Presenting Author

Abstract Title

Talk/Poster

Absolon, Dominic

Multi-haplotype curation for high ploidy level plant genomes—The Urtica dioica story

talk

Adams, Jenea I

rMATS-turbo—An efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data

poster

Ahmad, Tanveer

Haplotype-specific karyotypes reconstruction and copy number aberrations/profiling from long reads sequencing data

poster

Ahmed, Omar J

Compressed linear pangenome indexes for more robust read classification

talk

Allert, Mattea

Composition, function and strain-sharing between maternal breast milk and the infant gut microbiome

poster

Almodaresi, Fatemeh B

Long-read sequencing-based pipeline for Neo-epitope candidates for immunotherapeotic targeting of U1 snRNA mutation in cancer

poster

Antipov, Dmitry

Verkko’s approaches for one-button T2T resolution for diploid human-sized genome

talk

Arabzadeh, Mona N

Integrated analysis of imbalanced allelic expression to infer gene regulatory patterns in cancer

poster

Avihai, Byron

Longitudinal single-cell genomic and transcriptomic analysis of relapsed pediatric AML

poster

Baradaran, Morteza

Enhancing pandemic preparedness—A novel partial matching approach for identifying similar genetic material from diverse sources for pathogen surveillance

poster

Bartom, Elizabeth T

Automated cancer cell line validation from sequencing data

poster

Belay, Kassaye H

Enhanced genome-based taxonomy for precise identification of Fusarium pathogens

poster

Blankenberg, Daniel J

Quantum computing comes to the Galaxy

poster

Bradshaw, Michael

What about B.O.B.? Bio-Ontology-Biases—The effects of study bias on less studied groups and classes in knowledge graph embedding methods

poster

Bryant, Asher

Benchmarking long-read somatic structural variant callers on a collection of tumor/normal cell lines

poster

Buen Abad Najar, Carlos F

Reference-free differential isoform analysis using short-read RNA-seq data

talk

Cao, Lei

mEnrich-seq—Methylation-guided enrichment sequencing and novel informatic methods to investigate specific bacterial taxa of interest directly from microbiome

poster

Carey, Vincent

Genome representation in bioconductor

poster

Carpenter, Anne

Functional genomics using image-based profiling—From variant impact to drug screening

talk

Cavalier, Sheridan H

Single-cell, long-read sequencing of the mouse hippocampus reveals learning-induced alternative splicing patterns and transcript isoform expression across cell types

poster

Chao, Kuan-Hao

Splam—A deep-learning-based splice site predictor that improves spliced alignments

poster

Chen, Yuhang

TransferQTL expands existing eQTL catalogs across human tissues

talk

Cheng, Haoyu

Scalable telomere-to-telomere assembly for diploid, polyploid and cancer genomes with double graph

poster

Chikhi, Rayan

Current tools for peta-scale sequence exploration

talk

Choi, Eunwoo

Somatic driver gene alterations are associated with predictive anticancer response and prognostic assessment in pancreatic ductal adenocarcinoma

poster

Choi, Jinmyung

QuadST—A powerful and robust approach for identifying cell-cell interaction changed genes on spatially resolved transcriptomics

poster

Chougule, Kapeel M

Swift pan-genomic methods for comprehensive genome annotation in crop genomes

poster

Clawson, Hiram

GenArk—Towards a million UCSC genome browsers

poster

Coraor, Nathan

Adapting analysis tools to a workflow-centric world

talk

Curry, Kristen

RHEA: Recovering horizontal gene transfer events from metagenome assembly graphs

poster

Dahiya, Daisy

Development of a haplotype-aware assembly pipeline for analysis of rearrangements at the human CYP2D6 locus

poster

Damaraju, Nikhita

Long-read sequencing of 1000 genomes samples to build a comprehensive catalog of human genetic variation

talk

Das, Arun

Diversity and representation of South Asian genomes

poster

Davis, John

Data access architecture at "Galactic" scale—Lessons learned (so far)

poster

Davuluri, Ramana

DNABERT-2—Efficient foundation model for multi-species genomes

talk

Deng, Zhiqian

Capturing and functional annotating the immunoglobulin loci of various species with thrid-generation sequencing

