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Issue No.03 - July-September (2008 vol.5)
pp: 321-322
Published by the IEEE Computer Society
This special section includes a selection of papers presented at the Third International Symposium on Bioinformatics Research and Application (ISBRA 2007), which took place at Georgia State University, Atlanta, 7-10 May 2007. The ISBRA symposium provides a forum for the exchange of ideas and results among researchers, developers, and practitioners working on all aspects of bioinformatics and computational biology and their applications. ISBRA is the successor of the International Workshop on Bioinformatics Research and Applications, held on 22-25 May 2005 in Atlanta, Georgia, and on 28-31 May 2006 in Reading, United Kingdom, in conjunction with the International Conference on Computational Science.
In 2007, 146 papers were submitted in response to the call for papers, out of which 55 papers appeared in the ISBRA proceedings published as volume 4463 of Springer Verlag's Lecture Notes in Bioinformatics series. A small number of authors were invited to submit extended versions of their symposium papers to this special section. Following a rigorous review process, five papers were selected for publication.
The first paper, which has won the Best Paper Award, is by Srinath Sridhar, Fumai Lam, Guy E. Blelloch, R. Ravi, and Russell Schwartz. The authors consider the problem of reconstructing the most parsimonious intraspecies phylogenetic tree from biallelic variation data, which can be viewed as a Steiner tree problem in a $n{\hbox{-}}{\rm{dimensional}}$ cube, where $m$ is the number of characters. They reformulate this Steiner tree problem as a multicommodity flow-based integer linear program. Despite its exponential size, this integer linear program is solved very efficiently. Indeed, the runtime reported for solving large instances consisting of human mtDNA and Y-chromosome variation data is competitive with fast heuristics that do not guarantee optimality. They also propose an alternative integer linear program formulation of polynomial size, and present a web server implementing their methods.
The next two papers of the special section address problems related to genome rearrangements, a key approach in comparative genomics.
The paper by Matthias Bernt, Daniel Merkle, and Martin Middendorf addresses a variant of the well-known reversal median problem, which asks for the ancestral gene order that minimizes the total number of reversals needed to obtain the gene orders of all given taxa. It is known that certain gene groups are preserved during evolution. Biologically relevant rearrangement scenarios should therefore preferentially maintain such conserved groups. In the variant of the reversal median problem considered by the authors, it is required to preserve each interval of genes that is common to the gene orders of all given taxa. The authors propose an exact algorithm based on a tree-based data structure for representing common intervals. Although even computing the preserving minimum reversal distance is NP-hard, the proposed algorithm is shown to solve a large class of instances in polynomial time. Furthermore, the algorithm is shown to perform well on biological and simulated data sets.
Typically, there are multiple optimal solutions for sorting permutations by reversals. However, most existing algorithms only return a single such solution. The paper by Marília Braga, Marie-France Sagot, Celine Scornavacca, and Eric Tannier proposes methods for partitioning the solution space into equivalence classes, counting the number of solutions in each class, and identifying a representative solution from each class without exhaustive enumeration. The proposed methods are applied to analyze the possible scenarios of rearrangements between mammalian sex chromosomes.
The fourth paper of the special section, authored by Marco Vassura, Luciano Margara, Pietro Di Lena, Filippo Medri, Piero Fariselli, and R. Casadio, is devoted to the problem of reconstructing three-dimensional protein structures from residue contact maps. This is equivalent to the so-called unit-disk-graph realization problem, which is known to be NP-hard. However, the authors propose an efficient heuristic by using existing distance-geometry methods in an iterative refinement framework. Experimental results on simulated contact maps derived from known protein structures show that the heuristic is very fast and yields high-accuracy reconstructions.
The final paper, authored by George Lee, Carlos Rodriguez, and Anant Madabhushi, explores methods for dimensionality reduction, which is a critical step in many analyses of high-dimensionality biological data sets such as classification of gene- and protein-expression profiles. The authors systematically compare the classification accuracy of two commonly used supervised classifiers (Support Vector Machines and C4.5 Decision Trees) when combined with three nonlinear (Isomap, Locally Linear Embedding, and Laplacian Eigenmaps) and three linear dimensionality reduction schemes (PCA, Linear Discriminant Analysis, Multidimensional Scaling). The authors find a statistically significant improvement of nonlinear schemes over the linear ones on a diversity of both binary and nonbinary cancer classification problems, as well as superior performance of nonlinear schemes in the identification of putative novel cancer subtypes.
We would like to thank the Program Committee members and external reviewers for volunteering their time to review the submissions to the symposium and the special section. We would also like to thank the Editor-in-Chief, Professor Dan Gusfield, for continuing to provide us with the opportunity to showcase some of the exciting research presented at ISBRA in the IEEE/ACM Transactions on Computational Biology and Bioinformatics. Last, but not least, we would like to thank all authors—the symposium could not continue to thrive without their high-quality contributions.
Ion I. Mandoiu Yi Pan Alexander Zelikovsky Guest Editors

    I.I. Mandoiu is with the Computer Science and Engineering Department, University of Connecticut, 371 Fairfield Way, Unit 2155, Storrs, CT 06269-2155. E-mail: ion@engr.uconn.edu.

