Day 3: Highlights & Recap!
What a day ISMB 2022 just had! Half way through the conference and going strong. Thank you to everyone for their continued patience and kindness as we continue to work to make the remainder of the conference a smooth and enlightening experience for all attendees, both virtually and in person.
Highlights
Dr. Aida Ouangraoua brought us together this morning for our third keynote address of ISMB 2022 to discuss her research on the challenges and solutions of investigating gene evolution at the transcript level, which provides a more refined level of functional evolution and diversity than considering gene evolution at the gene level. Even with this greater refinement, however, are four distinct challenges to transcript-level investigations. For instance, gene alignment models must account for gene and exon-intron structure, transcript evolution models must account for changes at transcript and gene levels, gene orthology/paralogy definitions must be extended at the transcript level, and clean and complete transcriptome data are required for transcript-level exploration of gene evolution.
To address these challenges, Dr. Ouangraoua’s lab has made some great methodological contributions, namely, multiple spliced alignment, transcript tree–gene tree reconciliation, and developing a transcript-centric database (TranscriptDB). But, as with any scientific endeavour, there is still more work to be done! Dr. Ouangraoua rounded out her keynote address by presenting important perspectives to consider with the study of transcript-level gene evolution. Researchers will need to consider more complete models of gene family evolution, more complete models of gene structure evolution, and more complete models of transcript evolution. These more complete models can then be used to improve gene and species trees.
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COSI Recaps:
iRNA COSI
The 2022 iRNA COSI took place on July 11 and 12. Our first iRNA track talk was given by Kin Fai Au from Ohio State University who discussed analysis of sequencing considering long read sequencing for isoform identification and quantification, with very useful recommendations. This talk was followed by several long and short talks discussing the use of long read sequencing and its comparison to short read sequencing considering many different datasets, conditions and systems, enabling collectively a deeper and much increased exploration and knowledge of the transcriptome than what is known in current annotations. Near the end of the first day, we also heard about the analysis single-cell RNA-seq, tools and examples of applications. Our COSI dinner at The Great Dane Pub and Brewing Company, including our traditional quiz proved very entertaining, and led to the conclusion that we all need to improve our knowledge of Madison and Wisconsin. Our second day was kicked off by Liana Lareau from UC Berkeley who discussed the study of splicing in single-cell sequencing, presenting a new tool that addresses the low of sequencing depth per cell, leading to very insightful observations. The following talks explored the computational analysis of diverse levels of gene expression regulation, from splicing and 3’ end processing to translation in different systems. We also heard about tools for the prediction of CRISPR/Cas9 gRNA design and therapeutic siRNAs. Our last keynote, Chase Weidmann from the University of Michigan, discussed RNA-protein interactions and a chemical probing approach to investigate them. Overall, it was a very productive meeting.
VarI COSI
This year VarI COSI held its 12th session, bringing the latest developments and discoveries on variant interpretation to ISMB. The session included 11 talks, 1 proceedings presentation and 3 keynote speakers. The first keynote featured Nicole Sorenzo who opened with a complete overview of her major discoveries characterizing the genetic and epigenetic components associated to human heterogeneity across multiple ‘omics readouts and how they relate to complex phenotypes as well as to rare diseases. The second keynote was given by David Robertson who provided a comprehensive review of the current understanding of SARS-CoV-2 phylogenetic origins, the sequence and structural features associated to its spread in humans and its ongoing evolutionary dynamics. Nathaniel Sharp gave the third keynote on the rate of mutation accumulation in diploid versus haploid yeast and how copy number context can affect mutation rates. Talks and proceeding presentations covered major areas in the field of variant interpretation, including approaches based on protein structural features and protein-protein interaction networks (Missense3D-PPI and Network&AA methods); statistical genetics methods to enhance the detection of genotype-phenotype associations (e.g. PolarMorphism method and sex-specific effects in hypertension); somatic variant interpretation and evolutionary trajectories in cancer phylogenies (MASTRO method), comparative genomic approaches to detect sequence constraints in humans -including constraints on synonymous variants - and how these relate to pathogenic variants (e.g. the Homologous Missense Constraint score); studies for improved clinical assessment of genetic variants (CAGI experiments lessons and calibration approaches of computational scores); and the assessment of the regulatory role of RNA G-quadruplex (rG4). Finally, the session included a presentation by our sponsor Variantyx, where Shane Hussey presented the validation of WGS for clinical use down to 50ng of DNA using a PCR-Free tagmentation protocol. This year's session saw more than 150 delegate registrations, and active participation with questions and discussions both on site and virtual.
TransMed COSI
TransMed COSI 2022 started with a very insightful keynote talk by Prof. Anthony Brookes (Department of Genetics & Genome Biology, University of Leicester, UK) discussing solutions and infrastructures that are necessary for data science in biomedicine and the importance of data findability and reuse.
