Presenting Author

Abstract Title

Talk/Poster

Abdollahzadeh, Elnaz

AGOUTIC—an agentic framework for reproducible long-read genomic processing and analysis

poster

Abhyankar, Yash

Gain- and loss-of-function variant benchmarks are solved by gene lookup—how to evaluate variants that defy their gene

poster

Agarwala, Richa

Petabase-Scale deep and wide searches with Pebblescout and Logan

talk

Akter, Sultana

3PodR—An accessible and reproducible workflow for automated pathway analyses and drug repurposing

poster

Antipov, Dmitry

HPRC assemblies show active recombination between all pairs of heterologous human acrocentric chromosomes

poster

Arbabi, Keon

brisc—a multithreaded CPU toolkit for single-cell analysis

talk

Baharav, Tavor Z

Statistical integration of bulk and single-cell TCR sequencing to improve differential clonotype abundance testing

poster

Balachandran, Suhani

Measuring the copy number and active fraction of 5S and 45S rDNA units using long-read nanopore sequencing

poster

Ballal, Aditya

Path-likelihood algorithm—Semi-supervised classification of biological and biomedical data with limited labels

poster

Bass, David J

Improving gene expression tissue specificity metrics in samples with correlated tissues

poster

Benjamin, Kynon J

IsoGraph learns coordinated isoform-switching networks distinct from gene abundance in human brain transcriptomes

talk

Bhati, Umesh

HiC-Setu—Inferring 3D genome organization from condition-specific transcriptomic signals

poster

Braynen, Janeen C

Physiological and transcriptomic variation in Sorghum responses to iron stress and elevated temperature

poster

Brown, Nicole L

Haplotype architecture shapes phenotypic diversity across plant and animal pangenomes

talk

Burhans, Richard C

HighGen—Comparative genomics resources for cannabis

poster

Bustos Gutiérrez, Álvaro

Mapping lineage-defining gene regulation during stem-cell-to-β-cell differentiation

poster

Cain, Scott

Orbit and Galaxy user-defined tools for reproducible, auditable computational biology

poster

Campillo, Beatriz

Splicelogic—A software package for obtaining splicing events from transcript sets

poster

Chakrabarty, Souparna

dfPPI Analysis Platform—A web server for systems-level interpretation of interaction-state proteomics in disease

poster

Chat, Vylyny

Germline cancer susceptibility and immune variation shape somatic driver acquisition in breast cancer

poster

Chen, Aleysha T

Harmonization and integration of pharmacogenomics screens

poster

Chen, Hai

Discordant evolutionary signals challenge genomic language models for constraint inference

poster

Chen, Kuan-Lin

Integrating NGS signatures and protein language model embeddings to cluster and prioritize drug candidates

poster

Chen, Yu

Contribution of short tandem repeats to schizophrenia in 107,331 Asian individuals

talk

Cheong, Dayeon

Differential methylation analysis of genetically diverse mice using Fiber-seq and pyDSS

poster

Chikina, Maria

Exploiting latent structure under biological constraints

talk

Chilton, John M

From Nextflow, CWL, papers, and conversations to runnable Galaxy workflows

poster

Chilton, John M

From research code to reproducible infrastructure with Galaxy user-defined tools

poster

Chinnadurai, Nishanth

Transformer-based virtual cell modeling to uncover perturbations that enable exhaustion reversal in t cells within preinvasive lung adenocarcinoma

poster

Choubal, Urshila V

An information-theoretic approach to cell-type identification and metacell construction in scRNA-seq

poster

Chougule, Kapeel M

Chromosome-scale genome assemblies enable comparative analysis of Sorghum aphid tolerance in Sorghum

poster

Christensen, Trevor

From active learning to dataset design—Scaling laws for regulatory genomics

poster

Deng, Yuming

Cellarium—A cell-type-informed framework for improved cell segmentation in spatial transcriptomics

poster

Denning, Mia

Integrating podocyte injury signatures and gut microbiome features for a multi-omic view of chronic kidney disease

poster

Deosthale, Padmini

From latent classes to biological states—Paired host-microbial profiling in pediatric sepsis

