|
Presenting Author |
Abstract Title |
Talk/Poster |
|
Abdilleh, Kawther |
Large-scale cloud-based inference of differential breast cancer-related network gene hubs between patient cohorts |
poster |
|
Aboukhalil, Robert |
Supercharge genomics web applications with biowasm |
talk |
|
Adeluwa, Temidayo P |
Predicting drug-induced liver injury with machine learning incorporating a diverse set of public datasets |
poster |
|
Aggarwal, Manu |
The functional significance of topological features from large-scale biological datasets |
poster |
|
Aguilar, Robin D |
Tigerfish―A tool for designing oligo probes against satellite DNA genome wide |
poster |
|
Anekalla, Kishore R |
Juvenile alveolar epithelial cells have a delayed transcriptional response following Influenza A virus infection |
poster |
|
Aounallah, Khaled |
Ancestry-specific genomic multi-dimensional scaling |
poster |
|
Argelaguet, Ricard |
MOFA+―A statistical framework for comprehensive integration of multi-modal single-cell data |
poster |
|
Baker, Daniel N |
Scalable single-cell RNA-seq clustering with model-based distances |
poster |
|
Bandoy, Darwin R |
Deconvolution of clonal interference by D614G mutation in Sars-CoV-2 using Monte Carlo and epidemic modelling |
talk |
|
Bentsen, Mette S |
TOBIAS―An ATAC-seq footprinting tool to reveal dynamics of transcription factor binding |
poster |
|
Berg, Jordan |
Gazing into the metaboverse―Automated exploration and contextualization of metabolic data |
talk |
|
Bernstein, Matthew N |
CellO―Comprehensive and hierarchical cell type classification of human cells with the Cell Ontology |
poster |
|
Bhogale, Shounak |
Thermodynamics-based model of the "Transcription Factor Collective” mechanism reveals cis-regulatory code of mesoderm development in Drosophila |
poster |
|
Bollas, Audrey |
Accurate ancestry inference using gnomAD and 1000 Genomes datasets |
poster |
|
Bonneau, Richard A |
Combining spatial genomics and imaging data―Comparing multiple machine learning approaches |
talk |
|
Boucher, Christina |
Building an index for a large number of genomes |
talk |
|
Buen Abad Najar, Carlos F |
Coverage-dependent bias creates the appearance of binary splicing in single cells |
poster |
|
Burel, Jean-Marie |
Reusable analytical workflows for public bioimaging data in cloud-based environments |
poster |
|
Bzikadze, Andrey |
Human centromeres―From first automated assemblies to structural characterization and evolution |
poster |
|
Campbell, Kieran |
Probabilistic machine learning to automate cell identity inference across single-cell technologies |
talk |
|
Cauer, Alexandra G |
A multiresolution optimization strategy for inferring 3D genome architecture from Hi-C data |
poster |
|
Chamberlin, John |
Gene-level detection bias confounds biological interpretation of single-nucleus RNA-seq experiments |
talk |
|
Chang, Weizhong |
DAVID update―Expanded knowledgebase and analysis tools for the functional annotation of gene lists |
poster |
|
Chen, Chao |
Topology-preserving deep image segmentation and generation for fine-scale biomedical structures |
poster |
|
Chen, Nae-Chyun |
Improving variant calling using population data and deep learning |
poster |
|
Chen, Shang-Yang |
MAGNET---Macrophage Annotation of Gene Network Enrichment Tool |
poster |
|
Chen, Shuonan |
BARcode DEmixing through Non-negative Spatial Regression (BarDensr) |
talk |
|
Chen, Yun-Ching |
Changes in peripheral methylome and brain development are associated with symptom changes in attention deficit hyperactivity disorder (ADHD) |
poster |
|
Chhatbar, Kashyap |
Quantitative analysis questions the role of MeCP2 as a global regulator of alternative splicing |
poster |
|
Choudhary, Krishna |
Probability distributions of single-cell mRNA and protein counts derived by solving urn models for stochastic gene expression |
poster |
|
Chougule, Kapeel M |
Moving from a single maize genome to population-based references assemblies of plants and exploring its gene space using Gramene comparative genomics platform |
poster |
|
Conard, Ashley M |
TIMEOR―A web-based tool to uncover temporal regulatory mechanisms from multi-omics data |
talk |
|
Cresswell-Clay, Evan |
Large-scale phylogenetic prediction of protein contact networks |
poster |
|
Das, Arun |
Analysis of sketching and sampling approaches for fast and accurate read classification |