We had 5 proceedings, 12 talks and 40 posters. These covered different methodologies, especially machine learning, multi-layered clinical, translational data analysis and their applications in different translational medicine areas including different types of diseases (cancer, COVID19, endometriosis, paediatric sepsis), drug response, signalling networks, genotype-phenotype associations, cancer imaging and healthcare data.
Our COSI session closed with another great keynote talk by Dr. Elana J. Fertig (SKCCC / Johns Hopkins University, United States) on how spatial transcriptomics can be used to explore mechanisms of therapeutic response and resistance in clinical trials.
Education
The Education COSI featured an exciting and diverse program of talks, including invited keynotes, contributed abstract talks, and two talks from accepted proceedings papers. The ISCB education program kicked off with the Workshop on Education in Bioinformatics (WEB), a mix of talks and working sessions on the theme of sustainability. The main COSI program featured two eminent keynote speakers: Ben Moore of EMBL-EBI speaking about bioinformatics education in low and middle income countries (LMICs) and Charla Lambert of Cold Spring Harbor Labs (CSHL) speaking about inclusiveness in bioinformatics education. The contributed talks covered topics in infrastructure for supporting trainers and trainees, novel pedagogical ideas, and case studies in bioinformatics training for diverse audiences and training needs. We closed out the day’s program with a lively panel discussion continuing the conversation on inclusiveness in bioinformatics education, featuring our keynote speakers and Lucia Peixoto representing the ISCB Equity, Diversity, and Inclusion
(EDI) Committee.
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Technology Theatre
Today’s TechTrack talks provided a glimpse into some exciting tools available for scientists! A handful of useful and user friendly options for creating 3D models for protein structure were discussed (AlphaFold, IntFOLD, Phyre2, and CATH), as well as servers to analyse the impact of missense variants (Missense 3D), and to map these variants to protein complexes (GWYRE). There were also some great advances in spatial biology profiling technologies (Giotto Suite) discussed!
Notably, there was a distinct message of collaboration through the use of cloud-
based technology outlined in this morning’s TechTrack talks, specifically Google Cloud’s RAD Lab for Research, and the LaTeX Authoring Platform, Overleaf. The RAD Lab presentation pointed out some great benefits for researchers to store their work in, and work from, the cloud. They pointed out not only the security of the cloud, but the scalability of the cloud to handle growing data sets, that the cloud enables AI and machine learning on larger data sets with more/different computer power, that the cloud aids in the reproducibility of research, and, most notably, the cloud allows for easier and more streamlined collaboration of researchers within and between countries. Overleaf noted a similar collaborative benefit, especially with their professional and other upgraded account versions: users can invite an unlimited number of collaborators!
Finally, the idea of a holistic approach to publishing—that is, alternatives to the
traditional approach to academic publishing—was put forth by F1000 Research. It was pointed out that in the last two years, researchers have been moving away from traditional academic publishing that is behind a paywall, has a closed peer-review system, and an emphasis on journal-level metrics in favor of more open-access-friendly methods for both themselves and readers. F1000 notes that they provide open publishing solutions that include open access, open data, open source, open methods, and open peer review to help encourage interaction and collaboration within the scientific community. |
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| These talks are now available on ISMB On-Demand. |
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Tips & Tricks:
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As a reminder masks are required for in-person attendance at ISMB 2022 as outlined at: https://www.iscb.org/ismb2022-general/health-and-safety
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Navigate ISMB 2022 Like a Pro:
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| Wednesday, July 13: Highlights & Reminders
7:30AM - 8:30AM: Virtual Poster Session (via Conference Platform)
8:30AM - 8:45AM: Morning Welcome
8:45AM - 9:45AM: ISCB Accomplishments by a Senior Scientist Award Keynote: Ron Shamir, Integration, modularity and network analysis for understanding disease
9:45AM - 10:30AM: Caffeinate and Connect with exhibitors (Grand Terrace)
10:30AM - 12:30PM: Morning Sessions: RegSys COSI, HitSeq COSI, MLCSB COSI, BOSC COSI, 3DSIG COSI, MICROBIOME COSI, Evolution and Comparative Genomics COSI, BioVis COSI, Bio-Ontologies COSI
12:30PM - 2:30PM: Lunch and Ideation Hall (Poster Session B) Room: Exhibit Hall A (Level 1)
2:30PM - 3:30PM: Sessions Continue
3:30PM - 4:00PM: Caffeinate and Connect with exhibitors
4:00PM - 6:00PM: Sessions Continue
6:15PM - 7:15PM: Birds of a Feather (BoF):
Comparative Genomics Resource: a powerful tool for scientific discovery
Cloud Computing and Bioinformatics
6:15PM - 7:15PM: Virtual Poster Session (via Conference Platform)
6:15PM - 8:15PM: Protein Codeathon: Final Team Presentations
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Thank you to our generous sponsors!
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