Presenting Author

Abstract Title

Talk/Poster

Aboukhalil, Robert G

The best of both worlds—Bringing command-line speeds to interactive genomics web apps

talk

Adelaja, Adewunmi O

Characterizing stimulus encoding by NFκB signaling dynamics

talk

Adelson, Robert P

Design of a variant quality control pipeline for whole genome sequencing studies using replicate discordance

poster

Aganezov, Sergey

Reconstruction of clone- and haplotype-specific cancer genomes from bulk tumor samples

poster

Alonge, Michael

RaGOO—Fast reference-guided ordering and orienting of genome assembly contigs

poster

Anaparthy, Naishitha

Simultaneous sequencing of transcriptome and genome of a single cell in single tube

poster

Andrews, Brenda J

Machine learning and computer vision approaches for phenotypic profiling in yeast

talk

Arslan, Ahmed

High-throughput computational genetic discovery

poster

Avsec, Ziga

Kipoi—Accelerating the community exchange and reuse of predictive models for genomics

talk

Aziz, Mohammad

Molecular subtyping of colorectal cancer using gene expression profile of tumor samples

poster

Bennett, Christopher G

Accurate annotation of genomic variation and assembly of personalized individual genomes

poster

Biederstedt, Evan

NovoGraph—Genome graph construction from multiple long-read de novo assemblies

poster

Billmann, Maximilian

Genome-wide identification of genetic interactions in human cells using CRISPR/Cas9

talk

Blankenberg, Daniel J

Scaling scalable infrastructure to analysis tools

poster

Boca, Simina M

Visualizing patient-specific drug-gene networks for recommending targeted cancer therapies

talk

Bolipata, Christopher A

Roslin—A portable and reproducible workflow infrastructure for cancer genomic sequencing analysis

poster

Botev, Georgie

A heuristic algorithm for the k-ploid haplotype assembly problem

poster

Botvinnik, Olga

Fast approximate cell type identification via MinHash sketches of k-mers in single cell RNA-seq

talk

Breitweiser, Florian P.

KrakenUniq and Pavian—Confident and fast metagenomics classification and visualization using unique k-mer counts

poster

Cain, Scott

JBrowse Connect—Launch analysis tasks from the browser

poster

Carpenter, Anne

Making microscopy images as computable as genomes—Drug discovery in the age of deep learning

talk

Carroll, Andrew

Improving deep learning methods by identifying diverse and representative datasets

poster

Chapman, Lesley M

SVCurator—A Crowdsourcing app to visualize evidence of structural variants for the human genome

poster

Chin, Jason

Decomposing dynamics from different time scale for time-lapse image sequences with a deep convolutional network

talk

Collado Torres, Leonardo

Analysis  of gene expression in dorsolateral prefrontal cortex and hippocampus across development and in schizophrenia reveal striking regional heterogeneity

poster

Corrada Bravo, Héctor

What comes next? Beyond integration of visual and computational interactive data analysis

talk

Czech, Eric A

Cytokit—A single-cell analysis toolkit for high dimensional fluorescent microscopy imaging

talk

Daley, Timothy P

Mixture model based analysis for CRISPR pooled screens

poster

Dandage, Rohan A

beditor—Computational framework to explore mutagenesis potential of CRISPR base editors

poster

Davidge, Henry H

A unified platform for scalable genomic data analysis

poster

DeBlasio, Dan

Building an automated bioinformatician—More accurate, large-scale genomic discovery using parameter advising

talk

Diaz, Daniel

Single cell gene expression analysis to identify progenitor/stem cells in mechanosensory organs

poster

Dikow, Rebecca B

The genome of an undomesticated African oilseed crop, Centrapalus pauciflorus (Compositae)

poster

Dikow, Rebecca B

Using machine learning to distinguish between and discover patterns of biodiversity in insects

poster

Duffy, Fergal J

Immunometabolic signatures of risk for progression to active tuberculosis after household exposure

poster

Duma, Denise

Deep learning applications to explore and classify high-dimensional feature spaces of millions of genetic variants

