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Samantha Riesenfeld

TitleAssistant Professor
InstitutionUniversity of Chicago
DepartmentPritzker Institute for Molecular Engineering
AddressChicago IL 60637
Email
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    Using high-throughput genomic data, Riesenfeld Group develops approaches to computationally infer the circuits that regulate gene expression and cellular function. By iterating experimental perturbations, data modeling, and targeted validations, they aim to extract from noisy, large-scale data the signals to help answer complex questions about the immune system, such as: What drives tolerant versus inflammatory immune responses? How do immune pathways contribute to or disrupt tissue homeostasis? How can immune responses be manipulated to restore health?

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    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.
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    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. Hieromnimon HM, Dolezal J, Doytcheva K, Howard FM, Kochanny S, Zhang Z, Grossman RL, Tanager K, Wang C, Kather JN, Izumchenko E, Cipriani NA, Fertig EJ, Pearson AT, Riesenfeld SJ. Building digital histology models of transcriptional tumor programs with generative deep learning for pathology-based precision medicine. Genome Med. 2025 Aug 07; 17(1):87. PMID: 40775734; PMCID: PMC12329968.
      Citations:    Fields:    Translation:HumansCells
    2. Hieromnimon HM, Trzcinska A, Wen FT, Howard FM, Dolezal JM, Dyer E, Kochanny S, Schulte JJ, Wang C, Chen H, Chin J, Blair E, Agrawal N, Rosenberg A, Vokes E, Katipally R, Juloori A, Izumchenko E, Lingen MW, Cipriani N, Jalaly JB, Basu D, Riesenfeld SJ, Pearson AT. Corrigendum to "Analysis of AI foundation model features decodes the histopathologic landscape of HPV-positive head and neck squamous cell carcinomas". [Oral Oncol. 163 (2025) 107207]. Oral Oncol. 2025 Oct; 169:107510. PMID: 40721367.
      Citations:    Fields:    
    3. Lisicka W, Earley ZM, Sifakis JJ, Erickson SA, Mattingly JR, Wu-Woods NJ, Krishnamurthy SR, Belkaid Y, Ismagilov RF, Cyster JG, Riesenfeld SJ, Bendelac A, Jabri B. Immunoglobulin A controls intestinal virus colonization to preserve immune homeostasis. Cell Host Microbe. 2025 Apr 09; 33(4):498-511.e10. PMID: 40154490; PMCID: PMC12235565.
      Citations: 7     Fields:    Translation:AnimalsCells
    4. Hieromnimon HM, Trzcinska A, Wen FT, Howard FM, Dolezal JM, Dyer E, Kochanny S, Schulte JJ, Wang C, Chen H, Chin J, Blair E, Agrawal N, Rosenberg A, Vokes E, Katipally R, Juloori A, Izumchenko E, Lingen MW, Cipriani N, Jalaly JB, Basu D, Riesenfeld SJ, Pearson AT. Analysis of AI foundation model features decodes the histopathologic landscape of HPV-positive head and neck squamous cell carcinomas. Oral Oncol. 2025 Apr; 163:107207. PMID: 40043423.
      Citations:    Fields:    Translation:HumansCells
    5. Sangani KA, Parker ME, Anderson HD, Chen L, Pandey SP, Pierre JF, Meisel M, Riesenfeld SJ, Hinterleitner R, Jabri B. Epigenetic control of commensal induced Th2 Responses and Intestinal immunopathology. bioRxiv. 2024 Aug 30. PMID: 39257820; PMCID: PMC11383986.
      Citations:    
    6. Liang Z, Anderson HD, Locher V, O'Leary C, Riesenfeld SJ, Jabri B, McDonald BD, Bendelac A. Eomes expression identifies the early bone marrow precursor to classical NK cells. Nat Immunol. 2024 Jul; 25(7):1172-1182. PMID: 38871999; PMCID: PMC11409033.
      Citations: 5     Fields:    Translation:AnimalsCells
    7. Ramesh S, Tomesh T, Riesenfeld SJ, Chong FT, Pearson AT. Quantum computing for oncology. Nat Cancer. 2024 Jun; 5(6):811-816. PMID: 38760645.
      Citations: 1     Fields:    Translation:Humans
    8. van Elsas MJ, Middelburg J, Labrie C, Roelands J, Schaap G, Sluijter M, Tonea R, Ovcinnikovs V, Lloyd K, Schuurman J, Riesenfeld SJ, Gajewski TF, de Miranda NFCC, van Hall T, van der Burg SH. Immunotherapy-activated T cells recruit and skew late-stage activated M1-like macrophages that are critical for therapeutic efficacy. Cancer Cell. 2024 Jun 10; 42(6):1032-1050.e10. PMID: 38759656.
