The University of Chicago Header Logo

Aly Khan

TitleAssistant Professor
InstitutionUniversity of Chicago
DepartmentFamily Medicine
AddressChicago IL 60637
vCardDownload vCard

    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.

    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. Improved Diagnosis of Non-Melanoma Skin Cancer in Resource-Limited Settings. Cancer Epidemiol Biomarkers Prev. 2025 Apr 27. PMID: 40287980.
      Citations:    Fields:    
    2. Rocheleau G, Clarke SL, Auguste G, Hasbani NR, Morrison AC, Heath AS, Bielak LF, Iyer KR, Young EP, Stitziel NO, Jun G, Laurie C, Broome JG, Khan AT, Arnett DK, Becker LC, Bis JC, Boerwinkle E, Bowden DW, Carson AP, Ellinor PT, Fornage M, Franceschini N, Freedman BI, Heard-Costa NL, Hou L, Chen YI, Kenny EE, Kooperberg C, Kral BG, Loos RJF, Lutz SM, Manson JE, Martin LW, Mitchell BD, Nassir R, Palmer ND, Post WS, Preuss MH, Psaty BM, Raffield LM, Regan EA, Rich SS, Smith JA, Taylor KD, Yanek LR, Young KA, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Hilliard AT, Tcheandjieu C, Peyser PA, Vasan RS, Rotter JI, Miller CL, Assimes TL, de Vries PS, Do R. Rare variant contribution to the heritability of coronary artery disease. Nat Commun. 2024 Oct 09; 15(1):8741. PMID: 39384761; PMCID: PMC11464707.
      Citations: 1     Fields:    Translation:Humans
    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 Sep 03; 15(1):7688. PMID: 39227386; PMCID: PMC11372096.
      Citations: 2     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 Sep 11; 4(9):100637. PMID: 39208795; PMCID: PMC11480863.
      Citations:    Fields:    Translation:HumansCells
    5. Georgakis MK, Malik R, El Bounkari O, Hasbani NR, Li J, Huffman JE, Shakt G, Tack RWP, Kimball TN, Asare Y, Morrison AC, Tsao NL, Judy R, Mitchell BD, Xu H, Montasser ME, Do R, Kenny EE, Loos RJF, Terry JG, Carr JJ, Bis JC, Psaty BM, Longstreth WT, Young KA, Lutz SM, Cho MH, Broome J, Khan AT, Wang FF, Heard-Costa N, Seshadri S, Vasan RS, Palmer ND, Freedman BI, Bowden DW, Yanek LR, Kral BG, Becker LC, Peyser PA, Bielak LF, Ammous F, Carson AP, Hall ME, Raffield LM, Rich SS, Post WS, Tracy RP, Taylor KD, Guo X, Mahaney MC, Curran JE, Blangero J, Clarke SL, Haessler JW, Hu Y, Assimes TL, Kooperberg C, Bernhagen J, Anderson CD, Damrauer SM, Zand R, Rotter JI, de Vries PS, Dichgans M. Rare damaging CCR2 variants are associated with lower lifetime cardiovascular risk. medRxiv. 2024 Jun 26. PMID: 37645892; PMCID: PMC10462211.
      Citations:    
    6. Xia J, Phan HV, Vistain L, Chen M, Khan AA, Tay S. Computational prediction of protein interactions in single cells by proximity sequencing. PLoS Comput Biol. 2024 Mar; 20(3):e1011915. PMID: 38483861; PMCID: PMC10939233.
      Citations: 1     Fields:    
    7. 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:    
    8. Stergachis AB, Blue EE, Gillentine MA, Wang LK, Schwarze U, Cortés AS, Ranchalis J, Allworth A, Bland AE, Chanprasert S, Chen J, Doherty D, Folta AB, Glass I, Horike-Pyne M, Huang AY, Khan AT, Leppig KA, Miller DE, Mirzaa G, Parhin A, Raskind WH, Rosenthal EA, Sheppeard S, Strohbehn S, Sybert VP, Tran TT, Wener MH, for University of Washington Center for Mendelian Genomics (UW-CMG), and Undiagnosed Diseases Networ, Byers PHH, Nelson SF, Bamshad MJ, Dipple KM, Jarvik GP, Hoppins S, Hisama FM. Full-length Isoform Sequencing for Resolving the Molecular Basis of Charcot-Marie-Tooth 2A. Neurol Genet. 2023 Oct; 9(5):e200090. PMID: 37560121; PMCID: PMC10409571.
