Probabilistic Modeling in Genomics
March 5 - 8, 2025

You must register for the meeting in order to submit abstracts.
After registering you will be sent a web link for abstract submission by email.
You may copy and paste your abstract from Word, Google Docs, or Notepad; abstracts are limited to ~2900 characters.

Program information: An electronic version of the program abstract book will be sent three working days prior to the first day of the meeting, and hard copies will be available for collection upon your arrival at Cold Spring Harbor Laboratory. First night and keynote speakers are informed of their session date and time, otherwise program information is only available upon release of the electronic version of the abstract book. The reason we do this is to try and maximize interactions by encouraging participants to stay for the duration of the meeting.

Please check your email for talk length, poster instructions, and how to have your poster printed at CSHL for collection upon arrival. 

Abstract Status

Presenting Author

Abstract Title

Talk/Poster

Anderson-Trocme, Luke

Breaking boundaries—Leveraging continuous models for improved population genetics analyses

poster

Aw, Alan J

Gene-ancestry interactions mediate individual heterogeneity in causal effects on complex traits in admixed populations

poster

Bailey, Nick

Population genetic simulations of codon sequence evolution at phylogenetic scale

talk

Barton, John

Disentangling trait and allele-level selection in temporal genetic data

poster

Baumdicker, Franz

Simulation-based neural posterior estimation for population genetics

poster

Berg, Jeremy J

Population structure, PCA, and residual confounding in GWAS

talk

Cai, Jiachen

Hierarchical Dirichlet processes to study tumor-immune microenvironments in paired single-cell RNA-seq and spatial transcriptomics data

poster

Cao, Hongyuan

A new distinguishability criterion for assessing replicability in genomic studies

poster

Cao, Hongyuan

Heritability—A counterfactual perspective

poster

Carlson, Maryn

Robust detection of specific epistasis

poster

Chaffee, Ryan K

Population genetics consequences of habitat fragmentation for the conservation of wild populations

poster

Chakraborty, Shreya

Understanding polygenic score portability through the lens of local ancestry

poster

Charmouh, Anders Poulsen

Estimating gene conversion tract length and rate from PacBio HiFi data

poster

Charney, Max

A deep learning pipeline for pancancer survival modeling and the revealing of SNAPC3 as a biomarker candidate via adaptive feature gating

poster

Chen, Yang

Deciphering the contribution of 3D interactions between cis-regulatory elements and promoters to regulate gene expression using graph neural networks

poster

Chiang, Charleston

A genealogy-based framework to infer the demographic history, genetic structure, and phenotype association

poster

Chotai, Meera

Estimating dominance and selection coefficients from biobank-scale genotypes

talk

Christ, Ryan

Variant set distillation

poster

Cole, Jared M

A surprising driver of sign bias in allelic effects on complex traits

poster

Conover, Justin L

Flexible and biologically motivated genotyping priors improve genotyping accuracy along the autopolyploid-allopolyploid continuum

poster

Dabi, Amjad

Evolutionary rescue model informs strategies for driving cancer cell populations to extinction

poster

Danning, Rebecca

eTopic-SCORE—An ensemble machine learning method for robust natural language processing of single-cell transcriptomics data

poster

Degiorgio, Michael

Efficient detection and characterization of targets of natural selection using transfer learning

talk

DeHaas, Drew C

Joint parametric inference of complex demographic history using composite likelihood based on whole-genome genealogy

talk

Deng, Yun

Low dimensional embedding of the Ancestral Recombination Graph—A unified framework for population structure and local ancestry

poster

Diaz-Papkovich, Alex

Population genetics in the information ecosystem—The social consequences of probabilistic modelling of human populations

poster

Do, Dat

Large-sample theory and model selection in admixture models

poster

Dowell, Robin

A complete model of RNA polymerase II uncovers unique features of termination

talk

Dura, Katherine

Variant effect prediction across multiple experiments with BIRDBath

poster

Fariello, María Inés

Detecting selection in admixed populations using hapFLK

poster

Fortes-Lima, Cesar A

Spatial modelling and population genomics methods to investigate human history in Africa

