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 (Chair: Benedict Paten) |
|---|
| 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 |
| 11.55 am - 12.05 pm | Heather Lawson / Andre Kahles | Pitches: HPRC / Unconference |
| 12.15 pm - 01.45 pm | Lunch Break | |
| Session 2 - Graph references and annotation (Chair: Mario Stanke) |
|---|
| 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 (Chair: Gunnar Rätsch) |
|---|
| 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 (Chair: Andre Kahles) |
|---|
| 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 (Chair: Heather Lawson) |
|---|
| 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 (Chair: Mario Stanke) |
|---|
| 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 (Chair: Heather Lawson) |
|---|
| 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 (Chair: Gunnar Rätsch) |
|---|
| 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 | |
