Algorithms in Bioinformatics: 13th International Workshop, WABI 2013, Sophia Antipolis, France, September 2-4, 2013. Proceedings

389 Pages·2013·7.996 MB·English

by  Bernard M. E. Moret (auth.), Aaron Darling, Jens Stoye (eds.)

Aaron Darling
Jens Stoye (Eds.)
Algorithms
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13th International Workshop, WABI 2013
Sophia Antipolis, France, September 2013
Proceedings
123
Lecture Notes in Bioinformatics 8126
EditedbyS.Istrail,P.Pevzner,andM.Waterman
EditorialBoard: A.Apostolico S.Brunak M.Gelfand
T.Lengauer S.Miyano G.Myers M.-F.Sagot D.Sankoff
R.Shamir T.Speed M.Vingron W.Wong
Subseries of Lecture Notes in Computer Science
Aaron Darling Jens Stoye (Eds.)
Algorithms
in Bioinformatics
13th International Workshop, WABI 2013
Sophia Antipolis, France, September 2-4, 2013
Proceedings
1 3
VolumeEditors
AaronDarling
UniversityofTechnologySydney
ithreeinstitute
Ultimo,NSW2007,Australia
E-mail:[email protected]
JensStoye
BielefeldUniversity
FacultyofTechnology
Universitätsstraße25
33615Bielefeld,Germany
E-mail:[email protected]
ISSN0302-9743 e-ISSN1611-3349
ISBN978-3-642-40452-8 e-ISBN978-3-642-40453-5
DOI10.1007/978-3-642-40453-5
SpringerHeidelbergNewYorkDordrechtLondon
LibraryofCongressControlNumber:2013945447
CRSubjectClassification(1998):F.2,J.3,G.2.2,F.1,I.2.6,H.2.8,G.1.2
LNCSSublibrary:SL8–Bioinformatics
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Preface
It is our great pleasure to present the proceedings of the 13th Workshop on
Algorithms in Bioinformatics (WABI 2013), held at Sophia Antipolis, France,
September 2–4, 2013. The WABI 2013 workshop was part of the seven ALGO
2013 conference meetings, which included ESA, IPEC, WAOA, ALGOSEN-
SORS,MASSIVE,andATMOS.WABI2013washostedbyINRIAandCampus
SophiaTech, and sponsored by the European Association for Theoretical Com-
puterScience(EATCS)andtheInternationalSocietyforComputationalBiology
(ISCB). See http://algo2013.inria.fr/wabi.shtmlfor more details.
The Workshop on Algorithms in Bioinformatics highlights research in algo-
rithmicworkforbioinformatics,computationalbiologyandsystemsbiology.The
emphasis is mainly on discrete algorithms and machine-learning methods that
address important problems in molecular biology, that are founded on sound
models,thatarecomputationallyefficient,andthathavebeenimplementedand
testedinsimulationsandonrealdatasets.Thegoalis topresentrecentresearch
results,including significantwork-in-progress,andto identify andexploredirec-
tions of future research.
Original research papers (including significant work-in-progress)or state-of-
the-art surveys were solicited for WABI 2013 in all aspects of algorithms in
bioinformatics, computational biology and systems biology. In response to our
call, we received 61 submissions for papers and 27 were accepted. In addition,
WABI2013hostedapostersessionandadistinguishedlecturebyBernardMoret,
ofE´colePolytechniqueF´ed´eralede Lausanne(EPFL),Switzerland. Prof.Moret
founded the WABI series 13 years ago and provided leadership to expand the
meeting over the past 13 years. Last year Prof. Moret stepped down from his
position of steering the meeting and formed a Steering Committee to facilitate
the workshop’s continued success.
We would like to sincerely thank the authors of all submitted papers and
the conference participants. We also thank the Program Committee and their
sub-referees for their hard work in reviewing, discussing, and selecting papers
for this year’s workshop.
