Presenting Author

Abstract Title

Talk/Poster

Agarwala , Richa

Pebblescout Petabase-scale search index and protein query capabilities

poster

Alam, Md Nafis Ul

An efficient multiple genome alignment method to characterize selection of chromosomal rearrangements in higher eukaryotes

poster

Almeyda-Tejada, Jennifer Z

Comprehensive computational and evidence-based epitope profiling of Bordetella pertussis

poster

Al-Tohamy, Ahmed

Identification of MftP as a multidrug efflux pump in Burkholderia thailandensis—Integrative multi-omics highlights metabolic dynamics and urate as a key cellular substrate​

poster

Amarasinghe, Shanika

A spatial transcriptomic survey of the breast cancer microenvironment across subtypes and metastases

poster

Antipov, Dmitry

TTT—Automatic generation of model sequences for complex regions in assembly graphs

poster

Azbijari, Nima

Protein language model transfer learning for functional discovery in the microbial dark matter

poster

Bahramy, Afshin

From whole-slide images to genome study—ML-derived hippocampal sclerosis phenotypes and suggestive loci in ADRC brains

poster

Baranašic, Damir

Genomic foundation models reveal rules of promoter architecture

poster

Barthel, Floris P

Telomere dysfunction promotes remote recombination between telomeres, centromeres and ribosomal DNA catalyzed by long-range chromatin interactions

poster

Bartosz, Piotr

Exploring associations of genetic scores in breast cancer cell line RNA-seq data

poster

Bereta, Dominik

Decoding EMT plasticity—An integrated python pipeline for cross-metric analysis of cellular transition states

poster

Bhimsaria, Devesh

HT-SELEX to ChIP-seq—Complementary deep learning models for predicting transcription factor occupancy

poster

Brown, Nicole L

Identifying introgressions across pangenomes with Panagram

talk

Cabrera, Feresa Corazon P

The Aurelia labiata genome uncovers drivers of Scyphozoan evolution

poster

Calderon, Guadalupe C

Functional and genomic analyses of Streptococcus gallolyticus subspecies gallolyticus strains

poster

Chantzi, Nikol

Landscape and mutational dynamics of G-quadruplexes in the complete human genome and in haplotypes of diverse ancestry

poster

Chantzi, Nikol

The repertoire of short tandem repeats across the tree of life

talk

Chen, Bowen

Bigger isn’t always better—A small-window convolutional neural network outperforms large deep learning models in splice site and transcript evaluation

poster

Chen, Ke

A scalable and improved heuristic for flow decomposition

talk

Cheng, Haoyu

Efficient telomere-to-telomere assembly of ONT Simplex reads using hifiasm (ONT)

talk

Chougule, Kapeel M

Propagating rsIDs across crop pan-genomes in Gramene platform using the Ensembl Variant Remapping Pipeline

poster

Cicherski, Adam

AlfaPang—Rapid construction of pangenome graphs without alignment

poster

Civitarese, Jon C

Developing a metabarcoding workflow for untargeted pathogen surveillance in wildlife rehabilitation

poster

Cooper, Katherine I

Developmental and cell-specific transcriptome analysis of the mouse retina

poster

De Maio, Nicola

Maximum likelihood phylogenetics at pandemic scales

talk

DeGroat, William B

Mapping cell type–specific enhancer–gene interaction networks using massively parallel reporter assays

poster

Dong, Jiayu

Host-associated and spatiotemporal dynamics of Phytophthora nicotianae populations

poster

Donmez, Ataberk

Phasing tumor clones with variant graphs

poster

Du, Zezhen

Gfamap—A graph-based framework for error correction and downstream analysis in genome assemblies

talk

Eglinton, Hannah J

Unlocking disease-specific alternative splicing events for targeted therapeutics

poster

Ekim, Baris C

Adaptive short- to long-read alignment enables low-coverage de novo assembly at population scale

talk

Erdogdu, Beril

Isoswitching drives the aging process in human brains

poster

Eshghi, Iraj

Uncovering structural variant karyotypes using conformation capture and simulations

poster

Felton, Emily

Characterization of a rare hospital-associated “Snowbird” MRSA lineage

poster

Franceschini-Santos, Vinicius

PARM—MPRA-trained deep learning for dissecting the plasticity of regulatory grammar in human promoters

poster

Fu, Lianting

A long-read human pangenome initiative for comprehensive interpretation of nuclear-embedded mitochondrial DNA

talk

Gao, Yan

LongcallD—Joint calling of small variants and large structural variants from long reads

poster

Gao, Yifei

Genotyping CFTR with next-generation sequencing data using T1K

poster

Ge, Peter

Improving metagenomics classification with Kmask—Entropy-based masking of low-complexity regions

