2005 International Workshop on Bioinformatics Research and Applications

URL: http://www.cs.gsu.edu/pan/iwbra.htm

Emory University Atlanta, USA

May 22-25, 2005

in conjunction with

International Conference on Computational Science 2005

URL: http://www.mathcs.emory.edu/dcl/meetings/iccs2005/

Emory University Atlanta, USA

May 22-25, 2005

Call for Papers

*Instructions for Camera-ready paper submission*

*See list of accepted papers at the end of the page*

Research and development in bioinformatics and computational biology require the cooperation of specialists from the fields of biology, computer science, mathematics, statistics, physics, and such related sciences. It is the comprehensive application of mathematics (e.g., probability and graph theory), statistics, science (e.g., biochemistry), and computer science (e.g., computer algorithms and machine learning) to the understanding of living systems. Bioinformatics is fast emerging as an important discipline for academic research and industrial application. The aim of this workshop is to bring together researchers, developers and practitioners in order to discuss various aspects of bioinformatics and computational biology and their applications.

Authors are invited to submit manuscripts that demonstrate original unpublished research in all areas of bioinformatics research, including the development of experimental or commercial systems. Surveys of important recent results and directions are also welcome.

Topics of Interest Include but Are Not Limited To:

• Bioinformatic databases
• Biomedical image processing (segmentation, registration, fusion)
• Bio-ontology and data mining
• Computational biology
• Data visualization
• DNA assembly, clustering, and mapping
• Gene expression and micro-arrays
• Gene identification and annotation
• Molecular evolution and phylogeny
• Molecular modeling and simulation
• Molecular sequence analysis
• Parallel Bioinformatics Applications
• Protein structure prediction
• Sequence assembly
• Sequence search and alignment

Submission Guidelines:

Email the paper as an attachment (in PS or PDF format) to the workshop's Program Chairs Prof. Yi Pan pan@cs.gsu.edu or Prof. Alex Zelikovsky alexz@cs.gsu.edu. All papers will be reviewed and the accepted papers will be published in Springer's Lecture Notes in Computer Science (LNCS). For ICCS 2005, we are limiting the length of papers to 8 pages in the rather restrictive LNCS format (a 122 mm by 193 mm printed area, single column, 10 point font). The submitted paper must be camera-ready and formatted according to the rules of LNCS (for formatting information see Information for LNCS Authors). Submission implies the willingness of at least one of the authors to register and present the paper. A selection of the best papers for the conference will be published in a special issue of an international journal LNCS Transactions on Computational Systems Biology (http://www.springeronline.com/sgw/cda/frontpage/0,11855,4-164-2-109319-0,00.html).

Important Dates:

• Full papers submission: December 1, 2004
• Notification of acceptance of papers: January 20, 2005
• Camera ready papers: February 10, 2005 (Instructions for Camera-ready paper submission)
• Early registration: March 30, 2005

*Important Notes for Authors of Accepted papers:

REGISTRATION: At least one author of each paper *must* register for the ICCS2005 conference in order for your paper to be published in the proceedings. Please note that author registration deadline is 6pm EST on Friday March 11. We cannot guarantee inclusion of your paper if your registration is not received by the deadline. Registration is now open at: https://dcl.mathcs.emory.edu/iccs2005/registration.html.

PAPER INSTRUCTIONS: The camera ready version of your paper, formatted according to Springer-Verlag requirements, is due by 6pm EST on Monday, February 28. Limits of 8 pages for full papers and 4 pages for poster papers will be *strictly* enforced; unfortunately we are unable to accommodate length extensions. Please follow the formatting guidelines at: http://www.springer.de/comp/lncs/authors.html Submit papers via: http://www.iccs-meeting.org/papers/upload.php using the url already used for the review version. For each paper, please, provide the e-mail address for the responsible author so that we and Springer may contact him as needed.

COPYRIGHT: Papers *must* be accompanied by a signed copyright form, available at the Springer-Verlag website. A partially pre-filled form is available at http://www.mathcs.emory.edu/iccs2005/cr.pdf Completed forms should be faxed to +1 404 727 5611 or mailed to the address at http://www.mathcs.emory.edu/iccs2005/contact.html.

VISA LETTERS: Authors and attendees requiring visa letters should send an email to iccs2005@mathcs.emory.edu with the subject line "Visa letter request". Visa letters will only be issued to: authors/speakers/presenters/attendees who have paid their registration fee in full, and are not from one of the countries embargoed by the U.S. government. Visa letters will only state (1) the conference title, dates and location; (2) whether the requester is an author/speaker/presenter or attendee; (3) that they have paid their registration fees in full.

Registration and Accommodation:

For registration and accommodation information, please refer to ICCS 2005 web page http://www.mathcs.emory.edu/dcl/meetings/iccs2005/ for details.

