Program
| Wednesday, 11 June | |
| 09:00 - 14:00 |
Registration & sign-in
 reception desk
|
| 10:30 - 13:00 | Workshop: Statistics Approaches to Modern Biology Workshop Program |
| 13:00 - 14:00 | Welcome lunch buffet |
| 14:00 - 14:15 | Conference Opening - Welcome messages |
AI, Models and Tools chair(s) Claudia Angelini, Luca Alessandrì |
|
| 14:15 - 15:00 |
Sylvia Richardson MRC Biostatistics Unit, University of Cambridge & Norwegian Centre for Knowledge-driven Mach PREPARATA LECTURE Uncovering latent structure in omics features: a strategy to enhance discoveries in biomedicine |
| 15:00 | Matteo Manfredi |Oral Presentation| AlphaFold2 and ESMFold: A large-scale model comparison of the human proteome upon functional annotation |
| 15:15 | Tommaso Mazza |Oral Presentation| Beyond missense: Expanding APOGEE's reach to noncoding variants in mitochondrial diseases |
| 15:30 | Rossano Atzeni |Oral Presentation| Data-driven liquid biopsy: a scalable framework for somatic mutation analysis |
| 15:45 | Salvatore Alaimo |Oral Presentation| REFINET: Reference Tissue Identification using Neural Transformers |
| 16:00 - 16:30 | Poster session and coffee |
| 16:30 - 19:00 | BITS members Assembly |
| 19:30 - 21:00 | Social activity |
| Thursday, 12 June | |
AI, Models and Tools chair(s) Anna Marabotti, Roberto Tagliaferri |
|
| 09:00 | Luca Alessandri |Flash Talk| FAIR-Flow, A FAIR-Compliant and Customizable Pipeline Builder for Bioinformatics |
| 09:06 | Francesco Cecere |Flash Talk| scGraphVerse: A Unified Framework for Network Inference, Evaluation, and Visualization from Single-Cell Gene Expression Data |
| 09:12 | Giorgia Biddau |Flash Talk| Integration of a multi-resolution approach for automatic parameter selection in ASCAT |
| 09:18 | Michele Leone |Flash Talk| TaxonMatch: ML Integration of Taxonomic Sources to Leverage Genomic and Biodiversity Data |
| 09:24 | Davide Rigoni |Flash Talk| RGCVAE: relational graph conditioned variational autoencoder for molecule design |
| 09:30 | Giulio Caravagna |Oral Presentation| Timing the origin of immune-evasion in AML undergoing allo-genic transplants |
| 09:45 | Adele De Hoffer |Oral Presentation| PromoterGPT: AI-Driven Design of Cell-Type-Specific Promoters |
| 10:00 - 10:45 | Karine Audouze University Paris Cité, Paris, France INVITED SPEAKER Deciphering the Chemical Exposome Effects on Human Health Through Adverse Outcome Pathways (AOPs) using artificial intelligence |
| 10:45 - 11:15 | Poster session and coffee |
Genomics, Transcriptomics, and Metagenomics chair(s) Annamaria Carissimo, Vincenzo Bonnici |
|
| 11:15 - 12:00 |
Pantelis Bagos Department of Computer Science and Biomedical Informatics University of Thessaly, Greece INVITED SPEAKER GWAS summary statistics: Bioinformatics methods for post-GWAS analyses |
| 12:00 | Simone Tomè |Oral Presentation| Dissecting interactome-driven subtypes of Colorectal Cancer |
| 12:15 | Francesco Gazzo |Oral Presentation| VISMA: Vector Integration Site Mutation Analysis |
| 12:30 | Mirco Stradiotto |Oral Presentation| Improving the detection of viral circRNAs combining short and long read sequencing data |
| 12:45 | Dario Righelli |Flash Talk| SpaceTrooper, an R package for the preprocessing and quality control of imaging-based spatial transcriptomics data |
| 12:51 | Andrea Betti |Flash Talk| Benchmarking PWM and SVM-based Models for Transcription Factor Binding Site Prediction: A Comparative Analysis on Synthetic and Biological Data |
| 12:57 | Italia Elisa Mauriello |Flash Talk| Bridging gaps in marine metagenomics resources |
| 13:03 | Alisa Kumbara |Flash Talk| CRISPR-HAWK: Haplotype- and variant-aware guide design toolkit for CRISPR-Cas |
| 13:09 | Aurelia Iuliana Timis |Flash Talk| Validation of DeNovoCNN for De Novo Variant Detection |
| 13:15 - 14:30 | lunch buffet |
Translational Bioinformatics: Clinics, agriculture, environment, food chair(s) Angelo Facchiano, Ramona Palombo |
|
| 14:30 - 15:15 | Mario Nicodemi University of Naples Federico II, Naples, Italy INVITED LECTURE Chromatin 3D architecture: mechanisms and functions |
| 15:15 | Giulia De Riso |Oral Presentation| X-Pose: Unveiling skewed X Chromosome Inactivation Through Integration of DNA and RNA Sequencing |
| 15:30 | Roberto Pagliarini |Flash Talk| Studying Genetic Variability at Population Level |
