WABI 2009 -- Conference for Algorithms in Bioinformatics

What are algorithms in bioinformatics?

Bioinformatics is the application of staticstics and science to the field of molecular biology. The goal of it is to increase the understanding and practical uses of biological processes.

An example that is a hot button topic these days in the field of bioinformatics is alternative car fuels. Fuel is a major topic, especially among gearheads like us, so we thought it would be helpful for our customers to share updates about this and about the conference. Studies of algorithms in bioinformatics helps us identify and explore altenative fuels that can be used for cars. Companies like Toyota and Honda have developed hybrid car applications (Toyota Prius and some versions of the Honda Civic) as most of us are aware, but there is also exploration of other forms of fuel such as biodiesel fuel and hydro fuel. All these are considered "green" forms of car energy usage, and are the result of research in the algorithms in bioinformatics. In fact, cars that use alternative green forms of fuel are so popular now, that some companies specifically develop car parts for them. You can see example of "green car" parts, for cars such as the Prius and Civic, here: Toyota parts and Honda parts. These provide a way to see bioinformatics at its finest as evidenced by cutting edge car products.

Beyond that, many green cars are have fuel-specific parts being developed. To be more specific, it's probable that there are green-fuel types of specialty fuel pumps and fuel injectors being developed as we speak. The prevalence of new car parts markets for green-energy cars is evidence of how popular the green car fuel idea to people of the world, and therefore evidence of the impact of agorithms in bioinformatics. Very clearly, the conferences we hold each year are of great importance.

If you want to shop for parts on our site related to fuel delivery, check out these links: fuel pumps, fuel injectors, fuel rails, fuel pressure regulators, fuel filters, and fuel hoses.


All research on algorithmic work in bioinformatics and systems biology. The emphasis is on discrete algorithms and machine-learning methods that address important problems in molecular biology, that are founded on sound models, that are computationally efficient, and that have been implemented and tested in simulations and on real datasets. The goal is to present recent research results, including significant work-in-progress, and to identify and explore directions of future research. One such example of this emphasis is found in the research and development of alternative forms of car fuel, such as biodiesel car fuel and hydro car fuel.

The Workshop on Algorithms in Bioinformatics (WABI) is sponsored by EATCS (the European Association for Theoretical Computer Science) and ISCB (the International Society for Computational Biology). WABI09 is supported by the Penn Genome Frontiers Institute and the Penn Center for Bioinformatics.


Original research papers (including significant work-in-progress) are solicited in all aspects of algorithms in bioinformatics, including, but not limited to:

  • Exact, approximate, and machine-learning algorithms for sequence analysis, gene and signal recognition, alignment and assembly, molecular evolution, structure determination or prediction, gene expression, pathways, gene networks, proteomics, functional genomics, and drug design.
  • High-performance computing approaches to computationally hard learning and optimization problems in bioinformatics.
  • Methods, software and dataset repositories for development and testing of such algorithms and their underlying models.
  • Research about alternative car fuels, including but not limited to biodiesel car fuel and hydro car fuel.
  • Research about parts that can accommodate alternative fuel cars, and specific theses about the application of such specific green car parts.


Paper submission must be formatted in the Springer LNCS style (http://www.springer.de/comp/lncs/authors.html) and not exceed 12pp. Each paper must contain a succinct statement of the issues and of their motivation, a summary of the main results, and a brief explanation of their significance, all accessible to a non-specialist reader.

Electronic submission is required; procedures for submission can be found in the WABI'09 web site. In case of problems, authors may, by prior arrangement, email a PDF to the chairs, Steven Salzberg and Tandy Warnow.

Simultaneous submission to another conference with published proceedings is not permitted, but simultaneous submission to a journal is allowed, provided that the authors notify the program chairs and: (1) if published in a journal before the conference date, such a contribution will be published as a short abstract (1 page) in the WABI proceedings, (2) if published in a journal after the conference date, the journal version must carry as a footnote to the title "A preliminary version of this work appeared in the WABI'09 proceedings."


