Zhangyi He

Spatial resolution of transcriptomic plasticity states underpinning lethal morphologies in lung adenocarcinoma

This study uses spatial transcriptomics to analyze gene expression in lung adenocarcinoma morphologies, revealing plasticity and gene expression trajectories linked to lethal growth patterns.

Self-supervised AI reveals a lethal discohesive phenotype in lung adenocarcinoma

This paper uses self-supervised AI to identify under-appreciated stromal morphologies in lung adenocarcinoma linked to poor prognosis, independent of current clinical schemas.

Estimating temporally variable selection intensity from ancient DNA data II

This paper introduces a Bayesian framework for inferring time-varying selection from ancient DNA data, improving upon previous methods by addressing issues with allele age dependencies.

Estimating temporally variable selection intensity from ancient DNA data with the flexibility of modelling linkage and epistasis

This paper extends a method to infer temporally variable selection from ancient DNA data, accounting for linkage and epistasis, and applies it to horse pigmentation loci.

Estimating temporally variable selection intensity from ancient DNA data

This paper introduces a Bayesian framework to infer temporally variable selection from ancient DNA data by modeling genotype likelihoods and sample uncertainties, demonstrating improved selection inference using ancient horse coat color loci.

Inferring the timing and strength of natural selection and gene migration in the evolution of chicken from ancient DNA data

This paper introduces a Bayesian framework to estimate the timing and strength of natural selection and gene migration from ancient DNA data, applied to ancient chicken samples.

Moment-based approximations for the Wright-Fisher model of population dynamics under natural selection at two linked loci

This paper introduces two moment-based approximations for the Wright-Fisher model with natural selection at two linked loci, improving computational efficiency and avoiding distribution support issues.

Detecting and quantifying natural selection at two linked loci from time series data of allele frequencies with forward-in-time simulations

This paper develops a Bayesian framework to infer natural selection at linked loci using time series allele frequency data and forward simulations, showing improved accuracy with recombination and linkage modeling.

Maximum likelihood estimation of natural selection and allele age from time series data of allele frequencies

This paper develops a likelihood-based method to estimate natural selection and allele age from time series allele frequency data, showing improved accuracy over existing methods.

Numerical simulation of the two-locus Wright-Fisher stochastic differential equation with application to approximating transition probability densities

This paper develops a numerical scheme for solving the two-locus Wright-Fisher diffusion equation to approximate transition probability densities, improving computational efficiency and performance over existing methods.

Effects of the ordering of natural selection and population regulation mechanisms on Wright-Fisher models

This study examines how the order of natural selection and population regulation affects Wright-Fisher model dynamics, showing significant differences under strong selection and linkage disequilibrium.