Computational Biology & Cancer Regulatory Genomics Lab

Our Research Publications

We publish high-impact peer-reviewed research papers in leading journals across diverse topics from genomics, epigenomic, machine learning, cancer genomics, and science policy.

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All publications

2025

Evolutionary measures show that recurrence of DCIS is distinct from progression to breast cancer
Evolutionary measures show that recurrence of DCIS is distinct from progression to breast cancer
Angelo Fortunato, Diego Mallo, Luis Cisneros, Lorraine M. King, Aziz Khan, …, Joseph Y. Lo, Allison Hall, Jeffrey R. Marks, E. Shelley Hwang, Carlo C. Maley
Breast Cancer Research  ·  21 Mar 2025  ·  doi:10.1186/s13058-025-01966-2
Temporal and spatial composition of the tumor microenvironment predicts response to immune checkpoint inhibition
Temporal and spatial composition of the tumor microenvironment predicts response to immune checkpoint inhibition
Noah F. Greenwald, Iris Nederlof, Cameron Sowers, Daisy Yi Ding, Seongyeol Park, …, Robert Tibshirani, Hugo M. Horlings, Christina Curtis, Marleen Kok, Michael Angelo
Cold Spring Harbor Laboratory  ·  28 Jan 2025  ·  doi:10.1101/2025.01.26.634557
Complex rearrangements fuel ER and HER2 breast tumours
Complex rearrangements fuel ER+ and HER2+ breast tumours
Kathleen E. Houlahan, Lise Mangiante, Cristina Sotomayor-Vivas, Alvina Adimoelja, Seongyeol Park, Aziz Khan, Sophia J. Pribus, Zhicheng Ma, Jennifer L. Caswell-Jin, Christina Curtis
Nature  ·  08 Jan 2025  ·  doi:10.1038/s41586-024-08377-x

2024

Multiomic analysis of familial adenomatous polyposis reveals molecular pathways associated with early tumorigenesis
Multiomic analysis of familial adenomatous polyposis reveals molecular pathways associated with early tumorigenesis
Edward D. Esplin, Casey Hanson, Si Wu, Aaron M. Horning, Nasim Barapour, …, Anshul Kundaje, Christina Curtis, William J. Greenleaf, James M. Ford, Michael P. Snyder
Nature Cancer  ·  30 Oct 2024  ·  doi:10.1038/s43018-024-00831-z
Germline-mediated immunoediting sculpts breast cancer subtypes and metastatic proclivity
Germline-mediated immunoediting sculpts breast cancer subtypes and metastatic proclivity
Kathleen E. Houlahan, Aziz Khan, Noah F. Greenwald, Cristina Sotomayor Vivas, Robert B. West, Michael Angelo, Christina Curtis
Science  ·  31 May 2024  ·  doi:10.1126/science.adh8697

2023

JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles
JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles
Ieva Rauluseviciute, Rafael Riudavets-Puig, Romain Blanc-Mathieu, Jaime A Castro-Mondragon, Katalin Ferenc, …, Boris Lenhard, Albin Sandelin, Wyeth W Wasserman, François Parcy, Anthony Mathelier
Nucleic Acids Research  ·  14 Nov 2023  ·  doi:10.1093/nar/gkad1059
JASPAR
Deterministic evolution and stringent selection during preneoplasia
Deterministic evolution and stringent selection during preneoplasia
Kasper Karlsson, Moritz J. Przybilla, Eran Kotler, Aziz Khan, Hang Xu, …, Zhicheng Ma, Carlos J. Suarez, Chris P. Barnes, Calvin J. Kuo, Christina Curtis
Nature  ·  31 May 2023  ·  doi:10.1038/s41586-023-06102-8
Somatic variant detection from multi-sampled genomic sequencing data of tumor specimens using the ith.Variant pipeline
Somatic variant detection from multi-sampled genomic sequencing data of tumor specimens using the ith.Variant pipeline
Nicole Maeser, Aziz Khan, Ruping Sun
STAR Protocols  ·  01 Mar 2023  ·  doi:10.1016/j.xpro.2022.101927

2022

Molecular classification and biomarkers of clinical outcome in breast ductal carcinoma in situ: Analysis of TBCRC 038 and RAHBT cohorts.
Molecular classification and biomarkers of clinical outcome in breast ductal carcinoma in situ: Analysis of TBCRC 038 and RAHBT cohorts.
Siri H Strand, Belén Rivero-Gutiérrez, Kathleen E Houlahan, Jose A Seoane, Lorraine M King, …, Carlo Maley, Jeffrey R Marks, Graham A Colditz, E Shelley Hwang, Robert B West
Cancer cell  ·  17 Nov 2022  ·  pmid:36400020