Accepted papers will be published in the Springer series Lecture Notes in Bioinformatics and will be allotted 12 pages. Posters will not be included in the published proceedings. Previous proceedings of WABI appeared in LNCS/LNBI volumes 2149 (Aarhus 2001), 2452 (Rome 2002), 2812 (Budapest 2003), 3240 (Bergen 2004), 3692 (Mallorca 2005), 4175 (Zurich 2006), 4645 (Philadelphia 2007) and 5251 (Karlsruhe 2008). By arrangements with the Editor-in-Chief, selected papers from WABI will be invited for an extended publication in a special issue of Algorithms for Molecular Biology.

Address any questions to the program committee chairs, Steven Salzberg and Tandy Warnow.

Important Dates

Paper submission deadline      May 11, 2009
Notification to authors (extended)    June 1, 2009
Final version due June 15, 2009
Poster submission deadline midnight (EDT), June 30, 2009
Notification to authors July 14, 2009
Symposium September 12-13, 2009

Keynote Speakers

Program Committee

    Elizabeth Allman (University of Alaska Fairbanks, USA)

    Tanya Berger-Wolf (University of Illinois, USA)

    Paola Bonizzoni (Università Degli Studi di Milano-Bicocca, Italy)

    Dan Brown (University of Waterloo, Canada)

    Rita Casadio (Università di Bologna, Italy)

    Mark Clement (Brigham Young University, USA)

    Maxime Crochemore (Université Paris-Est, Marne-la-Vallée, France)

    Miklós Csurös (University of Montreal, Canada)

    Aaron Darling (UC Davis, USA)

    Nadia El-Mabrouk (Université de Montréal, Canada)

    Eleazar Eskin (UCLA, USA)

    Liliana Florea (University of Maryland, USA)

    Ganesh Ganapathy (NESCENT, USA)

    Olivier Gascuel (LIRMM-CNRS, France)

    Raffaele Giancarlo (Università degli Studi di Palermo, Italy)

    Concettina Guerra (Università di Padova, Italy)

    Roderic Guigó (Centre de Regulació Genòmica, Spain)

    Sridhar Hannenhalli (University of Pennsylvania, USA)

    Daniel Huson (Universität Tübingen, Germany)

    Shane Jensen (University of Pennsylvania -- Wharton, USA)

    Carl Kingsford (University of Maryland, USA)

    Ming Li (University of Waterloo, Canada)

    Randy Linder (University of Texas, USA)

    Stefano Lonardi (UC Riverside, USA)

    Jian Ma (UC Santa Cruz, USA)

    Erick Matsen (UC Berkeley, USA)

    István Miklós (Rényi Institute, Hungarian Academy of Sciences, Hungary)

    Bernard Moret (Swiss Federal Institute of Technology, Switzerland)

    Burkhard Morgenstern (University of Gottingen, Germany)

    Elchanan Mossel (Weizmann Institute of Science, Israel)

    Luay Nakhleh (Rice University, USA)

    Macha Nikolski (Université Bordeaux, France)

    Uwe Ohler (Duke University, USA)

    Laxmi Parida (IBM T.J. Watson Research Center, USA)

    Kunsoo Park (Seoul National University, Korea)

    Ron Pinter (Israel Institute of Technology, Israel)

    Cinzia Pizzi (University of Padova, Italy)

    David Posada (University of Vigo, Spain)

    Sven Rahmann (U. Dortmund, Germany)

    Ben Raphael (Brown University, USA)

    Knut Reinert (Freie Universität Berlin, Germany)

    Allen Rodrigo (U. Auckland, NZ)

    Mikhail Roytberg (Russian Academy of Sciences, Russia)

    Marie-France Sagot (Université Claude Bernard, Lyon I, France)

    Steven Salzberg (University of Maryland, USA) (co-chair)

    David Sankoff (University of Ottawa, Canada)

    Mona Singh (Princeton University, USA)

    Saurabh Sinha (University of Illinois, USA)

    Steven Skiena (SUNY Stony Brook, USA)

    Peter Stadler (Universität Leipzig, Germany)

    Alexis Stamatakis (Ludwig-Maximilians Universität, Germany)

    Jens Stoye (Universität Bielefeld, Germany)

    Jijun Tang (University of South Carolina, USA)

    Glenn Tesler (UC San Diego, USA)

    Olga Troyanskaya (Princeton University, USA)

