2025 SysMod annual meeting
Integrating systems biology and bioinformatics
July, 2025 | Liverpool, UK
Methods
Dynamical modelingFlux balance analysis
Logical modeling
Network modeling
Stochastic simulation
...
Systems
AnimalsBacteria
Humans
Plants
Yeast
…
Applications
BioengineeringCancer
Developmental biology
Immunology
Precision medicine
…
Prof. Jasmin Fisher,
UCL Cancer Institute
Prof. Ronan Fleming,
University of Galway
Overview
Advances in genomics are creating new opportunities to understand the biology that require both systems modeling and bioinformatics. The ninth annual SysMod meeting will be a forum for discussion about the combined use of systems biology modeling and bioinformatics to understand biology, and disease. The meeting will take place in July 2025, during the 2025 ISMB/ECCB conference 
in Liverpool, UK. The meeting will feature two keynote talks and contributed presentations.
Topics
Methods
Dynamical modeling Flux balance analysis Logical modeling Network modeling Stochastic simulation …
Systems
Animals Bacteria Humans Plants Yeast …
Applications
Bioengineering Cancer Developmental biology Immunology Precision medicine …
Keynote speakers
Jasmin Fisher
UCL Cancer Institute
University College London
Ronan Fleming
School of Medicine, University of Galway, Ireland
Schedule
Poster presentation:
| 10:00-11:20 and 16:00-16:40 | Poster Session with Lunch and Coffee Breaks |
|---|---|
| Poster Title Affiliation
ABSTRACT |
|
SysMod meeting:
| 11:20-13:00 | Session I: Computational Advances in Metabolic Modeling Moderator: Matteo Barberis, University of Surrey, United Kingdom |
|---|---|
| 11:20 – 11:30 | Welcome and Introduction to SysMod 2025 Matteo Barberis University of Surrey, United Kingdom
The community of special interest (COSI) in systems modeling (SysMod) organizes annual one-day gatherings. In 2025 the meeting comprises three sessions that cover a broad variety of topics, beginning with metabolic modeling, followed by the afternoon session on multiscale modeling and concludes with inference of cellular processes. This year’s meeting features two keynote speakers, Ronan Fleming and Jasmin Fisher. The event is hosted by Chiara Damiani and Matteo Barberis on behalf of the eight COSI organizers. This brief talk introduces all speakers, organizers, and main topics of the 2025 meeting. |
| 11:30-12:10 | Keynote talk: Variational kinetics: a variational formulation of reaction kinetics Ronan Fleming School of Medicine, University of Galway, University Rd, Galway, Ireland |
| 12:10-12:30 | A dynamic multi-tissue metabolic reconstruction reveals interindividual variation in postprandial metabolic fluxes Lisa Corbeij, Natal van Riel, and Shauna O’Donovan
Abstract |
| 12:30-12:50 | Decoding organ-specific breast cancer metastasis through single-cell metabolic modeling Garhima Arora and Samrat Chatterjee
Abstract |
| 12:50- 12:55 | Enzyme activation network facilitates regulatory crosstalk between metabolic pathways Sultana Al Zubaidi, Muhammad Ibtisam Nasar, Richard Notebaart, Markus Ralser, and Mohammad Tauqeer Alam
Abstract |
| 12:55- 13:00 | Cell-cycle dependent DNA repair and replication unifies patterns of chromosome instability Bingxin Lu, Samuel Winnall, Will Cross, and Chris Barnes
Abstract |
| 13:00- 14.00 | Lunch Break |
| 14.00-16.00 | Session II: Systems biology and multiscale modeling Moderator: Chiara Damiani, Università degli Studi di Milano-Bicocca, Italy |
| 14:40-14:40 | Keynote talk: Virtual Tumours for Predictive Precision Oncology Jasmin Fisher University of Galway, Ireland
Cancer is a complex systemic disease driven by genetic and epigenetic aberrations that impact a multitude of signalling pathways operating in different cell types. The dynamic, evolving nature of the disease leads to tumour heterogeneity and an inevitable resistance to treatment, which poses considerable challenges for the design of therapeutic strategies to combat cancer. In this talk, I will discuss some of the progress made towards addressing these challenges, using the design of computational models of cancer signalling programs (i.e., virtual tumours). I will showcase a growing library of mechanistic, data-driven computational models, focused on the intra- and inter-cellular signalling in various types of cancer (namely triple-negative breast cancer, non-small cell lung cancer, melanoma and glioblastoma). These computational models are predictive and mechanistically interpretable, enabling us to understand and anticipate emergent resistance mechanisms and to design patient-specific treatment strategies to improve outcomes for patients with hard-to-treat cancers. |
| 14:40-15:00 | A community benchmark of off-lattice multiscale modelling tools reveals differences in methods and across-scales integrations Thaleia Ntiniakou, Othmane Hayoun-Mya, Marco Ruscone, Alejandro Madrid Valiente, Adam Smelko, Jose Luis Estragués Muñoz, Jose Carbonell-Caballero, Alfonso Valencia, and Arnau Montagud
