CGSI 2025 CGSI Organizing Committee Irene Chen | UC Berkeley & UCSF Jason Ernst | University of California, Los Angeles Eleazar Eskin | University of California, Los Angeles Jo Hardin | Pomona College Shalmali Joshi | Columbia University Vanessa Jonsson – UC Santa Cruz Jaehee Kim | Cornell University Christoph Lippert | Hasso Plattner Institute Loes Olde Loohuis | University of California, Los Angeles Harold Pimentel | University of California, Los Angeles Rajesh Ranganath | New York University Sriram Sankararaman | University of California, Los Angeles Ritambhara Singh | Brown University Daniel Tward | University of California, Los Angeles Julia Vogt | ETH Zurich Faculty 2025 Ahmed Alaa | Evaluation of Generative AI Models in Healthcare Can Alkan | Acceleration of bioinformatics workloads Mohammed Alser | Georgia State University Valerie Arboleda | UCLA Brunilda Balliu | UCLA Vikas Bansal | Low mappability genes in the human genome challenges and opportunities Elias Bareinboim | Columbia University Kayhan Batmanghelich | Boston University Gurkan Bebek | Case Western Reserve University Elhanan Borenstein | Tel Aviv University Brian Browning | Methods for detecting identity-by-descent segments Na Cai | Invasion of the heritable confounders Shai Carmi | Evaluating the utility of IVF embryo screening for polygenic disease risk Francesco Paolo Casale | Bayesian aggregation of multiple annotations enhances rare variant association testing Francesco Paolo Casale | AI-Enabled Imaging Genetics and Causal Inference in Genetic Biobanks Tim Chang | UCLA Rayan Chikhi | Living in the past of Genomics Rayan Chikhi | Tutorial on accessing SRA data Ercument Cicek | Privacy challenges in genomic data sharing Andy Dahl | UChicago Jessica Dennis | Novel approaches to study DNA methylation as a marker of gene-environment interplay in population-based biobanks reveals time-dependent associations with prenatal and childhood exposures Mohammed El Kebir | Integer Linear Programming for Computational Biology Jason Ernst | Computational methods for modeling and analyzing epigenomic data Jason Ernst | Computational methods for identifying associations of de novo non-coding variants and epigenetic variation with Autism Spectrum Disorder Eleazar Eskin | Separating good kmers from bad kmers in viral metagenomics Nandita Garud | Pervasive selective sweeps across human gut microbiomes Steven Gazal | University of Southern California Amy Goldberg | UCLA Casey Greene | The data generating process matters a case study with single cell biology Casey Greene | Bringing genetics to the point of care Ilan Gronau | Stdpopsim – a community-maintained library of standard population genetic simulation models Gamze Gürsoy | Privacy enhancing technologies and their applications to genomics Juan Gutiérrez | A Mathematical Theory of Discursive Networks Iman Hajirasouliha | Metagenomics analysis systems Jo Hardin | Pomona College Jaana Hartiala | Statistical Frontiers in GxE Meta-analysis for Coronary Artery Disease: Lessons from UK Biobank and All of Us Fereydoun Hormozdiari | UC Davis Margaux Hujoel | UCLA Haky (Hae Kyung) Im | How to train genetic predictors of epigenetic features with a sample size of one Iuliana Ionita-Laza | Columbia University Vanessa Jonsson | UC Santa Cruz Shalmali Joshi | Foundation models in health and medicine Shalmali Joshi | What makes a foundation model in health and medicine? Aly Khan | University of Chicago Jaehee Kim | Cornell University David Knowles | Using the Pyro probabilistic programming language for statistical genomics David Koslicki | Prokrustean Graph A Substring Index for Rapid K Mer Size Analysis | CGSI 2025 David Koslicki | Sketching for fast metagenomic analysis Smita Krishnaswamy | Deep neural network models for inference of cellular dynamics and underlying regulatory networks: MIOflow (manifold interpolating flows) Christina Leslie | Decoding gene regulation in 3D and in single cells Wei Li | University of California, Irvine Jingyi Jessica Li | mcRigor: a statistical method to enhance the rigor of metacell partitioning in single-cell data analysis Qunhua Li | Measure reproducibility of high throughput experiments and LLM generated analyses Sheng Li | University of Southern California Christoph Lippert | Deep Learning for Statistical Inference in Imaging Genetics Christoph Lippert | Conformal Prediction in Time Series Cong Ma | Inference of copy number aberrations using bulk and single cell sequencing data Ying Ma | Statistical and Computational Methods for Cell Type Deconvolution in Spatial Transcriptomics Nick Mancuso | Efficient count-based models improve power and robustness for large-scale single-cell eQTL Nick Mancuso | Computationally Scalable Approaches for Inference in Genetics and Genomics Siavash Mirarab | Incomplete lineage sorting phylogenetics meets population genetics Hosein Mohimani | Discovering novel natural product drugs by computational mass spectrometry Erin Molloy | Dynamic programming for scalable cell lineage tree reconstruction with interpretable optimality guarantees Jazlyn Mooney | Population genetics in Wild and Captive Populations of Conservation Concern: Challenges and Opportunities John Novembre | Population structure in human genetic data A basic introduction and some challenges Layla Oesper | Computational methods for improved inference of tumor evolution Loes Olde Loohuis | Large Language Models for Psychiatric Phenotype Extraction from Electronic Healt Loes Olde Loohuis | Inclusion bias affects genetic analyses in biobanks Bogdan Pasaniuc | The Good, The Bad, and The Polygenic: Genetic Scoring in Precision Medicine Pavel Pevzner | Algorithmic challenges in complete genomics and metagenomics Teresa Przytycka | Mutational signatures in cancer interplay of DNA damage and repair Rajesh Ranganath | NYU Ben Raphael | Spatiotemporal alignment of developmental processes Saharon Rosset | Expectation Maximization: Intro and Examples Saharon Rosset | Dating ancient splits in phylogenetic trees, with application to the human-Neanderthal split Sushmita Roy | Unsupervised representation learning with applications to 3D genome organization and cell-type-specific gene regulatory programs Julia Salzman | Stanford University Kris Sankaran | Modular Software for Mediation Analysis of Microbiome Data Sriram Sankararaman | New approaches for causal inference from genomic data Sriram Sankararaman | Learning representations for biomedical 3D imaging and tabular data Palash Sashitta | Evolutionary models and algorithms for tumor phylogeny inference Matteo Sesia | Model-X statistical inference for GWAS data Sagiv Shifman | Genotype–phenotype heterogeneity in autism Ritambhara Singh | Integrative Deep Learning for Heterogeneous Biomedical Datasets Pavel Skums | University of Connecticut Sagi Snir | From Gene Trees to a Species Tree Starting from the Basics Paul Spellman | UCLA Matthew Stephens | Nonnegative matrix factorization of count data with the shifted log transform Matthew Stephens | Genetic fine mapping via the Sum of Single Effects SuSiE model Daniel Tward | Moment kernels: a simple and scalable approach for equivariance to rotations and reflections in deep convolutional networks Peter Visscher | University of Oxford and University of Queensland Julia Vogt | ETH Zurich Wei Wang | UCLA Wenyi Wang | A Guide to Transcriptomic Deconvolution in Cancer Tandy Warnow | Advances in Large scale Multiple Sequence Alignment Xinzhu “April” Wei | Cornell University Jennifer Wilson | Predicting new drug phenotype by simulating off target effects Jason Xu | Eliciting simple and transparent algorithms for statistical learning via Majorization-Minimization (MM) Chongzhi Zang | Predicting functional transcription factors from various genomics data Shaojie Zhang | University of Central Florida Jasmine Zhou | UCLA Or Zuk | Generative Models and Their Applications in Computational Biology