    Alfonso Valencia (Structural and Computational Biology Programme, Spain)

    Li-San Wang (University of Pennsylvania, USA)

    Lusheng Wang (City University of Hong Kong, HK)

    Tandy Warnow (University of Texas, USA) (co-chair)

    Chris Workman (Technical University of Denmark, Denmark)

Organizing Committee (University of Pennsylvania)

    Junhyong Kim (chair) Biology & Penn Genome Frontiers Institute

    Stephen Fisher Biology

    Li-San Wang Penn Institute on Aging

    Download program as pdf | Call For Papers


    Decoding the Genomic Architecture of Mammalian and Plant Genomes: Synteny Blocks and Large-Scale Duplications

    Qian Peng (Univ of California, San Diego, USA)

    Max Alekseyev (Univ of South Carolina, USA)

    Glenn Tesler (Univ of California, San Diego, USA)

    Pavel Pevzner (Univ of California, San Diego, USA)

    Linear-Time Protein 3-D Structure Searching with Insertions and Deletions

    Tetsuo Shibuya (Univ of Tokyo, Japan)

    Jesper Jansson (Ochanomizu Univ, Japan)

    Kunihiko Sadakane (National Institute of Informatic, Japan)

    K-partite RNA Secondary Structures

    Minghui Jiang (Utah State Univ, USA)

    Pedro J. Tejada (Utah State Univ, USA)

    Ramoni O. Lasisi (Utah State Univ, USA)

    Shanhong Cheng (Utah State Univ, USA)

    D. Scott Fechser (Utah State Univ, USA)

    A non-parametric Bayesian approach for predicting RNA secondary structures

    Kengo Sato (Japan Biological Informatics Consortium, Japan)

    Michiaki Hamada (Mizuho Information & Research Institute, Inc, Japan)

    Toutai Mituyama (National Institute of Advanced Industrial Science and Technology, Japan)

    Kiyoshi Asai (Univ of Tokyo, Japan)

    Yasubumi Sakakibara (Keio Univ, Japan)

    A Tree Based Method for the Rapid Screening of Chemical Fingerprints

    Thomas Greve Kristensen (Aarhus Univ, Denmark)

    Jesper Nielsen (Aarhus Univ, Denmark)

    Christian Nørgaard Storm Pedersen (Aarhus Univ, Denmark)

    Large-scale neighbor-joining with NINJA

    Travis Wheeler (Univ of Arizon, USA)

    A Unifying View on Approximation and FPT of Agreement Forests

    Chris Whidden (Dalhousie Univ, Canada)

    Norbert Zeh (Dalhousie Univ, Canada)

    On the upper bound of the prediction accuracy of residue contacts in proteins with correlated mutations: the case study of the similarity matrices

    Pietro Di Lena (Univ of Bologna, Italy)

    Piero Fariselli (Univ of Bologna, Italy)

    Luciano Margara (Univ of Bologna, Italy)

    Marco Vassura (Univ of Bologna, Italy)

    Rita Casadio (UNIB, Italy)

    A simulation study comparing supertree and combined analysis methods using SMIDGen

    M. Shel Swenson (Univ of Texas at Austin, USA)

    Francois Barbancon (Univ of Texas at Austin, USA)

    Randy Linder (Univ of Texas, USA)

    Tandy Warnow (Univ of Texas at Austin, USA)

    Minimum Factorization Agreement of Spliced ESTs

    Paola Bonizzoni (Univ di Milano-Bicocca, Italy)

    Gianluca Della Vedova (Univ degli Studi Milano-Bicocca, Italy)

    Riccardo Dondi (Univ degli Studi di Bergamo, Italy)

    Yuri Pirola (DISCo, Università di Milano-Bicocca, Italy)

    Raffaella Rizzi (Comunicazione Univ degli Studi di Milano - Bicocca, Italy)

    Annotating fragmentation patterns

    Sebastian Böcker (Jena Univ, Germany)

    Florian Rasche (Jena Univ, Germany)

    Tamara Steijger (Friedrich-Schiller-Univ Jen, Germany)

    Structural Alignment of RNA with Complex Pseudoknot Structure

    Thomas Wong (Univ of Hong Kong, Hong Kong)

