Leadership Structure
R. Gonzalo Parra, parra.gonzalo@gmail.com, Barcelona Supercomputing Center, PI, ES, Co-chair
Su Datt Lam, sudatt@ukm.edu.my, Universiti Kebangsaan Malaysia, PI, Malaysia, Co-chair
Douglas Pires, douglas.pires@unimelb.edu.au, University of Melbourne, PI, AU, Co-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
Alexander Monzon, monzon.alexander@gmail.com, Padova University, PI, IT, Track Editor
Javier Alfaro, javier.alfaro@proteogenomics.ca, International Center for Cancer Vaccine Science (University of Gdansk), PI, PL, Track Editor
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 Hackathon Coordinator
Carlos Rodrigues, carlosmr12@gmail.com, University of Queensland, Postdoc, AU, Training Coordinator and Hackathon 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
Serena Rosignoli, srosignoli@unimore.it, Unimore - University of Modena and Reggio Emilia, Postdoc, Italy, Webinars Organiser
Neeladri Sen, n.sen@ucl.ac.uk, University College London, Postdoc, UK, Webinars Organiser

Activities Over the Last Year
Summary of 2025:
ISMB was held in Liverpool, UK. This time we had 3 keynote speakers delivered by:

Prof. Adrian Mulholland (Bristol University, UK)
Prof. Franca Fraternalli (University College London, UK)
Prof. Diego U. Ferreiro (Buenos Aires University, Argentina)

The same procedure as for 3DSig 2025 was followed to fill the 2 days programme with selected talks.



ISMB track applicable
Number of total submissions: 84
Number of proceedings: 4
Number of keynote speakers: 3 How many were of a diverse nature: 1 from the Global South (Argentina).
Number of total talks within track: 27 many were of a diverse nature: NA
Total number of posters: 46
Sponsorship secured: 0
Travel fellowships issued: NA


Activities outside of ISMB:

1st ISCB 3DSIG / Elixir 3DBioinfo Joint Conference - Barcelona
We organized our 1st activity, in person, outside of ISMB. In March 2025, we held the 1st ISCB 3DSIG / 3DBioinfo event in Barcelona, at the Barcelona Supercomputing Center. The event was a success, with over a hundred attendees from all over Europe and some invited speakers from North America. A short report can be viewed here:
https://f1000research.com/documents/14-483

Webinars:
We kept organising our webinars in collaboration with the 3DBioinfo community from Elixir. Also, we added 1 webinar in collaboration with the ML4NGP COST Action project on the subject of intrinsically disordered proteins.

We had 5 Webinar Sessions this year:

1. January:
Prof. David Jones (University College London, UK)
“Exploring structural diversity across the protein universe with The Encyclopaedia of Domains”
https://youtu.be/D8S3xy1MNB4?si=J29TYk7Pplmic6JR

2. February:
Ondrej Vavra, Ph.D., Enantis, Czech Republic
“Large-scale annotation of biochemically relevant pockets and tunnels in cognate enzyme–ligand complexes”

Antonio Macchiarulo, Department of Pharmaceutical Sciences, University of Perugia, Italy
“Incorporating Molecular Dynamics and Biophysical Studies into a Structure-Based Approach to Identify Non-Amino Acidic Ligands of DDAH-1”
https://youtu.be/I-bpTQsJZEc?si=DKxw2ILlOCHFoIex

3. May:
Dr. Qian Cong (University of Texas Southwestern Medical Center)
“Computing the Human Interactome”
https://youtu.be/NT_VB6Ufng4?si=hZILXKiyjO1eT828

4. September
Prof Michele Vendruscolo
“Expediting Drug Discovery for Undruggable Targets Using AI”
University of Cambridge, UK

Dr. Zsuzsanna Dosztanyi
“Integrating Biophysics and Deep Learning for Interpretable IDP Prediction”
Eötvös Loránd University, Hungary

5. December:
Prof. Edward Marcotte, University of Austin, Texas.
“Modern cells, ancient proteins and complexes”
https://youtu.be/UP4Joa8CnGc?si=ZHFk0bhiHJuLVb0v


Feedback about existing ISCB activities and suggestions on new initiatives/activities/public policies that ISCB could participate in with the group to advance a shared mission:

Existing activities and new initiative plans for ISMB 2026
- The potential for a Hackathon is being considered
- Additional recruitment of student/postdoc volunteers, particularly to animate the slack channel
- Our collaboration with the ELIXIR 3DBioinfo community continues. A new joint event is planned for November 2026 in Rome, Italy, and we are also discussing additional forms of international collaboration.
- We will continue working with regional structural bioinformatics associations to organize seminars or joint meetings. Our involvement typically provides access to ISCB online resources (e.g., webinar platforms) and, in turn, may encourage members of these organizations to join ISCB.

At ISMB 2025 we had two non shows in virtual speakers. As a result, we will not accept virtual speakers for ISMB 2026.

Equity, Diversification, and Inclusion Efforts
Gender representation: We do not have access to any information relative to the distribution of sex or self-defined gender of participants. We strive to have a balance in terms of sex of keynotes at the level priorities of invitations. This year we decided to have two women as keynotes to balance past years like 2022 when none of the female (description of sex) invited speakers we able to accept our invitation.

Leadership Structure
In the past we have had a loose organizing committee with one or two people leading the detailed coordination with support from the others especially recruiting speakers and panelists. We met online monthly from March 2025 until ISMB. Some new people stepped up this year to help with different parts of the COSI session and an AI zoom in November.

Activities Over the Last Year
Our main focus was our (second full day) session at ISMB. We had talks, panels, and fruitful group discussions on topics relevant to core members.

Talks:
Damian Dalle Nogare - Bioimage analysis in the age of AI: lessons and a path forward from a core facility perspective. A thought-provoking keynote regarding some history of the computational imaging field and its journey into a fully AI mode. We can learn a lot from the things they have gone through, and we should work together.

Kübra Narcı - Benchmarking Variant-Calling Workflows: The nf-core/variantbenchmarking Pipeline within the GHGA Framework: Variant callers do all sorts of different things and comparing structural variants is non-trivial. This is an nf-core pipeline to handle this type of comparison that was developed for the GHGA and shared with the world.

Thomas Roder - Assembly Curator: rapid and interactive consensus assembly generation for bacterial genomes – A microbial assembly benchmarking paper (Wick and Holt) basically found no assembler worked well on all assemblies. Tricycler from Ryan Wick is good, but time consuming. The goal of this was to get 80% of the quality of Tricycler in 5% of the time. On github at https://github.com/MrTomRod/assembly-curator

Adam Giess - Long Read Sequencing at Genomics England: They’ve done 12,000 Nanopore Promethion flowcells and shared some of the details of their setup and approach.

Anil S. Thanki - Autonomous Single Cell Transcriptomics Analysis in Persist-seq: Multi-institutional effort to study early tumor environment. Diverse toolset included Kubernetes, Jenkins, Galaxy (workflow executer command line), AWS, and Slack.

Iris Diana Yu - Advancing the Expression Atlas Resources: A Scalable Single-Cell Transcriptomics Pipeline to Facilitate Scientific Discoveries: Expression Atlas and single cell expression atlas – ingest, annotate, curate, and serve data!

Ayushi Agrawal - Mixed effects models applied to single nucleus RNA-seq data identify cell types associated with animal level pathological trait of Alzheimer’s disease: LODopt model applied to single nucleus RNA-seq data. https://github.com/gladstone-institutes/LODopt

Natalie Gill - Optimizing Clustering Resolution for Multi-subject Single Cell Studies: Method of optimizing clustering by splitting PCs into odd and even. https://github.com/gladstone-institutes/clustOpt

Hubert Rehrauer - GEO Uploader: Simplifying the data deposition in the GEO repository: A tool to make it easier for researchers to upload their data to GEO: https://github.com/fgcz/geo-uploader

Carlos Prieto - Enhancing Bioinformatics Workflows with Analytical Visualization Tools: a series of impressive interactive tools and data visualizations – rjsplot, D3GB, looking4clusters, Rvisdiff, RD3plot. https://github.com/BioinfoUSAL

Patricia Carvajal-López - Competency framework profiles to reflect career progression within bioinformatics core facility scientists: A collaboration and community effort led by EBI to develop more robust career definitions and stages for people in core facilities. Publication out in Bioinformatics Advances (https://academic.oup.com/bioinformaticsadvances/article/5/1/vbaf206/8255757).

Panels:

The rise of computational imaging

Panelists: Damian Dalle Nogare, Jamie Soul, Syed Murtuza Baker, Emily Johnson

Imaging groups and bioinformatics groups feel themselves coming together, mainly due to spatial transcriptomics. How can these two groups interact and learn from each other to advance science? We saw issues with the software built-in to some commercial platforms in terms of calling cells correctly and more custom solutions are probably needed. Perhaps some things can be learned by the bioinformatics core community and some things will be a collaboration between the two groups, but we need to be clear who does what and who needs what files from who in order to accomplish things. In some ways imaging has transformed into a fully AI field and we can learn from their growing pains.

The practical use of AI in cores

Panelists: Madelaine Gogol, Ashley Sawle, Mohab Helmy, Ken Brewer

We discussed training users in the use of genAI (because we as bioinformaticians might be more experienced). Do we still need to teach coding? I think the consensus was at least some for some people, but it’s not really clear how much. How do we keep up with new tools? We need to be intentional about setting aside time for reading papers, experimenting, taking time to try things. Seqera AI was mentioned as a platform for writing NextFlow code (many of the models are not good at it yet). Multiqc has an argument now to generate an AI summary about the quality in the report. Could be used to take a collection of scripts and make it into a NextFlow pipeline with a little effort. University of Queensland fast AI course was mentioned as a potential source for upskilling. There were discussions of hiring in the age of AI with in-person interviews maybe more required and deep questions to check knowledge. Watch out for slopsquatting or bad prompting generating garbage for collaborators.

Breakout groups:

We broke into four breakout groups based on what the people in the room were interested in discussing.

Spatial / Imaging – Imaging and Bioinformatics groups can stay separate but improve communication and make sure it’s clear who does what. Bioinformaticians need to learn to perform common and easy image-based tasks, and to ask for help with the hard ones. We have a lot to learn from imaging groups so short trainings could help us be able to leverage some things for spatial transcriptomics.

