1st simbad Workshop

Cascina Fossata, Torino (IT), September 22-26, 2025 [map, weather, transit]

PROGRAMME

Monday Sept. 22 (morning)

(Cascina Fossata)

13:59 (1') Welcome
14 (40') Martin Weigt (Sorbonne) Data augmentation enables label-specific generation of protein sequences
14:40 (40') Pierre Barrat-Charlaix (Politecnico) Generative continuous time model reveals epistatic signatures in protein evolution
15:20 (20') Matteo De Leonardis (Politecnico) Modeling protein sequence evolution as an Ornstein-Uhlenbeck process in a latent space
15:40 (20') Francesco Caredda (Politecnico) Controllable protein design with Direct Coupling Analysis
16 (30') Coffee break
16:30 (40') Andrea Pagnani (IIGM & Politecnico) Prediction of protein fitness landscapes from screening experiments
17:10 (40') Juan Rodriguez Rivas (Politecnico) Generative diffusion models for protein domain sequence design
17:50 (40') Giovanni Peinetti (Sorbonne) Integrating experimental feedback improves generative models for biological sequences
18:30 | Session ends
19:30 | Welcome dinner at Ventuno

8:30 | Coffee
9 (40') Luca Ferretti (Oxford) Social interactions and genetic interactions
9:40 (40') Francesco Di Lauro (Oxford) The impact of sexual networks on HIV transmission clusters: a comparative analysis of selected countries in Europe and Sub - Saharan Africa
10:20 (20') Punya Alhakoon (Oxford) Tracking West Nile virus dynamics using viral loads from trapped mosquitoes
10:40 (20') Tarek Alrefae (Oxford) Bayesian Inference from Serum Titration Data
11 (30') Coffee break
11:30 (40') Luca Dall'Asta (Politecnico) Small-coupling approximation for dynamic cavity method
12:10 (20') Mattia Tarabolo (Politecnico) Sparse interactions reshape stability of complex ecosystems
12:30 (20') Anna Paola Muntoni (Politecnico) Epidemic inference from contact tracing data
12:50 | Lunch

14 (40') Alfredo Braunstein (Politecnico) Matrix-product belief propagation for inference in dynamics
14:40 (20') Federico Florio (Politecnico) Continuous-space Matrix-Product Belief Propagation
15 (40') David Margarit (UNGS) Hypergraph Analysis of a Cancer Stem Cell Marker Network
15:40 (20') Nadia Gonzalez (UNGS) Dynamics of System Perturbations: Transition from Healthy to Cancerous Tissue, Particularly in the Crypts of Lieberkühn
16 (30') Coffee break
16:30 (40') Marcela Reale (UNGS) Mathematical Modeling of HPV Transmission and the Evaluation of Immunization Strategies in Argentina
17:10(40') Charlie Hamilton (Oxford) Epi and evo transitions in the emergence of Zoonotic viruses
17:50 (40') Alejandro Lage (La Habana) Inference of contact tracing delays in first waves of COVID in Cuba
18:30 | Session ends

8:30 | Coffee
9 (40') Jotun Hein (Oxford) Algorithms for Reconstructing Ancestral Recombination Graphs
9:40 (20') Gustavo Paccosi (UNGS) Fractional Local derivatives in the context of Biological Time vs. Chronological Time
10 (20') Ariel Scagliotti (UNGS) Chasing atmospheric aerosols for epidemiological studies
10:20 (40') Carla Bosia (Politecnico) Ultrasensitive post-transcriptional regulation and frequency decoding
11 (30') Coffee break
11:30 (40') Tammy Boggiano (CIM) Increasing protein production of industrially relevant cell lines
12:10 (20') Lisandra Calzadilla (Politecnico) Metabolic and gene engineering in bioprocess development
12:30 (20') Ernesto Azahares (CIM) TBA
12:50 | Lunch

14 (40') [online] Emanuele Massa (Nijmegen) Statistical mechanics of Cox regression in the proportional regime
14:40 (40') Andrea De Martino (Politecnico) Metabolism: shifting the perspective
15:20 (40') Arián Ferrero (Instituto Biofisika) How metabolic heterogeneity shapes cyanobacterial strategies: insights from single-cell metabolic flux analysis
16 | Session ends, coffee break
16:30 | Meeting of Simbad node coordinators and management committee

(Egyptian museum, highly recommended)

(the Po and the Cappuccini [the hill, not the drinks])

(standard cityscape [from the Cappuccini])

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