RECOMB 2005 - Cambridge, MA - May 14-18, 2005
   

RECOMB 2005 Posters

RECOMB Insight Awards recognizing insight and innovation in computational biology.

Profiling Condition-Specific Regulation of mRNA Stability in Yeast Barrett C. Foat, S. Sean Houshmandi, Wendy M. Olivas, and Harmen J. Bussemaker, Columbia University

FINE SCALE ANALYSIS OF HAPLOTYPE STRUCTURE IN THE DOMESTIC DOG POPULATION Elinor K. Karlsson Claire M. Wade1,, E.J. Kulbokas1, Tara Biagi, Mark J. Daly, Michael C. Zody, Eric S. Lander, Kerstin Lindblad-Toh and the Dog Genome Sequencing Consortium, Boston University and Broad Institute

RECOMB & PDB Poster Awards recognizing insight and innovation in structural computational biology.

Comparative Modeling of Mainly- Proteins Profile Wrapping Andrew V. McDonnell, Matthew Menke, Nathan Palmer, King, Lenore Cowen, Bonnie Berger, MIT

MAPPIS: Multiple Alignment of Protein-Protein Interfaces Alexandra Shulman-Peleg, Maxim Shatsky, Ruth Nussinov and Haim J. Wolfson, Tel-Aviv University

Judges:

  • Bonnie Berger (MIT)
  • Peter Clote (BC)
  • Enoch Huang (Pfizer Discovery)
  • Simon Kasif (Boston University)
  • Jun Liu (Harvard)
  • T.M. Murali (VPI)
  • Fritz Roth (Harvard Medical School)
  • Russell Schwartz (CMU)
  • Lei Shen (Harvard)
  • Mona Singh (Princeton)


Topics
All (200)

 alternative splicing (2)

 Bayesian Networks (3)

 clustering (3)

 combinatorial optimization (1)

 comparative genomics (8)

 database construction (4)

 database searching (1)

 determining or using metabolic pathways and networks (3)

 determining or using regulatory pathways and networks (3)

 DNA sequencing (1)

 drug design (1)

 experiment design (1)

 gene expression analysis (13)

 gene networks (7)

 gene prediction (3)

 genome alignment/comparisons (1)

 genome annotation (3)

 genome evolution (3)

 genome rearrangements (2)

 haplotype modeling, finding, analysis (5)

 haplotype use (2)

 machine learning (7)

 mass-spec technologies (4)

 microarray design and/or data analysis (10)

 models of evolution (6)

 molecular evolution (2)

 molecular modeling and/or docking (3)

 multiple sequence alignment (3)

 new technologies (1)

 Other (7)

 pairwise sequence alignment (2)

 pattern and motif discovery (3)

 phylogenetic analysis (3)

 phylogenetics: algorithms (2)

 protein function prediction (17)

 protein interaction (8)

 protein structure comparison (10)

 protein structure prediction (9)

 quantitative or population genetics (3)

 regulatory region prediction (5)

 RNA structure comparison (2)

 RNA structure prediction (3)

 sequence assembly (4)

 SNP discovery or use (5)

 splice site recognition (2)

 statistics of motifs or strings (2)

 string algorithms (1)

 systems biology (6)
  1. Abyzov Alexej (Northeastern university) Statistical characteristics of the Delaunay Tessellation of protein structure

  2. adiwijaya, bambang (MIT) Understanding the design principles of biological networks using optimization

  3. Agarwal, Pratul (Oak Ridge National Laboratory) Multi-scale Modeling of Enzyme Catalysis, Biomolecular Recognition and Protein Folding

  4. Agrawal, Ritesh (Washington University) In Silico Characterization of Novel Alternative Splice Products

  5. Aksianov Evgeniy (Belozersky Institute, Moscow State University) Interlock structural motif is typical for beta sandwich domains

  6. Alekseyenko, Alexander (UCLA, Los Angeles, CA 90095) A stochastic model for creation and loss of genomic sequence blocks

  7. Alterovitz, Gil (Massachusetts Institute of Technology) The Human Massome of Protein Interactions: A New Mass Spectrometry-Based Perspective

