Day 1 (26 May, Tuesday)
| Time | Program |
|---|---|
| 09:00–09:05 | Welcome |
| 09:05–10:05 | Keynote 1: Paul Medvedev |
| 10:05–10:30 | Coffee Break I |
| 10:30–12:20 | Session 1: Sequence I Minimizer Density revisited: Models and Multiminimizers — Ingels et al. MaxGeomHash: An Algorithm for Variable-Size Random Sampling of Distinct Elements — Hera et al. Faster and Scalable Parallel External-Memory Construction of Colored Compacted de Bruijn Graphs with Cuttlefish 3 — Khan et al. Sequence-to-graph alignment based copy number calling using a network flow formulation — Magalhães et al. Privacy-Preserving Pangenome Graphs — Blindenbach et al. bronko: ultrarapid, alignment-free detection of viral genome variation — Doughty et al. |
| 12:20–13:30 | Lunch |
| 13:30–15:20 | Session 2: Protein/ML I Predicting interaction-specific protein–protein interaction perturbations by missense variants with MutPred-PPI — Stewart et al. Bacterial protein function prediction via multimodal deep learning — Muzio et al. Evolutionary profile enhancement improves protein function annotation — Dai et al. Integrative Multi-Scale Sequence–Structure Modeling for Antimicrobial Peptide Prediction and Design — Li et al. ProtFlow: Flow Matching-based Protein Sequence Design with Comprehensive Protein Semantic Distribution Learning and High-quality Generation — Kong et al. Transforming Biological Foundation Model Representations for Out-of-Distribution Data — Pratapa et al. |
| 15:20–15:50 | Coffee Break II |
| 15:50–17:05 | Session 3: Single-Cell I Random Matrix Theory-guided sparse PCA for single-cell RNA-seq data — Chardès Gene-First Identity Construction for Robust Cell Identification in Single-Cell Transcriptomics — Yang et al. Error Correction Algorithms for Efficient Gene Quantification in Single Cell Transcriptomics — Zentgraf et al. Nullstrap-DE: A General Framework for Calibrating FDR and Preserving Power in Differential Expression Methods — Jiang et al. |
| 17:05–19:00 | Poster Session I |
Day 2 (27 May, Wednesday)
| Time | Program |
|---|---|
| 09:00–10:00 | Keynote 2: Gene Myers |
| 10:00–10:25 | Coffee Break I |
| 10:25–12:20 | Session 4: Sequence II KuPID: Kmer-based Upstream Preprocessing of Long Reads for Isoform Discovery — Borowiak & Yu SLAB: A Sweep Line Algorithm in PBWT for Finding Haplotype Block Cores — Naseri et al. pHapCompass: Probabilistic Assembly and Uncertainty Quantification of Polyploid Haplotype Phase — Hosseini et al. On Deriving Synteny Blocks by Compacting Elements — Bohnenkämper et al. Compressed inverted indexes for scalable sequence similarity — Ingels et al. Fast and Flexible Flow Decompositions in General Graphs via Dominators — Sena & Tomescu |
| 12:20–13:30 | Lunch |
| 13:30–14:45 | Session 5: Multi-Omics Multimodal spatial alignment and morphology mapping with MOSAICField — Liu et al. Multi-modal tissue-aware graph neural network for in silico genetic discovery — Aggarwal et al. Modeling Multi-Modal Brain Connectomes for Brain Disorder Diagnosis via Graph Diffusion Optimal Transport Network — Sheng et al. Achieving spatial multi-omics integration from unaligned serial sections with DIME — Sun et al. |
| 14:45–15:20 | Session 6: Small Molecules SpecLig: Energy-Guided Hierarchical Model for Target-Specific 3D Ligand Design — Zhang et al. Joint Learning of Drug-Drug Combination and Drug-Drug Interaction via Coupled Tensor-Tensor Factorization with Side Information — Zhang et al. |
| 15:20–15:50 | Coffee Break II |
| 15:50–17:05 | Session 7: Transcriptomics Summarizing RNA Structural Ensembles via Maximum Agreement Secondary Structures — Gu et al. CLADES — Contrastive Learning Augmented DifferEntial Splicing with Orthologous Positive Pairs — Talukder et al. Alternet: Alternative splicing-aware gene regulatory network inference Deep genomic models of allele-specific measurements — Tu et al. |
| 17:05–19:00 | Poster Session II |
Day 3 (28 May, Thursday)
| Time | Program |
|---|---|
