papers

pre-prints

Giuliano Netto Flores Cruz, Keegan Korthauer. Bayesian Decision Curve Analysis with bayesDCA. arXiv preprint arXiv:2308.02067. 2023 Aug 3.

Keegan Korthauer, Rafael A Irizarry. Genome-wide repressive capacity of promoter DNA methylation is revealed through epigenomic manipulation. bioRxiv, doi: 10.1101/381145, 2018.

peer reviewed journal articles

Benjamin Life, Terri L. Petkau, Giuliano N.F. Cruz, Erick I. Navarro-Delgado, Ning Shen, Keegan Korthauer, Blair R. Leavitt. FTD-associated behavioural and transcriptomic abnormalities in ‘humanized’ progranulin-deficient mice: A novel model for progranulin-associated FTD. Neurobiology of Disease, doi: 10.1016/j.nbd.2023.106138, 182:106138, 2023.

Julien Richard Albert, Toshihiro Kobayashi, Azusa Inoue, Ana Monteagudo-Sánchez, Soichiro Kumamoto, Tomoya Takashima, Asuka Miura, Mami Oikawa, Fumihito Miura, Shuji Takada, Masumi Hirabayashi, Keegan Korthauer, Kazuki Kurimoto, Maxim VC Greenberg, Matthew C Lorincz, Hisato Kobayashi. Conservation and divergence of canonical and non-canonical imprinting in murids. Genome Biology, doi: 10.1186/s13059-023-02869-1, 24:48, 2023.

Patrick C Lee, Susan Klaeger^†, Phuong M Le^†, Keegan Korthauer^†, Jingwei Cheng^†, Varsha Ananthapadmanabhan, Thomas C Frost, Jonathan D Stevens, Alan YL Wong, J Bryan Iorgulescu, Anna Y Tarren, Vipheaviny A Chea, Isabel P Carulli, Camilla K Lemvigh, Christina B Pedersen, Ashley K Gartin, Siranush Sarkizova, Kyle T Wright, Letitia W Li, Jason Nomburg, Shuqiang Li, Teddy Huang, Xiaoxi Liu, Lucas Pomerance, Laura M Doherty, Annie M Apffel, Luke J Wallace, Suzanna Rachimi, Kristen D Felt, Jacquelyn O Wolff, Elizabeth Witten, Wandi Zhang, Donna Neuberg, William J Lane, Guanglan Zhang, Lars R Olsen, Manisha Thakuria, Scott J Rodig, Karl R Clauser, Gabriel J Starrett, John G Doench, Sara J Buhrlage, Steven A Carr, James A DeCaprio^‡, Catherine J Wu^‡, and Derin B Keskin^‡. Reversal of viral and epigenetic HLA class I repression in Merkel cell carcinoma. Journal of Clinical Investigation, doi: 10.1172/JCI151666, 132(13):e151666, 2022.

Jacob E Berchuck^†, Sylvan C Baca^†, Heather M McClure^†, Keegan Korthauer, Harrison K Tsai, Pier Vitale Nuzzo, Kaitlin M Kelleher, Monica He, John A Steinharter, Soumya Zacharia, Sandor Spisak, Ji-Heui Seo, Vincenza Conteduca, Olivier Elemento, Joonghoon Auh, Michael Sigouros, Eva Corey, Michelle S Hirsch, Mary-Ellen Taplin, Toni K Choueiri, Mark M Pomerantz, Himisha Beltran, Matthew L Freedman. Detecting Neuroendocrine Prostate Cancer Through Tissue-Informed Cell-Free DNA Methylation Analysis. Clinical Cancer Research, doi: 10.1158/1078-0432.CCR-21-3762, 28:928-938, 2022.

Haiyang Guo, Yiming Wu, Mannan Nouri, Sandor Spisak, Joshua W Russo, Adam G Sowalsky, Mark M Pomerantz, Zhao Wei, Keegan Korthauer, Ji-Heui Seo, Liyang Wang, Seiji Arai, Matthew L Freedman, Housheng Hansen He, Shaoyong Chen, Steven P Balk. Androgen receptor and MYC equilibration centralizes on developmental super-enhancer. Nature Communications, doi: 10.1038/s41467-021-27077-y, 12(7308), 2021.

Mark A Keibler, Wentao Dong, Keegan D Korthauer, Aaron M Hosios, Sun Jin Moon, Lucas B Sullivan, Nian Liu, Keene L Abbott, Orlando D Arevalo, Kailing Ho, Jennifer Lee, Aasavari S Phanse, Joanne K Kelleher, Othon Iliopoulos, Jonathan L Coloff, Matthew G Vander Heiden, Gregory Stephanopoulos. Differential Substrate Use in EGF‐and Oncogenic KRAS‐Stimulated Human Mammary Epithelial Cells. The FEBS Journal, doi: 10.1111/febs.15858, 288(19): 5629-5649, 2021.

