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Derek Reiman

TitleResearch Assistant Professor
InstitutionUniversity of Chicago
DepartmentFamily Medicine
AddressChicago IL 60637
ORCID ORCID Icon0000-0002-7955-3980 Additional info
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    Collapse Overview 
    Collapse overview
    My research focuses on developing and applying computational and artificial intelligence methods to understand human health and disease. I integrate machine learning with diverse biological and clinical data—including genomics, transcriptomics, single-cell and spatial data, immunological measurements, and medical imaging—to uncover mechanisms of disease and identify clinically meaningful patterns.

    A major focus of my work is understanding interactions between the immune system, microbiome, and human disease, with applications spanning cancer, autoimmune, and metabolic disorders. I am particularly interested in developing AI and foundation-model approaches that can integrate multimodal biomedical data and translate complex biological measurements into actionable insights for clinical decision-making, including in resource-limited healthcare settings.

    Collapse Biography 
    Collapse education and training
    University of North Texas, Denton, TXBS12/2010Computer Science
    University of Illinois at Chicago, Chicago, ILPhD09/2021Computational Biology and Bioinformatics

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Ellis S, Song S, Reiman D, Hui X, Zhang R, Shahriar MH, Argos M, Kamal M, Shea CR, Grossman RL, Khan AA, Ahsan H. AI-assisted Diagnosis of Nonmelanoma Skin Cancer in Resource-Limited Settings. Cancer Epidemiol Biomarkers Prev. 2025 Jul 01; 34(7):1080-1088. PMID: 40287980; PMCID: PMC12209823.
      Citations:    Fields:    Translation:Humans
    2. Mallott EK, Kuthyar S, Lee W, Reiman D, Jiang H, Chitta S, Waters EA, Layden BT, Sumagin R, Manzanares LD, Yang GY, Sardaro MLS, Gray S, Williams LE, Dai Y, Curley JP, Haney CR, Liechty ER, Kuzawa CW, Amato KR. The primate gut microbiota contributes to interspecific differences in host metabolism. Microb Genom. 2024 12; 10(12). PMID: 39620695; PMCID: PMC11893272.
      Citations: 1     Fields:    Translation:HumansAnimals
    3. Lee J, Yurkovetskiy LA, Reiman D, Frommer L, Strong Z, Chang A, Kahaly GJ, Khan AA, Chervonsky AV. Androgens contribute to sex bias of autoimmunity in mice by T cell-intrinsic regulation of Ptpn22 phosphatase expression. Nat Commun. 2024 09 03; 15(1):7688. PMID: 39227386; PMCID: PMC11372096.
      Citations: 3     Fields:    Translation:AnimalsCells
    4. Weber LL, Reiman D, Roddur MS, Qi Y, El-Kebir M, Khan AA. Isotype-aware inference of B cell clonal lineage trees from single-cell sequencing data. Cell Genom. 2024 09 11; 4(9):100637. PMID: 39208795; PMCID: PMC11480863.
      Citations:    Fields:    Translation:HumansCells
    5. Lee J, Reiman D, Singh S, Chang A, Morel L, Chervonsky AV. Microbial influences on severity and sex bias of systemic autoimmunity. Immunol Rev. 2024 08; 325(1):64-76. PMID: 38716867; PMCID: PMC11338725.
      Citations: 2     Fields:    Translation:HumansAnimals
    6. Weber LL, Reiman D, Roddur MS, Qi Y, El-Kebir M, Khan AA. TRIBAL: Tree Inference of B cell Clonal Lineages. bioRxiv. 2023 Nov 27. PMID: 38076836; PMCID: PMC10705245.
      Citations:    
