|
Presenting Author |
Abstract Title |
Talk/Poster |
|
Ahmed, Omar J |
Pan-genomic indexes for robust classification of nanopore and metagenomics reads |
talk |
|
Akagi, Keiko |
Resolution of genomic structural variation at the MYC locus “hotspot” for human papillomavirus (HPV) integration in human cancers |
poster |
|
Alam, Aqsa S |
Deep representation learning to predict function in non-coding regulatory regions |
poster |
|
Alvarez Jarreta, Jorge |
Deep learning homology relationships in an ever-growing environment |
talk |
|
Andreu Sanchez, Sergio |
Genetic, parental and lifestyle factors influence telomere length |
poster |
|
Baali, Ilyes |
Predicting in-vivo binding preferences of RNA-binding proteins using transfer learning |
poster |
|
Baghela, Arjun |
Predicting sepsis severity at first clinical presentation—The role of endotypes and mechanistic signatures |
poster |
|
Baker, Daniel N |
Dashing2—Scalable and flexible similarity search for genomic collections using locality-sensitive hashing and the SetSketch |
talk |
|
Balliu, Brunilda |
Fast and powerful statistical method for context-specific eQTL mapping in multi-context genomic studies |
talk |
|
Barreira, Sofia |
Determining the evolution history of the metazoan nucleolar transcription factor and its contribution to regeneration |
poster |
|
Behera, Sairam |
Comprehensive genomics at scale using DRAGEN pipeline |
poster |
|
Berk, Katrin |
Functionalization, adaptation and gain/loss dynamics of human de novo genes |
poster |
|
Blaxter, Mark |
Telomere to telomere genomes across the Tree of Life |
talk |
|
Bollas, Audrey E |
A machine learning approach to detect somatic variants in tumor RNA-Seq |
poster |
|
Bradshaw, III, Michael |
CNViz—A tool for the integration and visualization of multiple CNV callers |
poster |
|
Brechtmann, Felix |
A rare variant risk score (RVRS) and its utility for gene prioritization |
poster |
|
Bretschneider, Hannes |
A splicing code reveals an expanded landscape of brain microexons with direct genetic links to autism |
talk |
|
Brover, Vyacheslav |
Novel tool to build large phylogenetic trees with applications to NCBI genomes and rRNA sequences |
poster |
|
Brown, Stuart L |
Complex structural variants in high grade serous ovarian cancer |
poster |
|
Cain, Scott |
JBrowse 2—A data visualization platform with special features for comparative genomics and structural variant visualization |
poster |
|
Callejas Hernandez, Francisco |
Long-read and Hi-C sequencing of a bird parasite closely related to the human sexually transmitted parasite Trichomonas vaginalis for accurate transposable element assembly |
poster |
|
Canzar, Stefan |
Ladder-seq partitions RNA-seq reads to improve transcriptome reconstruction and reveals a critical role of m6A as a regulator of alternative splicing in neural progenitor cells |
talk |
|
Celik, Muhammed Hasan |
Analysis of alternative polyadenylation from long-read or short-read RNA-seq with LAPA |
poster |
|
Chen, Chujia |
Marker-assisted mapping enables forward genetic analysis in Aedes aegypti, an arboviral vector with vast recombination deserts |
poster |
|
Chen, Nae-Chyun |
Fast and accurate coordinate conversion between assemblies |
poster |
|
Chen, Yang |
DiffChIPL: A Differential binding analysis method based on limma for ChIP-seq data featuring biological replicates |
poster |
|
Chen, Ying |
A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines |
poster |
|
Cheng, Haoyu |
Robust haplotype-resolved assembly of diploid individuals without parental data |
talk |
|
Chin, Jason |
Boosting GWAS sensitivity and computational efficiency with word embedding vectors |
poster |
|
Choi, Jinlyung |
MTxQC—Flexible and automatic metagenomics/metatranscriptomics quality control service for Next Generation Sequencing(NGS) shotgun sequencing data in AWS cloud |
poster |
|
Chougule, Kapeel M |
Identifying protein coding genes in Maize using a hybrid annotation workflow |
poster |
|
Chu, Justin |
Sequence classification of short read sequence data to the of complex regions in the Human Pangenome |
poster |
|
Colomé-Tatché, Maria |
Analysis and integration of single cell epigenomics data |
talk |
|
Conesa, Ana V |
Combining long-read and single-cell RNA-seq to infer isoform co-expression networks reveals splicing regulation as a key determinant in cell type identity |
