Late-Breaking Research: Bioinformatics, Computational Biology, Systems Biology, and Convergent Science 1

• LB159 A practical guideline for benchmarking unimodal and multimodal foundation models on spatial transcriptomics data in oncology Anna C. Wahl (née Schaar), Dasha Valter, Lisa Sikkema, Stefan G. Stark, Zelda E. Mariet, Tokuwa Kanno, Ediem Al-Jibury, Tobias Heinen, Liam Gonzalez, Marin G. M. Scalbert
• LB160 · PDF SMURFS: A comprehensive Nextflow pipeline for consensus somatic variant detection Ting Yang, Rongjie Wu
• LB161 A comparative study of neoantigen discovery pipelines uncovers discrepancies in the generation of mutated neopeptide sequences Ibel Carri, Angela Frentzen Worley, Ashmitaa Logandha Ramamoorthy Premlal, Gauri Renjith, Malachi Griffith, Jason Greenbaum, Alessandro Sette, Bjoern Peters, Zeynep Kosaloglu-Yalcin
• LB162 Twistcgp pipeline: A portable, open-source workflow for comprehensive genomic profiling in translational oncology Nils Homer, Erin McAuley, Zach Norgaard, James Flynn, Rebecca Barnard, Tina Han
• LB163 Spatial analysis of head and neck cancer reveals two ecosystems with distinct modes of epithelial-to-mesenchymal transition Dor Simkin, Thomas F. Barrett, Lingling Zhang, Michael J. Moore, Alissa R. Greenwald, Noam G. Darnell, Michael Mints, Salma Ramadan, Victoria Yu, Riley DZ Mullins, Jesse Zaretsky, Porter Bischoff, Douglas Adkins, Wade L. Thorstad, Sana D. Karam, Randall C. Paniello, Jason T. Rich, Ryan S. Jackson, Patrik Pipkorn, Paul A. Zolkind, Guangyong Peng, R. Alex Harbison, Rebecca Chernock, Anuraag S. Parikh, Sidharth V. Puram, Itay Tirosh
• LB164 · PDF Mutational signatures associated with Western dietary patterns in colorectal cancer Mariya Kazachkova, Thomas Cattiaux, Ammal Abbasi, Mathilde Meyenberg, Joanna Loizou, Michael R. Stratton, Paul Brennan, Ludmil B. Alexandrov
• LB165 · PDF Predicting neoantigen immunogenicity through evolutionary selection pressure Timothy Sears, Ko-Han Lee, Maurizio Zanetti, Hannah Carter
• LB166 Genomic and transcriptomic changes associated with tucatinib exposure in HER2-positive breast cancer brain metastases Savannah C. Roy, Anna Guarnieri, Pradeep Bhartiya, Thomas Danhorn, Andrew Goodspeed, Hannah Parris, Virginia F. Borges, James Costello, David R. Ormond, Elena Shagisultanova
• LB168 Advancing peptide-MHC binding prediction with JANUS through iterative multi-allele deconvolution and ensemble deep learning Alan Perez-Rathke, Justin Balko, Jens Meiler
• LB169 scCAP: An ontology-aware large language model framework for hierarchical and standardized single-cell type annotation Dongkwan Shin, Seok-Won Jang, Jonghyun Lee, Juyeon Cho
• LB170 · PDF scVarID: Linking somatic variants to single-cell transcriptomes to reveal early cancer-associated cell states Dongkwan Shin, Juyeon Cho, Jonghyun Lee, Seok-Won Jang
• LB171 AI-based B2SC identifies pre-existing TOP2A/E2F-active populations driving resistance to T-DXd in HER2+ breast cancer Se-eun Han, Minwoo Jung, Taewoo Kim, Jaeeun Park, Minji Seo, Jangsoon Lee, Sang Youn Rhie
• LB172 RNA-seq-based molecular and microenvironmental stratification of colorectal cancer in a Korean real-world cohort Jinseon Yoo, Kyu Jin Song, Jimin Kim, Keeok Haam, Soobok Joe, Jongbum Jeon
• LB173 · PDF Mapping of somatic and RNA-level variants along the colorectal adenoma-carcinoma progression Dongkwan Shin, Jonghyun Lee, Juyeon Cho, Seok-Won Jang
• LB174 · PDF H-optimus-1: A foundation model for computational histopathology Marin Scalbert, Charlie Saillard, Thomas Peeters, Liam Gonzalez, Dasha Valter, Felipe Llinares-López, Zelda E. Mariet, Rodolphe Jenatton
• LB175 · PDF Weakly supervised deep learning enables spatially resolved cell type inference from H&E histopathology Andrew T. Wang, Saugato R. Dhruba, Emma M. Campagnolo, Kun Wang, Danh-Tai Hoang, Eldad D. Shulman, Eytan Ruppin

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