Papers (Program PDF)
| Saturday, September 8th | ||||||
| Keynote | 9:00 - 10:00 am | |||||
| Hall of Flags | ||||||
| Pavel Pevzner | ||||||
| Shotgun PROTEIN Sequencing. | ||||||
| Session 1-A | 10:10 - 11:50 am | |||||
| Protein Structure / Classification | Hall of Flags | |||||
| Predicting Protein Folding Kinetics via Temporal Logic Model Checking: | 10:10 - 10:35 am | |||||
| Extended Abstract. | ||||||
| Christopher Langmead (Carnegie Mellon Univ, USA) | ||||||
| Sumit Jha (Carnegie Mellon Univ, USA) | ||||||
| Efficient Algorithms to Explore Conformation Spaces of Flexible Protein Loops. | 10:35 - 11:00 am | |||||
| Ankur Dhanik (Stanford Univ, USA) | ||||||
| Peggy Yao (Stanford Univ, USA) | ||||||
| Nathan Marz (Stanford Univ, USA) | ||||||
| Ryan Propper (Stanford Univ, USA) | ||||||
| Charles Kou (Stanford Univ, USA) | ||||||
| Guanfeng Liu (Stanford Univ, USA) | ||||||
| Henry, van den Bedem (JCSG, SLAC, USA) | ||||||
| Jean-Claude Latombe (Stanford Univ, USA) | ||||||
| Fault Tolerance for Large Scale Protein 3D Reconstruction from Contact Maps. | 11:00 - 11:25 am | |||||
| Marco Vassura (Dept of Comp Sci, Univ of Bologna, Italy) | ||||||
| Luciano Margara (Dept of Comp Sci, Univ of Bologna, Italy) | ||||||
| Pietro Di Lena (Dept of Comp Sci, Univ of Bologna, Italy) | ||||||
| Medri Filippo (Dept of Comp Sci, Univ of Bologna, Italy) | ||||||
| Piero Fariselli (Dept of Biology, Univ of Bologna, Italy, Italy) | ||||||
| Rita Casadio (Dept of Biology UNIBO, Italy) | ||||||
| Bringing folding pathways into strand pairing prediction. | 11:25 - 11:50 am | |||||
| Jieun Jeong (Penn State Univ, USA) | ||||||
| Piotr Berman (Penn State Univ, USA) | ||||||
| Teresa Przytycka (National Center for Biotechnology Information, USA) | ||||||
| Session 1-B | 10:10 - 11:50 am | |||||
| SNPs and Haplotypes | Bodek Lounge | |||||
| A Fast and Accurate Heuristic for the Single Individual SNP Haplotyping Problem | 10:10 - 10:35 am | |||||
| with Many Gaps, High Reading Error Rate and Low Coverage. | ||||||
| Loredana Genovese (Institute for Informatics and Telematics of CNR, Italy) | ||||||
| Filippo Geraci (Institute for Informatics and Telematics of CNR, Italy) | ||||||
| Marco Pellegrini (Institute for Informatics and Telematics of CNR, Italy) | ||||||
| Two Birds, One Stone: Selecting Functionally Informative Tag SNPs for Disease | 10:35 - 11:00 am | |||||
| Association Studies. | ||||||
| Phil Hyoun Lee (Queen's Univ, Canada) | ||||||
| Hagit Shatkay (Comp Bio and Machine Learning Lab, School of Computing, Queen's Univ, Kingston, Ontario, Canada) | ||||||
| Genotype Error Detection using Hidden Markov Models of Haplotype Diversity. | 11:00 - 11:25 am | |||||
| Justin Kennedy (Univ of Connecticut, USA) | ||||||
| Bogdan Pasaniuc (Univ of Connecticut, USA) | ||||||
| Ion Mandoiu (Univ of Connecticut, USA) | ||||||
| Haplotype inference via genotype parsing. | 11:25 - 11:50 am | |||||
| Pasi Rastas (Univ of Helsinki, Dept of Comp Sci and Helsinki Institute for Info Tech HIIT, Finland) | ||||||
| Esko Ukkonen (Univ of Helsinki, Dept of Comp Sci and Helsinki Institute for Info Tech HIIT, Finland) | ||||||
| Session 2-A | 1:30 - 2:45 pm | |||||
| Evolution | Hall of Flags | |||||