poster

Garg, Prakriti

Graph representation learning framework for principled analysis of orthologous regulatory regions across more than two species

talk

Garud, Nandita

Pervasive selective sweeps within and across human gut microbiomes

talk

Ghosh, Deepjyoti

Accounting for recurrent mutation in the SFS of ultra-rare alleles

poster

Gibbon, Sam R

Modeling mutation-selection balance in allo- and autotetraploids

poster

Goldberg, Amy

An epidemiological-evolutionary model of complex pathogen lifecycle

poster

Green, Anna G

Forecasting antibiotic resistance using biophysics and machine learning

talk

Guez, Jeremy

Deep learning-augmented models of gnomAD v4 enable estimation of LoF mutational constraint for all human genes

poster

Gursoy, Gamze

Quantification of private information leakage from omics data

talk

Gutenkunst, Ryan N

GHIST1—The 1st Genomic History Inference Strategies Tournament

talk

Harris, Mariana

Removing the need for perfect simulations—Domain-adaptive neural network reveals hard selective sweeps dominate in aDNA

poster

Hingerl, Johannes

Scooby—Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution

talk

Holness, Shevaughn T

Impact of missing contexts and environmental variables on polygenic risk score calibration

poster

Hoyt, Stephanie

TrioBEAST—A Bayesian model for estimating allele-specific expression in familial trios

poster

Huang, Ziwei

A resampling-based framework for learning Markov networks from high-dimensional data

poster

Izarraras-Gomez, Alan

Inference of the distribution of fitness effects using local genealogies

talk

Johri, Parul

A gene-based model of fitness and its implications for genetic variation

talk

Kang, Yijie

Designing DNA with tunable regulatory activity using discrete diffusion

poster

Kanteh, Abdoulie

Phylodynamic analysis of SARS-CoV-2 infection in The Gambia—A 2-year genomic surveillance investigation

poster

Kaplan, Noam

Learning mechanistic probabilistic models of 3D genome organization de novo

poster

Kerdoncuff, Elise

Disentangling the role of admixture, founder events and selection—The case of lactase persistence in South Asia

talk

Kim, Jaehee

Bayesian phylodynamic inference of population dynamics with dormancy

talk

Koo, Peter

Uncertainty-aware genomic deep learning with knowledge distillation

poster

Korfmann, Kevin

Coalescence and translation—Leveraging large language models for population genetics

talk

Kuru, Nurdan

Leveraging ARGs for population-free PRS prediction

poster

Lee, Hanbin

tslmm—Complex trait modelling with ancestral recombination graphs

talk

Lemanczyk, Marta S

A toolkit for evaluating post-hoc interpretability in the genomic domain

poster

LeMay, Charlotte M

ARG inference for gene duplicates

poster

Li, Hui

FunKAT improves the power of gene-based association test by modeling the functional heterogeneity of variants within genes

poster

Li, Jinmin

Leveraging ancestral recombination graphs for artificial genome simulation

poster

Liang, Jiatong

A fast general framework for demographic inference using IICR curves

poster

Lim, Daven

The evolution of structural variation across the vertebrate tree of life

poster

Lin, Ying Fei

Root estimation in phylogenetic trees using deep learning

poster

Liu, Jiayi

Computational framework for predicting the effect of non-coding variation

poster

Liu, Yang

Monitoring rapid evolution of recombinant inbred lines with Pool-seq in plants

poster

Liu, Yuda

Multi-task matrix factorization for cell type-specific transcription factor activity estimation

poster

Loell, Kaiser

A systematic evaluation of the impact of output distribution and nonlinearity on genomic deep neural net training performance

poster

Long, Micaela

Genomic data visualization using graphs and Fermat distance

poster

Lorenz, Anna

Age-related protein changes in Hispanic/Latino individuals

poster

Lu, Wenhan

Heritability and effect-size distribution of rare and de novo protein-coding variation

talk

Machado, Luiz C

Ancestral recombination graphs for detecting adaptive introgression in the maize genome