poster

Duren, Zhana

Simultaneous clustering of single-cell genomics data and deconvolution of bulk chromatin interaction data

talk

Erdman, Lauren

Explaining gene expression—Massively parallel in-silico testing of gene expression regulators reveals large scale patterns of shared and divergent regulation across cancers and tissues

poster

Farek, Jesse

xAtlas—Scalable small variant calling for large and heterogeneous sample sets

poster

Ferrall-Fairbanks, Meghan C

Quantifying intraleukemic heterogeneity through single cell RNA sequencing

poster

Flores-Gonzalez, Mirella R

A tissue and host-specific expression atlas for Citrus sinensis and Diaphorina citri for exploring the citrusgreening disease complex  

poster

Fullem, Robert L

Improving the data ecosystem in genome medicine research consortia through implementation of modern data standards

poster

Fürth, Daniel

Paired-end in situ sequencing and cellular geometry of the Drosophila compound eye

talk

Gaye, Amadou

Transcriptome signature of hypertension in African Americans—Findings from machine learning

poster

Ge, Weihao

Search space reduction in stepwise modeling for GWAS

poster

Gerstein, Mark B.

Interpretable machine learning approaches for understanding functional genomics in the human brain

poster

Ghosh, Debarati

Labeling, imaging, and isolating invisible, marker-less cancer cells

poster

Giangreco, Nicholas P

Standardized and reproducible analysis enables identification of novel primary graft dysfunction biomarkers using exosome proteomics

poster

Gilbo, Philip

Machine learning—How tumor expression predicts response to checkpoint immunotherapy

poster

Goecks, Jeremy

Accessible and scalable machine learning for biomedical data analysis

poster

Gu, Tongjun

Integrating multi-platform genomic datasets for cancer subtype discovery using denoising autoencoders

poster

Guidi, Giulia

BELLA—Berkeley efficient long-read to long-read aligner and overlapper

poster

Gursoy, Gamze

Quantification of private information leakage from functional genomics data and practical file formats for privacy preservation

talk

Gymrek, Melissa A

Profiling the genome-wide landscape of tandem repeat expansions

talk

Hauser, Fritz

One medical life time history of a breast cancer patient and its pattern formations is the key for successful big data

poster

Helb, Danica

ClinEpiDB—The Clinical Epidemiology Database Resource

poster

Heydarian, Mo

Galaxy at scale—Automated analysis of thousands of single cell transcriptomes.

poster

Hoffman, Michael M

Virtual ChIP-seq—Predicting transcription factor binding by learning from the transcriptome

talk

Holmes, Susan

Tools for reproducible research that rise to the challenges of the analyses of multidomain longitudinal analyses of the human microbiome

talk

Hong, Changjin

Divine—Prioritizing genes for rare Mendelian disease in whole exome sequencing data

poster

Hosmani, Prashant

Sol Genomics Network (SGN) community resources and a high-quality tomato reference genome

poster

Hoyt, Stephanie

Characterization of bacterial endosymbionts and systems biology resources for Diaphorina citri, insect vector for the citrusgreening disease

poster

Huellein, Jennifer

Data management for integrative analysis of ex vivo drug screens and multi-omics data

poster

Hwang, Tae Hyun

Machine learning approach to identify clinically relevant biomarker and predict treatment response based on FDA-approved tumor genetic testing for genome-driven precision oncology care

poster

Irber Junior, Luiz Carlos

Building decentralized indexes for public genomic data to improve access speed and availability

poster

Jansen, Camden

Building gene regulatory networks from single-cell ATAC-seq and RNA-seq using linked self-organizing maps

talk

Jayakumaran, Gowtham

An ultrasensitive next generation sequencing assay using cfDNA for clinical utility

poster

Johnson, Benjamin K

Semi-supervised manifold learning of chromatin compartmentalization

talk

Jordan, William

The X in sex—Uncovering factors that promote Drosophila X-chromosome identification

poster

K C, Kishan

A deep framework for aggregating heterogeneous biological information for gene network inference