      Citations: 1     
    9. Aalbers SE, Khan AT, Weir BS. Perceptions of forensic scientists on statistical models, sequence data, and ethical implications for DNA evidence evaluations: A qualitative assessment. Forensic Sci Int Synerg. 2023; 6:100335. PMID: 37325613; PMCID: PMC10265457.
      Citations:    
    10. 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: 9     Fields:    Translation:Humans
    11. Stergachis AB, Blue EE, Gillentine MA, Wang LK, Schwarze U, Cortés AS, Ranchalis J, Allworth A, Bland AE, Chanprasert S, Chen J, Doherty D, Folta AB, Glass I, Horike-Pyne M, Huang AY, Khan AT, Leppig KA, Miller DE, Mirzaa G, Parhin A, Raskind W, Rosenthal EA, Sheppeard S, Strohbehn S, Sybert VP, Tran TT, Wener M, University of Washington Center for Mendelian Genomics (UW-CMG), Undiagnosed Diseases Network (UDN), Byers PH, Nelson SF, Bamshad MJ, Dipple KM, Jarvik GP, Hoppins S, Hisama FM. Full-length isoform sequencing for resolving the molecular basis of Charcot-Marie-Tooth 2A. bioRxiv. 2023 Feb 07. PMID: 36798371; PMCID: PMC9934537.
      Citations:    
    12. 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: 2     Fields:    Translation:HumansAnimalsCells
    13. 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: 5     Fields:    Translation:HumansAnimalsCells
    14. Khan AT, Gogarten SM, McHugh CP, Stilp AM, Sofer T, Bowers ML, Wong Q, Cupples LA, Hidalgo B, Johnson AD, McDonald MN, McGarvey ST, Taylor MRG, Fullerton SM, Conomos MP, Nelson SC. Recommendations on the use and reporting of race, ethnicity, and ancestry in genetic research: Experiences from the NHLBI TOPMed program. Cell Genom. 2022 Aug 10; 2(8). PMID: 36119389; PMCID: PMC9481067.
      Citations: 39     Fields:    
    15. 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: 13     Fields:    Translation:HumansCells
    16. Kelly TN, Sun X, He KY, Brown MR, Taliun SAG, Hellwege JN, Irvin MR, Mi X, Brody JA, Franceschini N, Guo X, Hwang SJ, de Vries PS, Gao Y, Moscati A, Nadkarni GN, Yanek LR, Elfassy T, Smith JA, Chung RH, Beitelshees AL, Patki A, Aslibekyan S, Blobner BM, Peralta JM, Assimes TL, Palmas WR, Liu C, Bress AP, Huang Z, Becker LC, Hwa CM, O'Connell JR, Carlson JC, Warren HR, Das S, Giri A, Martin LW, Craig Johnson W, Fox ER, Bottinger EP, Razavi AC, Vaidya D, Chuang LM, Chang YC, Naseri T, Jain D, Kang HM, Hung AM, Srinivasasainagendra V, Snively BM, Gu D, Montasser ME, Reupena MS, Heavner BD, LeFaive J, Hixson JE, Rice KM, Wang FF, Nielsen JB, Huang J, Khan AT, Zhou W, Nierenberg JL, Laurie CC, Armstrong ND, Shi M, Pan Y, Stilp AM, Emery L, Wong Q, Hawley NL, Minster RL, Curran JE, Munroe PB, Weeks DE, North KE, Tracy RP, Kenny EE, Shimbo D, Chakravarti A, Rich SS, Reiner AP, Blangero J, Redline S, Mitchell BD, Rao DC, Ida Chen YD, Kardia SLR, Kaplan RC, Mathias RA, He J, Psaty BM, Fornage M, Loos RJF, Correa A, Boerwinkle E, Rotter JI, Kooperberg C, Edwards TL, Abecasis GR, Zhu X, Levy D, Arnett DK, Morrison AC, Samoan Obesity, Lifestyle, and Genetic Adaptations Study (OLaGA) Group,‡ NHLBI Trans-Omics for Preci. Insights From a Large-Scale Whole-Genome Sequencing Study of Systolic Blood Pressure, Diastolic Blood Pressure, and Hypertension. Hypertension. 2022 08; 79(8):1656-1667. PMID: 35652341; PMCID: PMC9593435.
