ISMB 2025
This is a list of all sessions at ISMB 2025.
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Showing 38 talks
| When? | Room | Speaker | Title | Session | Abstract |
|---|---|---|---|---|---|
| 20 July 11:00-11:05 (add to calendar) | 02N | Raúl Fernández-Díaz | AutoPeptideML 2: An open source library for democratizing machine learning for peptide bioactivity prediction | SCS: Student Council Symposium | Peptides are a rapidly growing drug modality with diverse bioactivities and accessible synthesis, particularly for canonical peptides composed of the [...] |
| 20 July 15:20-15:40 (add to calendar) | - | Julio Saez-Rodriguez | Rethinking Rigor: Benchmarking in the Age of Foundation Models | Fellows Presentation | The abstract for this presentation will be shared by the presenter shortly [...] |
| 21 July 08:40-09:00 (add to calendar) | 01A | - | Morning Welcome and Keynote Introduction | Distinguished Keynotes | |
| 21 July 12:40-13:00 (add to calendar) | 01B | Laura-Jayne Gardiner | How can emerging AI technologies benefit multi-omic analysis for crop and soil sustainability | Bioinformatics in the UK | The field of AI is rapidly evolving. At IBM Research (UK), our work in molecular biology has developed from a focus on bioinformatics and computationa [...] |
| 21 July 14:00-14:15 (add to calendar) | 12 | Julio Saez-Rodriguez | Benchmarking foundation models in biology: where we are, and we where we want to go with the community | DREAM Challenges | The AI promise of powerful solutions to solve biomedical and healthcare related problems needs to be accompanied by a transparent evaluation and proof [...] |
| 21 July 15:00-15:20 (add to calendar) | 03A | Jose Espinosa-Carrasco | Empowering Bioinformatics Communities with nf-core: The success of an open-source bioinformatics ecosystem | BOSC: Bioinformatics Open Source Conference | The nf-core community exemplifies how open-source software development fosters collaboration, innovation, and sustainability in bioinformatics. nf-cor [...] |
| 21 July 15:00-15:15 (add to calendar) | 12 | Pablo Meyer-Rojas | AI Alliance: Benchmarking foundation models for drug discovery | DREAM Challenges | The AI Alliance is focused on fostering an open community and enabling developers and researchers to accelerate responsible innovation in AI while ens [...] |
| 21 July 15:00-15:10 (add to calendar) | 01A | Julián García-Vinuesa | PANDORA: Peptide-based ANtimicrobial Design Optimized by Reinforcement Automation | MLCSB: Machine Learning in Computational and Systems Biology | The global rise of antibiotic resistance, particularly in critical pathogens such as Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter [...] |
| 21 July 15:20-15:40 (add to calendar) | 03A | Sebastian Ayala-Ruano | VueGen: automating the generation of scientific reports | BOSC: Bioinformatics Open Source Conference | The analysis of omics data typically involves multiple bioinformatics tools and methods, each producing distinct output files. However, compiling thes [...] |
| 21 July 17:20-17:40 (add to calendar) | 03A | Monica Munoz-Torres | AI-readiness for biomedical data: Bridge2AI recommendations | BOSC: Bioinformatics Open Source Conference | The convergence of biomedical research and artificial intelligence (AI) promises unprecedented insights into complex biological systems. However, real [...] |
| 22 July 08:40-09:00 (add to calendar) | 01A | - | Morning Welcome and Keynote Introduction | Distinguished Keynotes | |
| 22 July 11:20-12:00 (add to calendar) | 04AB | Julio Saez-Rodriguez | Knowledge-based machine learning to study cellular regulation from spatial multi-omics data | CSI: Computational Systems Immunology | Multi-omics technologies, specially with single-cell and spatial resolution, provide unique opportunities to the key study intra- and inter-cellular p [...] |
| 22 July 11:30-12:10 (add to calendar) | 12 | Marc Robinson-Rechavi | Evolution of function in light of gene expression | EvolCompGen: Evolution & Comparative Genomics | One of the fundamental questions of genome evolution is how gene function changes or is constrained, whether between species (orthologs) or inside gen [...] |
| 22 July 11:30-12:10 (add to calendar) | 12 | Marc Robinson-Rechavi | Evolution of function in light of gene expression | Function: Gene and Protein Function Annotation | One of the fundamental questions of genome evolution is how gene function changes or is constrained, whether between species (orthologs) or inside gen [...] |
