Computational pangenomics course, conference, and biohackathon in Memphis, TN, exploring the cutting edge of pangenomes, biology, methods, software, and artificial intelligence (AI).
Important Dates
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Practical course/Conference/Biohackathon Registration Deadline: 13th April 2024
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Selected Participant will be notified by: 22nd April 2024
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Payment Deadline: 4th May 2024
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Practical course / Workshop: 18th-19th May 2024
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Conference: 20th May 2024
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Biohackathon: 21st-22nd May 2024
Venues
Practical course / Workshop
Freeman Auditorium at the Hamilton Eye Institute
930 Madison Ave,
3rd floor,
Memphis, TN 38103
United States
→ See the venue on the map
Conference
Freeman Auditorium at the Hamilton Eye Institute
930 Madison Ave,
3rd floor,
Memphis, TN 38103
United States
→ See the venue on the map
Biohackathon
Room 101, UTHSC Translational Research Science Building
71 S Manassas St,
Memphis, TN 38103
United States
→ See the venue on the map
Hotels in Memphis
Transportation in Memphis
If you stay in Downtown, the Medical District, South City, or New Chicago, you can reach the event venue by getting on-demand, convenient, and affordable rides with Groove On-Demand.
About the Practical Course / Workshop
Saturday, May 18, 2024 - Sunday, May 19, 2024
The use of a single reference genome in bioinformatics can lead to reference bias and miss important information about genome variability and relationships. New assembly methods have made it easier to generate high-quality complete genome assemblies, and using a pangenome graph that expresses many genomes and their mutual alignment can help address these issues.
This practical course / workshop will focus on building such graphs from whole genome assemblies and using them in various downstream applications in comparative genomics, evolution, variation analysis, sequence alignment, and phenotype association.
Participants will learn about pangenome concepts and gain practical experience building and analyzing pangenome graphs. They will apply these methods to complex research questions that require understanding the relationships between multiple genomes or accounting for variability when analyzing new genomes. By the end of the practical course / workshop, participants will have a strong understanding of pangenome methods based on whole genome assemblies.
About the Conference
Monday, May 20, 2024
We will gather for an in-person conference on the day after the practical course / workshop.
This will bring together practical course / workshop participants and virtual and in-person speakers who are actively working on diverse aspects of pangenome research.
The virtual meeting will be open to the public.
Speakers will cover topics at the intersection of pangenome methods and biology, including a focus on basic methods, data structures, genome assembly, data visualization, and public collaborative pangenome projects.
We expect to draw speakers from a diverse set of species contexts.
About the Biohackathon
People
Practical Course / Workshop Instructors
Erik Garrison - Assistant Professor
Genomicist with a quantitative social science background. I build methods that let us understand the precise relationships between thousands of genomes. In these, the genome is encoded in a graph that may represent a population sample of individuals from the same species, a metagenome, the diploid genome of a single individual, or any other useful collection of sequences.
Andrea Guarracino - Postdoctoral Scholar
Computer (bio)scientist dedicated to developing and applying new methods to analyze ever-larger collections of sequences (also called "pangenomes") in the tree of life.
Simon Heumos - PhD student
Bioinformatician by training. I am exploring methods to calculate and visualize pangenome graph layouts. These are key steps in pangenome graph construction and analysis pipelines. Cluster-scalable pangenomics is the next step.
Practical Course Helpers
Flavia Villani - PhD student
I have a master degree in Medical Biotechnology from the University of Naples Federico II. Currently, I am a PhD student at the University of Tennessee Health Science Center. I am building the pangenome of model organisms (inbred mice and rats) using a combination of second and third generation sequence data.
