Publications

  1. Nguyen AJ, Fogarty ZC, Davila J, Markovic SN, Wang C, Guo R. Uncovering the hidden risk of metastatic cutaneous basal cell carcinoma by molecular profiling: A retrospective review. JAAD Int. 2024 Sep; 16:189-191 Epub 2024 May 24
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  2. Mistry NA, Roellinger SE, Manninen MC, Gandham M, Koganti T, Balan J, Basu S, Blake EJ, Tandale PP, Holdren MA, Hoenig MF, Urban RM, Veith RL, Kendzior MC, Wang C, Gupta S, Shen W. Variant Detection in 3' Exons of PMS2 Using Exome Sequencing Data. J Mol Diagn. 2024 Sep; 26 (9):843-850 Epub 2024 June 24
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  3. Saner FAM, Takahashi K, Budden T, Pandey A, Ariyaratne D, Zwimpfer TA, Meagher NS, Fereday S, Twomey L, Pishas KI, Hoang T, Bolithon A, Traficante N, Alsop K, Christie EL, Kang EY, Nelson GS, Ghatage P, Lee CH, Riggan MJ, Alsop J, Beckmann MW, Boros J, Brand AH, Brooks-Wilson A, Carney ME, Coulson P, Courtney-Brooks M, Cushing-Haugen KL, Cybulski C, El-Bahrawy MA, Elishaev E, Erber R, Gayther SA, Gentry-Maharaj A, Gilks CB, Harnett PR, Harris HR, Hartmann A, Hein A, Hendley J, Hernandez BY, Jakubowska A, Jimenez-Linan M, Jones ME, Kaufmann SH, Kennedy CJ, Kluz T, Koziak JM, Kristjansdottir B, Le ND, Lener M, Lester J, Lubinski J, Mateoiu C, Orsulic S, Ruebner M, Schoemaker MJ, Shah M, Sharma R, Sherman ME, Shvetsov YB, Soong TR, Steed H, Sukumvanich P, Talhouk A, Taylor SE, Vierkant RA, Wang C, Widschwendter M, Wilkens LR, Winham SJ, Anglesio MS, Berchuck A, Brenton JD, Campbell I, Cook LS, Doherty JA, Fasching PA, Fortner RT, Goodman MT, Gronwald J, Huntsman DG, Karlan BY, Kelemen LE, Menon U, Modugno F, Pharoah PDP, Schildkraut JM, Sundfeldt K, Swerdlow AJ, Goode EL, DeFazio A, Kobel M, Ramus SJ, Bowtell DDL, Garsed DW, Australian Ovarian Cancer Study Group. Concurrent RB1 Loss and BRCA Deficiency Predicts Enhanced Immunologic Response and Long-term Survival in Tubo-ovarian High-grade Serous Carcinoma. Clin Cancer Res. 2024 Aug 15; 30 (16):3481-3498
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  4. Liu Y, Vierkant RA, Bhagwate A, Jons WA, Stallings-Mann ML, McCauley BM, Carter JM, Stephens MT, Pfrender ME, Littlepage LE, Radisky DC, Cunningham JM, Degnim AC, Winham SJ, Wang C. Evaluating cell type deconvolution in FFPE breast tissue: application to benign breast disease NAR Genomics and Bioinformatics. 2024.
  5. Yang Y, Wang J, Wan J, Cheng Q, Cheng Z, Zhou X, Wang O, Shi K, Wang L, Wang B, Zhu X, Chen J, Feng D, Liu Y, Jahan-Mihan Y, Haddock AN, Edenfield BH, Peng G, Hohenstein JD, McCabe CE, O'Brien DR, Wang C, Ilyas SI, Jiang L, Torbenson MS, Wang H, Nakhleh RE, Shi X, Wang Y, Bi Y, Gores GJ, Patel T, Ji B. PTEN deficiency induces an extrahepatic cholangitis-cholangiocarcinoma continuum via aurora kinase A in mice. J Hepatol. 2024 Jul; 81 (1):120-134 Epub 2024 Feb 28
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  6. Jackson LE, Tomlinson JL, Alva-Ruiz R, Gregory LA, Byeon SK, Abdelrahman AM, Mun DG, Grant CW, Fogarty ZC, Wang C, Roberts LR, Graham RP, Borad MJ, Ilyas SI, Gores GJ, Pandey A, Athreya AP, Smoot RL. Metabolome-wide association identifies altered metabolites and metabolic pathways in the serum of patients with cholangiocarcinoma. JHEP Rep. 2024 Jun; 6 (6):101068 Epub 2024 Mar 18
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  7. Grant P, Quinn M, O'Neill H, Ramachandran D, Tyrer JP, Kommoss S, DeFazio A, Riggan MJ, Webb PM, Fasching PA, Lambrechts D, Garcia MJ, Rodriguez-Antona C, Goodman MT, Modugno F, Moysich KB, Karlan BY, Lester J, Kjaer SK, Jensen A, Hogdall E, Goode EL, Cliby WA, Kumar A, Wang C, Cunningham JM, Winham SJ, Monteiro AN, Schildkraut JM, Cramer DW, Terry KL, Titus L, Bjorge L, Thomsen LCV, Pejovic T, Hogdall CK, McNeish IA, May T, Huntsman DG, Pfisterer J, Canzler U, Park-Simon TW, Schroder W, Belau A, Hanker L, Harter P, Sehouli J, Kimmig R, de Gregorio N, Schmalfeldt B, Baumann K, Hilpert F, Burges A, Winterhoff B, Schurmann P, Speith LM, Hillemanns P, Berchuck A, Johnatty SE, Ramus SJ, Chenevix-Trench G, Pharoah PDP, Dork T, Heitz F, AOCS Group//OPAL Study Group. Genome-wide association analyses of ovarian cancer patients undergoing primary debulking surgery identify candidate genes for residual disease. NPJ Genom Med. 2024 Mar 5; 9 (1):19 Epub 2024 Mar 05
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  8. Watkins R, Gamo A, Choi SH, Kumar M, Buckarma E, McCabe C, Tomlinson J, Pereya D, Lupse B, Geravandi S, Werneburg NW, Wang C, Starlinger P, Zhu S, Li S, Yu S, Surakattula M, Baguley T, Ardestani A, Maedler K, Roland J, Nguyen-Tran V, Joseph S, Petrassi M, Rogers N, Gores G, Chatterjee A, Tremblay M, Shen W, Smoot R. A small molecule MST1/2 inhibitor accelerates murine liver regeneration with improved survival in models of steatohepatitis. PNAS Nexus. 2024 Mar; 3 (3):pgae096 Epub 2024 Mar 01
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  9. Zhao Y, Dimou A, Fogarty ZC, Jiang J, Liu H, Wong WB, Wang C. Real-world Trends, Rural-urban Differences, and Socioeconomic Disparities in Utilization of Narrow versus Broad Next-generation Sequencing Panels. Cancer Res Commun. 2024 Feb 5; 4 (2):303-311
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  10. Walton NA, Nagarajan R, Wang C, Sincan M, Freimuth RR, Everman DB, Walton DC, McGrath SP, Lemas DJ, Benos PV, Alekseyenko AV, Song Q, Gamsiz Uzun E, Taylor CO, Uzun A, Person TN, Rappoport N, Zhao Z, Williams MS. Enabling the clinical application of artificial intelligence in genomics: a perspective of the AMIA Genomics and Translational Bioinformatics Workgroup. J Am Med Inform Assoc. 2024 Jan 18; 31 (2):536-541
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  11. Ye H, Zhang X, Wang C, Goode EL, Chen J. Batch-effect correction with sample remeasurement in highly confounded case-control studies. Nat Comput Sci. 2023 Aug; 3 (8):709-719 Epub 2023 Aug 23