AI – When users ask for AI, we need to find out if it’s the right tool and then guide them, otherwise they may pursue other less reputable sources. Upskilling our users in the use of AI could work better with free food. Assigning a few people in the team as AI experts could help the team learn and support users better.

Project Management and tools – Jira and Agile might help manage projects and time. Getting involved early can help avoid bad data. Some teams like strict scoping, others feel it’s not collaborative. Being able to say no is essential, and so is maintaining good relationships.

Reporting / communicating results – Quarto was mentioned as a great solution for updating reports and presentations when something changes. Containers and NextFlow are important for reproducibility, and clinical environments may be more resistant to changes.

Besides our session at ISMB, many of us have been participating in a working group to better define career roles for people working in bioinformatics cores (as presented by Patricia Carvajal Lopez at the conference). We have written a framework, surveyed people in cores, and the manuscript was published this year in bioinformatics advances. This will help to formalize our career paths and provide guidance to other people starting or working in cores.

This year after ISMB, some members still were interested in discussing some of the topics further, so Sivarajan Karunanithi and James Gilbert organized a zoom discussion on the topic. At least 14 people attended and generally we all found it informative and to be a useful way to share best practices and information on this rapidly evolving area.
Generally, people regularly interact through our slack and mailing list to get advice, find out how other people handle particular situations, share job postings, etc.

Equity, Diversification, and Inclusion Efforts
We have been lucky enough to be (at least for a while now) organized by a group that is itself represented by different groups in a number of ways - gender, geography, country of origin, and work role. Since people working in cores tend to come from all different backgrounds, we seem to be above average within the conference at identifying a diverse group of people to participate in talks and panels. Our selection of talks is currently based mainly on the relevance of the topic to our audience, but our speakers have luckily tended to be pretty diverse. This year we offered complimentary registration for our speakers and a free ISMB t-shirt to our panelists, which might encourage some people to attend who might not be able to otherwise. Since cores work in an interdisciplinary field, we also tend to try to be pretty inclusive in terms of both topic areas and people’s backgrounds. The breakout sessions also allow for a more comfortable means of sharing of information for people who don’t necessarily want to give a talk or even sit on a panel, but still might have a lot of wisdom and insight to share. We have not been able to really afford sponsoring travel fellowships for students, which is a potential area of growth - it’s not as applicable for our COSI since we tend to be more of a professional-oriented group. Another potential area of growth for us might be to examine our keynote speaker selection process. We have had quite a run of male keynote speakers, for example, and it might be good to examine how we are identifying those speakers to ensure we aren’t passing valid people over for the opportunity.

Leadership Structure
General Chairs
Qianwen Wang, University of Minnesota, USA
Zeynep Gümüş, Icahn School of Medicine at Mount Sinai, USA
Website Chair
Kari Lavikka, University of Helsinki, Finland
Publicity Chair
Astrid van den Brandt, Eindhoven University of Technology, The Netherlands
BioVis COSI @ ISMB 2025 Abstracts Chairs
Jen Rogers, University of Utah, USA
Robert Krueger, New York University, USA
Aditeya Pandey, Regeneron Genetics Center, United States


ISMB Liaison Chairs
Jim Procter, University of Dundee, UK
Bio+MedVis Challenge @ IEEE VIS 2025 Chairs
Barbora Kozlikova, Masaryk University, Czech Republic
Nils Gehlenborg, Harvard Medical School, USA
Laura Garrison, University of Bergen, Norway
Eric Mörth, Harvard Medical School, USA
Simon Warchol, Harvard University, USA
Morgan Turner, Harvard Medical School, USA


BioVis Meetup 2025 Chairs
Helena Jambor, TU Dresden, Germany
Zeynep Gümüş, Icahn School of Medicine at Mount Sinai, USA




Steering Committee
Jan Aerts, KU Leuven and U Hasselt, Belgium
Jan Byska, Masaryk University, Czech Republic and University of Bergen, Norway
Helena Jambor, TU Dresden, Germany
Michael Krone, Stuttgart Technical University of Applied Sciences, Germany
G. Elisabeta Marai, University of Illinois at Chicago, USA
Jim Procter, University of Dundee, UK
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 2025 main event at ISMB featured two distinguished keynote speakers. Kay Nieselt presented The Visual Genome: An attempt to classify multi-omics visualization, discussing emerging needs for clearer conceptual frameworks to support interpretation of complex multi-omics data. Ingrid Hotz delivered Visual Data Analysis Research in Biomedical Applications: Navigating the Line Between Scientific Novelty and Practical Impact, addressing challenges in translating visualization research into practical biomedical impact. In addition to the keynote program, the meeting included contributed talks and posters spanning methods, systems, and applications in biological data visualization, reflecting broad international participation across academia and industry. Most notably, Submission 927, “GENET: AI-Powered Interactive Visualization Workflows to Explore Biomedical Entity Networks,” received the Best Abstract Award, authored by Bum Chul Kwon, Natasha Mulligan, Joao Bettencourt-Silva, Ta-Hsin Li, Bharath Dandala, Feng Lin, Ching-Huei Tsou, and Pablo Meyer, representing IBM Research (Healthcare and Life Sciences, Yorktown Heights, NY, USA) and Cleveland Clinic (Cleveland, OH, USA). The meeting was attended by a full audience, with certain talks (especially the keynote and AI-integrated tools) having a good number of standing attendees. The BioVis dinner was on the same day, attended by keynote speakers, chairs, and a BioVis speaker representing an initiative from an underserved African country.
Another important meeting was the Bio+MedVis Challenge @ IEEE VIS 2025 on November 2, 2025, in Vienna, as https://biovis.net/2025/biovisChallenges_vis/. The 2025 Challenge centered on designing alternative visualization approaches to better support biomedical interpretation tasks—particularly for magnetic resonance spectroscopy (MRS) data, where current practice makes it difficult to compare metabolite measurements, assess quality, and interpret relationships across patients and time. Submissions were eligible for recognition awards (e.g., Award of Merit / Award of Excellence), awarded at the discretion of the evaluators.
A number of notable entries received awards and recognition. MRSight (Ratio-Weighted Complete and Visibility Graphs for MRS data visualization and assessment) reports receiving an Award of Excellence (described by the authors as “first place”). BioSET: Biomarker-based Spatial co-Expression analysis in Tumor environments also received an Award of Excellence, highlighting the broader challenge theme of making high-dimensional biomedical measurements more interpretable for real analysis workflows. An additional Award of Merit went to t-SNE based Transfer Functions for Multi-attribute Volume Rendering, demonstrating the continued importance of interaction and multivariate encodings in biomedical volume exploration. Beyond the awardees, the 2025 Challenge showcased creative directions for both redesigning MRS interfaces (e.g., dual-view designs for ratio + quality and overview-to-detail exploration) and tissue/biomarker-driven ROI discovery approaches that combine computational methods with interactive visual analysis.


Finally, we continued the online BioVis meetup series. In 2025, the series ran monthly and was widely promoted across our channels (LinkedIn, Email list, and Slack Channels), helping sustain year-round engagement beyond the conference itself.

Equity, Diversification, and Inclusion Efforts
BioVis is committed to Equity, Diversity, and Inclusion (EDI) in both how we organize the community and how we shape the scientific program. We believe diverse perspectives strengthen the field, improve the quality of discussion, and broaden the impact of visualization research in the life sciences.
Concrete steps we have taken include:
Gender representation in high-visibility roles: In the current BioVis program, two of our keynote speakers are women, reflecting an intentional effort to ensure speaker diversity at the highest-profile parts of the meeting.
Dedicated platform for women’s voices and leadership: We host a BioVis Meetup speaker series featuring all women speakers, designed to amplify expertise, create visible role models, and strengthen professional connections and mentoring.
Diverse representation in organizing and leadership roles: Our organizing team includes members with diverse professional backgrounds, career stages, and lived experiences, distributed across key roles (e.g., chairs, program organization, community-facing efforts). This helps ensure that decisions about programming and community norms reflect more than a single perspective.
Balanced participation across career stages: We aim for a deliberate balance of junior and senior community members in both participation and organizational responsibilities, supporting inclusion, leadership development, and fair access to visibility and experience.
Intentional practices in program formation: We work to maintain gender balance among general chairs, keynote selections, and speakers chosen from abstracts, applying these considerations throughout planning rather than as an afterthought.
EDI is an ongoing effort. We will continue to evaluate our processes (e.g., speaker selection, leadership recruitment, community feedback) and refine our practices to better support an inclusive, respectful, and welcoming environment for all attendees.

Leadership Structure
COSI representative to committee: Robert Hoehndorf
COSI Alternate representative: Maxat Kulmanov
COSI Proceedings Liaison: Robert Hoehndorf
COSI Track Chair(s): Tiffany Callahan and Augustin Luna and Robert Hoehndorf

Activities Over the Last Year
Bio-Ontologies & Knowledge Representation (BOKR) is an ISMB Community of Special Interest (COSI) that covers research in the application of ontologies, knowledge graphs, and the organization, presentation, and dissemination of knowledge in biomedicine and the life sciences.

BOKR celebrated its 28th year at ISMB 2025 in Liverpool, UK. The COSI provides a platform for reporting novel methods and sharing experiences on the construction and application of semantic artifacts. This year's program featured 30 speakers, comprising 21 male and 9 female presenters. Participants benefited from a strongly interdisciplinary setting, engaging with members from the OBO Foundry, the W3C’s Healthcare and Life Sciences Community Group, and the wider AI community.
Day 1: Generative AI, FAIR Infrastructure, and Data Sustainability

The first day opened with a joint session with the Bioinformatics Open Source Conference (BOSC), focusing on the integration of Large Language Models (LLMs) with structured knowledge. The invited presentation discussed Open Knowledge Bases in the Age of Generative AI, exploring how structured data can ground AI to reduce hallucinations. Subsequent talks addressed generating molecular interaction graphs using LLMs, transcriptomic foundation models, and peptide bioactivity prediction. The session also covered transparency and reproducibility in machine learning via registry systems.