| Seeded Tree Alignment and Planar Tanglegram Layout. | 1:30 - 1:55 pm | |||||
| Antoni Lozano (Technical Univ of Catalonia, Spain) | ||||||
| Ron Pinter (Technion - Israel Institute of Technology, Israel) | ||||||
| Oleg Rokhlenko (Technion - Israel Institute of Technology, Israel) | ||||||
| Gabriel Valiente (Technical Univ of Catalonia, Spain) | ||||||
| Michal Ziv-Ukelson (Technion -- Israel Institute of Technology, Israel) | ||||||
| Inferring Models of Rearrangements, Recombinations and Horizontal Transfers | 1:55 - 2:20 pm | |||||
| by the Minimum Evolution Criterion. | ||||||
| Hadas Birin (Tel Aviv Univ, Israel) | ||||||
| Zohar Gal-or (Tel Aviv Univ, Israel) | ||||||
| Isaac Elias (KTH, Sweden) | ||||||
| Tamir Tuller (Tel Aviv Univ, Israel) | ||||||
| An $\Omega(n^2/\log n)$ Speed-Up of \TBR Heuristics for the | 2:20 - 2:45 pm | |||||
| Gene-Duplication Problem. | ||||||
| Mukul Bansal (Dept of Comp Sci, Iowa State Univ, Ames, IA, USA) | ||||||
| Oliver Eulenstein (Dept of Comp Sci, Iowa State Univ, Ames, IA, USA) | ||||||
| Session 2-B | 1:30 - 2:45 pm | |||||
| Motifs | Bodek Lounge | |||||
| Incremental Discovery of the Irredundant Motif Bases for all Suffixes of a String | 1:30 - 1:55 pm | |||||
| in $O(|\Sigma|n^2 \log n)$ Time. | ||||||
| Alberto Apostolico (Univ of Padova and Georgia Tech, Italy) | ||||||
| Claudia Tagliacollo (Univ of Padova & Georgia Tech, Italy) | ||||||
| A Graph Clustering Approach to Weak Motif Recognition. | 1:55 - 2:20 pm | |||||
| Christina Boucher (Univ of Waterloo, Canada) | ||||||
| Daniel Brown (Cheriton School of Comp Sci, Univ of Waterloo, Canada) | ||||||
| Paul Church (Univ of Waterloo, Canada) | ||||||
| Informative Motifs in Protein Family Alignments. | 2:20 - 2:45 pm | |||||
| Hatice Gulcin Ozer (Ohio State Univ, USA) | ||||||
| William C Ray (The Ohio State Univ, USA) | ||||||
| Session 3-A | 3:15 - 4:55 pm | |||||
| Protein Folding / Alignment | Hall of Flags | |||||
| Topology Independent Protein Structural Alignment. | 3:15 - 3:40 pm | |||||
| Joe Dundas (Dept of Bioengineering, Univ of Illinois at Chicago, USA) | ||||||
| Andrew Binkowski (Dept of Bioengineering, Univ of Illinois at Chicago, USA) | ||||||
| Bhaskar DasGupta (Dept of Comp Sci, Univ of Illinois at Chicago, USA) | ||||||
| Jie Liang (Dept of Bioengineering, Univ of Illinois at Chicago, USA) | ||||||
| Generalized Pattern Search and Mesh Adaptive Direct Search Algorithms for | 3:40 - 4:05 pm | |||||
| Protein Structure Prediction. | ||||||
| Vincenzo Cutello (Dept of Mathematics and Comp Sci, Univ of Catania, Italy) | ||||||
| Giuseppe Nicosia (Univ of Catania, Italy) | ||||||
| Giovanni Stracquadanio (Univ of Catania, Italy) | ||||||
| Alignment-Free Local Structural Search by Writhe Decomposition. | 4:05 - 4:30 pm | |||||
| Degui Zhi (Univ of California, Berkeley, USA) | ||||||
| Maxim Shatsky (Univ of California, Berkeley, USA) | ||||||
| Steven Brenner (Univ of California, Berkeley, USA) | ||||||
| Defining and Computing Optimum RMSD for Gapped Multiple Structure Alignment. | 4:30 - 4:55 pm | |||||
| Xueyi Wang (UNC Chapel Hill, USA) | ||||||
| Jack Snoeyink (Dept of Comp Sci, UNC Chapel Hill, USA) | ||||||
| Session 3-B | 3:15 - 4:55 pm | |||||
| Sequence Analysis | Bodek Lounge | |||||
