COSI Information

Leadership Structure
Name Email Institution Position Country Position
Rafael Najmanovich rafael.najmanovich@umontreal.ca University of Montreal PI CA Chair
Douglas Pires douglas.pires@unimelb.edu.au University of Melbourne PI AU Chair
Alexey Porollo Alexey.Porollo@cchmc.org Cincinnati Children's Hospital Medical Center PI US Track Editor
Anna Marabotti amarabotti@unisa.it University of Salerno PI IT Track Editor
Ray Arjun rayarjun@gmail.com Indraprastha Institute of Information Technology (IIIT) PI IN Track Editor
Javier Alfaro javier.alfaro@proteogenomics.ca International Center for Cancer Vaccine Science (University of Gdansk) PI PL/ Track Editor
Lam Su Datt sudatt@ukm.edu.my Universiti Kebangsaan Malaysia PI Malaysia Track Editor and Webinar Coordinator
Stephen Yi Stephen.yi@austin.utexas.edu The University of Texas at Austin PI US Webinar Coordinator
Daniel Buchan daniel.buchan@ucl.ac.uk UCL PI UK Track Editor and Training Coordinator
Rafaela Ferreira rafaelasalgadoferreira@gmail.com Universidade Federal de Minas Gerais PI Brazil Track Editor
Chris Kieslich kieslich@auburn.edu Auburn University PI US Track Editor and Training Coordinator
Stuart MacGowan s.macgowan@dundee.ac.uk University of Dundee PI UK Track Editor and Comms Coordinator
S. Byamal sbyamal@gmail.com University of Kansas Postdoc US Track Editor
Ravinder Abrol ravinder.abrol@csun.edu California State University PI US Track Editor and Hackaton Coordinator
Carlos Rodrigues carlosmr12@gmail.com University of Queensland Postdoc AU Training Coordinator and Hackaton Coordinator + Comms
Sara Capponi sara.capponi@ibm.com IBM Research NA US Track Editor
Bruna Moreira munamomo@gmail.com University of Melbourne PhD Student AU Training Coordinator + Comms
Sandro Izidoro sandroizidoro@unifei.edu.br Universidade Federal de Itajubá PI Brazil Track Editor
Raul Secchi raul.secchi@nbi.ku.dk University of Copenhagen Postdoc Denmark Track Editor

Activities Over the Last Year
3DSIG is an ISMB Community of Special Interest (COSI) that covers the latest and most innovative research in the all aspects of molecular biology and biophysics informed by structural data through computational methods.

3DSIG was formed in 2004 by Ilan Samish and John Moult initially as a satellite meeting. In 2006 3DSIG had its second installment and with the inclusion of Rafael Najmanovich to the organizing committee in 2006, it became an annual event. Over the years 3DSIG has had a broad selection of keynote speakers. Most notably in 2022, our one of our keynote speakers was David Baker (U. Washington), who we have been trying to have as a keynote for more than a decade. The two keynotes in 2022, Robert Jernigan and David Baker spoke for the first time in 3DSIG but we hope to invite them again in the future, as we consider anew the impact of their publications ever since they last appeared in 3DSIG. In general, the mechanism to select keynote speakers include considerations of geographic location relative to the meeting, past presentations at 3DSIG, life-time contributions to structural bioinformatics and computational biophysics as well as recent specific contributions.

The selection of oral presentations from contributed abstracts at 3DSIG has always been the result of an independent vote by a committee (track reviewers). In the past it included the co-chairs of 3DSIG as well as keynote speakers. More recently, since 2021 only track editors and co-chairs have been involved. The vote is independent, and voting is prevented in specific cases of conflicts of interest, such as a member voting for his own contributions. As a result of this methodology, no one has any control over the selection of oral presentations. For example, in 2022, three graduate students in the Najmanovich group were selected for oral presentations. This came about as a result of voting by at least 4 track editors, and their PI, Rafael Najmanovich had no saying or right to vote.

3DSIG always accepts at least 2 proceedings papers and has in the past accepted up to four during the 2 days.

After all accepted oral presentations and proceedings papers were selected, the Co-chairs build the 2 day program trying to group contributions into themes that are presented in specific sessions during 3DSIG.

In terms of activities outside ISMB, 3DSIG hosted 2 seminars in 2022 for the ISCBAcademy:
- February 15, 2022: Critical Assessment of Computational Hit-finding Experiments (CACHE): An Initiative to Guide Future Computational Drug Design by Matthieu Schapira
- September 6, 2022: Functional variomics: Systematic annotation of somatic mutations and gene fusions in cancer by Nidhi Sahni

Our Slack community (3dsig-cosi.slack.com) currently has 272 members. In 2022, 80 new members joined. Among those, 31 joined before 3DSIG at ISMB 2022, 23 joined during 3DSIG (July 13 and 14, 2022) and 26 joined after 3DSIG. This is encouraging and shows that interest for the 3DSIG COSI does not peak solely during 3DSIG or as a result of having submitted an abstract to ISMB.

The entire leadership team (see table above) started as of January 2023 to meet monthly to discuss the development of 3DSIG and its activities.

Equity, Diversification, and Inclusion Efforts
We strive to have a balance in terms of sex of keynotes at the level priorities of invitations but in 2022, none of the female (description of sex) invited speakers we able to accept our invitation.

Leadership Structure
COSI representative to committee: Núria Queralt Rosinach
COSI Alternate representative: Maxat Kulmanov
COSI Proceedings Liaison: Robert Hoehndorf and Tiffany Callahan as alternate

COSI Track Chair(s):
Tiffany Callahan and Robert Hoehndorf as alternate

COSI Programming Coordinator for ISCBacademy: Núria Queralt Rosinach

Activities Over the Last Year
Bio-Ontologies (#bioontologies; http://www.bio-ontologies.org.uk/) is an ISMB Community of Special Interest (COSI) that covers the latest and most innovative research in the application of ontologies and the organization, presentation, and dissemination of knowledge in biomedicine and the life sciences.

Bio-Ontologies celebrated its 25th year at ISMB 2022, held both virtually and in-person in Madison Wisconsin on July 10-14, 2022. The Bio-Ontologies is one of the oldest COSIs and provides a vibrant environment for reporting novel methods, exchanging knowledge and sharing experiences on the construction and application of ontologies in the life sciences. The COSI run track offers a constructive environment to nurture discussion of innovative and scientifically sound work that ranges from preliminary to completed, from both young and experienced investigators alike. Bio-Ontologies participants also benefit from a strongly interdisciplinary setting, where ISMB attendees intermingle with members from American Medical Informatics Association (AMIA), the W3C’s Healthcare and Life Sciences Community Group (HCLSCG), and the National COVID Cohort Collaborative (N3C) thereby increasing impact through new collaborations and broader dissemination. Furthermore, the COSI participates in the ISCBAcademy running two webinars every year to both provide to junior and senior researchers another platform for dissemination, instruction and discussion on current topics of interest in academia, and to provide the opportunity to students and junior researchers to chair the session to foster their involvement, empowerment and networking within the community. We aim at broadening the range of talks by inviting industry speakers with current interesting topics for the bio-ontologies community.

Day 1 of the Bio-ontologies track included a keynote delivered by Dr. Maria Keet on “Encoding Biases’ Influences on Development and Use of Ontologies in the Life Sciences” where she shared her ideas on the importance of knowledge representation when designing ontologies. She demonstrated through several interesting examples, how different decisions during the ontology development process can result in different types of biases. This talk drew a sizable in-person and online crowd and elicited a lively discussion. Bio-ontologies also featured many exciting talks. The day featured 10 talks covering applications of FAIR for vascular anomaly and breast cancer research; the use of knowledge graphs and ontologies to improve named entity recognition, genome annotations, and cluster phenotypes; and the development of new ontologies and updates of existing ontologies. This day also featured a proceedings talk, which presented a novel method for detecting inconsistencies in literature-based annotation via the Gene Ontology. The day closed with a brief plenary discussion which focused on ways to expand the Bio-Ontologies community and ways to engage existing community members through novel community-based tasks, inviting relevant external speakers for ISCB webinars, and the development of new social media-based avenues for communication.

Day 2 of the Bio-ontologies track included a keynote that was shared with the BOSC COSI and delivered by Dr. Melissa Haendel on “The Open Data Highway: Turbo-Boosting Translational Traffic with Ontologies” where she discussed the need for better data integration in order to improve our ability to model complex phenomena. This talk was shared with the BOSC COSI and also drew a sizable crowd and elicited a lively discussion. Bio-ontologies also featured 10 exciting talks on tools to improve the development, evaluation, and use of ontologies. This day also featured a proceedings talk, which presented a novel zero-shot learning method designed to improve the prediction of protein function from sequencing data.

The COSI sessions also had a social media impact on Twitter (activity under #BioOnt2022 tag) and on Slack (67 members currently registered on the bio-ontologies workspace) and our LinkedIn group (Bio-Ontologies; https://www.linkedin.com/groups/13998260/), which currently has 101 members, which represent both academic and industry settings.

