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Aly Khan

TitleAssistant Professor
InstitutionUniversity of Chicago
DepartmentFamily Medicine
AddressChicago IL 60637
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    Collapse Overview 
    Collapse overview
    My research lab focuses on developing novel computational methods to better understand the complex interactions between immune cells, their environment, and the microbiome. Our goal is to uncover clinically relevant insights and pave the way for new diagnostics and therapies that can improve human 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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    1. Spring J, Khan AA, Lara S, O'Grady K, Wilks J, Gurbuxani S, Erickson S, Fischbach M, Jacobson A, Chervonsky A, Golovkina T. Gut commensal bacteria enhance pathogenesis of a tumorigenic murine retrovirus. Cell Rep. 2022 09 13; 40(11):111341. PMID: 36103821.
      View in: PubMed
    2. Lau D, Khare S, Stein MM, Jain P, Gao Y, BenTaieb A, Rand TA, Salahudeen AA, Khan AA. Integration of tumor extrinsic and intrinsic features associates with immunotherapy response in non-small cell lung cancer. Nat Commun. 2022 07 13; 13(1):4053. PMID: 35831288.
      View in: PubMed
    3. Larsen BM, Kannan M, Langer LF, Leibowitz BD, Bentaieb A, Cancino A, Dolgalev I, Drummond BE, Dry JR, Ho CS, Khullar G, Krantz BA, Mapes B, McKinnon KE, Metti J, Perera JF, Rand TA, Sanchez-Freire V, Shaxted JM, Stein MM, Streit MA, Tan YC, Zhang Y, Zhao E, Venkataraman J, Stumpe MC, Borgia JA, Masood A, Catenacci DVT, Mathews JV, Gursel DB, Wei JJ, Welling TH, Simeone DM, White KP, Khan AA, Igartua C, Salahudeen AA. A pan-cancer organoid platform for precision medicine. Cell Rep. 2021 07 27; 36(4):109429. PMID: 34320344.
      View in: PubMed
    4. Li L, Dugan HL, Stamper CT, Lan LY, Asby NW, Knight M, Stovicek O, Zheng NY, Madariaga ML, Shanmugarajah K, Jansen MO, Changrob S, Utset HA, Henry C, Nelson C, Jedrzejczak RP, Fremont DH, Joachimiak A, Krammer F, Huang J, Khan AA, Wilson PC. Improved integration of single-cell transcriptome and surface protein expression by LinQ-View. Cell Rep Methods. 2021 Aug 23; 1(4):100056. PMID: 35475142.
      View in: PubMed
    5. Asano Y, Daccache J, Jain D, Ko K, Kinloch A, Veselits M, Wolfgeher D, Chang A, Josephson M, Cunningham P, Tambur A, Khan AA, Pillai S, Chong AS, Clark MR. Innate-like self-reactive B cells infiltrate human renal allografts during transplant rejection. Nat Commun. 2021 07 16; 12(1):4372. PMID: 34272370.
      View in: PubMed
    6. 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.
      View in: PubMed
    7. Khan AA, Yurkovetskiy L, O'Grady K, Pickard JM, de Pooter R, Antonopoulos DA, Golovkina T, Chervonsky A. Polymorphic Immune Mechanisms Regulate Commensal Repertoire. Cell Rep. 2019 10 15; 29(3):541-550.e4. PMID: 31618625.
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    8. Beaubier N, Bontrager M, Huether R, Igartua C, Lau D, Tell R, Bobe AM, Bush S, Chang AL, Hoskinson DC, Khan AA, Kudalkar E, Leibowitz BD, Lozachmeur A, Michuda J, Parsons J, Perera JF, Salahudeen A, Shah KP, Taxter T, Zhu W, White KP. Integrated genomic profiling expands clinical options for patients with cancer. Nat Biotechnol. 2019 11; 37(11):1351-1360. PMID: 31570899.
      View in: PubMed
    9. Lau D, Bobe AM, Khan AA. RNA Sequencing of the Tumor Microenvironment in Precision Cancer Immunotherapy. Trends Cancer. 2019 03; 5(3):149-156. PMID: 30898262.
      View in: PubMed
    10. 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.
      View in: PubMed
    11. Neu KE, Guthmiller JJ, Huang M, La J, Vieira MC, Kim K, Zheng NY, Cortese M, Tepora ME, Hamel NJ, Rojas KT, Henry C, Shaw D, Dulberger CL, Pulendran B, Cobey S, Khan AA, Wilson PC. Spec-seq unveils transcriptional subpopulations of antibody-secreting cells following influenza vaccination. J Clin Invest. 2019 01 02; 129(1):93-105. PMID: 30457979.
      View in: PubMed
    12. Hashemifar S, Neyshabur B, Khan AA, Xu J. Predicting protein-protein interactions through sequence-based deep learning. Bioinformatics. 2018 09 01; 34(17):i802-i810. PMID: 30423091.