poster

Markarian, Nicholas

Mixtures of Gaussian latent variable models

talk

Martens, Laura D

Dissecting single-cell gene regulation with scooby—From eQTLs to organoid development

poster

Martí-Gómez, Carlos

Learning sequence-function relationships with scalable and biologically interpretable gaussian process models

poster

Massey, Dashiell

Instability in the inference of parental global ancestry proportion from offspring

poster

Matthews, Jamie E

Liabilideep—A deep learning approach to modeling covariates in non-randomly ascertained genetic association studies

poster

Mawass, Walid

Evaluating confounding bias in polygenic score associations due to imperfect control of population stratification

poster

Mazzeo, Giovanni R

Inferring fluctuating selection from a snapshot of genetic variation

poster

Medina Tretmanis, Jazeps

Joint inference of continental and archaic ancestry—A deep learning approach

talk

Messer, Conor

Applying statistics-first, reference-free genomics analysis to diverse human whole genome data

poster

Mies, Georgia

Evaluating local ancestry inference methods to identify post-admixture adaptation in Neolithic Europe

poster

Munch, Kasper

Probabilistic modeling in genomics

poster

Narayanan, Manikandan

MultiPopPred—A trans-ethnic disease risk prediction method, and its application to the South Asian population

poster

Nordborg, Magnus

Towards an unbiased characterization of genetic polymorphism

poster

Ortega-Del Vecchyo, Diego

Natural selection acting on complex traits hampers the predictive accuracy of polygenic scores in ancient samples

talk

Osele, Metu

DeepTaxon—Using deep learning for biological classification

talk

Pacheco, Antonio F

Balancing, linkage and effects of selection—a deep learning approach

poster

Palpant, Nathan

Combinatorial multivariate epigenomic patterns reveal the genomic basis of cell phenotypes underpinning complex traits

poster

Pedersen, Bjarke M

Correlated landscapes of genomic diversity across primates are driven by non-neutral processes

poster

Pe'er, Dana

Through the Wasserstein Wormhole—Exploring tissue biology

talk

Pennell, Matt

Macroevolutionary divergence in gene expression driven by selection on protein abundance

talk

Poon, Yeuk Pin Gladys

Multi-state evolutionary model quantifies tumour cellular plasticity

talk

Ragsdale, Aaron P

Stabilizing selection shapes the distribution of shared variation after introgression

poster

Rahman Hera, Mahmudur

Fast and scalable genome-wide mutation rate calculation using k-mers and sketching

poster

Rahman, Amatur

Efficient and robust computation of EHH-based statistics for large-scale data

poster

Ralph, Peter

Dating large ARGs, with clinical applications

talk

Riall, Kellen T

Information about the derived orientation of disease risk-increasing variants provides power to detect signals of directional selection on diseases

poster

Robson, Eyes S

The ACGTs of language modeling

poster

Roshani, Rashedeh

Gene and protein expression changes associated with liver disease in Hispanic/Latino population at risk for metabolic-associated fatty liver disease

poster

Sadowski, Michal

Towards resolving scaling and endogeneity induced confounding in gene-environment interaction tests

poster

Schraiber, Joshua G

An evolution-guided genetic relatedness matrix reveals the action of natural selection in shaping complex trait variation

talk

Schrider, Daniel

Rapid adaptation via soft sweeps in Aedes aegypti

poster

Schroeder, Jeremy

ShapeME—A tool and web front-end for de novo discovery of structural motifs underpinning protein-DNA interactions

poster

Scicluna, Matthew C

PHATE effectively captures continuous population structure in human genomic data

poster

Seitz, Evan

Deciphering the determinants of mechanistic variation in regulatory sequences

poster

Sgarlata, Gabriele M

Quantifying the genome-wide effect of polygenic selection over a single generation

talk

Shastry, Vivaswat

Computing likelihoods for genealogies under selection

poster

Shi, Zhuozheng

Genetic causal effect similarity across local ancestries in Hispanic Latino Americans