Conference Invited speakers
Organizers
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Andrea Guarracino, University of Tennessee Health Science Center, Memphis, TN, US
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Erik Garrison, University of Tennessee Health Science Center, Memphis, TN, US
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Flavia Villani, University of Tennessee Health Science Center, Memphis, TN, US
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Pjotr Prins, University of Tennessee Health Science Center, Memphis, TN, US
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Shelby Solomon Darnell, University of Tennessee Health Science Center, Memphis, TN, US
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Simon Heumos, Quantitative Biology Center (QBiC), Tübingen, BW, DE
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Vincenza Colonna, University of Tennessee Health Science Center, Memphis, TN, US
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Tamara Brock, University of Tennessee Health Science Center, Memphis, TN, US
University of Tennessee Health Science Center, Department of Genetics, Genomics and Informatics
Program
Practical course / Workshop
Time: Saturday-Sunday, 18th-19th May 2024
| Day | Time | Speaker(s) | Topic |
|---|---|---|---|
Saturday, May 18, 2024 |
09:30-10:00 |
Presentation: Introduction to pangenomics |
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10:00-10:30 |
Everyone |
Practical |
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10:30-11:00 |
Everyone |
Coffee break |
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11:00-12:30 |
Everyone |
Practical |
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12:30-14:00 |
Everyone |
Lunch (provided) |
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14:00-14:30 |
Presentation: Understanding pangenomes |
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14:30-15:30 |
Everyone |
Practical |
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15:30-16:00 |
Everyone |
Coffee break |
|
16:00-16:45 |
Everyone |
Practical |
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16:45-17:00 |
Everyone |
Q&A, Day 1 Survey |
| Day | Time | Speaker(s) | Topic |
|---|---|---|---|
Sunday, May 19, 2024 |
09:30-10:00 |
Everyone |
Discussion about previous day activities |
10:00-10:30 |
Presentation: Heterologous recombination in the human pangenome |
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10:30-11:00 |
Everyone |
Coffee break |
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11:00-12:30 |
Everyone |
Practical |
|
12:30-14:00 |
Everyone |
Lunch (provided) |
|
14:00-14:30 |
Presentation: nf-core/pangenome, pangenome growth |
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14:30-16:00 |
Everyone |
Practical |
|
16:00-16:30 |
Everyone |
Coffee break |
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16:00-16:45 |
Everyone |
Practical |
|
16:45-17:00 |
Everyone |
Q&A, Day 2 Survey |
Conference
Time: Monday, 20 May 2024
| Chair | Time | Talk | Speaker |
|---|---|---|---|
09:20 - 09:30 |
Conference Opening |
Erik Garrison |
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09:30 - 10:00 |
Counting K-mers on distributed memory efficiently with sorting and task-based parallelism |
Yifan Li (VIRTUAL) |
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10:00 - 10:30 |
Towards the Mouse Pangenome: Complete sequence representation of diverse mouse haplotypes and genes |
Mohab Helmy (VIRTUAL) |
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10:30 - 11:00 |
Coffee break |
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11:00 - 11:30 |
Toward Hardware-Accelerated Pangenome Analyses |
Adrian Sampson |
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11:30 - 12:00 |
Scalability and Productivity in Genomics on Massively Parallel Systems |
Giulia Guidi |
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12:00 - 12:30 |
A*PA & A*PA2: Up to 20 times faster exact global alignment |
Ragnar Groot Koerkamp |
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12:30 - 14:00 |
Lunch |
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14:00 - 14:30 |
Restoration of Ancient Genomes with the PanGenome: The good, the bad and the ugly |
Brandi Cantarel |
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14:30 - 15:00 |
GWAS on an Arabidopsis MAGIC pangenome |
Arun Isaac |
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15:00 - 15:10 |
Conference Closing |
Vincenza Colonna |
Biohackathon
Time: Tuesday-Wednesday, 21st-22nd May 2024
| Day | Time | Speaker(s) | Topic |
|---|---|---|---|
Tuesday, May 21, 2024 |
09:30-10:30 |
Everyone |
Hacking |
10:30-11:00 |
Everyone |
Coffee break |
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11:00-12:30 |
Everyone |
Hacking |
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12:30-14:30 |
Everyone |
Lunch |
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14:30-15:30 |
Everyone |
Hacking |
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15:30-16:00 |
Everyone |
Coffee break |
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16:00-17:00 |
Everyone |
Hacking |
| Day | Time | Speaker(s) | Topic |
|---|---|---|---|
Wednesday, May 22, 2024 |
09:30-10:30 |
Everyone |
Hacking |
10:30-11:00 |
Everyone |
Coffee break |
|
11:00-12:30 |
Everyone |
Hacking |
|
12:30-14:30 |
Everyone |
Lunch |
|
14:30-15:30 |
Everyone |
Hacking |
|
15:30-16:00 |
Everyone |
Coffee break |
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16:00-17:00 |
Everyone |
Hacking |
Registration and Practical Information
Conference pre-registration for speakers: ended
Registration for event attendees: ended
Registration includes access to: all lectures and practical sessions, all course materials.
Cost
The cost includes all expenses associated with the event, with lunches, coffee, and snacks. In certain circumstances, we can waive the fees.
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Academic - $200, with financial support if needed
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Industry - $400
Selection criteria
This practical course / workshop is intended for biologists and bioinformaticians interested in studying organisms with high genetic diversity or without a reference genome, as well as those involved in comparative genomics and the assembly of pangenomes for any species.
Selection of participants will be based on:
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good knowledge of Linux operating system and basic shell commands. This will be a mandatory prerequisite.
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familiarity with genomics data formats (e.g., FASTA, VCF, BED, …) is a plus.
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impact of the practical course / workshop for the participant and his/her research group.
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stage of the research project: priority will be given to participants with data already available and ready to be analyzed (participants data will not be analyzed during the practical course / workshop).
Fulfillment of these conditions by participants will be assessed through the registration form.
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