Xiuyu Ma, Keegan Korthauer, Christina Kendziorski, Michael A. Newton. A compositional model to assess expression changes from single-cell RNA-seq data. Annals of Applied Statistics, doi: 10.1214/20-AOAS1423, 15(2): 880-901, 2021.

Sylvan C Baca, David Y Takeda, Ji-Heui Seo, Justin Hwang, Sheng Yu Ku, Rand Arafeh, Taylor Arnoff, Supreet Agarwal, Connor Bell, Edward O’Connor, Xintao Qiu, Sarah Abou Alaiwi, Rosario I Corona, Marcos AS Fonseca, Claudia Giambartolomei, Paloma Cejas, Klothilda Lim, Monica He, Anjali Sheahan, Amin Nassar, Jacob E Berchuck, Lisha Brown, Holly M Nguyen, Ilsa M Coleman, Arja Kaipainen, Navonil De Sarkar, Peter S Nelson, Colm Morrissey, Keegan Korthauer, Mark M Pomerantz, Leigh Ellis, Bogdan Pasaniuc, Kate Lawrenson, Kathleen Kelly, Amina Zoubeidi, William C Hahn, Himisha Beltran, Henry W Long, Myles Brown, Eva Corey, Matthew L Freedman. Reprogramming of the FOXA1 cistrome in treatment-emergent neuroendocrine prostate cancer. Nature Communications, doi: 10.1038/s41467-021-22139-7, 12(1): 1-12, 2021.

April C Watt, Paloma Cejas, Molly J DeCristo, Otto Metzger-Filho, Enid YN Lam, Xintao Qiu, Haley BrinJones, Nikolas Kesten, Rhiannon Coulson, Alba Font-Tello, Klothilda Lim, Raga Vadhi, Veerle W Daniels, Joan Montero, Len Taing, Clifford A Meyer, Omer Gilan, Charles C Bell, Keegan D Korthauer, Claudia Giambartolomei, Bogdan Pasaniuc, Ji-Heui Seo, Matthew L Freedman, Cynthia Ma, Matthew J Ellis, Ian Krop, Eric Winer, Anthony Letai, Myles Brown, Mark A Dawson, Henry W Long, Jean J Zhao, Shom Goel. CDK4/6 inhibition reprograms the breast cancer enhancer landscape by stimulating AP-1 transcriptional activity. Nature Cancer, doi: 10.1038/s43018-020-00135-y, 2(1): 34-48, 2021.

Benjamin Haibe-Kains, George Alexandru Adam, Ahmed Hosny, Farnoosh Khodakarami, Levi Waldron, Bo Wang, Chris McIntosh, Anna Goldenberg, Anshul Kundaje, Casey S Greene, Tamara Broderick, Michael M Hoffman, Jeffrey T Leek, Keegan Korthauer, Wolfgang Huber, Alvis Brazma, Joelle Pineau, Robert Tibshirani, Trevor Hastie, John PA Ioannidis, John Quackenbush, Hugo JWL Aerts. Transparency and reproducibility in artificial intelligence. Nature, doi: 10.1038/s41586-020-2766-y, 586(7829): E14-E16, 2021.

Mark M Pomerantz^†, Xintao Qiu^†, Yanyun Zhu^†, David Y Takeda, Wenting Pan, Sylvan C Baca, Alexander Gusev, Keegan Korthauer, Tesa M Severson, Gavin Ha, Srinivas R Viswanathan, Ji-Heui Seo, Holly M Nguyen, Baohui Zhang, Bogdan Pasaniuc, Claudia Giambartolomei, Sarah A Alaiwi, Connor A Bell, Edward P O’Connor, Matthew S Chabot, David R Stillman, Rosina Lis, Alba Font-Tello, Lewyn Li, Paloma Cejas, Andries M Bergman, Joyce Sanders, Henk G van der Poel, Simon A Gayther, Kate Lawrenson, Marcos A S Fonseca, Jessica Reddy, Rosario I Corona, Gleb Martovetsky, Brian Egan, Toni Choueiri, Leigh Ellis, Isla P Garraway, Gwo-Shu Mary Lee, Eva Corey, Henry W Long, Wilbert Zwart, Matthew L Freedman. Prostate cancer reactivates developmental epigenomic programs during metastatic progression. Nature Genetics, doi: 10.1038/s41588-020-0664-8, 52(8): 790-799, 2020.