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  12. Kobel M, Kang EY, Weir A, Rambau PF, Lee CH, Nelson GS, Ghatage P, Meagher NS, Riggan MJ, Alsop J, Anglesio MS, Beckmann MW, Bisinotto C, Boisen M, Boros J, Brand AH, Brooks-Wilson A, Carney ME, Coulson P, Courtney-Brooks M, Cushing-Haugen KL, Cybulski C, Deen S, El-Bahrawy MA, Elishaev E, Erber R, Fereday S, Fischer A, Gayther SA, Barquin-Garcia A, Gentry-Maharaj A, Gilks CB, Gronwald H, Grube M, Harnett PR, Harris HR, Hartkopf AD, Hartmann A, Hein A, Hendley J, Hernandez BY, Huang Y, Jakubowska A, Jimenez-Linan M, Jones ME, Kennedy CJ, Kluz T, Koziak JM, Lesnock J, Lester J, Lubinski J, Longacre TA, Lycke M, Mateoiu C, McCauley BM, McGuire V, Ney B, Olawaiye A, Orsulic S, Osorio A, Paz-Ares L, Ramon Y Cajal T, Rothstein JH, Ruebner M, Schoemaker MJ, Shah M, Sharma R, Sherman ME, Shvetsov YB, Singh N, Steed H, Storr SJ, Talhouk A, Traficante N, Wang C, Whittemore AS, Widschwendter M, Wilkens LR, Winham SJ, Benitez J, Berchuck A, Bowtell DD, Candido Dos Reis FJ, Campbell I, Cook LS, DeFazio A, Doherty JA, Fasching PA, Fortner RT, Garcia MJ, Goodman MT, Goode EL, Gronwald J, Huntsman DG, Karlan BY, Kelemen LE, Kommoss S, Le ND, Martin SG, Menon U, Modugno F, Pharoah PD, Schildkraut JM, Sieh W, Staebler A, Sundfeldt K, Swerdlow AJ, Ramus SJ, Brenton JD, AOCS Group. p53 and ovarian carcinoma survival: an Ovarian Tumor Tissue Analysis consortium study. J Pathol Clin Res. 2023 May; 9 (3):208-222 Epub 2023 Mar 22
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  13. Wang C, Block MS, Cunningham JM, Sherman ME, McCauley BM, Armasu SM, Vierkant RA, Traficante N, Talhouk A, Ramus SJ, Pejovic N, Kobel M, Jorgensen BD, Garsed DW, Fereday S, Doherty JA, Ariyaratne D, Anglesio MS, Widschwendter M, Pejovic T, Bosquet JG, Bowtell DD, Winham SJ, Goode EL, Australian Ovarian Cancer Study Group. Methylation Signature Implicated in Immuno-Suppressive Activities in Tubo-Ovarian High-Grade Serous Carcinoma. Cancer Epidemiol Biomarkers Prev. 2023 Apr 3; 32 (4):542-549
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  14. Starlinger P, Brunnthaler L, McCabe C, Pereyra D, Santol J, Steadman J, Hackl M, Skalicky S, Hackl H, Gronauer R, O'Brien D, Kain R, Hirsova P, Gores GJ, Wang C, Gruenberger T, Smoot RL, Assinger A. Transcriptomic landscapes of effective and failed liver regeneration in humans. JHEP Rep. 2023 Apr; 5 (4):100683 Epub 2023 Feb 02
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  15. Mitchell A, Ruiz M, Yang S, Wang C, Davila JI. Excerno: Using Mutational Signatures in Sequencing Data to Filter False Variants Caused by Clinical Archival. J Comput Biol. 2023 Apr; 30 (4):366-375 Epub 2022 Nov 02
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  16. Jiang J, Moore R, Jordan CE, Guo R, Maus RL, Liu H, Goode E, Markovic SN, Wang C. Multiplex Immunofluorescence Image Quality Checking Using DAPI Channel-referenced Evaluation. J Histochem Cytochem. 2023 Mar; 71 (3):121-130 Epub 2023 Mar 24
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  17. Kang EY, Weir A, Meagher NS, Farrington K, Nelson GS, Ghatage P, Lee CH, Riggan MJ, Bolithon A, Popovic G, Leung B, Tang K, Lambie N, Millstein J, Alsop J, Anglesio MS, Ataseven B, Barlow E, Beckmann MW, Berger J, Bisinotto C, Bösmüller H, Boros J, Brand AH, Brooks-Wilson A, Brucker SY, Carney ME, Casablanca Y, Cazorla-Jiménez A, Cohen PA, Conrads TP, Cook LS, Coulson P, Courtney-Brooks M, Cramer DW, Crowe P, Cunningham JM, Cybulski C, Darcy KM, El-Bahrawy MA, Elishaev E, Erber R, Farrell R, Fereday S, Fischer A, García MJ, Gayther SA, Gentry-Maharaj A, Gilks CB, AOCS Group, Grube M, Harnett PR, Harrington SP, Harter P, Hartmann A, Hecht JL, Heikaus S, Hein A, Heitz F, Hendley J, Hernandez BY, Polo SH, Heublein S, Hirasawa A, Høgdall E, Høgdall CK, Horlings HM, Huntsman DG, Huzarski T, Jewell A, Jimenez-Linan M, Jones ME, Kaufmann SH, Kennedy CJ, Khabele D, Kommoss FKF, Kruitwagen RFPM, Lambrechts D, Le ND, Lener M, Lester J, Leung Y, Linder A, Loverix L, Lubinski J, Madan R, Maxwell GL, Modugno F, Neuhausen SL, Olawaiye A, Olbrecht S, Orsulic S, Palacios J, Pearce CL, Pike MC, Quinn CM, Mohan GR, Rodríguez-Antona C, Ruebner M, Ryan A, Salfinger SG, Sasamoto N, Schildkraut JM, Schoemaker MJ, Shah M, Sharma R, Shvetsov YB, Singh N, Sonke GS, Steele L, Stewart CJR, Sundfeldt K, Swerdlow AJ, Talhouk A, Tan A, Taylor SE, Terry KL, Toloczko A, Traficante N, Van de Vijver KK, van der Aa MA, Van Gorp T, Van Nieuwenhuysen E, van-Wagensveld L, Vergote I, Vierkant RA, Wang C, Wilkens LR, Winham SJ, Wu AH, Benitez J, Berchuck A, Candido Dos Reis FJ, DeFazio A, Fasching PA, Goode EL, Goodman MT, Gronwald J, Karlan BY, Kommoss S, Menon U, Sinn HP, Staebler A, Brenton JD, Bowtell DD, Pharoah PDP, Ramus SJ, Köbel M. CCNE1 and survival of patients with tubo-ovarian high-grade serous carcinoma: An Ovarian Tumor Tissue Analysis consortium study. Cancer. 2023 Mar 01; 129(5):697-713. Epub 2022 Dec 26.
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  18. Weir A, Kang EY, Meagher NS, Nelson GS, Ghatage P, Lee CH, Riggan MJ, Gentry-Maharaj A, Ryan A, Singh N, Widschwendter M, Alsop J, Anglesio MS, Beckmann MW, Berger J, Bisinotto C, Boros J, Brand AH, Brenton JD, Brooks-Wilson A, Carney ME, Cunningham JM, Cushing-Haugen KL, Cybulski C, Elishaev E, Erber R, Fereday S, Fischer A, Paz-Ares L, Gayarre J, Gilks BC, Grube M, Harnett PR, Harris HR, Hartmann A, Hein A, Hendley J, Hernandez BY, Heublein S, Huang Y, Huzarski T, Jakubowska A, Jimenez-Linan M, Kennedy CJ, Kommoss FKF, Koziak JM, Kraemer B, Le ND, Lesnock J, Lester J, Lubinski J, Menkiszak J, Ney B, Olawaiye A, Orsulic S, Osorio A, Robles-Díaz L, Ruebner M, Shah M, Sharma R, Shvetsov YB, Steed H, Talhouk A, Taylor SE, Traficante N, Vierkant RA, Wang C, Wilkens LR, Winham SJ, Benitez J, Berchuck A, Bowtell DD, Candido Dos Reis FJ, Cook LS, DeFazio A, AOCs group, Doherty JA, Fasching PA, García MJ, Goode EL, Goodman MT, Gronwald J, Huntsman DG, Karlan BY, Kommoss S, Modugno F, Schildkraut JM, Sinn HP, Staebler A, Kelemen LE, Ford CE, Menon U, Pharoah PDP, Köbel M, Ramus SJ. Increased FOXJ1 protein expression is associated with improved overall survival in high-grade serous ovarian carcinoma: an Ovarian Tumor Tissue Analysis Consortium Study. Br J Cancer. 2023 Jan; 128(1):137-147. Epub 2022 Nov 02.
