Conference Agenda
RT Regular Talk

HT Highlight Talk

Monday – September 4
7:30 pm
8:15 am

8:25 am
8:30 am

9:00 am

9:30 am
10:00 am

10:30 am

10:50am
11:20 am

11:50 pm

12:20 pm

1:30 pm
2:00 pm

2:30 pm

thRegistration
Opening Remarks
Session 1: Phylogenetics
Chair: Mohammed El-Kebir
Short welcome message by PC chairs
RT (WABI-[002]): EMMA: Adding Sequences into a Constraint Alignment with High Accuracy
and Scalability.
Authors: Chengze Shen, Baqiao Liu, Kelly P. Williams, and Tandy Warnow
RT (WABI-[003]): BATCH-SCAMPP: Scaling phylogenetic placement methods to place many
sequences
Authors: Eleanor Wedell, Chengze Shen, and Tandy Warnow
RT (WABI-[004]): Optimal Subtree Prune and Regraft for Quartet Score in Sub-quadratic Time
Authors: Shayesteh Arasti and Siavash Mirarab
RT (WABI-[005]): Leveraging constraints plus dynamic programming for the large Dolloparsimony problem
Authors: Junyan Dai, Tobias Rubel, Yunheng Han, and Erin K. Molloy
BreakSession 2: Networks – Cancer phylogenetics
Chair: Christina Boucher
RT (WABI-[007]): Making a Network Orchard by Adding LeavesAuthors: Leo van Iersel, Mark Jones, Esther Julien, and Yukihiro Murakami
RT (WABI-[008]): Quartets enable statistically consistent estimation of cell lineage trees underan unbiased error and missingness model
Authors: Yunheng Han and Erin K. Molloy
RT (WABI-[009]): Inferring Temporally Consistent Migration Histories
Authors: Mrinmoy Saha Roddur, Sagi Snir, and Mohammed El-Kebir
Lunch
Session 3: Reconciliation – Genome rearrangement - Planning
Chair: Yukihiro Murakami
RT (WABI-[006]): Simultaneous reconstruction of duplication episodes and gene-species mappingsAuthors: Paweł Górecki, Natalia Rutecka, Agnieszka Mykowiecka, and Jarosław Paszek
RT (WABI-[022]): Bridging Disparate Views on the DCJ-indel model for a Capping-free Solution
to the Natural Distance ProblemAuthors: Leonard Bohnenkämper
RT (WABI-[023]): Reinforcement Learning for Robotic Liquid Handler PlanningAuthors: Mohsen Ferdosi, Yuejun Ge, and Carl Kingsford

3:00 pmBreak

3:30 pm

Opening Keynote: Teresa M. Przytycka. Delineating relation between mutagenic signatures,
cellular processes, and environment through computational approaches
General assembly & SIGBIO General Meeting
Poster Session & Reception

5:00 pm
6:00 pm
8:00 pm

Tuesday – September 5th

8:15 am
8:45 am
9:15 am

9:45 am
10:15 am

Session 4: Pattern Matching
Chair: Travis Gagie
RT (WABI-[010]): Finding Maximal Exact Matches in GraphsAuthors: Nicola Rizzo, Manuel Cáceres, and Veli Mäkinen
RT (WABI-[011]): Revisiting the Complexity of and Algorithms for the Graph Traversal Edit
Distance and Its Variants
Authors: Yutong Qiu, Yihang Shen, and Carl Kingsford
RT (WABI-[012]): Co-linear Chaining on Pangenome Graphs
Authors: Jyotshna Rajput, Ghanshyam Chandra, and Chirag Jain
Session of Highlights: Theory and Applications of r-index in Bioinformatics
Chair: Jens Stoye
HT: Pangenome Alignment via Recursive Prefix-free Parsing
Authors: Ben Langmead, Travis Gagie, Marco Oliva, and Christina Boucher
HT: The r-index and friends
Authors: Travis Gagie and friends

10:45 amBreak

11:00 amKeynote 2: Nora Franceschini. Genomics and Human Population Diversity

12:00 pm

2:30 pm

Lunch
Session 5: Pattern Matching
Chair: Rob Patro
RT (WABI-[013]): Acceleration of FM-index Queries Through Prefix-free Parsing
Authors: Aaron Hong, Marco Oliva, Dominik Köppl, Hideo Bannai, Christina Boucher, and Travis
Gagie
RT (WABI-[014]): Exact sketch-based read mapping
Authors: Tizian Schulz and Paul Medvedev
RT (WABI-[015]): Fractional Hitting Sets for Efficient and Lightweight Genomic Data Sketching
Authors: Timothé Rouzé, Igor Martayan, Camille Marchet, and Antoine Limasset

3:00 pm

Break

1:30pm

2:00 pm

3:30 pm
4:00 pm
4:30 pm

6:15 pm
8:00 pm

Session 6: Pattern Matching - Compression
Chair: Erin Molloy
RT (WABI-[016]): Fast, Parallel, and Cache-friendly Suffix Array Construction
Authors: Jamshed Khan, Tobias Rubel, Laxman Dhulipala, Erin Molloy, and Rob Patro
RT (WABI-[017]): Compression algorithm for colored de Bruijn graphs
Authors: Amatur Rahman, Yoann Dufresne, and Paul Medvedev
RT (WABI-[018]): Fulgor: A fast and compact k-mer index for large-scale matching and color
queries
Authors: Jason Fan, Noor Pratap Singh, Jamshed Khan, Giulio Ermanno Pibiri, and Rob Patro
Conference Banquet2

Wednesday – September 6th

09:00 am
09:30 am

10:00 am

Session 7: RNA Bioinformatics
Chair: Jaroslaw Paszek
RT (WABI-[019]): SparseRNAFolD: Sparse RNA pseudoknot-free Folding including DanglesAuthors: Mateo Gray, Sebastian Will, and Hosna Jabbari
RT (WABI-[020]): Automatic exploration of the natural variability of RNA non-canonical geometricpatterns with a parameterized sampling technique
Authors: Théo Boury, Yann Ponty, and Vladimir Reinharz
RT (WABI-[021]): Balancing Minimum Free Energy and Codon Adaptation Index for ParetoOptimal RNA DesignAuthors: Xinyu Gu, Yuanyuan Qi, and Mohammed El-Kebir

10:30 amBreak

11:00 am

Closing Keynote: Weida Tong. The Ascent of AI: Predicting Drug-Induced Liver Injury

12:00 pm

Lunch

1:30 pm

Session 8: Future WABIs - Your inputs
Chair: Jens Stoye
Information about WABI 2023; Future plans for WABI

3:00 pm
3:30 pm

Closing Ceremony

3