      View in: PubMed
    13. Cho S, Lee HM, Yu IS, Choi YS, Huang HY, Hashemifar SS, Lin LL, Chen MC, Afanasiev ND, Khan AA, Lin SW, Rudensky AY, Crotty S, Lu LF. Differential cell-intrinsic regulations of germinal center B and T cells by miR-146a and miR-146b. Nat Commun. 2018 07 16; 9(1):2757. PMID: 30013024.
      View in: PubMed
    14. Denzin LK, Khan AA, Virdis F, Wilks J, Kane M, Beilinson HA, Dikiy S, Case LK, Roopenian D, Witkowski M, Chervonsky AV, Golovkina TV. Neutralizing Antibody Responses to Viral Infections Are Linked to the Non-classical MHC Class II Gene H2-Ob. Immunity. 2017 08 15; 47(2):310-322.e7. PMID: 28813660.
      View in: PubMed
    15. Canzar S, Neu KE, Tang Q, Wilson PC, Khan AA. BASIC: BCR assembly from single cells. Bioinformatics. 2017 02 01; 33(3):425-427. PMID: 28172415.
      View in: PubMed
    16. Vander Lugt B, Riddell J, Khan AA, Hackney JA, Lesch J, DeVoss J, Weirauch MT, Singh H, Mellman I. Transcriptional determinants of tolerogenic and immunogenic states during dendritic cell maturation. J Cell Biol. 2017 03 06; 216(3):779-792. PMID: 28130292.
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    17. Neu KE, Tang Q, Wilson PC, Khan AA. Single-Cell Genomics: Approaches and Utility in Immunology. Trends Immunol. 2017 02; 38(2):140-149. PMID: 28094102.
      View in: PubMed
    18. Cruz LO, Hashemifar SS, Wu CJ, Cho S, Nguyen DT, Lin LL, Khan AA, Lu LF. Excessive expression of miR-27 impairs Treg-mediated immunological tolerance. J Clin Invest. 2017 Feb 01; 127(2):530-542. PMID: 28067667.
      View in: PubMed
    19. Varanasi V, Khan AA, Chervonsky AV. Loss of the death receptor CD95 (Fas) expression by dendritic cells protects from a chronic viral infection. Proc Natl Acad Sci U S A. 2014 Jun 10; 111(23):8559-64. PMID: 24912151.
      View in: PubMed
    20. Singh H, Khan AA, Dinner AR. Gene regulatory networks in the immune system. Trends Immunol. 2014 May; 35(5):211-8. PMID: 24768519.
      View in: PubMed
    21. Vander Lugt B, Khan AA, Hackney JA, Agrawal S, Lesch J, Zhou M, Lee WP, Park S, Xu M, DeVoss J, Spooner CJ, Chalouni C, Delamarre L, Mellman I, Singh H. Transcriptional programming of dendritic cells for enhanced MHC class II antigen presentation. Nat Immunol. 2014 Feb; 15(2):161-7. PMID: 24362890.
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    22. Spooner CJ, Lesch J, Yan D, Khan AA, Abbas A, Ramirez-Carrozzi V, Zhou M, Soriano R, Eastham-Anderson J, Diehl L, Lee WP, Modrusan Z, Pappu R, Xu M, DeVoss J, Singh H. Specification of type 2 innate lymphocytes by the transcriptional determinant Gfi1. Nat Immunol. 2013 Dec; 14(12):1229-36. PMID: 24141388.
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    23. Yurkovetskiy L, Burrows M, Khan AA, Graham L, Volchkov P, Becker L, Antonopoulos D, Umesaki Y, Chervonsky AV. Gender bias in autoimmunity is influenced by microbiota. Immunity. 2013 Aug 22; 39(2):400-12. PMID: 23973225.
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    24. Glasmacher E, Agrawal S, Chang AB, Murphy TL, Zeng W, Vander Lugt B, Khan AA, Ciofani M, Spooner CJ, Rutz S, Hackney J, Nurieva R, Escalante CR, Ouyang W, Littman DR, Murphy KM, Singh H. A genomic regulatory element that directs assembly and function of immune-specific AP-1-IRF complexes. Science. 2012 Nov 16; 338(6109):975-80. PMID: 22983707.
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    25. Setty M, Helmy K, Khan AA, Silber J, Arvey A, Neezen F, Agius P, Huse JT, Holland EC, Leslie CS. Inferring transcriptional and microRNA-mediated regulatory programs in glioblastoma. Mol Syst Biol. 2012; 8:605. PMID: 22929615.
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    26. Mavrakis KJ, Van Der Meulen J, Wolfe AL, Liu X, Mets E, Taghon T, Khan AA, Setty M, Setti M, Rondou P, Vandenberghe P, Delabesse E, Benoit Y, Socci NB, Leslie CS, Van Vlierberghe P, Speleman F, Wendel HG. A cooperative microRNA-tumor suppressor gene network in acute T-cell lymphoblastic leukemia (T-ALL). Nat Genet. 2011 Jun 05; 43(7):673-8. PMID: 21642990.
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    27. Khan AA, Betel D, Miller ML, Sander C, Leslie CS, Marks DS. Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nat Biotechnol. 2009 Jun; 27(6):549-55. PMID: 19465925.
      View in: PubMed
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