Workshop Chairs

Dr. Yi Pan Department of Computer Science Georgia State University Atlanta, GA 30302-4110, USA Phone: (404) 651-0649 Fax: (404) 463-9912 Email: pan@cs.gsu.edu http://www.cs.gsu.edu/pan

Dr. Alexander Zelikovsky Department of Computer Science Georgia State University Atlanta, GA 30302-4110, USA Phone: (404) 651-0676 Fax: (815) 642-0052 Email: alexz@cs.gsu.edu http://www.cs.gsu.edu/~cscazz/

Program Committee

Piotr Berman Penn State, USA Paola Bonizzoni Universita degli Studi di Milano-Bicocca, Italy Liming Cai University of Georgia, USA Jake Yue Chen IUPUI, USA Bhaskar Dasgupta University of Illinois at Chicago, USA Juntao Guo University of Georgia, USA Tony Hu Drexel University, USA Bin Ma University of West Ontario, Canada Ion Mandoiu University of Connecticut, USA

Kayvan Najarian University of North Carolina at Charlotte, USA Giri Narasimhan Florida International University, USA Jun Ni University of Iowa, USA Mathew Palakal IUPUI, USA Pavel Pevzner University of California at San Diego, USA Gwenn Volkert Kent State University, USA Kaizhong Zhang University of West Ontario, Canada Wei-Mou Zheng Chinese Academy of Sciences, China

Accepted Papers (in no particular order)

1. Yen Huang Chen, Hsueh-I Lu and Chuan Yi Tang, “Non-overlapping Segments with Maximum Density”.
2. Sergey Bereg and Hao Wang, “Wiener Indices of Balanced Binary Trees”.
3. Guillaume Blin, Guillaume Fertin, Romeo Rizzi and Stephane Vialette, “What makes the ARC-Preserving Subsequence Problem hard?”.
4. Guangming Tan, Xinchun Liu and Ninghui Sun, “An Efficient Dynamic Programming Algorithm and Implementation for RNA Secondary Structure Prediction”.
5. Haifeng Liu and Loo-Nin Teow, “Performance Evaluation of Protein Sequence Clustering Tools”.
6. Rastislav Lukac, Konstantinos N. Plataniotis, Bogdan Smolka and Anastasios N. Venetsanopoulos, “A Data-Adaptive Approach to cDNA Microarray Image Enhancement”.
7. Shibin Qiu, Coenraad M Adema, Wenzhong Zhao and Terran Lane, “Evaluating Off-Target Effects of RNA Interference Using String Kernels of Imperfect Matches”.
8. Zhengdeng Lei and Yang Dai, “A New Kernel based on a Matrix of High-scored Pairs of Tri-peptides and Its Application in Prediction of Protein Subcelluar Location”.
9. Osamu Maruyama, Akiko Matsuda and Satoru Kuhara, “Reconstructing Phylogenetic Trees of Prokaryote Genomes by Randomly Sampling Oligopeptides”.
10. Luay Nakhleh and Li-San Wang, “Phylogenetic Networks, Trees, and Clusters”.
11. Yifeng Li and Hesham H. Ali, “SWAT: A New Spliced Alignment Tool Tailored for Handling More Sequencing Errors”.
12. Beeta Masoumi and Marcel Turcotte, “Simultaneous Alignment and Structure Prediction of RNAs Are Three Input Sequences Better than Two”.
13. Yong Wang, Chengyong Yang, Kalai Mathee and Giri Narasimhan, “Clustering using Adaptive Self-Organizing Maps (ASOM) and Applications”.
14. Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi and Lorenzo Mariani “Experimental Analysis of a New Algorithm for Partial Haplotype Completion”.
15. Bin Ma, Lieyu Wu, and Kaizhong Zhang, “Improving the Sensitivity and Specificity of Protein Homology Search by Incorporating Predicted Secondary Structures”.
16. Chunmei Liu, Yinglei Song, Russell Malmberg and Liming Cai “Profiling and Searching for RNA Pseudoknot structures in Genomes”.
17. Min Song, Il-Yeol Song, Xiaohua Hu and Robert B. Allen, “Integrating Text Chunking with Mixture Hidden Markov Models for Effective Biomedical Information Extraction”.
18. Francis Y.L. Chin, Qiangfeng Zhang and Hong Shen, “k-Recombination Haplotype Inference in Pedigrees”.
19. Ion I. Mandoiu, Claudia Prajescu, and Dragos Trinca “Improved Tag Set Design and Multiplexing Algorithms for Universal Arrays”.
20. Vijaya Smitha Kolli, Hui Liu, Michelle Hong Miao, and Yi Pan, “A Parallel Implementation for Determining Genomic Distances under Deletion and Insertion”.
21. Dima Brinza, Jingwu He, Weidong Mao and Alex Zelikovsky, “Phasing and Missing data recovery in Family Trios”.
22. Wei-Mou Zheng and Xin Liu, “A Protein Structural Alphabet and Its Substitution Matrix CLESUM”.
23. Bhaskar DasGupta, Kishori M. Konwar, Ion I. Mandoiu, and Alex A. Shvartsman, “Highly Scalable Algorithms for Robust String Barcoding”.
24. F Cicalese, P. Damaschke and U.Vaccaro, “Optimal Group Testing Strategies with Interval Queries and Their Application to Splice Site Detection”.
25. Xian Xu and Aidong Zhang, “Virtual Gene: a Gene Selection Algorithm for Sample Classification on Microarray Datasets”.