Armita Nourmohammad
Associate Professor of Immunobiology and Biomedical EngineeringCards
About
Research
Publications
2026
Experimental immunologists in the era of artificial intelligence
Wang Y, Ouyang W, Wang C, Nourmohammad A, Liu G, Wu N. Experimental immunologists in the era of artificial intelligence. Trends In Immunology 2026 PMID: 41856883, DOI: 10.1016/j.it.2026.01.003.Peer-Reviewed Original Research
2025
T cell receptor specificity landscape revealed through de novo peptide design
Visani G, Pun M, Minervina A, Bradley P, Thomas P, Nourmohammad A. T cell receptor specificity landscape revealed through de novo peptide design. Proceedings Of The National Academy Of Sciences Of The United States Of America 2025, 122: e2504783122. PMID: 41100668, PMCID: PMC12557503, DOI: 10.1073/pnas.2504783122.Peer-Reviewed Original ResearchConceptsT cell receptorDe novo designAmino acid preferencesTCR-pMHCDe novo peptide designProtein universeDiverse pathogensTCR-MHCSpecificity landscapeMHC-I allelesT cell receptor interactionT cell specificityCancer epitopesT-cell receptor specificityPeptide designPathogensPeptideT cellsBinding affinityImmunogenic peptidesMachine learning modelsHistocompatibility complexAdaptive immunityEffective bindingT cell activationDesign of high-specificity binders for peptide–MHC-I complexes
Liu B, Greenwood N, Bonzanini J, Motmaen A, Meyerberg J, Dao T, Xiang X, Ault R, Sharp J, Wang C, Visani G, Vafeados D, Roullier N, Nourmohammad A, Scheinberg D, Garcia K, Baker D. Design of high-specificity binders for peptide–MHC-I complexes. Science 2025, 389: 386-391. PMID: 40705892, DOI: 10.1126/science.adv0185.Peer-Reviewed Original ResearchConceptsAmino acid residuesPeptide-MHC-IAcid residuesDisease-associated peptidesCell surfaceDiseased cellsPeptide-specific T-cell activationChimeric antigen receptorT cell activationClass I major histocompatibility complexHistocompatibility complexProteinPeptidePeptide-MHC I complexesAntigen receptorImmune surveillanceIntracellular antigensCellsTherapeutic utilityResiduesTarget
2024
Holographic-(V)AE: An end-to-end SO(3)-equivariant (variational) autoencoder in Fourier space
Visani G, Pun M, Angaji A, Nourmohammad A. Holographic-(V)AE: An end-to-end SO(3)-equivariant (variational) autoencoder in Fourier space. Physical Review Research 2024, 6: 023006. PMID: 39711614, PMCID: PMC11661850, DOI: 10.1103/physrevresearch.6.023006.Peer-Reviewed Original ResearchLow-dimensional representationEnd-to-endLatent spaceState-of-the-art predictionsCategorical featuresPrediction of protein-ligand binding affinitiesLearned latent spaceState-of-the-artProtein-ligand binding affinityModel complex dataUnsupervised tasksUnsupervised learningExpressive representationNeural networkRandom forest regressorSpherical imagesComplex dataDiverse datasetsGeneration of dataLearning tasksForest regressorFourier encodingTaskEfficient approachRepresentationLocal and Global Variability in Developing Human T-Cell Repertoires
Isacchini G, Quiniou V, Barennes P, Mhanna V, Vantomme H, Stys P, Mariotti-Ferrandiz E, Klatzmann D, Walczak A, Mora T, Nourmohammad A. Local and Global Variability in Developing Human T-Cell Repertoires. PRX Life 2024, 2: 013011. PMID: 39582620, PMCID: PMC11583800, DOI: 10.1103/prxlife.2.013011.Peer-Reviewed Original ResearchT cell receptorCell typesT cell maturationAdaptive immune responsesT cellsStages of T cell maturationDiversity of T-cell receptorsHuman TCR repertoirePhenotypic specializationT-cell maturation stagesV(D)J recombinationImmune responseT cell receptor repertoireInterindividual variabilityHuman T cell repertoireT-cell receptor sequencingT cell repertoireSimilarity networkReceptor sequencesTCR repertoireThymocyte subsetsSequenceRepertoireCellsPathogensLearning the shape of protein microenvironments with a holographic convolutional neural network
