Program

Program Overview (tentative)

	Sunday	Monday	Tuesday	Wednesday	Thursday
Morning Session (9.00am - 12.00pm)		Algorithms and Computational Models (Part I)	Human Pan-Genome	Non-human Pan-Genomes / Metagenomics	Graph Construction and Assembly
Lunch
Afternoon Session (2.00pm - 5.30pm)	Arrival	Algorithms and Computational Models (Part II)	HPP Global Outreach and ELSI	Excursion	References and Annotation
Dinner
Evening Session (7.30pm - 9.30pm)	Welcome Reception	Poster Session / Networking	Unconference / Special interest groups	Conference Dinner	Departure

Schedule

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

Sunday, June 30, 2024

Welcome

06.00 pm - 06.45 pm	Keynote Presentation: Ewan Birney	The past, present and future of genomics
07.00 pm - 09.30 pm	Welcome Reception

Monday, July 1, 2024

Welcome

08.45 am - 09.00 am	Welcome - CSF

Session 1 - Algorithms and Computational Models I

09.00 am - 09.45 am	Keynote Presentation: Ben Langmead	Pan-genomic methods for fighting reference bias
09.45 am - 10.05 am	Davide Bolognini	Pangenome-based inference of structurally complex haplotypes from short read data
10.05 am - 10.25 am	Kai Ye	Somatic structural variant discovery with SVision-pro
10.25 am - 10.45 am	Timofey Prodanov	Locityper - genotyping complex polymorphic loci using both short- and long-read whole genome sequencing
10.45 am - 11.15 am	Coffee Break
11.15 am - 12.00 pm	Keynote Presentation: Jasmijn Baaijens	Graph-based approaches to viral lineage quantification
12.15 pm - 02.00 pm	Lunch Break

Session 2 - Algorithms and Computational Models II

02.00 pm - 02.20 pm	Xian Chang	Long-read-to-pangenome mapping with Giraffe
02.20 pm - 02.40 pm	Hufsah Ashraf	Detecting recurrent inversion polymorphisms in human pan-genomes
02.40 pm - 03.00 pm	Jouni Sirén	Personalized Pangenome References
03.00 pm - 03.45 pm	Coffee Break
03.45 pm - 04.30 pm	Keynote: Marinka Zitnik	Building Multimodal Language Models for Genome Knowledge Graphs
04.30 pm - 04.50 pm	Peter Heringer	Bridging Patient Data and Pangenome Graphs
04.50 pm - 05.10 pm	Daniel Dörr	GFAffix: Collapsing walk-preserving shared affixes in variation graphs
05.10 pm - 05.30 pm	Ragnar Groot Koerkamp	Speeding up A*PA
06.00 pm - 07.30 pm	Dinner Break

Session 3 - Poster Session

07.30 pm - 09.30 pm	Poster Session

Tuesday, July 2, 2024

Session 4 - Human Pangenome I

09.00 am - 09.45 am	Keynote Presentation: Eimear Kenny	Representation and Sampling for the Human Pangenome
09.45 am - 10.05 am	Peter Sudmant	Understanding Human Evolution through Amylase Gene Diversity
10.05 am - 10.25 am	Jean Monlong	Characterising the CYP21A2 gene with Parakit
10.25 am - 10.55 am	Coffee Break
10.55 am - 11.15 am	Dylan Duchen	Genotyping immunoglobulin and other highly polymorphic immune-related genes using variation graphs and short read sequencing data
11.15 am - 11.35 am	Matthew Jensen	Graph-based personal genomes improve regulatory element identification across tissues in the EN-TEx resource
11.35 am - 11.55 am	Qian Zeng	Graph Genome for NGS-Based Clinical Testing
12.15 pm - 02.00 pm	Lunch Break

Session 5 - Human Pangenome II

02.00 pm - 02.20 pm	Andrea Guarracino	The complete sequence of human Robertsonian chromosomes
02.20 pm - 02.40 pm	Yoshihiko Suzuki	The Japanese pangenome
02.40 pm - 03.00 pm	Dr Nasna Nassir	The Arab pangenome
03.00 pm - 04.00 pm	Coffee Break
04.00 pm - 04.20 pm	Hardip Patel	The Indigenous Australian pangenome
04.20 pm - 04.40 pm	Anna-Sophie Fiston-Lavier	The diversity of human transposable elements
04.40 pm - 05.00 pm	Nicolas Robine	The Polyethnic-1000 project
05.00 pm - 05.20 pm	Jonathan LoTempio	A bioethical framework of pangenomics
06.00 pm - 07.30 pm	Dinner Break

Session 6 - Unconference

07.30 pm - 09.30 pm	Breakout groups

Wednesday, July 3, 2024

Session 7 - Non-Human Pangenomes/ Metagenomics

08.45 am - 09.30 am	Keynote Presentation: Zamin Iqbal	Pangenomes for bacteria and mobile elements, new problems and old
09.30 am - 09.50 am	Paulo Jorge Dias	Construction and Analysis of the Graph-based Pangenomes of two Lactic Acid Bacteria (LAB), Lactococcus lactis and Lactococcus cremoris
09.50 am - 10.10 am	Harun Mustafa	Large-scale multi-genome representation and microbiome analysis with the MetaGraph framework
10.10 am - 10.30 am	Alex Leonard	The Bovine Pangenome
10.30 am - 11.00 am	Coffee Break
11.00 am - 11.45 am	Keynote Presentation: Kateryna Makova	The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes
11.45 am - 12.05 pm	Byron Smith	Quantitative metagenome assembly
12.05 pm - 12.25 pm	Zhigui Bao	Understanding mutational processes from plant pangenome graphs
12.30 pm - 02.00 pm	Lunch Break

Thursday, July 4, 2024

Session 8 - Graph Construction and Assembly

09.00 am - 09.45 am	Keynote Presentation: Camille Marchet	The de Bruijn graph, a computational structure for pangenomes
09.45 am - 10.05 am	Jordan Eizenga	Multiple sequence alignments of human centromeres
10.05 am - 10.25 am	Leon Rauschning	Finding structurally conserved and variable regions in multiple genomes using msyd
10.25 am - 10.45 am	Guillaume Holley	The Emblask-Weaver pipeline: hybrid assembly and short-read mapping to the Icelandic pangenome graph
10.45 am - 11.15 am	Coffee Break
11.15 am - 11.35 am	Simon Heumos	The nf-core pangenome pipeline
11.35 am - 11.55 am	Mira Mastoras	Highly accurate assembly polishing with DeepPolisher
11.55 am - 12.15 pm	Mikko Rautiainen	Ribotin: Automated assembly and phasing of rDNA morphs.
12.15 pm - 02.00 pm	Lunch Break

Session 9 - References and Annotations

02.00 pm - 02.45 pm	Keynote Presentation: Arang Rhie	Utilizing the most out of one T2T reference genome
02.45 pm - 03.05 pm	Adam Frankish	Gene annotation on the Pangenome
03.05 pm - 03.25 pm	Fergal Martin	Ensembl pangenome resources
03.25 pm - 03.45 pm	Closing remarks