poster

Diaz de la Vega Gonzalez, Alejandro

Widespread functional translation of downstream open reading frames across the human transcriptome

talk

Farias-Virgens, Madza

Sex differences in cell type composition and molecular specializations in a vocal motor circuit

poster

Farmer, Rohit

Stability of antibody repertoires in astronauts during long-term spaceflight

poster

Finazzi, Veronica

Charting transposable element expression across human development in vivo and in vitro using single-cell transcriptomics

poster

Finucane, Hilary

Systematic identification of disease-associated 3D neighborhoods in protein structures

talk

Formenti, Giulio

GAIA—Transforming planetary-scale genome curation and conservation with machine learning

poster

Founta, Kyriaki

Characterization of genome-wide DNA methylation variability across human populations

poster

Frost, Rob

LRSPAT—A low-rank framework for spatial omics statistics

poster

Gerhardt, Kenji

TEsorter2—Fast and divergence-robust classification of transposable elements

poster

Gilbert, Jacob

Identifying robust subclonal structures through tumor progression tree alignment

poster

Goecks, Jeremy

Artificial intelligence and machine learning advances in the Galaxy Computational Workbench

talk

Goldman, Matthew

Bad neighborhood? evaluating spatial niche identification tools on mouse leukemia tissues

poster

González Isa, Jacob

The single-molecule, long-read meiotic recombination landscapes in Arabidopsis pollen and human sperm

poster

Gorski, Jack

The perturbation of an established CD8 T cell ecosystem by an influenza virus re-exposure

poster

Guo, Boyi

Benchmarking imputation methods for imaging-based spatial transcriptomics in postmortem human brain

poster

Guo, Boyi

labWeaver—reliable agentic data analysis grounded in laboratory knowledge

poster

Hamilton, Nolan H

Consensus multi-sample signal estimation in epigenomic sequencing cohorts with sample- and locus-specific uncertainty

talk

Han, Shuying

Quantifying cell and gene repositioning across tissue states using tissue-intrinsic geometric coordinates

poster

Han, Yunheng

∆-PRO—Scalable variant-aware multiplex primer design

poster

Hoffman, Jill M

Gene co-expression modules as a scalable search space for trans-QTL and core gene discovery

poster

Hogstrom, Larson

Cross-technology assessment of vector integration site detection in biomanufacturing cell banks—Short-read WGS vs shallow nanopore

poster

Hrytsenko, Yana

Alignment‑free genome analysis for population structure and phylogenetics

poster

Hu, Gary

Mapping spatial omics slices to reference atlases via induced clustering

poster

Hu, Kevin L

Mapping human prefrontal cortex aging across lifespan at single-cell resolution

talk

Huang, Emma Yu-Chen Y

JUPITER—Leveraging junction usage and haplotype specific paired read evidence to prioritize transcripts underlying splicing quantitative trait loci

poster

Hwang, Nahee

Spatial transcriptomics reveals a disease-associated myofibroblast niche shaping invasive progression in colitis-associated colorectal cancer

poster

Ishar, Jaspreet

Celldega—Integrated toolkit for visualization and analysis of spatial data

poster

Ito, Yu

Scarpia enables haplotype-resolved germline assembly from matched tumor/normal long reads without Hi-C or parental data

talk

Jajoo, Aarti

Integrating circular RNAs into transcriptomic and genetic analyses reveals distinct disease‑specific regulation and brain imaging signatures

poster

Jakobson, Chris

A comprehensive diagram of the protein wiring from the genome to heritable traits

poster

Jamsandekar, Minal

Genomic Annotation Infrastructure (GAIn)—A software architecture for reproducible genomic annotation

poster

Jangi, Radhika

Multiome profiling across differentiating cells refines context resolution and reveals dynamic genetic effects

talk

Jiang, Wengyao

Spatial biomarker transformer learns molecular-spatial representations of cells across multiplexed imaging studies

talk

Jin, Yucheng

Consistent modeling of genetic interactions in large-scale perturbation screens

poster

Job, Kim P

Improving consistency and accuracy of 3D spatial gene expression reconstruction from tomo-seq data

