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Arjun Raman

TitleAssistant Professor
InstitutionUniversity of Chicago
DepartmentPathology
AddressChicago IL 60637
Email
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    Collapse Overview 
    Collapse overview
    Biological systems are thought to be exceedingly 'complex'--comprised of many parts and sets of unintuitive interactions between parts conferring system function. My lab is interested in elucidating principles of structure, function, and adaptability relationships with the ultimate goals of (i) characterizing 'personalized' variation in biological systems with high-fidelity, (ii) creating tools to genetically engineer variation in a rational way, and (iii) engineering natural-like, adaptive systems de novo. We use a blend of theory, computation, and experiment applied to a range of model systems spanning neural networks to electronic health record data to complex ecosystems inhabiting humans in addressing these concepts.

    Collapse Biography 
    Collapse education and training
    University of Chicago, ChicagoB.A.06/2008Physics
    University of Chicago, ChicagoB.S.06/2008Chemistry (Honors)
    University of Texas at Southwestern, DallasM.D.06/2017Medicine
    University of Texas at Southwestern, DallasPh.D.06/2017Molecular Biophysics
    Washington University in St. Louis, St. Louis06/2020Clinical Pathology

    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. Behera V, Guzzetta A, Giba H, Pen UY, Di Lello A, Pandey B, Doran BA, Esposito A, Pezeshk A, Husain A, Bestvina CM, Kline J, Garassino MC, Raman AS. Pan-tumor spatial transcriptomics reveals conserved properties of tumor organization. Cell Rep Med. 2026 Sep 15; 7(9):103013. PMID: 42664957; PMCID: PMC13589502.
      Citations:    
    2. Carroll DD, Cira K, Archer J, Shapiro J, Shah H, Pen UY, Tieri D, Leonor L, Roofchayee ND, Yee SS, Wahab M, Koralnik IJ, Alverdy JC, Raman AS, Visvabharathy L. Post-COVID impairment of T cell responses to community-acquired pathogens can be modified by activating cellular metabolism. PLoS Pathog. 2026 07; 22(7):e1013860. PMID: 42531297; PMCID: PMC13441075.
      Citations:    Fields:    Translation:HumansCells
    3. Ramachandran SL, Pasupuleti N, Abdill RJ, Adikari G, Ahlawat B, Blekhman R, Burgo V, Davenport ER, Dwivedi A, Gupta S, Ijinu TP, Jamir T, Karu R, Kaushik A, Komarabathini JM, Lalzarliana J, Norbu T, Pautu T, Pawar K, Raman AS, Ramaswamy R, Ranasinghe R, Sasidharan SP, Satheesh T, Shaji S, Shapiro JW, Singh E, Singson V, Sundararajan A, Kamani H T, Tetso D, Urban Aragon JA, Welikala AHJ, Yhome RR, Rai N, Raghavan M. Distinct trajectories of urbanization shape the human gut microbiome across South Asia. Gut Microbes. 2026 Dec 31; 18(1):2700042. PMID: 42444491; PMCID: PMC13371495.
      Citations:    Fields:    Translation:HumansCells
    4. Dea A, Lan Y, Doran BA, Ali A, Igarashi MG, Dyer L, Aksianiuk V, Pincus D, Raman AS. Physiological architecture and evolutionary origins of cellular adaptability. bioRxiv. 2026 Apr 11. PMID: 41993285; PMCID: PMC13081815.
      Citations:    
    5. Ramachandran SL, Pasupuleti N, Abdill RJ, Adikari G, Ahlawat B, Blekhman R, Burgo V, Davenport ER, Dwivedi A, Gupta S, Ijinu TP, Jamir T, Karu R, Kaushik A, Komarabathini JM, Lalzarliana J, Norbu T, Pautu T, Pawar K, Raman AS, Ramaswamy R, Ranasinghe R, Sasidharan SP, Satheesh T, Shaji S, Shapiro JW, Singh E, Singson V, Sundararajan A, Tennekoon KH, Tetso D, Aragon JAU, Welikala AHJ, Yhome RR, Rai N, Raghavan M. Distinct trajectories of urbanization shape the human gut microbiome across South Asia. bioRxiv. 2026 Jan 23. PMID: 41648281; PMCID: PMC12871693.