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  19. Garsed DW, Pandey A, Fereday S, Kennedy CJ, Takahashi K, Alsop K, Hamilton PT, Hendley J, Chiew YE, Traficante N, Provan P, Ariyaratne D, Au-Yeung G, Bateman NW, Bowes L, Brand A, Christie EL, Cunningham JM, Friedlander M, Grout B, Harnett P, Hung J, McCauley B, McNally O, Piskorz AM, Saner FAM, Vierkant RA, Wang C, Winham SJ, Pharoah PDP, Brenton JD, Conrads TP, Maxwell GL, Ramus SJ, Pearce CL, Pike MC, Nelson BH, Goode EL, DeFazio A, Bowtell DDL. The genomic and immune landscape of long-term survivors of high-grade serous ovarian cancer. Nat Genet. 2022 Dec; 54 (12):1853-1864 Epub 2022 Dec 01
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  20. Zhao Y, Brush M, Wang C, Wagner AH, Liu H, Freimuth RR. Leveraging a pharmacogenomics knowledgebase to formulate a drug response phenotype terminology for genomic medicine. Bioinformatics. 2022 Nov 30; 38 (23):5279-5287
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  21. Liu Y, Bhagwate A, Winham SJ, Stephens MT, Harker BW, McDonough SJ, Stallings-Mann ML, Heinzen EP, Vierkant RA, Hoskin TL, Frost MH, Carter JM, Pfrender ME, Littlepage L, Radisky DC, Cunningham JM, Degnim AC, Wang C. Quality control recommendations for RNASeq using FFPE samples based on pre-sequencing lab metrics and post-sequencing bioinformatics metrics. BMC Med Genomics. 2022 Sep 16; 15 (1):195 Epub 2022 Sept 16
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  22. Kumar A, Wang C, Sheedy SP, McCauley BM, Winham SJ, Ramus SJ, Anglesio MS, Kim B, Torres D, Keeney GL, Cliby WA, Goode EL. Into the future: A pilot study combining imaging with molecular profiling to predict resectability in ovarian cancer. Gynecol Oncol. 2022 Sep; 166 (3):508-514 Epub 2022 Aug 02
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  23. Watkins RD, Buckarma EH, Tomlinson JL, McCabe CE, Yonkus JA, Werneburg NW, Bayer RL, Starlinger PP, Robertson KD, Wang C, Gores GJ, Smoot RL. SHP2 inhibition enhances Yes-associated protein-mediated liver regeneration in murine partial hepatectomy models. JCI Insight. 2022 Aug 8; 7 (15) Epub 2022 Aug 08
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  24. Zhao Y, Dimou A, Shen F, Zong N, Davila JI, Liu H, Wang C. PO2RDF: representation of real-world data for precision oncology using resource description framework. BMC Med Genomics. 2022 Jul 30; 15 (1):167 Epub 2022 July 30
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  25. Guo Y, Wang C, Moore R, Liu H, Shen F. POKR: Building a Computable Heterogeneous Knowledge Resource for Precision Oncology. Stud Health Technol Inform. 2022 Jun 6; 290:243-247
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  26. Thompson SM, Suman G, Torbenson MS, Chen ZE, Jondal DE, Patra A, Ehman EC, Andrews JC, Fleming CJ, Welch BT, Kurup AN, Roberts LR, Watt KD, Truty MJ, Cleary SP, Smoot RL, Heimbach JK, Tran NH, Mahipal A, Yin J, Zemla T, Wang C, Fogarty Z, Jacobson M, Kemp BJ, Venkatesh SK, Johnson GB, Woodrum DA, Goenka AH. PSMA as a Theranostic Target in Hepatocellular Carcinoma: Immunohistochemistry and (68) Ga-PSMA-11 PET Using Cyclotron-Produced (68) Ga. Hepatol Commun. 2022 May; 6 (5):1172-1185 Epub 2021 Nov 15
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  27. Kang EY, Millstein J, Popovic G, Meagher NS, Bolithon A, Talhouk A, Chiu DS, Anglesio MS, Leung B, Tang K, Lambie N, Pavanello M, Da-Anoy A, Lambrechts D, Loverix L, Olbrecht S, Bisinotto C, Garcia-Donas J, Ruiz-Llorente S, Yague-Fernandez M, Edwards RP, Elishaev E, Olawaiye A, Taylor S, Ataseven B, du Bois A, Harter P, Lester J, Hogdall CK, Armasu SM, Huang Y, Vierkant RA, Wang C, Winham SJ, Heublein S, Kommoss FKF, Cramer DW, Sasamoto N, van-Wagensveld L, Lycke M, Mateoiu C, Joseph J, Pike MC, Odunsi K, Tseng CC, Pearce CL, Bilic S, Conrads TP, Hartmann A, Hein A, Jones ME, Leung Y, Beckmann MW, Ruebner M, Schoemaker MJ, Terry KL, El-Bahrawy MA, Coulson P, Etter JL, LaVigne-Mager K, Andress J, Grube M, Fischer A, Neudeck N, Robertson G, Farrell R, Barlow E, Quinn C, Hettiaratchi A, Casablanca Y, Erber R, Stewart CJR, Tan A, Yu Y, Boros J, Brand AH, Harnett PR, Kennedy CJ, Nevins N, Morgan T, Fasching PA, Vergote I, Swerdlow AJ, Candido Dos Reis FJ, Maxwell GL, Neuhausen SL, Barquin-Garcia A, Modugno F, Moysich KB, Crowe PJ, Hirasawa A, Heitz F, Karlan BY, Goode EL, Sinn P, Horlings HM, Hogdall E, Sundfeldt K, Kommoss S, Staebler A, Wu AH, Cohen PA, DeFazio A, Lee CH, Steed H, Le ND, Gayther SA, Lawrenson K, Pharoah PDP, Konecny G, Cook LS, Ramus SJ, Kelemen LE, Kobel M. MCM3 is a novel proliferation marker associated with longer survival for patients with tubo-ovarian high-grade serous carcinoma. Virchows Arch. 2022 Apr; 480 (4):855-871 Epub 2021 Nov 15
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  28. Torbenson M, McCabe CE, O'Brien DR, Yin J, Bainter T, Tran NH, Yasir S, Chen ZE, Dhanasekaran R, Ahn KS, Roberts LR, Wang C. Morphological heterogeneity in beta-catenin-mutated hepatocellular carcinomas: implications for tumor molecular classification. Hum Pathol. 2022 Jan; 119:15-27 Epub 2021 Sept 27
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  29. Cunningham JM, Winham SJ, Wang C, Weiglt B, Fu Z, Armasu SM, McCauley BM, Brand AH, Chiew YE, Elishaev E, Gourley C, Kennedy CJ, Laslavic A, Lester J, Piskorz A, Sekowska M, Brenton JD, Churchman M, DeFazio A, Drapkin R, Elias KM, Huntsman DG, Karlan BY, Kobel M, Konner J, Lawrenson K, Papaemmanuil E, Bolton KL, Modugno F, Goode EL. DNA Methylation Profiles of Ovarian Clear Cell Carcinoma. Cancer Epidemiol Biomarkers Prev. 2022 Jan; 31 (1):132-141 Epub 2021 Oct 25
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  30. Jiang J, Tekin B, Yuan L, Armasu S, Winham SJ, Goode EL, Liu H, Huang Y, Guo R, Wang C. Computational tumor stroma reaction evaluation led to novel prognosis-associated fibrosis and molecular signature discoveries in high-grade serous ovarian carcinoma. Front Med (Lausanne). 2022; 9:994467 Epub 2022 Sept 07
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  31. Na J, Zong N, Wang C, Midthun DE, Luo Y, Yang P, Jiang G. Characterizing phenotypic abnormalities associated with high-risk individuals developing lung cancer using electronic health records from the All of Us researcher workbench. J Am Med Inform Assoc. 2021 Oct 12; 28 (11):2313-2324
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  32. Winham SJ, Wang C, Heinzen EP, Bhagwate A, Liu Y, McDonough SJ, Stallings-Mann ML, Frost MH, Vierkant RA, Denison LA, Carter JM, Sherman ME, Radisky DC, Degnim AC, Cunningham JM. Somatic mutations in benign breast disease tissues and association with breast cancer risk. BMC Med Genomics. 2021 Jul 14; 14 (1):185 Epub 2021 July 14
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  33. Yi S, Zhang X, Yang L, Huang J, Liu Y, Wang C, Schaid DJ, Chen J. 2dFDR: a new approach to confounder adjustment substantially increases detection power in omics association studies. Genome Biol. 2021 Jul 13; 22 (1):208 Epub 2021 July 13
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  34. Feng T, Davila JI, Liu Y, Lin S, Huang S, Wang C. Semi-Supervised Topological Analysis for Elucidating Hidden Structures in High-Dimensional Transcriptome Datasets. IEEE/ACM Trans Comput Biol Bioinform. 2021 Jul-Aug; 18 (4):1620-1631 Epub 2021 Aug 06
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  35. Davila JI, Chanana P, Sarangi V, Fogarty ZC, Weroha SJ, Guo R, Goode EL, Huang Y, Wang C. Frequent POLE-driven hypermutation in ovarian endometrioid cancer revealed by mutational signatures in RNA sequencing. BMC Med Genomics. 2021 Jun 22; 14 (1):165 Epub 2021 June 22
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  36. Zong N, Ngo V, Stone DJ, Wen A, Zhao Y, Yu Y, Liu S, Huang M, Wang C, Jiang G. Leveraging Genetic Reports and Electronic Health Records for the Prediction of Primary Cancers: Algorithm Development and Validation Study. JMIR Med Inform. 2021 May 25; 9 (5):e23586
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  37. Jessen E, Liu Y, Davila J, Kocher JP, Wang C. Determining mutational burden and signature using RNA-seq from tumor-only samples. BMC Med Genomics. 2021 Mar 1; 14 (1):65 Epub 2021 Mar 01
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  38. Zhao Y, Weroha SJ, Goode EL, Liu H, Wang C. Generating real-world evidence from unstructured clinical notes to examine clinical utility of genetic tests: use case in BRCAness. BMC Med Inform Decis Mak. 2021 Jan 6; 21 (1):3 Epub 2021 Jan 06
