Algorithms for Computational Biology: First International Conference, AlCoB 2014, Tarragona, Spain, July 1-3, 2014, Proceedigns

285 Pages·2014·7.132 MB·English

by  Adrian-Horia Dediu, Carlos Martín-Vide, Bianca Truthe (eds.)

Adrian-Horia Dediu
Carlos Martín-Vide
Bianca Truthe (Eds.)
2
Algorithms for
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B Computational Biology
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First International Conference, AlCoB 2014
Tarragona, Spain, July 1–3, 2014
Proceedings
123
Lecture Notes in Bioinformatics 8542
Subseries of Lecture Notes in Computer Science
LNBISeriesEditors
SorinIstrail
BrownUniversity,Providence,RI,USA
PavelPevzner
UniversityofCalifornia,SanDiego,CA,USA
MichaelWaterman
UniversityofSouthernCalifornia,LosAngeles,CA,USA
LNBIEditorialBoard
AlbertoApostolico
GeorgiaInstituteofTechnology,Atlanta,GA,USA
SørenBrunak
TechnicalUniversityofDenmarkKongensLyngby,Denmark
MikhailS.Gelfand
IITP,ResearchandTrainingCenteronBioinformatics,Moscow,Russia
ThomasLengauer
MaxPlanckInstituteforInformatics,Saarbrücken,Germany
SatoruMiyano
UniversityofTokyo,Japan
EugeneMyers
MaxPlanckInstituteofMolecularCellBiologyandGenetics
Dresden,Germany
Marie-FranceSagot
UniversitéLyon1,Villeurbanne,France
DavidSankoff
UniversityofOttawa,Canada
RonShamir
TelAvivUniversity,RamatAviv,TelAviv,Israel
TerrySpeed
WalterandElizaHallInstituteofMedicalResearch
Melbourne,VIC,Australia
MartinVingron
MaxPlanckInstituteforMolecularGenetics,Berlin,Germany
W.EricWong
UniversityofTexasatDallas,Richardson,TX,USA
Adrian-Horia Dediu Carlos Martín-Vide
Bianca Truthe (Eds.)
Algorithms for
Computational Biology
First International Conference, AlCoB 2014
Tarragona, Spain, July 1-3, 2014
Proceedings
1 3
VolumeEditors
Adrian-HoriaDediu
RoviraiVirgiliUniversity,ResearchGrouponMathematicalLinguistics
AvingudaCatalunya,35,43002Tarragona,Spain
E-mail:[email protected]
CarlosMartín-Vide
RoviraiVirgiliUniversity,ResearchGrouponMathematicalLinguistics
AvingudaCatalunya,35,43002Tarragona,Spain
E-mail:[email protected]
BiancaTruthe
Justus-Liebig-Universität,Fachbereich07,InstitutfürInformatik
Arndtstraße2,35392Gießen,Germany
E-mail:[email protected]
ISSN0302-9743 e-ISSN1611-3349
ISBN978-3-319-07952-3 e-ISBN978-3-319-07953-0
DOI10.1007/978-3-319-07953-0
SpringerChamHeidelbergNewYorkDordrechtLondon
LibraryofCongressControlNumber:2014940380
LNCSSublibrary:SL8–Bioinformatics
©SpringerInternationalPublishingSwitzerland2014
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Preface
These proceedings contain the papers that were presented at the First Interna-
tionalConferenceonAlgorithmsforComputationalBiology(AlCoB2014),held
in Tarragona,Spain, during July 1–3, 2014.
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, etc.
– Transcriptomics: splicing variants, isoform inference and quantification, dif-
ferential analysis, etc.
– Next-generationsequencing: populationgenomics, metagenomics, metatran-
scriptomics, etc.
– Microbiome analysis
– Systems biology
AlCoB 2014 received 39 submissions. Most papers were reviewed by three and
some by two Program Committee members. There were also several external
referees consulted; we acknowledge all the reviewers in the next section. After
a thorough and vivid discussion phase, the committee decided to accept 20 pa-
pers (which represents an acceptance rate of 51.28%). The conference program
also included two invited talks and one invited tutorial. Part of the success in
the management of this number of submissions is due to the excellent facilities
provided by the EasyChair conference management system.