poster

Khalfan, Mohammed

Modify reference sequence and annotation files quickly and easily with reform

poster

Khilji, Saadia

Residue-specific histone acetylation associated with transcriptional co-activator p300 in early myoblast differentiation

poster

Khodadadi-Jamayran, Alireza

scSeqR—An interactive R package to work with high-throughput single cell sequencing technologies

poster

Khosravi, Pegah

Deep neural networks reliably assess human blastocyst quality and assist in predicting implantation success upon in vitro fertilization

poster

Kirsche, Michael

SAPLING—Suffix Array Piecewise Linear INdex for Genomics

poster

Kissinger, Jessica

EuPathDB—Insights from 15 years experience developing, scaling and deploying an integrated omics, data-mining and visualization platform for >300 pathogens and a user community of >50,000

talk

Kovaka, Sam C

UNCALLED—Rapid streaming mapping of raw nanopore signal to large references

poster

Kucukural, Alper

DEBrowser—Interactive differential expression analysis and visualization tool for count data

poster

Kumar, Vivek

Integrating data, tools and knowledge to accelerate scientific discovery using open-science, collaborative platform of KBase

poster

Lariviere, Delphine M

Bacterial genomic at large scale with Galaxy—A Tn-SEQ example

poster

Laserson, Uri

Scaling up single-cell analysis with distributed computing

poster

Lee, Je H

Unmasking functional genetic mosaicism in single cells

talk

Lemmon, Gordon H

A best practice approach to mining structured electronic medical records in search of comorbidities

poster

Levitin, Hanna M

De novo gene signature identification from single-cell RNA-seq with hierarchical poisson factorization

poster

Ling, Jonathan

ASCOT identifies key regulators of photoreceptor-specific splicing

poster

Loh, Jui Wan

Inference of specimen purity from variant allele frequencies in tumor-only clinical sequencing data

poster

Looso, Mario

Webbased interactive omics visualization (WIlsON) in a cloud based infrastructure

poster

Lu, Alex X

Learning unsupervised feature representations for single cell microscopy images with paired cell inpainting

talk

Lu, Jennifer

Identifying and removing contamination in bacterial, archaeal, and eukaryotic genomic databases

poster

Lu, Jennifer

Re-releasing the Kraken—More efficient and more accurate metagenomic analysis with Kraken 2

poster

Lu, Zhenyuan

SciApps.org—An XSEDE and CyVerse powered platform for reproducible bioinformatics workflows

poster

MacDonald, Madolyn L

EvalDNA—A machine learning-based tool for the comprehensive evaluation of genome assembly quality

poster

Madden, Tom

BLAST in the cloud

poster

Madduri, Kamesh

Harnessing multi-node parallelism for terascale genomic data analysis

poster

Maity, Sayak

Cell migratory mode classification system using artificial neural networks—A novel method for cancer detection and drug discovery

poster

Mak, Lauren

PoolHapX—de novo haplotype reconstruction from pooled pathogen next-generation sequencing data

poster

Malikic, Salem

PhISCS—A combinatorial approach for sub-perfect tumor phylogeny reconstruction via integrative use of single cell and bulk sequencing data

talk

Medina, Santiago G

Deciphering mRNA decay programs during embryogenesis

poster

Melamed, Rachel D

Causal inference to repurpose FDA-approved drugs for cancer therapy and prevention

poster

Miron, Michelle

Mapping memory T-cell clones in human tissues

talk

Mohsen, Hussein

Deep neural networks to identify somatic-germline interactions in cancer

poster

Morrison, Norman

The Human Cell Atlas Data Coordination Platform

talk

Moshiri, Niema

Flipping computational courses using massive adaptive interactive texts

poster

Mun, Taher K

Improving variation-aware alignment using the run-length FM index

talk

Munoz, Adriana

Role of de novo intronic indels in autism

poster

Nafees, Saba

Analyzing genomic data using tensor-based orthogonal polynomials

poster

Narechania, Apurva

Information theoretic detection of horizontal gene transfer

poster

Navarro, Fabio CP

Developing a comprehensive resource of the human body epigenome with a new integrated annotation of tissue-specific regulatory elements and networks

talk

Nekrutenko, Anton

Can UI handle 10^x datasets where X > 3? Yes, it can!