    Tak-Wah Lam (Univ of Hong Kong, Hong Kong)

    Wing-Kin Sung (Nuational Univ of Singapore, Singapore)

    SM Yiu (Univ of Hong Kong, Hong Kong)

    MPSCAN: fast localisation of multiple reads in genomes

    Eric Rivals (LIRMM - UMR 5506 CNRS UM2, France)

    Leena Salmela (Helsinki Univ of Technology, Finland)

    Petteri Kiiskinen (Helsinki Univ of Technology, Finland)

    Petri Kalsi (Helsinki Univ of Technology, Finland)

    Jorma Tarhio (Helsinki Univ of Technology, Finland)

    Phylogenetic Comparative Assembly

    Peter Husemann (Bielefeld Univ, Germany)

    Jens Stoye (Bielefeld Univ, Germany)

    Back-translation for discovering distant protein homologies

    Marta Girdea (LIFL - Univ Lille 1 / INRIA Lille - Nord Europe, France)

    Laurent Noé (LIFL - Univ Lille 1 / INRIA Lille - Nord Europe, France)

    Gregory Kucherov (LIFL/CNRS/INRIA, France)

    Predicting Gene Structures from Multiple RT-PCR Tests

    Jakub Kovac (fmfi uk, Slovakia)

    Tomas Vinar (Comenius Univ in Bratislava, Slovakia)

    Bronislava Brejova (Comenius Univ in Bratislava, Slovakia)

    PMFastR: A New Approach to Multiple RNA Structure Alignment

    Daniel DeBlasio (Univ of Central Florida, USA)

    Jocelyne Bruand (Univ of California, San Diego, USA)

    Shaojie Zhang (Univ of Central Florida, USA)

    SCJ: a variant of breakpoint distance for which sorting, genome median and genome halving problems are easy

    Pedro Feijão (UNICAMP - Univ of Campinas, Brazil)

    João Meidanis (Univ of Campinas / Scylla Bioinformatics, Brazil)

    Generalizing the Four Gamete Condition and Splits Equivalence Theorem: Perfect Phylogeny on Three State Characters

    Fumei Lam (Univ of California, Davis, USA)

    Dan Gusfield (Univ of California, Davis, USA)

    Srinath Sridhar (Carnegie Mellon Univ, USA)

    biRNA: Fast RNA-RNA Binding Sites Prediction

    Hamidreza Chitsaz (Simon Fraser Univ, Canada)

    Rolf Backofen (Albert-Ludwigs-Univ Freiburg, Germany)

    S. Cenk Sahinalp (Simon Fraser Univ, Canada)

    Improving Inference of Transcriptional Regulatory Networks Based on Network Evolutionary Models

    Xiuwei Zhang (EPFL, Switzerland)

    Bernard Moret (EPFL, Switzerland)

    Aligning Biomolecular Networks Using Modular Graph Kernels

    Fadi Towfic (Iowa State Univ, Ames, IA, USA)

    M. Heather West Greenlee (Iowa State Univ, Ames, IA, USA)

    Vasant Honavar (Iowa State Univ, USA)

    MADMX: A Novel Strategy for Maximal Dense Motif Extraction

    Fabio Vandin (Univ of Padova, Italy)

    Roberto Grossi (Univ di Pisa, Italy)

    Andrea Pietracaprina (Univ of Padova, Italy)

    Nadia Pisanti (Univ di Pisa, Italy)

    Geppino Pucci (DEI - Univ di Padova, Italy)

    Eli Upfal (Brown Univ, USA)

    Fast prediction of RNA-RNA Interaction

    Raheleh Salari (Simon Fraser Univ, Canada)

    Rolf Backofen (Albert-Ludwigs-Univ Freiburg, Germany)

    S. Cenk Sahinalp (Simon Fraser Univ, Canada)

    A Markov Classification Model for Metabolic Pathways

    Timothy Hancock (Kyoto Univ, Japan)

    Hiroshi Mamitsuka (Kyoto Univ, Japan)

    FlexSnap: Flexible Non-Sequential Protein Structure Alignment

    Saeed Salem (RPI, USA)

    Mohammed Zaki (RPI, USA)

    Chris Bystroff (Rensselaer Polytechnic Institute, USA)

