Program

 

Tuesday, November 9

  • 09:00 - 09:30 Registration

  • 09:30 - 09:40 Opening

  • 09:40 - 10:30 Tamar Schlick. Folding Genes at Nucleosome Resolution - Invited lecture

  • 10:30 - 10:50 Break

  • 10:50 - 12:05

    • —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
    • —Gabriel Siqueira, Klairton Lima Brito, Ulisses Dias, and Zanoni Dias. Heuristics for Reversal Distance between Genomes with Duplicated Genes

  • 12:05 - 13:35 Lunch

  • 13:35 - 14:50:

    • —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
    • —Hannah Brown, Lei Zuo, and Dan Gusfield. Comparing Integer Linear Programming to SAT-solving for Hard Problems in Computational and Systems Biology

  • 14:50 - 15:10 Break

  • 15:10 - 16:25:

    • —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

  • 16:25 - 16:45 Break

  • 16:45 - 17:15 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. Algorithms for Mining Massive Metagenome Repositories to Detect Novel Enzymes - 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 - 13:25 Lunch

  • 13:25 - 14:40:

    • —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

  • 14:40 - 15:00 Break

  • 15:00 - 16:15:

    • —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

  • 16:15 - 16:35 Break

  • 16:35 - 17:15 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 - 13:25 Lunch

  • 13:25 - 14:40

    • —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

  • 14:40 - 15:00 Break

  • 15:00 - 16:15

    • —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

  • 16:15 - 16:35 Break

  • 16:35 - 17:05 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

  • 17:05 - 17:15 Closing