Keegan Korthauer
PhD
Investigator, BC Children's Hospital
JCO Precision Oncology
Giuliano Netto Flores Cruz and Keegan Korthauer
DOI: 10.1200/PO-25-0027912 / 2025
Genome Biology
Erick I. Navarro-Delgado and Darina Czamara and Karlie Edwards and Maggie P. Fu and Sarah M. Merrill and Chaini Konwar and Julie L. MacIsaac and David T.S. Lin and Piush Mandhane and Elinor Simons and Padmaja Subbarao and Theo J. Moraes and Jari Lahti and Gregory E. Miller and Elisabeth B. Binder and Katri Rikknen and Stuart E. Turvey and Keegan Korthauer and Michael S. Kobor
DOI: 10.1186/s13059-025-03864-412 / 2025
Genomics, Proteomics & Bioinformatics
Zheng Dong and Nicole Gladish and Maggie P Y Fu and Samantha L Schaffner and Keegan Korthauer and Michael S Kobor
DOI: 10.1093/gpbjnl/qzaf09611 / 2025
Gina L. McNeill and Giada Guntri and Ida Calvi and Alastair H. Kyle and Hans-Rudolf Hotz and Victoria M. Leonard and Willie Wu and Matthew J. Shannon and Andrew I. Minchinton and Keegan Korthauer and Margherita Y. Turco and Alexander G. Beristain
DOI: 10.1101/2025.10.29.68538710 / 2025
Biorxiv
Shen, N. and Zhang, Z. and Baca, S. and Korthauer, K.
DOI: 10.1101/2025.05.09.653152Cell Reports
Dong, Z. and Whitehead, J. and Fu, M. and MacIsaac, J.L. and Rehkopf, D.H. and Rosero-Bixby, L. and Kobor, M.S. and Korthauer, K.
DOI: 10.1016/j.celrep.2025.115755Life Science Alliance
Zhuang, B.C. and Jude, M.S. and Konwar, C. and Yusupov, N. and Ryan, C.P. and Engelbrecht, H.-R. and Whitehead, J. and Halberstam, A.A. and Macisaac, J.L. and Dever, K. and Tran, T.K. and Korinek, K. and Zimmer, Z. and Lee, N.R. and McDade, T.W. and Kuzawa, C.W. and Huffman, K.M. and Belsky, D.W. and Binder, E.B. and Czamara, D. and Korthauer, K. and Kobor, M.S.
DOI: 10.26508/lsa.202403155STAR Protocols
Fu, M.P.-Y. and Merrill, S.M. and Korthauer, K. and Kobor, M.S.
DOI: 10.1016/j.xpro.2025.103638Zheng Dong and Samantha Schaffner and Maggie Fu and Joanne Whitehead and Julia L. MacIsaac and David H. Rehkopf and W. Thomas Boyce and Luis Rosero-Bixby and Lluis Quintana-Murci and Etienne Patin and Gregory E. Miller and Keegan Korthauer and Michael S. Kobor
DOI: 10.1101/2024.11.07.62247411 / 2024
Biorxiv
Dong, Z.J. and Whitehead, J. and Fu, M. and MacIsaac, J.L. and Rehkopf, D.H. and Rosero-Bixby, L. and Kobor, M.S. and Korthauer, K.
DOI: 10.1101/2024.10.07.617116Biorxiv
Zhuang, B.C. and Jude, M.S. and Konwar, C. and Yusupov, N. and Ryan, C.P. and Engelbrecht, H.-R. and Whitehead, J. and Halberstam, A.A. and MacIsaac, J.L. and Dever, K. and Tran, T.K. and Korinek, K. and Zimmer, Z. and Lee, N.R. and McDade, T.W. and Kuzawa, C.W. and Huffman, K.M. and Belsky, D.W. and Binder, E.B. and Czamara, D. and Korthauer, K. and Kobor, M.S.
DOI: 10.1101/2024.07.02.600461Statistics in Medicine
Netto Flores Cruz, G. and Korthauer, K.
