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Guest Editors' Introduction to the Special Section on Algorithms in Bioinformatics (WABI '07)

Raffaele Giancarlo
Sridhar Hannenhalli

Pages: pp. 482-483


This special section presents a selection of papers that appeared originally as extended abstracts in the Proceedings of the Seventh Workshop on Algorithms in Bioinformatics (WABI 2007), which took place in Philadelphia on 8-9 September 2007, under the auspices of the International Society for Computational Biology (ISCB), the European Association for Theoretical Computer Science (EATCS), the Penn Genomics Institute, and the Penn Center for Bioinformatics.

The Workshop on Algorithms in Bioinformatics covers research in all aspects of algorithmic work in bioinformatics. The emphasis is on discrete algorithms 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 data sets. The goal is to present recent research results, including significant work-in-progress, and to identify andexplore directions of future research. Specific topics of interest include, but are not limited to:

  • exact, approximate, and machine-learning algorithms for genomics, sequence analysis, gene and signal recognition, alignment, molecular evolution, polymorphisms and population genetics, protein and RNA structure determination or prediction, gene expression and gene networks, proteomics, functional genomics, and drug design;
  • methods, software, and data set repositories for development and testing of such algorithms and their underlying models; and
  • high-performance approaches to computationally hard problems in bioinformatics, particularly optimization problems.

A major goal of the workshop is to bring together researchers working in a wide spectrum of areas in bioinformatics, ranging from abstract algorithm design to biological data analysis so as to enable a dialogue between application specialists and algorithm designers, mediated by algorithm engineers and high-performance computing specialists. We believe that such a dialogue is necessary for the progress of computational biology, inasmuch as application specialists cannot analyze their data sets without fast and robust algorithms and, conversely, algorithm designers cannot produce useful algorithms without being conversant with the problems faced by biologists.

The eight papers that appear in this special section are the highest ranking among the 133 extended abstracts submitted to the conference. Those contributions, duly expanded, were invited for publication in this special section and they were peer-reviewed according to the procedures that TCBB applies to its standard submissions.

The selected papers offer a vivid snapshot of the spectrum of computational biology problems addressed via algorithmic and machine learning techniques. Some of the contributions report progress in well-recognized areas of computational biology, such as protein structure predic-tion, alignments of sequences, trees, and structures. Others address relatively novel issues related to single nucleotide polymorphism and optimal design of genomic tiling arrays.


Raffaele Giancarlo acknowledges the support of the Italian Ministry of Research, International Italy-Israel Firb Project Pattern Discovery in Discrete Structures with Applications to Bioinformatics and by FIRB Project Bioinformatics for Genomics and Proteomics. Sridhar Hannenhalli acknowledges the support of the US National Institutes of Health.

About the Authors

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Raffaele Giancarlo received the BS degree in computer science from the University of Salerno in 1982 (summa cum laude) and the PhD degree in computer science from the School of Arts and Sciences, Columbia University, New York, in 1990. He has been a full professor of computer science at the University of Palermo, Italy, since 2000. His doctoral dissertation is among the first to systematically explore algorithmic issues for biological sequence analysis (alignments and RNA secondary structure prediction). In the fall of 1990, he was awarded the prestigious Post-Doctoral Fellowship for the Mathematical and Information Sciences by AT&T Bell Laboratories. Over the years, he has been a member of many institutions, either permanent or as a visiting scientist: the Universitá degli Studi di Salerno, AT&T Bell Laboratories, AT&T Research Labs, Bell Labs of Lucent Technologies, INRIA, Max Plank Institute for Molecular Genetics, and CNRS. He contributed in founding many initiatives in bioinformatics: the Workshop on Algorithms in Bioinformatics, the journal Algorithms for Molecular Biology, and the International Annual Lipari Summer School in Bioinformatics and Computational Biology. Currently, he serves on the editorial boards of: the Journal of Discrete Algorithms, BioMed Central Research Notes, BMC Bioinformatics, and Algorithms for Molecular Biology, for the last three, as an associate editor. He has had the privilege of being invited speaker at numerous scientific events, including the Annual Meeting of SIAM and the Ettore Majorana Center for the Advancement of Science. He also serves as a regular reviewer for many international funding agencies, in Europe and elsewhere. He is the author of more then 80 scientific papers, published in international journals and conference proceedings. Thanks to solid ties with industrial research, he has been awarded four international patents by the US Patent Office, all for algorithms related to information retrieval, voice recognition, and dynamic management of large software systems. His current research interests are in discrete algorithms, statistical methods for data analysis, combinatorics on words, and multidimensional data structures.
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Sridhar Hannenhalli received the BTech degree in computer science from the Institute of Technology at Varanasi, India, and the PhD degree in computer science from the Pennsylvania State University at State College in 1996. He is an assistant profesor of bioinformatics in the Department of Genetics at the University of Pennsylvania's School of Medicine. He additionally holds a secondary appointment in the Department of Computer and Information Sciences. His doctoral work focussed on combinatorial algorithms for genome rearrangement problems and resulted in the first polynomial solution for the problem of sorting by reversals. After his postdoctoral fellowship at the University of Southern California, he spent six years in industry as a computational biologist, first at Glaxo Smith-Kline and then at Celera Genomics. He has been at the University of Pennsylvania School of Medicine since the fall of 2003. His current focus of research is in the area of transcriptional regulation and its evolution. He is a regular reviewer for numerous journals, serves on program committees for several leading bioinformatics conferences, and has organized RECOMB and served as the program chair for WABI. He has also served as a panelist for US National Science Foundation grant review and currently serves as an academic editor for the journal PLoS ONE. He has coauthored more than 50 papers in leading computer science and bioinformatics publications.
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