talk

Georgakopoulos-Soares, Ilias

Non-B DNA as driver of genome variation and evolution

talk

Goldenberg, Miles D

Comparative analysis of 16S rRNA and metagenomic sequencing for clinical applications of vaginal microbiome profiling

poster

Goretsky, Anton

Long-read sequencing of single cell-derived melanoma subclones reveals divergent and parallel genomic and epigenomic evolutionary trajectories

talk

Hernandez, Rian

Insight into Streptococcus gallolyticus subsp. gallolyticus virulence mechanisms

poster

Hirsch, Mary G

Mathematical and experimental models of interactions among subclones and immunity in  melanoma

poster

Hu, Kevin

Phylogenetic analysis with stochastic context-free grammars

poster

Jain, Chirag

Pangenome-based genome reference using integer programming

talk

Jamsandekar, Minal

Unheralded high MHC Class II polymorphism in the abundant Atlantic herring resolved by long-read sequencing

poster

Jones, Robert E

PhyloFisher v2—Advancing accuracy and reproducibility in deep phylogenomics

talk

Jones, Ronald G

Single-nucleus transcriptomic signatures of single and repeated MYC pulses in adult murine skeletal muscle

poster

Kang, Yijie

Decoding the sequence basis of Pol II elongation with deep learning

talk

Kaplow, Irene M

Challenges in predicting enhancer activity differences between species

talk

Kaur, Sehgeet

From species to strains—Developing metagenomics for fast, accurate, and precise pathogen identification

poster

Keskus, Ayse

Severus and Wakhan—Long-read tools for haplotype-aware reconstruction of complex cancer genomes

poster

Kim, Anastasiia

Practical assessment of “limited-data” algorithms versus neighbor-Joining

poster

Kim, Minju

Predictive modeling of rice phenotypes with multi-omics and environmental data—Generalization tests and consilience with association studies

poster

Koo, Peter

Explainable AI–guided virtual experiments reveal how DNA sequence context shapes gene regulation

talk

Kundaje, Anshul B

Deep learning models of regulatory DNA—A comparison of model design choices

talk

Lariviere, Delphine

Dual curation improves the quality of genome assemblies

poster

Le, Megan

DeKnot—Local haplotype-resolved assembly with k-syncmer-based multiplex De Bruijn graphs

talk

Lees, John

Comparing millions of bacterial genomes with GPU-accelerated sketching

talk

Li, Wei Vivian

Unified spatial transcriptomics analysis across single-slice and multi-slice data

poster

Li, Yifan

Counting K-mers on distributed memory efficiently

poster

Lin, Mao-Jan

impuT2T—Genome assembly scaffolding and patching with pangenome awareness

poster

Linderman, Michael

Leveraging simulation, deep learning, and variation graphs for structural variant genotyping in short-read genome sequencing

poster

Liu, Jiayi

Computational framework for predicting the effect of non-coding variation

poster

Liu, Xiran

Clustering alignment for single cell analyses—Streamlining model comparison and revealing informative genes

talk

Lotfi, Maryam

plsMD—A plasmid reconstruction tool from short-read assemblies

poster

Lui, Wui Wang

SpliSync—Genomic-language-model-driven splice site correction of long RNA sequencing reads

talk

Ma, Cong

COMPOSITION—Efficient modeling of cell type and spatial organization for high resolution spatial transcriptomics

talk

Ma, Lawrence

Prediction of in vivo G-quadruplex formation using multi-modal hybrid transformer-CNN models

poster

Maddamsetti, Rohan

Scaling laws of bacterial and archaeal plasmids

poster

Majidian, Sina

MetaKpick—Machine learning–based metagenomic classification with multi k-mer-based pangenome indexes

poster

Malikic, Salem

A Bi-partition function algorithm to evaluate inferred subclonal structures in single-cell sequencing data

talk

Malnak, Julia C

Uncovering acquisition events and human-specific folds with pairwise comparisons of the predicted viral proteome

talk

Mankame, Sharvari

Utilizing alignment-free classification of cell-free DNA sequencing reads to monitor tumor burden in primary brain tumors

poster

Manzo, Gaetano

DeepFootprinting—A deep learning framework for explainable footprinting of transcription factors in the human genome

poster

Marin, Maximillian G

Personalized transcriptome annotation across the Human Pangenome Reference Consortium

talk

Martin Linares, Cristina

Minimal reconstruction of SpliceAI using distilled matryoshka sparse autoencoders

poster

Martino, Florencia

Topology-aware graph mapping improves classification of circular genomes

poster

May, Vinzenz

SvirlPool—Multiple sample structural variant detection with local assemblies from Nanopore long reads