The afternoon focused on ontology infrastructure and FAIR data standards. Presentations provided updates on biomedical ontology repositories and introduced frameworks for integrating knowledge graphs with LLMs. Significant attention was given to FAIR standards, with talks on Bioschemas and RO-Crate for research outputs. Additional topics included scalable phenotyping systems and the use of the Ontology Development Kit (ODK) for managing legal compliance in ontology creation. The day concluded with a retrospective on 10 years of ontology repository development, a review of global biodata infrastructure, and a panel discussion on Data Sustainability.
Day 2: Knowledge Graphs, Disease Mechanisms, and Theory

The second day concentrated on the application of Knowledge Graphs (KGs) to disease and microbial research. Presentations detailed KG-driven microbial growth predictions, resources for disease-associated genes, and causal KG analysis for identifying adverse drug effects. A unified KG approach for heterogeneous data representation was also presented. Short talks covered technical challenges such as benchmarking data leakage in link prediction and extracting biological pathway knowledge from literature.

The afternoon proceedings session featured a novel method leveraging the Gene Ontology to find functionally analogous cell types across species. Other sessions addressed autoantibody knowledge integration, ontology pre-training for metabolite property prediction, and the development of the Aging Biomarkers Ontology. Further talks explored the Cell Knowledge Network and genomic knowledge curation frameworks. The meeting concluded with an invited presentation on Knowledge Graph Theory and Applications, followed by flash talks on LLM-enhanced ontology translation, FAIR single-cell data management, and the Cancer Complexity Knowledge Portal.
Community Engagement

The COSI sessions maintained a strong social media presence. The community currently engages through the Bio-Ontologies Slack workspace (69 members) and a LinkedIn group with 117 members representing both academic and industry settings.

Equity, Diversification, and Inclusion Efforts
The Bio-Ontologies COSI did not implement specific Equity, Diversity, and Inclusion (EDI) initiatives for the 2025 conference year. The program focused strictly on scientific merit and technical relevance in its selection and organization processes.

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 President, Nomi Harris as Vice-President, and Heather Wiencko as Treasurer.

BOSC (https://www.open-bio.org/events/bosc-2025/) continues to be chaired by Nomi Harris, who has chaired or co-chaired the meeting since 2010. For 2026, the BOSC organizing committee includes 9 people. Newly added is Van Truong (University of Pennsylvania).

Activities Over the Last Year
OBF accomplishments over the past year include:
- OBF Event Fellowships: In 2025, 9 people were awarded funds to attend in-person or virtual events related to open source / open science, including conferences such as BioHackathon Europe 2025, the 2025 International Statistical Genetics Workshop, and ISMB/ECCB 2025.
- OBF newsletters went out in February and November 2025: https://github.com/OBF/newsletter/tree/master/newsletters. We welcome suggestions from the community about relevant content (related to open source / open science) to include in future issues.
- In Feb-March 2025, we migrated the OBF/BOSC website from WordPress to a site created by the open source static site generator Hugo, with the pages stored on GitHub, which allows the public to easily propose improvements to our website or draft new posts. As part of this move, our website is now also archived with Rogue Scholar, ensuring the blog posts will remain part of the long-term scientific record and have their own citable DOI. For details, see https://www.open-bio.org/posts/2025-03-04-new-website/
- OBF and BOSC remain active on social media. There were 22 posts on our blog (open-bio.org/blog/) as well as emails to our subscribers, posts on LinkedIn and Bluesky, and messages in public Slack channels. As of January 13, 2026, OBF has 1.6K followers on Bluesky (https://bsky.app/profile/openbio.bsky.social) and 688 group members in our LinkedIn group (https://www.linkedin.com/groups/9539620/)

BOSC accomplishments over the past year include:
- Our report about BOSC 2025 can be found at https://f1000research.com/articles/14-887
- BOSC 2025, the 26th annual Bioinformatics Open Source Conference, was part of ISMB/ECCB 2025 in Liverpool, UK, and online. Attendance at BOSC peaked at 283 in-person attendees, with additional online participants.
- BOSC 2025 included two full days of talks and posters covering a wide range of topics in open science and open source bioinformatics, with two keynote talks and a panel discussion. The second day of BOSC was a joint session with the Bio-Ontologies and Knowledge Representation (BOKR) track.
- BOSC 2025 covered a wide range of topics in open science and open source bioinformatics, organized into the following session topics: Open Science; Analytic tools, pipelines, toolkits, and platforms; Open Data; AI; Ontologies & knowledge representation; The global biodata infrastructure
- The first keynote talk was delivered by Christine Orengo: “Working together to develop, promote and protect our data resources: Lessons learnt developing CATH and TED.” The joint BOSC/BOKR session included a keynote talk by Chris Mungall entitled “Open Knowledge Bases in the Age of Generative AI”.
- In addition to the two keynotes, BOSC 2025 included 34 talks chosen from submitted abstracts and 43 in-person posters, plus 4 online posters. The complete lists of talks and posters can be found at www.open-bio.org/events/bosc-2025/bosc-2025-schedule.
- A closing panel on Data Sustainability, moderated by Mónica Muñoz Torres, featured panelists Scott Edmunds, Varsha Khodiyar, Tony Burdett, Nicky Mulder, and Chris Mungall..
- CollaborationFest, a collaborative work event that typically precedes or follows ISMB, was incorporated as part of the main conference and organized by BOSC with help from the Function and 3D-SIG tracks. Over 60 people participated in ISMB CoFest, collaborating on nine different projects.
- BOSC’s social media presence is growing. As of January 15, 2026, the BOSC group on LinkedIn (https://www.linkedin.com/groups/14344023/) has 754 members (up from 385 a year ago). On Bluesky (https://bsky.app/profile/bosc.bsky.social), BOSC has 675 followers (up from 351). The BOSC Slack workspace has 552 members.

Equity, Diversification, and Inclusion Efforts
- The OBF Event Fellowship program is aimed at improving diversity at events related to open science or open-source bioinformatics by helping to make events financially accessible to people from groups that are traditionally underrepresented in these fields. Originally called 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/).
- As in previous years, BOSC prioritized its time and funds to ensure our meeting was more diverse and inclusive. Anyone who submitted an abstract to BOSC could request fee assistance by checking a box on the submission form. Additionally, participants were encouraged to apply for OBF Event Fellowships. In 2025, 14 people (12 from underrepresented groups) were granted free registration to ISMB/BOSC thanks to a combination of registration fee waivers and OBF Event Fellowships (funded by sponsorships).
- Our keynote speaker selection process is designed to be inclusive and transparent. In the first phase, we invite as broad a community as possible to nominate potential speakers. After that, we apply our Invited Speaker Rubric (https://github.com/OBF/bosc_materials/blob/master/invited-speaker-process.md) to narrow down the list of candidates and solicit community feedback. This process has helped us choose keynote speakers who represent a diversity of backgrounds and ideas. In the first few years of BOSC, the two keynote speakers were often both white men. In more recent years, that has not been the case.
- We offer honoraria to our keynote speakers, in recognition of the fact that not all researchers are privileged to be able to donate their time. Those who do not want to accept honoraria were given the option to donate it back to help support future DEI-related endeavors.
- The BOSC Organizing Committee and Review Committee are both diverse, with wide representation from people of different ethnicities and geographical locations. We hope to continue making both of these committees, as well as BOSC participation in general, even more representative of the whole world, particularly the Global South.
- A page on our website (https://www.open-bio.org/bosc-dei/) provides more information about how BOSC has supported diversity, inclusion and accessibility (also known as DEI or EDI).

Leadership Structure
CAMDA is co-chaired by Wenzhong Xiao (Harvard/Stanford), Joaquin Dopazo (Spanish Health Ministry), David Kreil (Vienna), and Pawel Labaj (Jagiellonian University, 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.
With novel challenges appearing in CAMDA portfolio of competition topics every year we take pride to involve a diverse group young and talented researchers.

Activities Over the Last Year
The main activity of the COSI is the preparation and running of competitions throughout the year, culminating in discussions at the CAMDA conference in ISMB, followed by a special proceedings volume.
The competition challenges for CAMDA 2025 were advertised early in the year and included:
- The Anti-Microbial Resistance Prediction Challenge featured the CABBAGE project’s unique curated genotype-phenotype database. Apply diverse ML strategies and language models to predict antimicrobial resistance across more than 5,000 bacterial strains!
- The Gut Microbiota Challenge focused on deriving new microbiome health indices that integrate taxonomy and function under the "Theatre of Activity" concept. Develop ensemble approaches to outperform existing indices and stratify healthy vs. unhealthy microbiomes!
- The Synthetic Clinical Health Records Challenge provided a rich set of highly realistic Electronic Health Records (EHRs) tracing the diagnosis trajectories, distilling information from 1.2 million real diabetic patients. Leverage these data to predict diabetic complications using deep learning frameworks!
- The Health Privacy Challenge presented an interactive platform under the ELSA initiative, utilizing a Blue Team vs Red Team format. Achieve trust and robustness in the generation of privacy-preserving synthetic gene expression datasets!
The last challenge was connected with Panel Discussion hosted by Hakime Öztürk (EMBL Germany) on The Health Privacy in which we hosted: Spiros Denaxas (UCL, U.K.), Antti Honkela (UoH, FI), David Kreil (BOKU, AT), Wenzhong Xiao (MGH/Stanford, U.S.A.), Joaquin Dopazo (FPS, ES).

The scientific program included keynotes by leading researchers in the field: Spiros Denaxas (University College London), discussing how electronic health records are reshaping biomedical research and enabling the simultaneous analysis of thousands of conditions. In 2025 we also had an opportunity to learn more about the computational prediction of microbial phenotypic traits using neural networks by Thomas Rattei (University of Vienna).

The last session featured the CAMDA Trophy Ceremony with the First Prize going to Anton Pashkov from ENES Morelia, UNAM, Mexico. The Second Prize went to Rafael Pérez-Estrada from Centro de Ciencias Matemáticas, UNAM, Mexico, and the Third Prize to Owen Visser from the University of Florida, U.S.A. An Honourable Mention for Sustainability was awarded to Serghei Mangul, University of Suceava, Romania.

At CAMDA, after critical assessment and discussion during the conference, participants are invited to submit a full manuscript incorporating new insights from the meeting for review and publication in the CAMDA Proceedings, published in the well established journal Frontiers in Genetics.

