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Algorithms for Computational Biology

First International Conference, AlCoB 2014, Tarragona, Spain, July 1-3, 2014, Proceedings

  • Conference proceedings
  • © 2014

Overview

Editors:
  1. Adrian-Horia Dediu

    1. Research Group on Mathematical Linguistics, Rovira i Virgili University, Tarragona, Spain

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  2. Carlos Martín-Vide

    1. Research Group on Mathematical Linguistics, Rovira i Virgili University, Tarragona, Spain

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    You can also search for this editor in PubMed   Google Scholar

  3. Bianca Truthe

    1. Fachbereich 07, Institut für Informatik, Justus-Liebig-Universität, Gießen, Germany

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Part of the book series: Lecture Notes in Computer Science (LNCS, volume 8542)

Part of the book sub series: Lecture Notes in Bioinformatics (LNBI)

Included in the following conference series:

Conference proceedings info: AlCoB 2014.

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Table of contents (21 papers)

  1. Front Matter

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  2. Invited Talks

    1. Comparative Genomics Approaches to Identifying Functionally Related Genes

      • Michael Y. Galperin, Eugene V. Koonin
      Pages 1-24

  3. Regular Papers

    1. A Greedy Algorithm for Hierarchical Complete Linkage Clustering

      • Ernst Althaus, Andreas Hildebrandt, Anna Katharina Hildebrandt
      Pages 25-34

    2. Vester’s Sensitivity Model for Genetic Networks with Time-Discrete Dynamics

      • Liana Amaya Moreno, Ozlem Defterli, Armin Fügenschuh, Gerhard-Wilhelm Weber
      Pages 35-46

    3. Complexity and Polynomial-Time Approximation Algorithms around the Scaffolding Problem

      • Annie Chateau, Rodolphe Giroudeau
      Pages 47-58

    4. Heuristics for the Sorting by Length-Weighted Inversions Problem on Signed Permutations

      • Thiago da Silva Arruda, Ulisses Dias, Zanoni Dias
      Pages 59-70

    5. On Low Treewidth Graphs and Supertrees

      • Alexander Grigoriev, Steven Kelk, Nela Lekić
      Pages 71-82

    6. On Optimal Read Trimming in Next Generation Sequencing and Its Complexity

      • Ivo Hedtke, Ioana Lemnian, Matthias Müller-Hannemann, Ivo Grosse
      Pages 83-94

    7. On the Implementation of Quantitative Model Refinement

      • Bogdan Iancu, Diana-Elena Gratie, Sepinoud Azimi, Ion Petre
      Pages 95-106

    8. HapMonster: A Statistically Unified Approach for Variant Calling and Haplotyping Based on Phase-Informative Reads

      • Kaname Kojima, Naoki Nariai, Takahiro Mimori, Yumi Yamaguchi-Kabata, Yukuto Sato, Yosuke Kawai et al.
      Pages 107-118

    9. Mapping-Free and Assembly-Free Discovery of Inversion Breakpoints from Raw NGS Reads

      • Claire Lemaitre, Liviu Ciortuz, Pierre Peterlongo
      Pages 119-130

    10. Modeling the Geometry of the Endoplasmic Reticulum Network

      • Laurent Lemarchand, Reinhardt Euler, Congping Lin, Imogen Sparkes
      Pages 131-145

    11. On Sorting of Signed Permutations by Prefix and Suffix Reversals and Transpositions

      • Carla Negri Lintzmayer, Zanoni Dias
      Pages 146-157

    12. On the Diameter of Rearrangement Problems

      • Carla Negri Lintzmayer, Zanoni Dias
      Pages 158-170

    13. Efficiently Enumerating All Connected Induced Subgraphs of a Large Molecular Network

      • Sean Maxwell, Mark R. Chance, Mehmet Koyutürk
      Pages 171-182

    14. On Algorithmic Complexity of Biomolecular Sequence Assembly Problem

      • Giuseppe Narzisi, Bud Mishra, Michael C. Schatz
      Pages 183-195

    15. A Closed-Form Solution for Transcription Factor Activity Estimation Using Network Component Analysis

      • Amina Noor, Aitzaz Ahmad, Bilal Wajid, Erchin Serpedin, Mohamed Nounou, Hazem Nounou
      Pages 196-207

    16. SVEM: A Structural Variant Estimation Method Using Multi-mapped Reads on Breakpoints

      • Tomohiko Ohtsuki, Naoki Nariai, Kaname Kojima, Takahiro Mimori, Yukuto Sato, Yosuke Kawai et al.
      Pages 208-219

    17. Analysis and Classification of Constrained DNA Elements with N-gram Graphs and Genomic Signatures

      • Dimitris Polychronopoulos, Anastasia Krithara, Christoforos Nikolaou, Giorgos Paliouras, Yannis Almirantis, George Giannakopoulos
      Pages 220-234

    18. Inference of Boolean Networks from Gene Interaction Graphs Using a SAT Solver

      • David A. Rosenblueth, Stalin Muñoz, Miguel Carrillo, Eugenio Azpeitia
      Pages 235-246
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  1. Algorithms for Computational Biology

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About this book

This book constitutes the refereed proceedings of the First International Conference, AlCoB 2014, held in July 2014 in Tarragona, Spain.

The 20 revised full papers were carefully reviewed and selected from 39 submissions. The scope of AlCoB includes topics of either theoretical or applied interest, namely: exact sequence analysis, approximate sequence analysis, pairwise sequence alignment, multiple sequence alignment, sequence assembly, genome rearrangement, regulatory motif finding, phylogeny reconstruction, phylogeny comparison, structure prediction, proteomics: molecular pathways, interaction networks, transcriptomics: splicing variants, isoform inference and quantification, differential analysis, next-generation sequencing: population genomics, metagenomics, metatranscriptomics, microbiome analysis, systems biology.

Editors and Affiliations

  • Research Group on Mathematical Linguistics, Rovira i Virgili University, Tarragona, Spain

    Adrian-Horia Dediu, Carlos Martín-Vide

  • Fachbereich 07, Institut für Informatik, Justus-Liebig-Universität, Gießen, Germany

    Bianca Truthe

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