We would like to thank all invited speakers and authors for their contri-
butions, the Program Committee and the reviewers for their cooperation, and
Springer for its very professional publishing work.
April 2014 Adrian-Horia Dediu
Carlos Mart´ın-Vide
Bianca Truthe
Organization
AlCoB2014wasorganizedbytheResearchGrouponMathematicalLinguistics–
GRLMC, from Rovira i Virgili University, Tarragona.
Program Committee
Tatsuya Akutsu Kyoto University, Japan
Amihood Amir Bar-Ilan University, Ramat-Gan, Israel
Alberto Apostolico Georgia Institute of Technology, Atlanta, USA
Joel Bader Johns Hopkins University, Baltimore, USA
Pierre Baldi University of California, Irvine, USA
Serafim Batzoglou Stanford University, USA
Bonnie Berger Massachusetts Institute of Technology,
Cambridge, USA
Francis Y.L. Chin University of Hong Kong, Hong Kong
Benny Chor Tel Aviv University, Israel
Keith A. Crandall George Washington University,
Washington DC, USA
Bhaskar DasGupta University of Illinois, Chicago, USA
Joaqu´ınDopazo Pr´ıncipe Felipe Research Center,
Valencia, Spain
Liliana Florea Johns Hopkins University, Baltimore, USA
Olivier Gascuel LIRMM-CNRS, Montpellier, France
David Gilbert Brunel University, Uxbridge, UK
Gaston H. Gonnet ETH Zu¨rich, Switzerland
Roderic Guig´o Center for Genomic Regulation, Barcelona,
Spain
Dan Gusfield University of California, Davis, USA
Vasant Honavar PennsylvaniaStateUniversity,UniversityPark,
USA
Sorin Istrail Brown University, Providence, USA
Tao Jiang University of California, Riverside, USA
Inge Jonassen University of Bergen, Norway
Anders Krogh University of Copenhagen, Denmark
Giovanni Manzini University of Eastern Piedmont, Alessandria,
Italy
Carlos Mart´ın-Vide (Chair) Rovira i Virgili University, Tarragona,Spain
Satoru Miyano University of Tokyo, Japan
Burkhard Morgenstern University of G¨ottingen, Germany
VIII Organization
Shinichi Morishita University of Tokyo, Japan
C´edric Notredame Center for Genomic Regulation, Barcelona,
Spain
Graziano Pesole National Research Council, Bari, Italy
Mark Ragan University of Queensland, Brisbane, Australia
Timothy Ravasi King Abdullah University of Science and
Technology, Thuwal, Saudi Arabia
Allen G. Rodrigo Duke University, Durham, USA
Steven Salzberg Johns Hopkins University, Baltimore, USA
David Sankoff University of Ottawa, Canada
Thomas Schiex INRA Toulouse, France
Jo˜ao Carlos Setubal University of Sa˜o Paulo, Brazil
Steven Skiena Stony Brook University, USA
Peter F. Stadler University of Leipzig, Germany
Wing-Kin Sung National University of Singapore, Singapore
Alfonso Valencia Spanish National Cancer Research Centre,
Madrid, Spain
Jacques van Helden University of Aix-Marseille, France
Arndt von Haeseler Center for Integrative Bioinformatics Vienna,
Austria
Lusheng Wang City University of Hong Kong, Hong Kong
Limsoon Wong National University of Singapore, Singapore
Xiaohui Xie University of California, Irvine, USA
Dong Xu University of Missouri, Columbia, USA
Zohar Yakhini Agilent Laboratories, Santa Clara, USA
Alex Zelikovsky Georgia State University, Atlanta, USA
Michael Q. Zhang University of Texas, Dallas, USA
External Reviewers
Artyomenko, Alexander Leibovich, Limor
Chateau, Annie Leung, Henry
De Givry, Simon Mandric, Igor
Doi, Koichiro Park, Hee-Won
Ehsani, Sepehr Puglisi, Simon J.
Gonnet, Pedro Sheridan, Paul
Hamelryck, Thomas Srihari, Sriganesh
Hermelin, Danny Swenson, Krister M.
