Prashant Emani, PhD
Associate Research ScientistCards
Appointments
Contact Info
About
Titles
Associate Research Scientist
Appointments
Molecular Biophysics and Biochemistry
Associate Research ScientistPrimary
Other Departments & Organizations
Education & Training
- PhD
- University of Washington, Physics (2012)
- MS
- University of Washington, Physics (2007)
- BS
- University of Minnesota, Twin Cities, Physics and Astrophysics (2006)
Research
Research at a Glance
Yale Co-Authors
Frequent collaborators of Prashant Emani's published research.
Publications Timeline
A big-picture view of Prashant Emani's research output by year.
Mark Gerstein, PhD
Nenad Sestan, MD, PhD
Alexander Urban, PhD
Alexej Abyzov, PhD
Andrew Miranker, PhD
Chao Cheng
7Publications
117Citations
Publications
Featured Publications
Single-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, 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 tissuesExpressionCellsChromatinLociMultiomicsAssessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases
Emani P, Geradi M, Gürsoy G, Grasty M, Miranker A, Gerstein M. Assessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases. Genome Research 2023, 33: 2156-2173. PMID: 38097386, PMCID: PMC10760520, DOI: 10.1101/gr.278322.123.Peer-Reviewed Original ResearchCitationsAltmetricInsights 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 ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsQuantum 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 studyComputerQuantum computing at the frontiers of biological sciences
Emani PS, Warrell J, Anticevic A, Bekiranov S, Gandal M, McConnell MJ, Sapiro G, Aspuru-Guzik A, Baker JT, Bastiani M, Murray JD, Sotiropoulos SN, Taylor J, Senthil G, Lehner T, Gerstein MB, Harrow AW. Quantum computing at the frontiers of biological sciences. Nature Methods 2021, 18: 701-709. PMID: 33398186, PMCID: PMC8254820, DOI: 10.1038/s41592-020-01004-3.Peer-Reviewed Original ResearchCitationsAltmetric
2024
The single-cell opioid responses in the context of HIV (SCORCH) consortium
Ament S, Campbell R, Lobo M, Receveur J, Agrawal K, Borjabad A, Byrareddy S, Chang L, Clarke D, Emani P, Gabuzda D, Gaulton K, Giglio M, Giorgi F, Gok B, Guda C, Hadas E, Herb B, Hu W, Huttner A, Ishmam M, Jacobs M, Kelschenbach J, Kim D, Lee C, Liu S, Liu X, Madras B, Mahurkar A, Mash D, Mukamel E, Niu M, O’Connor R, Pagan C, Pang A, Pillai P, Repunte-Canonigo V, Ruzicka W, Stanley J, Tickle T, Tsai S, Wang A, Wills L, Wilson A, Wright S, Xu S, Yang J, Zand M, Zhang L, Zhang J, Akbarian S, Buch S, Cheng C, Corley M, Fox H, Gerstein M, Gummuluru S, Heiman M, Ho Y, Kellis M, Kenny P, Kluger Y, Milner T, Moore D, Morgello S, Ndhlovu L, Rana T, Sanna P, Satterlee J, Sestan N, Spector S, Spudich S, Tilgner H, Volsky D, White O, Williams D, Zeng H. The single-cell opioid responses in the context of HIV (SCORCH) consortium. Molecular Psychiatry 2024, 1-12. PMID: 38879719, DOI: 10.1038/s41380-024-02620-7.Peer-Reviewed Original ResearchAltmetricConceptsContext of human immunodeficiency virusHuman immunodeficiency virusSubstance use disordersOpioid responseAnimal modelsEffects of substance use disordersOpioid pain medicationsPrevalence of co-morbid conditionsChronic pain syndromesStage of diseaseCell typesAffected cell typesCo-morbid conditionsPain syndromeImmunodeficiency virusPain medicationOpioid addictionIncreased riskRisk factorsHuman cohortsDrug addictionBrain tissue collectionBrain cell typesTissue collectionSingle-cell level
2023
Binding peptide generation for MHC Class I proteins with deep reinforcement learning
Chen Z, Zhang B, Guo H, Emani P, Clancy T, Jiang C, Gerstein M, Ning X, Cheng C, Min M. Binding peptide generation for MHC Class I proteins with deep reinforcement learning. Bioinformatics 2023, 39: btad055. PMID: 36692135, PMCID: PMC9907221, DOI: 10.1093/bioinformatics/btad055.Peer-Reviewed Original ResearchCitationsAltmetric
1996
Unifying Solution and Solid‐State NMR Studies of Nucleic Acid Dynamics
Pederson K, Echodu D, Emani P, Olsen G, Bardaro M, Shajani Z, Meints G, Miller P, Varani G, Drobny G. Unifying Solution and Solid‐State NMR Studies of Nucleic Acid Dynamics. 1996 DOI: 10.1002/9780470034590.emrstm1173.Peer-Reviewed Original ResearchCitationsConceptsSolid-state NMRSolid-state NMR studiesNucleic acidsNucleic acid systemsNMR relaxation techniquesInternal molecular motionsNucleic acid dynamicsNMR line shapesMolecular recognitionPresence of ligandsNMR ViewNMR studiesBiomolecular systemsDescription of DNAMolecular motionSpectroscopic measurementsBiophysical techniquesDynamic spectroscopyAcid systemHhaI methyltransferaseConformational transitionConformational adaptationProtein motionsProtein foldingNMR