  8. Alterovitz, Gil (MIT) Protein Network Topology Metric Conservation: From Yeast to Human

  9. Altschuler, Josiah (Harvard University) A gene set repository for model organisms

  10. Anton, Brian (Boston University) Phylogenetic Detection of Conserved Gene Clusters in Microbial Genomes

  11. Arai, Masafumi (Hirosaki University) Domain Architecture of Transmembrane Proteins: Focusing on Single-Spanning Proteins First

  12. Asai, Kiyoshi (University of Tokyo) Comparing RNA sequences based on the alignment of stem candidates

  13. Ashwin Sivakumar (Bioinformatics group, Institute of Biotechnology, University of Helsinki) Approaches to determine biological ?function?- Dissecting the diverse Crotonase Superfamily

  14. Awadalla, Saria (Rochester Institute of Technology) Prediction of trans-Splicing Sites Using a Genetic Algorithm

  15. Barenboim Maxim (George Mason University) Neuro-Fuzzy Approach to Classification of Human Non-Synonymous SNPs Based upon Statistical Geometry

  16. Beerenwinkel, Niko (Department of Mathematics, University of California at Berkeley) Algebraic Invariants of Mutagenetic Trees

  17. Bell, George (Whitehead Institute for Biomedical Research) Design of Oligonucleotide Microarrays for Vertebrate Chromatin Immunoprecipitation: From Promoters to Whole Genomes

  18. Benovoy, David (University of Ottawa) Processed pseudogenes,processed genes and spontaneous mutations in the Arabidopsis genome

  19. Berger-Wolf, Tanya (DIMACS) Combinatorial Reconstruction of Sibling Groups

  20. Bhanot, Gyan (Institute for Advanced Study) Robust meta-analysis of genomic data for cancer diagnosis

  21. Birkland, Aaron (Cornell University) BIOZON: a system for unification, management and analysis of heterogeneous biological data

  22. Bogdan Pasaniuc (University of Connecticut) Hoplotype Inference by Entropy Minimization

  23. Bradt, Dirck (The Jackson Laboratory) From Genotype to Phenotype in the Mouse Genome Informatics (MGI) Database: Integrating Quantitative Trait Loci with the Annotated Mouse Genome

  24. Brejova, Brona (University of Waterloo) ExonHunter: A Comprehensive Approach to Gene Finding

  25. Brinza, Dumitru (Georgia State University) Family Trios Phasing and Missing data recovery

  26. Brockman, J. Michael (The Jackson Laboratory) PACdb: PolyA Cleavage Site and 3'-UTR Database

  27. Bujnicki, Janusz, M. (Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, POLAND) Protein structure prediction by combination of fold-recognition with de novo folding

  28. Butler, Jonathan (The Broad Institute at MIT and Harvard) ALLPATHS: A New Genome Assembly Algorithm that Preserves Intrinsic Ambiguity

  29. Cafrey Daniel (Pfizer) Protein Fami ly Alignment Annotation T ool

  30. Cai, Hong (University of Texas at San Antonio) Analysis of Transcriptomic Profiles of Malaria Parasite using Wavelet Decomposition

  31. Caspi, Anat (University of California, Berkeley) Homology mapping with Markov random fields

  32. Chang, Li-Wei (Washington University ) Predicting Transcription Regulatory Mechanisms by Systematic Promoter Analysis

  33. Chang, Yi-Feng (Institute of Bioinformatics, NYMU, Taiwan) Identification and Characterization of Conserved Overlapping Genes in Vibrio Genomes

  34. Chanyong Park (Electronics and Telecommunications Research Institute) A Protein Structure Retrieval System Using 3D LRA

  35. Chiu, Hua-Sheng (Department of Computer Science and Information Engineering, National Taiwan University, Taiwan) Biclustering Gene Expression Data by Using Iterative Genetic Algorithm

  36. Chua, Cyril (Singapore Polytechnic) Study of pseudogenes and splice sites in the annotated C. elegans genome

  37. Clarke IV, Thomas (University of Notre Dame) Influence of translation rate on co-translational folding intermediates

  38. Dalgin, Gul S. (Boston University) Simple discriminant functions identify numerous small sets of genes that stratify breast cancer grades and stages

  39. Davies, Christopher (Affymetrix ) Leveraging Complete Genome Sequences in the Design of a Compact Multi-organism E. coli mRNA Expression MicroArray

  40. de Carvalho Jr., Sergio A. (University Bielefeld) Analyzing the Layout of Affymetrix Microarrays