| 15:36 | Riccardo Pizzichemi |Flash Talk| New Frontiers in Genotoxicity Detection by Multiparametric Analyses for Gene Therapy |
| 15:42 | Enrico Blanzieri |Flash Talk| Applying OneGenE causality discovery on different grapevine transcriptomic datasets unveiled effects of gene expression profiles on consensus. |
| 15:48 - 16:00 | BatchX: Bioinformatics at Scale - Sponsored communication: David Castillo, Sequentia |
| 16:00 - 16:30 | Poster session and coffee |
Special session: Sustainable bioinformatics: infrastructure, interoperability, and data sharing chair(s) Matteo Pallocca, Alessandro Cestaro |
|
| 16:30 - 17:00 | Marialuisa Lavitrano KEYNOTE Research Infrastructures in the EOSC Landscape |
| 17:00 | Giacomo Baruzzo |Oral Presentation| Sustainable computation on large, sparse omics matrices with quickSparseM |
| 17:15 | Pietro Pinoli |Oral Presentation| Federated Learning in Practice: The BETTER Project’s Approach to Rare Disease Research and Data Governance |
| 17:30 | Damiano Piovesan |Flash Talk| MobiDB in 2025: integrating ensemble properties and function annotations for intrinsically disordered proteins |
| 17:36 | Sandro Gepiro Contaldo |Flash Talk| Building FAIR and Sustainable Infrastructure: The Italian Collaborative Platform for Microbial Research |
| 17:42 | Claudio Lo Giudice |Flash Talk| BioRepository@ELIXIR-IT: a secure environment for storing and sharing human genetic data |
| 17:48 - 18:00 | End of session and day - Communications by Conference Organizers for participants to the social dinner |
| Friday, 13 June | |
Systems Biology and Multi-Omics chair(s) Raffaele Calogero, Giacomo Baruzzo, Simone Pernice |
|
| 09:00 | Alice Chiodi |Oral Presentation| Ulisse: a tool for intracellular and intercellular crosstalk analysis in omics data |
| 09:15 | Daniela Volpatto |Oral Presentation| Simulating tumor evolution with functional stochastic branching models: a framework for testing evolutionary hypotheses |
| 09:30 | Riccardo Aucello |Oral Presentation| Computational Analysis of Function-Specific Minimal Microbiomes in Multiple Sclerosis |
| 09:45 | Elisabetta Sciacca |Oral Presentation| Graph-driven multi-omic tool for differential network analysis and feature selection in machine learning |
| 10:00 - 10:45 | Vincenza Colonna University of Tennesse Health and Science Center, US BITS LECTURE Integrating genetic ancestry, environmental exposure and health equity |
| 10:45 - 11:15 | Poster session and coffee |
| 11:15 | Elvira Toscano |Flash Talk| SimulCell reproduces a wide range of cell features and can predict the behaviour of transformed cell populations |
| 11:22 | Lorenzo Federico Signorini |Flash Talk| NetCos: a Network-Enhanced Connectivity Score for Drug Repurposing |
Proteins chair(s) Bruno Hay Mele, Pasqualina D'Ursi |
|
| 11:30 | Sol C Begue |Flash Talk| RING 4.0: Analyzing proteins through Residue Interaction Networks |
| 11:40 - 12:25 | Romina Oliva University of Naples "Parthenope", Naples, Italy INVITED SPEAKER Tools for the analysis of biomolecular complexes |
| 12:25 - 12:40 | BioHackathon Report |
| 12:40 - 13:00 | Announcement: BITS2026 |
| 13:00 - 14:00 | lunch buffet |
| 14:00 - 15:00 |
Round Table: Prospective of AI and LLM for bioinformatics Chair: Bruno Hay Mele |
| 15:00 - 15:15 | BITS2025 Closure and announcements |
| 15:15 - 15:30 |
Presentation of YOUNG BITS, RSG-Italy, CINI Young-InfoLife groups
Giulia Cesaro, Simone Pernice, Giacomo Baruzzo
|
| 15:15 - 17:00 | Symposium organized by YOUNG BITS, RSG-Italy & CINI Young-InfoLife |
| 15:30 - 15:45 | Remarks on the First International BioHackathon of BITS |
| 15:45 - 16:00 | Domain-Informed Representation Learning for Drug–Gene Interactions via Multimodal Pretrained Embeddings Francesca Pia Panaccione |
| 16:00 - 16:15 | Re-analyzing Sequencing Data with High-Precision Pipeline for Variant Detection and Prioritization in Rare Genetic Diseases Harsh Poddar |
| 16:15 - 16:30 | GenePrior: a modular R-based workflow for variant prioritization and multi-omics integration in mendelian disease diagnosis Amalia Chiariello |
| 16:30 - 16:45 | Enabling Cell-Free DNA Deconvolution Across Sequencing Depths Through Deep Neural Networks Carlo Ciprian |
| 16:45 - 17:00 | Final remarks/Group photo |
For any query regarding the BITS2025 congress, please write to: congress AT bioinformatics.it