poster

Dias, Paulo J

Graph-based and gene-based pangenome of Lactococcus lactis and Lactococcus cremoris

talk

Diaz Ortiz, Gerardo R

Comparison of 16s rRNA gene sequencing and shotgun metagenomic sequencing for rumen microbiome analysis

poster

Diaz Ortiz, Gerardo R

A metagenomic investigation of the work-related microbiome in US swine workers

poster

Donmez, Ataberk

Strainy—Assembly-based metagenomic strain phasing using long reads

talk

Dubinkina, Veronika

Phylogenetic diversity patterns among gastrointestinal bacterial strains

poster

Eddy, Sean

Computational analysis of RNA structure and function

talk

Eraslan, Basak

PerturbDecode, a probabilistic analysis framework to recover regulatory circuits and predict genetic interactions from large-scale perturbation screens

talk

Erdogdu, Beril

Detecting differential transcript usage in complex diseases with SPIT

poster

Esiri-Bloom, Edward

Investigating the origins and impacts of structural variation and DNA methylation in high-grade serous ovarian cancer

poster

Feng, Xiaowen

Strain-resolution long read metagenome assembly

poster

Frost, Hildreth R

A quaternion model for single cell transcriptomics

poster

Frost, Hildreth R

Reconstruction Set Test (RESET)—A computationally efficient method for single sample gene set testing based on randomized reduced rank reconstruction error

poster

Gao, Teng

Sensitive and specific detection of mosaic chromosomal alterations from large-scale RNA-seq datasets

poster

Ge, Peter

Re-analysis of microbial content found in tumors sequenced by The Cancer Genome Atlas Project

poster

Geraghty, Sara

Integrative computational framework, Dyscovr, links mutated driver genes to metabolic dysregulation across 22 cancer types

poster

Gibson, Sophia B

Haplotype-resolved characterization of repeat expansions and patterns of methylation from 1000 Genomes ONT Consortium data

talk

Gohar, Yomna

Characterizing host-pathogen interaction dynamics for Toxoplasma gondii with single-cell RNA sequencing—A pilot study

poster

Goretsky, Anton

Multi-sample Nanopore sequencing provides insights into melanoma heterogeneity and evolution

poster

Govada, Pravallika

Landscape of differentiation induced oncogenesis regulated by pseudogenes—A neural network based study of gastrointestinal tract

poster

Gulhan, A. Burak

Speeding up whole genome alignment by increasing hardware utilization

poster

Guo, Yujie

Evaluation of haplotype-aware long-read error correction with hifieval

poster

Harazono, Yoritaka

For the development of a PCR primer design pipeline for detection of contamination in foods

poster

Harris, Andrew J

Toward telomere-to-telomere Felid genomes

poster

Hickman, Allison

TEM-seq—An ultrasensitive multiomic platform for epitope-targeted DNA methylation mapping

poster

Hicks, Parker C

Interpretable text-based machine learning for inferring systematic tissue and disease annotations of public transcriptome samples

poster

Holcik, Laurenz

GC-bias aware species abundance estimation from metagenomic data with GuaCAMOLE increases accuracy and comparability

talk

Huang, Neng

Compleasm—A faster and more accurate reimplementation of BUSCO

poster

Huang, Rongting

Computational analysis of copy number variations in spatial transcriptomics data

poster

Husted, Christopher

Environmental and genetic insights into carcinogenesis—An approach using passive sampling and CHIP analysis in the companion dog

poster

Hwang, Stephen

Compressed indexing for pangenome substring queries

poster

Irber Junior, Luiz Carlos

Enabling petabase-scale search of millions of metagenomes with branchwater

talk

Isaev, Karin

Investigating RNA splicing as a source of cellular diversity using a binomial mixture model

poster

Jenike, Katharine M

Panagram—Alignment-free and interactive pan-genome visualization

talk

Kadam, Aditee

Detection, characterization, and prevention of MMEJ deletions

poster

Kamath, Sudhanva S

Telomere-to-telomere genome assembly by preserving contained reads

poster

Katsoula, Georgi

The molecular environment of osteoarthritis risk genes in primary cartilage

talk

Kelso, Janet

Understanding genetic variation in modern and archaic human genomes

talk

Keskus, Ayse

Severus—A tool for automatic characterization of complex germline and somatic rearrangements in cancer using long-read sequencing.