Abstract |
| 15:00-15:20 | Multi-objective Reinforcement Learning for Optimizing JAK/STAT Pathway Interventions: A Quantitative System Pharmacology Study Nhung Duong, Tuan Do, Tien Nguyen, Hoa Vu, and Lap Nguyen
Abstract |
| 15:20-15:40 | Decoding CXCL9 regulatory mechanisms by integrating perturbation screenings with active learning of mechanistic logic-ODE models Bi-Rong Wang, Maaruthy Yelleswarapu, and Federica Eduati
Abstract |
| 15:40-16:00 | ARTEMIS integrates autoencoders and Schrödinger Bridges to predict continuous dynamics of gene expression, cell population and perturbation from time-series single-cell data Sayali Anil Alatkar
Cellular processes like development, differentiation, and disease progression are highly complex and dynamic (e.g., gene expression). These processes often undergo cell population changes driven by cell birth, proliferation, and death. Single-cell sequencing enables gene expression measurement at the cellular resolution, allowing us to decipher cellular and molecular dynamics underlying these processes. However, the high costs and destructive nature of sequencing restrict observations to snapshots of unaligned cells at discrete timepoints, limiting our understanding of these processes and complicating the reconstruction of cellular trajectories. To address this challenge, we propose ARTEMIS, a generative model integrating a variational autoencoder (VAE) with unbalanced Diffusion Schrödinger Bridge (uDSB) to model cellular processes by reconstructing cellular trajectories, reveal gene expression dynamics, and recover cell population changes. The VAE maps input time-series single-cell data to a continuous latent space, where trajectories are reconstructed by solving the Schrödinger bridge problem using forward-backward stochastic differential equations (SDEs). A drift function in the SDEs captures deterministic gene expression trends. An additional neural network estimates time-varying kill rates for single cells along trajectories, enabling recovery of cell population changes. Using three scRNA-seq datasets—pancreatic β-cell differentiation, zebrafish embryogenesis, and epithelial-mesenchymal transition (EMT) in cancer cells—we demonstrate that ARTEMIS: (i) outperforms state-of-art methods to predict held-out timepoints, (ii) recovers relative cell population changes over time, and (iii) identifies “drift” genes driving deterministic expression trends in cell trajectories. Furthermore, in silico perturbations show that these genes influence processes like EMT. The code for ARTEMIS: https://github.com/daifengwanglab/ARTEMIS. |
| 16:00- 16.40 | Coffee Break |
| 16.40-18.00 | Session III: Analysis of single cells and and inference of cellular processes Moderator: |
| 16:40-17:00 | Calibrating agent‐based models of colicin-mediated inhibition in microfluidic traps using single-cell time-lapse microscopy Ati Ahmadi, Samantha Schwartz, and Brian Ingalls
Abstract |
| 17:00-17:20 | Inferring metabolic activities from single-cell and spatial transcriptomic atlases Erick Armingol, James Ashcroft, Magda Mareckova, Martin Prete, Valentina Lorenzi, Cecilia Icoresi Mazzeo, Jimmy Tsz Hang Lee, Marie Moullet, Christian Becker, Krina Zondervan, Omer Ali Bayraktar, Luz Garcia-Alonso, Nathan E. Lewis, and Roser Vento-Tormo
Abstract |
| 17:20-17:40 | Spatiotemporal Variational Autoencoders for Continuous Single-Cell Tissue Dynamics Koichiro Majima and Teppei Shimamura
Abstract |
| 17:40-17:45 | Computational Modeling of Shortening and Reconstruction of Telomeres Marek Kimmel, Marie Doumic, Leonard Mauvernay, and Teresa Teixeira
Abstract |
| 17:45-17:50 | TFvelo: gene regulation inspired RNA velocity estimation Jiachen Li, Xiaoyong Pan, Ye Yuan, and Hong-Bin Shen
Abstract |
| 17:50-18:00 | Closing Remarks Chiara Damiani Università degli Studi di Milano-Bicocca, Italy
This concluding talk aims to briefly discuss the diversity of topics presented at the “Computational Modeling of Biological Systems” (SysMod) COSI track. This diversity illustrates the importance of the field and the broad range of applications in systems biology and disease. Then, forthcoming meetings of interest will be announced, and the three poster awards will be delivered as a closing event. |
Key Dates
April 17, 2025
Abstract submission deadline
May 13, 2025
Abstract acceptance notification
May 15, 2025
Late poster submissions deadline
May 22, 2025
Late poster acceptance notifications
Sunday-Thursday July 20-24, 2025
ISMB/ECCB conference
July 22, 2025
SysMod meeting
Registration and fees
Please register for the SysMod meeting through the ISMB conference registration .
Accomodation
Accommodations will be available through the ISMB/ECCB conference. Please see the ISMB/ECCB website for more information.
More information
For more information, please contact the SysMod coordinators 🔗.