      Citations: 65     Fields:    Translation:HumansAnimalsCells
    9. Gao CF, Vaikuntanathan S, Riesenfeld SJ. Dissection and integration of bursty transcriptional dynamics for complex systems. Proc Natl Acad Sci U S A. 2024 Apr 30; 121(18):e2306901121. PMID: 38669186; PMCID: PMC11067469.
      Citations: 5     Fields:    Translation:HumansAnimalsCells
    10. Gao CF, Vaikuntanathan S, Riesenfeld SJ. Dissection and Integration of Bursty Transcriptional Dynamics for Complex Systems. bioRxiv. 2023 Jun 13. PMID: 37398022; PMCID: PMC10312759.
      Citations:    
    11. Earley ZM, Lisicka W, Sifakis JJ, Kowalczyk A, Barlow JT, Shaw DG, Discepolo V, Tan IL, Gona S, Ernest JD, Matzinger P, Barreiro LB, Morgun A, Bendelac A, Ismagilov RF, Shulzhenko N, Riesenfeld SJ, Jabri B, Aguirre-Gamboa R. GATA4 controls regionalization of tissue immunity and commensal-driven immunopathology. Immunity. 2023 01 10; 56(1):43-57.e10. PMID: 36630917; PMCID: PMC10262782.
      Citations: 14     Fields:    Translation:HumansAnimalsCells
    12. Yang D, Jacobson A, Meerschaert KA, Sifakis JJ, Wu M, Chen X, Yang T, Zhou Y, Anekal PV, Rucker RA, Sharma D, Sontheimer-Phelps A, Wu GS, Deng L, Anderson MD, Choi S, Neel D, Lee N, Kasper DL, Jabri B, Huh JR, Johansson M, Thiagarajah JR, Riesenfeld SJ, Chiu IM. Nociceptor neurons direct goblet cells via a CGRP-RAMP1 axis to drive mucus production and gut barrier protection. Cell. 2022 10 27; 185(22):4190-4205.e25. PMID: 36243004; PMCID: PMC9617795.
      Citations: 96     Fields:    Translation:HumansAnimalsCells
    13. Pawlak M, DeTomaso D, Schnell A, Meyer Zu Horste G, Lee Y, Nyman J, Dionne D, Regan BML, Singh V, Delorey T, Schramm MA, Wang C, Wallrapp A, Burkett PR, Riesenfeld SJ, Anderson AC, Regev A, Xavier RJ, Yosef N, Kuchroo VK. Induction of a colitogenic phenotype in Th1-like cells depends on interleukin-23 receptor signaling. Immunity. 2022 09 13; 55(9):1663-1679.e6. PMID: 36070768; PMCID: PMC9808605.
      Citations: 21     Fields:    Translation:AnimalsCells
    14. Kaur G, Porter CBM, Ashenberg O, Lee J, Riesenfeld SJ, Hofree M, Aggelakopoulou M, Subramanian A, Kuttikkatte SB, Attfield KE, Desel CAE, Davies JL, Evans HG, Avraham-Davidi I, Nguyen LT, Dionne DA, Neumann AE, Jensen LT, Barber TR, Soilleux E, Carrington M, McVean G, Rozenblatt-Rosen O, Regev A, Fugger L. Mouse fetal growth restriction through parental and fetal immune gene variation and intercellular communications cascade. Nat Commun. 2022 07 29; 13(1):4398. PMID: 35906236; PMCID: PMC9338297.
      Citations: 10     Fields:    Translation:AnimalsCells
    15. Dani N, Herbst RH, McCabe C, Green GS, Kaiser K, Head JP, Cui J, Shipley FB, Jang A, Dionne D, Nguyen L, Rodman C, Riesenfeld SJ, Prochazka J, Prochazkova M, Sedlacek R, Zhang F, Bryja V, Rozenblatt-Rosen O, Habib N, Regev A, Lehtinen MK. A cellular and spatial map of the choroid plexus across brain ventricles and ages. Cell. 2021 05 27; 184(11):3056-3074.e21. PMID: 33932339; PMCID: PMC8214809.
      Citations: 181     Fields:    Translation:AnimalsCells
    16. Bielecki P, Riesenfeld SJ, Hütter JC, Torlai Triglia E, Kowalczyk MS, Ricardo-Gonzalez RR, Lian M, Amezcua Vesely MC, Kroehling L, Xu H, Slyper M, Muus C, Ludwig LS, Christian E, Tao L, Kedaigle AJ, Steach HR, York AG, Skadow MH, Yaghoubi P, Dionne D, Jarret A, McGee HM, Porter CBM, Licona-Limón P, Bailis W, Jackson R, Gagliani N, Gasteiger G, Locksley RM, Regev A, Flavell RA. Skin-resident innate lymphoid cells converge on a pathogenic effector state. Nature. 2021 04; 592(7852):128-132. PMID: 33536623; PMCID: PMC8336632.