Equity, Diversification, and Inclusion Efforts
In past years CAMDA has managed to have a good gender balance among keynotes and invited speakers. Last year we were hosting Ms Dr Hakime Öztürk nad Ms Dr Kinga Zielinska as an invited speaker. CAMDA also puts a lot of efforts to especially promote young researchers at the beginning of their scientific career. CAMDA featured speakers from: Austria, China, Finland, Germany, Mexico, Israel, Poland, Palestine, Romania, Spain, U.S.A.

Leadership Structure
The CompMS COSI is led by a mix of academic and industry researchers. The current CompMS COSI leadership consists of Wout Bittremieux (University of Antwerp, Belgium), Timo Sachsenberg (University of Tübingen, Germany), Isabell Bludau (Heidelberg University Hospital, Germany), Marie Brunet (University of Sherbrooke, CA), and Lindsay Pino (Talus Bio, WA, USA).

Activities Over the Last Year
Over the past year, the CompMS COSI’s activities were primarily centered around the ISMB/ECCB 2025 conference in Liverpool, UK. Our dedicated CompMS track once again highlighted state-of-the-art developments in computational mass spectrometry, with broad relevance across multiple omics domains, most notably proteomics, metabolomics, and lipidomics. The program featured keynote lectures by Prof. Rick Dunn on computational approaches for small molecule structural annotation and by Dr. Tine Claeys on making proteomics AI-ready. In addition, the track included 16 oral presentations, predominantly delivered by early-career researchers, and 24 poster presentations, providing a strong platform for emerging scientists. The CompMS COSI also actively participated in the ISMB CollaborationFest organized by the BOSC COSI, fostering cross-community interaction and collaboration.

Beyond ISMB/ECCB, CompMS continued to promote computational mass spectrometry at major international meetings. This included organizing the Informatics Hub at the American Society for Mass Spectrometry (ASMS) conference and contributing to the Bioinformatics Hub at the Human Proteome Organization (HUPO) World Congress. Additionally, CompMS members supported community training through hands-on workshops and tutorials focused on bioinformatics and machine learning approaches for mass spectrometry data analysis across these and other events.

In terms of scholarly output, CompMS published a Perspectives on Computational Mass Spectrometry viewpoint article in Bioinformatics Advances [1], outlining recent methodological advances, current challenges, and emerging opportunities for the field.

Finally, the CompMS Slack workspace (https://compms.slack.com/) continued to expand as a central community resource, growing to 506 members. The workspace serves as an active forum for discussing new scientific developments, sharing expertise and resources, and supporting professional networking within the computational mass spectrometry community.

[1] Sachsenberg, T. et al. Perspectives in Computational Mass Spectrometry: Recent Developments and Key Challenges. Bioinformatics Advances 5, vbaf301 (2025).

Equity, Diversification, and Inclusion Efforts
Equity, diversity, and inclusion are core priorities of the CompMS COSI. We actively strive for balanced gender and geographic representation across our leadership, speakers, and program activities. This commitment was reflected at ISMB/ECCB 2025, where the CompMS keynote program achieved equal representation of female and male speakers, alongside broad international participation.

Supporting early-career researchers (ECRs) remains a central pillar of our EDI efforts. For the third consecutive year, CompMS awarded dedicated travel grants to enable early-career members to attend ISMB/ECCB. Feedback from previous award recipients at this year’s conference explicitly highlighted the positive impact of these grants on their career development, reinforcing the value of this initiative and motivating its continuation.

In addition, CompMS contributes to improving global access to training in computational mass spectrometry. As part of our educational activities, we collaborated with local mass spectrometry organizations and communities in the Global South, delivering hands-on workshops in regions including South Africa and the Philippines. These efforts aim to lower barriers to participation, strengthen local expertise, and broaden the global reach of computational mass spectrometry.

Leadership Structure
Ferhat Ay - co-chair
Jishnu Das - co-chair
Yuri Pritykin - Organizing Committee Member
Hatice Ulku Osmanbeyoglu - Organizing Committee Member
Aly Azeem Khan - Organizing Committee Member

Activities Over the Last Year
2025 marked the first year of Computational and Systems Immunology, CSI for short, COSI. We were excited to start the CSI's day-long program with a packed room for Dr. Julio-Saez Rodriguez's Keynote talk on use of multiomic and spatial data alongside biological knowledge to model gene regulatory and signalling networks. This was followed by a talk from founder and former chair of the Computational Biology Department at Carnegie Mellon, Dr. Robert F. Murphy, on their vision transformer based cell annotation method for highly multiplexed tissue images. The morning session continued with talks on protein expression imputation from spatial transcriptomics data and spatial and single-cell study of the human thymus to understand how it becomes dysfunctional as we age.


The afternoon session started with a remote talk from Dr. Harinder Singh on deciphering transcriptional regulatory code of immune cells using an expanded DNA motif lexicon (such as composite TF motifs). Following talks by trainees looked at transcriptional regulators of Tfh differentiation, double negative B cells in cancer and prediction of pairing of heavy and light immunoglobulin chains. These were followed by talks on incorporation of phylogeny information for B cell epitope prediction, improvements for TCR-epitope binding prediction models and prediction of neoantigen immunogenicity in cancer. The last full talk of the afternoon introduced SHISMA, a novel tool to infer significant cell type-specific regulatory patterns with strong statistical guarantees. The day and the COSI session for this year was concluded with 5-minute short talks selected from submitted abstracts.

Equity, Diversification, and Inclusion Efforts
We value diversity of backgrounds, expertise and opinion in our organizing committee, steering committee as well as our keynote speakers and invited speakers for the COSI track. Last year, although we invited, we did not have a female keynote speaker. This year our proposed keynote speaker list will feature more female scientists and scientists from outside North America. We will also ensure at least one relatively junior faculty who is doing high impact work in the recent years will be invited as a keynote. When selecting invited talks, we considered the balance in topics covered and in representation of different career stages. This year we will further seek out speakers from underrepresented groups in the field, including women, racial and ethnic minorities, and individuals from diverse geographic regions. We will also make a concerted effort to include voices from non-traditional academic or research settings, such as industry, to reflect the full spectrum of the Systems Immunology field. We have done a good job at this in 2025 with multiple attendees from industry who were active participants and gave good feedback in industry involvement for the next year. The ultimate goal of the meeting is to provide a platform for information exchange and stimulate collaborations in the broad field of Systems Immunology among a diverse set of attendees that is representative of the general ISMB audience

Leadership Structure
Pablo Meyer, Julio Saez Rodriguez, Gustavo Stolovitzky co-chairs of COSI
Track Chair: Laura Heiser
Submitted Talks chair: Adi Tarca
Submitted Poster chair: Kyle Elrott

Activities Over the Last Year
We organized a workshop on "Benchmarking Foundation Models in Biology", also discussing where we are, and we where we want to go with the community.
Inivited speakers were John Moult, Maria Brbic, Elizabeth Fahsbender, Justin Guinney and Anshul Kundaje

Equity, Diversification, and Inclusion Efforts
We are in the planning phase for this topic

Leadership Structure
The COSI is managed by two co-chairs: Russell Schwartz and Wai Keat Yam.

Activities Over the Last Year
The most prominent activity of the COSI each year is running the Education Track of ISMB. This year, the COSI session featured two exciting keynotes. The opening keynote, from Gabriel Rustici of AstraZeneca on sharing her experiences with bioinformatics training, emphasizing partnerships between industry and academia training and some of the challenges and opportunities that entails. The session bridged and aligned with the Workshop on Education in Bioinformatics (WEB) theme on the role of industry in bioinformatics education. The closing keynote by Patricia Carvajal-López of EMBL/EBI, was a chance to hear about her work on communities of practice in the field and her experiences co-hosting the most recent Global Bioinformatics Education Summit. The track also included two proceedings talks and eight contributed abstracts covering covered a wide range of ongoing and emerging topics in bioinformatics education, including computational and quantitative education of experimental biologists and public health workers, new pedagogy models and use cases, meeting challenges of content delivery in resource-limited environments, and the use of large language models (LLMs) to facilitate bioinformatics education. This was supplemented by a vibrant program of education poster presentations.

The COSI was also active in other educational meetings and related activities. This included co-sponsoring the 2025 Global Bioinformatics Education Summit, held in Mexico City in May 2025, and organizing tracks of the summit related to COSI initiatives in applying competencies to degree assessment. It also included contributing educational sessions and talks to several other ISCB-affiliated meetings, such as the Great Lakes Bioinformatics Conference. COSI leadership was active in follow-up initiatives of the bioinformatics education community, including active participation in the Global Organisation for Bioinformatics Learning, Education and Training (GOBLET) and several working groups of the Education Summit community that continue their activities throughout the year. The COSI also served the community through donations of funding to travel awards.

Equity, Diversification, and Inclusion Efforts
The Education COSI strives to be representative of the diversity of its membership and the global bioinformatics education community. This is best reflected in the ISMB COSI program, which has long featured an exceptional diversity of invited and contributed speakers, reflecting the global nature of educational community. It is also reflected in the range of topics for both invited and contributed talks, including keynotes highlighting the role of bioinformatics education in industry and efforts to expand bioinformatics in Latin America, and contributed talks covering such diverse areas as education of rural youth in Ukraine, pathogen surveillance in South Africa, and massive open online courses.

Leadership Structure
2025 Leadership

- COSI representatives, track chairs: Lars Arvestad, Dannie Durand
- Abstract chairs: Nadia El-Mabrouk, Katharina Jahn, Giltae Song
- Award chairs: Louxin Zhang, Giltae Song, Alexey Markin, Maureen Stolzer.
- ISCBacademy: Alexey Markin and Valeriia Vasylieva
- Communication/website managers: Aida Ouangraoua


COSI steering committee

- Lars Arvestad, Stockholm University, https://www.su.se/english/profiles/arve-1.232358
- Edward Braun, University of Florida, https://people.clas.ufl.edu/ebraun/
- Dannie Durand, Carnegie Mellon University, https://www.cmu.edu/bio/people/faculty/durand.html
- Nadia El-Mabrouk, Université de Montréal, http://www.iro.umontreal.ca/~mabrouk/
- Katharine Jahn, University of Berlin, https://www.mi.fu-berlin.de/en/inf/groups/ag-bds/staff/jahn.html
- Alexey Markin, staff scientist at USDA, https://markin-alex.github.io/publications.html
- Erin Molloy, University of Maryland, https://www.umiacs.umd.edu/people/emolloy
- Aida Ouangraoua, University of Sherbrooke, https://www.chairs-chaires.gc.ca/chairholders-titulaires/profile-eng.aspx
- Janani Ravi, Michigan State University, https://cvm.msu.edu/directory/ravi
- Celine Scornavacca, University of Montpellier, https://sites.google.com/view/celinescornavacca
- Giltae Song, Pusan National University. https://dmb.pusan.ac.kr/dmb/26323/subview.do
- Louxin Zhang, National University of Singapore, https://discovery.nus.edu.sg/822-louxin-zhang

COSI leadership represents 34 members, total.