talk |
|
Cook, Daniel E |
DeepConsensus—Using transformers for long-read consensus generation |
poster |
|
Darmofal, Madison |
Clinically-implemented targeted genomic panels support better tumor type classification than pre-clinical technologies |
poster |
|
Das, Arun |
Analysis of sketching and sampling approaches for fast and accurate long read classification |
poster |
|
De La Vega, Francisco |
Accurate germline variant calling from RNA-seq data using deep learning |
poster |
|
Desai, Jairav |
The Precision Health Cloud—Tackling the challenges of big data in precision medicine |
poster |
|
Duncan, Andrew |
Sequence features distinguish STARR-seq enhancer activity from activity in a native chromatin context |
poster |
|
Engelhardt, Barbara |
Structured dimension reduction for single cell observations |
talk |
|
Feng, Xiaowen |
Metagenome assembly with Hifi reads |
talk |
|
Fischer, Stephan |
Performance curvature meta-analysis characterizes the generalizability of computational inference of gene function |
poster |
|
Franklin, Samuel J |
Short tandem repeat characterization in a cohort of rare diseases families |
poster |
|
Gagalova, Kristina |
Genome size expansion in the North American forest pest, Pissodes strobi, and evidence of a Wolbachia endosymbiont |
poster |
|
Ghotra, Rohan S |
Interpreting motif interactions from self-attention-based networks for regulatory genomics |
poster |
|
Goktas, Talha Murathan |
LINKS 2.0—Optimized alignment-free and scalable de novo genome scaffolding with long reads |
poster |
|
Gonzalez, Josefa |
Population-scale long-read sequencing uncovers transposable elements contributing to gene expression variation and adaptation in Drosophila |
talk |
|
Goodman, Jack |
Estimation of metabolic activity profiles across tissues of origin via aggregate and single-cell RNA-seq improve survival prediction |
poster |
|
Green, Anna G |
Genome-wide detection of mutational dependence in naturally evolving Mycobacterium tuberculosis populations |
talk |
|
Greenberg, Grant |
A TNF-based orientation test to improve bacterial genome assembly |
poster |
|
Groza, Cristian |
Genome graphs detect human mobile element polymorphisms in active epigenomic states |
poster |
|
Guijarro, Cristina |
Ensembl comparative genomic resources—Supporting large scale genome sequencing projects |
poster |
|
Hafezqorani, Saber |
ntEmbd—Deep learning embedding for nucleotide sequences |
poster |
|
Haghani, Viktoria |
Rocketchip—A comprehensive bioinformatics workflow for ChIP-seq data analysis |
poster |
|
Halabian, Reza |
DNA transductions mediated by non-LTR retroelements in the complete human genome (T2T-CHM13) |
poster |
|
Harrigan, Caitlin |
Dirichlet allocation of mutations as a function of both damage and DNA repair |
talk |
|
Harris, Benjamin |
A meta-analytic single-cell atlas of mouse bone marrow hematopoietic development |
poster |
|
He, Zitong |
Predicting alternative splicing regulation and the effects of sequence variation with a Probabilistic Deep Learning model |
poster |
|
Heidari, Elyas |
Spatial reconstruction of dissociated single-cell data using graph neural networks |
talk |
|
Hitz, Benjamin C |
Functional impact of genomic variation—The latest consortium for functional genomics |
poster |
|
Holmes, Edward |
Viral metagenomics at the human-animal interface |
talk |
|
Hu, Zhiqiang |
Biological discovery and consumer genomics activate latent privacy risk in functional genomics data |
poster |
|
Huang, Yue |
Increased burden of somatic mutations in Alzheimer’s disease revealed by single neuron whole-genome sequencing |
talk |
|
Imami, Ali S |
BORE—Detecting RNA editing events comfortably |
poster |
|
Iqbal, Zamin |
Variant analysis in bacterial pan-genomes---New solutions and open problems |
talk |
|
Jenike, Katharine M |
HetTrek—Improving assembly accuracy and contiguity of highly heterozygous genomes |
poster |
|
Jimenez-Barron, Laura T |
Identification of in vitro model systems capable of capturing the polygenic basis of mental illness |
poster |
|
Jin, Xiaofan |
Phylogenetic models identify genetic basis of spatial structure in microbial communities |
poster |
|
Kamps-Hughes, Nicholas |
Sensitive detection of pathogenic splice variants from human blood samples |
poster |
|
Kaphle, Anubhav |