poster |
|
Davila, Jaime I |
Mutational signatures from clinical genomic panels elucidate origins of hyper-mutated tumors of unknown primary |
poster |
|
Davis, Phillip E |
A continuous featuring engineering and explanatory modeling paradigm for data-mining genomics data |
poster |
|
Davis-Marcisak, Emily F |
Matrix factorization of single-cell RNA-sequencing identifies immune cell states that project across species, cancer type, and infectious disease |
poster |
|
Daw, Joyjit |
A deep learning framework for genomic read variation analysis |
poster |
|
Dibaeinia, Payam |
SERGIO―A single-cell expression simulator guided by gene regulatory networks |
poster |
|
Dobin, Alexander |
STARsolo―Ultra-fast comprehensive single-cell RNA-seq quantification beyond gene expression |
poster |
|
Doing, Georgia |
De-noising autoencoder-derived gene expression signatures for Pseudomonas aeruginosa elucidate virulence-promoting characteristics of ex vivo sputum from persons with cystic fibrosis |
poster |
|
Dyjack, Nathan |
Robust multinomial-based distance metrics for scRNA-seq data |
poster |
|
Egieyeh, Samuel |
Molecular and mechanistic insight into the varied rate of metabolism by allele of CYP3A4 enzyme |
poster |
|
Ewing, Ailith |
Integrative analysis of novel genomic and transcriptomic datasets from high grade serous ovarian cancer reveals structural variants at BRCA1/2 are a common source of homologous repair deficiency |
poster |
|
Fansler, Mervin M |
A rapid pipeline to detect and quantify differential 3’ UTR isoform usage in single-cell RNA-seq |
poster |
|
Farmer, Rohit |
Stim Cell Selector―An R package for the identification of responding cells in cytometry stimulation assays |
poster |
|
Fischer, Stephan |
Quantifying tradeoffs in the transcriptional definition of cell types |
poster |
|
Fitzgerald, Donnacha |
Single-cell multi-omics captures the inter and intra-tumor heterogeneity of nodal B-cell non-Hodgkin lymphomas. |
poster |
|
Forbes, Kwame K |
Integration of preprocessed single-cell datasets with bulk differential analysis results for DESeq2 |
poster |
|
Foroughi pour, Ali |
Interpreting deep learning features via integrative analysis with gene expressions |
poster |
|
Frise, Erwin |
Artificial intelligence-driven scoring of structural variations for the diagnosis of rare genetic disease from genome sequencing |
poster |
|
Gabel, Alexander |
Normalization of comparative transcriptomics data across species and organs |
poster |
|
Gerstein, Mark |
Abstract |
talk |
|
Gharavi, Erfaneh |
Embeddings of genomic region sets capture rich biological associations in low dimensions |
poster |
|
Gosline, Sara JC |
Employing a hybrid graph reduction and community detection algorithm on multi-graphs to identify disease-specific pathway signatures in cancer |
poster |
|
Han, Jungmin |
Using scientific machine learning to infer a mechanistic gene network from spatiotemporal single cell data |
poster |
|
Hansen, Nancy |
SVanalyzer―Sequence similarity-aware tools for accurate representation and comparison of genomic structural variants |
poster |
|
Hao, Yuhan |
Multi-modal representation and mapping of single-cell data |
talk |
|
Harris, Benjamin |
Multiscale co-expression in the brain |
poster |
|
Harrow, Jennifer |
ELIXIR―Establishing a sustainable infrastructure for managing and analysing distributed data at scale |
talk |
|
He, Di |
A cross-level information transmission network for predicting phenotype from new genotype―Application to cancer precision medicine |
poster |
|
Heil, Benjamin J |
Integrating tools and practices to make computational research reproducible |
poster |
|
Hicks, Stephanie C |
Scaling up single-cell data analyses in Bioconductor |
talk |
|
Hippen Anderson, Ariel A |
Quality control for single-cell RNA-seq data through Bayesian inference |
talk |
|
Holmes, Ian |
JBrowse 2 visualizes synteny and structural variation |
talk |
|
Hu, Minjie |
Lineage dynamics of the endosymbiotic cell type in the soft coral Xenia |
poster |
|
Jain, Chirag |
Accurately mapping long reads to highly repetitive reference sequences |
talk |
|
Joglekar, Anoushka |
Cell type signatures of brain-region specific splicing in postnatal development |
poster |
|
Johansen, Nelson |
Deconvolving multi-modal assays to uncover associations in spatial and neuro-electrophysiological data modalities |
