Jason Liu
Postdoctoral AssociateAbout
Titles
Postdoctoral Associate
Appointments
Molecular Biophysics and Biochemistry
Postdoctoral AssociatePrimary
Other Departments & Organizations
Education & Training
- Postdoctoral Associate
- Yale University
- PhD
- Yale University, Computational Biology and Bioinformatics (2024)
- MSc
- Yale University, Computational Biology and Bioinformatics
- BA
- Yale University, Applied Math and Statistics (2017)
Research
Research at a Glance
Yale Co-Authors
Frequent collaborators of Jason Liu's published research.
Publications Timeline
A big-picture view of Jason Liu's research output by year.
Garrett Ash, PhD
Henry Pratt
Timur Galeev
Albert Higgins-Chen, MD/PhD
Alexander Urban, PhD
Alexej Abyzov, PhD
17Publications
1,986Citations
Publications
2024
Digital phenotyping from wearables using AI characterizes psychiatric disorders and identifies genetic associations
1. Liu J*, Borsari B*, Li Y, Liu S, Gao Y, Xin X, Lou S, Jensen M, Garrido-Martín D, Verplaetse T, Ash G, Zhang J, Girgenti M, Roberts W, Gerstein M. Digital phenotyping from wearables using AI characterizes psychiatric disorders and identifies genetic associations. In press. Cell 2024.Peer-Reviewed Original Research In PressSingle-cell genomics and regulatory networks for 388 human brains
Emani P, Liu J, Clarke D, Jensen M, Warrell J, Gupta C, Meng R, Lee C, Xu S, Dursun C, Lou S, Chen Y, Chu Z, Galeev T, Hwang A, Li Y, Ni P, Zhou X, Bakken T, Bendl J, Bicks L, Chatterjee T, Cheng L, Cheng Y, Dai Y, Duan Z, Flaherty M, Fullard J, Gancz M, Garrido-Martín D, Gaynor-Gillett S, Grundman J, Hawken N, Henry E, Hoffman G, Huang A, Jiang Y, Jin T, Jorstad N, Kawaguchi R, Khullar S, Liu J, Liu J, Liu S, Ma S, Margolis M, Mazariegos S, Moore J, Moran J, Nguyen E, Phalke N, Pjanic M, Pratt H, Quintero D, Rajagopalan A, Riesenmy T, Shedd N, Shi M, Spector M, Terwilliger R, Travaglini K, Wamsley B, Wang G, Xia Y, Xiao S, Yang A, Zheng S, Gandal M, Lee D, Lein E, Roussos P, Sestan N, Weng Z, White K, Won H, Girgenti M, Zhang J, Wang D, Geschwind D, Gerstein M, Akbarian S, Abyzov A, Ahituv N, Arasappan D, Almagro Armenteros J, Beliveau B, Berretta S, Bharadwaj R, Bhattacharya A, Brennand K, Capauto D, Champagne F, Chatzinakos C, Chen H, Cheng L, Chess A, Chien J, Clement A, Collado-Torres L, Cooper G, Crawford G, Dai R, Daskalakis N, Davila-Velderrain J, Deep-Soboslay A, Deng C, DiPietro C, Dracheva S, Drusinsky S, Duong D, Eagles N, Edelstein J, Galani K, Girdhar K, Goes F, Greenleaf W, Guo H, Guo Q, Hadas Y, Hallmayer J, Han X, Haroutunian V, He C, Hicks S, Ho M, Ho L, Huang Y, Huuki-Myers L, Hyde T, Iatrou A, Inoue F, Jajoo A, Jiang L, Jin P, Jops C, Jourdon A, Kellis M, Kleinman J, Kleopoulos S, Kozlenkov A, Kriegstein A, Kundaje A, Kundu S, Li J, Li M, Lin X, Liu S, Liu C, Loupe J, Lu D, Ma L, Mariani J, Martinowich K, Maynard K, Myers R, Micallef C, Mikhailova T, Ming G, Mohammadi S, Monte E, Montgomery K, Mukamel E, Nairn A, Nemeroff C, Norton S, Nowakowski T, Omberg L, Page S, Park S, Patowary A, Pattni R, Pertea G, Peters M, Pinto D, Pochareddy S, Pollard K, Pollen A, Przytycki P, Purmann C, Qin Z, Qu P, Raj T, Reach S, Reimonn T, Ressler K, Ross D, Rozowsky J, Ruth M, Ruzicka W, Sanders S, Schneider J, Scuderi S, Sebra R, Seyfried N, Shao Z, Shieh A, Shin J, Skarica M, Snijders C, Song H, State M, Stein J, Steyert M, Subburaju S, Sudhof T, Snyder M, Tao R, Therrien K, Tsai L, Urban A, Vaccarino F, van Bakel H, Vo D, Voloudakis G, Wang T, Wang S, Wang Y, Wei Y, Weimer A, Weinberger D, Wen C, Whalen S, Willsey A, Wong W, Wu H, Wu F, Wuchty S, Wylie D, Yap C, Zeng B, Zhang P, Zhang C, Zhang B, Zhang Y, Ziffra R, Zeier Z, Zintel T. Single-cell genomics and regulatory networks for 388 human brains. Science 2024, 384: eadi5199. PMID: 38781369, PMCID: PMC11365579, DOI: 10.1126/science.adi5199.