| Using protein domains to improve the accuracy of ab initio gene finding. | 3:15 - 3:40 pm | |||||
| Mihaela Pertea (UMD, USA) | ||||||
| Steven Salzberg (UMD, USA) | ||||||
| Genomic signatures in de Bruijn chains. | 3:40 - 4:05 pm | |||||
| Lenwood Heath (Virginia Tech, USA) | ||||||
| Amrita Pati (Virginia Tech, USA) | ||||||
| Fast kernel methods for SVM sequence classifiers. | 4:05 - 4:30 pm | |||||
| Pavel Kuksa (Rutgers Univ, Piscataway, NJ 08854, USA) | ||||||
| Vladimir Pavlovic (Rutgers Univ, Piscataway, NJ 08854, USA) | ||||||
| On-line Viterbi Algorithm for Analysis of Long Biological Sequences. | 4:30 - 4:55 pm | |||||
| Rastislav Sramek (Comenius Univ Bratislava, Slovakia) | ||||||
| Brona Brejova (Cornell Univ, USA) | ||||||
| Tomas Vinar (Cornell Univ, USA) | ||||||
| Sunday, September 9th | ||||||
| Session 4-A | 9:10 - 10:00 am | |||||
| Protein Folding | Hall of Flags | |||||
| Locality Kernels for Protein Classification. | 9:10 - 9:35 am | |||||
| Evgeni Tsivtsivadze (Turku Centre for Comp Sci, Finland) | ||||||
| Jorma Boberg (Dept of IT, Univ of Turku, Finland) | ||||||
| Tapio Salakoski (Dept of IT, Univ of Turku, Finland) | ||||||
| When Less is More: Improving Classification of Protein Families with a Minimal | 9:35 - 10:00 am | |||||
| Set of Global Features. | ||||||
| Roy Varshavsky (Hebew Univ, Jerusalem, Israel) | ||||||
| Menachem Fromer (Hebew Univ, Jerusalem, Israel) | ||||||
| Amit Man (Hebew Univ, Jerusalem, Israel) | ||||||
| Michal Linial (The Hebrew Univ of Jerusalem, Israel) | ||||||
| Session 4-B | 9:10 - 10:00 am | |||||
| Similarity Search | Bodek Lounge | |||||
| Homology Search with Fragmented Nucleic Acid Sequence Patterns. | 9:10 - 9:35 am | |||||
| Axel Mosig (PICB Shanghai, China) | ||||||
| Jiunn-Linag (Julian) Chen (School of Life Sci and Dept of Chem, Arizona State Univ, Tempe, AZ, USA) | ||||||
| Peter F Stadler (Haertelstr 16-18, 04107 Leipzig, Germany) | ||||||
| Fast computation of good multiple spaced seeds. | 9:35 - 10:00 am | |||||
| Lucian Ilie (Univ of Western Ontario, Canada) | ||||||
| Silvana Ilie (Ontario Research Centre for Computer Algebra, Canada) | ||||||
| Session 5-A | 10:10 - 11:25 am | |||||
| RNA World | Hall of Flags | |||||
| Fast Algorithms for Selecting Specific siRNA in Complete mRNA Data. | 10:10 - 10:35 am | |||||
| Jaime Davila (CSE Dept at Univ of Connecticut, USA) | ||||||
| Sudha Balla (Dept of Comp Sci, Univ of Connecticut, USA) | ||||||
| Sanguthevar Rajasekaran (Univ of Connecticut, USA) | ||||||
| RNA Folding Including Pseudoknots: A New Parameterized Algorithm and | 10:35 - 11:00 am | |||||
| Improved Upper Bound. | ||||||
| Chunmei Liu (Howard Univ, USA) | ||||||
| Yinglei Song (Univ of Maryland, Eastern Shore, USA) | ||||||
| Louis Shapiro (Dept of Math, Howard Univ, USA) | ||||||
| HFold: RNA Pseudoknotted Secondary Structure Prediction Using | 11:00 - 11:25 am | |||||
| Hierarchical Folding. | ||||||
| Hosna Jabbari (Univ of British Columbia, Canada) | ||||||
| Anne Condon (Univ of British Columbia, Canada) | ||||||
| Ana Pop (Univ of British Columbia, Canada) | ||||||
| Cristina Pop (Univ of British Columbia, Canada) | ||||||
| Yinglei Zhao (Univ of British Columbia, Canada) | ||||||
| Session 5-B | 10:10 - 11:25 am | |||||
