Volume 1, 2006

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  Burkhard Morgenstern, Peter F. Stadler: New journal: Algorithms for Molecular Biology.
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  Xiaowen Liu, Lusheng Wang: Finding the region of pseudo-periodic tandem repeats in biological sequences.
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  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.
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  Alberto Apostolico, Matteo Comin, Laxmi Parida: Mining, compressing and classifying with extensible motifs.
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  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.
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  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.
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  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.
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  Peter Meinicke, Thomas Brodag, Wolfgang Florian Fricke, Stephan Waack: P-value based visualization of codon usage data.
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  James Lu, Heinz W. Engl, Peter Schuster: Inverse bifurcation analysis: application to simple gene systems.
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  Giuseppe Lancia, Romeo Rizzi: The approximability of the String Barcoding problem.
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  Elena Zaslavsky, Mona Singh: A combinatorial optimization approach for diverse motif finding applications.
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  Jonathan E. Allen, Steven L. Salzberg: A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons.
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  Gregory A. Grothaus, Adeel Mufti, T. M. Murali: Automatic layout and visualization of biclusters.
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  Chris Christiansen, Thomas Mailund, Christian N. S. Pedersen, Martin Randers, Martin Stig Stissing: Fast calculation of the quartet distance between trees of arbitrary degrees.
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  Grégory Nuel: Pattern statistics on Markov chains and sensitivity to parameter estimation.
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  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.
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  Yongqiang Zhang, Mohammed J. Zaki: SMOTIF: efficient structured pattern and profile motif search.
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  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.
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  Alexander L. Tournier, Paul W. Fitzjohn, Paul A. Bates: Probability-based model of protein-protein interactions on biological timescales.

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