    7. Funsten MC, Yurkovetskiy LA, Kuznetsov A, Reiman D, Hansen CHF, Senter KI, Lee J, Ratiu J, Dahal-Koirala S, Antonopoulos DA, Dunny GM, Sollid LM, Serreze D, Khan AA, Chervonsky AV. Microbiota-dependent proteolysis of gluten subverts diet-mediated protection against type 1 diabetes. Cell Host Microbe. 2023 02 08; 31(2):213-227.e9. PMID: 36603588; PMCID: PMC9911364.
      Citations: 4     Fields:    Translation:HumansAnimalsCells
    8. Dotts AJ, Reiman D, Yin P, Kujawa S, Grobman WA, Dai Y, Bulun SE. In Vivo Genome-Wide PGR Binding in Pregnant Human Myometrium Identifies Potential Regulators of Labor. Reprod Sci. 2023 02; 30(2):544-559. PMID: 35732928; PMCID: PMC9988762.
      Citations: 7     Fields:    Translation:HumansCells
    9. Priyadarshini M, Navarro G, Reiman DJ, Sharma A, Xu K, Lednovich K, Manzella CR, Khan MW, Garcia MS, Allard S, Wicksteed B, Chlipala GE, Szynal B, Bernabe BP, Maki PM, Gill RK, Perdew GH, Gilbert J, Dai Y, Layden BT. Gestational Insulin Resistance Is Mediated by the Gut Microbiome-Indoleamine 2,3-Dioxygenase Axis. Gastroenterology. 2022 05; 162(6):1675-1689.e11. PMID: 35032499; PMCID: PMC9040389.
      Citations: 18     Fields:    Translation:HumansAnimals
    10. Ringeling FR, Chakraborty S, Vissers C, Reiman D, Patel AM, Lee KH, Hong A, Park CW, Reska T, Gagneur J, Chang H, Spletter ML, Yoon KJ, Ming GL, Song H, Canzar S. Partitioning RNAs by length improves transcriptome reconstruction from short-read RNA-seq data. Nat Biotechnol. 2022 05; 40(5):741-750. PMID: 35013600; PMCID: PMC11332977.
      Citations: 7     Fields:    Translation:Cells
    11. Reiman D, Layden BT, Dai Y. MiMeNet: Exploring microbiome-metabolome relationships using neural networks. PLoS Comput Biol. 2021 05; 17(5):e1009021. PMID: 33999922; PMCID: PMC8158931.
      Citations: 37     Fields:    Translation:Humans
    12. Reiman D, Manakkat Vijay GK, Xu H, Sonin A, Chen D, Salomonis N, Singh H, Khan AA. Pseudocell Tracer-A method for inferring dynamic trajectories using scRNAseq and its application to B cells undergoing immunoglobulin class switch recombination. PLoS Comput Biol. 2021 05; 17(5):e1008094. PMID: 33939691; PMCID: PMC8118552.
      Citations: 4     Fields:    Translation:AnimalsCells
    13. Reiman D, Farhat AM, Dai Y. Predicting Host Phenotype Based on Gut Microbiome Using a Convolutional Neural Network Approach. Methods Mol Biol. 2021; 2190:249-266. PMID: 32804370.
      Citations: 3     Fields:    Translation:Humans
    14. Reiman D, Metwally AA, Sun J, Dai Y. PopPhy-CNN: A Phylogenetic Tree Embedded Architecture for Convolutional Neural Networks to Predict Host Phenotype From Metagenomic Data. IEEE J Biomed Health Inform. 2020 10; 24(10):2993-3001. PMID: 32396115.
      Citations: 47     Fields:    
    15. Metwally AA, Yu PS, Reiman D, Dai Y, Finn PW, Perkins DL. Utilizing longitudinal microbiome taxonomic profiles to predict food allergy via Long Short-Term Memory networks. PLoS Comput Biol. 2019 02; 15(2):e1006693. PMID: 30716085; PMCID: PMC6361419.
      Citations: 21     Fields:    Translation:Humans
    16. Reiman D, Sha L, Ho I, Tan T, Lau D, Khan AA. Integrating RNA expression and visual features for immune infiltrate prediction. Pac Symp Biocomput. 2019; 24:284-295. PMID: 30864330.
      Citations: 7     Fields:    Translation:HumansCells
    17. Reiman D, Metwally A. Using convolutional neural networks to explore the microbiome. Annu Int Conf IEEE Eng Med Biol Soc. 2017 Jul; 2017:4269-4272. PMID: 29060840.
      Citations: 20     Fields:    
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