Equity, Diversification, and Inclusion Efforts
Gender representation: The majority of Bio-Ontology COSI presenters were male (80%)

World research representation: The majority of Bio-Ontology COSI researchers were from Europe (45.8%), North America (27.5%), Africa (14.5%), Asia (11.5%), and South America (0.8%)

Leadership Structure
Madelaine Gogol, Stowers Institute, United States
Alastair Kerr, CRUK-MI, University of Manchester, United Kingdom
Brent Richter, Partners HealthCare of Massachusetts General and Brigham and Women’s Hospitals, United States
Alberto Riva, University of Florida, United States
Rodrigo Polo, Agriculture and Agri-Food Canada, Canada

Activities Over the Last Year
We focused on the organization of the workshop session at ISMB. We had six speakers from organizations in Brazil, the USA, Canada and the Netherlands. We also recruited our first keynote speaker, Johannes Koster, who provided an overview and updates of the Snakemake workflow management system. This keynote talk was also re-broadcasted at the ISCBacademy event on September 28th and can be found in YouTube: https://www.youtube.com/watch?v=LchfsoH1ITg.
As it is our COSI's tradition, we had workshops following the speaker presentations and the keynote talk. This year, the workshop sessions were very dynamic and included the following topics: project management, core facilities during the pandemic, protected data and knowledge sharing. It was a very rich exchange of ideas were the workshop attendees as we as the organizers learned from the expertise and experience of each other.

Equity, Diversification, and Inclusion Efforts
In the Bioinfo-Core session at ISMB three out of six speakers were women, and four out of six speakers were from underrepresented groups. Besides the USA, we had representation from speakers from Brazil, the Netherlands, Canada and Germany. We hope to work on more inclusive efforts and to attract speakers from countries and groups not traditionally represented in our session and ISMB. We believe there is a lot to learn from the experiences and challenges from colleagues who have the task of establishing core facilities from the ground up in adverse situations and we hope to provide a session at ISMB and a place in our Slack group where they can learn from other colleagues who have core facilities that are a bit more established.

Leadership Structure
BioVis 2022
General chairs
Helena Jambor, TU Dresden, Germany
Michael Krone, University of Tübingen, Germany

Website chair
Kari Lavikka, University of Helsinki, Finland

Publicity chair
Jen Rogers, University of Utah, USA

BioVis COSI @ ISMB 2022
Abstracts Chairs
Jan Byska, Masaryk University, Czech Republic and University of Bergen, Norway
Heba Sailem, University of Oxford, UK
Qianwen Wang, Harvard University, USA

ISMB Liaison Chairs
Jim Procter, University of Dundee, UK

BioVis Workshop @ IEEE VIS 2022 Chairs
Zeynep H Gumus, Icahn School of Medicine at Mount Sinai, USA
Thomas Höllt, Leiden University Medical Center, The Netherlands
Daniel Jönsson, Linköping University, Sweden
Renata Raidou, TU Wien, Austria

Steering Committee
Jan Aerts, KU Leuven and U Hasselt, Belgium
G. Elisabeta Marai, University of Illinois at Chicago, USA
Kay Nieselt, University of Tübingen, Germany
Jim Procter, University of Dundee, UK
Marc Streit, Johannes Kepler University Linz, Austria
Cagatay Turkay, University of Warwick, UK

Honored Members
Michel Westenberg, (passed away April 2021) Eindhoven University of Technology, The Netherlands

Activities Over the Last Year
The BioVis COSI 2022 started with a keynote by Tatiana von Landesberger (University of Cologne, Germany) on the very timely topic of visual analytics approaches for pandemic data. This included efforts on containing the ‘silent pandemic’ of antibiotic resistant pathogens and of course the ongoing COVID-19 pandemic, as well as reflections and lessons learned. The keynote was followed by one long abstract talk and four short ones. The talks in this session focused on single-cell data analysis and clustering approaches. In the lunch break, the posters were presented, leading to many lively discussions. The second session featured more abstract talks, ranging from metagenomic profile visualization to cohort analysis and the visual analysis of tumor phylogenies. The closing session featured another long abstract talk as well as lightning talks by all poster presenters and a keynote talk by Lennart Martens (Ghent University, Belgium), who shared his research and insights on new perspectives on proteomics through machine learning, especially on post-translational modifications of proteins and the visualization challenges that come with this. Overall, more than two thirds of the talks were given live from the venue. We had a very active participation not only by the on-site attendees but also from the online participants. Posters were awarded to: Mark Keller for his contribution “Polyphony: an Interactive Transfer Learning Framework for Single-Cell Data Analysis” and Camilo Valdes for his contribution “Microbiome Maps: Hilbert Curve Visualizations of Metagenomic Profiles”.

For advancement of bioinformatics and visualisation of biological data, we continued the BioVis meetups, which ran throughout 2022 with a total of 5 meetups. The aim is to enable members of the BioVis community to meet regularly at a smaller scale than international conferences. The series covered the following talk attended by up to 200 participants online and included:
BioVis Meetup #1: Changing the world with data visualization Jan 25, 2022, with Matthias Stahl from DER SPIEGEL. Matthias is a PhD scientist, founder of design studio higsch, and now co-lead of Graphics & Interactive department at a leading German weekly.
BioVis Meetup #2: Visualisation of Spatial and Image Data Mar 22, 2022, with Speakers: Fabian Theis and Heba Sailem.
BioVis Meetup #3: A pandemic of bad charts May 24, 2022, with Martin Krzywinski (@MKrzywinski), known for his work in bioinformatics, data visualization and the interface of science and art and co-author of Nature Method’s Points of View and Points of Significance columns.
BioVis Meetup #4: Surgery visualizations: leveraging AI in the healthcare setting Sep 27, 2022 with Stephanie Speidel, Prof. Translational Surgery, NCT-UCC at the University Hospital Dresden/Germany
BioVis Meetup #5: Visualising science: Communicating complex research with information graphics at Nature Nov 29, 2022, with Nik Spencer – Art editor, Nature and Jasiek Krzysztofiak – Art Editor, Nature.
For 2023 the series is planned to be continued and will star
BioVis Meetup #6: Communicating Scientific Concepts Through Art Jan 31, 2023 with Beata Edyta Mierzwa, PhD - Molecular Biologist and Science Artist, Ludwig Institute for Cancer Research and UC San Diego and “Beata Science Art”.
All meetups are recorded and available to the community through YouTube.

Another important meeting was the BioVis Workshop @ IEEE VIS 2022. This event serves as a platform for visualization researchers to increase the impact of visualization approaches in biology and medicine. Prior to the workshop we invited ressearchers to participate in a visualisation challenge. This year's topic was on protein translation modifications, for which we asked for design and redesign visualisations that help to visually understand where protein modifications are most likely to occur, and whether these are in loci with known connections to specific rare diseases. A total of 10 submissions were evaluated by a jury, and each gave a talk during the workshop. In addition, we invited four keynote speakers: The challenge was introduced by an invited talk of Enrico Massignani, Flanders Institute for Biotechnology. His presentation was entitled "Deciphering Protein Modifications with the Power of Visualization". Haichao Miao spoke about "Visual Analysis of Large-scale Biological Data to Understand Microbial Threats", Yihan Shao introduced "A Heatmap for Enzyme Engineering", and Barbora Kozlikova concluded with a capstone talk about "Bio+MedVis: Current and future opportunities".

Equity, Diversification, and Inclusion Efforts
BioVis strives to achieve equity and diversity both in its management and operational structures. We actively recruit junior members of the community to organisational roles and offer more senior roles as they gain experience. We aim to achieve a gender balance in the curation of the organising committees and also in curating the programme where we have control. In curating the invited talk programme, for instance, we aim for a gender balance as is evidenced from the keynote selections in the past five years where we always had a male and a female invited keynote speaker. Similarly, we also aim for gender balance when distributing the session chair roles.

Leadership Structure
The Open Bioinformatics Foundation (OBF), an all-volunteer organization that is responsible for BOSC, is led by an elected Board that currently includes 9 members (https://www.open-bio.org/board/), with Peter Cock as the president. Malvika Sharan finished her term this year and stepped down from the Board (see https://www.open-bio.org/2022/07/25/reflections-malvika-2022/). Iddo Friedberg (Iowa State University) was elected on 2022-10-21 as a new member-at-large. Board member Nomi Harris was elected as Secretary, replacing Chris Fields.

BOSC (https://www.open-bio.org/events/bosc/) continues to be chaired by Nomi Harris, who has chaired or co-chaired the meeting since 2010. For 2023, our organizing committee includes 9 people. Newly added is Radhika Khetani of the Harvard T.H. Chan School of Public Health.

Activities Over the Last Year
OBF accomplishments over the past year include:
- Held public OBF Board meeting in October 2022 (https://www.open-bio.org/2022/09/29/obf-public-board-meeting-2022-10-21/), at which one new member-at-large and one new officer were elected (see Leadership Structure section).
- Participated in Google Summer of Code 2022 https://summerofcode.withgoogle.com/programs/2022/organizations/open-bioinformatics-foundation-obf). Five students, all from underrepresented groups, worked on open source bioinformatics related projects under the OBF umbrella.
- OBF Event Fellowships: In 2022, 19 people were awarded funds to attend virtual events (12 for ISMB 2022 and 7 for other events related to open science).
- OBF/BOSC ISCBacademy talk in February 2022 (https://www.open-bio.org/2022/02/23/watch-the-recording-of-the-iscbacademy-webinar-on-growing-open-source-communities/): Yo Yehudi discussed how internship programs such as Google Summer of Code or Outreachy can be a great way to grow your open source community.
- Volunteer Geraldine van der Auwera put together an issue of the OBF newsletter: https://github.com/OBF/newsletter/blob/master/newsletters/2022-07.md
- OBF/BOSC activity on social media included 19 blog posts (open-bio.org/blog/) as well as many tweets, email to our subscribers, and public Slack channels. In December 2022, we also joined Mastodon (@OpenBio@genomic.social and @BOSC@genomic.social).

