CGSI 2024

CGSI Organizing Committee

Faculty 2024

Ahmed Alaa | Applications of Conformal Prediction in Medicine

Can Alkan | Acceleration of bioinformatics workloads through hardware-algorithm co-design and processing-in-memory technologies

Corey Arnold | Corey Arnold | Applications of AI in Healthcare: From the EHR to Imaging

Vineet Bafna | ecDNA and Breakage Fusion Bridge: two facets of oncogene amplification in cancer

Vikas Bansal | Detection of genetic variation in highly homologous genes using short read sequencing

Lisa Bastarache | The real world phenotypic presentation of Mendelian disease

Kayhan Batmanghelich | Kayhan Batmanghelich | Synthetic Data In Medical Imaging: Are we there yet?

Brian Browning | Compression of Phased Sequence Data

Brian Browning | Bref4 compression: increasing the analyses that can be performed directly on compressed sequence data

Na Cai | Helmholtz Zentrum München

Francesco Paolo Casale | ML-enabled Genetic Association Studies of High-Content Phenotypes

Tim Chang | Modeling Alzheimer’s disease Risk in Real World Data

Han Chen | StocSum: a reference panel free summary statistics framework for diverse populations

Irene Chen | Leveraging Large Datasets and Large Language Models for Healthcare

Haoyu Cheng | Reconstructing Every Haplotype with De Novo Assembly

Jeffrey Chiang | Towards foundation models for Electronic Health Records

Rayan Chikhi | Project Logan Assembling all public sequencing data

Rayan Chikhi | A Chalk Talk on Applications of K-mers

Ercument Cicek Bilkent | University & Carnegie Mellon University

Andrew Dahl | University of Chicago

Jessica Dennis | University of British Columbia

Mohammed El-Kebir | Introduction to Integer Linear Programming

Jason Ernst | Computational Methods for Cross-species Epigenomic Analyses

Jason Ernst | Computational Methods for Modeling and Analyzing Epigenomic Data

Eleazar Eskin | Challenges in Developing a Universal Metagenomic Diagnostic Test

Nandita Garud | Inference of the selective effects and demographic histories of human gut commensals

Casey Greene | Some issues with deconvolution using single-cell profiles

Gamze Gürsoy | Privacy-preserving techniques for precision medicine

Juan Gutierrez | The Flaws of Others: Large Language Models in Biomedical Research

Iman Hajirasouliha | Iman Hajirasouliha | AI Models in Reproductive Medicine

Jo Hardin | Fitting time-dependent models using sicegar with applications to the timing of transcription of RpoS-dependent genes in E-coli

Fereydoun Hormozdiari | University of California, Davis

Haky (Hae Kyung) Im | On the problem of inflation in TWAS and other xWAS

Evan Johnson | Rutgers New Jersey Medical School

Vanessa Jonsson | UCSC

Shalmali Joshi | Columbia University

Aly Azeem Khan | University of Chicago

Jaehee Kim | Cornell University

David Knowles | Using the Pyro probabilistic programming language for statistical genomics

David Koslicki | YACHT: an ANI-based statistical test to detect microbial presence or absence in metagenomes

Rahul Krishnan | Bridging the gap: Deep Learning and Causality

Smita Krishnaswamy | Uncovering Cellular dynamics and metabolism with Geometric deep learning and optimal transport

Kenneth Lange | Examples of MM Algorithms

Iuliana Laza | Columbia University

Christina Leslie | New Machine Learning Models for Single-cell and Regulatory Genomics

Jingyi (Jessica) Li | Categorization of 31 computational methods to detect spatially variable genes from spatially resolved transcriptomics data

Qunhua Li | Pennsylvania State University

Wei (April) Li | Genotype Representation Graph/ Enabling Efficient Analysis of Biobank-Scale Data

Christoph Lippert Hasso | Conservation of Historic Patient Records from Walter Kempner’s Rice Diet for Hypertension

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

Jian Ma | Carnegie Mellon University

Nick Mancuso | Variational Inference for Fun and Profit

Jazlyn Mooney | Using dogs as a model system in genomics

Loes Olde Loohuis | Using biobanks to study people that are not in it

Loes Olde Loohuis | Psychiatric phenotyping from EHR, yes, we can!

Pavel Pevzner | Uni-alignment: A Parameter-free Framework for Fast and Accurate Sequence Alignment

Harold Pimentel | Hierarchical Models for Deep Mutational Scans

Rajesh Ranganath | Digging into the foundations of generative AI for healthcare

Ben Raphael | Princeton University

Saharon Rosset | Using Classical Algorithms for Modern Applications/ MCMC for Tail Calculations, EM for PET reconstruction

Sushmita Roy | Matrix factorization and applications to bulk and single cell omic datasets

Julia Salzman | SPLASH: Statistical signal extraction for unified genomic discovery

Kris Sankaran | Topic Models for Multiscale Analysis

Sriram Sankararaman | Methods for Analyzing Biobank Data: Statistical, Computational, and Privacy Challenges

Ayellet Segre | Harvard Medical School

Sagiv Shifman | Using pooled CRISPR screens to study biology

Ritambhara Singh | An introduction to graph neural networks

Pavel Skums | Harnessing Computational Genomics for Predicting Viral Evolution

Sagi Snir | Assembling the Tree of Life in Light of Conflicting Signals

Paul Spellman | Constraints on Tumor Development

Matthew Stephens | Empirical Bayes Matrix Factorization and Parts-based Representations

Matthew Stephens | Empirical Bayes and its applications: shrinkage, hypothesis testing, and more

Daniel Tward | Classical and Deep Learning Approaches to Longitudinal Modeling in Neuroimages

Julia Vogt | Echoes Over Time: Detecting Heart Defects in Newborns

Wei Wang | Information Retrieval in the Era of Large Language Models

Wenyi Wang | A Guide to Perform Transcriptomic Deconvolution in Cancer

Tandy Warnow | Statistically consistent estimation of level-1 phylogenetic networks from SNPs

Xinzhu (APRIL) Wei | Genotype Representation Graph/ Enabling Efficient Analysis of Biobank-Scale Data

Jason Xu | Improving k means clustering via simple iterative optimization

Loic Yengo | University of Queensland, Australia

Chongzhi Zang | University of Virginia

Alex Zelikovsky | SARS CoV 2 Saltations and Punctuational Evolution

Jing Zhang | Dissecting the Gene Regulatory Grammer at a Single cell Resolution

Shaojie Zhang | PBWT-based Algorithms for Large Cohort Genetics

Xinjun Zhang | Promises and Pitfalls of Scaling in Population Genetic Simulations

Zijun (Frank) Zhang | Cedars-Sinai Medical Center

Hua Zhou | Statistical and Computational Algorithms for Analyzing Biobank Data

James Zou | Stanford University