Algorithms for Molecular Biology, Volume 1

Volume 1, 2006

• Burkhard Morgenstern, Peter F. Stadler:
  New journal: Algorithms for Molecular Biology.
  
• Xiaowen Liu, Lusheng Wang:
  Finding the region of pseudo-periodic tandem repeats in biological sequences.
  
• Stephan H. F. Bernhart, Hakim Tafer, Ulrike Mückstein, Christoph Flamm, Peter F. Stadler, Ivo L. Hofacker:
  Partition function and base pairing probabilities of RNA heterodimers.
  
• Alberto Apostolico, Matteo Comin, Laxmi Parida:
  Mining, compressing and classifying with extensible motifs.
  
• Grégory Nuel:
  Effective p-value computations using Finite Markov Chain Imbedding (FMCI): application to local score and to pattern statistics.
  
• Burkhard Morgenstern, Sonja J. Prohaska, Dirk Pöhler, Peter F. Stadler:
  Multiple sequence alignment with user-defined anchor points.
  
• Elena Zotenko, Katia S. Guimarães, Raja Jothi, Teresa M. Przytycka:
  Decomposition of overlapping protein complexes: A graph theoretical method for analyzing static and dynamic protein associations.
  
• Nan Li, Martin Tompa:
  Analysis of computational approaches for motif discovery.
  
• Katharina Anna Lehmann, Michael Kaufmann, Stephan Steigele, Kay Nieselt:
  On the maximal cliques in c-max-tolerance graphs and their application in clustering molecular sequences.
  
• Peter Meinicke, Thomas Brodag, Wolfgang Florian Fricke, Stephan Waack:
  P-value based visualization of codon usage data.
  
• James Lu, Heinz W. Engl, Peter Schuster:
  Inverse bifurcation analysis: application to simple gene systems.
  
• Giuseppe Lancia, Romeo Rizzi:
  The approximability of the String Barcoding problem.
  
• Elena Zaslavsky, Mona Singh:
  A combinatorial optimization approach for diverse motif finding applications.
  
• Jonathan E. Allen, Steven L. Salzberg:
  A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons.
  
• Gregory A. Grothaus, Adeel Mufti, T. M. Murali:
  Automatic layout and visualization of biclusters.
  
• Chris Christiansen, Thomas Mailund, Christian N. S. Pedersen, Martin Randers, Martin Stig Stissing:
  Fast calculation of the quartet distance between trees of arbitrary degrees.
  
• Grégory Nuel:
  Pattern statistics on Markov chains and sensitivity to parameter estimation.
  
• Jonas S. Almeida, Susana Vinga:
  Computing distribution of scale independent motifs in biological sequences.
  
• Andreas Wilm, Indra Mainz, Gerhard Steger:
  An enhanced RNA alignment benchmark for sequence alignment programs.
  
• Martin Paluszewski, Thomas Hamelryck, Pawel Winter:
  Reconstructing protein structure from solvent exposure using tabu search.
  
• Yongqiang Zhang, Mohammed J. Zaki:
  EXMOTIF: efficient structured motif extraction.
  
• Yongqiang Zhang, Mohammed J. Zaki:
  SMOTIF: efficient structured pattern and profile motif search.
  
• Chandan K. Reddy, Yao-Chung Weng, Hsiao-Dong Chiang:
  Refining motifs by improving information content scores using neighborhood profile search.
  
• Woochang Hwang, Young-Rae Cho, Aidong Zhang, Murali Ramanathan:
  A novel functional module detection algorithm for protein-protein interaction networks.
  
• Alexander L. Tournier, Paul W. Fitzjohn, Paul A. Bates:
  Probability-based model of protein-protein interactions on biological timescales.