09:40 - 10:30 Tamar Schlick. Biomolecular Modeling and Simulation Thriving in the Age of Technology - Invited lecture
10:30 - 10:50 Break
10:50 - 12:05
Hannah Brown, Lei Zuo, and Dan Gusfield. Comparing Integer Linear Programming to SAT-solving for Hard Problems in Computational and Systems Biology
Md Momin Al Aziz, Parimala Thulasiraman, and Noman Mohammed. Parallel Generalized Suffix Tree Construction for Genomic Data
Andre Rodrigues Oliveira, Géraldine Jean, Guillaume Fertin, Klairton Lima Brito, Ulisses Dias, and Zanoni Dias. A 3.5-Approximation Algorithm for Sorting by Intergenic Transpositions
12:05 - 12:25 Break
12:25 - 13:40
Gabriel Siqueira, Klairton Lima Brito, Ulisses Dias, and Zanoni Dias. Heuristics for Reversal Distance between Genomes with Duplicated Genes
Lucia Williams and Brendan Mumey. Extending Maximal Perfect Haplotype Blocks to the Realm of Pangenomics
Zhe Yu, Chunfang Zheng, and David Sankoff. Gaps and Runs in Syntenic Alignments
13:40 - 14:00 Break
14:00 - 15:15
Remie Janssen, Mark Jones, and Yukihiro Murakami. Combining Networks Using Cherry Picking Sequences
Remie Janssen and Yukihiro Murakami. Linear Time Algorithm for Tree-child Network Containment
Mohsen Katebi, Pedro Feijao, Julius Booth, Mehrdad Mansouri, Sean La, Alex Sweeten, Reza Miraskarshahi, Matthew Nguyen, Johnathan Wong, William Hsiao, Cedric Chauve, and Leonid Chindelevitch. PathOGiST: A Novel Method for Clustering Pathogen Isolates by Combining Multiple Genotyping Signals
15:15 - 15:35 Break
15:35 - 16:05 Poster session I
Tathagata Debnath and Mingzhou Song. Local Clustering inside a Genome
Matthew Hayes, Derrick Mullins, and Angela Nguyen. Complex Germline Structural Variant Discovery via Discordant Cluster Normalization
Nick Steinauer, Chun Guo, and Jinsong Zhang. Deciphering Gene Regulatory Networks via Logistic Regression of Cistromic and Transcriptomic Features in Disease Models
Wednesday, November 10
09:30 - 10:20 Christine Orengo. Protein Structure Informs Functional Mechanisms and the Risk of Disease - Invited lecture
10:20 - 10:40 Break
10:40 - 11:55
Misagh Kordi and Mukul S. Bansal. TreeSolve: Rapid Error-correction of Microbial Gene Trees
Edward E. Allen, John Farrell, Alexandria F. Harkey, David J. John, Gloria Muday, James L. Norris, and Bo Wu. Time Series Adjustment Enhancement of Hierarchical Modeling of Arabidopsis Thaliana Gene Interactions
Jiarui Chen, Hong-Hin Cheong, and Shirley Weng In Siu. BESTox: A Convolutional Neural Network Regression Model Based on Binary-encoded SMILES for Acute Oral Toxicity Prediction of Chemical Compounds
11:55 - 12:15 Break
12:15 - 13:30
Shaoheng Liang, Qingnan Liang, Rui Chen, and Ken Chen. Stratified Test Alleviates Batch Effects in Single-cell Data
Sayan Mandal, Aldo Guzmán-Sáenz, Niina Haiminen, Saugata Basu, and Laxmi Parida. A Topological Data Analysis Approach on Predicting Phenotypes from Gene Expression Data
Shunfu Mao, Yihan Jiang, Edwin Basil Mathew, and Sreeram Kannan. BOAssembler: A Bayesian Optimization Framework to Improve RNA-Seq Assembly Performance
13:30 - 13:50 Break
13:50 - 15:05
Ernst Althaus, Andreas Hildebrandt, and Domenico Mosca. Learning Molecular Classes from Small Numbers of Positive Examples Using Graph Grammars
Paola Bonizzoni, Clelia De Felice, Alessia Petescia, Yuri Pirola, Raffaella Rizzi, Jens Stoye, Rocco Zaccagnino, and Rosalba Zizza. Can We Replace Reads by Numeric Signatures? Lyndon Fingerprints as Representations of Sequencing Reads for Machine Learning
Wenwen Ju and Chenqi Mou. Exploiting Variable Sparsity in Computing Equilibria of Biological Dynamical Systems by Triangular Decomposition
15:05 - 15:25 Break
15:25 - 16:05 Poster session II
Tim Anderson and Travis Wheeler. An Optimized FM-index Library for Nucleotide and Amino Acid Search
Conner Copeland, George Lesica, Jack Roddy, and Travis Wheeler. Identifying and Visualizing Bacterial Prophage Integration Patterns
Huyen Trang Dang, Shi Jie Samuel Tan, and Sara Mathieson. Improvements to Ancestral Haplotype Reconstruction in Pedigrees
Alex Nord and Travis Wheeler. Oasis Locates and Contextualizes Unannotated Exons
Thursday, November 11
09:30 - 10:20 Terry Gaasterland. Genetic Risk of Disease through Genome Variation and Regulation of Transcription - Invited lecture
10:20 - 10:40 Break
10:40 - 11:55
Yining Liu, Sachin Kadyan, and Itsik Pe’er. A Recovery Algorithm and Pooling Designs for One-stage Noisy Group Testing Under the Probabilistic Framework
Kaari Landry, Aivee Teodocio, Manuel Lafond, and Olivier Tremblay-Savard. Novel Phylogenetic Network Distances Based on Cherry Picking
David Schaller, Manuela Geiß, Marc Hellmuth, and Peter F. Stadler. Best Match Graphs with Binary Trees
11:55 - 12:15 Break
12:15 - 13:30
Eleanor Wedell, Yirong Cai, and Tandy Warnow. Scalable and Accurate Phylogenetic Placement Using pplacer-XR
James Willson, Mrinmoy Saha Roddur, and Tandy Warnow. Comparing Methods for Species Tree Estimation with Gene Duplication and Loss
Alexsandro Oliveira Alexandrino, Klairton Lima Brito, Andre Rodrigues Oliveira, Ulisses Dias, and Zanoni Dias. Reversal Distance on Genomes with Different Gene Content and Intergenic Regions Information
13:30 - 13:50 Break
13:50 - 15:05
Klairton Lima Brito, Alexsandro Oliveira Alexandrino, Andre Rodrigues Oliveira, Ulisses Dias, and Zanoni Dias. Reversals Distance Considering Flexible Intergenic Regions Sizes
Yin Yao and Martin C. Frith. Improved DNA-versus-Protein Homology Search for Protein Fossils
Paul Zaharias, Vladimir Smirnov, and Tandy Warnow. The Maximum Weight Trace Alignment Merging Problem
15:05 - 15:25 Break
15:25 - 15:55 Poster session III
Daniel Olson, Vishwesh Venkatraman, Amitava Roy, and Travis Wheeler. Predicting Binding Affinity of Protein-pocket and Ligand Pairs with ANNs
Audrey Shingleton, Travis Wheeler, Kaitlin Carey, and George Lesica. Improved Representation and Adjudication of Subfamilies for Reliable Sequence Annotation
Huan Zhang. Detecting “Hybrid Transposable Elements” Formed by Homologous Recombination