Program
Program Overview
Sunday | Monday | Tuesday | Wednesday | Thursday | |
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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 | ||
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06.30 pm - 09.30 pm | Welcome Reception |
Monday, July 4, 2022
Session 1 - Pangenome representation (Chair: Benedict Paten) |
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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) |
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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 |
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07.30 pm - 09.30 pm | Poster Session | |
Tuesday, July 5, 2022
Session 4 - Algorithms on genome graphs (Chair: Gunnar Rätsch) |
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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) |
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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 |
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07.30 pm - 09.30 pm | Breakout groups | |
Session 6B - HPRC Satellite (Chair: Heather Lawson) |
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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) |
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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) |
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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) |
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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 | |