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Constraints in Bioinformatics

Edited by Rolf Backofen, Alessandro Dal Palu', Agostino Dovier, and Sebastian Will

The technology of Constraint and Constraint Logic Programming has shown to be effective for a multitude of computational problems of modern bio-sciences, which are typically complex and often NP-hard. Constraint-based methods contribute essentially to the tool set of Bioinformatics, due to their ability to simplify problem modeling and face computationally challenging problems. These techniques emerged in bioinformatics more than 10 years ago, introduced at the workshops Constraints and Bioinformatics/Biocomputing associated to CP97 and CP98. Since 2005, the Workshops on Constraint based methods for Bioinformatics (WCB series) haven taken place annually. Topics of particular interest comprise (but are not limited to) sequence analysis, biological systems simulations, protein structure prediction and docking, structure alignment, pedigree analysis, and haplotype inference. The thematic series is open to any original paper in the area that has not been published elsewhere. In particular, we encourage the submission of full papers corresponding to presentations in recent editions of the WCB series.

View all collections published in Algorithms for Molecular Biology.

  1. This paper addresses the problem of finding attractors in biological regulatory networks. We focus here on non-deterministic synchronous and asynchronous multi-valued networks, modeled using automata networks ...

    Authors: Emna Ben Abdallah, Maxime Folschette, Olivier Roux and Morgan Magnin
    Citation: Algorithms for Molecular Biology 2017 12:20
  2. Numerous cellular differentiation processes can be captured using discrete qualitative models of biological regulatory networks. These models describe the temporal evolution of the state of the network subject...

    Authors: Louis Fippo Fitime, Olivier Roux, Carito Guziolowski and Loïc Paulevé
    Citation: Algorithms for Molecular Biology 2017 12:19
  3. Pyrosequencing Allele Quantification (AQ) is a cost-effective DNA sequencing method that can be used for detecting somatic mutations in formalin-fixed paraffin-embedded (FFPE) samples. The method displays a lo...

    Authors: Jerome Ambroise, Jamal Badir, Louise Nienhaus, Annie Robert, Anne-France Dekairelle and Jean-Luc Gala
    Citation: Algorithms for Molecular Biology 2016 11:24
  4. Chemical reactions are rearrangements of chemical bonds. Each atom in an educt molecule thus appears again in a specific position of one of the reaction products. This bijection between educt and product atoms...

    Authors: Martin Mann, Feras Nahar, Norah Schnorr, Rolf Backofen, Peter F Stadler and Christoph Flamm
    Citation: Algorithms for Molecular Biology 2014 9:23
  5. Analysis of elementary modes (EMs) is proven to be a powerful constraint-based method in the study of metabolic networks. However, enumeration of EMs is a hard computational task. Additionally, due to their la...

    Authors: Sayed-Amir Marashi, Laszlo David and Alexander Bockmayr
    Citation: Algorithms for Molecular Biology 2012 7:17
  6. For many predictive applications a large number of models is generated and later clustered in subsets based on structure similarity. In most clustering algorithms an all-vs-all root mean square deviation (RMSD...

    Authors: Federico Fogolari, Alessandra Corazza, Paolo Viglino and Gennaro Esposito
    Citation: Algorithms for Molecular Biology 2012 7:16