Invited lectures: 45 minutes for presentation + 5 minutes for questions

Contributed talks: 23 minutes for presentation + 2 minutes for questions

Tuesday, May 28

  • 09:00 - 09:30 Registration

  • 09:30 - 09:40 Opening

  • 09:40 - 10:30 Igor Jurisica. Explanable AI for Data-driven Medicine - Invited lecture

  • 10:30 - 10:45 Break

  • 10:45 - 12:00

    • Tom Davot, Annie Chateau, Rodolphe Giroudeau and Mathias Weller. New Polynomial-time Algorithm around the Scaffolding Problem

    • Ozan Kahramanogullari. Enumerating Dominant Pathways in Biological Networks by Information Flow Analysis

    • Sridevi Maharaj, Zarin Ohiba and Wayne Hayes. Comparing Different Graphlet Measures for Evaluating Network Model Fits to BioGRID PPI Networks

  • 12:00 - 13:30 Lunch

  • 13:30 - 14:20 Lior Pachter. Algorithms for Single-cell Genomics - Invited lecture

  • 14:20 - 14:35 Break

  • 14:35 - 15:50

    • Louis Petingi and Tamar Schlick. Graph-theoretic Partitioning of RNAs and Classification of Pseudoknots

    • Alexander Shlemov and Anton Korobeynikov. PathRacer: Racing Profile HMM Paths on Assembly Graph

    • Pavel Avdeyev, Maria Atamanova, and Max A. Alekseyev. A Uniform Theory of Adequate Subgraphs for the Genome Median, Halving, and Aliquoting Problems

  • 15:50 - 17:00 Poster session I:

    • Tim Anderson and Travis Wheeler. Havac: A Scalable, Highly Parallelized FPGA Accelerator Architecture for Profile Hidden Markov Model Sequence Database Search

    • Kaitlin Carey and Travis Wheeler. Annotation Confidence Estimates Improve Sequence Annotation with Subfamilies

    • Artem Danilevsky and Noam Shomron. Applied Deep Learning for the Analysis of High-throughput DNA Sequencing Data

    • Edward Harry and Zemin Ning. Visualization of Genome Scaffolding Using Hi-C Paired-end Reads

    • Sean La and Leonid Chindelevitch. PathOGiST: Calibrated Multi-criterion Genomic Analysis for Public Health Microbiology

    • Erin Molloy and Tandy Warnow. A Nearly Alignment-free Approach to Large-scale Gene Tree Estimation Using TreeMerge

Wednesday, May 29

  • 09:30 - 10:20 Pavel A. Pevzner. Bioinformatics: A Servant or the Queen of Molecular Biology? - Invited lecture

  • 10:20 - 10:35 Break

  • 10:35 - 11:50

    • Veronica Guerrini and Giovanna Rosone. Lightweight Metagenomic Classification via eBWT

    • Christopher Wright, Sriram Krishnamoorty and Milind Kulkarni. MULKSG: MULtiple K Simultaneous Graph Assembly

    • Joao Paulo Pereira Zanetti, Leonid Chindelevitch and Joao Meidanis. Counting Sorting Scenarios and Intermediate Genomes for the Rank Distance

  • 11:50 - 13:20 Group photo and Lunch

  • 13:20 - 14:10 Teresa Przytycka. Exploring Phenotypic Heterogeneity across Tissues and Conditions with Network-based Approaches - Invited lecture

  • 14:10 - 14:25 Break

  • 14:25 - 15:40

    • Joao Paulo Pereira Zanetti, Leonid Chindelevitch and Joao Meidanis. Generalizations of the Genomic Rank Distance to Indels

    • Thien Le, Aaron Sy, Erin K. Molloy, Qiuyi (Richard) Zhang, Satish Rao and Tandy Warnow. Using INC within Divide-and-Conquer Phylogeny Estimation

    • Alona Levy-Jurgenson, Xavier Tekpli, Vessela N. Kristensen and Zohar Yakhini. Predicting Methylation from Sequence and Gene Expression Using Deep Learning with Attention

  • 15:40 - 16:50 Poster session II:

    • Alex Nord and Travis Wheeler. Splice-aware Translated Homology Search

    • Daniel Olson and Travis Wheeler. Finding Repeats with Ultra

    • Jack Roddy and Travis Wheeler. A Convolutional Neural Network to Trim Sequence Alignment Overextension

    • Titli Sarkar, V. Sarika Kondra, Wu Xu and Vijay Raghavan. On the Effectiveness of Triangular Spatial Relationship for Regulatory Motif Discovery in Proteins

    • Sarah Walling, Kaitlin Carey, Alex Nord and Travis Wheeler. Alternatively Spliced Dual-coding Exons: Expression and Conservation

    • Yifan Zhang, Chi-Man Liu, Ruibang Luo and Tak-Wah Lam. Deep Learning Enabling Rapid and Accurate Genome Assembly Consensus of Single Molecule Long Reads

  • 17:00 Walk around the campus

Thursday, May 30

  • 09:30 - 10:20 Tandy Warnow. Advances in Mathematical Approaches to Constructing the Tree of Life - Invited lecture

  • 10:20 - 10:35 Break

  • 10:35 - 11:50

    • Kari Nousiainen, Jukka Intosalmi and Harri Lähdesmäki. A Mathematical Model for Enhancer Activation Kinetics during Cell Differentiation

    • Atif Rahman and Lior Pachter. Transcript Abundance Estimation and the Laminar Packing Problem

    • Peng Xiao, Xingyu Cai and Sanguthevar Rajasekaran. Efficient Algorithms for Finding Edit-distance Based Motifs

  • 11:50 - 12:00 Closing

  • 12:00 Lunch