| 09:00–10:00 | Session 8: Phylogeny I Constrained diffusion as a paradigm for evolution — Lazarev et al. Deconvolving Phylogenetic Distance Mixtures — Arasti et al. A Cophylogenetic Approach for Virus-Host Interaction Prediction — Chowdhury et al. |
| 10:00–10:25 | Coffee Break I |
| 10:25–12:20 | Session 9: Single-Cell II scDesignPop generates population-scale single-cell RNA-seq data for power analysis, method benchmarking, and privacy protection — Dong et al. scProfiterole: Clustering of Single-Cell Proteomic Data Using Graph Contrastive Learning via Spectral Filters — Coşkun et al. Integrating morphology and gene expression in unpaired single-cell data using GeoAdvAE — Du & Lin MOSAIC: A Spectral Framework for Integrative Phenotypic Characterization Using Population-Level Single-Cell Multi-Omics — Lu et al. Integrative Inference of Spatially Informed Cell Lineage Trees using LineageMap — Pan et al. Causal gene regulatory network inference from Perturb-seq via adaptive instrumental variable modeling — Sun et al. |
| 12:20–13:30 | Lunch |
| 13:30–14:30 | Keynote 3: Alexandros Stamatakis |
| 14:30–15:25 | Session 10: Phylogeny II Quartet-based species tree methods enable fast and consistent tree of blobs reconstruction under the network multispecies coalescent — Dai et al. STELAR-X: Scaling Coalescent-Based Species Tree Inference to 100,000 Species and Beyond — Saha & Bayzid PaNDA: Efficient Optimization of Phylogenetic Diversity in Networks — Holtgrefe et al. |
| 15:25–15:55 | Coffee Break II |
| 15:55–17:10 | Session 11: Cancer & Evolution Arborist: Prioritizing Bulk DNA Inferred Tumor Phylogenies via Low-pass Single-cell DNA Sequencing Data — Weber et al. Identifying Robust Subclonal Structures Through Tumor Progression Tree Alignment — Wu et al. Fast and accurate resolution of ecDNA sequence using Cycle-Extractor — Faizrahnemoon et al. POTTR: Identifying Recurrent Trajectories in Evolutionary and Developmental Processes using Posets — Käufler et al. |
| 17:10–17:50 | Business Meeting |
| 19:00 | Gala Dinner |
Day 4 (29 May, Friday)
| Time | Program |
|---|---|
| 09:00–10:00 | Keynote 4: Sara Mostafavi |
| 10:00–10:25 | Coffee Break I |
| 10:25–12:20 | Session 12: Protein/ML II Fast, accurate construction of multiple sequence alignments from protein language embeddings — Hoang et al. Generating Hybrid Proteins with the MSA-Transformer — Tule et al. Deconvolving mutation effects on protein stability and function with disentangled protein language models — Ding et al. Quantum and Temporal Graph Neural Networks Reveal New Accuracy Limits in Predicting Protein–Ligand Dissociation Kinetics — Salamatov et al. Protein Compositional Ratio Representation (PCRR) Systematically Improves Human Disease Prediction — Madduri et al. Uncertainty-aware synthetic lethality prediction with pretrained foundation models — Hua et al. |
| 12:20–13:30 | Lunch |
| 13:30–15:25 | Session 13: Statistical Genetics Prediction of lifetime disease liability from EHR features — Di & Cai Private Information Leakage from Polygenic Risk Scores — Nikitin & Gürsoy A biobank-scale method for learning environmental modulators of gene–environment interaction underlying complex traits — Liu et al. Bias in genome-wide association test statistics due to omitted interactions — Yelmen et al. GOPHER: Optimization-based Phenotype Randomization for Genome-Wide Association Studies with Differential Privacy — Nandi et al. Evolutionary dynamics under phenotypic uncertainty — Mohanty et al. |
| 15:25–15:55 | Coffee Break II |
| 15:55–17:30 | Session 14: Single-Cell III CAMP: Coreset Accelerated Metacell Partitioning enables scalable analysis of single-cell data — Li et al. DeltaNMF: A Two-Stage Neural NMF for Differential Gene Program Discovery — Karpurapu et al. Information Geometry Reconciles Discrete and Continuous Variation in Single-Cell and Spatial Transcriptomic Analysis — Cai et al. DiCoLo: Integration-free and cluster-free detection of localized differential gene co-expression in single-cell data — Li et al. CycleGRN: Inferring Gene Regulatory Networks from Cyclic Flow Dynamics in Single-Cell RNA-seq — Zhao et al. |
| 17:30–18:30 | Closing & Awards |
*Time Zone: GMT+3