Korthauer Lab Statistics + Genomics

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

SUBJECTIVE AND OBJECTIVE SOCIOECONOMIC STATUS AND CONTROL OF HYPERTENSION AND DIABETES
SUBJECTIVE AND OBJECTIVE SOCIOECONOMIC STATUS AND CONTROL OF HYPERTENSION AND DIABETES
[no author info]
Journal of General Internal Medicine   ·   05 Feb 2024   ·   wosuid:WOS:000209142900506
IdentifyingIdentifying regulators of reversible MHC I loss in Markel cell carcinoma through genome-scale screens
IdentifyingIdentifying regulators of reversible MHC I loss in Markel cell carcinoma through genome-scale screens
[no author info]
The Journal of Immunology   ·   05 Feb 2024   ·   wosuid:WOS:000589972403168
Virally mediated mechanisms of HLA class I loss in Merkel cell carcinoma and implications for viral epitope presentation
Virally mediated mechanisms of HLA class I loss in Merkel cell carcinoma and implications for viral epitope presentation
[no author info]
Journal of Investigative Dermatology   ·   05 Feb 2024   ·   wosuid:WOS:000888821100019
Virally mediated mechanisms of HLA class I loss in Merkel cell carcinoma and implications for viral epitope presentation
Virally mediated mechanisms of HLA class I loss in Merkel cell carcinoma and implications for viral epitope presentation
[no author info]
Journal of Investigative Dermatology   ·   05 Feb 2024   ·   wosuid:WOS:000929815500012

2023

vmrseq: Probabilistic Modeling of Single-cell Methylation Heterogeneity
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
Bayesian Decision Curve Analysis with bayesDCA
Bayesian Decision Curve Analysis with bayesDCA
Giuliano N. F. Cruz, Keegan Korthauer
arXiv   ·   03 Aug 2023   ·   doi:10.48550/arXiv.2308.02067
FTD-associated behavioural and transcriptomic abnormalities in ‘humanized’ progranulin-deficient mice: A novel model for progranulin-associated FTD
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
Conservation and divergence of canonical and non-canonical imprinting in murids
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

2022

Reversal of viral and epigenetic HLA class I repression in Merkel cell carcinoma
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
Conservation and divergence of canonical and non-canonical imprinting in murids
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 Greenberg, Matthew Lorincz, Hisato Kobayashi
Cold Spring Harbor Laboratory   ·   21 Apr 2022   ·   doi:10.1101/2022.04.21.488764
Detecting Neuroendocrine Prostate Cancer Through Tissue-Informed Cell-Free DNA Methylation Analysis
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
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
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
Differential substrate use in EGF‐ and oncogenic KRAS‐stimulated human mammary epithelial cells
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
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
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
Reprogramming of the FOXA1 cistrome in treatment-emergent neuroendocrine prostate cancer
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
Cold Spring Harbor Laboratory   ·   24 Oct 2020   ·   doi:10.1101/2020.10.23.350793
Transparency and reproducibility in artificial intelligence
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
Author Correction: Detection of renal cell carcinoma using plasma and urine cell-free DNA methylomes
Author Correction: 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   ·   07 Sep 2020   ·   doi:10.1038/s41591-020-1078-y
Plasma cell-free DNA variant analysis compared with methylated DNA analysis in renal cell carcinoma
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
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
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
Sensitive detection of renal cell carcinoma using plasma and urine cell-free DNA methylomes.
Sensitive detection of renal cell carcinoma using plasma and urine cell-free DNA methylomes.
Pier Vitale Nuzzo, Jacob E Berchuck, Sandor Spisak, Keegan Korthauer, Amin Nassar, ..., Rafael A. Irizarry, Mark Pomerantz, Daniel De Carvalho, Matthew L. Freedman, Toni K. Choueiri
Journal of Clinical Oncology   ·   20 Feb 2020   ·   doi:10.1200/JCO.2020.38.6_SUPPL.728

2019

Detection and accurate false discovery rate control of differentially methylated regions from whole genome bisulfite sequencing
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
A practical guide to methods controlling false discoveries in computational biology
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

2018

Genome-wide repressive capacity of promoter DNA methylation is revealed through epigenomic manipulation
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
A Somatically Acquired Enhancer of the Androgen Receptor Is a Noncoding Driver in Advanced Prostate Cancer
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
            <scp>RNA</scp>
            nuclear enrichment sequences
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
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
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
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
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
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
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
            <sup>+</sup>
            T Cells: Robust Activation and Proliferation with Weak Effector Function during Recall
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

2011

Use and Evaluation of Disposable Absorbent Products for Managing Fecal Incontinence by Community-Living People
Use and Evaluation of Disposable Absorbent Products for Managing Fecal Incontinence by Community-Living People
Donna Z. Bliss, Jaclyn Lewis, Keegan Hasselman, Kay Savik, Ann Lowry, Robin Whitebird
Journal of Wound, Ostomy & Continence Nursing   ·   01 May 2011   ·   doi:10.1097/WON.0B013E31821530CA

2008

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