DOI: 10.1002/sim.10277Molecular Nutrition and Food Research
Tello-Palencia, M.A. and Yang, T. and Sularz, O. and Demers, L.E. and Ma, Y. and Boycott, C. and Zhang, H.A. and Lubecka-Gajewska, K. and Kumar, S. and Ramsey, B.S. and Torregrosa-Allen, S. and Elzey, B.D. and Lanman, N.A. and Korthauer, K. and Stefanska, B.
DOI: 10.1002/mnfr.202400662Biorxiv
Shen, N. and Korthauer, K.
DOI: 10.1101/2023.11.20.567911Neurobiology of Disease
DOI: 10.1016/J.NBD.2023.106138Genome Biology
DOI: 10.1186/S13059-023-02869-1Journal of Clinical Investigation
DOI: 10.1172/JCI151666Clinical Cancer Research
DOI: 10.1158/1078-0432.CCR-21-3762The FEBS journal
Keibler MA and Dong W and Korthauer KD and Hosios AM and Moon SJ and Sullivan LB and Liu N and Abbott KL and Arevalo OD and Ho K and Lee J and Phanse AS and Kelleher JK and Iliopoulos O and Stephanopoulos G
DOI: 10.1111/febs.15858 PubMed: 3381172904 / 2021
Annals of Applied Statistics
Ma, X. and Korthauer, K. and Kendziorski, C. and Newton, M.A.
DOI: 10.1214/20-AOAS1423Nature Communications
Baca, S.C. and Takeda, D.Y. and Seo, J.-H. and Hwang, J. and Ku, S.Y. and Arafeh, R. and Arnoff, T. and Agarwal, S. and Bell, C. and O?Connor, E. and Qiu, X. and Alaiwi, S.A. and Corona, R.I. and Fonseca, M.A.S. and Giambartolomei, C. and Cejas, P. and Lim, K. and He, M. and Sheahan, A. and Nassar, A. and Berchuck, J.E. and Brown, L. and Nguyen, H.M. and Coleman, I.M. and Kaipainen, A. and De Sarkar, N. and Nelson, P.S. and Morrissey, C. and Korthauer, K. and Pomerantz, M.M. and Ellis, L. and Pasaniuc, B. and Lawrenson, K. and Kelly, K. and Zoubeidi, A. and Hahn, W.C. and Beltran, H. and Long, H.W. and Brown, M. and Corey, E. and Freedman, M.L.
DOI: 10.1038/s41467-021-22139-7Nature Communications
DOI: 10.1038/S41467-021-27077-YNature Cancer
April C. Watt and Paloma Cejas and Molly J. DeCristo and Otto Metzger-Filho and Enid Y. N. Lam and Xintao Qiu and Haley BrinJones and Nikolas Kesten and Rhiannon Coulson and Alba Font-Tello and Klothilda Lim and Raga Vadhi and Veerle W. Daniels and Joan Montero and Len Taing and Clifford A. Meyer and Omer Gilan and Charles C. Bell and Keegan D. Korthauer and Claudia Giambartolomei and Bogdan Pasaniuc and Ji-Heui Seo and Matthew L. Freedman and Cynthia Ma and Matthew J. Ellis and Ian Krop and Eric Winer and Anthony Letai and Myles Brown and Mark A. Dawson and Henry W. Long and Jean J. Zhao and Shom Goel
DOI: 10.1038/s43018-020-00135-y11 / 2020
Nature
Haibe-Kains B and Adam GA and Hosny A and Khodakarami F and Massive Analysis Quality Control (MAQC) Society Board of Directors and Waldron L and Wang B and McIntosh C and Aerts HJWL
DOI: 10.1038/s41586-020-2766-y PubMed: 3305721710 / 2020
Journal of Clinical Oncology
DOI: 10.1200/jco.2020.38.15_suppl.504605 / 2020
Nature Medicine
Nuzzo, P.V. and Berchuck, J.E. and Korthauer, K. and Spisak, S. and Nassar, A.H. and Alaiwi, S.A. and Chakravarthy, A. and Shen, S.Y. and Bakouny, Z. and Boccardo, F. and Steinharter, J. and Bouchard, G. and Curran, C.R. and Pan, W. and Baca, S.C. and Seo, J.-H. and Lee, G.-S.M. and Michaelson, M.D. and Chang, S.L. and Waikar, S.S. and Sonpavde, G. and Irizarry, R.A. and Pomerantz, M. and De Carvalho, D.D. and Choueiri, T.K. and Freedman, M.L.
