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Computational techniques

An Integrated Pipeline for the Genome-Wide Analysis of Transcription Factor Binding Sites from ChIP-Seq

Eloi Mercier, Arnaud Droit, [ ... ], Raphael Gottardo

Error and Error Mitigation in Low-Coverage Genome Assemblies

Melissa J. Hubisz, Michael F. Lin, Manolis Kellis, Adam Siepel

Considering Transposable Element Diversification in De Novo Annotation Approaches

Timothée Flutre, Elodie Duprat, Catherine Feuillet, Hadi Quesneville

Odorant Binding Proteins of the Red Imported Fire Ant, Solenopsis invicta: An Example of the Problems Facing the Analysis of Widely Divergent Proteins

Dietrich Gotzek, Hugh M. Robertson, Yannick Wurm, DeWayne Shoemaker

Sequence Alignment, Mutual Information, and Dissimilarity Measures for Constructing Phylogenies

Orion Penner, Peter Grassberger, Maya Paczuski

Evolutionary Distances in the Twilight Zone—A Rational Kernel Approach

Roland F. Schwarz, William Fletcher, [ ... ], Florian Markowetz

Robust Computational Analysis of rRNA Hypervariable Tag Datasets

Maksim Sipos, Patricio Jeraldo, [ ... ], Nigel Goldenfeld

The Bacterial Intimins and Invasins: A Large and Novel Family of Secreted Proteins

Jennifer C. Tsai, Ming-Ren Yen, [ ... ], Milton H. Saier Jr

MPI-PHYLIP: Parallelizing Computationally Intensive Phylogenetic Analysis Routines for the Analysis of Large Protein Families

Alexander J. Ropelewski, Hugh B. Nicholas Jr, Ricardo R. Gonzalez Mendez

Structural Relationships in the Lysozyme Superfamily: Significant Evidence for Glycoside Hydrolase Signature Motifs

Alexandre Wohlkönig, Joëlle Huet, Yvan Looze, René Wintjens

HMMSplicer: A Tool for Efficient and Sensitive Discovery of Known and Novel Splice Junctions in RNA-Seq Data

Michelle T. Dimon, Katherine Sorber, Joseph L. DeRisi

The Threshold Bootstrap Clustering: A New Approach to Find Families or Transmission Clusters within Molecular Quasispecies

Mattia C. F. Prosperi, Andrea De Luca, [ ... ], Marco Salemi

Adaptive GDDA-BLAST: Fast and Efficient Algorithm for Protein Sequence Embedding

Yoojin Hong, Jaewoo Kang, Dongwon Lee, Damian B. van Rossum

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