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  39. Jiang J, Tekin B, Guo R, Liu H, Huang Y, Wang C. Digital Pathology-based Study of Cell- and Tissue-level Morphologic Features in Serous Borderline Ovarian Tumor and High-grade Serous Ovarian Cancer. J Pathol Inform. 2021; 12:24 Epub 2021 June 05
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  40. Zong N, Stone DJ, Sharma DK, Wen A, Wang C, Yu Y, Huang M, Liu S, Liu H, Shi Q, Jiang G. Modeling cancer clinical trials using HL7 FHIR to support downstream applications: A case study with colorectal cancer data. Int J Med Inform. 2021 Jan; 145:104308 Epub 2020 Oct 22
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  41. Talhouk A, George J, Wang C, Budden T, Tan TZ, Chiu DS, Kommoss S, Leong HS, Chen S, Intermaggio MP, Gilks B, Nazeran TM, Volchek M, Elatre W, Bentley RC, Senz J, Lum A, Chow V, Sudderuddin H, Mackenzie R, Leong SCY, Liu G, Johnson D, Chen B, Group A, Alsop J, Banerjee SN, Behrens S, Bodelon C, Brand AH, Brinton L, Carney ME, Chiew YE, Cushing-Haugen KL, Cybulski C, Ennis D, Fereday S, Fortner RT, Garcia-Donas J, Gentry-Maharaj A, Glasspool R, Goranova T, Greene CS, Haluska P, Harris HR, Hendley J, Hernandez BY, Herpel E, Jimenez-Linan M, Karpinskyj C, Kaufmann SH, Keeney GL, Kennedy CJ, Kobel M, Koziak JM, Larson MC, Lester J, Lewsley LA, Lissowska J, Lubinski J, Luk H, Macintyre G, Mahner S, McNeish IA, Menkiszak J, Nevins N, Osorio A, Oszurek O, Palacios J, Hinsley S, Pearce CL, Pike MC, Piskorz AM, Ray-Coquard I, Rhenius V, Rodriguez-Antona C, Sharma R, Sherman ME, De Silva D, Singh N, Sinn P, Slamon D, Song H, Steed H, Stronach EA, Thompson PJ, Toloczko A, Trabert B, Traficante N, Tseng CC, Widschwendter M, Wilkens LR, Winham SJ, Winterhoff B, Beeghly-Fadiel A, Benitez J, Berchuck A, Brenton JD, Brown R, Chang-Claude J, Chenevix-Trench G, deFazio A, Fasching PA, Garcia MJ, Gayther SA, Goodman MT, Gronwald J, Henderson MJ, Karlan BY, Kelemen LE, Menon U, Orsulic S, Pharoah PDP, Wentzensen N, Wu AH, Schildkraut JM, Rossing MA, Konecny GE, Huntsman DG, Huang RY, Goode EL, Ramus SJ, Doherty JA, Bowtell DD, Anglesio MS. Development and Validation of the Gene Expression Predictor of High-grade Serous Ovarian Carcinoma Molecular SubTYPE (PrOTYPE). Clin Cancer Res. 2020 Oct 15; 26 (20):5411-5423 Epub 2020 June 17
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  42. Buckarma EH, Werneburg NW, Conboy CB, Kabashima A, O'Brien DR, Wang C, Ilyas SI, Smoot RL. The YAP-Interacting Phosphatase SHP2 Can Regulate Transcriptional Coactivity and Modulate Sensitivity to Chemotherapy in Cholangiocarcinoma. Mol Cancer Res. 2020 Oct; 18 (10):1574-1588 Epub 2020 July 09
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  43. Loeuillard E, Yang J, Buckarma E, Wang J, Liu Y, Conboy C, Pavelko KD, Li Y, O'Brien D, Wang C, Graham RP, Smoot RL, Dong H, Ilyas S. Targeting tumor-associated macrophages and granulocytic myeloid-derived suppressor cells augments PD-1 blockade in cholangiocarcinoma. J Clin Invest. 2020 Oct 1; 130 (10):5380-5396
    View PubMed
  44. White J, Ball C, Young C, Bell D, Hall C, Healy T, Allen D, Phillips K, Millstein J, Budden T, Goode EL, Anglesio MS, Talhouk A, Intermaggio MP, Leong HS, Chen S, Elatre W, Gilks B, Nazeran T, Volchek M, Bentley RC, Wang C, Chiu DS, Kommoss S, Leung SCY, Senz J, Lum A, Chow V, Sudderuddin H, Mackenzie R, George J, Fereday S, Hendley J, Traficante N, Steed H, Koziak JM, Kobel M, McNeish IA, Goranova T, Ennis D, Macintyre G, Silva De Silva D, Ramon Y Cajal T, Garcia-Donas J, Hernando Polo S, Rodriguez GC, Cushing-Haugen KL, Harris HR, Greene CS, Zelaya RA, Behrens S, Fortner RT, Sinn P, Herpel E, Lester J, Lubinski J, Oszurek O, Toloczko A, Cybulski C, Menkiszak J, Pearce CL, Pike MC, Tseng C, Alsop J, Rhenius V, Song H, Jimenez-Linan M, Piskorz AM, Gentry-Maharaj A, Karpinskyj C, Widschwendter M, Singh N, Kennedy CJ, Sharma R, Harnett PR, Gao B, Johnatty SE, Sayer R, Boros J, Winham SJ, Keeney GL, Kaufmann SH, Larson MC, Larson MC, Luk H, Hernandez BY, Thompson PJ, Wilkens LR, Carney ME, Trabert B, Lissowska J, Brinton L, Sherman ME, Bodelon C, Hinsley S, Lewsley LA, Glasspool R, Banerjee SN, Stronach EA, Haluska P, Ray-Coquard I, Mahner S, Winterhoff B, Slamon D, Levine DA, Kelemen LE, Benitez J, Chang-Claude J, Gronwald J, Wu AH, Menon U, Goodman MT, Schildkraut JM, Wentzensen N, Brown R, Berchuck A, Chenevix-Trench G, deFazio A, Gayther SA, Garcia MJ, Henderson MJ, Rossing MA, Beeghly-Fadiel A, Fasching PA, Orsulic S, Karlan BY, Konecny GE, Huntsman DG, Bowtell DD, Brenton JD, Doherty JA, Pharoah PDP, Ramus SJ, AOCS Group. Prognostic gene expression signature for high-grade serous ovarian cancer. Ann Oncol. 2020 Sep; 31 (9):1240-1250 Epub 2020 May 28
    View PubMed
  45. Zong N, Wen A, Stone DJ, Sharma DK, Wang C, Yu Y, Liu H, Shi Q, Jiang G. Developing an FHIR-Based Computational Pipeline for Automatic Population of Case Report Forms for Colorectal Cancer Clinical Trials Using Electronic Health Records. JCO Clin Cancer Inform. 2020 Mar; 4:201-209.
    View PubMed
  46. Sangtani A, Wang C, Weaver A, Hoppman NL, Kerr SE, Abyzov A, Shridhar V, Staub J, Kocher JA, Voss JS, Podratz KC, Wentzensen N, Kisiel JB, Sherman ME, Bakkum-Gamez JN. Combining copy number, methylation markers, and mutations as a panel for endometrial cancer detection via intravaginal tampon collection. Gynecol Oncol. 2020 Feb; 156 (2):387-392 Epub 2019 Nov 28
    View PubMed
  47. Zhao Y, Yu H, Fu S, Shen F, Davila JI, Liu H, Wang C. Data-driven Sublanguage Analysis for Cancer Genomics Knowledge Modeling: Applications in Mining Oncological Genetics Information from Patients' Genetic Reports. AMIA Jt Summits Transl Sci Proc. 2020; 2020:720-729 Epub 2020 May 30
    View PubMed
  48. Zong N, Sharma DK, Yu Y, Egan JB, Davila JI, Wang C, Jiang G. Developing a FHIR-based Framework for Phenome Wide Association Studies: A Case Study with A Pan-Cancer Cohort. AMIA Jt Summits Transl Sci Proc. 2020; 2020:750-759 Epub 2020 May 30
    View PubMed
  49. Larson NB, Larson MC, Na J, Sosa CP, Wang C, Kocher JP, Rowsey R. Coverage profile correction of shallow-depth circulating cell-free DNA sequencing via multidistance learning. Pac Symp Biocomput. 2020; 25:599-610
    View PubMed
  50. Heitz F, Kommoss S, Tourani R, Grandelis A, Uppendahl L, Aliferis C, Burges A, Wang C, Canzler U, Wang J, Belau A, Prader S, Hanker L, Ma S, Ataseven B, Hilpert F, Schneider S, Sehouli J, Kimmig R, Kurzeder C, Schmalfeldt B, Braicu EI, Harter P, Dowdy SC, Winterhoff BJ, Pfisterer J, du Bois A. Dilution of Molecular-Pathologic Gene Signatures by Medically Associated Factors Might Prevent Prediction of Resection Status After Debulking Surgery in Patients With Advanced Ovarian Cancer. Clin Cancer Res 2020 Jan 1; 26 (1):213-219 Epub 2019 Sept 16
    View PubMed
  51. Hong N, Wen A, Shen F, Sohn S, Wang C, Liu H, Jiang G. Developing a scalable FHIR-based clinical data normalization pipeline for standardizing and integrating unstructured and structured electronic health record data. JAMIA Open. 2019 Dec; 2 (4):570-579 Epub 2019 Oct 18
    View PubMed
  52. Bhagwate AV, Liu Y, Winham SJ, McDonough SJ, Stallings-Mann ML, Heinzen EP, Davila JI, Vierkant RA, Hoskin TL, Frost M, Carter JM, Radisky DC, Cunningham JM, Degnim AC, Wang C. Bioinformatics and DNA-extraction strategies to reliably detect genetic variants from FFPE breast tissue samples. BMC Genomics. 2019 Sep 2; 20 (1):689 Epub 2019 Sept 02
    View PubMed
  53. Mariani A, Wang C, Oberg AL, Riska SM, Torres M, Kumka J, Multinu F, Sagar G, Roy D, Jung DB, Zhang Q, Grassi T, Visscher DW, Patel VP, Jin L, Staub JK, Cliby WA, Weroha SJ, Kalli KR, Hartmann LC, Kaufmann SH, Goode EL, Shridhar V. Genes associated with bowel metastases in ovarian cancer. Gynecol Oncol. 2019 Sep; 154 (3):495-504 Epub 2019 June 14
    View PubMed
  54. Liu Y, Chanana P, Davila JI, Hou X, Zanfagnin V, McGehee CD, Goode EL, Polley EC, Haluska P, Weroha SJ, Wang C. Gene expression differences between matched pairs of ovarian cancer patient tumors and patient-derived xenografts. Sci Rep. 2019 Apr 19; 9 (1):6314
    View PubMed
  55. Winham SJ, Larson NB, Armasu SM, Fogarty ZC, Larson MC, McCauley BM, Wang C, Lawrenson K, Gayther S, Cunningham JM, Fridley BL, Goode EL. Molecular signatures of X chromosome inactivation and associations with clinical outcomes in epithelial ovarian cancer. Hum Mol Genet. 2019 Apr 15; 28 (8):1331-1342
    View PubMed
  56. Torres D, Kumar A, Bakkum-Gamez JN, Weaver AL, McGree ME, Wang C, Langstraat CL, Cliby WA. Mesenchymal molecular subtype is an independent predictor of severe postoperative complications after primary debulking surgery for advanced ovarian cancer. Gynecol Oncol. 2019 Feb; 152(2):223-227. Epub 2018 Nov 28.