Activities Over the Last Year
We organized the EvolCompGen track at ISMB 2025 in Liverpool.
The track received 79 abstract submissions. Of these, 51 were accepted as poster presentations and 27 were accepted as oral presentations. In addition, three proceedings talks were presented in the EvolCompGen track.

This year's EvolCompGen track comprised six sessions with 30 presentations, in total, spread over the first two days of the conference. One of these sessions was jointly organized with the Function COSI. EvolCompGen presentations included three proceedings talks and a mix of short and long talks selected from contributed abstracts.

A session devoted to cancer phylogenetics was a great success - every seat was filled, with a line of people standing at the door. The work presented focused on fast reconstruction of tumor cell evolution, including efficient selection of molecular features in various data types and identification structural variants. Presentations explored the striking variety of molecular data that can be used for tracking cancer progression.

Subsequent sessions considered evolutionary questions on a very different time scale. These included phylogeny- and orthology-related studies, covering issues important for function prediction, and phylogenetic sequence and tree based methods for investigating protein family evolution. The problem of scalability in the face of the data deluge received particular attention. Presentations in the session used a refreshing variety of computational techniques, ranging from machine learning and Bayesian statistics to algorithm theory and combinatorial optimization.

Tuesday started with a joint session with the Function COSI focused on orthology, paralogy and changes in gene function over evolutionary history.
Keynote speaker Marc Robinson-Rechavi presented the current state of the debate on the ortholog conjecture and made a compelling case for best practices and infrastructure supporting rigorous assessment of functional conservation among related genes. These themes were echoed by contributed talks throughout the session, which nicely melded topics in both evolution and function

The final session closed with a panel discussion of current and future directions in Evolution and Comparative Genomics, moderated by Christophe Dessimoz. Ed Braun, Russell Schwartz and Dannie Durand served as panelists.
It was noted that for both "classical" phylogeny and cell-trajectory studies, AI methods have not had the same driving force as in many other areas of computational biology. This led to a spirited exchange on future roles for AI in evolutionary studies, with much participation from the audience. Friendly bickering about the impact of AI methods in evolutionary studies ensued and a good time was had by all.

Awards
- Vikram Shivakumar (Johns Hopkins University) won best poster prize (100 USD) for his poster on "Mumemto: efficient maximal matching across pangenomes."
- The award for best short talk (150 USD) went to Maureen Stolzer, Carnegie Mellon University for her presentation on "Evolution of the Metazoan Protein Domain Toolkit Revealed by a Birth-Death-Gain Model"
- Emilia Hurtado (UBC) won the best long talk award (200 USD) for "A Probabilistic Method for Inferring Cell Phylogenies from Mitochondrial Variants"

ISCBAcademy seminars, with speakers:
- May 2, 2025 - Billera-Holmes-Vogtmann (BHV) Phylogenetic Tree Space: Algorithms and Applications to Evolutionary Biology by Megan Owen, Lehman College, CUNY
- December 5, 2025 - Experimental evolution of evolvability by Michael Barnett, Max Planck Institute for Evolutionairy Biology

Ongoing activities
The EvolCompGen COSI represents a cohesive community that interacts throughout the year through related professional activities. In 2025, Giltae Song, EvolCompGen steering committee member, served as program chair for the Recomb satellite conference on Comparative Genomics (RCG). EvolCompGen members served on the RCG program committee and/or contributed manuscripts. There is also substantial overlap between the EvolCompGen communities and Quest for Orthologs, a community standards initiative to promote, improve and standardize orthology predictions through collaboration and the use of shared reference datasets. In 2025, advances in ortholog prediction were highlighted in a Quest for Orthologs special issue (Journal of Mol. Evol., Dec, 2025) to which several EvolCompGen members contributed. Another example is the workshop on Novel Mathematical Paradigm for Phylogenomics in Banff International Research Station organized by steering committee member Nadia El-Mabrouk and her colleagues in September 2025, where multiple EvolCompGen members met and shared ideas.

Equity, Diversification, and Inclusion Efforts
The EvolCompGen COSI is committed to fostering interactions among a diverse group of computational biologists that include researchers from all parts of the global community. At present, our COSI leadership includes representatives from a diversity of career stages, ranging from post-doctoral scientists to established professors. Our leadership has almost equal gender representation (7 women, 5 men) and includes scientists from Africa, Asia, Europe, and North America.

We have asked two younger scientists to spearhead the organization of the COSI webinar series to ensure equitable representation of speakers, especially at the level of career stage.

We are committed to expanding representation, especially to scholars in Africa and South America. During abstract selection for the ISMB/ECCB meeting in Liverpool, we focused on increasing participation from parts of the globe that have been underrepresented in computational evolutionary biology. We are conscious of the fact that there are structural barriers to engagement by computational biologists in the Global South and seek opportunities to be as inclusive as possible.

Leadership Structure
COSI co-chairs alphabetically: Iddo Friedberg, Jason McDermott, Dukka KC, Ana Rojas, Mark Wass

Activities Over the Last Year
The CAFA competition (CAFA 6), an integral part of the Function COSI, is currently taking place and receiving a large number of entries (https://www.kaggle.com/competitions/cafa-6-protein-function-prediction). We plan to report on the outcome of the competition at the meeting this year, including a talk by the winning group. Previously, the CAFA competition, has received a grant of $1,800,000 USD from the NIH for continuing its activities. Some of these moneys are slated for conference travel to the Function COSI. Additionally, at ISMB 2025 we participated in organizing the CollaborationFest led by BOSC. This demonstrates the large extent of the outreach and the work run by the Function COSI.

Equity, Diversification, and Inclusion Efforts
We consider diversity when selecting presentations for the COSI looking for those form underrepresented groups and geographical regions, especially with respect to trainees. The COSI leadership structure includes two minorities and one woman. Keynote speakers over the years were female majority.

Leadership Structure
Can Alkan, PhD
Bilkent University, Ankara, Turkey

Christina Boucher, PhD
University of Florida, Gainesville, FL, USA.

Brona Brejová, PhD
Comenius University in Bratislava, Slovakia

Ana Conesa, PhD
Spanish National Research Council, I2SysBio, Paterna, Spain and University of Florida, Gainesville, FL, USA.

Francisco M. De la Vega, D.Sc.
Stanford University and Tempus AI, USA

Kjong Lehman, PhD
Centre of Medical Technology, Aachen, Germany

Kristoffer Sahlin, PhD
Stockholm University, Stockholm, Sweden

Dirk Evers, PhD
Dr. Dirk Evers Consulting, Enger, Germany

STUDENT -PhD Student- Ana Isabel Castillo Orozco MSc
McGill University, Montreal, Canada

Activities Over the Last Year
* In preparations for the HiTSeq Track (ISMB, 2025, Liverpool, United Kingdom), we acquired three keynote speakers, Valentina Boeva, Jonathan Göke, and Tobias Marschall.

* Sponsorship: HiTSeq acquired sponsorships from Pacific Biosciences and Oxford Nanopore Technologies, contributing to five student travel fellowships of $1000 each, and $300 in prize money each for the best talk and poster presentations.

* BioinfoBridges Podcast: We have collaborated with the ISCB Student Council to develop episodes for the Science Communication Initiative Podcast “Bioinfobridges.”. Dr. Ana Conesa (S1. Ep. 1) and Dr Christina Boucher (S2 Ep. 2) have been guests in the podcast.
Podcast Link:
https://open.spotify.com/show/201oMlCIEZRQElbE6yWdk8


* HitSeq Track (ISMB, 2024, Montreal, Canada):

HitSeq Track (ISMB, 2025, Liverpool, United Kingdom):

HiTSeq track statistics
Number of total submissions: 81 abstract submissions.
Number of proceedings programmed: 9
Number of keynote speakers: 3
Number of total talks within track: 25
Total number of posters: 60 (56 in person and 4 virtual)
Sponsorships secured: 2
Travel fellowships issued: 5 ($1,000 each)
Best talk prize: $300
Best poster prize: $300

We designed a program that spanned several key areas in high-throughput sequence analysis, including statistical and machine learning methods for analyzing large sequencing datasets, methods for pangenome analysis, structural variation detection, genome assembly, long-read transcriptomics analysis, data structures for representing large sequence datasets, and methods for cancer genomics.

The HiTSeq 2025 conference opened with a keynote presentation from Valentina Boeva, who delivered a talk entitled “Learning variant effects on chromatin accessibility and 3D structure without matched Hi-C data.” She presented a comprehensive modeling framework connecting DNA sequence variation to chromatin accessibility, 3D genome folding, and RNA expression levels — effectively closing the loop from DNA to RNA. Dr. Boeva discussed how her models can predict the impact of in-silico genomic perturbations and non-coding variants on chromatin folding in a cell-type–specific manner, thereby enabling more accurate interpretation of regulatory variants even in the absence of matched Hi-C data.