July 2013 Aaron Darling
Jens Stoye
Organization
Steering Committee
Bernard Moret EPFL, Switzerland
Vincent Moulton University of East Anglia, UK
Jens Stoye Bielefeld University, Germany
Tandy Warnow The University of Texas at Austin, USA
Program Committee
Mohamed Abouelhoda Cairo University, Egypt
Tatsuya Akutsu Kyoto University, Japan
Anne Bergeron University of Quebec at Montreal, Canada
Paola Bonizzoni Universita` di Milano-Bicocca, Italy
Guillaume Bourque McGill University, Canada
Marilia Braga Inmetro - Ditel, Brazil
C. Titus Brown Michigan State University, USA
Daniel Brown University of Waterloo, Canada
David Bryant University of Otago, New Zealand
Philipp Bucher Swiss Institute for Experimental Cancer
Research, Switzerland
Sebastian B¨ocker Friedrich Schiller University Jena, Germany
Rita Casadio UNIBO, Italy
Cedric Chauve Simon Fraser University, Canada
Benny Chor Tel Aviv University, Israel
Lachlan Coin The University of Queensland, Australia
Lenore Cowen Tufts University, USA
Keith Crandall George Washington University, USA
Aaron Darling University of Technology Sydney, Australia
Nadia El-Mabrouk University of Montreal, Canada
Eleazar Eskin University of California, Los Angeles, USA
Liliana Florea Johns Hopkins University, USA
Martin Frith CBRC, AIST, Japan
Anna Gambin Warsaw University, Poland
Olivier Gascuel LIRMM, CNRS - University of Montpellier 2,
France
Nicholas Hamilton The University of Queensland, Australia
Barbara Holland University of Tasmania, Australia
Katharina Huber University of East Anglia, UK
Carl Kingsford Carnegie Mellon University, USA
Jinyan Li University of Technology Sydney, Australia
VIII Organization
Zsuzsanna Lipta´k University of Verona, Italy
Stefano Lonardi UC Riverside, USA
Ion Mandoiu University of Connecticut, USA
Giovanni Manzini University of Eastern Piedmont, Italy
Paul Medvedev Pennsylvania State University, USA
Joao Meidanis UniversityofCampinas/ScyllaBioinformatics,
Brazil
Istvan Miklos Renyi Institute, Hungary
Satoru Miyano University of Tokyo, Japan
Bernard Moret EPFL, Switzerland
Burkhard Morgenstern University of G¨ottingen, Germany
Vincent Moulton University of East Anglia, UK
Gene Myers MPI Cell Biology and Genetics, Germany
Veli M¨akinen University of Helsinki, Finland
Luay Nakhleh Rice University, USA
Nadia Pisanti UniversityofPisa, Italyand LeidenUniversity,
The Netherlands
Teresa Przytycka NIH, USA
Sven Rahmann University of Duisburg-Essen, Germany
Ben Raphael Brown University, USA
Knut Reinert FU Berlin, Germany
Marie-France Sagot INRIA Grenoble Rhoˆne-Alpes and Universit´e
de Lyon 1, Villeurbanne, France
S. Cenk Sahinalp Simon Fraser University, Canada
David Sankoff University of Ottawa, Canada
Russell Schwartz Carnegie Mellon University, USA
Joao Setubal University of Sa˜o Paulo, Brazil
Saurabh Sinha University of Illinois, USA
Jens Stoye Bielefeld University, Germany
Krister Swenson Universit´e de Montr´eal / McGill University,
Canada
Jijun Tang University of South Carolina, USA
Eric Tannier INRIA, France
Glenn Tesler University of California, San Diego, USA
Lusheng Wang City University of Hong Kong, China
Yuzhen Ye Indiana University, USA
Louxin Zhang National University of Singapore, Singapore
Michal Ziv-Ukelson Ben-Gurion University of the Negev, Israel
Additional Reviewers
Aiche, Stephan Cicalese, Ferdinando
Badr, Ghada Conrad, Tim
Biller, Priscila D’Addario, Marianna
Chateau, Annie Dao, Phuong
Organization IX
Dittwald, Piotr Pinhas, Tamar
Donmez, Nilgun Pizzi, Cinzia
Drori, Hagai Polishko, Anton
Duggal, Geet Rizzi, Raffaella
Duma, Denisa Sadakane, Kunihiko
Goldberg, Tatyana Scheubert, Kerstin
Gorecki, Pawel Scornavacca, Celine
Hazelhurst, Scott Sheridan, Paul
Higashi, Susan Sinaimeri, Blerina
Hormozdiari, Farhad Snir, Sagi
Hufsky, Franziska Startek, Micha(cid:4)l
Kluge, Bogusl(cid:4)aw Tomescu, Alexandru
Kocsis, Levente Wang, Zhanyong
Lacroix, Vincent White, Walton Timothy James
Leoncini, Mauro Wohlers, Inken
Marino, Andrea Yakhini, Zohar
McPherson, Andrew Yasuda, Tomohiro
Mirebrahim, Seyed Yue, Feng
Oesper, Layla Zakov, Shay