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsSingle-cell genomicsSingle-cell expression quantitative trait locusExpression quantitative trait lociDrug targetsQuantitative trait lociPopulation-level variationSingle-cell expressionCell typesDisease-risk genesTrait lociGene familyRegulatory networksGene expressionCell-typeMultiomics datasetsSingle-nucleiGenomeGenesCellular changesHeterogeneous tissuesExpressionCellsChromatinLociMultiomics
2023
More than bad luck: Cancer and aging are linked to replication-driven changes to the epigenome
Minteer C, Thrush K, Gonzalez J, Niimi P, Rozenblit M, Rozowsky J, Liu J, Frank M, McCabe T, Sehgal R, Higgins-Chen A, Hofstatter E, Pusztai L, Beckman K, Gerstein M, Levine M. More than bad luck: Cancer and aging are linked to replication-driven changes to the epigenome. Science Advances 2023, 9: eadf4163. PMID: 37467337, PMCID: PMC10355820, DOI: 10.1126/sciadv.adf4163.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsStem cell divisionImmortalized human cellsTissue-specific cancer riskTumorigenic stateCell divisionDNA methylationEpigenetic changesAge-related accumulationHuman cellsMultiple tissuesSomatic mutationsClinical tissuesTissue differencesEpigenomeCellsTissueNormal tissuesMethylationMutationsReplicationNormal breast tissueSignaturesVitroAccumulationDivisionThe EN-TEx resource of multi-tissue personal epigenomes & variant-impact models
Rozowsky J, Gao J, Borsari B, Yang Y, Galeev T, Gürsoy G, Epstein C, Xiong K, Xu J, Li T, Liu J, Yu K, Berthel A, Chen Z, Navarro F, Sun M, Wright J, Chang J, Cameron C, Shoresh N, Gaskell E, Drenkow J, Adrian J, Aganezov S, Aguet F, Balderrama-Gutierrez G, Banskota S, Corona G, Chee S, Chhetri S, Cortez Martins G, Danyko C, Davis C, Farid D, Farrell N, Gabdank I, Gofin Y, Gorkin D, Gu M, Hecht V, Hitz B, Issner R, Jiang Y, Kirsche M, Kong X, Lam B, Li S, Li B, Li X, Lin K, Luo R, Mackiewicz M, Meng R, Moore J, Mudge J, Nelson N, Nusbaum C, Popov I, Pratt H, Qiu Y, Ramakrishnan S, Raymond J, Salichos L, Scavelli A, Schreiber J, Sedlazeck F, See L, Sherman R, Shi X, Shi M, Sloan C, Strattan J, Tan Z, Tanaka F, Vlasova A, Wang J, Werner J, Williams B, Xu M, Yan C, Yu L, Zaleski C, Zhang J, Ardlie K, Cherry J, Mendenhall E, Noble W, Weng Z, Levine M, Dobin A, Wold B, Mortazavi A, Ren B, Gillis J, Myers R, Snyder M, Choudhary J, Milosavljevic A, Schatz M, Bernstein B, Guigó R, Gingeras T, Gerstein M. The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models. Cell 2023, 186: 1493-1511.e40. PMID: 37001506, PMCID: PMC10074325, DOI: 10.1016/j.cell.2023.02.018.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and Concepts
2022
Forest Fire Clustering for single-cell sequencing combines iterative label propagation with parallelized Monte Carlo simulations
Chen Z, Goldwasser J, Tuckman P, Liu J, Zhang J, Gerstein M. Forest Fire Clustering for single-cell sequencing combines iterative label propagation with parallelized Monte Carlo simulations. Nature Communications 2022, 13: 3538. PMID: 35725981, PMCID: PMC9209427, DOI: 10.1038/s41467-022-31107-8.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and Concepts