    Y. Pan and A. Zelikovsky are with the Department of Computer Science, Georgia State University, 34 Peachtree Street, Atlanta, GA 30302-4110. E-mail: {pan, alexz}@cs.gsu.edu.

For information on obtaining reprints of this article, please send e-mail to: tcbb@computer.org.



Ion I. Mandoiu received the MS degree from Bucharest University in 1992 and the PhD degree from the Georgia Institute of Technology in 2000, both in computer science. Between 2000 and 2003, he was a post-doctoral researcher and then research scientist at the University of California at Los Angeles and at San Diego. Since 2003, he has been with the Computer Science and Engineering Department at the University of Connecticut, Storrs, where he is currently an associate professor. His main research interests are in the design and analysis of approximation algorithms for NP-hard optimization problems, particularly in the areas of bioinformatics, design automation, and ad hoc wireless networks, areas in which he has authored more than 60 refereed journal and conference proceeding papers. He has also coedited (with A. Zelikovsky) the book Bioinformatics Algorithms: Techniques and Applications published in the Wiley Book Series on Bioinformatics. Dr. Mandoiu is a member of the Association for Computing Machinery and of the International Society for Computational Biology. He has served as general and program committee chair for numerous international workshops and conferences, including the International Symposium on Bioinformatics Research and Applications (ISBRA) and the System Level Interconnect Prediction Workshop (SLIP). He also serves on the editorial board of the International Journal of Bioinformatics Research and Applications, and is a guest editor for the IEEE/ACM Transactions on Computational Biology and Bioinformatics, the IEEE Transactions on Nanobiosciences, the International Journal of Wireless and Mobile Computing, and the Journal of Universal Computer Science. Dr. Mandoiu received the best paper award at the joint Asia-South Pacific Design Automation/VLSI Design Conferences in 2003, and the best poster award at the Annual BACUS Symposium on Photomask Technology in 2005. He is a 2006 recipient of the US National Science Foundation Faculty Early Career Development Award.



Yi Pan received the BEng and MEng degrees in computer engineering from Tsinghua University, China, in 1982 and 1984, respectively, and the PhD degree in computer science from the University of Pittsburgh, Pennsylvania, in 1991. He is the chair and a professor in the Department of Computer Science and a professor in the Department of Computer Information Systems at Georgia State University. Dr. Pan's research interests include parallel and distributed computing, networks, and bioinformatics. Dr. Pan has published more than 100 journal papers with 37 papers published in various IEEE journals. In addition, he has published more than 100 papers in refereed conferences. He has also authored/edited 34 books (including proceedings) and contributed many book chapters. Dr. Pan has served as an editor-in-chief or editorial board member for 15 journals including five IEEE Transactions, and a guest editor for 10 journals including, the IEEE/ACM Transactions on Computational Biology and Bioinformatics and the IEEE Transactions on NanoBioscience. He has organized several international conferences and workshops and has also served as a program committee member for several major international conferences such as INFOCOM, GLOBECOM, ICC, IPDPS, and ICPP. Dr. Pan has delivered more than 10 keynote speeches at many international conferences and is a speaker for several distinguished speaker series. He is listed in Men of Achievement, Who's Who in Midwest, Who's Who in America, Who's Who in American Education, Who's Who in Computational Science and Engineering, and Who's Who of Asian Americans.



Alexander Zelikovsky received the PhD degree in computer science from the Institute of Mathematics of the Belorussian Academy of Sciences in Minsk, Belarus, in 1989 and worked at the Institute of Mathematics in Kishinev, Moldova from 1989-1995. Between 1992 and 1995, he visited Bonn University and the Institut fur Informatik in Saarbrueken, Germany. Dr. Zelikovsky was a research scientist at the University of Virginia from 1995-1997 and a postdoctoral scholar at the University of California, Los Angeles, from 1997-1998. He is an associate professor in the Computer Science Department at Georgia State University, which he joined in 1999. Dr. Zelikovsky's research interests include bioinformatics, discrete and approximation algorithms, combinatorial optimization, VLSI physical layout design, and ad hoc wireless networks. He is the author of more than 150 refereed publications and coeditor (with I. Mandoiu) of the book Bioinformatics Algorithms: Techniques and Applications published in the Wiley Book Series on Bioinformatics. Dr. Zelikovsky is the founding cochair of the ACIS International Workshop on Self-Assembling Wireless Networks (SAWN) and the International Workshop on Bioinformatics Research and Applications (IWBRA). He is program committee cochair of the 2007 and 2008 International Symposium on Bioinformatics Research and Applications (ISBRA). He also serves on the editorial boards of the International Journal of Bioinformatics Research and Applications and Advances in Bioinformatics, and is a guest editor for the LNCS Transactions on Computational Systems Biology, the IEEE/ACM Transactions on Computational Biology and Bioinformatics, the IEEE Transactions on Nanobiosciences, and the Journal of Universal Computer Science. Dr. Zelikovsky received the SIAM Outstanding Paper Prize in 2007, the best paper award at the joint Asia-South Pacific Design Automation/VLSI Design Conferences in 2003, and the best poster awards at the Annual BACUS Symposium on Photomask Technology in 2005 and the Fifth Georgia Tech International Conference on Bioinformatics in 2005.
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