BOSC accomplishments over the past year include:
- BOSC 2022 was part of ISMB 2022 (in Madison, WI, and online – the first hybrid ISMB). Approximately 200 people participated in BOSC sessions, which included 28 talks chosen from submitted abstracts, 46 posters, a panel discussion and two keynote talks. The BOSC 2022 schedule can be found at https://www.open-bio.org/events/bosc-2022/bosc-2022-schedule/.
- BOSC 2022 reports:
- F1000: https://f1000research.com/articles/11-1034/v1
- Festus Nyasimi, a co-founder and lead of the Bioinformatics Hub of Kenya Initiative (BHKi), shared the story of his journey to the ISMB/BOSC 2022 conference on an OBF Event Fellowship: https://www.open-bio.org/2022/08/01/obf-event-fellow2022-fnyasimi/
- Geraldine Van der Auwera collected impressions from multiple BOSC participants in a blog that will make you wistful if you missed BOSC 2022: https://www.open-bio.org/2022/08/16/crowdsourced-highlights-from-bosc-2022/
- BOSC 2022 included joint sessions with two other COSIs (Education COSI and Bio-Ontologies). Jason Williams gave a BOSC / Education COSI keynote entitled "Riding the bicycle: Including all scientists on a path to excellence". A joint session with Bio-Ontologies featured a keynote by Melissa Haendel, “The open data highway: turbo-boosting translational traffic with ontologies.”
- BOSC 2022 included a panel, which we had not attempted to offer during the two years (2020 and 2021) when the meeting was held virtually. “Building and Sustaining Inclusive Open Science Communities” featured panelists who not only are known for supporting diversity and inclusion, but also themselves are members of groups that are underrepresented in our field. This lively, interactive panel focused on the “what next?” part -- what needs to come after the initial steps to diversify an open source project or community.
- As usual, BOSC was followed by a two-day CollaborationFest (CoFest). A hands-on-keyboards event that has been held after BOSC for the last twelve years, CoFest 2022 was a hybrid meeting. Participants worked together on six collaborative projects, three primarily involving in-person participants and three online.

Equity, Diversification, and Inclusion Efforts
- As in previous years, BOSC prioritized its time and funds to ensure our meeting was more diverse and inclusive. With help from our sponsors, we granted free registration to 12 participants, including 11 from groups that are underrepresented in bioinformatics, and covered travel expenses for several of the panelists and keynote speakers. Those submitting abstracts were able to request fee assistance by checking a box on the submission form. Additionally, participants were encouraged to apply for OBF Event Fellowships.
- Our Event Fellowship program is specifically aimed at improving diversity at bioinformatics-related events by helping to make events financially accessible to people from groups that are traditionally underrepresented in bioinformatics and open science. Formerly the OBF Travel Fellowship, the program was extended in 2020 to cover costs associated with participating in online events such as virtual conference fees, headsets, high speed internet, etc. (https://www.open-bio.org/event-awards/).
- We began offering keynote speaker honoraria last year, in recognition of the fact that not all researchers are privileged to be able to gift their time. Those who did not want to accept honoraria were given the option to donate it back to help support future EDI endeavors. We see the honorarium program as one aspect to our inclusiveness in choosing keynote speakers, which we are still striving to improve.
- In the past 11 years, BOSC has had 22 keynote speakers. 10 were women or non-binary people; 4 were non-white (all of whom were in the past 5 years).
- Diversity, Equity and Inclusion was a focus of several of the BOSC sessions, including the panel (see above) and the session on Inclusion & Open Science.
- As far as we are aware, BOSC 2022 was the first BOSC, possibly even the first ISMB, to include a service dog (assisting a blind panelist), demonstrating tangible progress in our efforts to make BOSC more inclusive and accessible.

Leadership Structure
CAMDA is co-chaired by Wenzhong Xiao (Harvard/Stanford), Joaquin Dopazo (Spanish Health Ministry), David Kreil (Vienna), and Pawel Labaj, a young group leader at a top university in Poland.
The chairs are supported by a Scientific Committee which features a good mix of senior established researchers like Wolfgang Huber and young talent in the field. We are actively working to invite additional young promising members, with Maria Pena Chilet recently joining us, a highly cited young researcher from Andalusia.

Activities Over the Last Year
The challenges for CAMDA 2022 were advertised early in the year and included:
- The Extended Literature AI for Drug Induced Liver Injury Challenge provides biomedical publications curated by FDA experts on DILI. Build their digital twin to identify the sparse positives and demonstrate robustness under distributional shifts!
- The Anti-Microbial Resistance Forensics Challenge features diverse metagenomics profiles from urban and non-urban areas. Track emerging AMR and its relationship with phages!
- The Disease Maps to Modelling COVID-19 Challenge provides highly detailed expert-curated molecular mechanistic maps for COVID-19. Combine them with available omic data to expand the current biological knowledge on COVID-19 mechanism of infection and downstream consequences!

Lynn Schriml (University of Maryland, Baltimore, U.S.A.) started the first day with her keynote on Addressing standardization challenges through integrated approaches in biomedical and genomic data. She has reviewed the development and utilization of standards for characterizing complex disease mechanisms and genomic metadata integration. She also has examined sources of unrecognized bias of collected data and highlighted standardized approaches to address these challenges among genomic and cancer resources. Krista Ryon subsequently provided a focus on metagenomics, sharing highlights from recent efforts of the MetaSUB Consortium in global-scale characterization of urban microbiomes and antimicrobial resistance. Both presentations were highly topical for the metagenomics challenges CAMDA has been running since 2017. Looking into the future, Leonid Chindelevitch (Imperial College London, U.K.) presented an outlook on antimicrobial resistance prediction from whole-genome sequence and metagenomic data, which is now actively being considered for one of the upcoming CAMDA 2023 challenges.

In an ISMB Proceeding presentation fitting well into this area, Tianqi Tang explained how a convolutional neural network could predict phage–host matches based on relatively short contigs. This is a key advancement for metagenomics studies, where instead of wholly assembled genomes typically only contigs are available, which can be as short as a few hundred bases. The second part of the session comprised four short talks on data quality and availability, as well as the challenges of benchmarking in the life sciences. These issues are all central for the reproducibility of science, as also discussed in the day’s keynote. Examples highlighted in the short talks included the incompleteness of public metadata accompanying omics studies, inconsistencies in immunogenetics databases across diverse populations, as well as the limited availability of open T-Cell Receptor Repertoire data. A shared-hub for Universal Benchmarking of Machine Learning-Based Protein Functional Annotation was presented as a possible solution towards greater reproducibility in that field.

The next session started with an overview of past metagenomics challenges at CAMDA, study highlights, and novel research projects evolving from them presented by Paweł Łabaj. Following that Deisy Gysi (Harvard & Northeastern, U.S.A.) outlined the pandemic-time application of AI graph network based methods to drug repurposing. The COVID-19 pandemic highlighted the importance of prioritizing candidates from drugs approved already for other diseases for potential repurposing in the treatment of SARS-CoV-2 infections. Her lab led by Barabasi evaluated existing drug-repurposing methodologies and used a consensus algorithm to increase the accuracy of the predictions. The top-ranked drugs were eventually screened for activity in human cells, identifying six drug candidates that reduced viral infection, four of which were considered promising for further investigation. Notably the presented strategy is data efficient and thus has significance beyond COVID-19, allowing the identification of drug-repurposing candidates for neglected or rare diseases. Mitsuhiro Odaka also reported COVID pandemic related research. Although intercellular attachment between cells are potentially significant in COVID-19, the interactions between the molecules involved have received little attention. The limited understanding of how they are regulated in COVID-19 is thus responsible for our incomplete knowledge of relevant signaling pathways. Speaker demonstrated how data-driven and knowledge-based approaches could be combined to gene network inference for pathway construction, repairing and completing known pathways and improving our current understanding of COVID-19 mechanisms. Joaquin Dopazo closed the day with the 20th anniversary presentation CAMDA Highlights - Making History.

Zhiyong Lu (NCBI, NLM, NIH) kicked off the second day of the conference with his keynote PubMed and Beyond: Biomedical Text Mining for Knowledge Discovery, highlighting the power and breadth of applications of modern text mining methods for finding and extracting knowledge from the biomedical literature. The keynote incidentally served as a great introduction to the subsequent session on the Extended Literature AI for Drug Induced Liver Injury Challenge.

The session featured 4 talks on the topic. Jung Hun Oh (MSK Cancer Center) demonstrated how a combination of word2vec and tf-idf embeddings yielded a better performance in the identification of papers relevant to Drug Induced Liver Injury than either alone. Amongst the models trained on this embedding, the best performance was achieved using a  linear support vector machine. Already at CAMDA’21 Malik Yousef (Zefat College, Israel) went beyond the ‘bag of words’ concept by instead introducing a ‘bag of topics’ extracted by LDA, and ranked by Random Forest with Monte-Carlo stratified cross-validation, this year further refining their choice of thresholds. Ihor Stepanov (National Academy of Sciences of Ukraine) joined us remotely to share a comparative analysis of information theory based statistical methods and transformer-based machine learning techniques for scientific literature classification. Finally, Xianghao Zhan (Stanford University) examined the reliability of DILI relevance predictions by conformality. Overall, both an ensemble model and a TF-IDF model reached satisfactory classification results but TF-IDF had much lower computational costs. In fact, its high performance on the seven hold-out datasets gave the TF-IDF model the top score in several of the challenge leaderboards.

Last but not least, Eunyoung Kim won this year’s CAMDA Trophy for her presentation of late breaking research on the interpretable prediction of drug-drug interactions from drug-induced gene expression signatures (data featured in the CAMDA CMap Drug Safety Challenges). First, drug induced gene expression patterns are learned from the structure and properties of drug compounds, allowing inference also for drugs without expression profiling experiments. An attention mechanism learns which genes are important for drug interactions. Translation embedding is used to represent side effects, which are learned from an older version of DrugBank, with predictions validated on a newer version.