The following proceedings sessions showcased a range of innovative methods and applications. Laura Martens presented a benchmark of deconvolution tools for estimating cell fractions in spatial transcriptomic data using ATAC- or RNA-based references. Her results demonstrated that methods originally designed for spatial transcriptomics, such as Cell2location and RCTD, generalize well to spatial chromatin accessibility data, providing robust cell-type resolution across various simulation frameworks.
Zahra Jousheghani introduced Oarfish, a novel approach to improve the accuracy of long-read transcriptome quantification. The method incorporates dynamic coverage modeling to better capture biases in complex genomic regions, improving quantification consistency across datasets.
Noor Pratap presented Alevin-fry-atac, an efficient tool for mapping single-cell ATAC-seq data using virtual color encoding for precise genomic pseudoalignment, significantly reducing memory and computational requirements while maintaining mapping accuracy.
Two new algorithms introduced during HiTSeq 2025 drew particular attention. HiCONA presented a unified representation of the multilayered chromatin structure using nested hierarchical clustering and entropy-based compartment identification. The method revealed how structural rearrangements, such as those induced by cohesin depletion, can be captured within a single hierarchical framework. SplitSync, another highlight, leveraged deep learning to improve splice-site correction in long RNA reads. By learning from genomic context, SplitSync enhances splice site accuracy and can detect novel splice events, thereby improving downstream isoform reconstruction — a particularly valuable feature for species with incomplete gene annotations.
Our sponsor, Pacific Biosciences (PacBio), was represented by Elizabeth Tseng, who delivered the talk “Bioinformatics analysis for long-read RNA sequencing: challenges and promises.” She discussed the latest advances in PacBio sequencing throughput and basecalling accuracy, as well as computational opportunities for transcriptome analysis in the era of duplex sequencing and machine-learning–based error correction.
The first day of HitSeq ended with our second keynote speaker, Jonathan Göke, who presented “Quantifying RNA Expression and Modifications using Long-Read RNA-Seq.” Dr. Göke explored how long-read sequencing can provide a more complete and quantitative view of the transcriptome, enabling direct detection of isoforms and RNA modifications at single-molecule resolution. He also highlighted challenges in accuracy, throughput, and computational analysis, outlining promising directions for integrating long-read data into single-cell and multi-omics pipelines.

The second day of HiTSeq 2025 began with our third keynote speaker, Tobias Marschall, who spoke on “Pangenome-based analysis of structural variation.” Dr. Marschall described the emerging opportunities and challenges in building and using pangenome references, highlighting the PanGenie and SAGA frameworks and the ongoing efforts within HGSVC3 to assemble high-quality human genomes at near completion.
Subsequent talks on the second day featured diverse topics, including CNV detection in ancient genomes, long-read quality assessment with SQANTI-reads, and the Lyceum framework for learning robust CNV calling models on noisy, low-coverage ancient DNA data. Collectively, these presentations illustrated the vibrant methodological landscape at the intersection of long-read sequencing, single-cell analysis, and 3D genome organization.
Then, our second sponsor, Oxford Nanopore Technologies, gave a promotional talk, with Mike Vella, Senior Director of Machine Learning at Oxford Nanopore Technologies, as the designated speaker. According to Mike, base calling is one of the most critical challenges for long-read sequencing data. He introduced us to duplex basecalling and how machine learning is allowing us to solve several issues that previously were so hard without machine learning implementation for base calling
HiTSeq 2025 once again provided a dynamic and interdisciplinary forum for researchers developing and applying algorithms for high-throughput sequencing data. The sessions reflected the continued convergence of machine learning, statistical modeling, and large-scale data integration in computational genomics.
Through acquired sponsorship funding, HiTSeq awarded a Best Presentation Award and a Best Poster Award. The best presentation award ($300) was awarded to Netanya Keil, graduate assistant, Florida State University, for her talk titled “Quality assessment of long read data in multisample lrRNA-seq experiments using SQANTI-reads”, and the best poster presentation ($300) was awarded to Qiuyu Lian for the poster titled "Harmonization, integration, and annotation of single-cell protein and transcriptomic atlases via unified cell ontology learning".

Equity, Diversification, and Inclusion Efforts
To support DEI efforts, we aimed to achieve a balanced representation of male and female speakers at the annual HiTSeq meeting. We had one female and two male keynote speakers. As for the remaining 22 talks (including the sponsored talks), 9 of the presentations were given by females.

Leadership Structure
Leadership Structure
Organizing Committee
Athma Pai, UMass Medical School, USA
Michelle Scott, Université de Sherbrooke, Canada
Hagen Tilgner, Weill Cornell Medicine, USA
Maayan Salton, Hebrew University, Israel
Eduardo Eyras, Australian National University, Australia

Abstract Committee
Michelle Scott, Université de Sherbrooke, Canada
Hagen Tilgner, Weill Cornell Medicine, USA
Maayan Salton, Hebrew University, Israel
Eduardo Eyras, Australian National University, Australia

Activities Over the Last Year
iRNA is a two-day COSI at ISMB typically attracting 150-200 participants. For 2025, the iRNA COSI featured 3 keynotes from Steven West from Exeter University, Roser Vento-Tormo from the Wellcome Sanger Institute, Yiliang Ding from John Innes Centre as well as 2 proceedings talks and 23 talks from abstracts covering subjects from methods for the identification, regulation and function of diverse RNAs and their modifications to RNA interactions and RNA design. iRNA 2025 also featured a special session on ‘Building the future of RNA tools’ with a keynote talk by Blake Sweeney from the EMBL/EBI and talks from abstracts on current tools for the characterization of RNA biology, finishing with a thought-provoking panel discussion with Ana Conesa (University of Valencia), Jan Gorodkin (University of Copenhagen), Lina Ma (Beijing Institute of Genomics) and Yaron Orenstein (Bar-Ilan University). Through numerous questions from the audience, the panel highlighted the importance of generating more quality data to study different RNA characteristics and most particularly RNA structure, better covering the whole RNA space. The iRNA COSI also featured the iRNA dinner within the ISMB networking event at Punch Tarmey’s and the traditional iRNA quiz which was won ex aequo by ChatGPT and a team of dedicated students.

iRNA gave three 150$ poster prizes at ISMB 2025, to Rahaf Issa from Florian Erhard's lab at the University of Regensburg in Germany, Yu-Jen Lin from Steven Brenner's lab at the University of California Berkeley in USA and Louis-Philippe Chaumont from Karine Choquet's lab at Université de Sherbrooke in Canada.

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 equity, diversity and inclusion 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
Yesid Cuesta Astroz , Claudia Gonzaga Jauregui, and Melike Donertas serve as the JPI co-leads.

Activities Over the Last Year
The JPI COSI maintains a New PI Slack ISCB channel and participates in the ISCB webinar series. Typically, the JPI COSI strives to plan and moderate a track session and a Birds of a Feather session at ISMB annually. We have now recruited co-leads based in North America and Europe and recommend this moving forward to better facilitate sustained international community-building efforts.

Equity, Diversification, and Inclusion Efforts
As part of ISCB, the JPI COSI values diverse and inclusive participation across the computational biology and bioinformatics community. To that end, our goal is to support community building that is broadly accessible by facilitating virtual and in-person networking, education, and scientific events.

Leadership Structure
Alice McHardy, Helmholtz Centre for Infection Research, Germany
Alexander Sczyrba, University of Bielefeld, Germany

Activities Over the Last Year
The MICROBIOME COSI 2025 featured two keynote talks: (1) Fiona Brinkman from Simon Fraser University, Burnaby, Canada, on “Microbiome multitudes and metadata madness,” and (2) Christopher Quince from the Earlham Institute, United Kingdom, on “Genome-resolved metagenomics for complex microbiomes with long reads.” On February 25, 2025, we hosted the ISCB Academy webinar “Modeling microbe evolution due to immune system pressure,” presented by Nico Pfeifer from the University of Tübingen, Germany.

Equity, Diversification, and Inclusion Efforts
The COSI invited an equal number of male and female keynote speakers, and has a gender- balanced COSI leadership team.

Leadership Structure
Anshul Kundaje and Oznur Tastan are MLCSB co-presidents and are supported by the MLCSB board.
Other leaders were as follows:
Track Chair: Sara Mostafavi
Track Chair: Barbara Elizabeth Engelhardt
Abstract Chair: Sara Mostafavi
Abstract Chair: Barbara Elizabeth Engelhardt

Activities Over the Last Year
The MLCSB track was run over two days and hosted 30 talks, including 4 invited speakers, 10 long proceedings talks, and 16 short abstract talks.
The invited speakers incuded: Sanmi Koyejo, Maria Brbic, Julien Gagneur, Maria Chikina

Throughout the year, communication within the research community was primarily maintained through the MLCSB Google Group (https://groups.google.com/a/iscb.org/g/mlcsb.cosi
), which serves as an active forum for exchanging job postings, webinar announcements, open positions, and information on related community activities.
As well as running the MLCSB COSI, we also provide support the MLCB meeting which is now a standalone meeting, typically US-based, with several MLCB organisers on our board.

Equity, Diversification, and Inclusion Efforts
MLCSB encourages diversity and representation within its leadership. Chairs are frequently invited to become board members after ISMB and this ensures the board also has good gender representation. 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. We also allocate travel fellowships diversely.

Leadership Structure
Committee Representative: Martina Summer-Kutmon
Alt. Committee Representative: Mehmet Koyuturk
Track Chair: Anaïs Baudot
Track Chair: Chad Myers
Proceedings Liaison: Martina Summer-Kutmon
Abstract Chair: Deisy Morselli Gysi
Abstract Chair: Jishnu Das

ISCBacademy program coordinator: Alexandros Xenos
Liaison ISBC Student Council: Pradeep Eranti
Outreach/conferences: Noel Malod Dognin

Activities Over the Last Year
The primary activity in 2025 was organizing the 1½-day NetBio COSI session at ISMB/ECCB 2025 in Liverpool, UK. In a very well-attended session, the program featured three distinguished keynote speakers: Prof. Laura Cantini (Institut Pasteur, France), Prof. Jan Baumbach (University of Hamburg, Germany), and Prof. Fiona Brinkman (Simon Fraser University, Canada), who delivered a shared keynote with the Microbiome COSI. The session included three proceedings presentations and fourteen contributed talks that showcased cutting-edge advances in network biology methods, applications, and tools/resources.

With strong community engagement, we hosted two poster sessions featuring 52 NetBio posters showcasing innovative work across the network biology field. We were pleased to recognize outstanding contributions through our awards program: Beatriz Urda-Garcia received the Best Talk prize, while poster prizes were awarded to Arne Wehling (Best Method), Sebastian Urquiza-Zurich (Best Application), and Estefania Torrejon (Best Resource/Tool).

Additionally, we organised a Cytoscape visualization contest and showcased beautiful network pictures. The winners of the Cytoscape contest were Alejandra Paulina Perez Gonzalez, Jong Lim, and Michael Constanzo.

