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July 15: ISMB Day 4 Recap

On our second last day of ISMB 2024, the schedule was as full as ever, with 8 COSI tracks, the General Computational Biology track, more Technology Track presentations, and 2 special sessions, including the Equity and Diversity in Computational Biology Research session, and the WEB 2024 session on Experiential Learning on How to Implement AI in Bioinformatics Training.

In addition, this evening was also when the ISCB Town Hall was held, allowing conference participants to learn about the latest programs and initiatives from ISCB, as well as upcoming conferences. At this meeting, they were also able to provide feedback and suggestions to help shape the future of the society.

**Please make sure to read the “Important Notes” section below.**

 

Keynote Address

Dr. Martin Steinegger, the 2024 ISCB Overton Prize Award winner, kicked off day four of ISMB 2024 with his keynote address entitled, “Supercharged Protein Analysis in the Era of Accurate Structure Prediction,” in which he focused on accelerating biological science through fast, open-source methods, the main mission of his lab.

He then went on to introduce MMseq2, an ultrafast and sensitive sequence comparison tool that achieves an unmatched tradeoff in speed versus sensitivity, crucial for annotating difficult cases. The Big Fantastic Database (BFD), a huge protein reference catalog, was highlighted for its enormous diversity and utility in searching for newly discovered proteins.

A significant focus of Dr. Steinegger’s talk was on recent advancements in protein structure prediction, notably AlphaFold2—an accurate predictor of protein structures that uses multiple sequence alignments (MSA) of homologous proteins. Dr. Steinegger then introduced Foldseek, a groundbreaking tool for ultra-fast searching and clustering of protein structures. This tool encodes structures as sequences by discretizing tertiary interactions, allowing for rapid searches across billions of structures with high sensitivity and alignment quality comparable to TMalign, but significantly faster.

Dr. Steinegger concluded with a discussion of clustering protein structures and analyzing the protein universe using MMseq2 and Foldseek. This analysis revealed that 35% of clusters lack annotation, with known proteins tending to cluster together. He also touched on Foldseek-multimer, which addresses the problem of chain mapping in multichain alignments.

Dr. Steinegger concluded his talk by stating that while sequence analysis remains fundamental to protein structure studies, new structural tools are now supercharging this analysis, opening up exciting possibilities in biological research!

 

 

Quick reminder that tomorrow, July 16, there will be an LGBTQI+ lunch meetup. Grab your lunch from the poster hall and head to room 523b!

 

Session Recaps

 

NetBio

We had an exciting full-day program at the NetBio session.

 Morning Session: A Dynamic Start
The NetBio session today began with an inspiring keynote by Anne-Claude Gingras, who presented her work on "Using proximity-dependent biotinylation to understand dynamic cell organization." Gingras showcased approaches for studying the spatial and temporal aspects of protein interactions within cells, providing invaluable insights into subcellular organization and dynamics.

Merel Kuijs continued the program with her presentation of their proceedings paper on the GraphCompass (10.1093/bioinformatics/btae242). After two selected talks on network approaches for MS proteomics data, we had our first NetBio poster session over lunch with lots of discussions and networking.

Afternoon Session: Bridging Disciplines
The afternoon session opened with Chao Deng presenting their proceeding paper (10.1093/bioinformatics/btae257) on candidate gene identification using hypergraph neural networks. The following selected talks covered topics around link prediction, multi-layer networks, machine learning, and protein sequenced-based LLMs.

Dongmin Bang highlighted their approaches for drug response prediction described in their proceeding paper (10.1093/bioinformatics/btae249) before we concluded our session with a fantastic keynote by Patrick Aloy on “Blending Biology, Chemistry and AI through network embeddings”.

 What’s coming up
Don’t forget to stop by the second half of the NetBio posters tomorrow during the lunch break! We are also excited that our best talk and poster prizes will be announced during the ISMB2024 award presentation session on Tuesday afternoon.

 Thank you
A big thank you to all presenters, both for their talks and posters, for their invaluable contributions to the success of today's session. Special thanks to the COSI organizing team for putting together an exciting program highlighting the diverse applications of network biology ranging from novel methods and innovative research applications to important tools and resources that advance the field. Also, a thank you to the technical support staff at the conference and the ISCB staff that is always ready to help.

TransMed

We kicked off our TransMed meeting at ISMB 2024 this afternoon! Reinhard Schneider (University of Luxembourg) presented brief updates of our community since the previous edition and introduced the current meeting that will run until tomorrow afternoon. This year, we will have a new session dedicated to Poster Flash Talks, 12 - 12.20pm tomorrow. Today, we had two proceedings (TA-RNN: https://doi.org/10.1093/bioinformatics/btae264 and PhiHER2: https://doi.org/10.1093/bioinformatics/btae236) and three selected talks covering methods and tools for cancer research, including the eHDPrep package for electronic health data preparation, identification of candidate drugs for repurposing for breast cancer and investigation of the impact of clinically relevant gene fusions in head and neck cancer. We thank all our speakers and participants and we are looking forward to continuing tomorrow with our keynotes, selected and flash talks as well as with the poster presentations.

 

Important Notes

POSTERS
All posters must be taken down by 3pm tomorrow, Tuesday, July 16.

LUGGAGE
We do not have a supervised luggage check this year.

If you’re leaving right after the conference and your hotel is nearby, you can ask the staff at the front desk of your hotel if they can hold your luggage for you. If your hotel isn’t nearby, you will be able to place your luggage in the space to the left of the registration desk, but note that neither ISCB event staff nor the Palais staff will be responsible for your luggage.

LOST ITEMS
If you’ve lost something while attending sessions during the conference, please visit the ISMB registration desk as many lost items have been dropped off there.

TRANSPORTATION TO THE AIRPORT
Bus:
The 747 Express bus will take you from the Station Place D’Armes (accessible on the 1st floor of the Palais de congrès de Montréal) to the Montréal Airport (YUL).

From the city of Montréal’s website regarding 747 bus travel:

Don’t miss this step! Whether you’re leaving the airport or going to the airport, it’s best to get your ticket before boarding. At the airport, buy a ticket at one of the four vending machines in the international arrivals area. If you’re downtown, visit any of the Métro stations. You can pay in cash, by debit card, or with VISA or MasterCard credit card. You will need the 24-hour ticket, which currently costs $11. (Note: it is possible to purchase a ticket on board, but you’ll need exact fare: $11 in coins.)”

Ride Share: If you want to travel by Uber to the airport, consider the ‘Share’ option to lower travel expenses, or connect with other conference attendees and split the fare for an Uber or taxi.

 

Coming Up Tomorrow, Tuesday, July 16

Abridged Agenda
Detailed Agenda
 
 
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