The final ISMB Proceeding talk at CAMDA introduced a novel hierarchical framework for the discovery of structured associations from paired high-dimensional datasets, efficiently integrating hierarchical hypothesis testing with FDR corrections to reveal significant linear and non-linear block-wise relationships among continuous or categorical data.
The last session featured the CAMDA Trophy Ceremony with the first prize going to Eunyoung Kim from the Gwangju Institute of Science and Technology in South Korea. Xianghao Zhan from Stanford University and Ihor Stepanov from The National Academy of Sciences of Ukraine tied for a double-second prize right. The competition was tight, and a an honourable mention went to Jung Hun Oh from Memorial Sloan Kettering Cancer Center in USA. The conference then concluded with discussions about new directions and future CAMDA challenges in the traditional CAMDA Caffé.

Throughout the year CAMDA hosted dedicated Google Group based forums for the different CAMDA challenge communities. CAMDA2021 Trophy Winners were invited to present their latest research in the ISCB Academy webinar series. On October 2021 Roumyana Yordanova of Hokkaido University and the Bulgarian Academy of Sciences shared her Alternative approach for discovering relationship between bacteriophages and antimicrobial resistance in the ISCB Academy, and March 2022 Xianghao Zhan from Stanford University showed how to effectively Filter Drug-induced Liver Injury (DILI) Literature with Natural Language Processing and Ensemble Learning.

Equity, Diversification, and Inclusion Efforts
Among keynotes of CAMDA 2022 half were female: Lynn Schriml, a President of the Genomic Standards Consortium and leader at the Human Disease Ontology project, University of Maryland, Baltimore, U.S.A. In addition, we invited: a presentation by Krista Ryon, a young executive director of MetaSUB International Consortium and a researcher at Weill Cornell Medicine, NY, U.S.A,; and presentation by Deisy Morselli Gysi, a young but already successful researcher from Harvard Medical School & Northeastern University, U.S.A.

CAMDA featured speakers from: France, Israel, Japan, Poland, Spain, South Korea, U.K., Ukraine, and U.S.A.

Leadership Structure
The CompMS COSI is led by a mix of early-career researchers from academia and industry. The CompMS COSI leadership for 2023 consists of Wout Bittremieux (University of Antwerp), Timo Sachsenberg (University of Tübingen), Isabell Bludau (Max Planck Institute of Biochemistry), and Lindsay Pino (Talus Bio).

Activities Over the Last Year
The CompMS COSI received one proceedings submission and 15 abstract submissions for the ISMB 2022 conference, spanning computational mass spectrometry research in various fields, including proteomics, metabolomics, and lipidomics. The CompMS program featured four keynote presentations, by Brian Searle (Ohio State University) on “Machine Learning Methods for Proteomics,” by Gary Patti (Washington University) on “Advancing Metabolomics for Precision Medicine,” by Ying Ge (University of Wisconsin) on “Novel CompMS Approaches for Top-down Proteomics toward Precision Medicine,” and by Michael Shortreed (University of Wisconsin) on “Unveiling the Hidden Proteome With Software.” The session additionally included one proceedings presentation on deep kernel learning to improve molecular fingerprint prediction from tandem mass spectra, four long presentations (20 minutes), four short presentations (10 minutes), and seven poster presentations. Meeting participants presented high-quality research in computational mass spectrometry, covering topics in metabolomics and proteomics. Daniela Klaproth-Andrade (Technical University of Munich) and Chathurani Ranathunge (Eastern Virginia Medical School) were the winners of the best oral presentation and best poster presentation awards, respectively.

Besides the CompMS COSI session at ISMB 2022, COSI representatives actively engaged with the computational mass spectrometry community at various international meetings and conferences. These activities included co-organizing the European Bioinformatics Community for Mass Spectrometry Winter School 2022 (Oeiras, Portugal), providing educational sessions at the annual conference of the American Society for Mass Spectrometry (Minneapolis, MN), and co-organizing the Bioinformatics Hub at the annual conference of the Human Proteome Organization (Cancun, Mexico). COSI representatives have also engaged in science popularization events by promoting computational mass spectrometry during multiple podcast interview sessions.

Equity, Diversification, and Inclusion Efforts
As the CompMS COSI leadership consists of early-career researchers in academia and industry, we are strongly committed to promoting the work of early-career researchers. Additionally, we strive towards having a balanced gender and geographical representation at CompMS COSI activities through keynote invitations and promoting our efforts with a diverse audience. Unfortunately, in 2022 we did not fully succeed in achieving gender parity for our keynote presentations at the ISMB 2022 conference, with three male keynote speakers and one female keynote speaker. Gender representation for the selected oral presentations from the abstracts was similarly skewed, with six male speakers and two female speakers.

Leadership Structure
Education COSI Chairs: Russell Schwartz (Carnegie Mellon University, USA), Patricia Palagi (SIB Swiss Institute of Bioinformatics, Switzerland), Annette McGrath (CSIRO, Australia).

Activities Over the Last Year
The COSI works to bring bioinformatics education to the agenda of the ISCB community and to collaborate with education efforts in computational biology and life sciences internationally. It started many years ago with a plan of explicitly bringing together the ISCB Education community with the Global Organisation for Bioinformatics Learning, Education & Training (GOBLET). However, it has since broadened its mission to be an interface between the ISCB education community and the international bioinformatics education community broadly defined.
Each year, the significant Education COSI efforts lay in the ISMB educational program and associated activities, where we seek to create a community discussion on education within ISMB, bring in voices from outside ISCB to work with us, and highlight some of the most exciting work in the field. In 2022, the Education COSI program at ISMB kicked off with the Workshop on Education in Bioinformatics (WEB), a mix of talks and working sessions on sustainability. It continued then with a vibrant 1.5-day program of invited Keynote speakers, submitted talks and two proceedings talks, posters, and a lively panel discussion continuing the conversation on inclusiveness in bioinformatics education, featuring our keynote speakers and a representative of the ISCB Equity, Diversity, and Inclusion (EDI) Committee.
The COSI also works to bring education topics to other meetings of the community. We participated in the APBIOnet’s International Conference on Bioinformatics (InCOB) as well as GOBLET’s COBLET conference. We have also continued to encourage education components in society affiliated meetings in the past year. In addition, we worked with the ISCBacademy to identify speakers to represent the COSI, hosting two talks for the academy in the past year.
The COSI has also been very active in a series of collaborative education initiatives organized around what has become an annual Bioinformatics Education Summit, held virtually again in 2022. The summit series, led by Nicky Mulder and Sarah Morgan aims to define and improve standards for bioinformatics education, to produce papers and other resources and training materials for the community, and to work with the ISCB on initiatives such as the short course affiliation and degree program endorsement processes now being put in place. The particular focuses of the past year were extending the competency framework to biomedical and health sciences, virtual education and training, and building education and training in low and middle income countries (LMICS).
The COSI leadership bridges between the large trainers community and the ISCB Education Committee and other ISCB community meetings. In this context, topics receiving ongoing attention in the past year have included the imminent publication of the latest edition of the ISCB competencies framework, development of new web resources for the ISCB education community, the short course affiliation and degree program endorsement processes, and reaching out to potential partners for initiative such as a student supercomputing challenge and ISCB Wikipedia efforts. For example, the affiliation and endorsement process has been working to recruit submissions to pilot and refine its review processes.

Equity, Diversification, and Inclusion Efforts
We have sought to promote Equity, Diversity, and Inclusion through consideration for a diverse and inclusive selection of speakers for the education COSI program at ISMB each year. For example, the ISMB program this year featured 8 speakers out of which 4 were women. Membership in the Education COSI is open to anyone interested in the topic and so we do not specifically select for diversity, but strive to be welcoming to all. The committee also made EDI efforts a focus of the program, for example through a keynote talk on education in low and middle income countries and a keynote and panel discussion on inclusiveness in bioinformatics education.

Leadership Structure
• Nadia El Mabrouk; COSI co-chair; University of Montreal
• Janani Ravi; COSI co-chair; Michigan State University
• Lars Arvestad; Proceedings liaison; Stockholm University
• Lars Arvestad; Area co-chair, Stockholm University
• Céline Scornavacca; Area co-chair; University of Montpellier
• Giltae Song; Abstract co-chair; Pusan National University
• Wataru Iwasaki, Abstract co-chair; University of Tokyo
• Dannie Durand; Abstract co-chair; Carnegie Mellon University
• Edward Braun; Communication/website; University of Florida
• Erin Molloy; Webinar; University of Maryland
• Aïda Ouangraoua; Award co-chair; University of Sherbrooke
• Louxin Zhang; Award co-chair; National University of Singapore

Activities Over the Last Year
The Evolution and Comparative Genomics (EvolCompGen) COSI hosted a two-day program at the hybrid ISMB ’22 meeting from July 13–14, 2022. The sessions included seven ISMB proceedings talks and 16 contributed talks with a concluding panel discussion, where in-person and virtual attendees exchanged ideas on fundamental questions related to gene/synteny/domain/isoform evolution and large-scale phylogenetics. Most contributed talks were accompanied by a poster, in addition to 17 other posters, presented onsite and discussed with the presenters during poster sessions. These two days provided us all the opportunity to enjoy fantastic presentations and posters from researchers around the world on subjects as diverse as protein evolution, comparative genomics applied to brain tumors, the evolution of cancer tissues, genetic features associated with diseases driven by pathogens, machine learning for identifying molecular features of antibiotic resistance, studying the evolution of the CRISPR-Cas systems to cite a few.

The talk award winners (nominees: trainee non-proceedings talks) were Taeyoung Kim and Joel Nitta, with special mentions to Mathiew Gacson and Yuting Xiao. The best poster award was won by Sungsik Kong, with special mentions to Ethan Wolfe, Chao Chun Liu, and Yiyan Yang. The awardees were voted for by the committee based on the significance and novelty of their work, visual appeal, and flow of their oral/poster presentation.