Pier Vitale Nuzzo^†, Jacob E Berchuck^†, Keegan Korthauer^†, Sandor Spisak^†, Amin H Nassar, Sarah A Alaiwi, Ankur Chakravarthy, Shu Y Shen, Ziad Bakouny, Francesco Boccardo, John Steinharter, Gabrielle Bouchard, Catherine R Curran, Wenting Pan, Sylvan C Baca, Ji-Heui Seo, Gwo-Shu M Lee, M Dror Michaelson, Steven L Chang, Sushrut S Waikar, Guru Sonpavde, Rafael A Irizarry, Mark Pomerantz, Daniel D De Carvalho^‡, Toni K Choueiri^‡, Matthew L Freedman^‡. Detection of renal cell carcinoma using plasma and urine cell-free DNA methylomes. Nature Medicine, 26:1041-1043, doi: 10.1038/s41591-020-0933-1, 26(7): 1041-1043, 2020.

Kathryn Lasseter^†, Amin H Nassar^†, Lana Hamieh^†, Jacob E Berchuck^†, Pier Vitale Nuzzo^†, Keegan Korthauer, Atul B Shinagare, Barbara Ogorek, Rana McKay, Aaron R Thorner, Gwo-Shu Mary Lee, David A Braun, Rupal S Bhatt, Matthew Freedman^‡, Toni K Choueiri^‡, David J Kwiatkowski^‡. Plasma cell-free DNA mutation analysis compared to methylated DNA analysis in renal cell carcinoma. Genetics in Medicine, doi: 10.1038/s41436-020-0801-x, 22(8): 1366-1373, 2020.

Keegan Korthauer, Sutirtha Chakraborty, Yuval Benjamini, Rafael A Irizarry. Detection and accurate False Discovery Rate control of differentially methylated regions from Whole Genome Bisulfite Sequencing. Biostatistics. doi: 10.1093/biostatistics/kxy007, , 20(3):367-383, 2019.

Keegan Korthauer^†, Patrick K Kimes^†, Claire Duvallet^‡, Alejandro Reyes^‡, Ayshwarya Subramanian^‡, Mingxiang Teng, Chinmay Shukla, Eric J Alm, and Stephanie C Hicks. A practical guide to methods controlling false discovery rates. Genome Biology. doi: 10.1186/s13059-019-1716-1, 20:118, 2019.

David Y Takeda^†, Sándor Spisák^†, Ji-Heui Seo, Connor Bell, Edward O’Connor, Keegan Korthauer, Dezső Ribli, István Csabai, Norbert Solymosi, Zoltán Szállási, David R Stillman, Paloma Cejas, Xintao Qiu, Henry W Long, Viktória Tisza, Pier Vitale Nuzzo, Mersedeh Rohanizadegan, Mark M Pomerantz, William C Hahn, Matthew L Freedman. A somatically acquired enhancer of the androgen receptor is a noncoding driver in advanced prostate cancer. Cell. doi: 10.1016/j.cell.2018.05.037, 20:118, 2018.

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. High-throughput identification of RNA nuclear enrichment sequences. The EMBO Journal, 37:e98452. doi: 10.15252/embj.201798452, 2018.

Jeea Choi, Shuyun Ye, Kevin H Eng, Keegan Korthauer, William H Bradley, Janet S Rader, Christina Kendziorski. IPI59: an actionable biomarker to improve treatment response in serous ovarian carcinoma patients. Statistics in Biosciences, 9(1):1-12. doi: 10.1007/s12561-016-9144-1, 2017.

Keegan D Korthauer, Li-Fang Chu, Michael A Newton, Yuan Li, James Thomson, Ron Stewart, Christina Kendziorski. A statistical approach for identifying differential distributions in single-cell RNA-seq experiments. Genome Biology, 17:222. doi: 10.1186/s13059-016-1077-y, 2016.

Clara Bodelon, Svetlana Vinokurova, Joshua N Sampson, Johan A den Boon, Joan L Walker, Mark A Horswill, Keegan Korthauer, Mark Schiffman, Mark E Sherman, Rosemary E Zuna, Jason Mitchell, Xijun Zhang, Joseph F Boland, Anil K Chaturvedi, S Terence Dunn, Michael A Newton, Paul Ahlquist, Sophia S Wang, Nicolas Wentzensen. Copy number alterations and HPV integration in cervical precancer and invasive cancer. Carcinogenesis, 37(2):188-196. doi: 10.1093/carcin/bgv171, 2016.

Keegan Korthauer, Christina Kendziorski. MADGiC: a model-based approach for identifying driver genes in cancer. Bioinformatics, 31(10): 1526–1535. doi: 10.1093/bioinformatics/btu858, 2015.