| Sequence Assembly / Alignment | Bodek Lounge | |||||
| Algorithms for the extraction of synteny blocks from comparative maps. | 10:10 - 10:35 am | |||||
| Vicky Choi (Virginia Tech, USA) | ||||||
| Chunfang Zheng (Univ of Ottawa, Canada) | ||||||
| Qian Zhu (Univ of Ottawa, Canada) | ||||||
| David Sankoff (Univ of Ottawa, Canada) | ||||||
| Inverse sequence alignment from partial examples. | 10:35 - 11:00 am | |||||
| Eagu Kim (Univ of Arizona, USA) | ||||||
| John Kececiogu (Univ of Arizona, USA) | ||||||
| Computability and Equivalence of Models for Sequence Assembly. | 11:00 - 11:25 am | |||||
| Paul Medvedev (Univ of Toronto, Canada) | ||||||
| Konstantinos Georgiou (Univ of Toronto, Canada) | ||||||
| Eugene Myers (HHMI Janelia Farm Research Campus, USA) | ||||||
| Michael Brudno (Univ of Toronto, Canada) | ||||||
| Keynote | 1:00 - 2:00 pm | |||||
| Hall of Flags | ||||||
| Maja Bucan | ||||||
| Novel approaches in psychiatric genomics. | ||||||
| Session 6-A | 2:10 - 3:25 pm | |||||
| Mapping / Tiling | Hall of Flags | |||||
| The Point Placement Problem on a Line – Improved Bounds for Pairwise | 2:10 - 2:35 pm | |||||
| Distance Queries. | ||||||
| Francis Chin (The Univ of Hong Kong, Hong Kong) | ||||||
| Chi Ming Leung (Univ of Hong Kong, Hong Kong) | ||||||
| Wing-Kin Sung (Nuational Univ of Singapore, Singapore) | ||||||
| SM Yiu (The Univ of Hong Kong, Hong Kong) | ||||||
| Efficient computational design of tiling arrays using a shortest path approach. | 2:35 - 3:00 pm | |||||
| Alexander Schliep (Max Planck Institute for Moelcular Genetics, Germany) | ||||||
| Roland Krause (Max Planck Institute for Moelcular Genetics, Germany) | ||||||
| Efficient and accurate construction of genetic linkage maps from noisy and | 3:00 - 3:25 pm | |||||
| missing genotyping data. | ||||||
| Yonghui Wu (UC Riverside, USA) | ||||||
| Stefano Lonardi (UC Riverside, USA) | ||||||
| Prasanna Bhat (UC Riverside, USA) | ||||||
| Timothy Close (UC Riverside, USA) | ||||||
| Session 6-B | 2:10 - 3:00 pm | |||||
| Pathways | Bodek Lounge | |||||
| A Novel Method for Signal Transduction Network Inference from Indirect | 2:10 - 2:35 pm | |||||
| Experimental Evidence. | ||||||
| Reka Albert (Penn State Univ, USA) | ||||||
| Bhaskar DasGupta (Dept of Comp Sci, Univ of Illinois at Chicago, USA) | ||||||
| Riccardo Dondi (Dipartimento di Scienze dei Linguaggi, Universita degli Studi di Bergamo, Italy) | ||||||
| Semen Kachalo (Dept of Bioengineering, Univ of Illinois at Chicago, USA) | ||||||
| Eduardo Sontag (Dept of Mathematics, Rutgers Univ, USA) | ||||||
| Alexander Zelikovsky (Dept of Comp Sci, Georgia State Univ, USA) | ||||||
| Kelly Westbrooks (Dept of Comp Sci, Georgia State Univ, USA) | ||||||
| Composing Globally Consistent Pathway Parameter Estimates through | 2:35 - 3:00 pm | |||||
| Belief Propagation. | ||||||
| Geoffrey Koh (NUS Graduate School for Integrative Sciences and Engineering, Singapore) | ||||||
| Lisa Tucker-Kellogg (Dept of Comp Sci, National Univ of Singapore, Singapore) | ||||||
| David Hsu (Dept of Comp Sci, National Univ of Singapore, Singapore) | ||||||
| P S Thiagarajan (National Univ of Singapore, Singapore) | ||||||
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