Beyond ISMB/ECCB, we co-hosted the NetBioMed satellite meeting at NetSci 2025 in Maastricht, Netherlands in June, and continued our webinar series with Dr. Judith Bernett presenting "Pushing the limits of sequence-based protein-protein interaction prediction" in May. We also introduced our new NetBio COSI logo, designed by Romana Yáñez.

These activities continued to demonstrate the interest in network biology and its role in advancing computational approaches to understanding biological systems.

Equity, Diversification, and Inclusion Efforts
Careful attention is paid to equity, diversity, and inclusion when selecting committee members and speakers for all organized events and activities. In 2025, half of the chair positions in our organizing committee were held by women. At our ISMB session, we aim for diversity among our keynote speakers and selected speakers (45% female) with presenters from Europe (12), North America (7), and Asia (1). We also aim to maintain diversity and inclusion across different areas of computational biology as they intersect with network biology (e.g., organisms, data types, etc.).

Leadership Structure
The COSI has a steering committee with three co-chairs which are listed below.
Steering Committee:
Stein Aerts
Ferhat Ay
Jason Ernst (Co-Chair)
Manolis Kellis
Christina Leslie
Jian Ma
Shaun Mahony
Anthony Mathelier
Alejandra Medina-Rivera
Sushmita Roy (Co-Chair)
Saurabh Sinha (Co-Chair)
Lonnie Welch
Judith Zaugg
Julia Zeitlinger

Additional individuals participate in the organization of COSI run meetings.

Activities Over the Last Year
The activities of the group over the past year were:
1. Regulatory & Systems Genomics 2-day COSI Track at ISMB/ECCB
2. Publishing an invited perspective article in Bioinformatics Advances (https://doi.org/10.1093/bioadv/vbaf106)
3. Making plans for the continuation of the previous RSG portion of the RECOMB/ISCB RSGDREAM meeting. The RSG portion of the meeting will now be a co-located satellite to the main RECOMB meeting


Additional details on the first item is below:
Day 1 (Wednesday, July 23rd)

The RegSys track opened with a keynote presentation by Vera Pancaldi on cellular plasticity and 4D epigenomes in cancer, emphasizing how chromatin topology and specific regulatory marks shift during differentiation and can be “reversed” in oncogenesis, with an explicit focus on how the tumour microenvironment shapes plasticity and how regulatory networks can be inferred in controlled in vitro systems.

The track followed with proceedings presentations highlighting method development for regulatory inference and benchmarking: GRIP (Gene Regulation Inference by considering TF Proximity) introduced the idea of constraining inferred regulators by their physical proximity in protein–protein interaction networks, aiming to improve TF selection and agreement with orthogonal ground truth; miRBench addressed a critical evaluation issue in microRNA target prediction by proposing bias-mitigating negative-sample generation and releasing benchmark datasets and a supporting package to lower barriers for ML reuse and comparison.

The morning session was wrapped up with a flash-talk block spanning hematopoietic fate plasticity, JASPAR extension with deep learning for TF-DNA interaction, replication timing regulation, and confounders in RNA–DNA interaction data.

The afternoon session focused on single-cell and multi-omic regulatory modeling. Talks covered blind super-resolution for single-cell Hi-C enhancement and 3D reconstruction (Unicorn/3DUnicorn) and gene-specific predictive modeling that integrates scATAC-seq and scRNA-seq to prioritize enhancer-gene links (MetaFR).

Next, we dove into deep learning with: cell2state framing TF-DNA sequence logic with biophysical constraints to predict chromatin accessibility across developmental cell populations; Nona providing a multimodal masked-modeling paradigm operating at base-pair resolution across sequence and epigenetic tracks; SCRIMPy proposing replication-driven signals in multiome ATAC data for cell-cycle inference beyond expression markers; and a systems immunology application describing dynamic and state-specific GRNs underlying bifurcating human B cell states, linking interpretable latent programs with stochastic ODE-based network dynamics.

The next session followed with an explicit regulatory sequence design arc: Ledidi and Lilliput showcased optimization- and model-guided strategies to design/edit cis-regulatory elements, including compact, cell-type-specific mini-enhancers relevant to vector size constraints.

The day finished with the a keynote talk by Mafalda Dias who connected regulatory genomics to disease through deep learning over evolutionary sequence diversity to decode constraints and improve variant interpretation.

Day 2 (Thursday, July 24th)

RegSys day 2 opened with a keynote talk by Roser Vento-Tormo emphasizing systems-level gene regulation in human tissues, integrating single-cell and spatial assays with microscopy to build reference maps and then using computational tools to quantitatively compare and interpret in vitro models against these tissue atlases.

The next session started with a proceedings talk introducing Sardine, which allows for spatially localized density comparison for anomaly/region detection across conditions in spatial transcriptomics. The session closed with flash talks spanning interpretable sequence models of nucleosome positioning, multi-species regulatory element cataloguing, reproducible frameworks for gene–environment effects, and protein-interaction affinity modeling in signaling domains.

The next session concentrated on computational frameworks for extracting regulatory structure from spatial and single-cell data with: GASTON-Mix modeling tissues as a mixture of spatial domains plus within-domain continuous gradients; providing refinement strategies for the Tangram approach improving stability and consistency in single-cell-to-spatial mapping; an optimal-transport approach encode chromatin accessibility as per-base probability distributions to better capture footprint/positioning information; Scooby extending sequence-to-profile modeling into single-cell resolution multi-modal prediction; and Soffritto to predict high-resolution replication timing from lower-resolution inputs and auxiliary genomic features.

The afternoon session lined up talks presenting: FineDMR to study spatial dependency across CpGs and improve cell-type-specific association detection in EWAS; MutBERT proposing probabilistic genome representations that prioritize informative variation for foundation modeling; hashFrag to address homology-driven data leakage in genome-trained sequence models; and a large-scale yeast promoter study (Camformer) using MPRA-scale training data plus explainability to reveal motif hierarchy and cis-regulatory logic.

The RegSys track concluded with a keynote talk by Luca Pinello on learning the regulatory genome “by destruction and creation,” centered on dense perturbation mapping (CRISPR-CLEAR) and generative design as complementary strategies for decoding regulatory grammar. The contributions presented in the RegSys track this year at ISMB illustrate the complexity of computational models that combine different types of data to illuminate how genomes are regulated and how we can perturb them to design experiments and reveal novel concepts of regulation.

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
A team of six coordinators and one volunteer, who virtually meet once per month, jointly organize the SysMod COSI.

Executive chairperson:
Bhanwar Lal Puniya, University of Nebraska–Lincoln, US

COSI Coordinators (alphabetical order):
Nantia Leonidou, German Cancer Research Center (DKFZ), Heidelberg, DE
Matteo Barberis, University of Surrey, UK
Shaimaa Bakr, Stanford University, US,
Chiara Damiani, Università degli Studi di Milano-Bicocca, IT,
Reihaneh Mostolizadeh, Justus Liebig University Giessen, DE
Meghna Verma, AstraZeneca, US

COSI volunteer:
Bruno Giovanni Galuzzi

Primary COSI representative:
Bhanwar Lal Puniya, University of Nebraska–Lincoln, US

Alternate COSI representative: None

COSI Programming Coordinators for ISCBacademy (alphabetical order):
Nantia Leonidou, German Cancer Research Center (DKFZ), Heidelberg, DE
Meghna Verma, AstraZeneca, US

Activities Over the Last Year

The primary activity of SysMod is the annual one-day meeting at the ISMB/ECCB 2025 conference. It provides a platform for the latest developments in mechanistic and predictive modeling of biological systems and applications across disciplines. SysMod community hosts webinars and is also engaged in communication with community members via Google group, X (formerly Twitter), and LinkedIn pages.

ISMB-2025: Dr. Chiara Damiani and Dr. Matteo Barberis hosted the SysMod event in 2025 in Liverpool, UK. The event featured two keynote talks, 13 contributed talks, and 44 posters on topics including modeling of metabolic processes, immune processing, regulatory processes in epithelial to mesenchymal transition, and infection with pathogens. Jasmin Fisher (UCL Cancer Institute, University College London) and Ronan Fleming (School of Medicine, University of Galway, Ireland) delivered the keynote talks. SysMod awarded three poster prizes to Yanjun Liu (1st prize), Rupinder Kaur (2nd prize), and Sebastian Huß (3rd prize). The conference updates and talks were well received, and the keynote speaker sessions were well attended. The conference speaker session pictures were posted on our LinkedInLinkedIN SysMod COSI page.

Webinars: In 2025, SysMod organized one ISCB Academy webinar by Nick Quinn-Bohmann focused on how metabolic modeling reveals determinants of synbiotic efficacy in a human intervention trial. The recording of the webinar was uploaded on ISCB YouTubeyoutube.

Publication from COSI: - Perspectives on computational modeling of biological systems and the significance of the SysMod community
Bhanwar Lal Puniya, Meghna Verma, Chiara Damiani, Shaimaa Bakr, Andreas Dräger

Outreach and other activities: Over the past year, SysMod has 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). It has an active Google group with 300 active members. Additionally, SysMod maintains a LinkedIn page with about 354 followers and an X account with about 600 followers.

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 indicates. From its inception, scientific quality has been the first criterion 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 assuring a gender balance, 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
Representative: Robert Leaman
Track Chairs: Robert Leaman, Lars Juhl Jensen, Cecilia Arighi, Zhiyong Lu

Activities Over the Last Year
The ISMB/ECCB 2023 text mining track was a one-day event featuring two keynote speakers and extensive range of scientific presentations and posters. It also hosted highly attended panel discussion on the implications of large language models, such as ChatGPT, in biology and medicine.
- The COSI track explored methodological advances and developing resources, especially for advanced language models. Recurring themes included extracting relations from the literature, manual annotation for training and evaluation, leveraging weak supervision, and integrating text data with other modalities. Practical applications spanned clinical and bioinformatics research.
- COSI track keynote speaker Martin Krallinger discussed creating natural language processing (NLP) components and resources for shared tasks in collaboration with clinical domain experts. His presentation discussed a spectrum of applications including biomaterial research, cardiology, occupational health and phenotypes, with increasing emphasis on multilingual applications. COSI track keynote speaker Aurélie Névéol discussed the complexities of reproducibility in biomedical NLP, examining how these challenges interact with issues like data privacy. She offered recommendations for enhancing reproducibility for biomedical NLP systems and how NLP systems themselves might help improve reproducibility across science.
- The COSI track ended with a very well attended panel on the applications of ChatGPT and large language models (LLMs) in biology and medicine. Panelist Larry Hunter discussed the tension between the utility of LLMs and how their fluency can be misleading. Panelist Harry Caufield discussed using LLMs to create knowledge graphs, particularly noting recent work mitigating “hallucination” by grounding responses in established ontologies. Panelist Chris Dallego discussed industrial LLM applications in healthcare and science. Audience questions focused on trustworthiness, data protections, addressing bias, democratizing the training and use of LLMs, alongside benchmarking and evaluation.
In January 2023, the COSI hosted Søren Brunak, professor of Disease Systems Biology at the University of Copenhagen, for a ISCB Academy lecture. He shared strategies for text mining to construct disease trajectories at scale by incorporating deep temporal information from patient records.

