2025
Intelligence at the Edge of Chaos
Zhang, Shiyang, et al. "Intelligence at the Edge of Chaos." arXiv preprint arXiv:2410.02536 (2024).Peer-Reviewed Original Research
2024
HEART: Learning better representation of EHR data with a heterogeneous relation-aware transformer
Huang T, Rizvi S, Thakur R, Socrates V, Gupta M, van Dijk D, Taylor R, Ying R. HEART: Learning better representation of EHR data with a heterogeneous relation-aware transformer. Journal Of Biomedical Informatics 2024, 159: 104741. PMID: 39476994, DOI: 10.1016/j.jbi.2024.104741.Peer-Reviewed Original ResearchElectronic health recordsElectronic health record datasetDownstream tasksLanguage modelModeling electronic health recordsLearning better representationsPretrained language modelsEntity predictionRepresentation learningAnomaly detectionAttention weightsRelation embeddingsHealthcare applicationsEncoding schemeMed-BERTHigher-order representationsInput sequenceComputational costReadmission predictionPairwise relationshipsEHR dataElectronic health record dataSuperior performanceHeterogeneous contextsMedical entitiesLearning integral operators via neural integral equations
Zappala, E., Fonseca, A.H.d.O., Caro, J.O. et al. Learning integral operators via neural integral equations. Nat Mach Intell 6, 1046–1062 (2024). https://doi.org/10.1038/s42256-024-00886-8Peer-Reviewed Original ResearchLearning Integral Operators with Neural Integral Equations
Zappala, E., Fonseca, A. H. D. O., Caro, J. O., & van Dijk, D. (2022). Neural integral equations. arXiv preprint arXiv:2209.15190. (published at Nature Machine Intelligence)Peer-Reviewed Original ResearchBrainLM: A foundation model for brain activity recordings
Ortega Caro, J., Oliveira Fonseca, A. H., Averill, C., Rizvi, S. A., Rosati, M., Cross, J. L., ... & van Dijk, D. (2023). BrainLM: A foundation model for brain activity recordings. bioRxiv, 2023-09. (Published at ICLR 2024)Peer-Reviewed Original ResearchThe Role of Epstein-Barr Virus in Long COVID
Alexandra Tabachnikova, Jon Klein, Jamie Wood, Jillian Jaycox, Rahul Dhodapkar, Peiwen Lu, Jeff Gehlhausen, Bornali Bhattacharjee, David van Dijk, Aaron Ring, David Putrino, Akiko Iwasaki, The Role of Epstein-Barr Virus in Long COVID, The Journal of Immunology, Volume 212, Issue 1_Supplement, May 2024, Page 1121_6087, https://doi.org/10.4049/jimmunol.212.supp.1121.6087Peer-Reviewed Original ResearchSex differences in symptomatology and immune profiles of Long COVID.
Silva J, Takahashi T, Wood J, Lu P, Tabachnikova A, Gehlhausen JR, Greene K, Bhattacharjee B, Monteiro VS, Lucas C, Dhodapkar RM, Tabacof L, Peña-Hernandez M, Kamath K, Mao T, Mccarthy D, Medzhitov R, van Dijk D, Krumholz HM, Guan L, Putrino D, Iwasaki A. Sex differences in symptomatology and immune profiles of Long COVID. MedRxiv 2024 PMID: 38496502, DOI: 10.1101/2024.02.29.24303568.Peer-Reviewed Original ResearchCell2sentence: Teaching large language models the language of biology
Levine, D., Lévy, S., Rizvi, S. A., Pallikkavaliyaveetil, N., Chen, X., Zhang, D., ... & van Dijk, D. (2023). Cell2sentence: Teaching large language models the language of biology. bioRxiv, 2023-09. (Published at ICML 2024)Peer-Reviewed Original Research
2023
scNAT: a deep learning method for integrating paired single-cell RNA and T cell receptor sequencing profiles
Zhu B, Wang Y, Ku L, van Dijk D, Zhang L, Hafler D, Zhao H. scNAT: a deep learning method for integrating paired single-cell RNA and T cell receptor sequencing profiles. Genome Biology 2023, 24: 292. PMID: 38111007, PMCID: PMC10726524, DOI: 10.1186/s13059-023-03129-y.Peer-Reviewed Original ResearchLongitudinal single-cell transcriptional dynamics throughout neurodegeneration in SCA1
