David van Dijk, PhD, MSc, BSc
Assistant Professor of Medicine (Cardiovascular Medicine) and of Computer ScienceCards
Appointments
Contact Info
Yale School of Medicine
300 George Street, 2nd Floor, rm 2312
New Haven, Connecticut 06511
United States
About
Titles
Assistant Professor of Medicine (Cardiovascular Medicine) and of Computer Science
Biography
Dr. David van Dijk is Assistant Professor at Yale Dept. of Internal Medicine and Yale Dept. of Computer Science where he leads a research group that focuses on the cutting-edge application of machine learning methods to big biomedical data. His group develops new algorithms for discovering hidden structure, signals, and patterns in complex high-dimensional and high-throughput data, including single-cell RNA sequencing, microbiome, medical imaging, and electronic health records. His research team comprises trainees from diverse backgrounds, including computer science, mathematics, physics, biology, medicine, and neuroscience. Dr. van Dijk completed his PhD in Computer Science at the University of Amsterdam and the Weizmann Institute of Science, where he used machine learning to understand how gene regulation is encoded in DNA sequence. As a postdoc at Yale Genetics and Computer Science, he developed machine learning methods for single-cell data that are widely used in the biomedical community.
Website: vandijklab.org
Appointments
Cardiovascular Medicine
Assistant ProfessorPrimary
Other Departments & Organizations
- Cardiovascular Medicine
- Center for Biomedical Data Science
- Center for Infection and Immunity
- Center for RNA Science and Medicine
- Computational Biology and Biomedical Informatics
- Interdepartmental Neuroscience Program
- Internal Medicine
- Neuroscience Track
- Wu Tsai Institute
- Yale Cardiovascular Research Center (YCVRC)
- Yale Combined Program in the Biological and Biomedical Sciences (BBS)
Education & Training
- Postdoctoral Fellow
- Columbia University (2015)
- PhD
- University of Amsterdam, Computer Science (2013)
- Postdoctoral Fellow
- Weizmann Institute of Science (2013)
- MSc
- Free University of Amsterdam, Computer Science (2008)
- BSc
- Free University of Amsterdam, Computer Science (2005)
Research
Overview
Medical Research Interests
ORCID
0000-0003-3911-9925- View Lab Website
David van Dijk
Research at a Glance
Yale Co-Authors
Publications Timeline
Research Interests
David A. Hafler, MD, FANA
Akiko Iwasaki, PhD
F. Perry Wilson, MD, MSCE
Ruth R Montgomery, PhD
Smita Krishnaswamy, PhD
Craig B. Wilen, MD, PhD
Single-Cell Analysis
Computational Biology
Machine Learning
Deep Learning
Publications
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 ResearchConceptsElectronic 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 Research
Academic Achievements & Community Involvement
activity Yale CBB program
CommitteesCommittee MemberDetailsPhD qualifying committee member for Eric Ni, Yale CBB program2022 - Presentactivity CBB/BIDS Seminar Series
Meeting Planning and ParticipationCo-OrganizerDetails09/01/2022 - Presentactivity Learning the Language of Biology: Transforming Biomedical Discovery with Foundation Models and Causal Inference
Oral PresentationSTATGEN 2025Details05/21/2025 - PresentMinneapolis, MN, United StatesCollaboratorsactivity Learning the Language of Biology: Transforming Biomedical Discovery with Foundation Models and Causal Inference
Oral Presentation19th Wisconsin Stem Cell Symposium: Translational and Commercial Applications of Stem Cell-Derived TechnologiesDetails04/02/2025 - PresentMadison, WI, United Statesactivity Single-Cell Analysis in the Age of LLMs
Oral PresentationENAR 2025Details03/26/2025 - PresentNew Orleans, LA, United StatesCollaborators
Teaching & Mentoring
Mentoring
Emanuele Zappala
Postdoc2022 - 2024Neal Ravindra
Postdoc2019 - 2022Antonio Oliveira Fonseca
Graduate student2019 - 2024
News
News
- July 11, 2024Source: Yale Ventures
11 Yale Projects Receive Awards from the Colton Center for Autoimmunity
- November 27, 2023
Yale Researchers Shed Light on the Progression of Neurodegeneration
- November 02, 2023
Discovering the 'Cytokine Language' That Activates Immune Responses
- April 13, 2023
Discoveries & Impact (April 2023)
Get In Touch
Contacts
Yale School of Medicine
300 George Street, 2nd Floor, rm 2312
New Haven, Connecticut 06511
United States