Throughout the year, the EvolCompGen outreach and research community collaboration continues through webinars and communication through Twitter: @EvolComp, Website: https://evolcompgen.org, or Slack: bit.ly/join_evolcompgen.

We are also pleased to announce a new Evolutionary Bioinformatics collection launched on the F1000Research platform, aiming to publish articles highlighting the diverse portfolio of our COSI.
https://f1000research.com/collections/evolutionary-bioinformatics/about-this-collection
We encourage you to participate by submitting proposals.

Equity, Diversification, and Inclusion Efforts
The diversity of our COSI is perfectly reflected in the leadership structure with members that span early-career and established professors from all corners of the world (Asia, Africa, Europe, United States), with a balanced gender distribution. We had trainees and PIs from diverse backgrounds attend our two-day session at ISMB ’22, facilitated greatly by the meeting's inclusive hybrid format. To further improve along the diversity axes in the upcoming meeting, we will proactively use available COSI funds to help support the travel costs of students at significant distances from the conference venue, particularly trainees from Asia and Africa. In addition, it would be great to provide registration/travel waivers to trainees and PIs from low-income countries. Also, we will work with ISMB/ECCB central into accessibility of all kinds, including vision/hearing would be most helpful to ensure better inclusion.

Leadership Structure
The COSI is led by Iddo Friedberg, Kimberly Reynolds, Mark Wass and Dukka KC, who all act together as Track Chairs.

The Critical Assessment of Functional Annotation (CAFA) is closely associated with Function COSI. The CAFA organisers are: Iddo Friedberg, Predrag Radivojac, Sean Mooney

Activities Over the Last Year
The Function Community of Special Interest (COSI, http://www.biofunctionprediction.org) covers the latest developments in the computational biology applications to functional annotation of proteins and understanding protein function.

At ISMB2022 the Function COSI held its 16th meeting, and first hybrid meeting. The keynote speaker was Lukasz Kurgan, a professor from the Virginia Commonwealth University, he spoke about the methods he has developed for the analysis of protein disorder and protein function.
The one day Function track also saw the presentation of one proceedings paper along with 22 talks selected from submitted abstracts, which covered diverse topics within Function including the identification of moonlighting proteins and applications of deep learning to functional annotation including AlphaFold.

Over the past year we have sought continued funding from NIH for the Critical Assessment of Functional Annotation (CAFA) Challenge. Despite extensive support from the community (in the form of letters of support), the application was unsuccessful. We are now in discussions with Kaggle (a Google subsidiary) to investigate the potential for running the next round of CAFA as a Kaggle challenge. This would open CAFA to the large Kaggle user base and attract new researchers to this field (especially data scientists). At a recent Open Meeting with the Function COSI Community we discussed this opportunity and what it would mean for CAFA.

Equity, Diversification, and Inclusion Efforts
The COSI considers EDI when identifying potential keynote speakers

Leadership Structure
HitSeq is organized by an organizing committee made up currently of seven members. Founding member Francisco De La Vega and Dirk Evers serve as steering group of HiTseq.

Activities Over the Last Year
This year HiTSeq featured three keynote speakers. Benedict Paten from University of California,
Santa Cruz, was covering the latest advances on a draft of the human pangenome reference.
In particular, in his keynote address, he presented his latest results on Giraffe and VG, which
are graph-based representations of pangenome. At the time, the work was submitted to biorxiv
but since this time the published findings appeared in Science. He also discussed some work
in progress and problems that need further consideration, such as visualizing complicated
regions of the genomes (e.g.: HLA regions), and applications to pangenomics (such as cancer
genomics). Tightly related to the representation of the human pangenome is structural variant
detection since the most immediate downstream analysis is to identify variants from the
alignment. DeepVariant was used in combination with Giraffe and VG and demonstrated that
the Giraffe alignments produced variants were significantly more accurate (reduced the false
positive) in comparison to the VG alignments. Giraffe is also significantly faster. An important
note that was made is that the increased accuracy was not seen across the entire genome.
There was great interest in the talk by the audience as demonstrated by a great number of
questions. At least a dozen people wanted to ask a question and we had to cut the questions
due to this. Most of the questions focused on the application of pangenomics and whether any
of the results of Giraffe were surprising or counterintuitive. Dr. Paten answered that a number of
methods did not improve in performance when pangenomics alignments were used, and the
drop of performance was sometimes significant. In addition, there were questions related to the
application of pangenomics to cancer genomics, i.e., pangenomics assists in identifying the
difference between germline variants.
Cole Trapnell, from Washington University, showed approaches using thousands of
individuals, single cells, and CRISPR to track the genetic basis of embryonic development at the
single-cell level. Yuzhen Ye from Indiana University, presented her recent work on utilizing
multi-omics, networks and bacterial immune system to understand the microbiome. She
presented an amazing array of approaches to characterizing the composition of communities
using multi-omics data, including metaproteomics, metatranscriptomics and MAGs. She also

presented her approaches for genome-wide metabolic reconstruction of microbial communities
and using the CRISPR-cas system to study species heterogeneity.
In the 2022 edition of HiTSeq the mixture of proceedings and abstract talks highlighted the
following topics: (1) improvements to genome assembly and RNA sequencing through new
methods and linked/long reads; (2) the analysis of genome structure, genome editing and
genomic databased ; (3) indexing, error correction, tracking, and manipulation of sequencing
data; (4) methods for single-cell DNA and RNA sequencing to study cell type composition and
RNA velocity; (5) analysis of immune repertoire using long reads sequencing. Here, we briefly
discuss some of these presentations.
Yutong Qiu and Carl Kingsford presented some of their work related to genome graph
expressiveness and described how graph decomposition can directly link the genome graph
with the sequences it represents. In addition, it allows for the comparison between two graphs,
i.e., one can compare the genome graph expressiveness in order to compare two genome
graphs. There were multiple questions from the audience, many of which were focused on
whether an approximation to the graph decomposition can be used to develop a more efficient
algorithm. Yutong replied that it may be possible and could lead to some interesting future
work.
Armaghan Sarvar et al. presented a concept called stochastic tile hashing, which they refer to
as “Stashing”. Stashing is the concept of a lossy tile hashing representation that is used to
describe large collections of k-mers that are used for genome assembly or other downstream
analyses. They are currently focusing on using stashing to align pairs of genomic sequences,
such as contigs, scaffolds, or even reads, and then using this alignment to identify
misassembled regions in the genome.
Belbasi et al. presented some work that describes that the assumption about the Jaccard
estimator is biased. Sketching is now widely used in bioinformatics in order to reduce data
size and increase efficiency. In particular, the Jaccard similarity metric is commonly used as an
estimator for minimizers. The authors here demonstrate that this measurement can be
inaccurate, and thus, has many implications. Many of the questions from the audience focused
on what the implications of the findings are.
Other notable presentations on the last day of the schedule include those from Alanko et al.,
Askar et al., and Wong et al. Alanko et al. presented some work from the University of Heliski
on what they refer to as “Matchtigs”, which are defined as the minimum representation of a set
of k-mers. Determining this minimum representation is potentially an NP-complete problem (it has
yet to be resolved) so Alanko et al. give a polynomial time heuristic for this problem and an
efficient near-minimum greedy heuristic. There were a couple of questions for the audience. One
interesting question was how well the author's method would be affected by spurious–or
incorrect– k-mers, and whether there was a relationship to the Minimum Path Cover. Askar et
al. show that finding the p-values under the typically used null hypothesis is NP-hard, and
demonstrate that the problem can be reformulated by calculating the null hypothesis using
Markov chains. Wong et al. presented GoldRush-Path, which is a de novo assembler for long reads. In fact,
they present their method as a collection of tools and show that long-read assembly can be
represented and solved using a multi-color bloom filter. A member of the audience asked what
the number of misassemblies was on standard genome assemblies, i.e., E Coli and human,
and if there was improved accuracy over existing methods, such as Flye and Canu.
Some technical issues persisted and some of the authors, including Giulio Ermanno Pibiri, and
Kendell Clement could not get their video work, even after some persistence. Lastly, it is worth
mentioning some of the strongest presentations, including that of Aubin et al. and Marmot-
Lassauzaie et al., who were both candidates for the best paper. Both presentations gave a
strong balance between biological findings, novel algorithmic expertise, and innovative use and
analysis of high throughput sequencing data, which is paramount to HitSeq.

Equity, Diversification, and Inclusion Efforts
We strive to add additional co-chairs from all backgrounds and regions and ensure female co-chairs are recruited. We also strive to balance the keynote invitations that have equal numbers of female and male speakers. Final keynote speakers depende on acceptance to our invitations. Abstracts for talk are selected purely on a score basis, and authors decide who presents at the conference.

