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Computational techniques

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

Correlation Analysis for Protein Evolutionary Family Based on Amino Acid Position Mutations and Application in PDZ Domain

Qi-Shi Du, Cheng-Hua Wang, Si-Ming Liao, Ri-Bo Huang

Insight into Antigenic Diversity of VAR2CSA-DBL5ε Domain from Multiple Plasmodium falciparum Placental Isolates

Sédami Gnidehou, Leon Jessen, [ ... ], Nicaise Tuikue Ndam

Neuroimaging Study Designs, Computational Analyses and Data Provenance Using the LONI Pipeline

Ivo Dinov, Kamen Lozev, [ ... ], Arthur Toga

Adjacent Nucleotide Dependence in ncRNA and Order-1 SCFG for ncRNA Identification

Thomas K. F. Wong, Tak-Wah Lam, Wing-Kin Sung, Siu-Ming Yiu

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