Research

Our interdisciplinary research lies at the interface of statistics and genomics. With our methods development work, we aim to advance statistical methodology and computational tools for the analysis of high-dimensional biological data. Our work is also highly collaborative; we routinely work alongside experimentalists and clinicians to apply cutting edge bioinformatics tools to uncover new molecular signals in cancer, child health, and development. We are especially interested in advancing understanding of epigenetics - the study of how gene activity is controlled through mechanisms that don’t involve changes in the DNA sequence itself - at the genome scale. You can check out our publications listed below, or find them listed on Google Scholar.

2024

Bayesian Decision Curve Analysis With Bayesdca

Giuliano Netto Flores Cruz, Keegan Korthauer

Statistics in Medicine  ·  01 Dec 2024  ·  doi:10.1002/sim.10277

Source code

R Package

Pterostilbene Targets Hallmarks of Aging in the Gene Expression Landscape in Blood of Healthy Rats

Marco A. Tello‐Palencia, Tony Yang, Olga Sularz, Louis Erik Demers, Yuexi Ma, …, Sandra Torregrosa‐Allen, Bennett D. Elzey, Nadia Atallah Lanman, Keegan Korthauer, Barbara Stefanska

Molecular Nutrition & Food Research  ·  19 Nov 2024  ·  doi:10.1002/mnfr.202400662

Genetic Basis, Quantitative Nature, and Functional Relevance of Evolutionarily Conserved DNA Methylation

Zheng (Joe) Dong, Samantha Schaffner, Maggie Fu, Joanne Whitehead, Julia L. MacIsaac, …, Lluis Quintana-Murci, Etienne Patin, Gregory E. Miller, Keegan Korthauer, Michael S. Kobor

Cold Spring Harbor Laboratory  ·  09 Nov 2024  ·  doi:10.1101/2024.11.07.622474

Complete Reference Genome and Pangenome Expand Biologically Relevant Information for Genome-Wide DNA Methylation Analysis Using Short-Read Sequencing and Array Data

Zheng (Joe) Dong, Joanne Whitehead, Maggie Fu, Julia L. MacIsaac, David H. Rehkopf, Luis Rosero-Bixby, Michael S. Kobor, Keegan Korthauer

Cold Spring Harbor Laboratory  ·  11 Oct 2024  ·  doi:10.1101/2024.10.07.617116

Discrepancies in readouts between Infinium MethylationEPIC v2.0 and v1.0 reflected in DNA methylation-based tools: implications and considerations for human population epigenetic studies

Beryl C. Zhuang, Marcia Smiti Jude, Chaini Konwar, Natan Yusupov, Calen Patrick Ryan, …, Daniel W. Belsky, Elisabeth B. Binder, Darina Czamara, Keegan Korthauer, Michael Steffen Kobor

Cold Spring Harbor Laboratory  ·  03 Jul 2024  ·  doi:10.1101/2024.07.02.600461

2023

vmrseq: Probabilistic Modeling of Single-cell Methylation Heterogeneity

Ning Shen, Keegan Korthauer

Cold Spring Harbor Laboratory  ·  21 Nov 2023  ·  doi:10.1101/2023.11.20.567911

Source code

R package

FTD-associated behavioural and transcriptomic abnormalities in ‘humanized’ progranulin-deficient mice: A novel model for progranulin-associated FTD

Benjamin Life, Terri L. Petkau, Giuliano N.F. Cruz, Erick I. Navarro-Delgado, Ning Shen, Keegan Korthauer, Blair R. Leavitt

Neurobiology of Disease  ·  01 Jun 2023  ·  doi:10.1016/j.nbd.2023.106138

Source code

Conservation and divergence of canonical and non-canonical imprinting in murids

Julien Richard Albert, Toshihiro Kobayashi, Azusa Inoue, Ana Monteagudo-Sánchez, Soichiro Kumamoto, …, Keegan Korthauer, Kazuki Kurimoto, Maxim V. C. Greenberg, Matthew Lorincz, Hisato Kobayashi

Genome Biology  ·  14 Mar 2023  ·  doi:10.1186/s13059-023-02869-1

Source code

2022

Reversal of viral and epigenetic HLA class I repression in Merkel cell carcinoma

Patrick C. Lee, Susan Klaeger, Phuong M. Le, Keegan Korthauer, Jingwei Cheng, …, Sara J. Buhrlage, Steven A. Carr, James A. DeCaprio, Catherine J. Wu, Derin B. Keskin

Journal of Clinical Investigation  ·  01 Jul 2022  ·  doi:10.1172/JCI151666

Source code

Detecting Neuroendocrine Prostate Cancer Through Tissue-Informed Cell-Free DNA Methylation Analysis