    Constructing Majority-Rule Supertrees

    Jianrong Dong (Iowa State Univ, Ames, IA, USA)

    David Fernández-Baca (Iowa State Univ, Ames, IA, USA)

    F.R. McMorris (Illinois Institute of Technology, USA)

    Mimosa – Mixture model of co-expression to detect modulators of regulatory interaction

    Matthew Hansen (Univ of Pennsylvania, USA)

    Logan Everett (Univ of Pennsylvania, USA)

    Larry Singh (Univ of Pennsylvania, USA)

    Sridhar Hannenhalli (Univ of Pennsylvania, USA)

    Efficient Algorithms for Analyzing Segmental Duplications, Deletions, and Inversions in Genomes

    Crystal Kahn (Brown Univ, USA)

    Shay Mozes (Brown Univ, USA)

    Ben Raphael (Brown Univ, USA)

    Exact Score Distribution Computation for Similarity Searches in Ontologies

    Marcel Schulz (Max Planck Institute for Molecular Genetics, Germany)

    Sebastian Köhler (Institut for Medizinische Genetik, Charite Universitätsmedizin Berlin, Germany)

    Sebastian Bauer (Institut fuer Medizinische Genetik, Charite Universitätsmedizin Berlin, Germany)

    Martin Vingron (Max Planck Institut fuer molekulare Genetik, Germany)

    Peter Robinson (Charite Univ tsmedizin Berlin, Germany)

    Quantifying Systemic Evolutionary Changes by Color Coding Confidence-Scored PPI Networks

    Phuong Dao (Simon Fraser Univ, Canada)

    Alexander Schonhuth (Simon Fraser Univ, Canada)

    Fereydoun Hormozdiari (Simon Fraser Univ, Canada)

    Iman Hajirasouliha (Simon Fraser Univ, Canada)

    S. Cenk Sahinalp (Simon Fraser Univ, Canada)

    Martin Ester (Simon Fraser Univ, Canada)

    A General Framework for Local Pairwise Alignment Statistics with Gaps

    Pasi Rastas (Helsinki Institute for Information Technology HIIT, Helsinki Univ of Technology and Univ of Helsinki, Finland)

    Visualizing Phylogenetic Treespace Using Cartographic Projections

    Kenneth Sundberg (Brigham Young Univ, USA)

    Mark Clement (Brigham Young Univ, USA)

    Quinn Snell (Brigham Young Univ, USA)

    A simple practical and complete 0 (n^3/log(n)) - time Algorithm for RNA folding

    Yelena Frid (Univ of California, Davis, USA)

    Dan Gusfield (Univ of California, Davis, USA)

    SATe: Simultaneous Alignment and Tree Estimation

    Kevin Liu (University of Texas at Austin, USA)

    Serita Nelson (University of Texas at Austin, USA)

    Randy Linder (University of Texas at Austin, USA)

    Tandy Warnow (University of Texas at Austin, USA)

    Upper bounds on the ability to reconstruct prokaryotic genomes with next generation sequencing technologies

    Joshua Wetzel (Rutgers University, USA)

    Mike Schatz (University of Maryland, USA)

    Carl Kingsford (University of Maryland, USA)

    Mihai Pop (University of Maryland, USA)


    CentroidFold: predictions of RNA secondary structure for estimating accurate base-pairs

    Michiaki Hamada (Mizuho Information & Research Institute, Inc., Japan)

    Kengo Sato (Japan Biological Informatics Consortium, Japan)

    Hisanori Kiryu (University of Tokyo, Japan)

    Toutai Mituyama (Comp. Bio. Res. Ctr., National Institute of Advanced Industrial Sci. and Tech., Japan)

    Kiyoshi Asai (University of Tokyo, Japan)

    The Power of Protein Interaction Networks for Associating Genes with Diseases

    Saket Navlakha (University of Maryland, United States)

    Carl Kingsford (University of Maryland, College Park, United States)

    Rescuing concatenation with maximum likelihood using supermatrix rooted triples

    Michael DeGiorgio (University of Michigan, United States)

    James Degnan (University of Canterbury, New Zealand)

    Exhaustive mitochondrial phylogenies: challenges and solutions

    Roberto Blanco (University of Zaragoza, Spain)

