Meeting Agenda

Program Day 1. Sep 3, 2024

8:00a    Breakfast & Registration

9:00a    Welcome Address (Adam Phillippy)

9:10a - 11:30a  Session 1: Complete genomes and pangenomes

(20 minutes  followed by 5-minute Q/A)
9:10  “On the road to ruminant T2T genomics”  Tim Smith; U.S. Meat Animal Research Center, USDA ARS

9:35  “T2T: shining a light on repeats, dynamic centromeres and chromosome evolution” Rachel O'Neill; Institute for Systems Genomics, UConn

10:00  "New fast alignment software and data structures for genomes across the tree of life" Richard Durbin; Department of Genetics, University of Cambridge

10:25  Coffee Break

10:35 “DiMeLo-seq, a method for mapping protein-DNA interactions genome-wide with long-read sequencing”; Aaron Streets; Center for Computational Biology, UC Berkeley

11:00  “Implicit pangenomics” Erik Garrison; Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center

11:25  “Enhancing Genomic Accuracy with Deep Learning and pangenomes: Advancements in Assembly polishing, Somatic and Germline Variant Calling"  Kishwar Shafin; Google Inc.

11:50-1:30 Lunch (Mediterranean cuisine)

1:30p - 3:00p   Flash Talk Session 2: "T2T all the things!" (8 min ea., followed by 10 min panel Q/A) 

Brief Introduction (Discussion Lead: Karen)
1:30 “The rapid karyotype evolution of small apes” Lucia Carbone; Oregon Health and Science University
1:40 “Recurrent evolution and selection shape structural diversity in humans and non-human primates” Peter Sudmant; University of California Berkeley
1:50 “Strategies and progress on assembling multiple zebrafish haplotypes” Shawn Burgess; Translational and Functional Genomics Branch, NHGRI
2:00 Q/A
2:10 Coffee Break
2:20 “Repetitive Sequences: Drivers of Genomic Instability and Evolution” Christine Beck; The Jackson Laboratory for Genomic Medicine, Farmington, CT
2:30 “Telomere-to-Telomere Assembly of an inbred Rattus norvegicus genome” Peter Doris; The Brown Foundation Institute of Molecular Medicine, Center for Human Genetics, University of Texas Health Science Center
2:40 “Challenges of songbird T2T genome assemblies” Inês Borges; Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
2:50 Q/A

3:00-4:00 Parallel session: T2T assembly troubleshooting / Networking

4:00p - 5:40p Flash Talk Session 3: Advancing T2T Tooling and Technology
Brief Introduction (Discussion Lead: Adam)
4:00 “HG002 Q100: benchmarking assembly and read accuracy with a near-perfect diploid genome” Nancy Hansen; Genome Informatics Section, Computational and Statistical Genomics Branch, NHGRI/NIH
4:10 “Assessing quality of HiFi read assemblies” Anton Bankevich; Computer Science and Engineering Department, Huck Institutes of Life Sciences, Pennsylvania State University
4:20 “Comparative studies of adaptive immune receptor loci in vertebrate genomes” Yana Safonova; Computer Science and Engineering Department, Huck Institutes of Life Sciences, Pennsylvania State University

4:30 Q/A
4:40 Refreshment Break

4:50 “T2T assemblies in the UCSC Genome Browser” Maximilian Haeussler; UC Santa Cruz Genomics Institute
5:00 “Better characterization of somatic variation in cancer with long-read sequencing” Mikhail Kolmogorov; Center for Cancer Research, NCI/NIH

5:10 “Fast and cost-efficient de novo assembly with the updated hifiasm.” Haoyu Cheng; Yale Biomedical Informatics & Data Science

5:20 "What good is near T2T? The HPRC Intermediate Assembly Release" Julian Lucas; Biomolecular Engineering Department, UC Santa Cruz 

5:30 Q/A

5:40p Closing Statement (Karen and Adam)
6:00p Beach bonfire (Twin Lakes; East Cliff Drive at 7th Avenue)