    View PubMed
  57. Zhang Q, Wang C, Cliby WA. Cancer-associated stroma significantly contributes to the mesenchymal subtype signature of serous ovarian cancer. Gynecol Oncol. 2019 Feb; 152 (2):368-374 Epub 2018 Nov 15
    View PubMed
  58. McDonough SJ, Bhagwate A, Sun Z, Wang C, Zschunke M, Gorman JA, Kopp KJ, Cunningham JM. Use of FFPE-derived DNA in next generation sequencing: DNA extraction methods. PLoS One. 2019; 14 (4):e0211400 Epub 2019 Apr 11
    View PubMed
  59. Stephens Z, Wang C, Iyer RK, Kocher JP. Detection and visualization of complex structural variants from long reads. BMC Bioinformatics. 2018 Dec 21; 19 (Suppl 20):508
    View PubMed
  60. Carter JM, Wu Y, Blessing MM, Folpe AL, Thorland EC, Spinner RJ, Jentoft ME, Wang C, Baheti S, Niu Z, Mauermann ML, Klein CJ. Recurrent Genomic Alterations in Soft Tissue Perineuriomas. Am J Surg Pathol. 2018 Dec; 42 (12):1708-1714
    View PubMed
  61. Lin S, Wang C, Zarei S, Bell DA, Kerr SE, Runger GC, Kocher JA. A data science approach for the classification of low-grade and high-grade ovarian serous carcinomas. BMC Genomics. 2018 Nov 27; 19 (1):841
    View PubMed
  62. Rambau PF, Vierkant RA, Intermaggio MP, Kelemen LE, Goodman MT, Herpel E, Pharoah PD, Kommoss S, Jimenez-Linan M, Karlan BY, Gentry-Maharaj A, Menon U, Polo SH, Candido Dos Reis FJ, Doherty JA, Gayther SA, Sharma R, Larson MC, Harnett PR, Hatfield E, de Andrade JM, Nelson GS, Steed H, Schildkraut JM, Carney ME, Hogdall E, Whittemore AS, Widschwendter M, Kennedy CJ, Wang F, Wang Q, Wang C, Armasu SM, Daley F, Coulson P, Jones ME, Anglesio MS, Chow C, de Fazio A, Garcia-Closas M, Brucker SY, Cybulski C, Harris HR, Hartkopf AD, Huzarski T, Jensen A, Lubinski J, Oszurek O, Benitez J, Mina F, Staebler A, Taran FA, Pasternak J, Talhouk A, Rossing MA, Hendley J, Edwards RP, Fereday S, Modugno F, Ness RB, Sieh W, El-Bahrawy MA, Winham SJ, Lester J, Kjaer SK, Gronwald J, Sinn P, Fasching PA, Chang-Claude J, Moysich KB, Bowtell DD, Hernandez BY, Luk H, Behrens S, Shah M, Jung A, Ghatage P, Alsop J, Alsop K, Garcia-Donas J, Thompson PJ, Swerdlow AJ, Karpinskyj C, Cazorla-Jimenez A, Garcia MJ, Deen S, Wilkens LR, Palacios J, Berchuck A, Koziak JM, Brenton JD, Cook LS, Goode EL, Huntsman DG, Ramus SJ, Kobel M, AOCS Group. Association of p16 expression with prognosis varies across ovarian carcinoma histotypes: an Ovarian Tumor Tissue Analysis consortium study. J Pathol Clin Res. 2018 Oct; 4 (4):250-261 Epub 2018 Sept 21
    View PubMed
  63. Larson NB, Wang C, Na J, Rowsey RA, Highsmith WE, Hoppman NL, Kocher JP, Klee EW. Improving Single-Nucleotide Polymorphism-Based Fetal Fraction Estimation of Maternal Plasma Circulating Cell-Free DNA Using Bayesian Hierarchical Models. J Comput Biol. 2018 Sep; 25 (9):1040-1049 Epub 2018 June 22
    View PubMed
  64. Fridley BL, Dai J, Raghavan R, Li Q, Winham SJ, Hou X, Weroha SJ, Wang C, Kalli KR, Cunningham JM, Lawrenson K, Gayther SA, Goode EL. Transcriptomic Characterization of Endometrioid, Clear Cell, and High-Grade Serous Epithelial Ovarian Carcinoma. Cancer Epidemiol Biomarkers Prev. 2018 Sep; 27(9):1101-1109. Epub 2018 Jul 02.
    View PubMed
  65. Torres D, Wang C, Kumar A, Bakkum-Gamez JN, Weaver AL, McGree ME, Konecny GE, Goode EL, Cliby WA. Factors that influence survival in high-grade serous ovarian cancer: A complex relationship between molecular subtype, disease dissemination, and operability. Gynecol Oncol. 2018 Aug; 150(2):227-232. Epub 2018 Jun 18.
    View PubMed
  66. Taylor AM, Shih J, Ha G, Gao GF, Zhang X, Berger AC, Schumacher SE, Wang C, Hu H, Liu J, Lazar AJ, Cherniack AD, Beroukhim R, Meyerson M, Cancer Genome Atlas Research Network. Genomic and Functional Approaches to Understanding Cancer Aneuploidy. Cancer Cell. 2018 Apr 9; 33 (4):676-689.e3 Epub 2018 Apr 02
    View PubMed
  67. Berger AC, Korkut A, Kanchi RS, Hegde AM, Lenoir W, Liu W, Liu Y, Fan H, Shen H, Ravikumar V, Rao A, Schultz A, Li X, Sumazin P, Williams C, Mestdagh P, Gunaratne PH, Yau C, Bowlby R, Robertson AG, Tiezzi DG, Wang C, Cherniack AD, Godwin AK, Kuderer NM, Rader JS, Zuna RE, Sood AK, Lazar AJ, Ojesina AI, Adebamowo C, Adebamowo SN, Baggerly KA, Chen TW, Chiu HS, Lefever S, Liu L, MacKenzie K, Orsulic S, Roszik J, Shelley CS, Song Q, Vellano CP, Wentzensen N, Weinstein JN, Mills GB, Levine DA, Akbani R, Cancer Genome Atlas Research Network. A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers. Cancer Cell. 2018 Apr 9; 33 (4):690-705.e9 Epub 2018 Apr 02
    View PubMed
  68. Huang KL, Mashl RJ, Wu Y, Ritter DI, Wang J, Oh C, Paczkowska M, Reynolds S, Wyczalkowski MA, Oak N, Scott AD, Krassowski M, Cherniack AD, Houlahan KE, Jayasinghe R, Wang LB, Zhou DC, Liu D, Cao S, Kim YW, Koire A, McMichael JF, Hucthagowder V, Kim TB, Hahn A, Wang C, McLellan MD, Al-Mulla F, Johnson KJ, Lichtarge O, Boutros PC, Raphael B, Lazar AJ, Zhang W, Wendl MC, Govindan R, Jain S, Wheeler D, Kulkarni S, Dipersio JF, Reimand J, Meric-Bernstam F, Chen K, Shmulevich I, Plon SE, Chen F, Ding L, Cancer Genome Atlas Research Network. Pathogenic Germline Variants in 10,389 Adult Cancers. Cell. 2018 Apr 5; 173 (2):355-370.e14
    View PubMed
  69. Sanchez-Vega F, Mina M, Armenia J, Chatila WK, Luna A, La KC, Dimitriadoy S, Liu DL, Kantheti HS, Saghafinia S, Chakravarty D, Daian F, Gao Q, Bailey MH, Liang WW, Foltz SM, Shmulevich I, Ding L, Heins Z, Ochoa A, Gross B, Gao J, Zhang H, Kundra R, Kandoth C, Bahceci I, Dervishi L, Dogrusoz U, Zhou W, Shen H, Laird PW, Way GP, Greene CS, Liang H, Xiao Y, Wang C, Iavarone A, Berger AH, Bivona TG, Lazar AJ, Hammer GD, Giordano T, Kwong LN, McArthur G, Huang C, Tward AD, Frederick MJ, McCormick F, Meyerson M, Van Allen EM, Cherniack AD, Ciriello G, Sander C, Schultz N, Cancer Genome Atlas Research Network. Oncogenic Signaling Pathways in The Cancer Genome Atlas. Cell. 2018 Apr 5; 173 (2):321-337.e10
    View PubMed
  70. Campbell JD, Yau C, Bowlby R, Liu Y, Brennan K, Fan H, Taylor AM, Wang C, Walter V, Akbani R, Byers LA, Creighton CJ, Coarfa C, Shih J, Cherniack AD, Gevaert O, Prunello M, Shen H, Anur P, Chen J, Cheng H, Hayes DN, Bullman S, Pedamallu CS, Ojesina AI, Sadeghi S, Mungall KL, Robertson AG, Benz C, Schultz A, Kanchi RS, Gay CM, Hegde A, Diao L, Wang J, Ma W, Sumazin P, Chiu HS, Chen TW, Gunaratne P, Donehower L, Rader JS, Zuna R, Al-Ahmadie H, Lazar AJ, Flores ER, Tsai KY, Zhou JH, Rustgi AK, Drill E, Shen R, Wong CK, Stuart JM, Laird PW, Hoadley KA, Weinstein JN, Peto M, Pickering CR, Chen Z, Van Waes C, Cancer Genome Atlas Research Network. Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas. Cell Rep. 2018 Apr 3; 23 (1):194-212.e6
    View PubMed