Tejwani L, Ravindra N, Lee C, Cheng Y, Nguyen B, Luttik K, Ni L, Zhang S, Morrison L, Gionco J, Xiang Y, Yoon J, Ro H, Haidery F, Grijalva R, Bae E, Kim K, Martuscello R, Orr H, Zoghbi H, McLoughlin H, Ranum L, Shakkottai V, Faust P, Wang S, van Dijk D, Lim J. Longitudinal single-cell transcriptional dynamics throughout neurodegeneration in SCA1. Neuron 2023, 112: 362-383.e15. PMID: 38016472, PMCID: PMC10922326, DOI: 10.1016/j.neuron.2023.10.039.Peer-Reviewed Original ResearchCausal identification of single-cell experimental perturbation effects with CINEMA-OT
Dong M, Wang B, Wei J, de O. Fonseca A, Perry C, Frey A, Ouerghi F, Foxman E, Ishizuka J, Dhodapkar R, van Dijk D. Causal identification of single-cell experimental perturbation effects with CINEMA-OT. Nature Methods 2023, 20: 1769-1779. PMID: 37919419, PMCID: PMC10630139, DOI: 10.1038/s41592-023-02040-5.Peer-Reviewed Original ResearchDistinguishing features of long COVID identified through immune profiling
Klein J, Wood J, Jaycox J, Dhodapkar R, Lu P, Gehlhausen J, Tabachnikova A, Greene K, Tabacof L, Malik A, Silva Monteiro V, Silva J, Kamath K, Zhang M, Dhal A, Ott I, Valle G, Peña-Hernández M, Mao T, Bhattacharjee B, Takahashi T, Lucas C, Song E, McCarthy D, Breyman E, Tosto-Mancuso J, Dai Y, Perotti E, Akduman K, Tzeng T, Xu L, Geraghty A, Monje M, Yildirim I, Shon J, Medzhitov R, Lutchmansingh D, Possick J, Kaminski N, Omer S, Krumholz H, Guan L, Dela Cruz C, van Dijk D, Ring A, Putrino D, Iwasaki A. Distinguishing features of long COVID identified through immune profiling. Nature 2023, 623: 139-148. PMID: 37748514, PMCID: PMC10620090, DOI: 10.1038/s41586-023-06651-y.Peer-Reviewed Original ResearchConceptsLong COVIDSARS-CoV-2Infection syndromeExaggerated humoral responseSoluble immune mediatorsEpstein-Barr virusPost-exertional malaiseCross-sectional studyHigher antibody responseImmune mediatorsImmune phenotypingImmune profilingHumoral responseAntibody responseLymphocyte populationsCOVID statusUnbiased machineCortisol levelsLC statusRelevant biomarkersViral pathogensSyndromeCOVIDFuture studiesBiological featuresAnatomical Diversity of the Adult Corticospinal Tract Revealed by Single-Cell Transcriptional Profiling
Golan N, Ehrlich D, Bonanno J, O'Brien R, Murillo M, Kauer S, Ravindra N, Van Dijk D, Cafferty W. Anatomical Diversity of the Adult Corticospinal Tract Revealed by Single-Cell Transcriptional Profiling. Journal Of Neuroscience 2023, 43: 7929-7945. PMID: 37748862, PMCID: PMC10669816, DOI: 10.1523/jneurosci.0811-22.2023.Peer-Reviewed Original ResearchConceptsCorticospinal tract neuronsCorticospinal tractAdult corticospinal tractIrreversible functional deficitsCortical layer 2/3Lumbar spinal cordSpinal cord injuryLayer 5 neuronsClasses of neuronsMolecular heterogeneityAxon collateralizationTract neuronsCord injuryRetrograde labelingMotor pathwaysFemale miceFunctional deficitsLayer 2/3Primary axonsSpinal cordTerminal fieldsNeuron subtypesAdult tractTherapeutic interventionsSingle-cell RNA sequencingContinuous Spatiotemporal Transformer
Fonseca, A. H. D. O., Zappala, E., Caro, J. O., & Van Dijk, D. (2023, July). Continuous Spatiotemporal Transformer. In International Conference on Machine Learning (pp. 7343-7365). PMLR.Peer-Reviewed Original ResearchNeural Integro-Differential Equations
Zappala E, de O. Fonseca A, Moberly A, Higley M, Abdallah C, Cardin J, Van Dijk D. Neural Integro-Differential Equations. Proceedings Of The AAAI Conference On Artificial Intelligence 2023, 37: 11104-11112. DOI: 10.1609/aaai.v37i9.26315.Peer-Reviewed Original ResearchIntegro-differential equationsIntegral operatorsDifferential equationsContinuous dynamical systemsNon-local dynamicsDynamical systemsInitial conditionsEquationsNeural networkTime extrapolationOperatorsIntegralsFundamental problemSuch dynamicsLatent spaceDynamicsNon-local processesBrain activity recordingsBrain dynamicsData scienceDifferential componentsIntegrandGeneralizationTheoryNetworkA machine learning method for the identification and characterization of novel COVID-19 drug targets.