poster

McCarthy, Shane A

Scaling reference-quality genome assemblies across the Tree of Life—Tools, workflows, and lessons from over 3,000 species

poster

McGimpsey, Stephanie R

Transmission of methicillin-resistant Staphylococcus aureus strain USA300 in Chicago over a 17-year time period

poster

McLamb, Flannery

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

poster

Meng, Ran

Machine learning models based on histological images from healthy donors identify tissue-specific ImageQTLs and predict chronological age

poster

Metpally, Agasthya

VarViz—A simple visual Interactive web framework for variant prioritization using population data, AI scores, and functional maps

poster

Miller, Chris

A deep transcriptional atlas of myeloid malignancies gives insight into splicing-factor mutant cancers

poster

Moore, Grace

Evolutionary origins of the Mycobacterium tuberculosis complex

poster

Moreno, Ryan R

Integrating single-cell omics data across species using matrix factorization regularized by gene-level phylogenies

talk

Mouratidis, Ioannis

MAFcounter—An efficient tool for counting the occurrences of k-mers in MAF files

poster

Moustafa, Ahmed M

Unraveling the epidemiological dynamics of Staphylococcus epidermidis in pediatric bacteremia

poster

Mustafa, Harun

Efficient, accurate, SRA-scale indexing and query

talk

Nekrutenko, Anton

Galaxy Filament—Bringing analyses to the data on a global scale

poster

Nguyen, Matthew

Refining Kraken2 long-read taxonomic classifications using convolutional neural networks

talk

Ochman, Maria

Challenges in defining circulating tumor cells from single-cell RNA sequencing in breast cancer

poster

Oh, Dong-Ha

Comparative genomics resource (CGR) at NCBI provides high-quality reference data and tools for eukaryotic genome analyses

poster

Oki, Shinya

ChIP-Atlas 3.0—A data-mining suite to explore chromosome architecture together with large-scale regulome data

poster

Olson, Andrew

Visualizing functional divergence and conservation in gene families with TBrowse

poster

Opara, Charles I

Prioritizing isoform-level transcriptome-wide association to link dysregulation of lipid metabolism in the liver

poster

Pardo, Katherine

Characterizing cell-type-specific isoforms using long-read transcriptomics to enhance rare disease variant detection and interpretation

poster

Park, Kwanwoo

Genetic study of extreme LDL cholesterol phenotypes in Koreans

poster

Phan , Lon

Multi-metric framework for deconvolving selection and demography in human genomes

poster

Phillippy, Adam M

The origin and evolution of acrocentric chromosomes in humans and the great apes

talk

Pierrot, Thomas

NTv3—Joint sequence-function multi-species modeling at scale for long-range genomic prediction

talk

Pizzi, Joseph R

Machine learning-based discovery of sex-specific bladder cancer biomarkers

poster

Prabakar, Rishvanth

gcat, it’s a scam—An open source pipeline for single cell data processing and quality control

poster

Qiu, Weigang

BpWrapper—A command-line toolkit for manipulations of sequences, alignments, and phylogenetic trees

poster

Raghavan, Vakul N

DNALaCT—Ultralong genomic sequence modeling with test-time training

poster

Ranallo-Benavidez, Timothy R

Sequence annotation using KaryoScope facilitates the rapid and accurate classification and quantification of repeats, genes, and other genomic elements

poster

Reale, McKenna

Exploring the gastrointestinal-autism spectrum disorder axis through a transfer-learning approach on shotgun metagenomic sequencing data

poster

Reichl, Stephan

MrBiomics—Composable modules and recipes for automated multi-omics data analysis

poster

Rice, Daniel

Computational methods for pandemic early warning through untargeted wastewater metagenomics

poster

Rodriguez Bouza, Victor

Sparrowhawk—Assembling bacterial genomes with WebAssembly

talk

Rudnick, Zoe C

Bramble—Efficient projection of spliced genomic alignments into transcriptomic space for accurate RNA-seq quantification

poster

Russell, Pamela

Computational pipeline for characterizing combinatorial antibody libraries from Oxford Nanopore sequencing data

poster

Safonova, Yana

Enabling biomedical discoveries through immunogenomics approaches

talk

Sahoo, Deepika

Integrated model of multi-omics features classifies AML patients over the age of 60 into distinct survival groups in ECOG-ACRIN Cancer Research Group's clinical trial E3999

poster

Sapoval, Nicolae

Theoretical and empirical performance of pseudo-likelihood-based Bayesian inference of species trees under the multispecies coalescent

talk

Sarno, Jakub

Predicting telomeric allelic imbalance from RNA-seq data using machine learning models

