Publications

Selected publications

See Dr. Korkola's full publication record here.

2018

  • Watson SS, Dane M, Chin K, Tatarova Z, Liu M, Liby T, Thompson W, Smith R, Nederlof M, Bucher E, Kilburn D, Whitman M, Sudar D, Mills GB, Heiser LM, Jonas O, Gray JW, Korkola JE. Microenvironment-Mediated Mechanisms of Resistance to HER2 Inhibitors Differ between HER2+ Breast Cancer Subtypes. Cell Systems. 2018 Mar 28;6(3):329-342.e6. PMC5927625.
  • Keenan AB, Jenkins SL, Jagodnik KM, Koplev S, He E, Torre D, Wang Z, Dohlman AB, Silverstein MC, Lachmann A, Kuleshov MV, Ma'ayan A, Stathias V, Terryn R, Cooper D, Forlin M, Koleti A, Vidovic D, Chung C, Schürer SC, Vasiliauskas J, Pilarczyk M, Shamsaei B, Fazel M, Ren Y, Niu W, Clark NA, White S, Mahi N, Zhang L, Kouril M, Reichard JF, Sivaganesan S, Medvedovic M, Meller J, Koch RJ, Birtwistle MR, Iyengar R, Sobie EA, Azeloglu EU, Kaye J, Osterloh J, Haston K, Kalra J, Finkbiener S, Li J, Milani P, Adam M, Escalante-Chong R, Sachs K, Lenail A, Ramamoorthy D, Fraenkel E, Daigle G, Hussain U, Coye A, Rothstein J, Sareen D, Ornelas L, Banuelos M, Mandefro B, Ho R, Svendsen CN, Lim RG, Stocksdale J, Casale MS, Thompson TG, Wu J, Thompson LM, Dardov V, Venkatraman V, Matlock A, Van Eyk JE, Jaffe JD, Papanastasiou M, Subramanian A, Golub TR, Erickson SD, Fallahi-Sichani M, Hafner M, Gray NS, Lin JR, Mills CE, Muhlich JL, Niepel M, Shamu CE, Williams EH, Wrobel D, Sorger PK, Heiser LM, Gray JW, Korkola JE, Mills GB, LaBarge M, Feiler HS, Dane MA, Bucher E, Nederlof M, Sudar D, Gross S, Kilburn DF, Smith R, Devlin K, Margolis R, Derr L, Lee A, Pillai A. The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations. Cell Systems. 2018 Jan 24;6(1):13-24. PMC29199020

2017

  • Hill SM, Nesser NK, Johnson-Camacho K, Jeffress M, Johnson A, Boniface C, Spencer SE, Lu Y, Heiser LM, Lawrence Y, Pande NT, Korkola JE, Gray JW, Mills GB, Mukherjee S, Spellman PT. Context Specificity in Causal Signaling Networks Revealed by Phosphoprotein Profiling. Cell Systems. 2017 Jan 25;4(1):73-83.e10. PMC28017544 
  • Hu Z, Mao JH, Curtis C, Huang G, Gu S, Heiser L, Lenburg ME, Korkola JE, Bayani N, Samarajiwa S, Seoane JA, Dane MA, Esch A, Feiler HS, Wang NJ, Hardwicke MA, Laquerre S, Jackson J, W Wood K, Weber B, Spellman PT, Aparicio S, Wooster R, Caldas C, Gray JW. Genome co-amplification upregulates a mitotic gene network activity that predicts outcome and response to mitotic protein inhibitors in breast cancer. Breast Cancer Research, 2016 Jul 1;18(1):70. PMC27368372