2021

JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles
JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles
Jaime A Castro-Mondragon, Rafael Riudavets-Puig, Ieva Rauluseviciute, Roza Berhanu Lemma, Laura Turchi, …, Boris Lenhard, Klaas Vandepoele, Wyeth W Wasserman, François Parcy, Anthony Mathelier
Nucleic Acids Research  ·  30 Nov 2021  ·  doi:10.1093/nar/gkab1113
JASPAR 2022
UniBind: maps of high-confidence direct TF-DNA interactions across nine species.
UniBind: maps of high-confidence direct TF-DNA interactions across nine species.
Rafael Riudavets Puig, Paul Boddie, Aziz Khan, Jaime Abraham Castro-Mondragon, Anthony Mathelier
BMC genomics  ·  26 Jun 2021  ·  pmid:34174819
Pakistan: anger mounts over threat to higher education.
Pakistan: anger mounts over threat to higher education.
Aziz Khan
Nature  ·  01 Apr 2021  ·  pmid:33907327
Changing scientific meetings for the better
Changing scientific meetings for the better
Sarvenaz Sarabipour, Aziz Khan, Yu Fen Samantha Seah, Aneth D. Mwakilili, Fiona N. Mumoki, Pablo J. Sáez, Benjamin Schwessinger, Humberto J. Debat, Tomislav Mestrovic
Nature Human Behaviour  ·  15 Mar 2021  ·  doi:10.1038/s41562-021-01067-y
A call to eradicate non-inclusive terms from the life sciences
A call to eradicate non-inclusive terms from the life sciences
Aziz Khan
eLife  ·  08 Feb 2021  ·  doi:10.7554/eLife.65604

2020

UniBind: maps of high-confidence direct TF-DNA interactions across nine species
UniBind: maps of high-confidence direct TF-DNA interactions across nine species
Rafael Riudavets Puig, Paul Boddie, Aziz Khan, Jaime Abraham Castro-Mondragon, Anthony Mathelier
Cold Spring Harbor Laboratory  ·  17 Nov 2020  ·  doi:10.1101/2020.11.17.384578
BiasAway: command-line and web server to generate nucleotide composition-matched DNA background sequences
BiasAway: command-line and web server to generate nucleotide composition-matched DNA background sequences
Aziz Khan, Rafael Riudavets Puig, Paul Boddie, Anthony Mathelier
Bioinformatics  ·  02 Nov 2020  ·  doi:10.1093/bioinformatics/btaa928
Source Code
open-source software
COVID-19: students caught in Pakistan s digital divide.
COVID-19: students caught in Pakistan's digital divide.
Aziz Khan
Nature  ·  01 Nov 2020  ·  pmid:33235363
The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution.
The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution.
Orit Rozenblatt-Rosen, Aviv Regev, Philipp Oberdoerffer, Tal Nawy, Anna Hupalowska, …, Avrum E Spira, Sudhir Srivastava, Kai Tan, Robert B West, Elizabeth H Williams
Cell  ·  16 Apr 2020  ·  pmid:32302568
Evaluating features of scientific conferences: A call for improvements
Evaluating features of scientific conferences: A call for improvements
Sarvenaz Sarabipour, Aziz Khan, Samantha Seah, Aneth D. Mwakilili, Fiona N. Mumoki, Pablo J. Sáez, Benjamin Schwessinger, Humberto J. Debat, Tomislav Mestrovic
Cold Spring Harbor Laboratory  ·  03 Apr 2020  ·  doi:10.1101/2020.04.02.022079
JASPAR 2020: update of the open-access database of transcription factor binding profiles.
JASPAR 2020: update of the open-access database of transcription factor binding profiles.
Oriol Fornes, Jaime A Castro-Mondragon, Aziz Khan, Robin van der Lee, Xi Zhang, …, François Parcy, Albin Sandelin, Boris Lenhard, Wyeth W Wasserman, Anthony Mathelier
Nucleic acids research  ·  08 Jan 2020  ·  pmid:31701148