Pun M, Ivanov A, Bellamy Q, Montague Z, LaMont C, Bradley P, Otwinowski J, Nourmohammad A. Learning the shape of protein microenvironments with a holographic convolutional neural network. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2300838121. PMID: 38300863, PMCID: PMC10861886, DOI: 10.1073/pnas.2300838121.Peer-Reviewed Original ResearchConceptsProtein structureBinding of protein complexesDesign of novel proteinsAmino acid preferencesImpact of mutationsProtein functionNovel proteinsProtein complexesProtein stabilityEvolutionary dataProteinPhysical interactionStructure-function mappingProtein microenvironmentFunctional informationSequenceAminoMutationsBindingBiologyH-CNNReversible, tunable epigenetic silencing of TCF1 generates flexibility in the T cell memory decision
Abadie K, Clark E, Valanparambil R, Ukogu O, Yang W, Daza R, Ng K, Fathima J, Wang A, Lee J, Nasti T, Bhandoola A, Nourmohammad A, Ahmed R, Shendure J, Cao J, Kueh H. Reversible, tunable epigenetic silencing of TCF1 generates flexibility in the T cell memory decision. Immunity 2024, 57: 271-286.e13. PMID: 38301652, PMCID: PMC10922671, DOI: 10.1016/j.immuni.2023.12.006.Peer-Reviewed Original ResearchConceptsT cellsCD8+ T cellsMemory T cell numbersT cell numbersOptimal immune responseImmune response magnitudeMemory potentialAcute infection modelResponse to stimulationImmune responseAntigen recognitionSelf-RenewalInfection modelPathogen clearanceMemory regulationCell numberEpigenetic silencingTCF1Response magnitudeCells
2023
Probabilities of developing HIV-1 bNAb sequence features in uninfected and chronically infected individuals
Kreer C, Lupo C, Ercanoglu M, Gieselmann L, Spisak N, Grossbach J, Schlotz M, Schommers P, Gruell H, Dold L, Beyer A, Nourmohammad A, Mora T, Walczak A, Klein F. Probabilities of developing HIV-1 bNAb sequence features in uninfected and chronically infected individuals. Nature Communications 2023, 14: 7137. PMID: 37932288, PMCID: PMC10628170, DOI: 10.1038/s41467-023-42906-y.Peer-Reviewed Original ResearchConceptsHIV-1BnAb developmentHIV-1-specific bnAbsHIV-1 neutralizing activityChronic HIV-1Generation of bnAbsHIV-1 vaccineB cell receptor repertoiresChronically infected individualsHCV-infected individualsBnAbsVaccine approachesChronic infectionNeutralizing antibodiesReceptor repertoireNeutralizing activityUninfected individualsUninfected peopleInfected individualsAntibodiesVaccineMolecular characteristicsInfectionChronicallyInductionSteering and controlling evolution — from bioengineering to fighting pathogens
Lässig M, Mustonen V, Nourmohammad A. Steering and controlling evolution — from bioengineering to fighting pathogens. Nature Reviews Genetics 2023, 24: 851-867. PMID: 37400577, PMCID: PMC11137064, DOI: 10.1038/s41576-023-00623-8.Peer-Reviewed Original Research
2022
Machine-Learning Model Reveals Protein-Folding Physics
Nourmohammad A, Pun M, Visani G. Machine-Learning Model Reveals Protein-Folding Physics. Physics 2022, 15: 183. DOI: 10.1103/physics.15.183.Peer-Reviewed Original Research
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