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July 13: ISMB Day 2 Highlights and Recap

Prior to the day’s keynote address, Day 2 of ISMB 2024 started off with a celebration of the ISCB 2024 Class of Fellows and presentation of the Fellows Awards to those that were in attendance, as well as the award presentation to Dr. Scott Markel, the recipient of the Outstanding Contributions to ISCB Award!

After the morning celebration and keynote talk, the remaining highlights for the day included the first day of the poster session, 8 COSI tracks, the NIH/ODSS special session, and Technology Track presentations.
 

Keynote Address

With her talk, “New Methods for Very Large-Scale Tree Estimation,” Dr. Tandy Warnow, the ISCB Accomplishments by a Senior Scientist Award keynote speaker, kicked off day two of the ISMB 2024 conference!

Dr. Warnow explored the complexities and advancements in phylogenomics, particularly focusing on the estimation of large-scale phylogenies and their applications to basic science questions, such as understanding the evolution of life on Earth. She highlighted the computational and statistical challenges posed by large datasets, including issues related to missing data, heterogeneity, and the sheer number of loci and species involved. Estimating these phylogenies, which can have potentially millions of leaves, requires sophisticated approaches due to the statistical and computational difficulties involved.

In response to the challenges posed by the phylogenetic estimations, Dr. Warnow emphasized the utility of divide-and-conquer approaches, such as supertrees and disjoint tree mergers (DTMs), to manage the challenges effectively, explaining that methods like Markov models and maximum likelihood tree estimation can help researchers infer phylogenies with improved statistical consistency and sample complexity. However, she noted that scalability and accuracy remain significant challenges, particularly for large datasets.

There is a need for new methods to handle discordance in species trees due to biological factors like gene duplication, loss, and incomplete lineage sorting. Dr. Warnow also addressed the importance of post-tree analyses, including rooting gene and species trees, estimating branch lengths, and dating internal nodes, which are essential for downstream analyses.

Finally, Dr. Warnow underscored ongoing efforts to develop better divide-and-conquer strategies, scalable supertree methods, and improved theoretical frameworks to enhance the accuracy and feasibility of large-scale phylogenetic analyses, inviting further research and innovation in this evolving field.
 

Session Recaps

Education

The Education COSI covered an exciting collection of contributed talks, proceedings talks, and keynotes.  The session opened with our first keynote speaker, Rolanda Julius, speaking about advances in data science training and health innovations in Africa.  Contributed talks spoke about familiar areas to the community, such as use of competency frameworks through talks by Marta Lloret Llinares, Nilson Coimbra, and Dusanka Nikolic.  New directions and case studies in bioinformatics education were presented in further contributed talks by Sara Fumagalli, Nia Hughes, and Ana Swan, and Priyanka Surana.  Michelle Brazas and Russell Schwartz gave a quick summary of many directions for the community covered at the most recent Bioinformatics Education Summit, an annual international meeting of the community held this past May in New York.   And our program for the first time featured two proceedings talks, by Pavlin Polikar and Selly Selem-Mojica.  Closing out the session was our second keynote, by Francis Ouellette, to provide a perspective on education and training efforts of our local hosts, Bioinformatics.ca, over the past 25 years. These and other topics will see further follow-up in through education posters and the Workshop on Education in Bioinformatics (WEB).

HiTSeq

HitSeq COSI was pleased to present today a total of 2 keynote speakers, 8 oral presentation from PhD students, postoc and principal investigators and a Invited presentation from PacBio, the sponsor for HitSeq this year.

  • The track debuted with keynote speaker Dr. Sushmita Roy, where she discussed how changes in 3D genome organization can lead to transcriptional changes and unsupervised learning methods for regulatory genomics.  

  • Talks from students comprised of presentations of tools and predictive models  to improve splicing status of scRNAseq reads, single-cell and spatial clustering, classification of nanopore singal and structural variant discovery.