poster

Kang, Yijie

Decoding the sequence basis of Pol II promoter-proximal pausing with deep learning

poster

Kaur, Sehgeet

Disease surveillance at infra species resolution using metagenomic classification in combination with enhanced taxonomy

poster

Kerr, Jennifer

From public repositories to classroom research—Cloud-based genomic data science miniCUREs for early-stage undergraduate biology courses

talk

Khan, Salaar

Optimizing multi-source training strategies for cross-species regulatory prediction

poster

Kim, Brian M

Measuring the efficacy of mixing RNA sequencing samples from different sequencing centers for expression outlier detection using OUTRIDER

poster

Kim, Sumin

Integrated multi-omics and spatial transcriptomic analysis identifies FSTL3 as a shared molecular feature of PSC and iCCA

poster

Kinney, Justin B

Maximum entropy libraries of biological sequences under additive constraints

poster

Koido, Masaru

A DNA sequence model conditioned on H&E histology predicts the spatial distribution of a transcript

talk

Koo, Peter

Dissecting and directing pathology foundation models

talk

Koul, Sneh

From proteomic mapping to predictive models of PARP1 target selection

poster

Kovaleva, Vasilisa

A probabilistic framework for de novo genomic annotation of immune receptor loci

talk

Kuru, Nurdan

SARGENT—A sparse Bayesian framework for heritability decomposition and population label-free polygenic prediction

talk

Laberge, Annika B

High-resolution, multimodal atlas using novel direct scATAC-seq methodology to characterize disease and healthy PBMCs

poster

Landis, Justin

plyxp facilitates feature aggregation and exploratory data analysis for omics datasets, bridging tidy grammar with Bioconductor data structures

poster

Lariviere, Delphine

Resolving both haplotypes of vertebrate genomes through dual curation with the VGP Galaxy workflows

poster

Lee, Chae Min

Endothelial cell senescence contributes to T cell remodeling in late-stage chronic obstructive pulmonary disease

poster

Lee, Hayan

StructurizeMe—Normalizing and visualizing DNA methylation data to reveal the yin-yang balance of paralogous gene biology

poster

Lee, YunJu

The role of sphingosine-1-phosphate signaling in idiopathic pulmonary fibrosis

poster

Li, Dongwei

Olivia—Learned sequence representations enable automated primer design for multiplex tiled amplicon sequencing of pathogens

poster

Li, Qiuhui

Population-scale long-read sequencing reveals molecular and clinical consequences of complex genetic variation in All of Us

talk

Likhite, Mary

Investigating the impact of promoter-promoter interactions on gene regulation

poster

Lin, Mao-Jan

ImpuT2T—Pangenome-based patching for human genome assemblies

talk

Liu, Di

Estimating selection coefficients of human missense variants with MisFit v2

poster

Liu, Xingyan

Geometry-guided phenotyping reveals interpretable spatial programs of Ebola infection beyond viral abundance

poster

Liu, Zhihan

PoolParty—streamlined design of DNA sequence libraries in Python

poster

Liu, Zhihan

S2F—A package for deep and mechanistic sequence-to-function modeling

poster

Lorv, Janet Sui Hoa

Streamlining metagenomic-based plant and animal disease diagnostics using a semi-automated web platform

poster

Love, Michael

Frameworks for multi-sample long-read RNA-seq analysis

talk

Ly, Lynn

Phasing and annotating paralogous regions with Oxford Nanopore Technologies sequencing

poster

Martin Linares, Cristina

A context-dependent foundation model for splicing

talk

McLamb, Flannery

Deciphering the contribution of cis-regulatory elements to gene expression in zebrafish using 3D interactions and graph neural networks

poster

Mehra, Anna Therese

Genome architecture and extreme stress tolerance in the antarctic midge Belgica antarctica

poster

Melamed, Rachel D

Connecting disease risk variants to spatial variation in gene regulation across the human brain with the Brain Ontology Expression (BRONTE) model

poster

Melsted, Pall

RNA-seq analysis in seconds using GPUs

poster

Miller, Danny E

A matched long-read DNA and RNA resource for structural and regulatory variation across ancestrally diverse populations

