Algorithms for Molecular Biology, Volume 2

Volume 2, 2007

• C. Steven Carmack, Lee Ann McCue, Lee Aaron Newberg, Charles E. Lawrence:
  PhyloScan: identification of transcription factor binding sites using cross-species evidence.
  
• Jingjun Sun, Kagan Tuncay, Alaa Abi Haidar, Lisa Ensman, Frank Stanley, Michael Trelinski, Peter J. Ortoleva:
  Transcriptional regulatory network discovery via multiple method integration: application to e. coli K12.
  
• Hui Yang, Srinivasan Parthasarathy, Duygu Ucar:
  A spatio-temporal mining approach towards summarizing and analyzing protein folding trajectories.
  
• Mohammed J. Zaki, George Karypis, Jiong Yang:
  Data Mining in Bioinformatics (BIOKDD).
  
• Koji Kadota, Ryoko Araki, Yuji Nakai, Masumi Abe:
  GOGOT: a method for the identification of differentially expressed fragments from cDNA-AFLP data.
  
• Kristin Reiche, Peter F. Stadler:
  RNAstrand: reading direction of structured RNAs in multiple sequence alignments.
  
• Chia Huey Ooi, Madhu Chetty, Shyh Wei Teng:
  Characteristics of predictor sets found using differential prioritization.
  
• David Bryant, Vincent Moulton, Andreas Spillner:
  Consistency of the Neighbor-Net Algorithm.
  
• Stefan Wolfsheimer, Bernd Burghardt, Alexander K. Hartmann:
  Local sequence alignments statistics: deviations from Gumbel statistics in the rare-event tail.
  
• Raffaele Giancarlo, Alessandro Siragusa, Enrico Siragusa, Filippo Utro:
  A basic analysis toolkit for biological sequences.
  
• Gilles Didier, Carito Guziolowski:
  Mapping sequences by parts.
  
• Rodrigo Gouveia-Oliveira, Anders Gorm Pedersen:
  Finding coevolving amino acid residues using row and column weighting of mutual information and multi-dimensional amino acid representation.
  
• Valentina Boeva, Julien Clément, Mireille Régnier, Mikhail A. Roytberg, Vsevolod Makeev:
  Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules.
  
• Andreas Spillner:
  Review of "Reconstructing Evolution: New mathematical and computational advances" edited by Olivier Gascuel and Mike Steel.
  
• Hélène Touzet, Jean-Stéphane Varré:
  Efficient and accurate P-value computation for Position Weight Matrices.
  
• Pedro Gabriel Ferreira, Paulo J. Azevedo:
  Evaluating deterministic motif significance measures in protein databases.