  • HitSeq was also pleased to hear from PacBio (sponsor) representant, Dr. Liz Tsent where she discussed how novel data requires new tools for analysis and diverse sequencing platforms such as isoform characterization, variant detection, phasing, and quantification. She recommend to read PacBio preprint Vollger et al. bioRxiv(2023) which delves into PaciBio efforts to analyze the multiome: genome + methylome + epigenome + transcriptome.

  • Finally, the amazing HitSeq day ended with the second keynote speaker of the day Dr. Evan Eichler, a fascinating talk about the importance of understanding the complexity of human genomes and how HiFi Pac Bio sequencing and Ultra Reads ONT have enabled us to understand human complexity and variation. He also discussed how pangenomes robustly represent human complexity. One pangenome can provide better resolution than 7 linear references.

No wonder why the audience was so engaged and having a lot of questions!

 

iRNA

The iRNA COSI started off with a keynote by Julia Salzman who presented SPLASH, a new statistics-first analytic approach which represents a paradigm shift in the analysis of sequencing datasets. We then had many talks discussing sequencing biases, new methods and approaches enabling a better resolution of the transcriptome/epitranscriptome and their application to specific contexts resulting in an increased understanding of the transcriptome, its regulation and its output. Our lively lunchtime poster session was advertised by nice concise, dynamic and original flash talks. Our last talk of the day was a keynote by Ashley Laughney who described tools to map genotypes to complex cellular and in vivo functions at scale and approaches that investigate the startling findings that activation of a given protein or signaling pathway can lead to very diverse functional outputs depending on the context.
 

🎉Youth Bioinformatics Symposium Winner🎉

Congratulations to Savanna Larson from Minnetonka High School for winning the 2024 YBS Student challenge with their submission "Evaluating the effects of sympatry on Canada lynx and bobcat population dynamics in Minnesota"
 

🧭 Career Compass Featured Jobs

Researcher, University of Oklahoma

From the job description: “Whether your degree is in Biomedical Sciences, Biochemistry, Molecular and Cellular Biology, Bioinformatics, Computer Science, or Mathematics, if you are passionate about working at the intersection of biology and computation, interested in functional genomics and thrive in a highly collaborative and dynamic environment, this is the perfect PhD or PostDoc opportunity for you.”

 

Protein Engineering Data Scientist, IFF, United States California Palo Alto

From the job description: “At IFF we are looking for an experienced machine learning oriented protein engineer. As part of our team, you will identify the state-of-the-art in data-driven methods for library design, adjust them to our purposes and help implement them for direct use in business projects. . . As a Protein Engineering Data Scientist, you will help to define our design strategy and to implement it so that it seamlessly integrates with our high-throughput screening workflows.”

 

PhD in Bioinformatics in Tropical Australia, James Cook University

From the job descrption: “Successful PhD candidate will work with leading immunologists and bioinformaticians across Australia in networks including the Centre for Personalised Immunology (www.cpi.org.au) and CIRCA (www.garvan.org.au/research/collaborative-programs/circa). This project will utilise the latest in sequencing technologies (including single cell and long reads) to discover the genetic contribution to human immunological diseases. This PhD would help develop cutting edge bioinformatics workflows and through collaborations with the Garvan Institute of Medical Research to further our understanding of the progression of autoimmune disease.”

 

Brue Mitchell fellow, Queen's University

From the job description: “We invite you to join our laboratory affiliated with Queen’s University, School of Medicine, and School of Computing. This prestigious Bruce Mitchell PhD fellowship offers an opportunity to work and receive training in computational methods and data analysis for studying the epigenetic mechanisms of cancer. The fellow is expected to collaborate closely with an experimental group from the Biology Department to elucidate the mechanisms of cancer mutations in histone and chromatin remodelers.”
 

Quick Updates and Reminders

  • If you’ve been referring to the detailed schedule that’s been displayed on the screens around level 5, you’re in luck! You can now download your own version. Click here or access it from the Quick Links menus on the ISMB home page!

  • Talk and poster presenters: Please review the details found on the Presenter Information Page.

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Coming Up Tomorrow, Sunday, July 14
Abridged Agenda
 
 
 
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