DOI: 10.1038/s41591-020-1078-yNature Genetics
Pomerantz, M.M. and Qiu, X. and Zhu, Y. and Takeda, D.Y. and Pan, W. and Baca, S.C. and Gusev, A. and Korthauer, K.D. and Severson, T.M. and Ha, G. and Viswanathan, S.R. and Seo, J.-H. and Nguyen, H.M. and Zhang, B. and Pasaniuc, B. and Giambartolomei, C. and Alaiwi, S.A. and Bell, C.A. and O?Connor, E.P. and Chabot, M.S. and Stillman, D.R. and Lis, R. and Font-Tello, A. and Li, L. and Cejas, P. and Bergman, A.M. and Sanders, J. and van der Poel, H.G. and Gayther, S.A. and Lawrenson, K. and Fonseca, M.A.S. and Reddy, J. and Corona, R.I. and Martovetsky, G. and Egan, B. and Choueiri, T. and Ellis, L. and Garraway, I.P. and Lee, G.-S.M. and Corey, E. and Long, H.W. and Zwart, W. and Freedman, M.L.
DOI: 10.1038/s41588-020-0664-8Genetics in Medicine
Lasseter, K. and Nassar, A.H. and Hamieh, L. and Berchuck, J.E. and Nuzzo, P.V. and Korthauer, K. and Shinagare, A.B. and Ogorek, B. and McKay, R. and Thorner, A.R. and Lee, G.-S.M. and Braun, D.A. and Bhatt, R.S. and Freedman, M. and Choueiri, T.K. and Kwiatkowski, D.J.
DOI: 10.1038/s41436-020-0801-xNature Medicine
Nuzzo, P.V. and Berchuck, J.E. and Korthauer, K. and Spisak, S. and Nassar, A.H. and Abou Alaiwi, S. and Chakravarthy, A. and Shen, S.Y. and Bakouny, Z. and Boccardo, F. and Steinharter, J. and Bouchard, G. and Curran, C.R. and Pan, W. and Baca, S.C. and Seo, J.-H. and Lee, G.-S.M. and Michaelson, M.D. and Chang, S.L. and Waikar, S.S. and Sonpavde, G. and Irizarry, R.A. and Pomerantz, M. and De Carvalho, D.D. and Choueiri, T.K. and Freedman, M.L.
DOI: 10.1038/s41591-020-0933-1Biostatistics (Oxford, England)
Korthauer K and Chakraborty S and Benjamini Y and Irizarry RA
DOI: 10.1093/biostatistics/kxy007 PubMed: 2948160407 / 2019
Genome Biology
Korthauer, K. and Kimes, P.K. and Duvallet, C. and Reyes, A. and Subramanian, A. and Teng, M. and Shukla, C. and Alm, E.J. and Hicks, S.C.
DOI: 10.1186/s13059-019-1716-1 PubMed: 31164141Keegan Korthauer and Rafael A. Irizarry
DOI: 10.1101/38114508 / 2018
The EMBO Journal
Chinmay J Shukla and Alexandra L McCorkindale and Chiara Gerhardinger and Keegan D Korthauer and Moran N Cabili and David M Shechner and Rafael A Irizarry and Philipp G Maass and John L Rinn
DOI: 10.15252/embj.20179845203 / 2018
Cell
Takeda, D.Y. and Spisk, S. and Seo, J.-H. and Bell, C. and O'Connor, E. and Korthauer, K. and Ribli, D. and Csabai, I. and Solymosi, N. and Szllsi, Z. and Stillman, D.R. and Cejas, P. and Qiu, X. and Long, H.W. and Tisza, V. and Nuzzo, P.V. and Rohanizadegan, M. and Pomerantz, M.M. and Hahn, W.C. and Freedman, M.L.