2019

A map of direct TF DNA interactions in the human genome
A map of direct TF–DNA interactions in the human genome
Marius Gheorghe, Geir Kjetil Sandve, Aziz Khan, Jeanne Chèneby, Benoit Ballester, Anthony Mathelier
Nucleic Acids Research  ·  28 Jun 2019  ·  doi:10.1093/nar/gkz582
Modeling RNA-Binding Protein Specificity In Vivo by Precisely Registering Protein-RNA Crosslink Sites.
Modeling RNA-Binding Protein Specificity In Vivo by Precisely Registering Protein-RNA Crosslink Sites.
Huijuan Feng, Suying Bao, Mohammad Alinoor Rahman, Sebastien M Weyn-Vanhentenryck, Aziz Khan, Justin Wong, Ankeeta Shah, Elise D Flynn, Adrian R Krainer, Chaolin Zhang
Molecular cell  ·  20 Jun 2019  ·  pmid:31226278
Integrative modeling reveals key chromatin and sequence signatures predicting super-enhancers
Integrative modeling reveals key chromatin and sequence signatures predicting super-enhancers
Aziz Khan, Xuegong Zhang
Scientific Reports  ·  27 Feb 2019  ·  doi:10.1038/s41598-019-38979-9
High OGT activity is essential for MYC-driven proliferation of prostate cancer cells
High OGT activity is essential for MYC-driven proliferation of prostate cancer cells
Harri M Itkonen, Alfonso Urbanucci, Sara ES Martin, Aziz Khan, Anthony Mathelier, Bernd Thiede, Suzanne Walker, Ian G Mills
Theranostics  ·  01 Jan 2019  ·  doi:10.7150/thno.30834

2018

A map of direct TF DNA interactions in the human genome
A map of direct TF–DNA interactions in the human genome
Marius Gheorghe, Geir Kjetil Sandve, Aziz Khan, Jeanne Chèneby, Benoit Ballester, Anthony Mathelier
Nucleic Acids Research  ·  04 Dec 2018  ·  doi:10.1093/nar/gky1210
Super-enhancers are transcriptionally more active and cell type-specific than stretch enhancers
Super-enhancers are transcriptionally more active and cell type-specific than stretch enhancers
Aziz Khan, Anthony Mathelier, Xuegong Zhang
Epigenetics  ·  02 Sep 2018  ·  doi:10.1080/15592294.2018.1514231
Making genome browsers portable and personal
Making genome browsers portable and personal
Aziz Khan, Xuegong Zhang
Genome Biology  ·  18 Jul 2018  ·  doi:10.1186/s13059-018-1470-9
Bioconda: sustainable and comprehensive software distribution for the life sciences.
Bioconda: sustainable and comprehensive software distribution for the life sciences.
Björn Grüning, Ryan Dale, Andreas Sjödin, Brad A Chapman, Jillian Rowe, Christopher H Tomkins-Tinch, Renan Valieris, Johannes Köster
Nature methods  ·  01 Jul 2018  ·  pmid:29967506
Super-enhancers are transcriptionally more active and cell-type-specific than stretch enhancers
Super-enhancers are transcriptionally more active and cell-type-specific than stretch enhancers
Aziz Khan, Anthony Mathelier, Xuegong Zhang
Cold Spring Harbor Laboratory  ·  30 Apr 2018  ·  doi:10.1101/310839
Put science first and formatting later
Put science first and formatting later
Aziz Khan, Alejandro Montenegro‐Montero, Anthony Mathelier
EMBO reports  ·  12 Apr 2018  ·  doi:10.15252/embr.201845731

2017

JASPAR RESTful API: accessing JASPAR data from any programming language
JASPAR RESTful API: accessing JASPAR data from any programming language
Aziz Khan, Anthony Mathelier
Bioinformatics  ·  15 Dec 2017  ·  doi:10.1093/bioinformatics/btx804
Source Code
open-source software
JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework
JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework
Aziz Khan, Oriol Fornes, Arnaud Stigliani, Marius Gheorghe, Jaime A Castro-Mondragon, …, Boris Lenhard, Benoît Ballester, Wyeth W Wasserman, François Parcy, Anthony Mathelier
Nucleic Acids Research  ·  13 Nov 2017  ·  doi:10.1093/nar/gkx1126
Bioconda: A sustainable and comprehensive software distribution for the life sciences
Bioconda: A sustainable and comprehensive software distribution for the life sciences
Björn Grüning, Ryan Dale, Andreas Sjödin, Brad A. Chapman, Jillian Rowe, …, Simon Dirmeier, Timothy H. Webster, Oleksandr Moskalenko, Gordon Stephen, Johannes Köster
Cold Spring Harbor Laboratory  ·  21 Oct 2017  ·  doi:10.1101/207092
Intervene: a tool for intersection and visualization of multiple gene or genomic region sets
Intervene: a tool for intersection and visualization of multiple gene or genomic region sets
Aziz Khan, Anthony Mathelier
BMC Bioinformatics  ·  31 May 2017  ·  doi:10.1186/s12859-017-1708-7

2016

dbSUPER: a database of super-enhancers in mouse and human genome
dbSUPER: a database of super-enhancers in mouse and human genome
Aziz Khan, Xuegong Zhang
Nucleic Acids Research  ·  04 Jan 2016  ·  doi:10.1093/nar/gkv1002
dbSUPER is the first database of super-enhancers and Aziz’s first publication
Website
open-source database