CGSI 2023

Faculty 2023

Alkan, Can | Characterization of Genomic Structural Variation Using Various Sequencing Technologies 

Arboleda, Valerie | Biobanks from a Pathologist’s Viewpoint

Bastarache, Lisa | From Population to Person How to Help a Single, Actual Person with Data Science

Bastarache, Lisa | Fun with Phecodes!

Batmanghelich, Kayhan | Divide and Conquer: Carving Out Symbolic Models out of BlackBox for More Efficient Domain Adaptation

Batmanghelich, Kayhan | Understanding Spurious Feature Learning Through the Lens of Task Difficulty

Cai, Na | Polygenic Means To Test And Refine Depression Disease Models

Casale, Francesco Paolo | Computational Analysis of Liver Whole slide Images Empowers Genomic Analyses of Historical Traits

Casale, Francesco Paolo | Mixed Models in Genomic Analyses and Imaging Studies

Chaisson, Mark | Design, Construction, and Usage of the Draft Pangenome

Chaisson, Mark | Genotyping Allele specific Copy Number Variants Using Pangenomes

Chen, Irene | Fairness and Equity in Machine Learning for Healthcare

Chiang, Jeffrey | Strategies for Integrating Deep Learning with Current Biomedical Research

Chikhi, Rayan | Living in the Future of Genomics

Chikhi, Rayan | mDBG and Alignment The Tumultuous Fate of Sequence Bioinformatics Ideas

Chopra, Sumit | Less is More Learning Signals to Learn Representations in Healthcare

Cox, Nancy | Ways to Find Confounding in Biobanks

Cox, Nancy | Confounding sneaks into biobanks in myriad ways…

El-Kebir, Mohammed | Inferring Parsimonious Migration Histories for Metastatic Cancers

Ernst, Jason | Leveraging High-throughput Functional Characterization Data to Dissect and Annotate Human Regulatory Regions

Ernst, Jason | Computational Methods for Modeling and Analyzing Epigenomic Data

Eskin, Eleazar | SwabSeq Sequencing based Detection of Pathogens

Garud, Nandita | Detection of Hard and Soft Sweeps from Population Genomic Data

Gazal, Steven | The Functional Architectures of Human Diseases and Complex Traits: From Polygenicity to Variant Function

Gravel, Simon | Population Genetics in Large Genealogies

Greene, Casey | Why is this so hard It should be easy

Gronau, Ilan | Generating Realistic Chromosome Scale Simulations for Population Genomics Studies

Gymrek, Melissa | Dissecting the Contribution of the Repeat ome to Complex Traits

Hajirasouliha, Iman | Applications of Deep Learning in Digital Pathology and Embryology

Hardin, Jo | Selecting Between-sample ChIP-Seq Normalization Methods From The Perspective of Their Assumptions

Im, Haky (Hae Kyung) | Predicting the Epigenome from DNA Sequence, Are you there yet

Joshi, Shalmali | Observational Causal Inference for Improving and Auditing ML for Healthcare

Khan, Aly Azeem | Computational Insights into Cancer Immunology

Krishnan, Rahul | Reliable Machine Learning in Healthcare

Krishnaswamy, Smita | Machine Learning via Graph Signal for Complex Biological Data

Krishnaswamy, Smita | Graph and Algebraic Signal Processing Basics for Computational Biology

Lange, Kenneth | MM Principle of Optimization

Leslie, Christina | Machine Learning Models for Single Cell and Regulatory Genomics

Li, Wei | Computational Biomedicine Epigenetics Liquid Biopsy and Alternative Polyadenylation Therapy

Lippert, Christoph | Performing GWAS of Images by Combining Deep Transfer Learning with Statistical Testing

Lippert, Christoph | Recent Advances in Normalizing Flows

Lonardi, Stefano | How to “Squeeze” the Best Genome Assembly From Your HiFi Reads

Loohuis, Loes Olde | Combining Biobanks and Cohort Studies. The Best of Both Worlds

Ma, Jian | Large Language Models for Computational Biology A Primer

Mancuso, Nicholas | Computationally Scalable Approaches for Characterizing Genetic Architectures in Diverse Ancestries

Moore, Jason | Automated Quantitative Trait Locus Analysis

Oesper, Layla | Tumor Evolution: Methods for Comparing, Summarizing and Visualizing Clonal Trees

Palacios, Julia | Inference from Single Cell Lineage Tracing Data Generated via Genome Editing

Przytycka, Teresa | From Mutagenic Processes to Mutational Signatures and Back

Raphael, Ben | Evolutionary Models for Cancer and Lineage Tracing

Raphael, Ben | Models and Methods for Spatial Transcriptomics

Ranganath, Rajesh | Revisiting Out of Distribution Generalization

Ranganath, Rajesh | Deep Generative Models in Medicine

Rosset, Saharon | Intuition and Paradoxes in Probability and Statistics

Rosset, Saharon | Multiple Testing: Methods for Low- and High-Dimensional Testing Problems in Biomed, and Some Optimality Results

Salzman, Julia | Statistical Reference free Genomics Solves Myriad Problems in Bioinformatics

Sankaran, Kris | Selective Inference for Computational Genomics

Shamir, Ron | Methods for Disease Analysis Using Multiomic Data

Singh, Ritambhara | Single cell Data Integration Using Optimal Transport

Snir, Sagi | Harnessing Genome Dynamics for Phylogenetic Reconstruction

Tward, Daniel Familywise Error Rate Control for Statistical Testing in Brain Image Ontologies

Wang, Wenyi | Statistical Methods for Cancer Risk Prediction Models

Warnow, Tandy | Advances in Large scale Multiple Sequence Alignment

Xie, Pengtao | Training Highly Generalizable Biomedical Image Segmentation Models with Very Few Annotations

Zang, Chongzhi | BART A Transcriptional Regulator Prediction Method for Functional Genomics

Zou, James | Modeling Spatial Omics and Cellular Niches with Graph Neural Networks

Zou, James | Leveraging Medical Twitter to Build a Visual-language AI Model for Pathology

Zuk, Or | Independence Tests and Dependence Measures, for Unbiased and Biased Samples