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 HealthcareCan Alkan | Acceleration of bioinformatics workloadsMohammed Alser | Georgia State UniversityValerie Arboleda | UCLABrunilda Balliu | Digital Phenotyping for Psychiatric GeneticsVikas Bansal | Low mappability genes in the human genome challenges and opportunitiesElias Bareinboim | Columbia UniversityLisa Bastarache | Finding and phenotype rare disease in the EHRLisa Bastarache | Fun with PhecodesKayhan Batmanghelich | Boston UniversityGurkan Bebek | Case Western Reserve UniversityElhanan Borenstein | Tel Aviv UniversityBrian Browning | Methods for detecting identity-by-descent segmentsNa Cai | Invasion of the heritable confoundersShai Carmi | Evaluating the utility of IVF embryo screening for polygenic disease riskFrancesco Paolo Casale | Bayesian aggregation of multiple annotations enhances rare variant association testingFrancesco Paolo Casale | AI-Enabled Imaging Genetics and Causal Inference in Genetic BiobanksTim Chang | UCLARayan Chikhi | Living in the past of GenomicsRayan Chikhi | Tutorial on accessing SRA dataErcument Cicek | Privacy challenges in genomic data sharingAndy Dahl | UChicagoJessica 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 exposuresMohammed El Kebir | Integer Linear Programming for Computational BiologyJason Ernst | Computational methods for modeling and analyzing epigenomic dataJason Ernst | Computational methods for identifying associations of de novo non-coding variants and epigenetic variation with Autism Spectrum DisorderEleazar Eskin | Separating good kmers from bad kmers in viral metagenomicsNandita Garud | Pervasive selective sweeps across human gut microbiomesSteven Gazal | University of Southern CaliforniaAmy Goldberg | UCLACasey Greene | The data generating process matters a case study with single cell biologyCasey Greene | Bringing genetics to the point of careIlan Gronau | Stdpopsim – a community-maintained library of standard population genetic simulation modelsGamze Gürsoy | Privacy enhancing technologies and their applications to genomicsJuan Gutiérrez | A Mathematical Theory of Discursive NetworksIman Hajirasouliha | Metagenomics analysis systemsJo Hardin | Pomona CollegeJaana Hartiala | Statistical Frontiers in GxE Meta-analysis for Coronary Artery Disease: Lessons from UK Biobank and All of UsFereydoun Hormozdiari | UC DavisMargaux Hujoel | UCLAHaky (Hae Kyung) Im | How to train genetic predictors of epigenetic features with a sample size of oneIuliana Ionita-Laza | Columbia UniversityVanessa Jonsson | UC Santa CruzShalmali Joshi | Foundation models in health and medicineShalmali Joshi | What makes a foundation model in health and medicine?Aly Khan | University of ChicagoJaehee Kim | Cornell UniversityDavid Knowles | Using the Pyro probabilistic programming language for statistical genomicsDavid Koslicki | Prokrustean Graph A Substring Index for Rapid K Mer Size Analysis | CGSI 2025David Koslicki | Sketching for fast metagenomic analysisSmita 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 cellsWei Li | University of California, IrvineJingyi Jessica Li | mcRigor: a statistical method to enhance the rigor of metacell partitioning in single-cell data analysisQunhua Li | Measure reproducibility of high throughput experiments and LLM generated analysesSheng Li | DNA Methylome Analysis: From Short-Read to Long-Read Sequencing TechnologiesChristoph Lippert | Deep Learning for Statistical Inference in Imaging GeneticsChristoph Lippert | Conformal Prediction in Time SeriesCong Ma | Inference of copy number aberrations using bulk and single cell sequencing dataYing Ma | Statistical and Computational Methods for Cell Type Deconvolution in Spatial TranscriptomicsNick Mancuso | Efficient count-based models improve power and robustness for large-scale single-cell eQTLNick Mancuso | Computationally Scalable Approaches for Inference in Genetics and GenomicsSiavash Mirarab | Incomplete lineage sorting phylogenetics meets population geneticsHosein Mohimani | Discovering novel natural product drugs by computational mass spectrometryErin Molloy | Dynamic programming for scalable cell lineage tree reconstruction with interpretable optimality guaranteesJazlyn Mooney | Population genetics in Wild and Captive Populations of Conservation Concern: Challenges and OpportunitiesJohn Novembre | Population structure in human genetic data A basic introduction and some challengesLayla Oesper | Computational methods for improved inference of tumor evolutionLoes Olde Loohuis | Large Language Models for Psychiatric Phenotype Extraction from Electronic HealtLoes Olde Loohuis | Inclusion bias affects genetic analyses in biobanksBogdan Pasaniuc | The Good, The Bad, and The Polygenic: Genetic Scoring in Precision Medicine Pavel Pevzner | Algorithmic challenges in complete genomics and metagenomicsTeresa Przytycka | Mutational signatures in cancer interplay of DNA damage and repairRajesh Ranganath | Developing the mathematical foundations of explainability and using them to catch an LLM in a lieRajesh Ranganath | Some fundamentals of generative modelsBen Raphael | Spatiotemporal alignment of developmental processesSaharon Rosset | Expectation Maximization: Intro and ExamplesSaharon Rosset | Dating ancient splits in phylogenetic trees, with application to the human-Neanderthal splitSushmita Roy | Unsupervised representation learning with applications to 3D genome organization and cell-type-specific gene regulatory programsJulia Salzman | Stanford UniversityKris Sankaran | Modular Software for Mediation Analysis of Microbiome DataSriram Sankararaman | New approaches for causal inference from genomic dataSriram Sankararaman | Learning representations for biomedical 3D imaging and tabular dataPalash Sashitta | Evolutionary models and algorithms for tumor phylogeny inferenceMatteo Sesia | Model-X statistical inference for GWAS dataSagiv Shifman | Genotype–phenotype heterogeneity in autismRitambhara Singh | Integrative Deep Learning for Heterogeneous Biomedical DatasetsPavel Skums | University of ConnecticutSagi Snir | From Gene Trees to a Species Tree Starting from the BasicsPaul Spellman | UCLAMatthew Stephens | Nonnegative matrix factorization of count data with the shifted log transformMatthew Stephens | Genetic fine mapping via the Sum of Single Effects SuSiE modelDaniel Tward | Moment kernels: a simple and scalable approach for equivariance to rotations and reflections in deep convolutional networksPeter Visscher | University of Oxford and University of QueenslandJulia Vogt | ETH ZurichWei Wang | UCLAWenyi Wang | A Guide to Transcriptomic Deconvolution in CancerTandy Warnow | Advances in Large scale Multiple Sequence AlignmentXinzhu “April” Wei | Cornell UniversityJennifer Wilson | Predicting new drug phenotype by simulating off target effectsJason Xu | Eliciting simple and transparent algorithms for statistical learning via Majorization-Minimization (MM)Chongzhi Zang | Predicting functional transcription factors from various genomics dataShaojie Zhang | University of Central FloridaJasmine Zhou | UCLAOr Zuk | Generative Models and Their Applications in Computational Biology