poster

Saunders, Christopher

Translating long-read alignments from personal diploid assemblies to reference genomes provides improved read alignment, phasing, and variant-calling for human rare-disease analysis

poster

Schatz, Michael

English is the new programming language—Reproducible, transparent and accessible agentic analysis with GalaxyMCP

poster

Schonhuth, Alexander

Generating synthetic genotypes using diffusion models

talk

Seitz, Evan

Decoding the mechanistic impact of genetic variation on regulatory sequences with deep learning

poster

Sen, Shurjo K

Rediscovering value—Insights from the life cycle of genomic datasets

poster

Serajian, Mohammadali

A GPU-accelerated, pangenome-scale framework for \textit{De Novo} resistance prediction in Mycobacterium tuberculosis

poster

Sharma, Era

Darkmatter—A new approach to annotation of hypothetical proteins in prokaryotes

poster

Sharma, Shubhangi

Fun30 binds chromatin boundaries and promotes controlled exit from quiescence

poster

Shaw, Jim

High-resolution metagenome assembly for modern long reads with myloasm

talk

Shiraishi, Yuichi

Centromere haplogroups unveiled by rare k-mers—Insights into human diversity and cancer translocations

poster

Shivakumar, Vikram

Bagpipe—Personalized genome browser for pangenome-based visualization

poster

Shivakumar, Vikram

Mumemto—Scalable multi-MUM finding for pangenomes

talk

Sikic, Mile

AI for genomes—Rethinking de novo assembly

talk

Sinha, Saurabh

Differential spatial transcriptomics with natural coordinate systems

talk

Soborowski, Andrew L

Multi-species approach for gene regulatory network inference in non-model organisms

poster

Song, Li

Quality control of single-cell ATAC-seq data without peak calling using Chromap

talk

Stasczak, Alicja

Dissecting mitochondrial, erythrocyte, and platelet signals in breast cancer circulating tumor cell transcriptomes

poster

Sun, Siqi

Targeting cell subpopulations critical to treatment response in autoimmune diseases

poster

Sun, Yidan

SpatialEnhancer maps cell-type–specific enhancer interaction alterations in Alzheimer’s disease

talk

Surana, Pallavi

PGViS—Personal Genome Variant interpretation Score for predicting lung cancer risk

poster

Sweeten, Alexander

ANI inferred annotation of satellite DNA

poster

Torcivia, John P

NCBI datasets—Applications, developer integration, and support for foundational AI

poster

Toussaint, Jacqueline

Constructing pan-genome gene graphs with hundreds of thousands of bacterial genomes

talk

Uzdenov, Azamat

Integrative selection of highly specific targets for gene-editing tasks

poster

Verma, Varinder

TransXplorer—An integrated platform for accelerating RNA-seq analysis from raw data to therapeutic insight

poster

von Wachsmann, Johanna

Gemsparcl—Rapid and consistent genome clustering for navigating bacterial diversity with millions of genomes

talk

Wan, Zhuoya

CRISPRScope—A comprehensive platform for single-cell CRISPR data analysis and visualization

poster

Wang, Hanchen

Biomni—A general-purpose biomedical AI agent

talk

Wick, Ryan

Perfecting genome assemblies with Autocycler

talk

Wu, David

Integrating long-read RNA sequencing with genomics and phenomics to discover novel disease-relevant splice-altering genetic variants

poster

Wu, Haonan

A k-mer-based estimator of the substitution rate between repetitive sequences

talk

Wynne, Jacob H

Integrating targeted experiments with deep learning to resolve biogeochemical mechanisms in an antarctic microbiome

talk

Xu, Ziang

Integrative genomics reveals developmental and cell-type-specific genetic architecture of autism

poster

Xu, Ziang

Multivariate genome-wide investigation uncovers molecular similarities and differences between psychiatric disorders and neurodegenerative diseases

poster

Yagudayeva, Genrietta

A reproducible RNA-seq pipeline for mitogenomics and barcoding phylogenetics in neglected biodiversity

talk

Yang, Tristan

Whole genome sequencing of 434 novel plant root-associated fungi reveals links between genomic content and ecological roles

poster

Yorki, Sosie

Analysis of sequence constraint across Cryptococcus and Kwoniella reveal unannotated regions

poster

Yu, Yun William

Average-case analysis of seed-chain-extend under random mutations

talk

Yu, Zhezhen

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

poster

Zhang, Shilong

A complete and near-perfect rhesus macaque reference genome and its biomedical insights

poster

Zhou, Ying

Characterize the gene associated structure variation in IG and TR regions

poster

Zitnik, Marinka

Empowering biomedical discovery with "AI scientists"

talk

Zunar, Bojan

Comparative CAGE analysis reveals 20 million years of yeast promoter evolution

poster