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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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    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. Kurniansyah N, Goodman MO, Khan AT, Wang J, Feofanova E, Bis JC, Wiggins KL, Huffman JE, Kelly T, Elfassy T, Guo X, Palmas W, Lin HJ, Hwang SJ, Gao Y, Young K, Kinney GL, Smith JA, Yu B, Liu S, Wassertheil-Smoller S, Manson JE, Zhu X, Chen YI, Lee IT, Gu CC, Lloyd-Jones DM, Zöllner S, Fornage M, Kooperberg C, Correa A, Psaty BM, Arnett DK, Isasi CR, Rich SS, Kaplan RC, Redline S, Mitchell BD, Franceschini N, Levy D, Rotter JI, Morrison AC, Sofer T. Evaluating the use of blood pressure polygenic risk scores across race/ethnic background groups. Nat Commun. 2023 06 02; 14(1):3202. PMID: 37268629; PMCID: PMC10238525.
      Citations: 2     Fields:    Translation:Humans
    2. 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; PMCID: PMC10226680.
      Citations: 2     Fields:    Translation:HumansAnimalsCells
    3. 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; PMCID: PMC9279502.
      Citations: 9     Fields:    Translation:HumansCells
    4. 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.
      Citations: 26     Fields:    Translation:HumansCells
    5. 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 08 23; 1(4):100056. PMID: 35475142; PMCID: PMC9017149.
      Citations: 4     Translation:HumansCells
    6. 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; PMCID: PMC8285506.
      Citations: 13     Fields:    Translation:HumansAnimalsCells
    7. 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: 2     Fields:    Translation:AnimalsCells
    8. Khan AA, Yurkovetskiy L, O'Grady K, Pickard JM, Antonopoulos DA, Golovkina T, Chervonsky A, de Pooter R. Polymorphic Immune Mechanisms Regulate Commensal Repertoire. Cell Rep. 2019 10 15; 29(3):541-550.e4. PMID: 31618625; PMCID: PMC6904226.
      Citations: 31     Fields:    Translation:AnimalsCells
    9. 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.
      Citations: 69     Fields:    Translation:Humans
    10. 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.
      Citations: 16     Fields:    Translation:HumansCells
    11. 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: 6     Fields:    Translation:HumansCells
    12. 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; PMCID: PMC6307935.
      Citations: 26     Fields:    Translation:HumansCellsPHPublic Health
    13. 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; PMCID: PMC6129267.
      Citations: 78     Fields:    Translation:HumansAnimalsCells
    14. 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; PMCID: PMC6048122.
      Citations: 35     Fields:    Translation:AnimalsCells
    15. 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; PMCID: PMC5568092.
      Citations: 31     Fields:    Translation:HumansAnimalsCells
    16. 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; PMCID: PMC5408917.
      Citations: 45     Fields:    Translation:Humans
    17. 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; PMCID: PMC5350508.
      Citations: 46     Fields:    Translation:AnimalsCells
    18. 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; PMCID: PMC5479322.
      Citations: 37     Fields:    Translation:HumansAnimals
    19. 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; PMCID: PMC5272185.
      Citations: 20     Fields:    Translation:AnimalsCells
    20. 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; PMCID: PMC4060656.
      Citations: 4     Fields:    Translation:HumansAnimalsCells
    21. Singh H, Khan AA, Dinner AR. Gene regulatory networks in the immune system. Trends Immunol. 2014 May; 35(5):211-8. PMID: 24768519.
      Citations: 40     Fields:    Translation:HumansAnimalsCells
    22. 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.
      Citations: 132     Fields:    Translation:AnimalsCells
    23. 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.
      Citations: 90     Fields:    Translation:AnimalsCells
    24. 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; PMCID: PMC3822899.
      Citations: 429     Fields:    Translation:AnimalsCells
    25. 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; PMCID: PMC5789805.
      Citations: 207     Fields:    Translation:HumansAnimalsCells
    26. 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; PMCID: PMC3435504.
      Citations: 59     Fields:    Translation:HumansAnimalsCells
    27. 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; PMCID: PMC4121855.
      Citations: 153     Fields:    Translation:HumansAnimalsCells
    28. 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; PMCID: PMC2782465.
      Citations: 282     Fields:    Translation:HumansCells
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