2016

  • Coleman DJ, Van Hook K, King CJ, Schwartzman J, Lisac R, Urrutia J, Sehrawat A, Woodward J, Wang NJ, Gulati R, Thomas GV, Beer TM, Gleave M, Korkola JE, Gao L, Heiser LM, Alumkal JJ. Cellular androgen content influences enzalutamide agonism of F877L mutant androgen receptor. Oncotarget, 2016;7(26):40690-703. PMC5130036 
  • Hu Z, Mao JH, Curtis C, Huang G, Gu S, Heiser L, Lenburg ME, Korkola JE, Bayani N, Samarajiwa S, Seoane JA, Dane MA, Esch A, Feiler HS, Wang NJ, Hardwicke MA, Laquerre A, Jackson J, Wood KW, Weber B, Spellman PT, Aparicio S, Wooster R, Caldas C, and Gray JW. Genomeco-amplification upregulates a mitotic gene network activity that predicts outcome and response to mitotic protein inhibitors in breast cancer. Breast Cancer Research, 2016;18(1):70. PMC4930593
  • Kushwaha R, Jagadish N, Kustagi M, Mendiratta G, Seandel M, Soni R, Korkola JE, Thodima V, Califano A, Bosl GJ, and  Chaganti RSK. Mechanism and role of sox2 repression in seminoma: relevance to human germline specification. Stem Cell Reports, 2016;6(5):772-83. PMC4939754
  • Hill SM, Nesser NK, Johnson-Camacho K, Jeffress M, Johnson A, Boniface C, Spencer SEF, Lu Y, Heise LM, Lawrence Y, Pande NT, Korkola JE, Gray JW, Mills GB, Mukherjee S, and Spellman PT. Context specificity in causal signaling networks revealed by phosphoprotein profiling. Cell Systems, 2017;4(1):73-83 e10. PMC5279869

2015

  • Butler TM, Johnson-Camacho K, Peto M, Wang NJ, Macey TA, Korkola JE, Koppie TM, Corless CL, Gray JW, and Spellman PT. Exome sequencing of cell-free DNA from metastatic cancer patients identifies clinically actionable mutations distinct from primary disease. PloS One, 2015;10(8):e0136407. PMC4552879
  • Chang YH, Korkola J, Amin DN, Moasser MM, Carmena JM, Gray JW, and Tomlin CL. Disentangling multidimensional spatio-temporal data into their common and aberrant responses. PloS One, 2015;10(4):e0121607. PMC4406848
  • Korkola JE, Collisson EA, Heiser L, Oates C, Bayani N, Itani S, Esch A, Thompson W, Griffith OL, Wang NJ, Kuo WL, Cooper B, Billig J, Ziyad S, Hung JL, Jakkula L, Feiler H, Lu Y, Mills GB, Spellman PT, Tomlin C, Mukherjee S, and Gray JW. Decoupling of the PI3K pathway via mutation necessitates combinatorial treatment in HER2+ breast cancer. PloS One, 2015;10(7):e0133219. PMC4504492
  • Korkola JE, Heck S, Olshen AB, Feldman DR, Reuter VE, Houldsworth J, Bosl GJ, Chaganti RSK. Development and validation of a gene-based model for outcome prediction in germ cell tumors using a combined genomic and expression profiling approach. PloS One, 2015;10(12):e0142846. PMC4666461
  • Kushwaha R, Jagadish N, Kustagi M, Tomishima MJ, Mendiratta G, Bansal M, Kim HR, Sumazin P, Alvarez MJ, Lefebvre C, Villagrasa-Gonzalez P, Viale A, Korkola JE, Houldsworth J, Feldman DR, Bosl GJ, Califano A, and Chaganti RSK. Interrogation of a context-specific transcription factor network identifies novel regulators of pluripotency. Stem Cells (Dayton, Ohio), 2015;33(2):367-77. PMC4305010

2014

  • Oates CJ, Dondelinger F, Bayani N, Korkola J, Gray JW, Mukherjee S. Causal network inference using biochemical kinetics. Bioinformatics (Oxford, England). 2014;30(17):i468-74. PMC4147905

2013

  • Daemen A, Griffith OL, Heiser LM, Wang NJ, Enache OM, Sanborn Z, Pepin F, Durinck S, Korkola JE, Griffith M, Hur JS, Huh N, Chung J, Cope L, Fackler MJ, Umbricht C, Sukumar S, Seth P, Sukhatme VP, Jakkula LR, Lu Y, Mills GB, Cho RJ, Collisson EA, van’t Veer LJ, Spellman PT, and Gray JW. Modeling precision treatment of breast cancer. Genome biology, 2013;14(10):R110. PMC3937590
  • Iacovides DC, Johnson AB, Wang N, Boddapati S, Korkola J, Gray JW. Identification and quantification of AKT isoforms and phosphoforms in breast cancer using a novel nanofluidic immunoassay. Molecular & Cellular Proteomics, 2013;12(11):3210-20. PMC3820934