Summary of Projects, 2023

The Human BioMolecular Atlas Program (HuBMAP)

HuBMAP Data Integration in Mixed Reality: Building an Immersive High-Resolution Human Atlas

Estimating dosage sensitivity using gene expression in copy-number-defined tumor subclones

Multimodal Pharmacology AI for Drug Interactions and Safety

Contextual Deep Learning on Knowledge Graphs for Precision Medicine in Neurological Disorders

Protein Function Prediction with Graph Neural Networks

Benchmarking Vision-Text Biomedical Models with CLIPContrast

AI in Pathology: Autonomous Microscopy for Brain Tumur Diagnosis

Beyond Data: Harnessing Computer Vision in the Operating Room

Unraveling CD8+ T cell development throughout childhood via multi-omics

Reducing the dimensions of the environment

Visualizing chronic disease burden and mobile health van presence across the United States

Identifying areas of highest need with a mobile clinics dashboard

Using KidneyDB to Examine the Inclusion of Race in Kidney Function Estimates

Cardiokid: R-based platform to generalize NHANES analysis

Fine-tuning LLMs to be copilots in high-quality epidemiological research

Characterizing Promoter Variation in Mycobacterium Tuberculosis to Predict Drug Resistance

Approaches for Generating Homoplasy Scores in SARS-COV-2 Without a Phylogenetic Tree

Summary of Projects, 2022

Developing a Method to Semi-Automate Harmonization of Clinical Variables Across Multiple Large-Scale Cohorts

Comparing the Predictive Value of Clinical Variables for Type 2 Diabetes Onset Based on Social Determinants of Health in the Framingham and Jackson Heart Studies

Multi-Cohort Variable Harmonization: Semantic and Variable Distribution Learning

Edge Bundling for Enhanced Genomics Visualizations

LINCS Compound Dataset And Causal-PPI

Assessing BMI and other Adiposity Measurements in Type 2 Diabetes Risk Prediction & the Variation in Differing Community Based Cohorts

Detection of Proper Endotracheal Tube Placement via Computer Vision

Developing Vitessce, a Single-Cell Sequencing Tool, to Investigate Immune Checkpoint Blockades 

Validation of GenTB Resistance Prediction with User-Submitted Mycobacterium tuberculosis Sequencing Data

Predicting the Onset of Diabetes Using Cardiac History and Social Determinants of Health

Mycobacterium Tuberculosis GWAS to Associate Genotype to Extrapulmonary TB

Prevalence and Selection of Pediatric Suicidality Cases in the Emergency Department Before and During the COVID-19 Pandemic

Genetic and Geospatial Shared Environment Associations with Individual-Level Exposures Expand Understanding of Cardiometabolic Health Etiology

Randomized Trials of AI in Clinical Practice

Finding Aberrant Gene Expression and Splice Junctions from RNA Sequencing Data in Undiagnosed Patients

Power Calculations for Genetic Variation Studies Focused on Severe COVID-19

PYPE: A Python Pipeline for PheWAS Execution, Visualization, and Interpretation

National Projections for Clinical Applications of New Kidney Function Equations in Asian Americans, 2011-2018

Automatic Detection of Endotracheal Tube Placement in Chest X-Rays

Using Multimodal Modeling for Novel Drug-Drug Interaction Prediction

Summary of Projects, 2021

Quantifying the Constraint on Missense and LoF Variants in the Human Genome Using a Fine-Scale Mutation Map

Designing a Mobile Platform for Personal Medical Data Exploration

Clinical Analysis and Evaluation of Gene-Phenotype Relationships in the Undiagnosed Disease Network

Liver Disease and Environmental Exposures: an Exposome-Wide Association Study

Somatic Mutation Calling in Slide-SEQ Prostate Cancer Samples

Marker Gene Panel Selection for Imaging-Based, Spatially-Resolved Transcriptions

Structural RNA Velocity

Role of Tandem Repeat Expansions in Ewing Sarcoma

Detecting Microsatellite Instability in Cancer Genomes

Translational Data Science Center for a Learning Healthcare System

Pediatric Reference Ranges: Applying Direct and Indirect Methods to NHANES Data

Race-Free Equations for Spirometry

What Do We Do When Machine Learning Models and Clinicians Disagree?

Ultra-Rare Epilepsy Genetics in the UDN

Co-Expression of Neighboring Genes Using Next Generation Sequencing

Network Diffusion Based Approach for Disease Gene Discovery

GraphXAI: Benchmarking Explainablity Methods for Graph Neural Networks

Characterizing Drug Mechanisms with Cell Type Specific Protein Networks

Segmenting Glioblastoma Slides Using Graphical Neural Networks

Genomic Data Visualization and the Implementation of Themes into Gosling


Intragenome Recombination in M. tuberculosis

Investigating Viral Genetics of SARS-CoV-2 Patients in Bahrain

Summary of Projects, 2020

Detecting Mutational Signatures in Cancer Cells

Analyzing Relationship Between Social Determinants of Health and Multidrug-Resistant
Tuberculosis and Developing Data Visualizations and Resistance Prediction Pipeline on the genTB

Predicting Bronchopulmonary Dysplasia in NICU Infants with Claims Data

Towards Deconvolution of Spatial Transcriptomics Data

Evolution of Mycobacterium Abscessus within Human Infection

Summary of Projects, 2019

Unsupervised Data Augmentation for Semisupervised Learning of Patient Outcomes

Analyzing the Source of Overdispersion in Allelic Imbalance Estimates

R Shiny App on HIV Positivity in Sub-Saharan Africa

Developing Infrastructure for Cell Set Operations and Organization in Single-Cell Visualization

Discerning Simple Phenotype from EEG: Patient Biometrics and Demographic Tasks using CNN Methodologies

'An Experimental Framework for Examining Hyperparameter Choices in Crowdsourced Environments

Of Mice and Men: Assessing Schizophrenia Drug Success in the Context of Human-Mouse Brain Homology

Prediction of Chronological and Biological Age from Laboratory Data

Investigating Biological Similarities among Rare Diseases