Daniel, Tesfaye Wubet

published 21 Feb 2012

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Exploiting Gene Families for Phylogenomic Analysis of Myzostomid Transcriptome Data

Stefanie Hartmann, Conrad Helm, Birgit Nickel, Matthias Meyer, Torsten H. Struck, Ralph Tiedemann, Joachim Selbig, Christoph Bleidorn

published 20 Jan 2012

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Accounting For Alignment Uncertainty in Phylogenomics

Martin Wu, Sourav Chatterji, Jonathan A. Eisen

published 17 Jan 2012

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Two-Stage Clustering (TSC): A Pipeline for Selecting Operational Taxonomic Units for the High-Throughput Sequencing of PCR Amplicons

Xiao-Tao Jiang, Hai Zhang, Hua-Fang Sheng, Yu Wang, Yan He, Fei Zou, Hong-Wei Zhou

published 11 Jan 2012

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Armadillo 1.1: An Original Workflow Platform for Designing and Conducting Phylogenetic Analysis and Simulations

Etienne Lord, Mickael Leclercq, Alix Boc, Abdoulaye Baniré Diallo, Vladimir Makarenkov

published 11 Jan 2012

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Identification of Domains and Amino Acids Essential to the Collagen Galactosyltransferase Activity of GLT25D1

Claire Perrin-Tricaud, Christoph Rutschmann, Thierry Hennet

published 21 Dec 2011

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Special Agents Can Promote Cooperation in the Population

Xin Wang, Jing Han, Huawei Han

published 21 Dec 2011

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