Jacob E. Berchuck, Sylvan C. Baca, Heather M. McClure, Keegan Korthauer, Harrison K. Tsai, …, Mary-Ellen Taplin, Toni K. Choueiri, Mark M. Pomerantz, Himisha Beltran, Matthew L. Freedman

Clinical Cancer Research  ·  01 Mar 2022  ·  doi:10.1158/1078-0432.CCR-21-3762

2021

Androgen receptor and MYC equilibration centralizes on developmental super-enhancer

Haiyang Guo, Yiming Wu, Mannan Nouri, Sandor Spisak, Joshua W. Russo, …, Seiji Arai, Matthew L. Freedman, Housheng Hansen He, Shaoyong Chen, Steven P. Balk

Nature Communications  ·  15 Dec 2021  ·  doi:10.1038/s41467-021-27077-y

A compositional model to assess expression changes from single-cell RNA-seq data

Xiuyu Ma, Keegan Korthauer, Christina Kendziorski, Michael A. Newton

The Annals of Applied Statistics  ·  01 Jun 2021  ·  doi:10.1214/20-AOAS1423

R package

Differential substrate use in EGF‐ and oncogenic KRAS‐stimulated human mammary epithelial cells

Mark A. Keibler, Wentao Dong, Keegan D. Korthauer, Aaron M. Hosios, Sun Jin Moon, …, Joanne K. Kelleher, Othon Iliopoulos, Jonathan L. Coloff, Matthew G. Vander Heiden, Gregory Stephanopoulos

The FEBS Journal  ·  13 May 2021  ·  doi:10.1111/febs.15858

Reprogramming of the FOXA1 cistrome in treatment-emergent neuroendocrine prostate cancer

Sylvan C. Baca, David Y. Takeda, Ji-Heui Seo, Justin Hwang, Sheng Yu Ku, …, Himisha Beltran, Henry W. Long, Myles Brown, Eva Corey, Matthew L. Freedman

Nature Communications  ·  30 Mar 2021  ·  doi:10.1038/s41467-021-22139-7

2020

CDK4/6 inhibition reprograms the breast cancer enhancer landscape by stimulating AP-1 transcriptional activity

April C. Watt, Paloma Cejas, Molly J. DeCristo, Otto Metzger-Filho, Enid Y. N. Lam, …, Myles Brown, Mark A. Dawson, Henry W. Long, Jean J. Zhao, Shom Goel

Nature Cancer  ·  09 Nov 2020  ·  doi:10.1038/s43018-020-00135-y

Transparency and reproducibility in artificial intelligence

Benjamin Haibe-Kains, George Alexandru Adam, Ahmed Hosny, Farnoosh Khodakarami, Thakkar Shraddha, …, Robert Tibshirani, Trevor Hastie, John P. A. Ioannidis, John Quackenbush, Hugo J. W. L. Aerts

Nature  ·  14 Oct 2020  ·  doi:10.1038/s41586-020-2766-y

Plasma cell-free DNA variant analysis compared with methylated DNA analysis in renal cell carcinoma

Kathryn Lasseter, Amin H. Nassar, Lana Hamieh, Jacob E. Berchuck, Pier Vitale Nuzzo, …, David A. Braun, Rupal S. Bhatt, Matthew Freedman, Toni K. Choueiri, David J. Kwiatkowski

Genetics in Medicine  ·  01 Aug 2020  ·  doi:10.1038/s41436-020-0801-x

Prostate cancer reactivates developmental epigenomic programs during metastatic progression

Mark M. Pomerantz, Xintao Qiu, Yanyun Zhu, David Y. Takeda, Wenting Pan, …, Gwo-Shu Mary Lee, Eva Corey, Henry W. Long, Wilbert Zwart, Matthew L. Freedman

Nature Genetics  ·  20 Jul 2020  ·  doi:10.1038/s41588-020-0664-8

Detection of renal cell carcinoma using plasma and urine cell-free DNA methylomes

Pier Vitale Nuzzo, Jacob E. Berchuck, Keegan Korthauer, Sandor Spisak, Amin H. Nassar, …, Rafael A. Irizarry, Mark Pomerantz, Daniel D. De Carvalho, Toni K. Choueiri, Matthew L. Freedman

Nature Medicine  ·  22 Jun 2020  ·  doi:10.1038/s41591-020-0933-1

Source code

2019

Detection and accurate false discovery rate control of differentially methylated regions from whole genome bisulfite sequencing

Keegan Korthauer, Sutirtha Chakraborty, Yuval Benjamini, Rafael A Irizarry

Biostatistics  ·  01 Jul 2019  ·  doi:10.1093/biostatistics/kxy007

Source code

R/Bioconductor package

A practical guide to methods controlling false discoveries in computational biology