2021
Cross-platform transcriptomic profiling of the response to recombinant human erythropoietin
Wang G, Kitaoka T, Crawford A, Mao Q, Hesketh A, Guppy FM, Ash GI, Liu J, Gerstein MB, Pitsiladis YP. Cross-platform transcriptomic profiling of the response to recombinant human erythropoietin. Scientific Reports 2021, 11: 21705. PMID: 34737331, PMCID: PMC8568984, DOI: 10.1038/s41598-021-00608-9.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsRNA-seqDifferential gene expressionPathway enrichment analysisRNA biologyTranscriptomic profilingTarget genesEnrichment analysisGene expressionEPO biologyMicroarray platformGene correlateCross-platform comparisonGenesBiologyImmune regulationHuman erythropoietinTissue protectionProfilingRegulationErythropoietinRecombinant human erythropoietinExpressionImportant toolErythropoiesisOxygen transportBayesian structural time series for biomedical sensor data: A flexible modeling framework for evaluating interventions
Liu J, Spakowicz DJ, Ash GI, Hoyd R, Ahluwalia R, Zhang A, Lou S, Lee D, Zhang J, Presley C, Greene A, Stults-Kolehmainen M, Nally LM, Baker JS, Fucito LM, Weinzimer SA, Papachristos AV, Gerstein M. Bayesian structural time series for biomedical sensor data: A flexible modeling framework for evaluating interventions. PLOS Computational Biology 2021, 17: e1009303. PMID: 34424894, PMCID: PMC8412351, DOI: 10.1371/journal.pcbi.1009303.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsDECODE: a Deep-learning framework for Condensing enhancers and refining boundaries with large-scale functional assays
Chen Z, Zhang J, Liu J, Dai Y, Lee D, Min MR, Xu M, Gerstein M. DECODE: a Deep-learning framework for Condensing enhancers and refining boundaries with large-scale functional assays. Bioinformatics 2021, 37: i280-i288. PMID: 34252960, PMCID: PMC8275369, DOI: 10.1093/bioinformatics/btab283.Peer-Reviewed Original ResearchCitationsAltmetricGene Tracer: a smart, interactive, voice-controlled Alexa skill For gene information retrieval and browsing, mutation annotation and network visualization
Lou S, Li T, Liu J, Gerstein M. Gene Tracer: a smart, interactive, voice-controlled Alexa skill For gene information retrieval and browsing, mutation annotation and network visualization. Bioinformatics 2021, 37: 2998-3000. PMID: 33792640, PMCID: PMC8479666, DOI: 10.1093/bioinformatics/btab107.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsAlexa skillAmazon Alexa skillInformation retrievalMutation annotationsVoice recognitionInteractive inputVisualization experienceDemonstration videoNetwork visualizationSupplementary dataGenome browserUsersMore flexibilityGene informationInformationQueriesBrowserBrowsingVideoKeyboardTechnological advancesRetrievalAnnotationNetworkBioinformaticsSCAN-ATAC-Sim: a scalable and efficient method for simulating single-cell ATAC-seq data from bulk-tissue experiments
Chen Z, Zhang J, Liu J, Zhang Z, Zhu J, Lee D, Xu M, Gerstein M. SCAN-ATAC-Sim: a scalable and efficient method for simulating single-cell ATAC-seq data from bulk-tissue experiments. Bioinformatics 2021, 37: 1756-1758. PMID: 33471102, PMCID: PMC8289380, DOI: 10.1093/bioinformatics/btaa1039.Peer-Reviewed Original ResearchCitationsAltmetric
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Graduate student2023 - 2024
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