      Citations:    
    6. Carroll DD, Cira K, Archer J, Shapiro J, Pen UY, Tieri D, Leonor L, Roofchayee ND, Yee SS, Wahab M, Koralnik IJ, Alverdy JC, Raman AS, Visvabharathy L. Post-COVID impairment of memory T cell responses to community-acquired pathogens can be rectified by activating cellular metabolism. bioRxiv. 2026 Jan 02. PMID: 41509309; PMCID: PMC12776401.
      Citations:    
    7. Oliveira RA, McSpadden E, Pandey B, Lee K, Yousef M, Chen RY, Triebold C, Haro F, Aksianiuk V, Patel R, Shriram K, Ramanujam R, Kuehn S, Raman AS. Statistical design of a synthetic microbiome that suppresses diverse gut pathogens. bioRxiv. 2025 Dec 31. PMID: 41502951; PMCID: PMC12773023.
      Citations:    
    8. Wu E, Bieniosek M, Wu Z, Thakkar N, Charville GW, Makky A, Schürch CM, Huyghe JR, Peters U, Li CI, Li L, Giba H, Behera V, Raman A, Trevino AE, Mayer AT, Zou J. ROSIE: AI generation of multiplex immunofluorescence staining from histopathology images. Nat Commun. 2025 Aug 16; 16(1):7633. PMID: 40819165; PMCID: PMC12357954.
      Citations: 5     Fields:    Translation:HumansCells
    9. Doran BA, Chen RY, Giba H, Behera V, Barat B, Sundararajan A, Lin H, Sidebottom A, Pamer EG, Raman AS. Subspecies phylogeny in the human gut revealed by co-evolutionary constraints across the bacterial kingdom. Cell Syst. 2025 02 19; 16(2):101167. PMID: 39826551; PMCID: PMC12626139.
      Citations:    Fields:    Translation:HumansCells
    10. Wu E, Bieniosek M, Wu Z, Thakkar N, Charville GW, Makky A, Schürch C, Huyghe JR, Peters U, Li CI, Li L, Giba H, Behera V, Raman A, Trevino AE, Mayer AT, Zou J. ROSIE: AI generation of multiplex immunofluorescence staining from histopathology images. bioRxiv. 2024 Nov 18. PMID: 39605711; PMCID: PMC11601356.
      Citations: 1     
    11. Raman AS. Combatting superbugs using the evolutionary record of microbial warfare. Cell Host Microbe. 2024 07 10; 32(7):1037-1039. PMID: 38991497.
      Citations: 1     Fields:    Translation:HumansCells
    12. Doran BA, Chen RY, Giba H, Behera V, Barat B, Sundararajan A, Lin H, Sidebottom A, Pamer EG, Raman AS. An evolution-based framework for describing human gut bacteria. bioRxiv. 2023 Dec 05. PMID: 38105970; PMCID: PMC10723311.
      Citations:    
    13. Skwara A, Gowda K, Yousef M, Diaz-Colunga J, Raman AS, Sanchez A, Tikhonov M, Kuehn S. Statistically learning the functional landscape of microbial communities. Nat Ecol Evol. 2023 11; 7(11):1823-1833. PMID: 37783827; PMCID: PMC11088814.
      Citations: 32     Fields:    Translation:Humans
    14. Zaydman MA, Little AS, Haro F, Aksianiuk V, Buchser WJ, DiAntonio A, Gordon JI, Milbrandt J, Raman AS. Defining hierarchical protein interaction networks from spectral analysis of bacterial proteomes. Elife. 2022 08 17; 11. PMID: 35976223; PMCID: PMC9427106.
      Citations: 4     Fields:    Translation:Cells
    15. Delannoy-Bruno O, Desai C, Raman AS, Chen RY, Hibberd MC, Cheng J, Han N, Castillo JJ, Couture G, Lebrilla CB, Barve RA, Leyn SA, Rodionov DA, Osterman AL, Hayashi DK, Meynier A, Vinoy S, Kirbach K, Wilmot T, Heath AC, Klein S, Barratt MJ, Gordon JI, Lombard V, Henrissat B. Evaluating microbiome-directed fibre snacks in gnotobiotic mice and humans. Nature. 2021 07; 595(7865):91-95. PMID: 34163075; PMCID: PMC8324079.