| 22 July 12:40-13:00 (add to calendar) | 03B | Wan-Chun Su | Virus targeting as a dominant driver of interfacial evolution in the structurally resolved human-virus protein-protein interaction network | 3DSIG: Structural Bioinformatics and Computational Biophysics | The competitive nature of host-virus protein-protein interactions drives an ongoing evolutionary arms race between hosts and viruses. The surface regi [...] |
| 22 July 12:40-13:00 (add to calendar) | 03A | Raúl Fernández-Díaz | AutoPeptideML 2: An open source library for democratizing machine learning for peptide bioactivity prediction | BOKR: Bio-Ontologies and Knowledge Representation | Peptides are a rapidly growing drug modality with diverse bioactivities and accessible synthesis, particularly for canonical peptides composed of the [...] |
| 22 July 12:40-13:00 (add to calendar) | 03A | Raúl Fernández-Díaz | AutoPeptideML 2: An open source library for democratizing machine learning for peptide bioactivity prediction | BOSC: Bioinformatics Open Source Conference | Peptides are a rapidly growing drug modality with diverse bioactivities and accessible synthesis, particularly for canonical peptides composed of the [...] |
| 22 July 14:40-14:50 (add to calendar) | 03B | Miguel Fernandez-Martin | Towards a Biophysical Description of the Protein Universe | 3DSIG: Structural Bioinformatics and Computational Biophysics | Understanding how protein families evolve and function remains a central question in molecular biophysics. By grouping evolutionarily related proteins [...] |
| 22 July 15:00-15:10 (add to calendar) | 11BC | Milana Frenkel-Morgenstern | Computational Genomics and Biosynthetic Potential Analysis of a Dead Sea Penicillium sp. | EvolCompGen: Evolution & Comparative Genomics | Extreme environments harbor unique microbial life with biotechnological potential. Here, we characterize a novel Penicillium sp. isolated from the hyp [...] |
| 22 July 15:00-15:20 (add to calendar) | 12 | Chih-Hsuan Wei | Contextual Gene Set Analysis with Large Language Models | Function: Gene and Protein Function Annotation | Gene set analysis (GSA) is a foundational technique in genomics research, enabling the identification of biological processes and disease mechanisms a [...] |
| 22 July 15:20-15:40 (add to calendar) | 03A | Damien Goutte-Gattat | The role of the Ontology Development Kit in supporting ontology compliance in adverse legal landscapes | BOKR: Bio-Ontologies and Knowledge Representation | Ontologies, like code, are a form of speech. As such, they can be subject to laws and other regulations that attempt to control how freedom of speech [...] |
| 22 July 15:20-15:40 (add to calendar) | 03A | Damien Goutte-Gattat | The role of the Ontology Development Kit in supporting ontology compliance in adverse legal landscapes | BOSC: Bioinformatics Open Source Conference | Ontologies, like code, are a form of speech. As such, they can be subject to laws and other regulations that attempt to control how freedom of speech [...] |
| 22 July 15:20-15:40 (add to calendar) | 01C | Bi-Rong Wang | Decoding CXCL9 regulatory mechanisms by integrating perturbation screenings with active learning of mechanistic logic-ODE models | SysMod: Computational Modeling of Biological Systems | Despite advances in immunotherapy, pancreatic cancer remains highly lethal due to an immunosuppressive tumor microenvironment characterized by immune [...] |
| 22 July 15:40-16:00 (add to calendar) | 01B | Beatriz Urda-García | Disentangling the genetic and non-genetic origin of disease co-occurrences | NetBio: Network Biology | Numerous diseases co-occur more than expected by chance, likely due to a combination of genetic and environmental factors. However, the extent to whic [...] |
| 22 July 17:00-17:20 (add to calendar) | 04AB | Ko-Han Lee | NeoPrecis: A Computational Framework for Assessing Neoantigen Immunogenicity to Advance Cancer Immunotherapy | CSI: Computational Systems Immunology | Cancer immunotherapy, including immune checkpoint inhibitors (ICIs) and personalized cancer vaccines, has transformed cancer treatment. However, respo [...] |
| 23 July 08:40-09:00 (add to calendar) | 01A | - | Morning Welcome and Keynote Introduction | Distinguished Keynotes | |