Equity, Diversification, and Inclusion Efforts
We support diversity in science and seek to create an inclusive community. We consider gender balance and underrepresented backgrounds when inviting keynote and invited speakers, and our scientific program reflects our commitment to promoting researchers from diverse backgrounds.

Leadership Structure
• Venkata Satagopam – TransMed COSI Representative, COSI Track Chair
  Head of Clinical & Translational Informatics Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg
• Maria Secrier – Alternate COSI Committee Representative, COSI Track Chair
 Associate Professor, University College London, UK
• Irene Ong – COSI Proceedings Liaison, COSI Track Chair
 Assistant Professor, University of Wisconsin–Madison, USA
• Anne Lorant – COSI Abstracts Chair, COSI Track Chair, ISCBacademy TransMed Program Coordinator
 Postdoctoral Researcher, Luxembourg Centre for Systems Biomedicine, University of Luxembourg
• Heba Sailem – COSI Track Chair
 Senior Lecturer, King’s College London, UK
• Mansoor Saqi – COSI Track Chair
  Head of Translational Bioinformatics, Institute of Cancer Research, UK
• Evert Bosdriesz – COSI Track Chair
 Assistant Professor, Vrije Universiteit Amsterdam, Netherlands
• Wei Gu – COSI Track Chair
 Scientific Coordinator & Deputy Head of ELIXIR Luxembourg Node, Luxembourg National Data Service
• Sikander Hayat – COSI Track Chair
 Group Leader, Institute of Experimental Medicine & Systems Biology, Univ. Hospital RWTH Aachen, Germany
• Irina Balaur – COSI Track Chair
 Senior Data Scientist, Luxembourg National Data Service
• Sandrine Medves – COSI Track Chair
 Project Manager, Luxembourg Centre for Systems Biomedicine, University of Luxembourg

Activities Over the Last Year
ISMB/ECCB 2025 Liverpool, United Kingdom – Scientific Program Summary

The TransMed COSI was featured again at ISMB/ECCB 2025 in Liverpool, with a strong and diverse scientific program:
• 2 Keynote Talks
• 3 Proceedings Talks
• 2 Long Talks (20-minute slots)
• 10 Short Talks (10-minute slots)
Selected from 122 submitted abstracts.

Keynote Speakers
Dr. Melanie Schirmer
Assistant Professor, Technical University of Munich
Talk Title: Gene-centric metagenomic analysis reveals functional insights into disease
Abstract: Dr. Schirmer presented a gene-centric framework for microbiome analysis using metagenomic assembly graphs. Applying this approach to over 9,000 stool samples across 24 cohorts, her team uncovered:
• Microbial gene signatures linked to IBD and colorectal cancer,
• A duplicated nar operon in Enterobacteriaceae, stress-specific in function,
• A mobile genetic element (Tn916-like) involved in antibiotic resistance.
This work show how structured gene-centric analyses can reveal key disease mechanisms in the microbiome.
Bio: Melanie studied mathematics (University of Bonn), earned her PhD in computational biology (University of Glasgow), and trained at the Broad Institute. She now leads a lab at TUM with ERC Starting and Emmy Noether funding, focused on integrating multi-omics and experimental data to study host-microbe interactions.

Dr. Jonathan Carlson
General manager, Microsoft Health Futures, Microsoft Research
Talk Title: The Emergence of General AI in Biomedicine
Abstract: Jonathan Carlson’s keynote explored the frontier of generative AI in biomedical research. He highlighted how such models are now capable of reasoning across modalities (language, images, proteins, and clinical data), driving innovation in:
• Diagnostics,
• Real-world evidence generation,
• Generative biology.
Bio: Dr. Carlson holds a PhD in computer science (University of Washington) and a biology degree (Dartmouth). With over 100 publications at the interface of AI, immunology, and virology, he now leads global initiatives at Microsoft to leverage AI for health.

TransMed COSI digest:
The TransMed COSI celebrated its 10th anniversary today at ISMB/ECCB 2025. The program began with welcome remarks by co-chair Venkata Satagopam, reflecting on a decade of progress at the interface of clinical research, multi-omics, and digital health. The session show how translational bioinformatics has evolved from proof-of-concept studies to real-world clinical integration.
The day opened with the keynote speaker Melanie Schirmer, who introduced a gene-centric metagenomic framework to identify disease-associated microbial genes and operon structures across 9,000+ microbiome samples, offering novel insights into IBD and colorectal cancer. The day featured a rich series of contributed talks showcasing a forward-looking agenda focused on translational bioinformatics, integrative multi-omic, and AI-powered approaches for improving diagnostics, patient stratification, and therapeutic development. It closed with Jonathan Carlson who delivered an inspiring invited talk on the rise of general AI in biomedicine, emphasizing how generative models are beginning to reason over proteins, images, and molecular systems—heralding a transformative shift in biomedical discovery.
TransMed’s anniversary celebration not only honored its past but also signaled a future driven by integrative, interpretable, and clinically actionable biomedical data science.

*Awards*
We also awarded Best Talk and Best Poster awards considering both the scores of the abstract reviews and presentations during the TransMed 2025 meeting as follows:
• Best Talk: Barry Ryan, University of Edinburgh, United Kingdom, Combining Clinical Embeddings with Multi-Omic Features for Improved Interpretability in Parkinson’s Disease Patient Classification.
• Best Talk: Sophia Krix, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany, Germany, Unraveling Early Changes in Alzheimer's Disease: Causal Relationships Among Sleep Behavior, Immune Dynamics, and Cognitive Performance Through Multimodal Data Fusion.
• Best Poster: Yang Yang, University of Chicago, United States, Transcription and DNA replication collisions lead to large tandem duplications and expose targetable therapeutic vulnerabilities in cancer.
• Best Poster: Gamze Yazgeldi Gunaydin, University of Helsinki, Finland, Signs of immune dysregulation in second trimester maternal blood RNA profiles in late-onset preeclampsia.

We awarded a Student Travel Fellowship using one of our complementary registrations:
• Travel awardee: Marcelo Hurtado, Cancer Research Center of Toulouse, France

*ISCBacademy Webinar (2025)*
January 28, 2025 – Dr. Venkata Satagopam
Title: Translational Medicine Informatics Approaches to Investigate Complex Diseases
Abstract:
Dr. Satagopam’s talk highlighted advanced informatics methods used to design and analyze clinical cohort studies for complex diseases such as Parkinson’s disease, IBD, MS, RA, and COVID-19. Key points included:
• Development of eCRFs encoded with controlled vocabularies and ontologies,
• Integration of multi-modal data (clinical, omics, imaging, wearable/sensor),
• FAIRification and harmonization challenges for large-scale data sharing,
• Application of ML and statistical methods for patient stratification and biomarker discovery,
• Mechanistic modeling through disease maps and knowledge graphs.
Bio: Dr. Satagopam is Deputy Head of the Bioinformatics Core at LCSB, University of Luxembourg, and Technical Coordinator of ELIXIR-Luxembourg. With over 20 years of experience in data integration, clinical informatics, and machine learning, he is also a co-founder of ITTM S.A. and has held senior roles at EMBL and LION bioscience AG. He holds a PhD in Bioinformatics from TUM.

Equity, Diversification, and Inclusion Efforts
We gave importance to gender balance and had a female and a male keynote speakers forTransMed 2025 COSI. In our COSI organising committee, we have 55% females.

Leadership Structure
Our COSI is led by 5 co-chairs: Julien Gagneur, Emidio Capriotti, Hannah Carter and Antonio Rausell, Tayo Obafemi-Ayaji

Activities Over the Last Year
This year, VariCOSI's primary activity was through the annual ISMB conference.

This year marked the 15th anniversary of the VarI COSI session at ISMB, showcasing cutting-edge advances in variant interpretation. The session received 57 abstract submissions (34 for talks, 23 for posters), with 13 selected talks and 3 keynote presentations.

The morning keynote featured Dr. Alexander Sasse from Heidelberg University, who explored how multi-task convolutional neural networks decode genomic regulatory patterns while addressing their limitations in predicting directional effects of genetic variants on gene expression - crucial for understanding disease mechanisms. The session continued with five talks on protein language models for missense variant effect prediction.

Dr. Ellen McDonagh delivered the second keynote, presenting OpenTargets' latest developments in multi-omics integration, AI-driven target prioritization, and collaborative tools for therapeutic discovery.

The final keynote by Dr. Andrew Lawson highlighted research on somatic mutations in normal tissues, introducing NanoSeq - an ultra-accurate duplex sequencing method that revealed extensive clonal selection patterns in human tissues, offering new insights into cancer development and aging.

The afternoon session featured eight talks showcasing major advances in genetic disease research. Presenters revealed novel insights into neurodevelopmental disorders, identifying unexpected cellular mechanisms beyond neurons. New computational tools improved predictions of splicing defects and cancer drug resistance using single-cell data, while cardiovascular studies uncovered hundreds of CAD-associated genes including non-coding RNAs. Breakthroughs in polygenic scoring addressed ethnic disparities and gender-related genetic factors, and cancer research uncovered protective gene effects and recessive inheritance patterns. Together, these studies demonstrated how multi-omics approaches and single-cell technologies are revolutionizing our understanding of disease genetics.

With 213 registered delegates, the session fostered active discussion.

Equity, Diversification, and Inclusion Efforts
We strive to be inclusive of all members of our scientific community and ensure representation at our annual meeting. We seek to represent the broader research community in our selection of invited speakers and to promote a positive environment for attendees and members.