poster |
|
Kahles, Andre |
MetaGraph―Representing sequence data at petabase-scale |
talk |
|
Kaminow, Benjamin |
The pan-human consensus performs best for RNA-seq alignment |
poster |
|
Kancherla, Jayaram |
Hierarchical interactive exploration and analysis of single cell RNA-seq datasets |
poster |
|
Kapourani, Chantriolnt-Andreas |
scMET―Bayesian modelling of DNA methylation heterogeneity at single-cell resolution |
poster |
|
Kindt, Alida |
Implementing disease-specific biomarkers for early detection of bronchopulmonary dysplasia |
poster |
|
Kirsche, Melanie |
Jasmine―Fast and accurate structural variant comparison across many individuals |
poster |
|
Knight, Spencer C |
COVID-19 susceptibility and severity risk modeling in over 500,000 individuals |
talk |
|
Koch, Clarissa M |
Time course analysis of gene expression following influenza infection reveals pathways associated with lung damage |
poster |
|
Koo, Peter |
Can we trust deep learning predictions in genomics? |
poster |
|
Kota, Pavan K |
Towards highly efficient pathogen diagnostics with compressed sensing and microfluidic cell capture |
poster |
|
Kovaka, Sam |
Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED |
poster |
|
Kreshuk, Anna |
Image segmentation at scale |
talk |
|
Krishnan, Arjun |
Harmonizing millions of transcriptomes by imputing unmeasured genes and predicting sample sources |
poster |
|
Kumar, Vivek |
Accelerating biological and environmental research using open-science, community platform of Systems Biology Knowledgebase (KBase) |
poster |
|
Kupkova, Kristyna |
Epigenomics of chronic child undernutrition |
talk |
|
Lannelongue, Loic |
The Green Algorithms project―Quantifying the carbon impact of bioinformatics and genomics |
talk |
|
Larsen, Joseph |
Modeling the onset of symptoms of COVID-19 |
poster |
|
Lawson, John |
COCOA―Coordinate covariation analysis to annotate epigenetic heterogeneity |
poster |
|
Lee, Alexandra |
Correcting for experiment-specific variability in expression compendia can remove underlying signals |
poster |
|
Lee, John |
CoCoCoNet―Conserved and comparative co-expression across a diverse set of species |
poster |
|
Lever, Jake |
CoronaCentral―Making sense of the vast coronavirus literature using manual curation and machine learning |
poster |
|
Li, Sijia |
Bayesian inference of gene regulatory network from single-cell data |
talk |
|
Li, Simon |
How to build and run an international open-data image repository |
poster |
|
Linan, Margaret |
GPU-accelerated next generation sequencing bioinformatic pipeline |
poster |
|
Liu, Jinlu |
Cell-clustering across single-cell RNA sequencing datasets with the hierarchical Dirichlet process |
poster |
|
Liu, Yunxi |
Squeegee―De novo computational detection of contaminants in low biomass microbiomes |
poster |
|
Lu, Junyan |
Multi-omics data integration identifies novel biomarkers for aggressive chronic lymphocytic leukaemia |
poster |
|
Lu, Shaina |
The replicability of spatial gene expression atlas data from the adult mouse brain |
poster |
|
Lucaci, Alexander |
Evaluating the impact of multi-nucleotide instantaneous mutations on evolutionary dynamics |
poster |
|
Luebeck, Jens |
AmpliconReconstructor integrates NGS and optical mapping to resolve the complex structures of focal amplifications |
poster |
|
Lyu, Xinrui |
DEspec―Protein abundance estimation and differential testing for DIA-MS data |
poster |
|
Marco, Cristina |
Undergraduate curation projects to improve gene annotations in maize |
talk |
|
Melamed, Rachel D |
Drug-wide association studies of cancer using real-world health data |
talk |
|
Min, Alan |
Matrix prior for data transfer between single cell data types in latent Dirichlet allocation models |
poster |
|
Minkin, Ilia |
Scalable multiple whole-genome alignment and locally collinear block construction with SibeliaZ |
poster |
|
Mitra, Ramkrishna |
Recurrence of microRNA-gene networks reveal unexpected pan-cancer cooperativity of 5p and 3p miRNA strands that impact patient survival |
poster |
|
Molik, David |
Automated text categorization and metabarcoding reinforces Cryptococcus neoformans–woody decomposition association |
poster |
|
Moore, Joshua |
Towards a next-generation format for sharing bioimaging data |
talk |
|
Morin, Susanna |
Predicting dynamic cell type-specific enhancers from transcriptomic data |