talk

Miraldi, Emily R

Multiome-seq links inflammatory bowel disease polygenic risk to TNF inhibitor response

poster

Moore, Jill E

Architectural chromatin interactions provide a framework for context-dependent gene regulation

talk

Moss, Matthew A

Per-locus quantification of microsatellite instability enables allele-resolved inference of shift dynamics and sensitive detection of endometrial and ovarian cancers

talk

Mpingirika, Eric

Targeting adaptive drug resistance in KEAP1/STK11-deficient lung adenocarcinoma

poster

Mukherjee, Aniruddha

Seqout—Metadata harmonisation for public genomic data discovery

poster

Murphy, Alan

AlphaGenome without the megabase—Fast, encoder-only transfer to short regulatory DNA with state-of-the-art performance

poster

Nagai, Masayuki

Causal refinement—Improving genomic deep learning models with perturbation data through continual learning

poster

Nair, Malavika

Evaluating short-read variant calling consistency across GRCh38 and T2T-CHM13 using 1000 genomes family trios

poster

Nakshi, Adrita Hossain

Sketching the SRA—Experiment-wide similarity search across 4.8 million metagenomes

talk

Nekrutenko, Anton

Orbit—Reproducible agentic workflow development with cloud execution included

poster

Newbury, Abigail M

Sparse covariate-aware non-negative extraction improves complex disease subtyping

poster

Nguyen, Cuong V

Molecular staging and dynamic expression mapping reveal regulatory variation in tomato fruit ripening

poster

Nguyen, Matthew

Foundation-model embeddings for pre-assembly binning of long metagenomic reads

poster

Nguyen, Matthew

Perseus—Lineage-aware refinement of Kraken2 taxonomic classification for long read metagenomes

poster

Nguyen, Thuy N

Genome-wide search for convergence of body mass variation among mammals

poster

Nugmanova, Aigul

PertSig—A data-driven collection of transcriptional perturbation signatures for human and mouse

poster

Obermayer, Alyssa

Quantifying treatment resistance with dysregulated splicing burden

talk

Oki, Shinya

ChIP-atlas update—Integration of the TAIR12 genome assembly and CUT&RUN/tag data for comprehensive plant and animal epigenomics

poster

Olson, Andrew

Tbrowse—An embeddable react component for exploring phylogenetic trees and associated data

poster

Osmanbeyoglu, Hatice U

Chromatin-informed multitask learning reveals cell-type-specific regulatory transitions in Alzheimer’s disease

poster

Osmanbeyoglu, Hatice U

HistoDGAT—Histology-guided multimodal learning for spatial protein inference

poster

Ostrovsky, Alex

Deduplication of pangenomic training data enhances genomic language model efficiency and accuracy

poster

Pandey, Anupam K

Calibrating single-cell developmental pseudotime using independently measured RNA decay rates

poster

Papineni, Nimisha

Regu-BERT—A ChIP-seq signal-augmented transformer for cross-species generalization and variant prediction of regulatory elements

poster

Pardo, Katherine

Identifying aberrant transcriptomic patterns in Undiagnosed Diseases Program (UDP) patients to enhance prioritization of candidate variants in rare disease diagnostics

poster

Park, Jung Won

Single-nucleus spatial genomic profiling of follicular lymphoma reveals pro-tumorigenic ligand-receptor interactions

poster

Pfenning, Andreas R

An epigenetic signature of vulnerable neurons is under selective pressure associated with longevity across placental mammals

talk

Pflug, Florian G

Learning genome replication programs from sequencing data

poster

Phan, Lon

ALFA Release 5—Scaling NCBI population allele frequencies for rare variant interpretation, cancer genomics, and ancestry-aware biomedical data science

poster

Pickard, Joshua M

Observable and controllable digital twins for improving sepsis care

poster

Prieto, Anatori

Calibrated and accurate inference of cell type-specific enhancer-gene links from single-cell multiome data

talk

Pybus, Alyssa

Machine learning predicts cancer immunotherapy outcomes in a national real-world clinical dataset

poster

Ramakrishnan, Abhirami

PolyApex—A toolkit and framework to investigate downstream functional consequences of alternative polyadenylation