  71. Kocher JP, Sun Q, Wu Y, Miller M, Zhang W, Wang J, Zhang J, Wong T, Lee S, Zhao F, Anderson ML, Brat DJ, Olson JJ, Sica G, Ahn K, Bell D, Borad M, Bryce AH, Castle E, Chandan V, Cheville J, Copland JA, Farnell M, Flotte T, Giama N, Ho T, Nagorney D, O'Brien D, O'Neill BP, Patel T, Petersen G, Que F, Rivera M, Roberts L, Smallridge R, Smyrk T, Stanton M, Thompson RH, Torbenson M, Zhang L, Guo C, Haydu L, Quinn M, Dhanasekaran R, Nguyen P, Peterson L, Knijnenburg TA, Wang L, Zimmermann MT, Chambwe N, Gao GF, Cherniack AD, Fan H, Shen H, Way GP, Greene CS, Liu Y, Akbani R, Feng B, Donehower LA, Miller C, Shen Y, Karimi M, Chen H, Kim P, Jia P, Shinbrot E, Zhang S, Liu J, Hu H, Bailey MH, Yau C, Wolf D, Zhao Z, Weinstein JN, Li L, Ding L, Mills GB, Laird PW, Wheeler DA, Shmulevich I, Monnat RJ Jr, Xiao Y, Wang C, Cancer Genome Atlas Research Network. Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas. Cell Rep. 2018 Apr 3; 23 (1):239-254.e6
    View PubMed
  72. Roy S, Coldren C, Karunamurthy A, Kip NS, Klee EW, Lincoln SE, Leon A, Pullambhatla M, Temple-Smolkin RL, Voelkerding KV, Wang C, Carter AB. Standards and Guidelines for Validating Next-Generation Sequencing Bioinformatics Pipelines: A Joint Recommendation of the Association for Molecular Pathology and the College of American Pathologists. J Mol Diagn. 2018 Jan; 20 (1):4-27 Epub 2017 Nov 21
    View PubMed
  73. Natanzon Y, Earp M, Cunningham JM, Kalli KR, Wang C, Armasu SM, Larson MC, Bowtell DD, Garsed DW, Fridley BL, Winham SJ, Goode EL. Genomic Analysis Using Regularized Regression in High-Grade Serous Ovarian Cancer. Cancer Inform. 2018; 17:1176935118755341 Epub 2018 Feb 01
    View PubMed
  74. Goode EL, Block MS, Kalli KR, Vierkant RA, Chen W, Fogarty ZC, Gentry-Maharaj A, Toloczko A, Hein A, Bouligny AL, Jensen A, Osorio A, Hartkopf A, Ryan A, Chudecka-Glaz A, Magliocco AM, Hartmann A, Jung AY, Gao B, Hernandez BY, Fridley BL, McCauley BM, Kennedy CJ, Wang C, Karpinskyj C, de Sousa CB, Tiezzi DG, Wachter DL, Herpel E, Taran FA, Modugno F, Nelson G, Lubinski J, Menkiszak J, Alsop J, Lester J, Garcia-Donas J, Nation J, Hung J, Palacios J, Rothstein JH, Kelley JL, de Andrade JM, Robles-Diaz L, Intermaggio MP, Widschwendter M, Beckmann MW, Ruebner M, Jimenez-Linan M, Singh N, Oszurek O, Harnett PR, Rambau PF, Sinn P, Wagner P, Ghatage P, Sharma R, Edwards RP, Ness RB, Orsulic S, Brucker SY, Johnatty SE, Longacre TA, Ursula E, McGuire V, Sieh W, Natanzon Y, Li Z, Whittemore AS, Anna A, Staebler A, Karlan BY, Gilks B, Bowtell DD, Hogdall E, Candido dos Reis FJ, Steed H, Campbell IG, Gronwald J, Benitez J, Koziak JM, Chang-Claude J, Moysich KB, Kelemen LE, Cook LS, Goodman MT, Garcia MJ, Fasching PA, Kommoss S, Deen S, Kjaer SK, Menon U, Brenton JD, Pharoah PDP, Chenevix-Trench G, Huntsman DG, Winham SJ, Kobel M, Ramus SJ, Ovarian Tumor Tissue Analysis (OTTA) Consortium. Dose-Response Association of CD8+ Tumor-Infiltrating Lymphocytes and Survival Time in High-Grade Serous Ovarian Cancer. JAMA Oncol. 2017 Dec 1; 3 (12):e173290
    View PubMed
  75. Torres D, Kumar A, Wallace SK, Bakkum-Gamez JN, Konecny GE, Weaver AL, McGree ME, Goode EL, Cliby WA, Wang C. Intraperitoneal disease dissemination patterns are associated with residual disease, extent of surgery, and molecular subtypes in advanced ovarian cancer. Gynecol Oncol. 2017 Dec; 147(3):503-508. Epub 2017 Sep 28.
    View PubMed
  76. Winham SJ, Mehner C, Heinzen EP, Broderick BT, Stallings-Mann M, Nassar A, Vierkant RA, Hoskin TL, Frank RD, Wang C, Denison LA, Vachon CM, Frost MH, Hartmann LC, Aubrey Thompson E, Sherman ME, Visscher DW, Degnim AC, Radisky DC. NanoString-based breast cancer risk prediction for women with sclerosing adenosis. Breast Cancer Res Treat. 2017 Nov; 166 (2):641-650 Epub 2017 Aug 10
    View PubMed
  77. Doherty JA, Peres LC, Wang C, Way GP, Greene CS, Schildkraut JM. Challenges and Opportunities in Studying the Epidemiology of Ovarian Cancer Subtypes. Curr Epidemiol Rep. 2017 Sep; 4 (3):211-220 Epub 2017 July 10
    View PubMed
  78. Wang C, Armasu SM, Kalli KR, Maurer MJ, Heinzen EP, Keeney GL, Cliby WA, Oberg AL, Kaufmann SH, Goode EL. Pooled Clustering of High-Grade Serous Ovarian Cancer Gene Expression Leads to Novel Consensus Subtypes Associated with Survival and Surgical Outcomes. Clin Cancer Res. 2017 Aug 1; 23 (15):4077-4085 Epub 2017 Mar 09
    View PubMed
  79. Earp MA, Raghavan R, Li Q, Dai J, Winham SJ, Cunningham JM, Natanzon Y, Kalli KR, Hou X, Weroha SJ, Haluska P, Lawrenson K, Gayther SA, Wang C, Goode EL, Fridley BL. Characterization of fusion genes in common and rare epithelial ovarian cancer histologic subtypes. Oncotarget. 2017 Jul 18; 8(29):46891-46899.
    View PubMed
  80. Kommoss S, Winterhoff B, Oberg AL, Konecny GE, Wang C, Riska SM, Fan JB, Maurer MJ, April C, Shridhar V, Kommoss F, du Bois A, Hilpert F, Mahner S, Baumann K, Schroeder W, Burges A, Canzler U, Chien J, Embleton AC, Parmar M, Kaplan R, Perren T, Hartmann LC, Goode EL, Dowdy SC, Pfisterer J. Bevacizumab May Differentially Improve Ovarian Cancer Outcome in Patients with Proliferative and Mesenchymal Molecular Subtypes. Clin Cancer Res. 2017 Jul 15; 23 (14):3794-3801 Epub 2017 Feb 03
    View PubMed
  81. Davila JI, Starr JS, Attia S, Wang C, Knudson RA, Necela BM, Sarangi V, Sun Z, Ren Y, Casler JD, Menke DM, Oliver GR, Joseph RW, Copland JA, Parker AS, Kocher JA, Thompson EA, Smallridge RC, Asmann YW. Comprehensive Genomic Profiling of a Rare Thyroid Follicular Dendritic Cell Sarcoma. Rare Tumors. 2017 Jul 3; 9 (2):6834 Epub 2017 Sept 15
    View PubMed
  82. Carrasquillo MM, Allen M, Burgess JD, Wang X, Strickland SL, Aryal S, Siuda J, Kachadoorian ML, Medway C, Younkin CS, Nair A, Wang C, Chanana P, Serie D, Nguyen T, Lincoln S, Malphrus KG, Morgan K, Golde TE, Price ND, White CC, De Jager PL, Bennett DA, Asmann YW, Crook JE, Petersen RC, Graff-Radford NR, Dickson DW, Younkin SG, Ertekin-Taner N. A candidate regulatory variant at the TREM gene cluster associates with decreased Alzheimer's disease risk and increased TREML1 and TREM2 brain gene expression. Alzheimers Dement. 2017 Jun; 13 (6):663-673 Epub 2016 Dec 08
    View PubMed
  83. Li Z, Hong N, Robertson M, Wang C, Jiang G. Preoperative red cell distribution width and neutrophil-to-lymphocyte ratio predict survival in patients with epithelial ovarian cancer. Sci Rep. 2017 Feb 22; 7:43001
    View PubMed
  84. Hong N, Prodduturi N, Wang C, Jiang G. Shiny FHIR: An Integrated Framework Leveraging Shiny R and HL7 FHIR to Empower Standards-Based Clinical Data Applications. Stud Health Technol Inform. 2017; 245:868-872
    View PubMed
  85. Hong N, Li Z, Kiefer RC, Robertson MS, Goode EL, Wang C, Jiang G. Building an i2b2-based integrated data repository for cancer research: A case study of ovarian cancer registry Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2017; 10186 LNCS:121-35.
