I am a computational biologist interested in gene regulation, cancer (epi)genomic, and chromatin regulatory dynamics of tumor growth.

I did my PhD in Bioinformatics at Tsinghua University, China with Prof. Xuegong Zhang followed by a three year Postdoc at NCMM, University of Oslo, Norway with Dr. Anthony Mathelier. During PhD and postdoctoral training my primary research emphasis was on regulatory genomics and epigenomics. I developed computational methods, tools, and resources to understand the (epi)genomic control of gene regulation in development and disease.

Currently in Dr. Christina Curtis’s lab at the Stanford Cancer Institute where I develop reproducible pipelines and computational methods for integrative analysis of multi-omics data at bulk and single-cell resolution to understand tumor evolution and chromatin regulatory dynamics of tumor growth.

Apart from research, I advocate for open science, open source, preprints, reproducibility in research and often tweet about it. I am a contributor for Bioconda and also developed several open source tools and resources such as JASPAR and ECRcentral.

Sarvenaz Sarabipour, Aziz Khan, et al. (2021). Changing scientific meetings for the better. Nature Human Behaviour, 5, 296–300.
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Aziz Khan (2021). A call to eradicate non-inclusive terms from the life sciences. eLife, 10:e65604.
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Aziz Khan (2020). COVID-19: students caught in Pakistan's digital divide. Nature, 587(7835):548.
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Rafael Riudavets Puig, Paul Boddie, Aziz Khan, Jaime Abraham Castro-Mondragon, Anthony Mathelier (2020). UniBind: maps of high-confidence direct TF-DNA interactions across nine species. bioRxiv, doi: 10.¹¹⁰¹⁄₂₀₂₀.11.17.384578.
Details PDF Code Project UniBind Preprint
Aziz Khan, Rafael Riudavets Puig, Paul Boddie, Anthony Mathelier (2020). BiasAway: command-line and web server to generate nucleotide composition-matched DNA background sequences. Bioinformatics, doi: 10.1093/bioinformatics/btaa928.
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Rozenblatt-Rosen O. et al. (2020). The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution. Cell, 2020;181(2):236-249.
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Oriol Fornes, Jaime A Castro-Mondragon, Aziz Khan, et al. (2019). JASPAR 2020: update of the open-access database of transcription factor binding profiles. Nucleic Acids Res, doi: 10.1093/nar/gkz1001.
Details PDF Code Project JASPAR 2020
Huijuan Feng, Suying Bao, Mohammad Alinoor Rahman, Sebastien M Weyn-Vanhentenryck, Aziz Khan, et al. (2019). Modeling RNA-Binding Protein Specificity In Vivo by Precisely Registering Protein-RNA Crosslink Sites. Mol. Cell 74(6):1189-1204.e6.
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Aziz Khan, Xuegong Zhang (2019). Integrative modeling reveals key chromatin and sequence signatures predicting super-enhancers. Scientific Reports 9, 2877; doi: 10.1038/s41598-019-38979-9.
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Harri M Itkonen, Alfonso Urbanucci, Sara ES Martin, Aziz Khan, Anthony Mathelier, Bernd Thiede, Suzanne Walker, Ian G Mills (2019). High OGT activity is essential for MYC-driven proliferation of prostate cancer cells. Theranostics, 9(8):2183-2197.
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Marius Gheorghe, Geir Kjetil Sandve, Aziz Khan, Jeanne Chèneby, Benoit Ballester, Anthony Mathelier (2018). A map of direct TF-DNA interactions in the human genome. Nucleic Acids Res, 47:4, e21.
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Aziz Khan, Anthony Mathelier, Xuegong Zhang (2018). Super-enhancers are transcriptionally more active and cell-type-specific than stretch enhancers. Epigenetics, 13:9, 910-922.
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Aziz Khan, Xuegong Zhang (2018). Making genome browsers portable and personal. Genome Biology, 19:93.
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Björn Grüning, …, The Bioconda Team, et al. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15, 475–476.
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Aziz Khan, Anthony Mathelier (2018). JASPAR RESTful API: accessing JASPAR data from any programming language. Bioinformatics, 34(9):1612-1614.
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Aziz Khan, Alejandro Montenegro-Montero, Anthony Mathelier (2018). Put science first and formatting later. EMBO reports, 19(5):e45731.
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Aziz Khan, Oriol Fornes, Arnaud Stigliani, et al. (2017). JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Res, 46(D1):D260-D26..
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Aziz Khan, Anthony Mathelier (2017). Intervene: a tool for intersection and visualization of multiple gene or genomic region sets. BMC Bioinformatics, 18:287.
Details PDF Code Project Shiny App Preprint

