Presenting Author

Abstract Title

Presentation

Antunes, Dinler

Structure-guided cancer immunotherapy design with HLA-Arena 2.0

talk

Belleau, Pascal

RAIDS—Software Framework for robust ancestry inference from challenging human molecular data

talk

Beruldsen, Finn

Composition-aware modeling of T-cell clonal competition in cancer immunotherapy

talk

Borges, Pamella

CrossDome 2.0—Improved off-target toxicity prediction through database expansion and algorithm refinement

talk

Byrd, Anna

ChEA-KG and ChEA-KG-TS—Network-based transcription factor enrichment analysis tool with a time series workflow

poster

Byrd, Anna

Identifying tumor-specific membrane targets, therapeutics, and matching cell lines for experimental validation with the Multiomics2Targets2 workflow

talk

Carri, Ibel

Systematic identification of noncanonical neoantigens from the dark genome in CEDAR using PEPMatch

talk

Carri, Ibel

The Cancer Epitope Database and Analysis Resource (CEDAR)

poster

CHIN, B B

Robust PET lesion detection using cross attention and patch contrastive learning

poster

Clarke, Daniel J

Codon-64—Scalable creation of bioinformatics tools with vibe coding

talk

Davis, Sean

Cancer genomics: Integrative and scalable solutions in R/Bioconductor—Progress update

poster

Del Fiol, Guilherme

GARDE chatbot platform for digital health interventions in cancer prevention

talk

Diamant, Ido

ARCHS4—Uniformly mining, processing, and serving human and mouse transcriptomics datasets from the Gene Expression Omnibus

poster

Dou, Yongchao

SEPepQuant2 enables interpretable protein isoform quantification for cancer proteogenomic studies

talk

Evangelista, John Erol

ARCHS4-seq—A metadata wheel user interface to interact with the ARCHS4 Database

poster

Fedorov, Andriy

NCI Imaging Data Commons—Cloud-based open access to 100 TB of cancer imaging with AI-enhanced discovery

talk

Gardner, John K

Perturb-Seqr—Comprehensive signature search engine integrating connectivity maps from multiple sources

poster

Goecks, Jeremy

Artificial intelligence and machine learning advances in the Galaxy Computational Workbench

talk

Goldman, Mary

UCSC Xena for embedding and mapping cancer single cell data using the Universal Cell Embedding (UCE) foundation model

talk

Gonzalez Camara, Pablo

ImmunoPheno—A computational framework for data-driven design and analysis of immunophenotyping experiments

talk

Griffin, Tim

Extensions to the immunopeptidogenomics (iPepGen) pipeline for characterizing the dark immunopeptidome and advancing immuno-oncology research

talk

Griffith, Malachi

AI-assisted, expert-governed curation of clinical cancer variant knowledge in CIViC

poster

Griffith, Obi

Advancing open somatic cancer variant interpretation through CIViC and ClinGen somatic cancer

talk

Hanauer, David

Chatting with clinical notes—Incorporating LLM-based question-and-answer capabilities into the EMERSE search engine and text processing tool

talk

Harris, Gordon

Open Health Imaging Foundation (OHIF) Viewer—Enhancing interoperability between the OHIF web viewer and 3D Slicer server-side applications

talk

Hochheiser, Harry

DeepPhe-Viz 2.0—Interactive cancer cohort discovery from electronic medical records

poster

Isaac, Kathryn

Impact of the ITN's educational support for cancer researchers

talk

Karchin, Rachel

From variants to insights—LLM-driven genomic annotation with the OpenCRAVAT MCP server

talk

Lee, Michael J

Resolving drug mechanisms of action using the MEDUSA web portal.

talk

Liang, Han

The Cancer Proteome Atlas—New web platform and foundation models for functional proteomics

talk

Lindsay, James

cBioPortal Chat—A work in progress to develop a tool-grounded conversational interface to access cancer genomics data

talk

Luo, Runpeng

Inferring allele-specific copy number aberrations across different sequencing technologies

talk

Nebbia, Giacomo

Learning temporal acetowhitening patterns for lesion localization in cervical colposcopy with quantum variational rewinding

talk

Nguyen, Tin C

BioGnosia—A graph-enhanced retrieval-augmented generation system for biomedical question answering

talk

Oh, Sehyun

MetaHarmonizer—A calibrated, locally deployable framework for biomedical schema matching and ontology grounding

talk

Osmanbeyoglu, Hatice U

DGAT—A dual-graph attention network for inferring spatial protein landscapes from transcriptomics

talk

Prabhakaran, Abinanda

Agentic AI report generation for the potential associations between understudied genes and liver diseases

poster

Prasanna, Prateek

Treatment-aware digital twins in oncology using diffusion models and standard-of-care tumor dynamics

talk

Roncali, Emilie

AI and theranostics digital twins for liver cancer radioembolization

talk

Rose, Johnie

Building PopCASE, a population cancer research tool—2 years in

talk

Shah, Pratik

Generative deep learning for computational destaining and restaining of unregistered digital pathology images

talk

Stein, Lincoln

Conversational AI workflows for cancer genomics data discovery and pathway interpretation

talk

Surana, Pallavi

Variant-informed pipeline for evidence-based drug target ranking (ViC targets)

talk

Taub, Lily

Integrating connectivity mapping resources with primary tumors, PDX models, and cell lines to prioritize drug candidates for individual triple negative breast cancer patients

poster

Tran, Vietbao N

Generative deep learning of immunohistochemistry staining patterns from native H&E whole slide images for cancer diagnosis

talk

Uttam, Shikhar

Three-dimensional spatial methods for characterizing the tumor microenvironment

talk

Wagner, Alex

Scaling cancer knowledge sharing with GA4GH standards

poster

Wang, Chi

Identification and evaluation of predictive biomarkers using ratios of time-to-event outcomes

talk

Yu, Haiyuan

Integrating structural homology with deep learning to achieve highly accurate 3D interactome modeling at full protoeme scale

talk