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. 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.
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.
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
- Shelley Berger (University of Pennsylvania, USA)
Elchanan Mossel (Weizmann Institute of Science, Israel)
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|
|Li-San Wang||Penn Institute on Aging|