Program

Program Overview

Sunday Monday Tuesday Wednesday Thursday
Morning Session
(9.00am - 12.00pm)
Pangenome representation Algorithms on genome graphs Quantitative methods on graphs Downstream applications and genomic privacy
Lunch
Afternoon Session
(2.00pm - 6.00pm)
Arrival Graph References and Annotation Telomere2Telomere Genome Assembly Excursion Genomic Diversity and ELSI
Dinner
Evening Session Welcome Reception Poster Session / Networking Unconference / Special interest groups / HPRC breakout Conference Dinner Departure

Schedule

The following schedule is preliminary and individual items can still be subject to change

Sunday, July 3, 2022

Arrival / Welcome
06.30 pm - 09.30 pm Welcome Reception

Monday, July 4, 2022

Session 1 - Pangenome representation
09.00 am - 09.15 am Welcome
09.15 am - 10.00 am Keynote Presentation: Richard Durbin Compressed data structures and algorithms on graphs for genetic variation: PBWT and GBWT
10.00 am - 10.20 am Erik Garrison Building Pangenome Graphs
10.20 am - 10.45 am Glenn Hickey HPRC Pangenome Construction
10.45 am - 11.15 am Coffee Break
11.15 am - 11.35 am Mikhail Karasikov Multi-genome representations with the MetaGraph framework
11.35 am - 11.55 am Nguyet Dang PARROT: PAngenome gRaph Related Output Transmutator
12.15 pm - 01.45 pm Lunch Break
     
Session 2 - Graph references and annotation
02.00 pm - 02.45 pm Keynote Presentation: Birte Kehr Detecting non-reference sequence variation using colored de Bruijn graphs.
02.45 pm - 03.10 pm Fergal Martin Ensembl Annotation of Human Pangenome Haplotypes
03.10 pm - 03.35 pm Deniz Turgut Graph-based genome reference representations (7BG)
03.35 pm - 04.05 pm Coffee Break
04.05 pm - 04.50 pm Keynote Presentation: Tobias Marschall Pangenome-Based Genome Inference
04.50 pm - 05.15 pm Nadia Pisanti The Elastic Degenerate String Matching (EDSM) problem
05.15 pm - 05.30 pm Shilpa Garg Chromosome-scale haplotype-resolved pangenomics
06.00 pm - 07.30 pm Dinner Break
     
Session 3 - Poster Session
07.30 pm - 09.30 pm Poster Session
     

Tuesday, July 5, 2022

Session 4 - Algorithms on genome graphs
09.00 am - 09.45 am Keynote Presentation: Christina Boucher Moni: A pangenomics aligner.
09.45 am - 10.10 am Harun Mustafa MSGAligner: a novel algorithm for multi-target alignment of sequences to annotated de Bruijn graphs
10.10 am - 10.30 am Daniel Doerr Founder set construction under allelic and non-allelic homologous recombination
10.30 am - 10.50 am Coffee Break
10.50 am - 11.35 am Keynote Presentation: Heng Li The assembly of a human pangenome
11.35 am - 12.00 pm Hannes Eggertson Weaver, a short-read mapper that supports pangenome reference graphs
12.00 pm - 12.30 pm Pesho Ivanov / Ragnar Groot Koerkamp Fast and Optimal Sequence Alignment using A*
12.30 pm - 02.00 pm Lunch Break
     
Session 5 - Telomere2Telomere genome assembly
02.30 pm - 03.15 pm Keynote Presentation: Karen Miga Modeling genetic and epigenetic maps of human centromeric regions
03.15 pm - 03.40 pm Mikko Rautiainen Verkko: automated telomere-to-telomere genome assembly with HiFi and nanopore reads
03.40 pm - 04.00 pm Max Brown Resolving mitochondrial genomes across vascular plants
04.00 pm - 04.30 pm Coffee Break
04.30 pm - 04.45 pm Andrews Frimpong Adu Benchmarking of ten assembly methods for assembling African genomes using PacBio HiFi sequencing data
04.45 pm - 05.05 pm Giulio Formenti Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs
05.05 pm - 05.25 pm Kai Ye A deep learning approach for the detection of complex structural variants
05.25 pm - 05.45 pm Christian Kubica panSV - graph based, reference free SV detection
06.00 pm - 07.30 pm Dinner Break
     
Session 6A - Unconference
07.30 pm - 09.30 pm Breakout groups
     
Session 6B - HPRC Satellite
07.30 pm - 07.40 pm Heather Lawson Welcome, Introduction to the Human Pangenome Project
07.40 pm - 07.55 pm Peter Goodhand and Susan Fairley GA4GH: developing global standards for genomics
07.55 pm - 08.10 pm Takako Takai-Igarashi Japanese Collaboration with HPRC/HPP on Pangenome
08.10 pm - 08.25 pm Shaun Aron Building an African Pangenome
08.25 pm - 08.40 pm Mile Sikic Asian Reference Genome Project
08.40 pm - 08.55 pm Kai Ye Phase 1 of Chinese Pangenome Project
09.00 pm - 09.30 pm Open Discussion
     

Wednesday, July 6, 2022

Session 7 - Quantitative Methods on Graphs
09.00 am - 09.45 am Keynote Presentation: Susan Holmes Graphs and Networks in the study of the Human Microbiome
09.45 am - 10.05 am Taylor Reiter An analysis framework for strain-resolved metagenome analysis
10.05 am - 10.20 am Anupam Gautam Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis
10.20 am - 10.50 am Coffee Break
10.50 am - 11.15 am Samuel Horsfield Graph Gene Caller: a novel approach to bacterial gene calling and gene discovery
11.15 am - 11.40 am Simon Heumos Graph layout algorithm using path-guided (PG) stochastic gradient descent (SGD): PG-SGD
11.40 am - 11.55 am Andrea Guarracino Chromosome communities in the human pangenome
12.15 pm - 02.00 pm Lunch Break
     

Thursday, July 7, 2022

Session 8 - Downstream applications and genomic privacy
09.00 am - 09.45 am Keynote Presentation: Jean Philippe Vert Embedding the de Bruijn graph, and applications to metagenomics
09.45 am - 10.05 am Jörg Hagmann Pantograph, an interactive and scalable pangenome graph browser.
10.05 am - 10.30 am Ian Fiddes Leveraging genome graphs to detect edits in multiplex genome engineering experiments
10.30 am - 10.50 am Coffee Break
10.50 am - 11.20 am Andrew Yates The GA4GH refget standard
11.20 am - 11.40 am Giuseppe Narzisi Somatic variant analysis using localized colored de Bruijn graphs
11.40 am - 11.55 am Mohammed Alser Intelligent Genome Analysis via Intelligent Algorithms and Architectures
12.15 pm - 01.45 pm Lunch Break
     
Session 9 - Genomic Diversity and ELSI
02.00 pm - 02.45 pm Keynote Presentation: Alice Popejoy Mapping Population Diversity: Technical Innovation and the Ethical, Legal, Social Implications (ELSI) of a Human Reference Genome Graph
02.45 pm - 03.05 pm Alex Wagner GA4GH Variation Representation Specification
03.05 pm - 03.25 pm Eef Jonkheer Exploring intra- and inter-genomic variation in haplotype-resolved genome assemblies
03.25 pm - 03.45 pm Closing Remarks