talk

Kim, Daniel

CCSA—Concurrent force-based position solving and quantization for multiple sequence alignment

poster

Kim, Juhyun

Revealing hidden transcripts with a complete reference and personalized transcriptome graph

poster

Kim, Yongjun

MOSCAL—Detection of mosaic variants using linked-read sequencing

poster

Kolora, Rohit

Leveraging public datasets to understand Parkinson's disease progression

poster

Kovaka, Sam

DNA and RNA modification detection via rapid nanopore signal alignment, analysis, and visualization with Uncalled4

talk

Krieger, Teresa G

Gene expression prediction from histopathology images of colorectal cancer

poster

Kucher, Natalie

The NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL)

poster

Kumar, Pankaj

Transcriptome analysis of Helicoverpa armigera (Hubner) (Lepidoptera: Noctuidae) infected with Metarhizium anisopliae

poster

Lariviere, Delphine

Automated reference genome assembly on public infrastructure with Galaxy

poster

Lazareva, Olga

SpaceTree—Deciphering Tumor microenvironments by joint modeling of cell states and genotype-phenotype relationships in spatial omics data

talk

Le, Denise

Exploring functional divergence in paralogs using embeddings from protein language models

poster

Lehner, Ben

Finding all our switches mutating everything to understand allostery

talk

Li, Feng

A fully assembled, phased yucatan reference genome enables accurate on-target and off-target analysis

poster

Li, Qiuhui

Analysis of pancreatic cancer risk variants using long read sequencing

poster

Li, Xiaoxu

Genetic and dietary modulators of the inflammatory response in the gastro-intestinal tract of the BXD mouse genetic reference population

poster

Li, Xiaoxu

Systems genetics of metabolic health in the BXD mouse genetic reference population

poster

Lin, Mao-Jan

Measuring, visualizing and diagnosing reference bias with biastools

poster

Lin, Yixin

Using Better Base Quality (BBQ) to detect low-frequency somatic mutations accurately

poster

Liu, Xiao

DNA bendability regulates transcription factor pioneer binding to nucleosomes

poster

Lou, Shaoke

PathwayGAT—A method to trace back biological interactions from microbes to host phenotypes

poster

Lu, Chenyue

Spatial transcriptomics data analyses revealed cancer-endothelial cell communication in hepatocellular carcinoma

poster

Lu, Jennifer

The Kraken protocol in action—Identifying potential pathogens in Ugandan individuals with unexplained acute febrile illness

poster

Mahmoud, Alexandru

Towards a cloud-agnostic scalable ecosystem for open genomic data science with Bioconductor and Galaxy

poster

Makinen, Veli

Pangenomics with founder sequences and graphs

talk

Malikic, Salem

Robust and scalable intratumor heterogeneity and tumor progression tree inference and assessment through single-cell RNA sequencing data

talk

Manpearl, Keenan

Leveraging representations of multi-species networks and ontologies to improve gene classification

poster

McCarthy, Shane A

Tools and workflows enabling scaling of genome assembly across the Tree of Life

poster

Miga, Karen H

Complete genomes to expand studies of genetic and epigenetic inheritance of centromeres

talk

Mikhalchenko, Aleksei

Understanding and mitigating amplification biases in single-cell DNA sequencing for accurate genotype calling

poster

Minkin, Ilia

Quality assessment of human splice site annotation based on conservation in 470 species

poster

Molik, David

OTB (Only The Best genome assembly tools)—A phased genome assembly nextflow pipeline

poster

Moltke, Ida

Insights into the genetic architecture of diabetes and other complex traits in the Greenlandic population

talk

Morina, Luke B

Cell-type deconvolution with long-read, single molecule methylation

poster

Moustafa, Ahmed M

Redcarpet—A tool for rapid recombination detection amidst expanding genomic databases

poster

Mulaudzi, Shandukani

Improving the accuracy of miro-variant detection in whole genome sequencing data

poster

Musunuri, Rajeeva Lochan

Lancet2—Improved performance and genotyping of somatic variants using localized genome graphs

poster

Nawaz, Urwah

Exploring gene expression properties of the human brain with BITHub

poster

Nazaretyan, Lusine

CADD v1.7—Using protein language models, regulatory CNNs and other nucleotide-level scores to improve genome-wide variant predictions