  86. Stephens ZD, Iyer RK, Wang C, Kocher JPA. Unraveling complex local genomic rearrangements from long-read data Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. 2017; 2017-January:181-7
  87. Way GP, Rudd J, Wang C, Hamidi H, Fridley BL, Konecny GE, Goode EL, Greene CS, Doherty JA. Comprehensive Cross-Population Analysis of High-Grade Serous Ovarian Cancer Supports No More Than Three Subtypes. G3 (Bethesda). 2016 Dec 7; 6 (12):4097-4103 Epub 2016 Dec 07
    View PubMed
  88. Wang W, Wu Y, Wang C, Jiao J, Klein CJ. Copy number analysis reveals a novel multiexon deletion of the COLQ gene in congenital myasthenia. Neurol Genet. 2016 Dec; 2 (6):e117 Epub 2016 Oct 31
    View PubMed
  89. Raghavan R, Hyter S, Pathak HB, Godwin AK, Konecny G, Wang C, Goode EL, Fridley BL. Drug discovery using clinical outcome-based Connectivity Mapping: application to ovarian cancer. BMC Genomics. 2016 Oct 19; 17 (1):811
    View PubMed
  90. Allen M, Carrasquillo MM, Funk C, Heavner BD, Zou F, Younkin CS, Burgess JD, Chai HS, Crook J, Eddy JA, Li H, Logsdon B, Peters MA, Dang KK, Wang X, Serie D, Wang C, Nguyen T, Lincoln S, Malphrus K, Bisceglio G, Li M, Golde TE, Mangravite LM, Asmann Y, Price ND, Petersen RC, Graff-Radford NR, Dickson DW, Younkin SG, Ertekin-Taner N. Human whole genome genotype and transcriptome data for Alzheimer's and other neurodegenerative diseases. Sci Data. 2016 Oct 11; 3:160089
    View PubMed
  91. Li Z, Block MS, Vierkant RA, Fogarty ZC, Winham SJ, Visscher DW, Kalli KR, Wang C, Goode EL. The inflammatory microenvironment in epithelial ovarian cancer: a role for TLR4 and MyD88 and related proteins. Tumour Biol. 2016 Oct; 37: (10)13279-13286.
    View PubMed
  92. Allen M, Burgess JD, Ballard T, Serie D, Wang X, Younkin CS, Sun Z, Kouri N, Baheti S, Wang C, Carrasquillo MM, Nguyen T, Lincoln S, Malphrus K, Murray M, Golde TE, Price ND, Younkin SG, Schellenberg GD, Asmann Y, Ordog T, Crook J, Dickson D, Ertekin-Taner N. Gene expression, methylation and neuropathology correlations at progressive supranuclear palsy risk loci. Acta Neuropathol. 2016 Aug; 132(2):197-211. Epub 2016 Apr 26.
    View PubMed
  93. Wang C, Winterhoff BJ, Kalli KR, Block MS, Armasu SM, Larson MC, Chen HW, Keeney GL, Hartmann LC, Shridhar V, Konecny GE, Goode EL, Fridley BL. Expression signature distinguishing two tumour transcriptome classes associated with progression-free survival among rare histological types of epithelial ovarian cancer. Br J Cancer. 2016 Jun 14; 114 (12):1412-20 Epub 2016 June 02
    View PubMed
  94. Wang W, Wang C, Dawson DB, Thorland EC, Lundquist PA, Eckloff BW, Wu Y, Baheti S, Evans JM, Scherer SS, Dyck PJ, Klein CJ. Target-enrichment sequencing and copy number evaluation in inherited polyneuropathy. Neurology. 2016 May 10; 86 (19):1762-71 Epub 2016 Apr 13
    View PubMed
  95. Konecny GE, Winterhoff B, Wang C. Gene-expression signatures in ovarian cancer: Promise and challenges for patient stratification. Gynecol Oncol. 2016 May; 141 (2):379-385 Epub 2016 Jan 28
    View PubMed
  96. Purrington KS, Visscher DW, Wang C, Yannoukakos D, Hamann U, Nevanlinna H, Cox A, Giles GG, Eckel-Passow JE, Lakis S, Kotoula V, Fountzilas G, Kabisch M, Rudiger T, Heikkila P, Blomqvist C, Cross SS, Southey MC, Olson JE, Gilbert J, Deming-Halverson S, Kosma VM, Clarke C, Scott R, Jones JL, Zheng W, Mannermaa A, Eccles DM, Vachon CM, Couch FJ, Jane Carpenter for ABCTC Investigators. Genes associated with histopathologic features of triple negative breast tumors predict molecular subtypes. Breast Cancer Res Treat. 2016 May; 157 (1):117-31 Epub 2016 Apr 15
    View PubMed
  97. Winterhoff B, Hamidi H, Wang C, Kalli KR, Fridley BL, Dering J, Chen HW, Cliby WA, Wang HJ, Dowdy S, Gostout BS, Keeney GL, Goode EL, Konecny GE. Molecular classification of high grade endometrioid and clear cell ovarian cancer using TCGA gene expression signatures. Gynecol Oncol. 2016 Apr; 141 (1):95-100
    View PubMed
  98. French JD, Johnatty SE, Lu Y, Beesley J, Gao B, Kalimutho M, Henderson MJ, Russell AJ, Kar S, Chen X, Hillman KM, Kaufmann S, Sivakumaran H, O'Reilly M, Wang C, Korbie DJ, Lambrechts D, Despierre E, Van Nieuwenhuysen E, Lambrechts S, Vergote I, Karlan B, Lester J, Orsulic S, Walsh C, Fasching PA, Beckmann MW, Ekici AB, Hein A, Matsuo K, Hosono S, Pisterer J, Hillemanns P, Nakanishi T, Yatabe Y, Goodman MT, Lurie G, Matsuno RK, Thompson PJ, Pejovic T, Bean Y, Heitz F, Harter P, du Bois A, Schwaab I, Hogdall E, Kjaer SK, Jensen A, Hogdall C, Lundvall L, Engelholm SA, Brown B, Flanagan JM, Metcalf MD, Siddiqui N, Sellers T, Fridley B, Cunningham J, Schildkraut JM, Iversen E, Weber RP, Brennan D, Berchuck A, Pharoah P, Harnett P, Norris MD, Haber M, Goode EL, Lee JS, Khanna KK, Meyer KB, Chenevix-Trench G, deFazio A, Edwards SL, MacGregor S, Australian Ovarian Cancer Study Group//Australian Ovarian Cancer Study//Ovarian Cancer Association Consortium. Germline polymorphisms in an enhancer of PSIP1 are associated with progression-free survival in epithelial ovarian cancer. Oncotarget. 2016 Feb 9; 7 (6):6353-68
    View PubMed
  99. Zimmermann MT, Jiang G, Wang C. Single-sample expression-based chemo-sensitivity score improves survival associations independently from genomic mutations for ovarian cancer Patients. AMIA Jt Summits Transl Sci Proc. 2016; 2016:94-100 Epub 2016 July 20
    View PubMed
  100. Novak AJ, Asmann YW, Maurer MJ, Wang C, Slager SL, Hodge LS, Manske M, Price-Troska T, Yang ZZ, Zimmermann MT, Nowakowski GS, Ansell SM, Witzig TE, McPhail E, Ketterling R, Feldman AL, Dogan A, Link BK, Habermann TM, Cerhan JR. Whole-exome analysis reveals novel somatic genomic alterations associated with outcome in immunochemotherapy-treated diffuse large B-cell lymphoma. Blood Cancer J. 2015 Aug 28; 5:e346
    View PubMed
  101. Chien J, Sicotte H, Fan JB, Humphray S, Cunningham JM, Kalli KR, Oberg AL, Hart SN, Li Y, Davila JI, Baheti S, Wang C, Dietmann S, Atkinson EJ, Asmann YW, Bell DA, Ota T, Tarabishy Y, Kuang R, Bibikova M, Cheetham RK, Grocock RJ, Swisher EM, Peden J, Bentley D, Kocher JP, Kaufmann SH, Hartmann LC, Shridhar V, Goode EL. TP53 mutations, tetraploidy and homologous recombination repair defects in early stage high-grade serous ovarian cancer. Nucleic Acids Res. 2015 Aug 18; 43 (14):6945-58 Epub 2015 Apr 27
    View PubMed
  102. Allen M, Kachadoorian M, Carrasquillo MM, Karhade A, Manly L, Burgess JD, Wang C, Serie D, Wang X, Siuda J, Zou F, Chai HS, Younkin C, Crook J, Medway C, Nguyen T, Ma L, Malphrus K, Lincoln S, Petersen RC, Graff-Radford NR, Asmann YW, Dickson DW, Younkin SG, Ertekin-Taner N. Late-onset Alzheimer disease risk variants mark brain regulatory loci. Neurol Genet. 2015 Aug; 1 (2):e15 Epub 2015 July 23
    View PubMed
  103. Degnim AC, Nassar A, Stallings-Mann M, Keith Anderson S, Oberg AL, Vierkant RA, Frank RD, Wang C, Winham SJ, Frost MH, Hartmann LC, Visscher DW, Radisky DC. Gene signature model for breast cancer risk prediction for women with sclerosing adenosis. Breast Cancer Res Treat. 2015 Aug; 152 (3):687-94 Epub 2015 July 23
    View PubMed
  104. Jiang G, Sohn S, Zimmermann MT, Wang C, Liu H, Chute CG. Drug Normalization for Cancer Therapeutic and Druggable Genome Target Discovery. AMIA Jt Summits Transl Sci Proc. 2015; 2015:72-6 Epub 2015 Mar 25
    View PubMed
  105. Priya S, Jiang G, Dasari S, Zimmermann MT, Wang C, Heflin J, Chute CG. A Semantic Web-based System for Mining Genetic Mutations in Cancer Clinical Trials. AMIA Jt Summits Transl Sci Proc. 2015; 2015:142-6 Epub 2015 Mar 25
    View PubMed
  106. Wang C, Zimmermann MT, Chute CG, Jiang G. Adverse Drug Events-based Tumor Stratification for Ovarian Cancer Patients Receiving Platinum Therapy. AMIA Jt Summits Transl Sci Proc. 2015; 2015:51-5 Epub 2015 Mar 23
    View PubMed
  107. Mansfield AS, Visscher DW, Hart SN, Wang C, Goetz MP, Oxvig C, Conover CA. Pregnancy-associated plasma protein-A expression in human breast cancer. Growth Horm IGF Res. 2014 Dec; 24(6):264-7.