Program Day 2. Sep 4, 2024

8:00a    Breakfast & Registration

9:00a    Welcome Address (Karen Miga)

9:10a - 11:30a  Session 4: "From filling sequence gaps to filling knowledge gaps"

(20 minutes  followed by 5-minute Q/A)
9:10  “Formation and propagation of human Robertsonian chromosomes” Jennifer Gerton; Stowers Institute for Medical Research and Andrea Guarracino; Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center 

9:35  “Gene regulation across the 6 Gbp diploid human genome”  Andrew Stergachis; Division of Medical Genetics, Department of Medicine, University of Washington

10:00  “Genome interpretation with sequence-to-function models” Nilah Ioannidis; Department of Electrical Engineering and Computer Sciences, UC Berkeley

10:25  Coffee Break

10:35  “Complete sequencing of ape genomes” Evan Eichler; Department of Genome Sciences, University of Washington

11:00  “New transcriptomics and epigenetics insights discovered by long reads sequencing” Kin Fai Au; Center for Computational Medicine and Bioinformatics, University of Michigan Medical School

11:25  “The X, Y, and Z: Reaching for the brass ring of the genome” Kateryna Makova; Penn State University

11:50-1:30 Lunch (Hawaiian Cruisine)

1:30p - 3:00p   Flash Talk Session 5: Long-Read Functional Analyses

Brief Introduction (Discussion Lead: Karen)
1:30 “CiFi: Accurate long-read chromatin conformation capture with low input requirements” Sean McGinty; (Dennis lab) Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, UC Davis
1:40 “Beyond assembly: annotations and function using the T2T genome” Winston Timp; Department of Biomedical Engineering, Molecular Biology and Genetics, and Genetic Medicine, Johns Hopkins University
1:50 “T2T Isogenomic Reference Genomes of Human Laboratory Cell Lines” Simona Giunta; Department of Biology and Biotechnology Charles Darwin, University of Rome “La Sapienza”
2:00 Q/A
2:10 Refreshment Break
2:20 “Nanopore Methylation – From Signal to Answers” Marcus Stoiber; Oxford Nanopore Technnoloiges
2:30 “Fiber-seq Inferred Regulatory Elements with diploid T2T genomes” Mitchell Vollger; Division of Medical Genetics, Department of Medicine, University of Washington
2:40 “Diversity of ribosomes at the level of rRNA variation associated with human health and disease” Daphna Rothschild; Department of Genetics, Stanford University
2:50 Q/A

3:00-4:00p Parallel session: Envisioning a future T2T functional map / Networking

4:00p - 5:40p Flash Talk Session 6: Uncovering new biology

Brief Introduction (Discussion Lead: Adam)
4:00 “CenMAP: An end-to-end pipeline to characterize centromere sequence and structure in T2T human genome assemblies” Keith Oshima; Department of Genetics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania
4:10 “Reference resources for novel variant discovery in T2T genomes” Arang Rhie; Genome Informatics Section, Computational and Statistical Genomics Branch, NHGRI/NIH
4:20 “A Complete Genome for the Common Marmoset” Prajna Hebbar; Biomolecular Engineering Department, UC Santa Cruz
4:30 Q/A
4:40 Refreshment Break
4:50 “Transposable elements shape primate genomes” Jessica Storer; Institute for Systems Genomics, UConn
5:00 “The variation in centromeres, telomeres, and acrocentric chromosomes across three generations using T2T assemblies” Monika Cechova; Biomolecular Engineering Department, UC Santa Cruz
5:10 “Genome assembly beyond the T2T: applications in cell lines, rare disease and cancer” T. Rhyker Ranallo-Benavidez; Translational Genomics Research Institute (TGen)
5:20 "A 1000 Genomes phased T2T reference panel improves phasing and imputation around common disease-causing SVs" Joe Lalli; Genetics Department,  University of Wisconsin-Madison
5:30 Q/A
5:40p Closing Statement (Karen and Adam) Wine/Cheese Networking
6:30p Dinner on your own