Computational pangenomics course, conference, and biohackathon in Memphis, TN, exploring the cutting edge of pangenomes, biology, methods, software, and artificial intelligence (AI).

400
400

Important Dates

  • Practical course/Conference/Biohackathon Registration Deadline: 13th April 2024

  • Selected Participant will be notified by: 22nd April 2024

  • Payment Deadline: 4th May 2024

  • Practical course / Workshop: 18th-19th May 2024

  • Conference: 20th May 2024

  • Biohackathon: 21st-22nd May 2024

Venues

Practical course / Workshop

University of Tennessee Health Science Center
Memphis, TN 38163
United States
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Conference

University of Tennessee Health Science Center
Memphis, TN 38163
United States
See the venue on the map

Biohackathon

University of Tennessee Health Science Center
Memphis, TN 38163
United States
See the venue on the map

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, 2023
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

Tuesday, May 21, 2024 - Wednesday, May 22, 2024

We have a focus on software. We will work with/on pangenomic tools (such as PGGB, WFMASH, SEQWISH, ODGI, SMOOTHXG, VG, VCFLIB, GEMMA) with software project leadership. You are welcome to bring your own projects!

People

Practical Course / Workshop Instructors

Erik Garrison - Assistant Professor

University of Tennessee Health Science Center, Memphis, TN, US

erik 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

University of Tennessee Health Science Center, Memphis, TN, US

erikComputer (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

Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, DE | Biomedical Data Science, Department of Computer Science, University of Tübingen, Tübingen, DE

simon

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

University of Tennessee Health Science Center, Memphis, TN, US

flavia 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

TBD


Organizers

  • Andrea Guarracino, University of Tennessee Health Science Center, Memphis, TN, US

  • Erik Garrison, University of Tennessee Health Science Center, Memphis, TN, US

  • Flavia Villani, University of Tennessee Health Science Center, Memphis, TN, US

  • Pjotr Prins, University of Tennessee Health Science Center, Memphis, TN, US

  • Vincenza Colonna, University of Tennessee Health Science Center, Memphis, TN, US

uthsc

University of Tennessee Health Science Center, Department of Genetics, Genomics and Informatics

College of Medicine, Department of Pediatrics

Program

Practical course / Workshop

Place: TBD

Day Time Speaker(s) Topic

Saturday, May 18, 2024

09:30-10:00

Erik Garrison

Presentation Introduction to pangenomics

10:00-10:30

Everyone

Practical

10:30-11:00

Everyone

Coffee break

11:00-12:30

Everyone

Practical

12:30-14:30

Everyone

Lunch (provided)

14:30-15:00

Andrea Guarracino

Presentation: Understanding pangenomes

15:00-16:00

Everyone

Practical

16:00-16:30

Everyone

Coffee break

16:30-17:15

Everyone

Practical

17:15-17:30

Everyone

Q&A, Day 1 Survey

Sunday, May 19, 2024

09:30-10:00

TBD

TBD

10:00-10:30

Everyone

Practical: TBD

10:30-11:00

Everyone

Coffee break

11:00-12:30

Everyone

Practical: TBD

12:30-14:30

Everyone

Lunch (provided)

14:30-15:00

Simon Heumos

Presentation: pangenome openness, nf-co.re/pangenome

15:00-16:00

Everyone

Practical: TBD

16:00-16:30

Everyone

Coffee break

16:30-17:15

Everyone

Practical: TBD

17:15-17:30

Everyone

Q&A, Day 2 Survey

Conference

Time: Monday, May 20, 2024
Place: TBD

Chair Time Talk Speaker

09:20 - 09:30

Conference Opening

TBD

Andrea Guarracino

09:30 - 10:00

TBD

TBD

10:00 - 10:30

TBD

TBD

10:30 - 11:00

Coffee break

Simon Heumos

11:00 - 11:30

TBD

TBD

11:30 - 12:00

TBD 

TBD

12:00 - 14:00

Lunch

Flavia Villani

14:00 - 14:30

TBD

TBD

14:30 - 15:00

TBD

TBD

15:00 - 15:10

Conference Closing

TBD

Biohackathon

TBD

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 is intended for the practical course / workshop. Conference and biohackaton are free. Meals (lunches) and coffee are included and provided for both 2 days during the Practical course / Workshop.

  • Academic - $200, with financial support if needed

  • 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:

  • good knowledge of Linux operating system and basic shell commands. This will be a mandatory prerequisite.

  • familiarity with genomics data formats (e.g., FASTA, VCF, BED, …​) is a plus.

  • impact of the practical course / workshop for the participant and his/her research group.

  • 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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