• ECRcentral: Bringing early-career researchers and funding opportunities together, ISMB/ECCB 2019, Basel. Jul 2019. - [Poster and Talk]

• Preprints in the life sciences, Sven Furberg Seminar in Bioinformatics and Statistical Genomics, Oslo, Norway. Jan 2019. - [Talk]

• A dynamic landscape of enhancer clusters during mouse development, CSHL meeting on Epigenetics & Chromatin, New York, USA. Sep 2018. - [Poster]

• Towards a format-free submission policy: Let’s put science first, 2nd annual conference of Digital Life Norway Research School, Stiklestad, Norway. Jun 2018. - [Talk]

• JASPAR: a comprehensive database of transcription factor binding profiles, 11th International Biocuration Conference, Shanghai. Apr 2018. - [Poster and Talk]

• Super-enhancers are transcriptionally more active and cell type-specific than stretch enhancers, Genomic Regulation 2018, Haute-Nendaz, Switzerland. Mar 2018. - [Poster]

• A novel web framework and RESTful API for the JASPAR database of transcription factor binding profiles, 3rd annual conference of NORBIS, Tromsø, Norway. Nov 2017. - [Poster]

• JASPAR RESTful API: accessing JASPAR data from any programming languages, GREEKC Training on Knowledge Commons and Tools interoperability, Lisbon, Portugal. Oct 2017. - [Talk]

• Intervene: a tool for intersection and visualization of multiple gene or genomic region sets, ISCB Student Council Symposium 2017, Prague, Czech Republic. Jul 2017. - [Talk]

• Intervene: a tool for intersection and visualization of multiple gene or genomic region sets, ISMB/ECCB 2017, Prague, Czech Republic. Jul 2017. - [Poster]

• Integrative analysis reveals significant differences between super and stretch enhancers, Gene Expression Data Analysis , Mainz, Germany. Nov 2016. - [Poster and Talk]

• Comprehensive analysis, prediction, and annotation of super-enhancers, Sven Furberg Seminar in Bioinformatics and Statistical Genomics, Oslo, Norway. Apr 2017. - [Talk]

• Computational prediction, characterization & annotation of super-enhancers & analysis of their key features, CSHA - Chromatin, Epigenetics & Transcription, Suzhou, China. May 2016. - [Poster]

• dbSUPER - an extensive and interactive database of super-enhancers, CSHA/AACR Meeting - Big Data, Comp. & Sys. Bio. in Cancer, Suzhou, China. Dec 2015. - [Poster]

• Super-enhancer prediction from epigenetic signatures and sequence motif data, ISMB/ECCB 2015, Dublin, Ireland. Jul 2015. - [Poster]

• An extensive and interactive database of super-enhancers – dbSUPER, ISCB Student Council Symposium 2015, Dublin, Ireland, Jul 2015. - [Poster]

• An extensive and interactive database of super-enhancers – dbSUPER, 8th International Biocuration Conference (IBC), Beijing. Apr 2015. - [Poster]

• Integration of ChIP-seq and machine learning reveals super-enhancers and features of biological significance, Synthetic Biology Workshops, Tsinghua University. May 2014. - [Talk]

Academic Activities

• Ambassador, eLife and ASAPbio (2018-2019)
• Member, International Society for Computational Biology (ISCB), 2015 – Present
• Member, International Society for Biocuration (ISB), 2015 – Present
• Curator, OMICtools, transcription factors and regulatory elements, 2014 – Present
• Co-Chair, Web Committee, ISCB Student Council, 2016 – Present
• Reviewer, ISCB Student Council Symposium, 2015, 2016, 2017, 2018
• Organizer, Young Investigator Meeting (YIM), University of Oslo, Norway, Sep 2018
• Chair Web Committee,ISCB African Student Symposium 2017, Entebbe, Uganda., Oct 2017
• Organizer, Young Investigator Meeting (YIM), University of Helsinki, Finland, Sep 2017
• Reviewer, for scientific journals. Check the eer review profile

Social activities

• Volunteer, ISMB/ECCB 2017, Prague, Czech Republic, Jul 2017
• Volunteer, ISMB/ECCB 2015, Dublin, Ireland, Jul 2015
• Volunteer, ICML 2014, Jun 2014
• Volunteer, RECOMB 2013, Beijing, Apr 2013
• Volunteer, Migrant Children’s Foundation (MCF), China, 2013 – present
• Founder, Gilgit-Baltistan Academia, an academic portal, 2011
• Participant, 3-Day Startup, Peking University, Beijing, China, 2012
• Participant, Beijing TechHive, Microsoft Research Asia, Beijing, Mar 2015
• Volunteer, to develop & maintain Tsinghua ENCODE Journal Club website, 2013

• azizk@stanford.edu
• C.J.Huang Building. 780 Welch Road, California 94305