Keegan Korthauer, Patrick K. Kimes, Claire Duvallet, Alejandro Reyes, Ayshwarya Subramanian, Mingxiang Teng, Chinmay Shukla, Eric J. Alm, Stephanie C. Hicks

Genome Biology  ·  04 Jun 2019  ·  doi:10.1186/s13059-019-1716-1

Source code

Data package

Shiny app

2018

Genome-wide repressive capacity of promoter DNA methylation is revealed through epigenomic manipulation

Keegan Korthauer, Rafael A. Irizarry

Cold Spring Harbor Laboratory  ·  01 Aug 2018  ·  doi:10.1101/381145

Source code

A Somatically Acquired Enhancer of the Androgen Receptor Is a Noncoding Driver in Advanced Prostate Cancer

David Y. Takeda, Sándor Spisák, Ji-Heui Seo, Connor Bell, Edward O’Connor, …, Pier Vitale Nuzzo, Mersedeh Rohanizadegan, Mark M. Pomerantz, William C. Hahn, Matthew L. Freedman

Cell  ·  01 Jul 2018  ·  doi:10.1016/j.cell.2018.05.037

High‐throughput identification of RNA nuclear enrichment sequences

Chinmay J Shukla, Alexandra L McCorkindale, Chiara Gerhardinger, Keegan D Korthauer, Moran N Cabili, David M Shechner, Rafael A Irizarry, Philipp G Maass, John L Rinn

The EMBO Journal  ·  15 Jan 2018  ·  doi:10.15252/embj.201798452

2017

IPI59: An Actionable Biomarker to Improve Treatment Response in Serous Ovarian Carcinoma Patients

J. Choi, S. Ye, K. H. Eng, K. Korthauer, W. H. Bradley, J. S. Rader, C. Kendziorski

Statistics in Biosciences  ·  01 Jun 2017  ·  doi:10.1007/s12561-016-9144-1

2016

A statistical approach for identifying differential distributions in single-cell RNA-seq experiments

Keegan D. Korthauer, Li-Fang Chu, Michael A. Newton, Yuan Li, James Thomson, Ron Stewart, Christina Kendziorski

Genome Biology  ·  25 Oct 2016  ·  doi:10.1186/s13059-016-1077-y

2015

Chromosomal copy number alterations and HPV integration in cervical precancer and invasive cancer

Clara Bodelon, Svetlana Vinokurova, Joshua N. Sampson, Johan A. den Boon, Joan L. Walker, …, S. Terence Dunn, Michael A. Newton, Paul Ahlquist, Sophia S. Wang, Nicolas Wentzensen

Carcinogenesis  ·  09 Dec 2015  ·  doi:10.1093/carcin/bgv171

MADGiC: a model-based approach for identifying driver genes in cancer

Keegan D. Korthauer, Christina Kendziorski

Bioinformatics  ·  07 Jan 2015  ·  doi:10.1093/bioinformatics/btu858

2014

Methods for Collapsing Multiple Rare Variants in Whole‐Genome Sequence Data

Yun Ju Sung, Keegan D. Korthauer, Michael D. Swartz, Corinne D. Engelman

Genetic Epidemiology  ·  11 Aug 2014  ·  doi:10.1002/gepi.21820

2013

Predicting Cancer Subtypes Using Survival-Supervised Latent Dirichlet Allocation Models

Keegan Korthauer, John Dawson, Christina Kendziorski

Advances in Statistical Bioinformatics  ·  10 Jun 2013  ·  doi:10.1017/cbo9781139226448.019

2012

Limited Model Antigen Expression by Transgenic Fungi Induces Disparate Fates during Differentiation of Adoptively Transferred T Cell Receptor Transgenic CD4 ⁺ T Cells: Robust Activation and Proliferation with Weak Effector Function during Recall

Marcel Wüthrich, Karen Ersland, John C. Pick-Jacobs, Benjamin H. Gern, Christopher A. Frye, …, Hanna I. Filutowicz, Kevin O’Brien, Keegan D. Korthauer, Stacey Schultz-Cherry, Bruce S. Klein

Infection and Immunity  ·  01 Feb 2012  ·  doi:10.1128/IAI.05326-11

2008

The Genetic Network Controlling the Arabidopsis Transcriptional Response to Pseudomonas syringae pv. maculicola: Roles of Major Regulators and the Phytotoxin Coronatine

Lin Wang, Raka M. Mitra, Keegan D. Hasselmann, Masanao Sato, Lisa Lenarz-Wyatt, Jerry D. Cohen, Fumiaki Katagiri, Jane Glazebrook

Molecular Plant-Microbe Interactions®  ·  01 Nov 2008  ·  doi:10.1094/mpmi-21-11-1408