talk

Nelson, Justin

Discovering novel genetic interactions using stress conditions in Saccharomyces cerevisiae

poster

Nguyen, Luong

Consistency between survey response and genetic information of AncestryDNA customers

poster

Ouyang, Zhengqing

Accurate reconstruction of cell trajectory and pseudo-time for massive single cell RNA-seq data

poster

Ozturk, Murat

Achieving portability and reproducibility in complex bioinformatics workflows using Singularity containers

poster

Park, YoSon

A platform for community-scale Mendelian randomization analysis

poster

Parmigiani, Giovanni

Training replicable predictors in multiple studies

talk

Patel, Deep S

Fostering FAIR genomic data in the NIEHS Data Commons

poster

Phan, Lon

Integrative analyses of dbSNP For variant prioritization and interpretation

poster

Phillippy, Adam

De novo assembly of haplotype-resolved genomes for a pan-human reference

talk

Pinello, Luca

CRISPResso2—Allele-specific quantification and visualization of genome editing events from CRISPR/Cas9, Cas12a (Cpf1) and base editors

poster

Pinello, Luca

Deconvolution of CRISPR tiling screen data for the discovery and dissection of functional non-coding elements

poster

Pinello, Luca

STREAM—Single-cell Trajectories Reconstruction, Exploration And Mapping of omics data

talk

Ploenzke, Matthew

Methods to encourage learning information-based genomic sequence motifs

talk

Prakash, Eva I

Efficient interpretation of nonlinear gapped-kmer support vector machines applied to transcription factor motif discovery

poster

Preussner, Jens

A scaleable framework for analysis of transcriptomic and epigenomic profiling of individual tumor cells in the cloud

talk

Prummer, Michael

Deciphering single-cell heterogeneity in melanoma for clinical decision support

poster

Ramakrishnan, Srividya

Benchmarking RNA-seq in plants

poster

Ranallo-Benavidez, Timothy R

GenomeScope 2.0—Reference-free genome profiling of polyploid genomes

poster

Reisman, Benjamin J

DebarcodeR—An approach for automated demultiplexing of fluorescent cell barcoded (FCB) samples for multiplexed flow cytometry

poster

Rosser, Gabriel

Characterising DNA methylation following reprogramming of terminally differentiated cells to a pluripotent state

poster

Rowell, William J

Comprehensive variant detection in a human genome with PacBio high-fidelity reads

poster

Russell, Pamela H

A large-scale analysis of bioinformatics code on GitHub

poster

Safikhani, Zhaleh

Personalized drug combination prediction in triple-negative breast cancer using single-cell sequencing

talk

Saha, Ashis

Alignment errors in RNA-sequencing produce false positives in association analyses

poster

Salzberg, Steven

Adventures and misadventures in genome data mining

talk

Sanchez, Diego F

Unraveling potential biomarkers with FC-R2—A comprehensive “ready-to-analyze” human gene expression resource

poster

Scheffler, Konrad

Strelka2—Fast and accurate calling of germline and somatic variants

talk

Schneider, Valerie A

Get more from your analyses—GRC and NCBI resources for enhanced use of the Human Reference Assembly

poster

Schneider, Vicky

Surrogate modelling and optimization made easier

poster

Schreiber, Jacob

Multi-scale deep tensor factorization learns a latent representation of the human epigenome

talk

Sedlazeck, Fritz J.