      Citations: 64     Fields:    Translation:HumansAnimalsCellsCTClinical Trials
    16. Chen RY, Mostafa I, Hibberd MC, Das S, Mahfuz M, Naila NN, Islam MM, Huq S, Alam MA, Zaman MU, Raman AS, Webber D, Zhou C, Sundaresan V, Ahsan K, Meier MF, Barratt MJ, Ahmed T, Gordon JI. A Microbiota-Directed Food Intervention for Undernourished Children. N Engl J Med. 2021 04 22; 384(16):1517-1528. PMID: 33826814; PMCID: PMC7993600.
      Citations: 142     Fields:    Translation:Humans
    17. López García de Lomana A, Kusebauch U, Raman AV, Pan M, Turkarslan S, Lorenzetti APR, Moritz RL, Baliga NS. Selective Translation of Low Abundance and Upregulated Transcripts in Halobacterium salinarum. mSystems. 2020 Jul 28; 5(4). PMID: 32723790; PMCID: PMC7394353.
      Citations: 7     Fields:    
    18. Bode L, Raman AS, Murch SH, Rollins NC, Gordon JI. Understanding the mother-breastmilk-infant "triad". Science. 2020 03 06; 367(6482):1070-1072. PMID: 32139527.
      Citations: 64     Fields:    Translation:Humans
    19. Feng L, Raman AS, Hibberd MC, Cheng J, Griffin NW, Peng Y, Leyn SA, Rodionov DA, Osterman AL, Gordon JI. Identifying determinants of bacterial fitness in a model of human gut microbial succession. Proc Natl Acad Sci U S A. 2020 02 04; 117(5):2622-2633. PMID: 31969452; PMCID: PMC7007522.
      Citations: 32     Fields:    Translation:HumansAnimalsCells
    20. Raman AS, Gehrig JL, Venkatesh S, Chang HW, Hibberd MC, Subramanian S, Kang G, Bessong PO, Kosek MN, Petri WA, Rodionov DA, Arzamasov AA, Leyn SA, Osterman AL, Huq S, Mostafa I, Islam M, Mahfuz M, Haque R, Ahmed T, Barratt MJ, Gordon JI, Lima AAM. A sparse covarying unit that describes healthy and impaired human gut microbiota development. Science. 2019 07 12; 365(6449). PMID: 31296739; PMCID: PMC6683326.
      Citations: 107     Fields:    Translation:HumansAnimalsCells
    21. Thompson AW, Turkarslan S, Arens CE, López García de Lomana A, Raman AV, Stahl DA, Baliga NS. Robustness of a model microbial community emerges from population structure among single cells of a clonal population. Environ Microbiol. 2017 08; 19(8):3059-3069. PMID: 28419704.
      Citations: 8     Fields:    Translation:Cells
    22. Turkarslan S, Raman AV, Thompson AW, Arens CE, Gillespie MA, von Netzer F, Hillesland KL, Stolyar S, López García de Lomana A, Reiss DJ, Gorman-Lewis D, Zane GM, Ranish JA, Wall JD, Stahl DA, Baliga NS. Mechanism for microbial population collapse in a fluctuating resource environment. Mol Syst Biol. 2017 03 20; 13(3):919. PMID: 28320772; PMCID: PMC5371734.
      Citations: 10     Fields:    Translation:Cells
    23. Raman AS, White KI, Ranganathan R. Origins of Allostery and Evolvability in Proteins: A Case Study. Cell. 2016 Jul 14; 166(2):468-480. PMID: 27321669.
      Citations: 74     Fields:    Translation:AnimalsCells
    24. Raman AV, Baliga NS. The universe under a microscope. Environ Microbiol Rep. 2015 Feb; 7(1):11-2. PMID: 25721591.
      Citations:    Fields:    Translation:Cells
    25. McLaughlin RN, Poelwijk FJ, Raman A, Gosal WS, Ranganathan R. The spatial architecture of protein function and adaptation. Nature. 2012 Nov 01; 491(7422):138-42. PMID: 23041932; PMCID: PMC3991786.
      Citations: 250     Fields:    Translation:Cells
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