Alan Murphy

Alan Murphy

he/him

Postdoctoral Research Scientist at CSHL | Deep learning for genomics

Alan Murphy

Computational Biologist | Postdoctoral Researcher, Cold Spring Harbor Laboratory, New York

   

Hi, I'm Alan Murphy, a computational biologist conducting my postdoctoral research in Dr. Peter Koo's lab at Cold Spring Harbor Laboratory. My research focuses on developing and refining sequence-to-function (seq2func) models that uncover the cis-regulatory code — the rules by which DNA sequence dictates gene regulatory activity — and that are interpretable, generalisable across contexts, and tightly coupled to experimental perturbations and functional readouts. Beyond research, I co-created and serve as editor for the Genomics × AI blog, a growing community hub highlighting methods and applications at the intersection of genomics and machine learning. This initiative reflects my dedication to scholarly leadership and knowledge sharing in computational biology.

 

Research Vision & Impact

I aim to uncover the cis-regulatory code — the rules by which DNA sequence dictates gene regulation — by developing interpretable, generalisable sequence-to-function (seq2func) models. My work integrates computational modeling and experimental perturbations, including functional assays, to systematically probe how regulatory sequences control cellular phenotypes.

Key goals of my research include:

  • Building models that generalise across cell types and experimental contexts, enabling predictive insights beyond the training data.
  • Improving interpretability, so that computational predictions reveal mechanistic principles of gene regulation.
  • Developing open-access tools and resources to promote reproducibility and empower the genomics community.

Through this approach, I seek to bridge predictive modeling with mechanistic understanding, advancing both fundamental insights into gene regulation and the methodological foundations of regulatory genomics.

 

Download CV Google Scholar Genomics × AI Blog

 

News

  • 2026-02-20

    Published a blog post on fine-tuning AlphaGenome for MPRA and STARR-seq data on the Genomics x AI blog, highlighting the approach of treating sequence-to-function models as modular regulatory encoders leading to state-of-the-art results across perturbation assays.

  • 2025-10-10

    Presented our work on causal refinement for genomic deep learning models through continual learning at MLCB 2025. Check out the talk on the MLCB YouTube channel.

  • 2025-03-03

    Joined Peter Koo’s group at Cold Spring Harbor Laboratory, New York to develop methods to improve genomic sequence-to-function and genomic language models.

  • 2024-12-11

    Our ChromExpress paper investigating the relationship of histone marks with expression using deep learning is out in Nucleic Acids Research (NAR)! See a quick overview on X/Twitter.

  • 2024-11-16

    Our Enformer Celltyping paper, a genomic DNN to accurately predict epigenetic signals in previously unseen cell types, is out in Nature Communications! See more on Twitter or on BlueSky.

  • 2023-12-04

    Our re-analysis paper of the first single-cell RNA-seq Alzheimer’s disease dataset is out in eLife! Check out an overview here.

  • 2023-09-25

    Presented my PhD work predicting the cell type-specific effects of genetic variants on the epigenome at the Kipoi Summit for computational regulatory genomics.

  • 2023-07-29

    Presented a session on single-cell genomics for Alzheimer’s disease as part of ADDI’s Summer Learning Series.

  • 2022-12-22

    Our paper benchmarking differential expression methods for single-cell RNA-seq is out in Nature Communications! Check out our overview here.

  • 2021-10-02

    MungeSumstats, our software for rapid standardisation and quality control of GWAS or QTL summary statistics, is now out in Bioinformatics.

  • 2021-07-19

    Thrilled to officially start my PhD with Dr. Nathan Skene’s group in the Department of Brain Sciences, Imperial College London as part of the UK DRI.

Selected Publications

This is a selection of recent work. For a complete and always up-to-date list, see my Google Scholar profile.