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Academic interests

My primary research interests are bioinformatics, computational biology, machine learning and integrative analysis of high throughput sequencing data including ChIP-seq, DNase-seq, RNA-seq, GRO-seq and Hi-C with an emphasis on regulatory genomics and epigenomics. The main focus of my recent research has been to develop computational methods and resources, and to perform integrative analysis, to help the research community in studying the functional importance of super-enhancers and to answer many outstanding questions.

My long-term research goal is to develop computational methods and tools for integrative analysis of heterogeneous, high-throughput sequencing data to understand the transcriptional and epigenetic control of gene regulation in development and disease.

Apart from research, I am a strong advocate of open science, open source, open access, and the use of social media in research as a way to advance research more broadly.



  • 2012 – 2016: Ph.D. in Bioinformatics, Tsinghua University, Beijing, China
  • 2008 – 2010: MS in Computer Science, National University of Computer & Emerging Sciences, Islamabad, Pakistan
  • 2006 – 2008: MSc in Information Technology, Quaid-I-Azam University, Islamabad, Pakistan
  • 2003 – 2005: BSc in Mathematics and Physics, Forman Christian College, Lahore, Pakistan


  • 2014 – 2015: Summer intern, Merck, Beijing, China
  • 2011 – 2016: Consultant, Microfinance Opportunities, Washington D.C., USA
  • 2010 – 2012: Freelance Website & Web Application Developer
  • 2009 – 2010: Web Intern, for a joint project by Harvard University & Aga Khan Development Network, Pakistan


  • CSC fully-funded PhD Scholarship, Tsinghua University, China - 2012 to 2016
  • TWAS BIOVISION.Next Fellowship - 2014, 2013
  • HEC Research Travel Grant, Higher Education Commission, Pakistan - 2012, 2016
Tags: Genetics, Bioinformatics, Computational Biology, Epigenetics, DNA sequence analysis, Gene regulation, Machine learning, Genomics


  • Feng, Huijuan; Bao, Suying; Rahman, Mohammad Alinoor; Weyn-Vanhentenryck, Sebastien M.; Khan, Aziz; Wong, Justin YY; Shah, Ankeeta; Flynn, Elise D.; Krainer, Adrian R. & Zhang, Chaolin (2019). Modeling RNA-Binding Protein Specificity In Vivo by Precisely Registering Protein-RNA Crosslink Sites. Molecular Cell.  ISSN 1097-2765.  74(6), s 1189- 1204 . doi: 10.1016/j.molcel.2019.02.002 Show summary
  • Fornes, Oriol; Castro Mondragón, Jaime Abraham; Khan, Aziz; Robin van der, Lee; Zhang, Xi; A. Richmond, Phillip; P. Modi, Bhavi; Correard, Solenne; Gheorghe, Marius; Baranasic, Damir; Santana-Garcia, Walter; Tan, Ge; Cheneby, Jeanne; Ballester, Benoit; Parcy, François; Sandelin, Albin; Lenhard, Boris; Wasserman, Wyeth W. & Mathelier, Anthony (2019). JASPAR 2020: update of the open-access database of transcription factor binding profiles. Nucleic Acids Research.  ISSN 0305-1048.  48, s 87- 92 . doi: 10.1093/nar/gkz1001 Show summary
  • Gheorghe, Marius; Sandve, Geir Kjetil; Khan, Aziz; Cheneby, Jeanne; Ballester, Benoit & Mathelier, Anthony (2019). A map of direct TF–DNA interactions in the human genome. Nucleic Acids Research.  ISSN 0305-1048.  47(4), s e21 . doi: 10.1093/nar/gky1210 Full text in Research Archive.
  • Itkonen, Harri; Urbanucci, Alfonso; Sara ES, Martin; Khan, Aziz; Mathelier, Anthony; Thiede, Bernd; Walker, Suzanne & Mills, Ian Geoffrey (2019). High OGT activity is essential for MYC-driven proliferation of prostate cancer cells. Theranostics.  ISSN 1838-7640.  9(8), s 2183- 2197 . doi: 10.7150/thno.30834 Full text in Research Archive.
  • Khan, Aziz & Zhang, Xuegong (2019). Integrative modeling reveals key chromatin and sequence signatures predicting super-enhancers. Scientific Reports.  ISSN 2045-2322.  9(1), s 1- 15 . doi: 10.1038/s41598-019-38979-9 Full text in Research Archive.
  • Khan, Aziz; Mathelier, Anthony & Zhang, Xuegong (2018). Super-enhancers are transcriptionally more active and cell type-specific than stretch enhancers. Epigenetics.  ISSN 1559-2294.  13(9), s 910- 922 . doi: 10.1080/15592294.2018.1514231
  • Khan, Aziz & Zhang, Xuegong (2018). Making genome browsers portable and personal. Genome Biology.  ISSN 1465-6906.  19(93) . doi: 10.1186/s13059-018-1470-9 Full text in Research Archive. Show summary
  • Khan, Aziz; Fornes, O; Stigliani, A; Gheorghe, Marius; Castro Mondragón, Jaime Abraham; van der Lee, R; Bessy, A; Cheneby, J; Kulkarni, SR; Tan, G; Baranasic, D; Arenillas, DJ; Sandelin, A; Vandepoele, K; Lenhard, B; Ballester, B; Wassermann, WW; Parcy, F & Mathelier, Anthony (2017). JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Research.  ISSN 0305-1048.  46(1), s D260- D266 . doi: 10.1093/nar/gkx1126 Full text in Research Archive.
  • Khan, Aziz & Mathelier, Anthony (2017). Intervene: a tool for intersection and visualization of multiple gene or genomic region sets. BMC Bioinformatics.  ISSN 1471-2105.  18(287) . doi: 10.1186/s12859-017-1708-7 Full text in Research Archive.
  • Khan, Aziz & Mathelier, Anthony (2017). JASPAR RESTful API: accessing JASPAR data from any programming language. Bioinformatics.  ISSN 1367-4803.  34(9), s 1612- 1614 . doi: 10.1093/bioinformatics/btx804 Full text in Research Archive.

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  • Khan, Aziz; Montenegro-Montero, Alejandro & Mathelier, Anthony (2018). Put science first and formatting later. EMBO Reports.  ISSN 1469-221X. . doi: 10.15252/embr.201845731

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Published Dec. 5, 2016 4:36 PM - Last modified Oct. 26, 2017 3:38 PM