  41. Deng, Chaoyang (Broad Institute of MIT and Harvard) A Functional Model of LRPPRC in LSFC

  42. Devay, Piroska (Novartis) Function prediction by automatized protein annotation

  43. Dhamdhere, Kedar (Carnegie Mellon University) Faster Reconstruction of Binary Near-Perfect Phylogenies

  44. Diskin, Sharon (University of Pennsylvania) Statistical Analysis of Array CGH (STAC): A Novel Approach to Analyzing Multiple Experiments

  45. Donald, Jason (Harvard University) Predicting Specificity-determing Residues for Eukaryotic Transcription Factors

  46. Drabikowski Micha? (Institute of Informatics) Local Descriptors' Library Models the Core of Protein Structures Accurately

  47. Elinor (B. U. Bioinformatics & Broad Institute) Fine Scale Analysis of Haplotype Structure in the Domestic Dog Population

  48. Eriksson, Nicholas (UC Berkeley) Tree construction using singular value decomposition

  49. Ferre Fabrizio (Boston College) Diresidue neural network for the prediction of disulfide connectivity and ligand-bound cysteines

  50. Flikka, Kristian (University of Bergen) Improving throughput and reliability of peptide identifications through spectrum quality evaluation

  51. Foat, Barrett (Columbia University, Department of Biological Sciences) Profiling Condition-Specific Regulation of mRNA Stability in Yeast

  52. Friedberg, Richard (Institute for Medical Research at NS-LIJ) Calibrating Genomic Distance via Universal Operation

  53. Friedman, Brad (MIT Department of Biology) Exonic splicing motif discovery using positional bias

  54. Gabriele Scheler (Stanford University) Dynamic Regulation of Receptor/G-protein coupling

  55. Gauthier, Olivier (Universit? de Montr?al) Consensus, Networks, and Information Content

  56. Gibbons, Francis (Harvard Medical School) Chipper: discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization.

  57. Gnerre, Sante (Broad Institute at MIT and Harvard) Syntey-Assisted Assembly of Genomes at Low Coverage

  58. Goldberg, Debra (Harvard Medical School) Breaking the Power Law: Improved Model Selection Reveals Increased Network Complexity

  59. Gorecki Pawel (Institute of Informatics, Warsaw University) Mathematically and biologically sound model for HGT-reconciliations

  60. Gorecki,A. (Warsaw University, Warsaw, Poland) Identification and Free Energy Simulations of Correlated Mutations in Proteins

  61. Grabherr, Manfred (Broad Institute at MIT and Harvard) Repeat Analysis to Improve Whole Genome Assembly

  62. Hak Yong (Chungbuk National University) Structural and Functional Characterization of Human Protein-Protein Interaction Network

  63. Hak Yong (Chungbuk National University) Functional Modules from Protein-Protein Interaction Network of Metabolite-Related Proteins in Saccharomyces cerevisiae

  64. Halasz, Gabor (Columbia University, Department of Biological Sciences) Detecting transcription levels above background using genomic tiling arrays

  65. Hautaniemi, Sampsa (Massachusetts Institute of Technology) High-throughput Phosphotyrosine Proteomics Analysis in EGFR Pathway using Self-Organizing Maps

  66. Hautaniemi, Sampsa (Massachusetts Institute of Technology) Modeling of Signal-Response Cascades using Decision Tree Analysis

  67. He, Jingwu (Georgia State University) Linearly Independent Tagging of Genotypes

  68. Heber, Steffen (NC State University) Evolutionary Conservation and Selection of Alternatively Spliced Human Genes

  69. Heitsch, Christine (University of Wisconsin -- Madison) Analyzing the Branching Degree of RNA Viral Genomes: A Hepatitis C Case Study

  70. Hernandez-Rosales Maribel (Centre for Genomic Sciences) No evidence for relation between Co-regulation and Regulatory Interactions in the evolution of Regulatory networks

  71. Hoffmann, Martin (Institute of Immunology, University of Rostock, Rostock, Germany) Robust computational reconstitution - a new method for the comparative analysis of mRNA expression in tissues and isolated cell fractions

  72. Hu, Hae-Jin (Georgia State University) Transmembrane Segments Prediction based on Support Vector Machine with Position Specific Scoring Matrix

