Publications

See my Google Scholar profile for an up-to-date list of publications.

2026 GenePT Revisited: Do Better Text Embeddings Make Better Gene Embeddings? bioRxiv LLMembeddingvirtual cell 2025 LangPert: LLM-Driven Contextual Synthesis for Perturbation Prediction MLGenX at ICLR 2025 LLMvirtual cellreasoning 2025 SynthPert: Enhancing LLM Biological Reasoning via Synthetic Reasoning Traces Arxiv LLMpost-trainingreasoningvirtual cell 2024 Enhancing Generative Perturbation Models with LLM-Informed Gene Embeddings MLGenX at ICLR 2024 LLMvirtual cellGaussian Process 2023 Disentangling Shared and Private Latent Factors in Multimodal VAEs MLCB VAEmulti-omics 2020 BasisVAE: Translation-Invariant Feature-Level Clustering with VAEs AISTATS VAEclusteringhierarchical Bayes 2020 Neural Decomposition: Functional ANOVA with Variational Autoencoders AISTATS VAEinterpretability 2019 Decomposing feature-level variation with Covariate Gaussian Process Latent Variable Models ICML 2019 Gaussian Processdimensionality reductiongene expression 2019 Augmented Ensemble MCMC sampling in Factorial Hidden Markov Models AISTATS 2019 MCMCHMMprobabilistic modeling 2016 seqlm: an MDL based method for identifying differentially methylated regions in high density methylation array data Bioinformatics 2016 methylationMDLR package 2016 Predicting quantitative traits from genome and phenome with near perfect accuracy Nature Communications 2016 genomicsquantitative geneticsprediction