2024
A variational graph-partitioning approach to modeling protein liquid-liquid phase separation
Wang G, Warrell J, Zheng S, Gerstein M. A variational graph-partitioning approach to modeling protein liquid-liquid phase separation. Cell Reports Physical Science 2024, 5: 102292. DOI: 10.1016/j.xcrp.2024.102292.Peer-Reviewed Original ResearchPredicting spatially resolved gene expression via tissue morphology using adaptive spatial GNNs
Song T, Cosatto E, Wang G, Kuang R, Gerstein M, Min M, Warrell J. Predicting spatially resolved gene expression via tissue morphology using adaptive spatial GNNs. Bioinformatics 2024, 40: ii111-ii119. PMID: 39230702, PMCID: PMC11373608, DOI: 10.1093/bioinformatics/btae383.Peer-Reviewed Original ResearchConceptsGene expressionSpatial gene expressionSpatial transcriptomics technologiesTissue histology imagesExpressed genesGene activationTranscriptomic technologiesMolecular underpinningsGraph neural networksState-of-the-artSpatial expressionGenesTissue architectureExpressionHistological imagesNeural network
2022
Insights from incorporating quantum computing into drug design workflows
Lau B, Emani P, Chapman J, Yao L, Lam T, Merrill P, Warrell J, Gerstein M, Lam H. Insights from incorporating quantum computing into drug design workflows. Bioinformatics 2022, 39: btac789. PMID: 36477833, PMCID: PMC9825754, DOI: 10.1093/bioinformatics/btac789.Peer-Reviewed Original ResearchConceptsQuantum machine learningComputer-aided drug designMachine-learning moduleQuantum computing methodsCommercial quantum computersMachine learningJupyter notebooksNeural networkComputing methodClassical baselinesDesign workflowQML modelsQuantum hardwarePython codeAcademic useSupplementary dataQuantum computerWorkflowJudicious partitioningModuleHardwareGitHubClassical counterpartCase studyComputer