SysMod

Chiara Damiani et al. combine data-driven and knowledge-based modeling to study tumor metabolism from high-resolution spatial transcriptomics data and apply the universal spFBA methodology in spatially resolved contexts. npj Systems Biology & Applications doi.org/10.1038/s41540…

We are glad to share this job opportunity with the SysMod community: the @KlippLindingLab is seeking a senior researcher at the interface of systems modeling, data science, and cell biology. linkedin.com/posts/klipp-ed…

🎄✨ Happy Holidays to all of you from SysMod! ✨🎄 We can’t wait to see you at our conference, July 12–16, 2026, in Washington, D.C., USA, to connect, share knowledge & continue advancing innovation in computational biology—mark your calendars & stay tuned for updates!

We are deeply saddened by the passing of @ChaouiyaC (1969–2025) – a cherished member of our community and coordinator (2018-2022), contributing with expertise & kindness. Her work on logical modeling of regulatory networks & dedication to SysMod left a lasting mark. We miss her.

SysMod just turned 10! 🎉 We continue to serve our community of systems modelers and researchers in computational systems biology. Join us and get involved, for instance, in our annual meetings at the ISMB conference. #MyXAnniversary

@iscb Congratulations from the Systems Modeling Community 👏🏻👏🏻👏🏻

The results of the ISCB Leadership vote are in!  Terms for the ISCB President-Elect and ISCB Vice President will start on January 21, 2026.

🎉 Congratulations to our poster prize winners of SysMod at #ISMBECCB2025! 🥁 Prizes: local food and beverages, and, as the first priue, a 20% discount to the 2026 meeting! ➢ 1st: Yanjun Liu @uniofgalway ➢ 2nd: Rupinder Kaur @kieluni ➢ 3rd: Sebastian Huß at the Uni Potsdam

Chiara Damiani (University of Milano-Bicocca) wraps up the 2025 SysMod Meeting at #ISMBECCB2025 with closing remarks and announcing the poster awards. Huge thanks to all participants and speakers for making it a vibrant showcase of systems biology! See you at #ISMB2026!

See the corresponding publication: doi.org/10.1038/s41467…

“TFvelo: gene regulation–inspired RNA velocity estimation” by Jiachen Li (Institute of Process Engineering) presents TFvelo—a tool that models RNA velocity without splicing info by leveraging regulatory networks, inferring cell trajectories & pseudotime. #ISMBECCB2025

Marek Kimmel (@RiceUniversity) on “Computational Modeling of Shortening and Reconstruction of Telomeres”: a stochastic branching-process model captures yeast telomere decay, cell death & alternate lengthening of telomeres-driven rebuilding—for human aging & cancer. #ISMBECCB2025

Koichiro Majima (@sciencetokyo_en) shows new spatiotemporal VAE models of continuous single-cell tissue dynamics—tracking growth, reorganization & gene expression from discrete snapshots. Applied to mouse embryogenesis, it reveals hidden developmental trajectories. #ISMBECCB2025

Erick Armingol presents at #ISMBECCB2025: scCellFie, a tool to infer metabolic activities from single-cell & spatial transcriptomics. Scaling to 30M cells, it maps human metabolism and uncovers rewired pathways in endometrium, endometriosis, and cancer. #SingleCell #Metabolism

Using single-cell time-lapse microscopy and agent-based #modeling, Ati Ahmad et al. (@UWaterloo) calibrate how colicin-producing E. coli kill susceptible strains in microfluidic traps—revealing how spatial structure shapes microbial competition #Microbiology #ISMBECCB2025

Next, Sayali Anil Alatkar (@UWMadison) presents ARTEMIS—a generative model combining autoencoders & Schrödinger Bridges at #ISMBECCB2025, aiming to predict continuous gene expression, cell population, and perturbation dynamics from time-series single-cell data. #SingleCell #AI

Now, Bi-Rong Wang (TU Eindhoven) presents at #ISMBECCB2025 how active learning + logic-ODE models decode CXCL9 regulation in pancreatic cancer. This approach speeds discovery of drug combos to boost T cell recruitment & tackle immune exclusion. #SystemsBiology #CancerImmunology

Using multi-objective reinforcement learning, Nhung Duong et al. (Hanoi University of Pharmacy) modeled JAK/STAT pathway for cancer therapies to balance tumor control, immune health, resistance & toxicity to reveal optimal strategies, towards personalized treatment. #ISMBECCB2025

Arnau Montagud introduces a community benchmark to compare leading off-lattice multiscale modeling tools (BioDynaMo, Chaste, PhysiCell, TiSim) for virtual human twin research, revealing performance gaps & needs for gold standards to advance biomedical simulations. #ISMBECCB2025

Virtual tumors are helping fight hard-to-treat cancers. Data-driven models of cancer signaling predict resistance, reveal mechanisms, & guide patient-specific therapies for TNBC, lung cancer, melanoma & glioblastoma. #CancerResearch #SystemsBiology

Jasmin Fisher, a professor at the @UCL, is delivering the second keynote talk in a full house on how computational models can decode complex cancer signalling networks at #ISMBECCB2025.