Pardi, Fabio Zanetti, Jo˜ao Paulo Pereira
Pardini, Giovanni L(cid:4) acki, Mateusz
(cid:2)
Patterson, Murray
Table of Contents
Extending the Reach of Phylogenetic Inference....................... 1
Bernard M.E. Moret
Protein(Multi-)LocationPrediction:UsingLocationInter-dependencies
in a Probabilistic Framework ...................................... 3
Ramanuja Simha and Hagit Shatkay
Towards Reliable Automatic Protein Structure Alignment............. 18
Xuefeng Cui, Shuai Cheng Li, Dongbo Bu, and Ming Li
A Minimum-Labeling Approach for Reconstructing Protein Networks
across Multiple Conditions ........................................ 33
Arnon Mazza, Irit Gat-Viks, Hesso Farhan, and Roded Sharan
Faster Mass Decomposition ....................................... 45
Kai Du¨hrkop, Marcus Ludwig, Marvin Meusel, and Sebastian B¨ocker
On NP-Hardness of the Paired de Bruijn Sound Cycle Problem ........ 59
Evgeny Kapun and Fedor Tsarev
Accurate Decoding of Pooled Sequenced Data Using Compressed
Sensing ......................................................... 70
Denisa Duma, Mary Wootters, Anna C. Gilbert, Hung Q. Ngo,
Atri Rudra, Matthew Alpert, Timothy J. Close,
Gianfranco Ciardo, and Stefano Lonardi
A Novel Combinatorial Method for Estimating Transcript Expression
with RNA-Seq: Bounding the Number of Paths ...................... 85
Alexandru I. Tomescu, Anna Kuosmanen, Romeo Rizzi, and
Veli M¨akinen
A Polynomial Delay Algorithm for the Enumeration of Bubbles with
Length Constraints in Directed Graphs and Its Application to the
Detection of Alternative Splicing in RNA-seq Data ................... 99
Gustavo Sacomoto, Vincent Lacroix, and Marie-France Sagot
Distribution of Graph-Distances in Boltzmann Ensembles of RNA
Secondary Structures............................................. 112
Rolf Backofen, Markus Fricke, Manja Marz, Jing Qin, and
Peter F. Stadler
XII Table of Contents
Faster Algorithms for RNA-Folding Using the Four-Russians Method ... 126
Balaji Venkatachalam, Dan Gusfield, and Yelena Frid
Algorithms for the Majority Rule (+) Consensus Tree and the
Frequency Difference Consensus Tree ............................... 141
Jesper Jansson, Chuanqi Shen, and Wing-Kin Sung
The Generalized Robinson-Foulds Metric............................ 156
Sebastian B¨ocker, Stefan Canzar, and Gunnar W. Klau
Computing the Skewness of the Phylogenetic Mean Pairwise Distance
in Linear Time .................................................. 170
Constantinos Tsirogiannis and Brody Sandel
Characterizing Compatibility and Agreement of Unrooted Trees via
Cuts in Graphs .................................................. 185
Sudheer Vakati and David Fern´andez-Baca
Unifying ParsimoniousTree Reconciliation .......................... 200
Nicolas Wieseke, Matthias Bernt, and Martin Middendorf
Sibelia: A Scalable and Comprehensive Synteny Block Generation Tool
for Closely Related Microbial Genomes ............................. 215
Ilya Minkin, Anand Patel, Mikhail Kolmogorov,
Nikolay Vyahhi, and Son Pham
On the Matrix Median Problem.................................... 230
Jo˜ao Paulo Pereira Zanetti, Priscila Biller, and Jo˜ao Meidanis
A Fixed-Parameter Algorithm for Minimum Common String Partition
with Few Duplications............................................ 244
Laurent Bulteau, Guillaume Fertin, Christian Komusiewicz, and
Irena Rusu
MSARC: Multiple Sequence Alignment by Residue Clustering ......... 259
Micha(cid:2)l Modzelewski and Norbert Dojer
Mutual Enrichment in Ranked Lists and the Statistical Assessment of
Position Weight Matrix Motifs..................................... 273
Limor Leibovich and Zohar Yakhini
Probabilistic Approaches to Alignment with Tandem Repeats.......... 287
Michal N´an´asi, Toma´ˇs Vinaˇr, and Bronˇa Brejov´a
Multiscale Identification of Topological Domains in Chromatin......... 300
Darya Filippova, Rob Patro, Geet Duggal, and Carl Kingsford
Modeling Intratumor Gene Copy Number Heterogeneity Using
Fluorescence in Situ Hybridization Data ............................ 313
Charalampos E. Tsourakakis