  73. Huang, Hailiang (Johns Hopkins University ) Probabilistic paths in protein interaction networks

  74. Huang, Hailiang (Johns Hopkins University ) Intrinsic Bayesian estimates of the eukaryotic protein interaction network complexity

  75. Hundewale Nisar (Georgia State University) Integrated Design Flow for Universal DNA Tag Arrays

  76. Husmeier, Dirk (Biomathematics & Statistics Scotland) Phylogenetic Factorial Hidden Markov Models

  77. Huson, Daniel H. (University of T?bingen) SplitsTree 4.0 - Computation of phylogenetic trees and networks

  78. Jack Y. Yang (Indiana University School of Medicine) Length-Dependent Amino Acid Compositions of Secondary Structure Segments and Disordered Regions

  79. Jagalur, Manjunatha (University of Massachusetts Amherst) Regulatory Network Dependencies From Quantitative Trait Loci

  80. Jang, Hyunchul (Electronics and Telecommunications Research Institute) A Corpus Tagging Tool for Extraction of Biological Relation Events

  81. Jang, Hyunchul (Electronics and Telecommunications Research Institute) Reducing Parsing Error of an Existing Parser for Extracting Biological Relation Events

  82. Joe Mellor (Boston University) Transcription Factor Binding Site Organization Influences Regulatory Logic in Yeast

  83. Jothi, Raja (NCBI/NLM/NIH) An Evolution-Based Clustering Method to Separate Orthologous Genes from Out-Paralogs

  84. JUNG JAEYOUNG (etri) A Function Prediction of Un-annotated Proteins Based on Interaction Generality

  85. Jung, Ho-Youl (ETRI) A New Clustering Method Starting From Seed Genes in Expression Profile Analysis

  86. Khrebtukova, Irina (Lynx Therapeutics, Inc.) Transcriptome Analysis Tools: Visualization and Management of Ultra-High Volume of DNA Sequence Data

  87. Kilel, Beatrice (George Mason University) Motif discovery in conserved regions of chloroplast genomes

  88. Kim, Changhoon (NCI/NIH) Improved probability calculation for DIALIGN2.

  89. Kim, Jong Hyun (University of Southern California) A Gibbs Sampling Approach to Diploid Genome Reconstruction

  90. Kim, Pan-Gyu (Dept. of Computer Science, Pusan National University, South Korea) An Integrated System for Microbial Genome Annotation and Comparative Genomic Analysis

  91. Kirschbaum-Slager, Natanja (Ludwig Institute for Cancer Research, Sao Paulo Branch) The use of expression data to study the association between alternative splicing and cancer

  92. Klee, Eric (University of Minnesota) AMOD: A morpholino oligonucleotide selection tool

  93. kreiman, gabriel (MIT) Transcription factor binding: does order matter?

  94. Kryukov, Kirill (National Institute of Genetics, Mishima, Japan) MISHIMA: a Method for Identifying Sequence History In terms of Multiple Alignment

  95. Ku, Chin-Jen (Cornell University) The Canonical Representation of Proteins: Application to Remote Homology Recognition

  96. Ku, Chin-Jen (Cornell University) Domain-based Protein Hierarchy and Detection of Semantically Significant Domain Architectures

  97. Kuska, Jacek (ICM UW) Variability Patterns in Kinase Subfamilies

  98. LaFramboise, Thomas (Dana-Farber Cancer Institute) Model-Based Genotyping and Allele-Specific Copy Number Analysis Using SNP Arrays

  99. Laramie, Jason (Boston University) HaploBuild: A Program for Constructing Haplotypes from High Density SNP Genotype Data

  100. Leach, Sonia (Brown University and Univ of CO) Investigating semantic similarity measures across the GeneOntology: the relationship between interaction and annotation

  101. Lee, Hyun-Sook (Bioinformatics Research Team, Electronics and Telecommunication Research Institute) Named Entity Recognition in Various Biomedical Domain

  102. Lehar, Joseph (CombinatoRx, Inc.) Probing Biological Networks with Chemical Combinations

  103. Leslin, Chesley (Northeastern University) TOPOFIT-DB and T-Server: A Database of structural alignments and a server for one-to-all protein structure comparisons based on the TOPOFIT method