poster

Si, Yichen

Genealogy-informed genotype calling of human Y chromosome in large scale sequencing data

poster

Simons, Yuval B

Stabilizing selection generates selection against introgressed DNA

poster

Singh, Vinod K

Methylation-based cell type classification at single DNA read level

poster

Smith, Megan

Accurate inferences of introgression in the presence of model violations using machine learning

talk

Smith, Thomas Q

Identifying evolutionary influences on local genomic patterns of genetic relatedness

poster

Snell, Hannah

WINDEX—A hierarchical integration of site- and window-based statistics for modeling the footprint of positive selection

poster

Specht, Ivan

PhyloSMC—Fast, parallel Bayesian phylogenetics via Sequential Monte Carlo

talk

Spence, Jeffrey P

Specificity, length, and luck—How genes are prioritized by rare and common variant association studies

poster

Staklinski, Stephen J

Bayesian inference of the metastasis graph from cancer cell lineage tracing data

talk

Stentella, Tommaso

A novel Bayesian method to perform demographic inference from genomic data

poster

Subramanian, Lakshminarayanan

The elusive search for a gold-standard zero imputation method

poster

Syed, Maha

plinkQC—A genomic ancestry and quality control R/CRAN package

poster

Tagami, Daiki

tstrait—A quantitative trait simulator for ancestral recombination graphs

poster

Tayeb, Karl

A Bayesian approach to gene set enrichment analysis that identifies redundant and complimentary gene sets

poster

Tella, Sri Manjusha

Cell type classification using deep learning models—Evaluating the impact of Hi-C data normalization on similarity measures

poster

Tian, Xiaohe

Assortative mating estimates between populations and confounding by socioeconomic status

poster

Tittes, Silas

Adding selection to stdpopsim

poster

Tomaz da Silva, Pedro

Nucleotide dependency analysis of DNA language models reveals genomic functional elements

poster

Tsai, Yi-Ting

Distance metrics and statistical summaries of labeled phylogenies

poster

Turfah, Ali

PHM—Multiresolution clustering of genomic data

poster

Valadares Barroso, Gustavo

A new model of background selection in non-equilibrium populations

poster

Vaughn, Andrew H

The impact of ancient selective pressures and dietary changes on obesity and weight-related diseases in modern Eurasian populations

poster

Wang, Bo

DAP-S—An improved variable selection approach for probabilistic fine-mapping analysis

poster

Wang, Jeremy

The problem with gestalt genetics—Genetic association does not commute with addition

poster

Wang, Qifan

Improving polygenic score portability using local BLUP

poster

Wang, Ting-Chen

Investigate sex-specific genetic effects on neurological traits and disorders through genetically regulated gene expression

poster

Willwerscheid, Jason

gEBMF—A fast and flexible matrix-factorization approach to discovering structure in multi-omics data.

poster

Xia, Ziyang

Patterns of genetic variation in populations with source-sink dynamics

poster

Xing, Jiawei

A modeling framework for differential gene expression analyses leveraging lineage phylogenies of metastatic cancers

poster

Xu, Bingxian M

Variational inference of single cell time series

poster

Xu, Perry Peiyu

Tree-based inference methods for Mycobacterium tuberculosis transmissibility

poster

Yao, Liwen

DeepCRE—A multimodal transformer framework for decoding and generating tissue-specific mammalian enhancers

poster

Yohannes, Mary T

Genomic variation and ethnolinguistic diversity in >42k eastern and southern Africans highlight the relationship between genetic variation and individuals’ cultural affiliations

talk

Zaidi, Arslan A

Behavior of random-effect SNP heritability estimators in admixed populations

poster

Zhang, Joy Zhichun

Efficient inference frameworks for the seedbank coalescent with a fixed genealogy

poster

Zhang, Yali

Prematurity and genetic liability for autism spectrum disorder

poster

Zhou, Juannan

importance of higher-order epistasis in protein sequence-function relationships

poster

Zhu, Yixin

Modeling the fitness effects of missense and non-coding variants using rare-variant genealogies

poster