DOI: 10.1016/j.cell.2018.05.037Keegan D. Korthauer and Sutirtha Chakraborty and Yuval Benjamini and Rafael A. Irizarry
DOI: 10.1101/18321008 / 2017
Statistics in Biosciences
Choi, J. and Ye, S. and Eng, K.H. and Korthauer, K. and Bradley, W.H. and Rader, J.S. and Kendziorski, C.
DOI: 10.1007/s12561-016-9144-1Genome Biology
Korthauer, K.D. and Chu, L.-F. and Newton, M.A. and Li, Y. and Thomson, J. and Stewart, R. and Kendziorski, C.
DOI: 10.1186/s13059-016-1077-yKorthauer KD and Chu L and Newton MA and Li Y and Thomson J and Stewart R and Kendziorski C
DOI: 10.1101/03550112 / 2015
Bioinformatics
Korthauer, K.D. and Kendziorski, C.
DOI: 10.1093/bioinformatics/btu858Carcinogenesis
Bodelon, C. and Vinokurova, S. and Sampson, J.N. and den Boon, J.A. and Walker, J.L. and Horswill, M.A. and Korthauer, K. and Schiffman, M. and Sherman, M.E. and Zuna, R.E. and Mitchell, J. and Zhang, X. and Boland, J.F. and Chaturvedi, A.K. and Dunn, S.T. and Newton, M.A. and Ahlquist, P. and Wang, S.S. and Wentzensen, N.
DOI: 10.1093/carcin/bgv171Genetic Epidemiology
Sung, Y.J. and Korthauer, K.D. and Swartz, M.D. and Engelman, C.D.
DOI: 10.1002/gepi.21820Infection and Immunity
Wthrich, M. and Ersland, K. and Pick-Jacobs, J.C. and Gern, B.H. and Frye, C.A. and Sullivan, T.D. and Brennan, M.B. and Filutowicz, H.I. and O'brien, K. and Korthauer, K.D. and Schultz-Cherry, S. and Klein, B.S.
DOI: 10.1128/IAI.05326-11Molecular Plant-Microbe Interactions
DOI: 10.1094/MPMI-21-11-1408Advances in Statistical Bioinformatics
Keegan Korthauer and John Dawson and Christina Kendziorski
DOI: 10.1017/cbo9781139226448.019A common task in the interpretation of epigenomic data, which holds information about the genome not encoded in the DNA sequence itself, is the detection and inference of regions of interest. For example, it is of interest to detect segments of the genome that show significantly higher or lower DNA methylation levels with respect to disease state or developmental stage, as this particular modification to the DNA is known to influence gene regulation. However, the number of possible segments of all possible sizes is near infinite, leading to a massive multiple testing problem. Our group develops tailored statistical and computational approaches for powerful detection and inference of region-based epigenomic signals, while paying particular attention to spatial patterns. We are interested in designing and applying these techniques for the analysis of DNA methylation, histone modification, and chromatin accessibility assay data.
It is widely known that epigenetic information, such as DNA methylation and histone modifications, plays a role in gene regulation. However, the prediction of gene expression from epigenomic signals is challenging due to interactions between different epigenomic marks as well as interactions between different regions of the genome. We are working on developing predictive models that account for these challenges and assess the predictive capacity for various epigenomic signals.
Our group develops computational approaches to study the genomic basis of a variety of complex traits. Our main focus areas currently include modeling the mutation spectrum of cancer genomes, revealing heterogeneity in single-cell gene expression during development, and characterizing the epigenomic landscape of prostate cancer. To maximize impact of our work, we also provide open source computational tools that enable other scientists to make meaningful biological insights.
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Congratulations to Dr. Megan Levings, recipient of a CIHR Team Grant: Preparation to Trial: Inflammation for Chronic Conditions for the project, "Allogeneic thymus-derived Tregs to prevent chronic inflammation in transplantation."
One of the biggest challenges with research into the genetic causes of illness used to be the time and cost of genomic sequencing. Today, thanks to significant advances in technology, the problem is no longer collecting the data; it’s mining the huge amount of information that can be pulled from a single patient sample to…
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