A better model for SNP-heritability and genomic prediction |
poster |
|
Karbalayghareh, Alireza |
Chromatin interaction aware gene regulatory modeling with graph attention networks |
talk |
|
Katz, Samuel |
An integrated method for gene prioritization and a statistical model for isoform ratios reveal splice variant selectivity as a critical regulator of the macrophage inflammatory state |
poster |
|
Kawaji, Hideya |
Unified identification of transcribed cis-regulatory elements |
talk |
|
Kempa, Dominik |
Speeding up the construction of pangenome data structures |
talk |
|
Khan, Samin R |
A deep learning model reveals sequence signatures associated with DNA bendability and links bendability-altering mutations with aberrant chromosomal conformation |
poster |
|
Kim, Sandy S |
Model-driven optimization of high-throughput in vivo CRISPR screen design |
poster |
|
Kinney, Justin B |
Learning genotype-phenotype maps from multiplex assays of variant effect using neural networks |
poster |
|
Kirsche, Melanie |
Jasmine—Population-scale structural variant comparison and analysis |
poster |
|
Kosiol, Carolin |
Genome-wide estimation and dating of species trees—Polymorphism-aware phylogenetic models meet RevBayes |
poster |
|
Kovaka, Sam |
Visualization and analysis of nanopore RNA and DNA signal alignments for modification detection, polishing, enrichment, and more with Uncalled4 |
poster |
|
Kucukural, Alper |
Dmeta—Automated data processing and management using ontology-based metadata tracking system |
poster |
|
Kulman, Ethan |
Pairtree—Accurate reconstruction of cancer evolution using bulk DNA samples |
poster |
|
Kumar, Vivek |
From sequences to functional-, comparative- and meta- genomics: Advancing systems biology of plants, microbes and their communities in KBase |
poster |
|
Labelson, Ethan L |
Towards reliable explanations of deep neural network predictions in regulatory genomics |
poster |
|
Ladewig, Erik |
Mutations in FOXA1 alter chromatin remodeling and cell fate in prostate organoids |
poster |
|
LaHaye, Stephanie D |
EnFusion—Discovery of clinically relevant fusions in pediatric cancer |
poster |
|
LaPierre, Nathan |
Accounting for isoform expression in eQTL mapping |
poster |
|
Lariviere, Delphine |
Enabling widespread use of Vertebrate Genome Project assembly pipeline by integration into Galaxy |
poster |
|
Lee, Nicholas |
Representation learning of genomic sequence motifs via information maximization |
poster |
|
Leslie, Christina S |
Advances in predictive models for regulatory genomics |
talk |
|
Li, Xuechan |
Robust explainable method to identify immune-related genes that predicts cancer survival |
poster |
|
Li, Yue |
Transfer learning of interpretable cellular and gene signature embeddings from single-cell transcriptomic data in diverse conditions |
poster |
|
Liebhoff, Anna |
Computational prediction of epitopes from protein sequences |
poster |
|
Lin, Mao-Jan |
Profiling germline adaptive immune receptor repertoire with gAIRR Suite |
poster |
|
Lin, Michael |
SQLite—Grand unified genomics file format? |
poster |
|
Lind, Abigail |
Eukdetect: Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing |
poster |
|
Linderman, Michael |
Machine-learning approaches to structural variant genotyping in whole genome sequencing data |
poster |
|
Listgarten, Jennifer |
Machine learning-based design of proteins |
talk |
|
Lu, Alex X |
Discovering molecular features of the intrinsically disordered proteome by using evolution for contrastive learning |
poster |
|
Lyudovyk, Olga |
Deep Learning model of T-cell recognition of antigens and its applications in cancer |
poster |
|
Madden, Tom |
Cloud-based BLAST resources from the NCBI |
poster |
|
Mahmoud, Medhat |
Long read based identification of HPV integration mediated molecular structure |
poster |
|
Manske, Felix |
High-performance microbiome analysis with MetaG |
poster |
|
Manukyan, Artur |
Dprofiler—A comparative profiling platform for diseases, phenotypes and experimental conditions |
poster |
|
Marschall, Tobias |
Structural variation and pangenome-based genome inference |
talk |
|
Minto, Melyssa S |
Beyond PWMs—Modeling sequence in context to reveal the multimodality of transcription factor binding and activity |
poster |
|
Mokrab, Younes |