Schultz B, DeLong LN, Masny A, Lentzen M, Raschka T, van Dijk D, Zaliani A, COPERIMOplus, Fröhlich H. A machine learning method for the identification and characterization of novel COVID-19 drug targets. Sci Rep 2023, 13: 7159. PMID: 37137934, DOI: 10.1038/s41598-023-34287-5.Peer-Reviewed Original ResearchNasal host response-based screening for undiagnosed respiratory viruses: a pathogen surveillance and detection study
Cheemarla N, Hanron A, Fauver J, Bishai J, Watkins T, Brito A, Zhao D, Alpert T, Vogels C, Ko A, Schulz W, Landry M, Grubaugh N, van Dijk D, Foxman E. Nasal host response-based screening for undiagnosed respiratory viruses: a pathogen surveillance and detection study. The Lancet Microbe 2023, 4: e38-e46. PMID: 36586415, PMCID: PMC9835789, DOI: 10.1016/s2666-5247(22)00296-8.Peer-Reviewed Original ResearchConceptsRespiratory virus panelPg/mLCXCL10 concentrationsSARS-CoV-2Bacterial pathobiontsRespiratory virusesSARS-CoV-2 negative samplesViral respiratory infectionsSARS-CoV-2 positive samplesClinical virology laboratoryHealth care systemVirus-positive samplesQuantitative RT-PCRInfluenza C virusSymptomatic patientsRespiratory infectionsSeasonal coronavirusesNasopharyngeal swabsVirus panelC virusCommon virusesCXCL10Host responseInterferon responseVirology laboratory
2022
Interspecies commensal interactions have nonlinear impacts on host immunity
Rice TA, Bielecka AA, Nguyen MT, Rosen CE, Song D, Sonnert ND, Yang Y, Cao Y, Khetrapal V, Catanzaro JR, Martin AL, Rashed SA, Leopold SR, Hao L, Yu X, van Dijk D, Ring AM, Flavell RA, de Zoete MR, Palm NW. Interspecies commensal interactions have nonlinear impacts on host immunity. Cell Host & Microbe 2022, 30: 988-1002.e6. PMID: 35640610, PMCID: PMC9283318, DOI: 10.1016/j.chom.2022.05.004.Peer-Reviewed Original ResearchConceptsImmunological outcomesCell activationIntestinal epithelial cell activationInflammatory bowel disease patientsBowel disease patientsDendritic cell activationMesenteric lymph nodesSystemic antibody responsesEpithelial cell activationImmunological milieuLymph nodesAntibody responseDisease patientsAkkermansia muciniphilaGnotobiotic miceHost immunityCommensal microbesHuman cohortsHuman gut bacteriaGut bacteriaMiceAllobaculumMuciniphilaDiseaseIncomplete penetranceSingle-cell multiomics reveals persistence of HIV-1 in expanded cytotoxic T cell clones
Collora JA, Liu R, Pinto-Santini D, Ravindra N, Ganoza C, Lama JR, Alfaro R, Chiarella J, Spudich S, Mounzer K, Tebas P, Montaner LJ, van Dijk D, Duerr A, Ho YC. Single-cell multiomics reveals persistence of HIV-1 in expanded cytotoxic T cell clones. Immunity 2022, 55: 1013-1031.e7. PMID: 35320704, PMCID: PMC9203927, DOI: 10.1016/j.immuni.2022.03.004.Peer-Reviewed Original ResearchConceptsHIV-1 eradicationHIV-1 RNAHIV-1Effector memory Th1 cellsHIV-1-infected individualsHIV-1-infected CD4Clonal expansionCell clonesMemory Th1 cellsCell clonal expansionPersistent antigenAntiretroviral therapyViral suppressionCytotoxic CD4Cytotoxic TTh1 cellsAntigen stimulationClonal expansion dynamicsUninfected individualsSurface protein expressionTNF responseUnstimulated conditionsTCR sequencesProtein expressionCD4Prdm6 controls heart development by regulating neural crest cell differentiation and migration
Hong L, Li N, Gasque V, Mehta S, Ye L, Wu Y, Li J, Gewies A, Ruland J, Hirschi KK, Eichmann A, Hendry C, van Dijk D, Mani A. Prdm6 controls heart development by regulating neural crest cell differentiation and migration. JCI Insight 2022, 7: e156046. PMID: 35108221, PMCID: PMC8876496, DOI: 10.1172/jci.insight.156046.Peer-Reviewed Original ResearchConceptsCardiac NCCNeural crest cell fateNeural crest cell differentiationSingle-cell RNA-seq analysisRNA-seq analysisDorsal neural tubeG1-S progressionFate-mapping approachCNCC migrationSpecification genesH4K20 monomethylationCell fateTranscriptomic analysisEpigenetic modifiersHeart developmentRegulated networkTranscript levelsKey regulatorMolecular mechanismsCell differentiationNeural tubePRDM6Ductus arteriosusPotential targetDifferentiation