      Citations: 12     Fields:    Translation:Humans
    17. Hindy G, Dornbos P, Chaffin MD, Liu DJ, Wang M, Selvaraj MS, Zhang D, Park J, Aguilar-Salinas CA, Antonacci-Fulton L, Ardissino D, Arnett DK, Aslibekyan S, Atzmon G, Ballantyne CM, Barajas-Olmos F, Barzilai N, Becker LC, Bielak LF, Bis JC, Blangero J, Boerwinkle E, Bonnycastle LL, Bottinger E, Bowden DW, Bown MJ, Brody JA, Broome JG, Burtt NP, Cade BE, Centeno-Cruz F, Chan E, Chang YC, Chen YI, Cheng CY, Choi WJ, Chowdhury R, Contreras-Cubas C, Córdova EJ, Correa A, Cupples LA, Curran JE, Danesh J, de Vries PS, DeFronzo RA, Doddapaneni H, Duggirala R, Dutcher SK, Ellinor PT, Emery LS, Florez JC, Fornage M, Freedman BI, Fuster V, Garay-Sevilla ME, García-Ortiz H, Germer S, Gibbs RA, Gieger C, Glaser B, Gonzalez C, Gonzalez-Villalpando ME, Graff M, Graham SE, Grarup N, Groop LC, Guo X, Gupta N, Han S, Hanis CL, Hansen T, He J, Heard-Costa NL, Hung YJ, Hwang MY, Irvin MR, Islas-Andrade S, Jarvik GP, Kang HM, Kardia SLR, Kelly T, Kenny EE, Khan AT, Kim BJ, Kim RW, Kim YJ, Koistinen HA, Kooperberg C, Kuusisto J, Kwak SH, Laakso M, Lange LA, Lee J, Lee J, Lee S, Lehman DM, Lemaitre RN, Linneberg A, Liu J, Loos RJF, Lubitz SA, Lyssenko V, Ma RCW, Martin LW, Martínez-Hernández A, Mathias RA, McGarvey ST, McPherson R, Meigs JB, Meitinger T, Melander O, Mendoza-Caamal E, Metcalf GA, Mi X, Mohlke KL, Montasser ME, Moon JY, Moreno-Macías H, Morrison AC, Muzny DM, Nelson SC, Nilsson PM, O'Connell JR, Orho-Melander M, Orozco L, Palmer CNA, Palmer ND, Park CJ, Park KS, Pedersen O, Peralta JM, Peyser PA, Post WS, Preuss M, Psaty BM, Qi Q, Rao DC, Redline S, Reiner AP, Revilla-Monsalve C, Rich SS, Samani N, Schunkert H, Schurmann C, Seo D, Seo JS, Sim X, Sladek R, Small KS, So WY, Stilp AM, Tai ES, Tam CHT, Taylor KD, Teo YY, Thameem F, Tomlinson B, Tsai MY, Tuomi T, Tuomilehto J, Tusié-Luna T, Udler MS, van Dam RM, Vasan RS, Viaud Martinez KA, Wang FF, Wang X, Watkins H, Weeks DE, Wilson JG, Witte DR, Wong TY, Yanek LR, AMP-T2D-GENES, Myocardial Infarction Genetics Consortium, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, NHLBI TOPMed Lipids Working Group, Kathiresan S, Rader DJ, Rotter JI, Boehnke M, McCarthy MI, Willer CJ, Natarajan P, Flannick JA, Khera AV, Peloso GM. Rare coding variants in 35 genes associate with circulating lipid levels-A multi-ancestry analysis of 170,000 exomes. Am J Hum Genet. 2022 01 06; 109(1):81-96. PMID: 34932938; PMCID: PMC8764201.