  104. Lieberman, Erez (Harvard/MIT) Evolutionary Dynamics on Graphs

  105. Lieberman, Erez (Harvard/MIT) Regulatory motif movement in promoter regions

  106. Lilburn, Timothy (American Type Culture Collection) Pathway Complements of Four Yersinia Strains

  107. Lim, Jaesoo (Electronics and Telecommunications Research Institute (ETRI)) Named Entity Recognition using Maximum Entropy Models on Biologists' Literature

  108. Lin, Michael (MIT) A Classification Approach to Comparative Gene Finding in Mammals

  109. Lippert, Ross (Dept of Mathematics, MIT) Space-efficient whole genome comparisons with Burrows-Wheeler transforms

  110. Lipshtat, Azi (Hebrew University) Bistability in Stochastic Mutual-Repression Circuits

  111. Livingston, Gary (University of Massachusetts Lowell) Finding Bayesian Difference Networks

  112. Lloyd, Peter (University of Minnesota) A Geometric Filter for Unbound Protein-Protein Docking

  113. Loganantharaj, Raja (University of Louisiana) Extension of Likelihood Ratio with Naive Bayes with Memory

  114. Lu, Long (Yale University) The Limit of Genomic Data Integration for Predicting Protein-Protein Interactions: An Assessment using Na?ve Bayes Classifier

  115. Mao, Weidong (Georgia State University) Prediction Methods for Inherited Disease

  116. Mary Qu Yang (Purdue University) Enhancing Joint Protein Structural Prediction by Ensemble Methods

  117. Mary Qu Yang (Purdue University) Extracting Features from Protein Primary Structure with Feature Selection to Enhance Protein Structural and Functional Prediction

  118. Masao Nagasaki (Human Genome Center, Institute of Medical Science, University of Tokyo) Genomic Object Net 1.6: A Platform for Biopathway Modeling and Simulation

  119. Masso, Majid (George Mason University) Automated Functional Inference of Enzyme Mutants Utilizing a Four-Body Statistical Potential

  120. Matukumalli, Lakshmi K (Bovine Functional Genomics Laboratory, USDA) Optimizing Bovine SNP discovery efforts

  121. McDonnell, Andrew (Massachusetts Institute of Technology) Comparative Modeling of Mainly-Beta Proteins by Profile Wrapping

  122. Minichiello, Mark (Wellcome Trust Sanger Institute) A heuristic algorithm for inferring possible ancestral recombination graphs from haplotype data

  123. Mizuta, Satoshi (Hirosaki University) Seeking Genome Rearrangements in Prokaryotic Genomes via Tandem Repeats

  124. Mounir Errami (Norhteastern University - Boston (MA)) Protein ? DNA interface: Structural Analysis of Contact Patches and Triplets by Specific Contact Mapping

  125. Mukherjee, Sach (University of Oxford) Data-adaptive test statistics for microarray data

  126. Myungguen, Chung (Electronics and Telecommunication Research Institute) Customized Biological Database Integration System for cDNA microarray

  127. Ndifon, Wilfred (Morgan State University) A new model for the kinetic folding of RNA

  128. Nowakowski, Szymon (Institute of Informatics, Warsaw University, Warszawa, Poland) Detecting Correct Structure of Protein Fragments in a Database of Motifs

  129. Park, Sung Hee (Electronics and Telecommunication Research Institute) Automatic Protein Structure Clustering Using Sequence of Secondary Structure Elements

  130. Park, Yonil (NCBI/NLM/NIH) Estimation of the Gumbel Scale Parameter for Local Alignment Score Distribution

  131. Park, Yuhyun (Harvard University/ Dana Farber Cancer Institute) A new method for biomarker detection: Quantitative assessment for contrasts between groups of subjects based on Mass Spec data

  132. Patrick Beaulieu (Ste-Justine Hospital, Montreal) THOR: a database for the management and analysis of regulatory regions functional assays

  133. Perdikuri Katerina (Research Academic Computer Technology Institute) Accelarating Sequence Alignments with the use of Suffix Trees

  134. Pertea, Mihaela (The Institute for Genomic Research) Sub-optimal predictions increase sensitivity of gene finders

  135. Peters, Bjoern (La Jolla Institute for Allergy and Immunology) A Framework for Automating the Generation and Evaluation of Tools Predicting Peptide Binding to MHC class I Molecules