Analysis of Qatari population genomes and transcriptomes provides novel insights into functional consequences of Middle Eastern genetic variation and their impact on human traits and disease |
poster |
|
Mokrab, Younes |
Ancestry prediction in Middle Eastern populations using deep neural networks |
poster |
|
Mokrab, Younes |
Thousands of Qatari genomes inform human migration history and improve imputation of Arab haplotypes |
poster |
|
Mokrab, Younes |
Using long-reads sequencing and optical mapping to generate genome references for Arab populations |
poster |
|
Moreland, Blythe S |
Information theoretic analysis of synonymous codon usage offers metrics to assess constraint on synonymous variants |
poster |
|
Morgan, Mike |
Milo—Differential cell state abundance testing using kNN-graphs |
talk |
|
Muralidharan, Harihara Subrahmaniam |
Comparative metagenomic genome analysis of Synechococcus spp. in microbial mats across a temperature gradient in hot springs from Yellowstone National Park |
poster |
|
Nachmanson, Daniela |
Characterization of genetic heterogeneity and clonal evolution in ductal carcinoma in situ |
poster |
|
Narechania, Apurva |
Is your species like my species? Using Hill numbers to quantify taxonomic diversity |
talk |
|
Nash, Eric B |
Tools to facilitate student metabarcoding research |
poster |
|
Navarro Gonzalez, Jairo |
UCSC Genome Browser in the cloud |
poster |
|
Ni, Bohan |
Modeling the effects of rare structural variants on gene expression across multiple tissues |
poster |
|
Nurk, Sergey |
Telomere-to-telomere assembly of human chromosome Y |
poster |
|
Oguz, Cihan |
High throughput sequencing of T and B cell receptors in healthy controls, and MIS-C and COVID-19 patients reveals predictive immune repertoire and HLA restriction signatures |
poster |
|
Olson, Andrew |
TBrowse—A modular gene tree viewer for exploring functional conservation |
poster |
|
Otero Bravo, Alejandro |
Additional filtering for somatic variants derived from FFPE tumor samples |
poster |
|
Pagadala, Meghana |
Germline variants that influence the tumor immune microenvironment also drive response to immunotherapy |
poster |
|
Penaloza, Jacqueline S |
Analysis of copy number variants in more than 1,300 patients with congenital heart disease |
poster |
|
Perez Fernandez, Cesar A |
Microbial endolithic communities are resilient to dramatic changes in humidity and temperature at the Atacama Desert, Chile |
poster |
|
Phillippy, Adam M |
The complete sequence of a human genome |
talk |
|
Pipes, Lenore |
Estimation of the composition of SARS-CoV-2 lineages in wastewater surveillance samples |
poster |
|
Prinster, Andrew J |
Assessing statistical significance and confidence of exogenous read taxonomic assignments and quantifications in exceRpt, the extracellular RNA sequencing pipeline |
poster |
|
Przytycki, Pawel F |
CellWalker integrates single-cell and bulk data to resolve regulatory elements across cell types in complex tissues |
poster |
|
Qiao, Jingping |
Evolutionary history and molecular heterogeneity of primary breast cancer |
talk |
|
Ramakrishnan, Srividya |
Reconstructing the genome of the living fossil conifer Wollemia nobilis using ONT long-read sequencing technology |
poster |
|
Ramos, Enrique I |
Functional characterization of estrogen-regulated divergent long noncoding RNAs in estrogen receptor-positive breast cancer |
poster |
|
Rao, Jingyou |
Quantifying uncertainty in estimation of isoform expression heritability |
poster |
|
Redekar, Neelam R |
Multiomics integration to investigate the role of insulin within energy dysregulation in Hepatitis C and associated liver disease |
poster |
|
Reisinger, Raquel M |
Data mining pedigrees with Probabilistic Graphical Models (PGMs)—A new tool for genetic disease discovery |
poster |
|
Rhie, Arang |
Merfin—Improved variant filtering and polishing via k-mer validation |
poster |
|
Rich, April A |
Exploring the unknown translatome using massively integrated coexpression analysis |
poster |
|
Richardson, Mary O |
A computational method to detect non-canonical translation events from Ribo-seq data |
talk |
|
Rodriguez, Matias |
Comprehensive analysis of transposable elements in 65 Apicomplexa genomes |
poster |
|
Rossi, Massimiliano |
MONI-align—A Pangenomics read aligner |
poster |
|
Rozowsky, Joel |
Integrative tools for the analysis of allele-specific behavior in multiple human tissues |