Leadership Structure
Organizing Committee
Athma Pai, UMass Medical School, USA
Michelle Scott, Université de Sherbrooke, Canada
Hagen Tilgner, Weill Cornell Medicine, USA

Abstract Committee
Athma Pai, UMass Medical School, USA
Michelle Scott, Université de Sherbrooke, Canada
Hagen Tilgner, Weill Cornell Medicine, USA
Maayan Salton, Hebrew University, Israel

Proceedings Liaison
Jérôme Waldispühl, McGill University, Canada

Activities Over the Last Year
Highlights of the RNA COSI at ISMB 2023:
The 2023 iRNA COSI took place on July 26 and 27. Our first iRNA track keynote talk was given by Irmtraud Meyer from the Berlin Institute for Medical Systems Biology who discussed several computational methods to study the dynamic RNA structure, forming as the RNA is being transcribed rather than assuming a fixed molecule. This talk was followed by several talks discussing optimized RNA design for vaccines, RNA interactions, RNA motifs, small RNAs and transcription start sites. Our second keynote, Julien Gagneur from the Technical University of Munich described the detection and prediction of aberrant splicing using machine learning algorithms before switching to discussing codon usage, relation to energy consumption and its effect on RNA stability. We ended the day with concise and entertaining flash talks advertising some of our posters and a lively poster session followed by our COSI dinner at the Park Brasserie. Our traditional dinner quiz was a great success, probing the depth of our knowledge of local trivia. Our second day featured talks on RNA localization, kinetics, CRISPR design, transcriptome reconstruction, RNA modification and RNA maturation including splicing and polyadenylation and their deregulation in disease. Our first keynote of the day, Maayan Salton from the Hebrew University discussed often disregarded but important regulatory relationships between promoters/enhancers and alternative splicing. The final keynote talk presented by Hagen Tilgner from Weill Cornell discussed recent advances in long reads technology and findings in spatial splicing analysis focused on mouse and human brains. Overall, the meeting provided an overview of new tools, technologies and many fascinating studies leading to a deeper exploration and increased understanding of the transcriptome.


Year-round activities
-Management of the iRNA COSI website to inform and mobilize the community: https://irbgroup.org/
-iRNA talks in the ISCB Academy: Christina Akirtava (CMU) discussed False-positive IRESes, mRNA annotation errors and a paradigm 'unshift' in mammalian development in November 2022 and Dr Matvei Khoroshkin (UCSF) talked about A systematic search for RNA structural switches across the human transcriptome in May 2023.
-Promotion of other meetings involving computational RNA research: EMBL-EBI course on Introduction to RNA-seq and functional interpretation and RiboClub 2023.

Equity, Diversification, and Inclusion Efforts
When choosing our COSI keynote speakers, in addition to well-known scientists in our field, we spend time searching for members of our community whose work we could highlight, who conduct excellent research but might not be senior sought-after speakers (yet), a good proportion of which are members of minorities. When selecting abstracts for our talks, we always consider simultaneously EDI and scientific excellence. Including all researchers that see themselves as computational RNA scientists regardless of their origin is a fundamental principle of our COSI and we are completely convinced that increasing diversity in members increases diversity in ideas, enriching our community.

Leadership Structure
Alejandra Medina-Rivera and Brittany Lasseigne are currently leading JPI.

Activities Over the Last Year
JPI's activities focus on peer mentoring and resource sharing for junior faculty in computational biology. We primarily carry out these activities on dedicated channels in the New PI Slack group. For example, we have 20 ISCB members in the New PI Slack #iscb_jpi channel. This year at ISMB 2022, we held a two-hour hybrid session on funding for computational labs that featured 7 program officers from NIH, CZI, and NSF. Speakers gave presentations as well as spoke on a panel about strategies and opportunities for computational funding. Additionally, we sponsored a Birds of a Feather meeting on Strategies for Team Science in the Age of Hybrid and Remote Work. We also worked to schedule seminars featuring junior PIs and distributed training and funding information to members.

Equity, Diversification, and Inclusion Efforts
This year our DEI efforts were predominantly focused on ensuring that our efforts were accessible to the global community. To that end, we ensured that our ISMB session included funding opportunities accessible internationally.

Leadership Structure
Alice McHardy; Helmholtz Centre for Infection Research; alice.mchardy@helmholtz-hzi.de
Alexander Sczyrba; University of Bielefeld; asczyrba@cebitec.uni-bielefeld.de

Activities Over the Last Year
The MICROBIOME COSI 2022 featured two keynote talks given by (1) Catherine Lozupone from the University of Colorado Denver, USA, on "Methods for integration and hypothesis generation from high dimensional biomedical microbiome datasets", and (2) Chirag Jain from the Indian Institute of Science, Bangalore, India, on " Revisiting string graph model for long-read assembly of genomes and metagenomes".
On 30th November 2021, we hosted the ISCB academy webinar "Longitudinal genome resolved metagenomics", by Christopher Quince from the University of Warwick, UK.
On 10th May 2022, we hosted the ISCB academy webinar "From hairballs to hypotheses: microbial network analysis", by Karoline Faust from the Rega Institute, Belgium, in collaboration with NetBio.
On 7th December 2022, we hosted the ISCB academy webinar "High- resolution, large scale metagenomics of the human microbiome" by Prof. Nicola Segat, University of Trento, Italy.
In 2022, we also published the second round of CAMI benchmarking challenges (Meyer, Fritz et al., Nature Methods 2022).

Equity, Diversification, and Inclusion Efforts
The COSI invited an equal number of male and female speakers.

Leadership Structure
Magnus Rattray and Chloe-Agathe Azencott are MLCSB co-presidents and are supported by the MLCSB board. Sayane Shome took on a new role as social media manager.

Activities Over the Last Year
This year's MLCSB track included a panel session on the important topic of Reproducibility and Transparency in ML: Training the Next Generation, chaired by Elena Fertig who was joined by Casey Greene and Florian Markowetz. As well as running the MLCSB COSI, we also support the MLCB meeting which is now a standalone meeting, typically US-based, with several MLCB organisers on our board. We run a COSI twitter account, managed by Sayane Shome, to advertise relevant events and activities. MLCSB co-president Rattray has joined the editorial board of Bioinformatics Advances.

Equity, Diversification, and Inclusion Efforts
MLCSB encourages diversity and representation within its leadership. The MLCSB meeting has had male and female co-chairs in 2019, 2020 and 2021 and female co-chairs in 2022 and 2023, and has female and male co-presidents. Chairs are invited to become board members after ISMB and this ensures the board also reflects this. We also pursue increasing diversity in terms of ethnicity and geography in our leadership by ensuring that our track chair selection lists are diverse, which then feeds into our board. Board ethn

Leadership Structure
Carlo Vittorio Cannistraci
Zhou Yahui Chair Professor
Chief Scientist, Tsinghua Laboratory of Brain and Intelligence (THBI)
Director, Center for Complex Network Intelligence (CCNI) at THBI
Department of Computer Science
Department of Biomedical Engineering
Tsinghua University, Beijing, China
https://brain.tsinghua.edu.cn/en/info/1010/1003.htm
NetBio COSI Committee Representative

Tijana Milenkovic
Frank M. Freimann Collegiate Professor of Engineering
University of Notre Dame
Board of Directors, International Society for Computational Biology
https://nd.edu/~tmilenko/
NetBio COSI Track Chair
NetBio COSI Proceedings Liaison

Marinka Zitnik
Assistant Professor
Harvard University
https://zitniklab.hms.harvard.edu/
NetBio COSI Track Chair

Martina Summer Kutmon
Assistant Professor
Maastricht University
https://www.maastrichtuniversity.nl/martina.kutmon
NetBio COSI Abstract Selection Chair

Anaïs Baudot
Principal Investigator
CNRS Researcher
Aix Marseille University
https://www.marseille medical genetics.org/a baudot/
NetBio COSI Alt. Committee Representative

Scooter Morris
Executive Director, Resource on Biocomputing, Visualization, and Informatics
Adjunct Assistant Professor
University of California, San Francisco
https://www.cgl.ucsf.edu/home/scooter/
NetBio COSI Finances
NetBio COSI Abstract Selection Committee

Frank Kramer
Professor
University of Augsburg
https://informatik.uni augsburg.de/
NetBio COSI Abstract Selection Committee

Noel Malod Dognin
Established Researcher
Barcelona Supercomputing Center
Honorary Senior Research Associate
University College London
http://www.black wind.com/
NetBio COSI Website and Calendar Manager

Alexandros Xenos
PhD student
Barcelona Supercomputing Center
ISCBacademy COSI Program Coordinator

Activities Over the Last Year
The essential activity in 2022 was the organization of the NetBio COSI sessions at ISMB 2022. We had a packed full-day slot. The program consisted of 2 keynote speakers (Dr. Teresa Przytycka, and Prof. Chad Myers), 2 proceedings presentations, 9 contributed talks, and 42 posters.

Regarding the ISCB academy webinars, we had two speakers:
⁃ 14/12/2021 A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks, by Elva Maria Novoa del Toro
⁃ 10/05/2022, jointly with the MICROBIOME COSI, From hairballs to hypotheses: microbial network analysis, by Karoline Faust & Sam Röttjers

Equity, Diversification, and Inclusion Efforts
A large portion (5/8) of the organizing committee are women. Half of the keynote speakers are women. Of other talk and poster presenters, about 35% are women (as compared to about 29% in 2021).

Leadership Structure
RegSys COSI Steering Committee
Stein Aerts
Jason Ernst (Co-Chair)
Manolis Kellis
Christina Leslie
Jian Ma
Saurabh Sinha (Co-Chair)
Lonnie Welch (Co-Chair)
Judith Zaugg
Julia Zeitlinger

Activities Over the Last Year
The Regulatory and Systems Genomics Community organizes the following activities each year:

1. ISMB Regulatory & Systems Genomics 2-day Track at ISMB

Day 1 Wednesday, July 13th

Day 1 of the RegSys COSI started with a virtual keynote by Julio Saez-Rodriguez from Heidelberg University, in which he discussed the integration of different information sources with single cell multi-omics data to build gene regulatory networks, a subject currently of high interest in the community. His talk launched interesting questions and discussions that continued in the JUNO platform after his participation. This allowed us to have a better engagement of the virtual attendees. This first session included one proceedings talk and three abstract selected talks focused on methods to integrate different sources of information to identify regulatory mechanisms.

