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AlCoB 2019

Berkeley, California, USA

May 28-30, 2019

Co-organized by:

University of California, Berkeley

Institute for Research Development, Training and Advice, Brussels/London


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


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

João Paulo Pereira Zanetti, Leonid Chindelevitch and João 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    

João Paulo Pereira Zanetti, Leonid Chindelevitch and João 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

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

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