  136. Phan, Vinhthuy (The University of Memphis) Formalizing a New Model-based Method of Classifying Gene Expressions

  137. Pinney, John (University of Leeds, UK) Decomposition of Biological Networks using Betweenness Centrality

  138. Popescu, Liviu (Cornell University) An EM algorithm for unambiguous assignment of genes to biochemical pathways

  139. Posy, Shoshana (Columbia University) Evolution and Structural Signature of the Cadherin Domain

  140. Presser, Aviva (Harvard University) How Do Genetic Networks Grow? Tracing the evolution of Saccharomyces cerevisiae using gene duplication events

  141. Purohit, Parul (University of California) Multivariate Analysis of Glycomic Mass Spectrometry Data

  142. Pyne, Saumyadipta (Stony Brook University, Stony Brook, NY 11794. USA.) Meta-analysis based on control of False Discovery Rate

  143. Qi, Yan (Johns Hopkins University) Genetic Interaction Motif Finding by Expectation Maximization ? a novel statistical framework for inferring gene modules from synthetic lethality

  144. Qiu, Jian (Cornell University) An alignment algorithm using structure-dependent substitution matrices and gap penalties learned from structurally aligned protein pairs

  145. Quo, Chang (Georgia Institute of Technology) Development of Information Management System for Bioinformatics Laboratory

  146. Rachlin, John (Boston University) The Limits of Multiplex PCR

  147. Raphael, Benjamin (University of California, San Diego) Unravelling the Architecture of Duplications in Tumor Genomes

  148. Rasmussen, Matthew (Massachusetts Institute of Technology) MultiBUS: An algorithm for resolving multi-species gene correspondence and gene family relationships

  149. RAUSCH, Christian (Center for Bioinformatics T?bingen (ZBIT), University of T?bingen, Germany) Classification of DNA methyltransferases with Profile Hidden Markov Models

  150. Rechtsteiner, Andreas (Portland State University & Los Alamos National Lab) Clustering of Protein Families in Literature Space

  151. Renaud, Gabriel (University of Waterloo) Ab initio secondary structure prediction using inter-residue contacts

  152. Richter, Daniel (Broad Institute) Automated Algorithms for Variation Detection in Diploid Resequencing Data

  153. Rodrigues, Thiago (Federal University of Minas Gerais, Brazil) Protein Classification with Extended Sequence Coding by Sliding Window

  154. Rother, Diego (University of Minnesota) Statistical Characterization of Protein Ensembles

  155. Ruan, Jianhua (Washington University in St Louis) A Two-dimensional Regression Tree Approach to the Modeling of Gene Expression Regulations

  156. Schatz, Michael (The Institute for Genomic Research) Improving Genome Assembly Without Sequencing

  157. Sebastian, Sethu (University of Massachussetts, Lowell) Using Machine Learning To Improve Gene Finding

  158. Shafer Paul (Cornell University) Hubs of Knowledge: using the functional link structure in Biozon to mine for biologically significant entities

  159. Shah, Ruchir (University of North Carolina at Chapel Hill) Structure Based Identification of Protein Family Signatures for Function Annotation

  160. Shamir, Ron (Tel-Aviv University) EXPANDER ? a 'one stop shop' for microarray data analysis

  161. Shankar Jata (Institute of Genomics and Integrative Biology ) Genome wide expression profiling of Aspergillus fumigatus against amphotericin B using a DNA Microarray

  162. Shchegrova, Svetlana (Agilent Technologies, Inc) Two color array normalization based on intensity of spiked in controls

  163. Shomron, Noam (MIT) Codon bias uncovers splicing regulatory sequences

  164. Shu-Hung,Lin (Institute of Biomedical Engineering, National Taiwan University, Taipei, Taiwan) Genomic Splicing Sites Prediction Algorithm Based on Nucleotide Sequence Pattern

  165. Shulman-Peleg Alexandra (Tel-Aviv University) MAPPIS: Multiple Alignment of Protein-Protein Interfaces

  166. Singh, Rohit (Massachusetts Institute of Technology) An Active Learning Approach for Appropriate Sampling During Time-Series Expression Experiments

  167. Song, Yun (Department of Computer Science, University of California, Davis) Efficient Computation of Close Lower and Upper Bounds on the Minimum Number of Recombinations in DNA Sequence Evolution

  168. Spiridonov Alexey (NCBI, NLM, NIH) Applying machine learning for rational siRNA design

  169. Stadler Michael (MIT) Neighborhood-Inference: Predicting Splicing Regulatory Elements Using Functionally Antagonistic Groups