      Citations: 111     Fields:    Translation:AnimalsCells
    17. Boroughs AC, Larson RC, Marjanovic ND, Gosik K, Castano AP, Porter CBM, Lorrey SJ, Ashenberg O, Jerby L, Hofree M, Smith-Rosario G, Morris R, Gould J, Riley LS, Berger TR, Riesenfeld SJ, Rozenblatt-Rosen O, Choi BD, Regev A, Maus MV. A Distinct Transcriptional Program in Human CAR T Cells Bearing the 4-1BB Signaling Domain Revealed by scRNA-Seq. Mol Ther. 2020 12 02; 28(12):2577-2592. PMID: 32755564; PMCID: PMC7704462.
      Citations: 61     Fields:    Translation:HumansCells
    18. Xu H, Ding J, Porter CBM, Wallrapp A, Tabaka M, Ma S, Fu S, Guo X, Riesenfeld SJ, Su C, Dionne D, Nguyen LT, Lefkovith A, Ashenberg O, Burkett PR, Shi HN, Rozenblatt-Rosen O, Graham DB, Kuchroo VK, Regev A, Xavier RJ. Transcriptional Atlas of Intestinal Immune Cells Reveals that Neuropeptide a-CGRP Modulates Group 2 Innate Lymphoid Cell Responses. Immunity. 2019 10 15; 51(4):696-708.e9. PMID: 31618654; PMCID: PMC6991097.
      Citations: 144     Fields:    Translation:AnimalsCells
    19. Wallrapp A, Burkett PR, Riesenfeld SJ, Kim SJ, Christian E, Abdulnour RE, Thakore PI, Schnell A, Lambden C, Herbst RH, Khan P, Tsujikawa K, Xavier RJ, Chiu IM, Levy BD, Regev A, Kuchroo VK. Calcitonin Gene-Related Peptide Negatively Regulates Alarmin-Driven Type 2 Innate Lymphoid Cell Responses. Immunity. 2019 10 15; 51(4):709-723.e6. PMID: 31604686; PMCID: PMC7076585.
      Citations: 135     Fields:    Translation:AnimalsCells
    20. Lun ATL, Riesenfeld S, Andrews T, Dao TP, Gomes T, participants in the 1st Human Cell Atlas Jamboree, Marioni JC. EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data. Genome Biol. 2019 03 22; 20(1):63. PMID: 30902100; PMCID: PMC6431044.
      Citations: 544     Fields:    Translation:HumansCells
    21. Wallrapp A, Riesenfeld SJ, Burkett PR, Kuchroo VK. Type 2 innate lymphoid cells in the induction and resolution of tissue inflammation. Immunol Rev. 2018 11; 286(1):53-73. PMID: 30294962; PMCID: PMC7370855.
      Citations: 30     Fields:    Translation:HumansAnimalsCells
    22. Farrell JA, Wang Y, Riesenfeld SJ, Shekhar K, Regev A, Schier AF. Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis. Science. 2018 06 01; 360(6392). PMID: 29700225; PMCID: PMC6247916.
      Citations: 389     Fields:    Translation:AnimalsCells
    23. Wallrapp A, Riesenfeld SJ, Burkett PR, Abdulnour RE, Nyman J, Dionne D, Hofree M, Cuoco MS, Rodman C, Farouq D, Haas BJ, Tickle TL, Trombetta JJ, Baral P, Klose CSN, Mahlakõiv T, Artis D, Rozenblatt-Rosen O, Chiu IM, Levy BD, Kowalczyk MS, Regev A, Kuchroo VK. Erratum: The neuropeptide NMU amplifies ILC2-driven allergic lung inflammation. Nature. 2017 11 30; 551(7682):658. PMID: 29143821.
      Citations: 7     Fields:    
    24. Wallrapp A, Riesenfeld SJ, Burkett PR, Abdulnour RE, Nyman J, Dionne D, Hofree M, Cuoco MS, Rodman C, Farouq D, Haas BJ, Tickle TL, Trombetta JJ, Baral P, Klose CSN, Mahlakõiv T, Artis D, Rozenblatt-Rosen O, Chiu IM, Levy BD, Kowalczyk MS, Regev A, Kuchroo VK. The neuropeptide NMU amplifies ILC2-driven allergic lung inflammation. Nature. 2017 09 21; 549(7672):351-356. PMID: 28902842; PMCID: PMC5746044.
      Citations: 360     Fields:    Translation:AnimalsCells
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