poster

Ramakrishnan, Srividya

Indirect genomic effects shape cancer risk across species

poster

Rashidi, Saadyeh

Exploring the dark immunopeptidome—Identification and characterization of eRNA-derived and HLA-presented peptides in cancer

talk

Rasolofomanana Rajery, Sakaiza

Cross-tissue inflammation signals related to T1D and gastrointestinal autoimmune conditions

poster

Revsine, Mahler

Pre-training dataset deduplication improves genomic language models

poster

Rhie, Arang

Djcounter—Biobank-scale genotyping of Robertsonian translocations reveals hidden structural variation on the human acrocentric chromosomes

talk

Rodrigues, Rhea Carmel Glen

Transfer learning-based classification of UV-induced skin damage from reflectance confocal microscopy images

poster

Romero, Juan Pablo

Longitudinal imaging of the same cell anchors transcriptional trajectories of adipogenic commitment

poster

Rube, Hans Tomas T

SPRINT-MS—A high-throughput platform for mapping protein–protein interactions using pooled IP-MS and compressed sensing

poster

Sakamoto, Yoshitaka

PRCGAP—Personalized diploid reference genomes enable comprehensive haplotype-resolved analysis of cancer genomes

poster

Salnikov, Mikhail

Benchmarking consensus peak methodologies for identifying differentially accessible regions in ATAC-seq data

poster

Saravanan, Sanjhna

Benchmarking zero-shot RNA generative models against continuous directed evolution for de novo cereblon aptamer discovery

poster

Sarkar, Hirak

SpaPRo—Adaptive RNA-to-protein decoding in spatial multi-omics data

poster

Sarkar, Hirak

Spindle—Scalable indexing of spatial-omics data for fast querying

poster

Schilder, Brian M

Exploring the genome at every scale—GPU-accelerated tools for genome-wide interaction calculations and visualization

talk

Schroeder, Robert

A multi-method approach to identify high confidence miRNA biomarkers for Alzheimer’s disease

poster

Schwerd-Kleine, Paul

PDX2PFS—A latent sensitivity model predicts clinical combination efficacy from single-agent xenograft data

talk

Seacord, Andrew C

Refining and enriching SRA metadata using deterministic logic and large language models

poster

Sedlazeck, Fritz J.

Cell-type-resolved somatic variant discovery from bulk long-read sequencing

poster

Seenivasa, Siddarth S

Sex-stratified phosphoproteomics reveals concordant male reductions in WAVE1-S550 across GRIN1 channelopathy models

poster

Severin, Jessica

Updates to the ZENBU interactive visualization system for the FANTOM6 interactome and IMMAGINE database projects

poster

Shedd, Nicole

Evolutionary remodeling of the human immune regulatory genome

poster

Sheffield, Nathan C

Refgenie reloaded—AI-ready reference genome asset management rebuilt on GA4GH identifiers

poster

Sheffield, Nathan C

RefgetStore—A fast, efficient, and cloud-friendly store for genomic sequence collections

poster

Sheffield, Nathan C

Researcher Profiles—a portable format for structured researcher expertise to power agentic and programmatic use

poster

Shiraishi, Yuichi

Centromeric alpha-satellite architecture and the formation of der(1;7) in myelodysplastic syndromes

poster

Singh, Neel

Quantitative seed phenotyping enables genome-wide association analysis of seed color in Sorghum bicolor

poster

Slota, Joanna

Redefining fibroblast cell types across organs through functional transcriptional modules

poster

Sollitto, Marco

A phylogenetically informed framework for reconstructing gene evolution across hundreds of vertebrate genomes

talk

Sonthalia, Radhika

HarmonyPath—Biology-guided batch correction of pathology foundation model embeddings

poster

Stein-O'Brien, Genevieve

Disentangling neurodegeneration one latent space at a time

poster

Sun, Mengyi

AI predictions and the expansion of scientific frontiers—Evidence from structural biology

poster

Sun, Mengyi

The strength of weird ties—Positive genetic interactions have greater scientific impact but are under-represented in the literature

