Aly Azeem Khan

Research Assistant Professor
Toyota Technological Institute at Chicago
Aly Azeem Khan, 

Contact info

Toyota Technological Institute at Chicago
6045 S. Kenwood Ave.
Chicago, Illinois 60637

Phone: +1-773-834-2623

Research Overview

I am a Research Assistant Professor at the Toyota Technological Institute at Chicago (TTIC), which is an academic computer science institute located on the campus of the University of Chicago. I direct a cross-disciplinary research program in computational immunology. My research focuses on understanding the molecular and cellular systems that control immune function. While I work on a wide range of problems in immunology, I tend to work on problems with a specific kind of personality; I am interested in problems that are clinically relevant, are amenable to machine learning, and allow for solutions that can be experimentally validated. Some of my past work includes developing a max-margin based approach to map all microRNA binding sites in T cells (CLIP base) and a minimum entropy based method to assemble immune repertoire genes from single cell RNA-seq data (BASIC).


I obtained my PhD from Cornell University, where I completed my graduate studies in computational biology in a joint program with Memorial Sloan Kettering Cancer Center under Christina Leslie (advisor), Alexander Rudensky and Chris Sander. In addition to my academic research, I worked at Merck on computational methods to improve drug target discovery [1⇗], and collaborated with Genentech on dissecting regulatory networks underlying immune cell function ([2⇗], [3⇗], [4⇗] and [5⇗]). I also took some time off during my PhD to study market impact and microstructure at Bank of America with Robert Almgren.

Selected Publications

Single cell immunology

  • Spec-seq unveils transcriptional subpopulations of antibody-secreting cells following influenza vaccination
    Neu KE, ... , Khan AA**, Wilson PC** (** co-corresponding)
    Data: GEO
    Journal of Clinical Investigation, 2019 Jan 2;129(1):93-105.

  • Single-Cell Genomics: Approaches and Utility in Immunology
    Neu KE, Tang Q, Wilson PC, Khan AA
    Trends in Immunology, 2017 Feb;2.

  • BASIC: BCR assembly from single cells
    Canzar S, Neu KE, Tang Q, Wilson PC, Khan AA
    Software: BASIC
    Bioinformatics, 2016 Oct;2.

Transcriptional genomics

  • Transcriptional programming of dendritic cells for enhanced MHC class II antigen presentation
    Lugt BV, 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
    Nature Immunology, 2014 Feb;15(2):161-7.

  • A genomic regulatory element that directs assembly and function of immune-specific AP-1-IRF complexes
    Glasmacher E, Agrawal S, Chang AB, Murphy TL, Zeng W, Vander Lugt B, Khan AA, Ciofani M, Spooner C, Rutz S, Hackney J, Nurieva R, Escalante CR, Ouyang W, Littman DR, Murphy KM, Singh H.
    Science, 2012 Nov 16;338(6109):975-80.

Microbiome and immunity

  • Gender bias in autoimmunity is influenced by microbiota
    Yurkovetskiy L*, Burrows M*, Khan AA*, Graham L, Volchkov P, Becker L, Antonopoulos D, Umesaki Y, Chervonsky AV
    (*Equal Contribution)
    Immunity, 2013 Aug 22;39(2):400-12.

small RNA genomics

  • Transcriptome-wide miR-155 binding map reveals widespread noncanonical microRNA targeting
    Loeb GB*, Khan AA*, Canner D, Hiatt JB, Shendure J, Darnell RB, Leslie CS, Rudensky AY.
    (*Equal Contribution)
    Server: CLIP-base
    Molecular Cell, 2012 Dec 14;48(5):760-70.

  • Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs
    Khan AA, Betel D, Miller ML, Sander C, Leslie CS, Marks DS.
    Nature Biotechnology, 2009 Jun;27(6):549-55.

For recent publications, check Google Scholar.

Random walk of ye olde websites

Aly Azeem Khan
Aly Azeem Khan