poster |
|
Moshiri, Niema |
ViralMSA―Massively scalable reference-guided multiple sequence alignment of viral genomes |
poster |
|
Mu, Wancen |
Differential allelic imbalance across groups of cells using adaptive generalized fused lasso with binomial likelihood |
poster |
|
Nair, Monica |
Single cell trajectory analysis to predict biomarkers of sustained CAR T cell response in non-Hodgkin lymphoma |
poster |
|
Nattestad, Maria |
DeepVariant 1.0 |
talk |
|
Nicholson, David N |
Linguistic analysis of the bioRxiv preprint landscape |
poster |
|
Nothaft, Frank A |
Glow―An industrial-scale library for rapidly analyzing large variation datasets |
poster |
|
Olivieri, Julia E |
Statistical splicing score enables robust differential splicing analysis in single-cell RNA-seq experiments |
talk |
|
Olson, Andrew |
Ranked choice voting for representative transcripts with TRaCE |
poster |
|
Onami, Shuichi |
SSBD:database and SSBD:repository―Online open resources for bioimages and quantitative data for biosystems dynamics |
talk |
|
Ouyang, Zhengqing |
Large-scale identification and analysis of RNA structural disruptions induced by single nucleotide variants |
poster |
|
Paropkari, Akshay |
Data driven discovery of transcription factor binding network with machine learning |
poster |
|
Patentreger, Andrew |
Developing a tool for capturing genomic regions of high density skin clonal mutations |
poster |
|
Penaloza, Jacqueline |
Constraint on single nucleotide variants disrupting non-coding RNA secondary structure |
poster |
|
Periwal, Vipul |
Expectation reflection for better biological and biomedical classification |
poster |
|
Phan, Lon |
NCBI ALFA―Open-access to dbGaP aggregated allele frequency for variant interpretation |
poster |
|
Piccolo, Stephen R |
Web-based tools for tidying, standardizing, and transforming high-throughput assay data and associated clinical annotations |
poster |
|
Pimentel, Harold |
Model driven design and analysis of quantitative phenotype screens |
talk |
|
Pividori, Milton |
PhenoPLIER―Integrating transcriptome-wide association studies with gene co-expression patterns |
poster |
|
Powell, Christopher L |
Pats―A taxon re-sampling pipeline to test phylogenetic stability in large datasets |
poster |
|
Prabhu, Gautam |
Structural variation in the human genome has significant effects on gene expression |
poster |
|
Prinster, Andrew J |
Exact sequence variant analysis of the gut microbiome and human psychometric phenotype conditional on host genetics |
talk |
|
Priya, Sambhawa |
A machine learning framework reveals patterns of host gene-microbiome interactions across human diseases |
talk |
|
Psomopoulos, Fotis |
"DOME" recommendations for machine learning validation in biology |
poster |
|
Rahman, Amatur |
Disk compression of k-mer sets |
talk |
|
Rando, Halie M |
Open publishing and the COVID-19 infodemic |
poster |
|
Rattray, Magnus |
Non-parametric modelling of temporal and spatial counts data from RNA-seq experiments |
talk |
|
Reynier, Jean-Baptiste |
COMIRI―Consensus meta-caller for immune receptor identification |
poster |
|
Roche, Kimberly |
Novel, scalable Bayesian methods to assess patterns of gut microbial covariation in a longitudinally-monitored wild baboon population |
talk |
|
Roche-Lima, Abiel |
Machine-learning-based in-hospital mortality prediction for transcatheter mitral valve repair in the United States |
poster |
|
Ronneberg, Leiv |
BayesSyneRgy―Flexible Bayesian modelling of synergistic interaction effects in in-vitro drug combination experiments |
poster |
|
Rosenbloom, Kate |
The UCSC Genome Browser in 2020―New data, visualizations and coronavirus resources |
poster |
|
Rowell, William J |
A workflow for the comprehensive detection and prioritization of variants in human genomes with PacBio HiFi reads |
poster |
|
Russell, Pamela |
BioCantor―A Python library for feature arithmetic in arbitrarily nested coordinate systems |
poster |
|
Safo, Sandra |
Integrating Omics and phenotypic data to advance precision medicine |
talk |
|
Salzman, Julia |
Statistical Inference for single-cell RNA seq |
poster |
|
Sampath, Dharanya |
Evaluation of bioinformatics tools to study clonal architecture in tumors |
poster |
|
Sarkar, Hirak |
Accurate, efficient, and uncertainty-aware expression quantification in single-cell RNA-seq data |