poster

Sun, Na

Decoding disease-associated changes in spatial tissue microenvironments

talk

Sun, Qingyao

Sparse linear algebra accelerates genotype representation graph computation at biobank scale

poster

Sung, Minjin

Spatial coupling of one-carbon metabolism and ECM remodeling in foamy macrophages during MASLD progression

poster

Sweeten, Alexander P

Evolutionary dynamics of the primate ACRO1 satellite

poster

Tanevski, Jovan

Context aware frameworks for multimodal integration and tissue dynamics

talk

Tang, Makayla

From annotation to steering—Sparse autoencoder features in kin, a DNA–protein language model

poster

Todorov, Kamen

From engineering excellence to AI-assisted scientific software

poster

Tokheim, Collin

An AI agent enables drug target identification from large-scale chemoproteomics of molecular glue degraders

poster

Tran, Tumi Ngoc

Perturbation prediction models that effectively use prior biological knowledge outperform foundation and reasoning model approaches and strong baselines

poster

Tsang, Josephine

Evaluating stability selected gene-ratio classifiers for the differentiation of feline LGITL from LPE

poster

Turco, Alexander

Diversity and genomic organization of non-B DNA motifs in haplotype-resolved human genome assemblies

poster

Varma, Mukund

Dynamic digital tumors for precision oncology—Selecting the right treatment, for the right patients, at the right time

poster

Vergis, John

Is biological information differentially preserved across reporter peptide, kinase activity, and pathway representations?

poster

Vishnubhatt, Surya P

Identification of blood-based DNA methylation biomarkers for the classification of feline LGITL vs. LPE

poster

Wang, Ryan

A Bayesian framework for gene regulatory network inference using multi-omics data

poster

Wardhana, Oliver

Cell-type separability predicts annotation accuracy and outweighs algorithm choice—a factorial benchmark across seven scRNA paradigms

poster

Wardhana, Oliver

Scaling reversal in hierarchical single-cell annotation—Model capacity, input width, and the bounds of cross-study transfer

poster

Wei, Sharon

SorghumBase—A FAIR and community-driven resource for Sorghum genomics, germplasm, and AI-ready data integration

poster

Wlodzimierz, Piotr

An integrated framework for de novo centromere and genome architecture annotation across eukaryotes

poster

Woyshner, Kyla

pyroNMF—Semi-supervised probabilistic NMF for spatial and single-cell transcriptomics

talk

Wu, Chih H

Determining optimal placement of copy number aberration impacted single nucleotide variants in a tumor progression history

poster

Xie, Shaojun

ProxiomeVis—Scalable interactive analysis of single-cell protein proximity data

poster

Xu, Linyi

RiboRAIL—Accurate isoform-level ribosome occupancy quantification from Ribo-seq

poster

Xu, Sangyu

Contextualized phenovectors reveal a Drosophila serotonergic circuit controlling satiety

poster

Yao, Hongcheng

Integration of large, complex single-cell datasets with Harmony2

talk

Yerukala Sathipati, Srinivasulu

Interpretable multi-omics machine learning identifies biomarkers predictive of ovarian cancer survival

poster

Yu, Qiyi

A multimodal framework maps spatial tumor-stromal metabolic ecosystems in bladder cancer

poster

Yu, Zhezhen

Expanding the readable genome—A novel approach for analyzing mononucleotide C repeats

poster

Zadorozhny, Nikola

TD2+—A universal method for recognizing protein-coding regions in RNA

poster

Zare Jousheghani, Zahra

alevin-fry-lr—Shift-tolerant and likelihood-informed UMI resolution for long-read single-cell RNA-seq

talk

Zhang, Kate

Identifying high-confidence RBP binding sites from eCLIP data

poster

Zheng, Xinchang

Evidence-based prioritization of isoforms from population-scale long-read transcriptomes

poster

Zhou, Juannan

Measuring epistatic effects of mutations with exact, scalable Shapley values

poster

Zhu, Wanying

Benchmarking computational HLA typing methods across diverse populations at biobank scale

poster

Zidan, Rahaf

From flies to primates—Cross-species evaluation of serine/threonine kinase activity using reporter-peptide activity arrays

poster