poster

Nguyen, Eric

Isoform quantitative trait loci analysis of neuropsychiatric disorders in adult brains at single-cell resolution

talk

Nguyen, Matthew

Genomic characterization and global contextualization of ESBL-producing E. coli from pediatric patients in Qatar

poster

Nitzan, Mor

Recovering hidden layers of information in single-cell data

talk

Ojukwu, Christopher E

STIX—A novel approach for comprehensive somatic structural variation detection and gene fusion identification

talk

Pal, Karol

Evolutionary insights into primate sex chromosomes—Sharing and gene content of palindromes

poster

Pani, Samarendra

Giggles—Pangenome-based genome inference using long reads

talk

Park, Dongwoo

Diagnosis of ocular infection using Nanopore metagenomic sequencing

poster

Peng, Pei-Hua

Detection of extrachromosomal DNAs (ecDNAs) in glioblastoma and in-depth investigation of their genome-wide interactions using advanced genome sequencing technology

poster

Perdomo, Jonathan E

ContextSV—A novel computational method for calling structural variants and integrating information across sequencing platforms

poster

Perez Ferandez, Cesar A

The effect of dynamic pressure on the gene expression of Deinococcus radiodurans R1

poster

Pflughaupt, Patrick

Sequence-associated mechanistic insights of DNA fragility

poster

Pietan, Lucas L

Prioritization of fluorescence in situ hybridization (FISH) probes for differentiating primary sites of neuroendocrine tumors with machine learning

poster

Qiu, Weilin

Integrative modeling of activity, responsiveness and contact (ARC) reveals enhancer-gene connections using single-cell data

poster

Rajput, Jyotshna

Co-linear chaining on pangenome graphs

talk

Ramdass, Amanda

Genomic analysis of novel hydrocarbonoclastic Chryseobacterium oranimense strain COTT, a putative bioremediation agent with multi-drug resistance and enzymes for industry

poster

Refahi, Mohammadsaleh

Leveraging large language models for metagenomic analysis

talk

Rivera, Alberto

Deducing the evolution of allorecognition and primordial immunity in Cnidarians

poster

Rosen, Gail

On-going sequencing and analysis of a new tumor cell line for development of a genome in a bottle tumor/normal benchmark

poster

Sakamoto, Yoshitaka

A novel structural variant detection pipeline in cancer genomes—The personalized matched-control reference-based approach

poster

Salick, Max R

Uncovering novel targets in human tuberous sclerosis and non-alcoholic fatty liver disease models by integrating multiomics and automation with pooled optical screening

talk

Salzberg, Steven

Major data analysis errors invalidate cancer microbiome findings

talk

Samart, Kewalin

Integrating multiple transcriptome-based methods to repurpose drugs for infectious diseases

poster

Sanchez, Sydney

Identifying niche-specific genetic adaptations in Acinetobacter baumannii

poster

Savage, Michelle

Biomedical and biological applications of machine learning using Galaxy Project

poster

Schiebout, Courtney T

Cell type-specific interaction analysis using doublets in scRNA-seq (CIcADA)

talk

Schneider, Kristen

Querying biobank-scale genomes to rapidly identify genetically matched cohorts

talk

Scott, Lucy

Cell lineage inference using patterns of DNA damage

poster

Segal, Eran

Personalized medicine based on deep human phenotyping

talk

Seitz, Evan

A surrogate modeling framework for interpreting deep neural networks in functional genomics

poster

Sen, Shurjo K

Democratizing access to genomics and data science education through the cloud—The GDSCN success story

poster

Serajian, Mohammadali

Classification of antibiotic resistance of Mycobacterium tuberculosis via linear and non-linear machine learning

poster

Shaw, Jim

Ultrafast, coverage-corrected genome similarity queries for metagenomic shotgun samples with sylph

talk

Shinder, Ida

EASTR—Identifying and eliminating systematic alignment errors in multi-exon genes

poster

Shiraishi, Yuichi

Precise characterization of somatic complex structural variations from tumor/control paired long-read sequencing data with nanomonsv

poster

Shiraishi, Yuichi

Systematic discovery of splice-site creating variants from massive publicly available transcriptome sequencing data