Illuminating the dark genome—Evaluation of technologies to assess medically relevant dark spots

poster

Sedlyarov, Vitaly

RESOLUTE—Research empowerment on solute carriers

poster

Sheffield, Nathan

Pepkit—A modular toolkit for organizing computational biology projects

poster

Sherman, Rachel M

Analyzing genetic instability in breast cancer with nanopore sequencing of patient-derived organoids

talk

Shi, Zhou

Comprehensive and ultra-rapid identification of genetic variants in human gut microbiome

talk

Shrikumar, Avanti

Suggested best practices for interpreting deep learning models of regulatory DNA

talk

Sick, Beate

Quantifying the trustability of an individual deep learning based image classification

talk

Simbirsky, Maria

A virtuous cycle of model training and execution demonstrated in the analysis of cancer transcriptional drivers

poster

Sisu, Cristina

Identification and analysis of unitary pseudogenes

poster

Sklavenitis-Pistofidis, Romanos

Founding precision therapy in 1q-amplified multiple myeloma

poster

Slotta, Douglas

Opening the NCBI prokaryotic annotation process to everyone

poster

Sokolowski, Dustin J

Identifying relevant RNA-seq experiments and candidate genes with the Reproducible Enrichment Tool.

poster

Stein-O'Brien, Genevieve

Decomposing cell identity for transfer learning across platforms, tissues and species

talk

Stoeger, Thomas

Large-scale investigation of the reasons why potentially important genes are ignored

poster

Strattan, J Seth

The ENCODE pipeline architecture—Containerization for reproducible and portable bioinformatics workflows

poster

Sugai, Shuhei S

Highly refined CRISPR target database for human and other organisms

poster

Tareen, Ammar

MPAthic—Quantitative modeling of sequence-function relationships for massively parallel assays

poster

Trizna, Michael

Applications of deep convolutional neural networks to digitized herbarium specimens

poster

Tsuchiya, Mirian

Designing the Smithsonian Genome Hub, a cloud based collaborative tool for biodiversity scientists

poster

Vallejos Meneses, Catalina A

Robust differential variability testing for single-cell RNA sequencing data

talk

Wang, Tingyou

Indel detection from DNA and RNA sequencing of primary and advanced prostate cancer

poster

Wayman, Joseph

Leveraging single-cell RNA-seq data for transcriptional regulatory network inference

poster

Webber, James T

Integrating ensembles of single-cell expression and drug response data

poster

Weinmann, Simone M

Ribonucleotide sequencing-by-ligation chemistry for functional genomics in single cells

poster

Wesolowski, Sergiusz

Probabilistic graphical models for patient cohort assembly and risk estimation using electronic medical records

talk

White, Alex

Modeling and visualizing ecological structure across the tropical-temperate divide

talk

Wilks, Christopher

Exploring transcription in tens of thousands of samples with Snaptron2

poster

Williams, Jason

Improving the bioinformatics curriculum

poster

Wright, Adam J

MP-BioPath—A computational tool for inferring the functional impact of mutational profiles on pathway level activity

poster

Wyman, Dana E

Building a comprehensive ENCODE long read transcriptome pipeline

talk

Xu, Hongming

A deep learning model for automatic nuclei segmentation in computational pathology

poster

Xue, Yaxin

Constructing ribosomal genes from meta-transcriptomic data

poster

Yan, Chengfei

A modularity-based approach to identify hierarchical chromatin domains

poster

Yaron, Tomer M

Applying machine learning and optimization algorithms to the tyrosine and serine/threonine kinomes

poster

Yu, Qichao

Dissecting the spatial heterogeneity of single circulating tumor cells reveals immune evasion through MAX regulated CCL5 overexpression in hepatocellular carcinoma

poster

Yukselen, Onur

DolphinNext—A graphical user interface for distributed data processing of high throughput genomics

poster

Zhang, Tongli

Integrating mechanistic modeling and machine learning to analyze biological data

poster

Zhang, Wei

Network-based learning methods to explore the role of post-transcriptional regulation in cancer

poster

Zhang, Yuping

Web server of principal trend analysis for longitudinal high-dimensional data

poster

Zhong, Yizhen

Elucidating novel gene regulation related to health disparities—Discovery of novel hepatic eQTLs in African Americans

poster

Zhong, Yu

Single-cell RNA-Seq deciphers endodermal origin and liver development by tracing FOXA2 lineage

poster

Zhu, Helen

Driver discovery in primary localized prostate cancer

poster