poster |
|
Satpathy, Sarthak |
Pan-cancer identification of sex-biased prognostic genes |
poster |
|
Schatz, Michael |
Streamlining accessibility and computability of large-scale genomic datasets with the NHGRI genome data science Analysis, Visualization, and Informatics Lab-Space (ANVIL) |
poster |
|
Scheben, Armin |
Unraveling molecular mechanisms of immunity, viral transmission and cancer-resistance using the genomes of the Jamaican fruit bat and Mesoamerican mustached bat |
poster |
|
Schreiber, Jacob |
Ledidi―Designing genomic edits that induce functional activity |
talk |
|
Sehlke, Robert |
Shedding light on primary human cancer models with single cell imaging and deep learning―The unique potential of functional testing for translational research |
poster |
|
Seifuddin, Fayaz |
Dysregulation of long non-coding RNA expression in bipolar disorder |
poster |
|
Sergushichev, Alexey |
FGSEA―Fast gene set enrichment analysis |
poster |
|
Sergushichev, Alexey |
Phantasus―A web-application for exploratory gene expression analysis and visualization |
poster |
|
Shajii, Ariya |
A Python-based paradigm for high-performance genomics |
poster |
|
Sheffield, Nathan |
Standardizing sample metadata with Portable Encapsulated Projects |
poster |
|
Shteyman, Alan |
GED―Learning to detect genetically modified organisms in Illumina data |
poster |
|
Shumate, Alaina |
Liftoff―An accurate genome annotation mapping tool |
talk |
|
Singh, Komudi |
SARS-CoV-2 infection of host cells perturbs autophagic and mitochondrial processes |
poster |
|
Smith, Jason P |
Quality control and processing of nascent RNA profiling data |
poster |
|
Sommer, Markus J |
Balrog―A universal protein model for prokaryotic gene prediction |
poster |
|
Speir, Matthew L |
UCSC Cell Browser―Visualization for single-cell transcriptomics data |
poster |
|
Stein-O'Brien, Genevieve |
Blueprinting the brain―Combinatorial use and reuse of latent spaces across space, time, and molecular assays |
poster |
|
Stolarczyk, Michal J |
Identity and compatibility of reference genome resources |
poster |
|
Tayeb, Karl |
Colocalization and fine-mapping of multiple traits in the presence of allelic heterogeneity |
talk |
|
Tseng, Alex |
Fourier-transform-based attribution priors improve the interpretability and stability of deep learning models for genomics |
poster |
|
Tuddenham, John F |
>200,000 single-cell transcriptomes uncover new human microglial diversity―Use of this reference to explore the glioblastoma microenvironment and the regulatory network of human microglia |
poster |
|
Twesigomwe, David |
CypGen―A Nextflow pipeline for calling star alleles in cytochrome P450 genes |
poster |
|
Verdezoto, Jose |
Bedbase―A unifying platform for genomic interval data |
poster |
|
Vulliard, Loan |
Understanding chemical-genetic interactions―Morphological screen of combined perturbations |
poster |
|
Wang, Liya |
SciApps.org―A web-based platform for reproducible bioinformatics analysis on the cloud |
poster |
|
Wang, Xiaotao |
A supervised learning framework for chromatin loop detection in genome-wide contact maps |
poster |
|
Wong, Frances |
The Image Data Resource―A scalable resource for FAIR biological imaging data |
talk |
|
Yang, Guangyu |
Accurate and scalable differential splicing detection with MntJULiP |
poster |
|
Yang, Xu |
A composable rootless container system for genomic analysis pipelines |
poster |
|
Yardimci, Galip G |
Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data |
poster |
|
Yip, Yuk-Lap (Kevin) |
A unified framework for integrative study of heterogeneous gene regulatory mechanisms |
poster |
|
Youtsey, Brett |
Kmerprof―A comparative k-mer tool tailored for distributed-memory parallel computers |
poster |
|
Zaitsev, Konstantin |
Single Cell Navigator allows cross-matching of public scRNA-seq data―Study case of tumor immune microenvironments |
poster |
|
Zaman, Sumaira |
EASEL―Efficient, Accurate, Scalable Eukaryotic modeLs for de novo genome annotation |
poster |
|
Zarate, Samantha |
Parliament2―Accurate structural variant calling at scale |
poster |
|
Zhu, Kaiyuan |
CAMMIQ―A combinatorial optimization method for accurate strain level metagenomic microbial detection and quantification |
poster |
|
Zhu, Xiang |
Modeling regulatory network topology improves genome-wide analyses of complex human traits |
poster |