Bioinformatics Research and Applications

1. Front Matter

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2. Evolution of Regulatory Systems in Bacteria (Invited Keynote Talk)

   • Mikhail S. Gelfand, Alexei E. Kazakov, Yuri D. Korostelev, Olga N. Laikova, Andrei A. Mironov, Alexandra B. Rakhmaninova et al.

   Pages 1-4

3. Integrating Multiple-Platform Expression Data through Gene Set Features

   • Matěj Holec, Filip Železný, Jiří Kléma, Jakub Tolar

   Pages 5-17

4. Practical Quality Assessment of Microarray Data by Simulation of Differential Gene Expression

   • Brian E. Howard, Beate Sick, Steffen Heber

   Pages 18-27

5. Mean Square Residue Biclustering with Missing Data and Row Inversions

   • Stefan Gremalschi, Gulsah Altun, Irina Astrovskaya, Alexander Zelikovsky

   Pages 28-39

6. Using Gene Expression Modeling to Determine Biological Relevance of Putative Regulatory Networks

   • Peter Larsen, Yang Dai

   Pages 40-51

7. Querying Protein-Protein Interaction Networks

   • Guillaume Blin, Florian Sikora, Stéphane Vialette

   Pages 52-62

8. Integrative Approach for Combining TNFα-NFκB Mathematical Model to a Protein Interaction Connectivity Map

   • Mahesh Visvanathan, Bernhard Pfeifer, Christian Baumgartner, Bernhard Tilg, Gerald Henry Lushington

   Pages 63-74

9. Hierarchical Organization of Functional Modules in Weighted Protein Interaction Networks Using Clustering Coefficient

   • Min Li, Jianxin Wang, Jianer Chen, Yi Pan

   Pages 75-86

10. Bioinformatics Challenges in Translational Research

    • Nicholas F. Tsinoremas

    Pages 87-87

11. Untangling Tanglegrams: Comparing Trees by Their Drawings

    • Balaji Venkatachalam, Jim Apple, Katherine St. John, Dan Gusfield

    Pages 88-99

12. An Experimental Analysis of Consensus Tree Algorithms for Large-Scale Tree Collections

    • Seung-Jin Sul, Tiffani L. Williams

    Pages 100-111

13. Counting Faces in Split Networks

    • Lichen Bao, Sergey Bereg

    Pages 112-123

14. Relationship between Amino Acids Sequences and Protein Structures: Folding Patterns and Sequence Patterns

    • Alexander Kister

    Pages 124-134

15. Improved Algorithms for Parsing ESLTAGs: A Grammatical Model Suitable for RNA Pseudoknots

    • Sanguthevar Rajasekaran, Sahar Al Seesi, Reda Ammar

    Pages 135-147

16. Efficient Algorithms for Self Assembling Triangular and Other Nano Structures

    • Vamsi Kundeti, Sanguthevar Rajasekaran

    Pages 148-158

17. Motif Construction from High–Throughput SELEX Data

    • Esko Ukkonen

    Pages 159-159

18. Rearrangement Phylogeny of Genomes in Contig Form

    • Adriana Muñoz, David Sankoff

    Pages 160-172

19. Prediction of Contiguous Regions in the Amniote Ancestral Genome

    • Aïda Ouangraoua, Frédéric Boyer, Andrew McPherson, Éric Tannier, Cedric Chauve

    Pages 173-185

20. Pure Parsimony Xor Haplotyping

    • Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola, Romeo Rizzi

    Pages 186-197

This book constitutes the refereed proceedings of the 5th International Symposium on Bioinformatics Research and Applications, ISBRA 2009, held in Fort Lauderdale, FL, USA, in May 2009. The 26 revised full papers presented together four invited papers were carefully reviewed and selected from a total of 55 submissions. The papers cover a wide range of topics, including clustering and classification, gene expression analysis, gene networks, genome analysis, motif finding, pathways, protein structure prediction, protein domain interactions, phylogenetics, and software tools.

• Clustering
• DOM
• amino acids sequences
• bioinformatics
• classification
• computational biology
• computational life science
• data mining
• dna
• feature selection
• genome
• microrna
• nano structures
• pattern matching
• protein analysis

• Computer Science & Engineering Department, University of Connecticut, Storrs, USA

  Ion Măndoiu

• Bioinformatics Research Group (BioRG), School of Computing and Information Sciences, Florida International University, Miami, USA

  Giri Narasimhan

• Department of Computer Science, Georgia State University, Atlanta, USA

  Yanqing Zhang

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