    Elvira Mayordomo (Universidad de Zaragoza, Spain)

    Parking functions, labeled trees and DCJ sorting scenarios

    Aida Ouangraoua (Department of Mathematics - Simon Fraser University, Canada)

    Anne Bergeron (Universite du Quebec a Montreal, Canada)

    Extracting Between Pathway Models from E­MAP Interactions Using Probabilistic Graph Summarization

    David Kelley (U. Maryland - College Park, United States)

    Carl Kingsford (University of Maryland, College Park, United States)

    An algorithmic method for building artificial DNA libraries

    Adam Kozak (Institute of Computing Science, Poznan University of Technology, Poland)

    Tomasz GÅ‚owacki (Institute of Computing Science, Poznan University of Technology, Poland)

    Piotr Formanowicz (Institute of Computing Science, Poznan University of Technology, Poland)

    SuperFine: a fast and accurate supertree method

    M. Shel Swenson (University of Texas at Austin, United States)

    Rahul Suri (University of Texas at Austin, Computer Science, United States)

    Young-Suk Lee (University of Texas, Computer Science, United States)

    Randy Linder (University of Texas, Integrative Biology, United States)

    Tandy Warnow (the university of texas at austin, United States)

    Detecting Coding Regions in Sequence Alignments With Spaced Seeds

    Leming Zhou (University of Pittsburgh, United States)

    Mihaela Pertea (UMD, United States)

    Liliana Florea (University of Maryland, United States)

    Read mapping tool for AB SOLiD data

    Marta Girdea (LIFL - Université Lille 1 / INRIA Lille - Nord Europe, France)

    Laurent Noé (LIFL - Université Lille 1 / INRIA Lille - Nord Europe, France)

    Gregory Kucherov (LIFL/CNRS/INRIA, France)

    Long peptides assembly method

    Tomasz GÅ‚owacki (Institute of Computing Science, Poznan University of Technology, Poland)

    Adam Kozak (Institute of Computing Science, Poznan University of Technology, Poland)

    Piotr Formanowicz (Institute of Computing Science, Poznan University of Technology, Poland)

    Efficient Error Detection and Removal Algorithm for Next Generation Sequencing Data

    Xiaohong Zhao (Siemens Corporate Research, United States)

    Lance Palmer (Siemens Corporate Research, United States)

    Randall Bolanos (Siemens Corporate Research, United States)

    Cristian Mircean (Siemens AG, Germany)

    Daniel Fasulo (454 Life Sciences, a Roche company, United States)

    Gayle Wittenberg (Siemens Corporate Research, United States)

    An angle based variant of Dynamic cross correlation metric

    Jyothish Soman (IIIT-hyderabad, India)

    Abhijit Mitra (IIIT Hyderabad, India)

    Large-Scale Simulating of RNA Evolution by an Energy-Dependent Fitness Model

    Sheng Guo (University of Pennsylvania, United States)

    Li-San Wang (University of Pennsylvania, United States)

    Junhyong Kim (University of Pennsylvania, United States)


    30 rooms have been reserved at Club Quarters in Philadelphia. Fifteen “Club Size” rooms are available at a rate of $99.00 per night, and fifteen “Standard” rooms are available for $114.00 per night. Rates do not include hotel taxes (currently 14%). This group discount is only valid until July 16, 2009.

    Hotels within a few blocks of the conference:

    Additional local hotel accommodations can be found on the University City District site and on the UPenn Admissions accomodations site.

    Getting Here

    • Getting to Penn
      • Air, train, bus
      • Driving
      • Public bus between the conference hotels and conference hall:
        • The 21 bus runs West along Walnut Ave from 2nd to 63rd St, and back East along Chestnut Ave from 63rd to 2nd St. You should get off at 34th St and walk one block South and one block East.
        • The 42 bus runs West along Walnut Ave, going from 17th and Walnut Street to 34th and Spruce Street. This bus returns East by circling around campus on the South side. You can catch it at 33rd and Spruce.
        • This bus costs $2 each way (exact change is required). Board the bus by placing the cash fare in to the farebox on the bus.
        • For more information about the bus you can contact SEPTA at http://www.septa.org or by phone at (215) 580-7800.

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