poster |
|
Saheb Kashaf, Sara M |
Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions |
poster |
|
Salmela, Leena |
Paired de Bruijn graphs meet viral quasispecies assembly |
talk |
|
Samartin Botezelli, Vitoria |
In embryo and in silico mapping of gene regulatory networks during commitment of sensory neurons |
poster |
|
Saunders, Christopher T |
Rapid and accurate genome-wide STR catalog genotyping |
poster |
|
Schatz, Michael |
Modeling the computing requirements and costs for genomics analysis in the cloud |
poster |
|
Scheben, Armin |
Long-read sequencing reveals rapid evolution of immunity- and cancer-related genes in bats |
poster |
|
Schneider, Kristen |
Enabling biobank-scale GWAS data sharing with efficient compression and indexing |
poster |
|
Schuetz, Robert |
Evaluation and optimization of a clinical support algorithm for rapid identification of pathogenic variants |
poster |
|
Sedlazeck, Fritz J. |
A genomic structural variant map of 945 Han Chinese individuals using long-read sequencing data |
poster |
|
Shafin, Kishwar |
Accurate small and structural variant calling with nanopore long-read sequencing data |
talk |
|
Shulgina, Yekaterina |
A computational screen for alternative genetic codes in over 250,000 genomes |
talk |
|
Silk, Ryan P |
Mitochondrial dysfunction and dynamics in high grade serous ovarian cancer |
poster |
|
Sim, Andre D |
Context-aware quantification of transcript expression with long read RNA-seq |
poster |
|
Singh, Kritika |
Investigating the shared functional biology of major depressive disorder and coronary artery disease reveals immune and inflammatory markers as a possible driver of the comorbidity |
poster |
|
Singhal, Pankhuri |
Genome-wide inter-chromosomal epistatic associations identified across complex diseases in ~300,000 participants from eMERGE and UK Biobank |
poster |
|
Smith, Jonathan T |
A 20x yield increase in accurate, full-length RNA sequencing data |
talk |
|
Stark, William |
A machine learning approach to gene symbol assignment |
poster |
|
Teer, Jamie K |
Workflow for all vs. all genotype comparison for quality control of massively parallel DNA and RNA sequencing data |
poster |
|
Thibaud Nissen, Francoise |
New developments in PGAP and RAPT—H\how you can produce a richer gene annotation for bacterial and archaeal isolates even faster |
poster |
|
Thybert, David |
Scaling whole-genome multiple alignment resources in Ensembl |
poster |
|
Tilgner, Hagen U |
Brain Isoforms in time, space and single cells |
talk |
|
Tseng, Elizabeth |
Allele-specific, isoform-resolution single-cell RNA-seq analysis using long read sequencing on concatenated single-cell molecule |
talk |
|
Vorperian, Sevahn K |
Cell types of origin in the cell free transcriptome in human health and disease |
poster |
|
Wagner, Nils |
Aberrant splicing prediction across human tissues |
poster |
|
Wang, Xiaotao |
Genome-wide detection of enhancer-hijacking events from chromatin interaction data in rearranged genomes |
poster |
|
Wei, Xiaoran |
DNA methylation regulates TrkB isoform expression in CNS |
poster |
|
Weissensteiner, Matthias H |
Motifs with non-B DNA forming potential affect accuracy and yield of major sequencing technologies |
poster |
|
West, Sean |
A comparison of RNA secondary structure prediction tools |
poster |
|
Wheeler, Gregory L |
A combined ensemble and machine learning method for improved accuracy of structural variant detection |
poster |
|
Wu, Thomas |
Transcriptome-guided genomic alignment |
poster |
|
Xiao, Chunlin |
Development and benchmarking of a SARS-CoV-2 Oxford Nanopore variation calling workflow |
poster |
|
Xue, Bingjie |
BEDbase—A unified platform and API for genomic region sets |
poster |
|
Yankee, Tara |
Transcriptome dynamics of developing human face reveal candidate disease genes |
talk |
|
You, Yupei |
NanoSplicer—Accurate identification of splice junctions using Oxford Nanopore sequencing |
poster |
|
Zarate, Samantha |
A complete reference genome improves analysis of mapping and variant calling across populations |
talk |
|
Zhang, Haowen |
Fast alignment and preprocessing of chromatin profiles with Chromap |
poster |
|
Zhang, Haowen |
Real-time mapping of nanopore raw signals |
poster |
|
Zimin, Alexey |
A reference-quality, fully annotated genome from a Puerto Rican individual |
poster |