      Citations: 22     Fields:    Translation:Humans
    18. Stilp AM, Emery LS, Broome JG, Buth EJ, Khan AT, Laurie CA, Wang FF, Wong Q, Chen D, D'Augustine CM, Heard-Costa NL, Hohensee CR, Johnson WC, Juarez LD, Liu J, Mutalik KM, Raffield LM, Wiggins KL, de Vries PS, Kelly TN, Kooperberg C, Natarajan P, Peloso GM, Peyser PA, Reiner AP, Arnett DK, Aslibekyan S, Barnes KC, Bielak LF, Bis JC, Cade BE, Chen MH, Correa A, Cupples LA, de Andrade M, Ellinor PT, Fornage M, Franceschini N, Gan W, Ganesh SK, Graffelman J, Grove ML, Guo X, Hawley NL, Hsu WL, Jackson RD, Jaquish CE, Johnson AD, Kardia SLR, Kelly S, Lee J, Mathias RA, McGarvey ST, Mitchell BD, Montasser ME, Morrison AC, North KE, Nouraie SM, Oelsner EC, Pankratz N, Rich SS, Rotter JI, Smith JA, Taylor KD, Vasan RS, Weeks DE, Weiss ST, Wilson CG, Yanek LR, Psaty BM, Heckbert SR, Laurie CC. A System for Phenotype Harmonization in the National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine (TOPMed) Program. Am J Epidemiol. 2021 10 01; 190(10):1977-1992. PMID: 33861317; PMCID: PMC8485147.
      Citations: 40     Fields:    Translation:Humans
    19. 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: 45     Fields:    Translation:HumansCells
    20. 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: 6     Fields:    Translation:HumansCells
    21. 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: 20     Fields:    Translation:HumansAnimalsCells
    22. 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
    23. Li X, Li Z, Zhou H, Gaynor SM, Liu Y, Chen H, Sun R, Dey R, Arnett DK, Aslibekyan S, Ballantyne CM, Bielak LF, Blangero J, Boerwinkle E, Bowden DW, Broome JG, Conomos MP, Correa A, Cupples LA, Curran JE, Freedman BI, Guo X, Hindy G, Irvin MR, Kardia SLR, Kathiresan S, Khan AT, Kooperberg CL, Laurie CC, Liu XS, Mahaney MC, Manichaikul AW, Martin LW, Mathias RA, McGarvey ST, Mitchell BD, Montasser ME, Moore JE, Morrison AC, O'Connell JR, Palmer ND, Pampana A, Peralta JM, Peyser PA, Psaty BM, Redline S, Rice KM, Rich SS, Smith JA, Tiwari HK, Tsai MY, Vasan RS, Wang FF, Weeks DE, Weng Z, Wilson JG, Yanek LR, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Lipids Working Group, Neale BM, Sunyaev SR, Rotter JI, Willer CJ, Peloso GM, Natarajan P, Lin X, Abecasis GR. Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale. Nat Genet. 2020 Sep; 52(9):969-983. PMID: 32839606; PMCID: PMC7483769.
      Citations: 125     Fields:    Translation:Humans
    24. 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: 38     Fields:    Translation:AnimalsCells
    25. 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: 82     Fields:    Translation:Humans
    26. 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: 17     Fields:    Translation:HumansCells
    27. 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
    28. 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
    29. 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: 100     Fields:    Translation:HumansAnimalsCells
    30. 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: 37     Fields:    Translation:AnimalsCells
    31. 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: 34     Fields:    Translation:HumansAnimalsCells
    32. 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: 52     Fields:    Translation:Humans
    33. 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: 50     Fields:    Translation:AnimalsCells
    34. 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: 40     Fields:    Translation:HumansAnimals
    35. 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: 23     Fields:    Translation:AnimalsCells
    36. 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
    37. Singh H, Khan AA, Dinner AR. Gene regulatory networks in the immune system. Trends Immunol. 2014 May; 35(5):211-8. PMID: 24768519.
      Citations: 47     Fields:    Translation:HumansAnimalsCells
    38. 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: 134     Fields:    Translation:AnimalsCells
    39. 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
    40. 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: 466     Fields:    Translation:AnimalsCells
    41. 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: 212     Fields:    Translation:HumansAnimalsCells
    42. 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: 64     Fields:    Translation:HumansAnimalsCells
    43. 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: 155     Fields:    Translation:HumansAnimalsCells
    44. 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: 283     Fields:    
    Khan's Networks
    Click the
    Explore
    buttons for more information and interactive visualizations!
    Concepts (254)
    Explore
    _
    Co-Authors (22)
    Explore
    _
    Similar People (60)
    Explore
    _
    Same Department Expand Description
    Explore
    _
    Physical Neighbors
    _