Katsirelos, George Wang, Yi
Kifer, Ilona Wood, Derrick
Kim, Daehwan Zagrovic, Bojan
Kurowski, Krzysztof Zheng, Chunfang
Organization IX
Organizing Committee
Adrian-Horia Dediu, Tarragona
Carlos Mart´ın-Vide, Tarragona (Chair)
Bianca Truthe, Gießen
Lilica Voicu, Tarragona
Table of Contents
Invited Talks
ComparativeGenomics Approaches to Identifying Functionally Related
Genes ........................................................... 1
Michael Y. Galperin and Eugene V. Koonin
Regular Papers
A Greedy Algorithm for Hierarchical Complete Linkage Clustering ..... 25
Ernst Althaus, Andreas Hildebrandt, and
Anna Katharina Hildebrandt
Vester’s Sensitivity Model for Genetic Networks with Time-Discrete
Dynamics ....................................................... 35
Liana Amaya Moreno, Ozlem Defterli, Armin Fu¨genschuh, and
Gerhard-Wilhelm Weber
Complexity and Polynomial-Time Approximation Algorithms around
the Scaffolding Problem........................................... 47
Annie Chateau and Rodolphe Giroudeau
Heuristics for the Sorting by Length-Weighted Inversions Problem on
Signed Permutations ............................................. 59
Thiago da Silva Arruda, Ulisses Dias, and Zanoni Dias
On Low Treewidth Graphs and Supertrees ........................... 71
Alexander Grigoriev, Steven Kelk, and Nela Leki´c
On Optimal Read Trimming in Next Generation Sequencing and Its
Complexity ..................................................... 83
Ivo Hedtke, Ioana Lemnian, Matthias Mu¨ller-Hannemann, and
Ivo Grosse
On the Implementation of Quantitative Model Refinement ............ 95
Bogdan Iancu, Diana-Elena Gratie, Sepinoud Azimi, and Ion Petre
HapMonster: A Statistically Unified Approach for Variant Calling and
Haplotyping Based on Phase-Informative Reads...................... 107
Kaname Kojima, Naoki Nariai, Takahiro Mimori,
Yumi Yamaguchi-Kabata, Yukuto Sato, Yosuke Kawai, and
Masao Nagasaki
XII Table of Contents
Mapping-Free and Assembly-Free Discovery of Inversion Breakpoints
from Raw NGS Reads ............................................ 119
Claire Lemaitre, Liviu Ciortuz, and Pierre Peterlongo
Modeling the Geometry of the Endoplasmic Reticulum Network ........ 131
Laurent Lemarchand, Reinhardt Euler, Congping Lin, and
Imogen Sparkes
On Sorting of Signed Permutations by Prefix and Suffix Reversals and
Transpositions................................................... 146
Carla Negri Lintzmayer and Zanoni Dias
On the Diameter of Rearrangement Problems........................ 158
Carla Negri Lintzmayer and Zanoni Dias
Efficiently Enumerating All Connected Induced Subgraphs of a Large
Molecular Network................................................ 171
Sean Maxwell, Mark R. Chance, and Mehmet Koyutu¨rk
On Algorithmic Complexity of Biomolecular Sequence Assembly
Problem ........................................................ 183
Giuseppe Narzisi, Bud Mishra, and Michael C. Schatz
A Closed-Form Solution for Transcription Factor Activity Estimation
Using Network Component Analysis................................ 196
Amina Noor, Aitzaz Ahmad, Bilal Wajid, Erchin Serpedin,
Mohamed Nounou, and Hazem Nounou
SVEM: A Structural Variant Estimation Method Using Multi-mapped
Reads on Breakpoints ............................................ 208
Tomohiko Ohtsuki, Naoki Nariai, Kaname Kojima,
Takahiro Mimori, Yukuto Sato, Yosuke Kawai,
Yumi Yamaguchi-Kabata, Testuo Shibuya, and
Masao Nagasaki
Analysis and Classificationof ConstrainedDNA Elements with N-gram
Graphs and Genomic Signatures ................................... 220
Dimitris Polychronopoulos, Anastasia Krithara,
Christoforos Nikolaou, Giorgos Paliouras, Yannis Almirantis, and
George Giannakopoulos
Inference of Boolean Networks from Gene Interaction Graphs Using a
SAT Solver...................................................... 235
David A. Rosenblueth, Stalin Mun˜oz, Miguel Carrillo, and
Eugenio Azpeitia