The second session of Day1 included an in-person keynote from Lucia Peixoto from Washington State University, where she shared her work on using epigenetic tools to understand sleep in Autism. This session also included a virtual keynote by Rahul Satija from New York University, discussing his work on dictionary learning methods to integrate single-cell data from different experiments and modalities. In this session, we had one proceedings talk and four abstract selected talks, with subjects mainly focused on single-cell data analysis, challenges, and opportunities for data integration in this emerging area.

Day 2 Thursday, July 14th

Day 2 of RegSys COSI started with an in-person keynote by Sushmita Roy, from the University of Wisconsin-Madison on the identification of cell type specific Gene Regulatory Networks during cell differentiation processes. Dr. Roy particularly focused on tree-structured NMF and other approaches that can effectively integrate multiple data modalities in branching differentiation processes. This session also had the presentation of four talks selected from abstracts, focused on machine learning approaches to integrate information to integrate gene regulatory networks.

The second session of Day 2 included a virtual keynote talk by Mayra Furlan-Magaril, from the National Autonomous University of Mexico, during which she shared her work on the determination of the spatial organization of chromatin during erythroid differentiation. This session also had a virtual keynote from Zhiping Weng from University of Massachusetts, where she discussed her work as part of the Zoonomia consortium on the evolutionary constraints of transcription factor binding sites in the mammalian lineage. Both keynotes had strong audience attendance and led to active in-person and virtual discussions through the JUNO app. In the second session, we heard five talks selected from abstracts, focused on methods to study 3D chromatin organization and machine learning approaches to analyze chromatin accessibility patterns and identify regulatory interactions.

The RegSys COSI congratulates the joint winners of our best talk award: Pia Rautenstrauch, Max-Delbrück-Center for Molecular Medicine (for her talk titled “Liam tackles complex multimodal single-cell data integration challenges”) and Anusri Pampari, Stanford University (for her talk titled “Base-resolution deep learning models of chromatin accessibility reveal combinatorial sequence motif syntax and regulatory variation”).

The RegSys COSI sessions were live tweeted via our Twitter account (@ISCB_RegSys) and discussion about the sessions continued on our community Slack (80 currently registered members).

2. RECOMB/ISCB Conference on Regulatory and Systems Genomics and DREAM Challenges

It was three years since the last DREAM conference in New York City in November 2019. Because of COVID-19 we, unfortunately, had to move the 2020 conference scheduled for Carnegie Mellon online; and we had to cancel the 2021 conference planned for Stanford University (due to COVID policies). With society reopening, we were eager to have the DREAM community reconvene in 2022. We were happy to see that the 14th annual DREAM-RSG conference in Las Vegas was a success! The easy-to-access and affordable location attracted people from all over the world; with attendees from Italy, Finland, South Korea, and Canada as well as all over the US. It was fantastic to be able to come together again to discuss science in the many different environments that Las Vegas provided.

The DREAM session of the conference, composed of 2 half-day sessions, kicked off with a Keynote by Lior Pachter from Caltech. Lior gave an amazing presentation on quantitative and computational biology, specifically addressing the paradox relative to the statistical models used to model single-cell RNAseq counts. This was followed by the presentations (4 talks) on the Preterm Birth Challenge and a panel discussion on DREAM. The next morning the Million promoter expression prediction (4 talks) and Anti-PD1 Response Prediction DREAM Challenge (4 talks) results were presented, and the DREAM portion closed with Melissa Handel’s amazing Keynote on how to build up Collaborative analytics at scale. We had a great time seeing everyone in the DREAM community again.

Regulatory and Systems Genomics (RSG) was a two-day event that occurred on Nov 10th-11th, in Las Vegas, NV, USA (co-located and consecutive with the meeting on DREAM challenges). RSG was co-chaired by Jason Ernst (UCLA), Anshul Kundaje (Stanford), and Sushmita Roy (UW Madison). Both days focused on open and emerging problems in gene regulation and regulatory genomics with talks organized into thematic groups of gene regulatory networks, single-cell genomics, spatial transcriptomics, genotype to phenotype, three-dimensional organization of the genome, and systems, network-based approaches for examining disease conditions, and comparative regulatory genomics. Day 1 started in the morning with a poster session, followed by talks on gene regulatory networks, chromatin state, 3D genome organization, network-based methods, and a keynote from Dr. Melissa Gymrek, UCSD, who talked about the importance of examining tandem repeats in gene regulatory studies. In particular, tandem repeats could influence splicing and transcription factor binding, among other processes. Interestingly, she noted that a significant portion of heritability in gene expression can be explained by tandem repeats. She introduced the current computational challenges and approaches developed by her group and others to address these challenges. Going forward she emphasized the importance of novel tools for examining tandem repeats and their contribution to genetic variation and enabling uniform access to large datasets needed for systematic studies of these repeats.

Day 2’s talks focused on single-cell and spatial transcriptomics, comparative genomics and gene regulation, and methods for understanding the relationship between genotype to phenotype. Day 2 ended with a keynote from Dr. Tiffany Amariuta-Bartell from UCSD. Dr. Amariuata-Bartell talked about the challenges in identifying disease-critical tissues. She introduced the method TCSC which helps to identify disease-relevant tissue contexts and combines Transcriptome Wide Association, eQTL, and GWAS datasets to predict key tissues of interest for a particular disease. One of the findings from her study was that cell type composition had a large effect on the results.

The poster session of RSG happened in person and virtually and featured a wide variety of methods, data, and tools in regulatory and systems genomics.

A word cloud was created from the submitted poster and talk abstracts:
https://twitter.com/sroyyors/status/1592778967408586752/photo/1

3. ISCBAcademy - RegSys

RegSys hosted a presentation by Rahul Satija of the New York Genome Center in January 2022:
Title: Integrated analysis of single-cell data across technologies and modalities
Host: Jason Ernst
URL: https://www.youtube.com/@ISCBtv/videos
Impact: Among all ISCB videos, the talk is currently ranked #31 of all time in terms of popularity (929 views) and #5 among those labeled as 1-year ago or more recent. [checked Feb. 6, 2022]

The DREAM challenges provide great educational value so we are featuring them in the ISCBAcademy. In January 2023 RegSys featured the talks of the winners of the Preterm Birth Prediction Microbiome DREAM Challenge. The challenge involved the following tasks:
Task 1 (Prediction of preterm birth) participants received processed vaginal microbiome data collected from pregnant people to develop prediction models to determine the risk of preterm birth (delivery <37 weeks vs. >=37 weeks).
Task 2 (Prediction of early preterm birth) participants received processed vaginal microbiome data collected from pregnant people to develop prediction models to determine the risk of preterm birth <32 weeks vs. >=32 weeks.
Date: January 10, 2023
Title: Preterm Birth Prediction Microbiome DREAM Challenge Rebroadcast
Presenters: Tomiko Oskotsky, Abigail Kuntzleman, and Eunyong Kim
URL: https://youtu.be/BHI6R83ecGM

4. Online community discussions via Twitter and Slack

Equity, Diversification, and Inclusion Efforts
Equity, diversity, and inclusion are given careful consideration during the selection of chairs and speakers for all events and activities organized by RegSys COSI. For instance, we have achieved gender diversity in the composition of leadership, committees, and speakers.

Leadership Structure
The SysMod COSI is jointly organized by a team of six coordinators, who virtually meet once per month. From 2018 to 2022, Andreas Dräger acted as the chairman and Tomáš Helikar as the primary COSI representative to ISCB. The session chairs for the 2022 annual meeting were Andreas Dräger, Bhanwar Lal Puniya, Anna Niarakis, and Reihaneh Mostolizadeh. In 2022, Bhanwar Lal Puniya was elected as the chairman and COSI representative (with Andreas Dräger as deputy).

The team of all current in alphabetical order includes Shaimaa Bakr (Stanford University, US), Matteo Barberis (University of Surrey, UK), Chiara Damiani (Università degli Studi di Milano-Bicocca, IT), Reihaneh Mostolizadeh (Eberhard Karl University of Tübingen, DE), Bhanwar Lal Puniya (University of Nebraska–Lincoln, US), and Meghna Verma (AstraZeneca, US).

The following SysMod coordinators stepped down in 2022: Marc Birtwistle (Clemson University, US), Laurence Calzone (Institut Curie, FR), Claudine Chaouiya (Gulbenkian Science Institute, PT), Andreas Dräger (University of Tübingen, DE), Jan Hasenauer (University of Bonn, DE), Tomáš Helikar (University of Nebraska–Lincoln, US), Jonathan Karr (Icahn School of Medicine at Mount Sinai, US), Anna Niarakis (Université d' Evry Val d' Essonne, FR), María Rodríguez Martínez (IBM Research Europe, CH), Julio Saez-Rodriguez (University of Heidelberg, DE), and Juilee Thakar (University of Rochester, US).

Activities Over the Last Year
The primary activity of SysMod is the annual one-day meeting at the ISMB/ECCB conference. The event featured three keynote talks, 12 contributed talks, two flash talks about poster highlights, and 23 posters.

Over the past year, SysMod has also maintained a community discussion list (e.g., the announcement of impactful new research, meetings, job opportunities, etc.) and a community calendar (e.g., conferences, workshops, and schools).

In a related meeting, the Basel Computational Biology Conference [BC]2, a group of SysMod coordinators annually organizes tutorials and workshops to provide an informal setting to learn about the latest bioinformatics methods, discuss technical issues, exchange research ideas, and share practical experiences on focused or emerging topics in bioinformatics.

Equity, Diversification, and Inclusion Efforts
Over the years, the SysMod coordinators have always promoted equal opportunities for researchers irrespective of their gender, beliefs, ethnicity, and other non-scientific aspects, as the highly diverse composition of the coordinators’ group, the scientific advisory board, and alumni indicate. From its inception, scientific quality has always been the first criterium for inviting keynote speakers. SysMod has always strived to achieve the highest scientific quality while inviting speakers from diverse countries with various backgrounds and ethnicities and with a balance in genders to present a wide variety of excellent researchers within the community. SysMod will continue to support underrepresented researchers when inviting keynote speakers. The submitted contributions, genders, and ethnicities will be balanced, depending on the potential presenting invited authors. Contributed talks and posters, on the other hand, are solely chosen based on scientific quality and soundness.