  170. Strope, Cory L. (University of Nebraska -- Lincoln) Simulation of Protein Families in the Twilight Zone

  171. Strope, Pooja (University of Nebraska - Lincoln) Comparative Analysis of Alignment-based and Alignment-free Protein Classifiers

  172. Szekely, Benjamin (Harvard University) Discovering Motif Regulatory Networks in Gene Promoter Regions

  173. Takakura, Takashi (Univ. of Electro-Communications) Efficient Tree Grammatical Modeling of RNA Secondary Structures from Alignment Data

  174. Taylor, Todd (George Mason University) A New Method for Protein Secondary Structure Assignment Based on a Simple Topological Descriptor

  175. Thompson Julie (Institut de Genomique et de Biologie Moleculaire et Cellulaire) MAO: Multiple Alignment Ontology

  176. Tian, Qi (University of Texas at San Antonio) Interactive Learning for Microarray Analysis

  177. Tseng, Yan Yuan (Department of Bioengineering, University of Illinois at Chicago) Evolutionary model for predicting protein function by matching local surfaces: a Bayesian Monte Carlo approach

  178. Turner, Frances (MRC Human Genetics Unit) Prioritisation of Positional Disease Gene Candidates

  179. Uzun, Alper (Northeastern University) Structure SNP (StSNP) Database: A tool for modeling nsSNPs locations on proteins and presenting their metabolic pathways

  180. Vibranovski, Maria D. (Ludwig Institute for Cancer Research, Sao Paulo Branch) Intron loss and gene size

  181. Vitol, Inna (Rensselaer Polytechnic Institute) SPOTCLUST: A Tool to Cluster Spoligotype Data for Tuberculosis Evolution and Epidemiology

  182. von Grotthuss, Marcin (BioInfoBank Institute) Ligand.Info, automated system for virtual high-throughput screening

  183. Waldispuhl Jerome (Boston College) A study of the folding energy spectrum of RNAs

  184. Wall, Dennis (Harvard Medical School) RoundUp: A comprehensive platform for exploration of orthologs

  185. Wang, Huiquan (Bioinformatics program in Genome Center, UC Davis) Strong SIDD (Stress Induced DNA Duplex Destabilization) sites occur at regulatory elements of the genes initiating responses to physiological and environmental stresses in E. coli

  186. Wang, Lu-yong (Siemens Corporate Research ) Boosting Methods in Classification and Analysis on mass spectrometry proteomic data

  187. Wang, Ting (Washington University) Prediction of Conserved Motif Networks based on Comparative Genomics

  188. Wu, Chunlei (Univ. of Texas-M.D. Anderson Cancer Center) A probe-to-transcripts mapping method for cross-platform comparisons of microarray data taking into account the effects of alternative splicing

  189. Xie, Xiaohui (MIT) Regulatory motif discovery in human promoters: motif evaluation, sequence space exploration, and functional validation.

  190. Xie, Xiaohui (MIT) Post-transcriptional regulation in the human genome:

  191. Xu, Yanlong (Louisiana State University) Protein evolution and divergence: the role of adjacent structures

  192. Ye, Ping (Johns Hopkins University) Commensurate Distances and Motifs from Genetic Congruence and Protein Interaction Networks in Yeast

  193. Zhang, Jinfeng (Harvard University) Study Near Native Protein Structures by Sequential Monte Carlo Method

  194. Zhang, Lan (Harvard Medical School) A Rich Probabilistic Model to Predict Yeast Gene Function

  195. Zhang, Naigong (George Washington University) Pairwise Decomposition of Many- body Energies using Generic Side-chains and Extreme Optimization in Computational Protein Design

  196. ZHANG, XU (University of Florida) A New Approach for Multiple Sequence Alignment

  197. Zhang, Ya (Penn State University) Protein Interaction Inference as a MAX-SAT Problem

  198. Zhao, Minglian (Department of Biological Sciences and Technology, Tsinghua University) Structural Insights into Biopolymer PHA Granular Phasins:Comparison Analysis and Function Validation

  199. Zhong,Wei (Georgia State University) Mining Relationship between Structural Homology and Frequency Profile for Structure Clusters

  200. Zhou, Ruhong (IBM TJ Watson Research Center) Screening and Refinement of Protein Structures from Fold Recognition