poster

Shivakumar, Vikram

Sigmoni—Classification of nanopore signal with a compressed pangenome index

poster

Shooshtari, Parisa

Assessing performance of supervised and unsupervised cell type labeling algorithms for cancer scRNA-seq data

talk

Shumate, Alaina

Claspy—Cell line authentication with STRs in Python

poster

Sikic, Mile

AI approach for de novo genome assembly

poster

Silk, Ryan P

Mitochondrial mutation and dysfunction in high grade serous ovarian cancer

poster

Simpson, Jared

Calling somatic mutations from long read tumors without matched normal samples

talk

Sims, Ying

TreeVal—Data generation for the curation of chromosome-scale genomes

poster

Singh, Amartya

Simplifying and improving single-cell gene expression analysis with Piccolo

poster

Solar, Steven J

TrioKala—A trio co-assembly approach for de novo variant detection

poster

Song, Li

Centrifuger—Lossless compression of microbiome genomes for efficient and accurate metagenomic sequence classification

talk

Standage, Daniel

MicroHapDB—A comprehensive catalog of human microhaplotype variation

poster

Stastny, Tiana H

CRISPRsc—Pooled CRISPR screening with single-cell transcriptome resolution

poster

Steenwyk, Jacob L

Innovation, constraint, and the evolution of genetic networks in major eukaryotic lineages

poster

Sun, Shixiang

SomaMutDB—A database of somatic mutations in normal human tissues

poster

Surana, Pallavi

Investigation of tissue-specific transcriptome at isoform-level in GTEx and TCGA datasets

poster

Sweeten, Alexander

ModDotPlot—A rapid and interactive visualization of tandem repeats

poster

Sztanka-Toth, Tamas Ryszard

Estimating background protein signals to enhance data normalization in CITE-Seq

poster

Tan, Luomeng

New computational methods for the analysis of transcription factor CUT&RUN data

poster

Tanay, Amos

Spatio-temporal quantitative models for embryonic development

talk

Teer, Jamie K

Less is more—Trimming long massively parallel sequence reads can improve mapping rates and depth of coverage

poster

Thai, Christopher

Guiding single-cell RNA-seq clustering with rank-based metrics

poster

Theiller, Erin M

Empowering global disease surveillance—The CURED tool for rapid identification of unique clonal biomarkers

talk

Trang, Khanh B

3D genomic features across >50 diverse cell types reveal insights into the differing genomic architectures of BMD determination and osteoporotic fracture pathogenesis

talk

Tutaj, Monika

Variant analysis in an inbred rat population—A lesson from the Hybrid Rat Diversity Panel

poster

Vaddadi, Naga Sai Kavya

Minimizing reference bias with an impute-first approach

talk

Varki, Rahul

MONI-Align—An r-index based pangenomics aligner

talk

Verburg, Jan C

Accurate comparison of insertion and deletion mutation rates using sequence composition correction with novel sequence ambiguity scoring

poster

Volden, Roger

Pbfusion—Detecting gene fusions and other transcriptional abnormalities using PacBio HiFi data

poster

Wright, Adam J

FAIR Bioheaders—Fair Header Reference genome (FHR)

poster

Xu, Zhuwei

Examining chromatin heterogeneity through PacBio long-read sequencing of M.EcoGII methylated genomes—An m⁶A detection efficiency and calling bias correcting pipeline

poster

Yan, Guanao

scReadSim—S single-cell RNA-seq and ATAC-seq read simulator

poster

Yang, Lixing

SFyNCS detects oncogenic fusions involving non-coding sequences in cancer

poster

Yang, Weiwei

A metagenomics genome-phenome association (MetaGPA) study reveals 2-aminoadenine (dZ) biosynthetic pathway in unculturable phage metagenome

poster

Yao, Yuelin

Stator---High order expression dependencies finely resolve cryptic states and subtypes in scRNA-seq data

poster

Zakeri, Mohsen

Real-time nanopore adaptive sampling with Movi

talk

Zeggini, Eleftheria

Translational genomics of complex disease

talk

Zhao, Yixin

Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells

poster

Zheng, Xinchang

Investigating mosaic structural variations across thousands of genomes with STIX

poster

Zimin, Alexey

Data beats machine learning for genome annotation

poster