| 23 July 14:00-14:20 (add to calendar) | 02N | Étienne Fafard-Couture | Predicting relevant snoRNA genes across any eukaryote genome using SnoBIRD | iRNA: Integrative RNA Biology | Small nucleolar RNAs (snoRNAs) are a group of noncoding RNAs identified in all eukaryotes. In human, C/D box snoRNAs are the most prevalent class, dis [...] |
| 23 July 15:00-15:20 (add to calendar) | 11A | Inimary Toby-Ogundeji | Integrating Bioinformatics into Undergraduate Biology Education: Innovation, Experiential Learning, and Sustainable Program Design | Education: Computational Biology and Bioinformatics Education and Training | As biology becomes increasingly data-driven, the integration of computational and quantitative skills into undergraduate life sciences education is es [...] |
| 23 July 15:20-15:40 (add to calendar) | 11A | Amanda Saravia-Butler | GeneLab for Colleges and Universities (GL4U): On-Demand Bioinformatics Training Using Space Biology Omics Data | Education: Computational Biology and Bioinformatics Education and Training | The NASA GeneLab project provides open access to space-relevant multi-omics data, hosted on the Open Science Data Repository (OSDR), which can be mine [...] |
| 23 July 16:40-17:00 (add to calendar) | 04AB | Patricia Carvajal-López | Competency framework profiles to reflect career progression within bioinformatics core facility scientists | BioInfo-Core | There is an expanding need for specialised services from Bioinformatics Core Facilities (BCF). Providing services for these infrastructures requires h [...] |
| 23 July 16:40-17:20 (add to calendar) | 02N | Roser Vento-Tormo | Gene regulation of human cell systems | iRNA: Integrative RNA Biology | The study of human tissues requires a systems biology approach. Their development starts in utero and during adulthood, they change their organization [...] |
| 23 July 17:20-18:00 (add to calendar) | 11A | Patricia Carvajal-López | Fostering communities of practice in bioinformatics education and training | Education: Computational Biology and Bioinformatics Education and Training | Communities of practice in bioinformatics education and training are essential, both for the technical training and professional development of bioinf [...] |
| 24 July 08:40-09:20 (add to calendar) | 11BC | Roser Vento-Tormo | “Gene regulation of human cell systems” | RegSys: Regulatory and Systems Genomics | “The study of human tissues requires a systems biology approach. Their development starts in utero and during adulthood, they change their organizatio [...] |
| 24 July 09:20-09:40 (add to calendar) | 03A | Gwang-Hyeon Yun | FACT: Feature Aggregation and Convolution with Transformers for predicting drug classification code | GenCompBio: General Computational Biology | Motivation: Drug repositioning, identifying new therapeutic applications for existing drugs, can significantly reduce the time and cost involved in dr [...] |
| 24 July 12:30-12:40 (add to calendar) | 01B | Daniel Gómez-Pérez | REMAG: recovery of eukaryotic genomes from metagenomes using reference-free contrastive learning | MICROBIOME | Assembly-based metagenomic approaches, including generation of metagenome‑assembled genome (MAG) catalogues, are pivotal for exploring and understandi [...] |
| 24 July 12:40-13:00 (add to calendar) | 04AB | Maik Wolfram-Schauerte | PhageExpressionAtlas - a comprehensive transcriptional atlas of phage infections of bacteria | BioVis: Biological Data Visualizations | Bacteriophages (phages) are bacterial viruses that infect and lyse their hosts. Phages shape microbial ecosystems and have contributed essential tools [...] |
| 24 July 14:00-14:20 (add to calendar) | 01A | Yu-Hsiang Tseng | Ultrafast and Ultralarge Multiple Sequence Alignments using TWILIGHT | HiTSeq: High Throughput Sequencing Algorithms & Applications | Motivation: Multiple sequence alignment (MSA) is a fundamental operation in bioinformatics, yet existing MSA tools are struggling to keep up with the [...] |
| 24 July 14:40-15:00 (add to calendar) | 12 | Chih-Hsuan Wei | Enhancing Biomedical Relation Extraction with Directionality | Text Mining: Text Mining for Healthcare and Biology | Biological relation networks contain rich information for understanding the biological mechanisms behind the relationship of entities such as genes, p [...] |