Leadership Structure
Organizing Committee:
Robert Leaman, NCBI/NLM/NIH, United States
Lars Juhl Jensen, University of Copenhagen, Denmark
Cecilia Arighi, University of Delaware, United States
Zhiyong Lu, NCBI/NLM/NIH, United States

Steering committee:
Russ Altman, Stanford, USA
Sophia Ananiadou, NaCTem, UK
Alex Bateman, EMBL-EBI, UK
Lynette Hirschman, MITRE Corporation, USA
Larry Hunter, University of Colorado, USA
Alfonso Valencia, BSC-CNS, Spain
Jonathan Wren, Oklahoma Medical Research Foundation, USA
Cathy Wu, University of Delaware, USA

Activities Over the Last Year
ISMB 2022 text mining track was a one-day five-hour event on July 11th, 2022. It was well attended: up to 50+ in-person attendees during the talks and many virtual attendees.
- The COSI track was centered on both methodology developments and applications of text mining, especially using advanced language models. Recurring themes included supporting manual data curation from the literature, literature indexing and search and pathway construction; other topics included new corpus development, enriching omics and gene lists.
- COSI track keynote speaker Andrey Rzhetsky presented on recent advances and applications of language embedding models for biomedical knowledge discovery. Keynote speaker Hongfang Liu presented on clinical natural language processing past and current progress. Furthermore, she discussed the significant opportunities present in translating the technology for support real world applications.
- COSI track had a panel on the broad topic of disease analysis with natural language processing (NLP) methods. Panelist Katerina Nastou from University of Copenhagen presented novel work on associating environmental factors with diseases from unstructured text. Panelist Liwei Wang from Mayo Clinic presented the applications of NLP methods in Cancer research using electronic health record (EHR) data. Panelist Gary Bader from the University of Toronto presented NLP research in gene and pathway analysis for disease treatment and drug discovery.

Equity, Diversification, and Inclusion Efforts
We actively sought to achieve gender / ethnic minority diversity in our program, as can be seen in our track statistics.

Leadership Structure
Venkata Satagopam is currently the TransMed COSI Representative and a COSI Track Chair. Maria Secrier is currently the alternate COSI Committee Representative, the COSI Proceedings Liaison and a COSI Track Chair. Wei Gu, Irina Balaur, Sanne Abeln and Heba Sailem serve as COSI Track Chairs. Irina Balaur also serves as the ICSBacademy TransMed Program Coordinator.

Activities Over the Last Year
TransMed 2022 meeting was held during the ISMB 2022 conference on July 10 - 14, 2022 in Madison, USA hosted by session chairs Dr. Anoop Mayampurath, and Dr. Irene Ong. TransMed 2022 had 2 keynote speakers invited:
- Dr. Elana J Fertig, SKCCC / Johns Hopkins University who is an Associate Professor of Oncology and Director of the Division/ Research Program in Quantitative Sciences, co-Director of the Convergence Institute, co-Director of the Single-Cell Training and Analysis Center, and Associate Director of Quantitative Sciences at the Johns Hopkins University Sidney Kimmel Comprehensive Cancer Center.
- Prof. Anthony Brookes, University of Leicester who is a Professor of Genomics and Health Data Research at the University of Leicester (UK), drives strategic initiatives as an Associate Director for the Health Data Research UK institute (HDRUK-Midlands) and is Director of the University’s ‘NUCLEUS’ Genomics Facility.

In total, TransMed 2022 had 5 proceedings, 12 short talks (10 min slot) selected from the abstracts and 42 posters.

TransMed 2022 started with a very insightful keynote talk by Prof. Anthony Brookes titled “Data Science: A trendy name for conventional research using data, or a truly revolutionary new discipline?” discussing the features of health data science, which is made of "a virtuous circle that connects novel research methods to innovative data engineering in order to access and leverage large or challenging datasets in new ways (thereby identifying the need for further new methods)". Prof. Brookes also presented some examples on how to increase the discoverability and reusability of the valuable and sensitive project assets (data, patients, samples, etc).

The last session of the TransMed 2022 started with another great keynote talk by Dr. Elana J Fertig titled "Learning cellular interactions from spatial transcriptomics with SpaceMarkers". Dr Fertig introduced the role of spatial molecular data - which permit characterization of the cellular and molecular interactions in human tissues and diseases - in understanding the mechanisms of the cancer therapeutic response and resistance. Moreover, she presented the SpaceMarkers newly-developed analysis approach that was applied to infer molecular changes from cell-cell interaction from latent space analysis of ST data from a liver cancer immunotherapy clinical trial. Dr. Fertig also discussed the benefits of using SpaceMarkers functionality in combination with other data types (e.g. scRNA-seq data).

We also selected 2 best talks and 2 best posters awards considering both the scores of the abstract reviews and presentation during the TransMed 2022 meeting as follows.

- Best Talk (Best Oral Presentation)
* Madison Darmofal, (Memorial Sloan Kettering, Weill Cornell Graduate School, United States) - “Genome-Derived Diagnosis: Deep Learning Model for Tumor Type Prediction using MSK-IMPACT data”
* Yue Wang, (University of Pittsburgh, United States) - “Perturbed Transcriptomic Analyses Identify Chemo-immunotherapy Synergisms to Shift Anti-PD1 Resistance in Cancer”

- Best Poster
* Junjie Peng, (University College London, United Kingdom) - “Patient-specific and disease-related determinants for cardiovascular disease (CVD) risk stratification in the APPLE (Atherosclerosis Prevention in Paediatric Lupus Erythematosus) clinical trial cohort”
* Jeppe Severens, (Leiden University Medical Center, Netherlands) - “Joint genetics and transcriptomics based classification of acute myeloid leukemia patients”

We welcomed new members of the TransMed COSI organizers (core team) at the TransMed 2022 at ISMB 2022:
- Irene Ong, PhD. - University of Wisconsin-Madison, USA, who continues to join our TransMed organizing team
- Anoop Mayampurath, PhD. - University of Wisconsin-Madison, USA, who had to step out of the activities of the organizing team after the ISMB 2022, but he will remain in the program committee.

Outreach at EATRIS:
- Irina Balaur gave an invited talk on the TransMed COSI activities (including the TransMed meetings, TransMed webinar at ICSBacademy etc.) at the European infrastructure for translational medicine (EATRIS: www.eatris.eu) on November 28, 2022. Discussions on potential collaborations between the TransMed and EATRIS groups follow.

TransMed ISCBacademy webinars:
We had 2 TransMed webinars at ISCBacademy, specifically,
- Marek Ostaszewski, (PhD., University of Luxembourg, Luxembourg) on community efforts from the COVID-19 Disease Map: https://covid.pages.uni.lu/ on February 1 and
- Maria Secrier, (PhD. University College London, UK) on cancer analytics approaches on June 29.

Our first TransMed ISCBacademy was on “COVID-19 Disease Map: building a computational repository of SARS-CoV-2 virus-host interaction mechanisms” given by Dr. Ostaszewski, who introduced the Disease Maps Project that develops computational and visual knowledge repositories constructed to catalogue, standardize, and model disease-related mechanisms towards contextualized data analysis and modeling of a given pathophysiology. Dr. Ostaszewski described in more detail the COVID-19 Disease Map project, a comprehensive interdisciplinary community scientific effort to study the mechanisms of the SARS-CoV-2 – host interactions, involving over 250 members (domain experts, diagram curators, analysts, and modelers). Dr. Ostaszewski also presented briefly both the challenges and lessons learnt from working in such large-scale scientific multidisciplinary collaboration.

Our second TransMed ISCBacademy was entitled “Reconstructing the mutational histories of healthy and cancer genomes” given by Dr. Maria Secrier, who introduced and explained the concept of "mutational signatures" as scars left in the genome by various mutational processes acting throughout an individual’s lifetime as a result of exposure to carcinogens, which lead to cancer development by inducing DNA damage in cells. Dr. Secrier also presented several state-of-the-art approaches on the identification and exploration of these mutational events in cancer genomes as well as applications of these methods in both healthy aging and cancer studies.

We disseminated information via several media channels, including LinkedIn webpage (Translational Medicine Informatics & Applications Group), the TransMed Slack and the @TransMedISMB Twitter account. We had comparable numbers of participants during the 3 sessions at the TransMed 2022 at ISMB 2022, (190, 105, and 150 attendees). During the 2 TransMed webinars, we had 22 and 23 registrations, respectively.

Equity, Diversification, and Inclusion Efforts
- We try to have gender and ethnicity balance in the leadership as well as in the selection of invited speakers.

Leadership Structure
This year Emidio Capriotti was COSI representative to committee and Antonio Rausell alternate representative. Hannah Carter was COSI Proceedings Liaison.

Activities Over the Last Year
This year VarI COSI reached held 12th session, bringing to ISMB the latest developments and discoveries on variant interpretation. The session included 11 talks, 1 proceedings presentation and 3 keynote speakers. Nicole Sorenzo opened with a complete overview of her major discoveries characterizing the genetics and epigenetics components associated to human heterogeneity across multiple ‘omics read outs 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.

Equity, Diversification, and Inclusion Efforts
We strive to be inclusive of all members of our scientific community and ensure representation at our annual meeting. The VarI COSI strongly promotes gender balance. currently Hannah Carter is our representative to the committee. We always promote keynotes talk from excellent female scientists.