Yun Ju Sung, Keegan D Korthauer, Michael D Swartz, Corinne D Engelman. Methods for Collapsing Multiple Rare Variants in Whole Genome Sequencing Data. Genetic Epidemiology, 38(S1):S13-S20. doi: doi.org/10.1002/gepi.21820, 2014.

Marcel Wüthrich, Karen Ersland, John C Pick-Jacobs, Benjamin H Gern, Christopher A Frye, Thomas D Sullivan, Meghan B Brennan, Hanna I Filutowicz, Kevin O’Brien, Keegan D Korthauer, Stacey Schultz-Cherry, Bruce S Klein. 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. Infection and immunity, 80(2): 787-797. doi: 10.1128/IAI.05326-11 2012.

Donna Z Bliss, Jaclyn Lewis, Keegan Hasselmann (now Korthauer), Kay Savik, Ann Lowry, Robin Whitebird. Use and evaluation of disposable absorbent products for managing fecal incontinence by community-living people. Journal of wound, ostomy, and continence nursing, 38(3):289. doi: 10.1097/WON.0b013e31821530ca, 2011.

Lin Wang, Raka M Mitra, Keegan D Hasselmann (now Korthauer), Masanao Sato, Lisa Lenarz-Wyatt, Jerry D Cohen, Fumiaki Katagiri, Jane Glazebrook. The genetic network controlling the Arabidopsis transcriptional response to Pseudomonas syringae pv. maculicola: roles of major regulators and the phytotoxin coronatine. Molecular plant-microbe interactions, 21(11): 1408-1420. doi: 10.1094/MPMI-21-11-1408, 2008.

book chapters

Keegan Korthauer, John Dawson and Christina Kendziorski. Predicting cancer subtypes using survival-supervised latent Dirichlet allocation models. In Advances in Statistical Bioinformatics: Models and Integrative Inference for High-Throughput Data, Kim-Anh Do, Zhaohui Steve Qin, Marina Vannucci (Eds). Cambridge University Press. doi: 10.1017/CBO9781139226448 2013.

conference proceedings

Pier Vitale Nuzzo, Sandor Spisak, Jacob E Berchuck, Sylvan Baca, Keegan Korthauer, Amin Nassar, Sarah Abou Alaiwi, Ziad Bakouny, Ronan Flippot, John A Steinharter, Catherine Curran, Gwo-Shu Mary Lee, Sushrut Waikar, Mark Pomerantz, Daniel De Carvalho, Guru Sonpavde, Matthew L Freedman, Toni K Choueiri. Detection of urothelial carcinoma using plasma cell-free methylated DNA. Journal of Clinical Oncology, doi: 10.1200/JCO.2020.38.15_suppl.5046, 2020.

Patrick C Lee, Phuong Le, Keegan Korthauer, Jingwei Cheng, John Doench, James A DeCaprio, Derin B Keskin, Catherine J Wu. Identifying regulators of reversible MHC I loss in Merkel cell carcinoma through genome-scale screens. The Journal of Immunology, url: https://www.jimmunol.org/content/204/1_Supplement/243.18, 2020.

Pier Vitale Nuzzo, Jacob E Berchuck, Sandor Spisak, Keegan Korthauer, Amin Nassar, Sarah Abou Alaiwi, Ankur Chakravarthy, Shu Yi Shen, Ziad Bakouny, Francesco Boccardo, Sylvan Baca, Gwo-Shu Mary Lee, Steven Lee Chang, Sushrut Waikar, Guru Sonpavde, Rafael A Irizarry, Mark Pomerantz, Daniel De Carvalho, Matthew L Freedman, Toni K Choueiri. Sensitive detection of renal cell carcinoma using plasma and urine cell-free DNA methylomes. Journal of Clinical Oncology, doi: 10.1200/JCO.2020.38.6_suppl.728, 2020.

Jose A Delgado, Elizabeth A Jacobs, Nancy E Adler, Keegan Korthauer, Alicia Fernandez. The relation between subjective socioeconomic status, depression and self-rated health in a population of African Americans, Hispanics and non-Hispanic whites with diabetes, Journal of General Internal Medicine, 28: S209. doi: 10.1007/s11606-013-2436-y, 2013.

Jose Delgado, Alicia Fernandez, Nancy E Adler, Keegan Korthauer, Elizabeth Jacobs Subjective and objective socioeconomic status and control of hypertension and diabetes. Journal of General Internal Medicine, 27:S312-S312. doi: 10.1007/s11606-012-2038-0, 2012.

phd dissertation

Keegan Korthauer. Bayesian hierarchical modeling of high-throughput genomic data with applications to cancer bioinformatics and stem cell differentiation, Ph.D. Thesis, University of Wisconsin, 2015.

† = co-first authorship; these authors contributed equally
‡ = co-second authorship; these authors contributed equally