    View PubMed
  108. Wang C, Davila JI, Baheti S, Bhagwate AV, Wang X, Kocher JP, Slager SL, Feldman AL, Novak AJ, Cerhan JR, Thompson EA, Asmann YW. RVboost: RNA-seq variants prioritization using a boosting method. Bioinformatics. 2014 Dec 1; 30 (23):3414-6 Epub 2014 Aug 27
    View PubMed
  109. Wang L, Chen J, Wang C, Uuskula-Reimand L, Chen K, Medina-Rivera A, Young EJ, Zimmermann MT, Yan H, Sun Z, Zhang Y, Wu ST, Huang H, Wilson MD, Kocher JP, Li W. MACE: model based analysis of ChIP-exo. Nucleic Acids Res. 2014 Nov 10; 42 (20):e156 Epub 2014 Sept 23
    View PubMed
  110. Asmann YW, Maurer MJ, Wang C, Sarangi V, Ansell SM, Feldman AL, Nowakowski GS, Manske M, Price-Troska T, Yang ZZ, Slager SL, Habermann TM, Cerhan JR, Novak AJ. Genetic diversity of newly diagnosed follicular lymphoma. Blood Cancer J 2014 Oct 31; 4:e256
    View PubMed
  111. Konecny GE, Wang C, Hamidi H, Winterhoff B, Kalli KR, Dering J, Ginther C, Chen HW, Dowdy S, Cliby W, Gostout B, Podratz KC, Keeney G, Wang HJ, Hartmann LC, Slamon DJ, Goode EL. Prognostic and therapeutic relevance of molecular subtypes in high-grade serous ovarian cancer. J Natl Cancer Inst. 2014 Oct; 106 (10) Epub 2014 Sept 30
    View PubMed
  112. Wang C, Evans JM, Bhagwate AV, Prodduturi N, Sarangi V, Middha M, Sicotte H, Vedell PT, Hart SN, Oliver GR, Kocher JP, Maurer MJ, Novak AJ, Slager SL, Cerhan JR, Asmann YW. PatternCNV: a versatile tool for detecting copy number changes from exome sequencing data. Bioinformatics. 2014 Sep 15; 30 (18):2678-80 Epub 2014 May 29
    View PubMed
  113. Wang C, Cicek MS, Charbonneau B, Kalli KR, Armasu SM, Larson MC, Konecny GE, Winterhoff B, Fan JB, Bibikova M, Chien J, Shridhar V, Block MS, Hartmann LC, Visscher DW, Cunningham JM, Knutson KL, Fridley BL, Goode EL. Tumor hypomethylation at 6p21.3 associates with longer time to recurrence of high-grade serous epithelial ovarian cancer. Cancer Res. 2014 Jun 1; 74 (11):3084-91 Epub 2014 Apr 11
    View PubMed
  114. Fridley BL, Armasu SM, Cicek MS, Larson MC, Wang C, Winham SJ, Kalli KR, Koestler DC, Rider DN, Shridhar V, Olson JE, Cunningham JM, Goode EL. Methylation of leukocyte DNA and ovarian cancer: relationships with disease status and outcome. BMC Med Genomics. 2014 Apr 28; 7:21.
    View PubMed
  115. Charbonneau B, Moysich KB, Kalli KR, Oberg AL, Vierkant RA, Fogarty ZC, Block MS, Maurer MJ, Goergen KM, Fridley BL, Cunningham JM, Rider DN, Preston C, Hartmann LC, Lawrenson K, Wang C, Tyrer J, Song H, deFazio A, Johnatty SE, Doherty JA, Phelan CM, Sellers TA, Ramirez SM, Vitonis AF, Terry KL, Van Den Berg D, Pike MC, Wu AH, Berchuck A, Gentry-Maharaj A, Ramus SJ, Diergaarde B, Shen H, Jensen A, Menkiszak J, Cybulski C, Lubilski J, Ziogas A, Rothstein JH, McGuire V, Sieh W, Lester J, Walsh C, Vergote I, Lambrechts S, Despierre E, Garcia-Closas M, Yang H, Brinton LA, Spiewankiewicz B, Rzepecka IK, Dansonka-Mieszkowska A, Seibold P, Rudolph A, Paddock LE, Orlow I, Lundvall L, Olson SH, Hogdall CK, Schwaab I, du Bois A, Harter P, Flanagan JM, Brown R, Paul J, Ekici AB, Beckmann MW, Hein A, Eccles D, Lurie G, Hays LE, Bean YT, Pejovic T, Goodman MT, Campbell I, Fasching PA, Konecny G, Kaye SB, Heitz F, Hogdall E, Bandera EV, Chang-Claude J, Kupryjanczyk J, Wentzensen N, Lambrechts D, Karlan BY, Whittemore AS, Culver HA, Gronwald J, Levine DA, Kjaer SK, Menon U, Schildkraut JM, Pearce CL, Cramer DW, Rossing MA, Chenevix-Trench G, AOCS group, Acs, Pharoah PD, Gayther SA, Ness RB, Odunsi K, Sucheston LE, Knutson KL, Goode EL. Large-scale evaluation of common variation in regulatory T cell-related genes and ovarian cancer outcome. Cancer Immunol Res. 2014 Apr; 2(4):332-40. Epub 2014 Jan 27.
    View PubMed
  116. Cunningham JM, Cicek MS, Larson NB, Davila J, Wang C, Larson MC, Song H, Dicks EM, Harrington P, Wick M, Winterhoff BJ, Hamidi H, Konecny GE, Chien J, Bibikova M, Fan JB, Kalli KR, Lindor NM, Fridley BL, Pharoah PP, Goode EL. Clinical characteristics of ovarian cancer classified by BRCA1, BRCA2, and RAD51C status. Sci Rep. 2014 Feb 7; 4:4026 Epub 2014 Feb 07
    View PubMed
  117. Wang C, Zimmermann MT, Prodduturi N, Chute CG, Jiang G. Adverse Drug Event-based Stratification of Tumor Mutations: A Case Study of Breast Cancer Patients Receiving Aromatase Inhibitors. AMIA Annu Symp Proc. 2014; 2014:1160-9 Epub 2014 Nov 14
    View PubMed
  118. Roy D, Mondal S, Wang C, He X, Khurana A, Giri S, Hoffmann R, Jung DB, Kim SH, Chini EN, Periera JC, Folmes CD, Mariani A, Dowdy SC, Bakkum-Gamez JN, Riska SM, Oberg AL, Karoly ED, Bell LN, Chien J, Shridhar V. Erratum to: Loss of HSulf-1 promotes altered lipid metabolism in ovarian cancer. Cancer Metab. 2014; 2:24 Epub 2014 Nov 04
    View PubMed
  119. Roy D, Mondal S, Wang C, He X, Khurana A, Giri S, Hoffmann R, Jung DB, Kim SH, Chini EN, Periera JC, Folmes CD, Mariani A, Dowdy SC, Bakkum-Gamez JN, Riska SM, Oberg AL, Karoly ED, Bell LN, Chien J, Shridhar V. Loss of HSulf-1 promotes altered lipid metabolism in ovarian cancer. Cancer Metab. 2014; 2:13 Epub 2014 Aug 18
    View PubMed
  120. Chen X, Xuan J, Wang C, Shajahan AN, Riggins RB, Clarke R. Reconstruction of transcriptional regulatory networks by stability-based network component analysis. IEEE/ACM Trans Comput Biol Bioinform. 2013 Nov-Dec; 10(6):1347-58.
    View PubMed
  121. Cicek MS, Koestler DC, Fridley BL, Kalli KR, Armasu SM, Larson MC, Wang C, Winham SJ, Vierkant RA, Rider DN, Block MS, Klotzle B, Konecny G, Winterhoff BJ, Hamidi H, Shridhar V, Fan JB, Visscher DW, Olson JE, Hartmann LC, Bibikova M, Chien J, Cunningham JM, Goode EL. Epigenome-wide ovarian cancer analysis identifies a methylation profile differentiating clear-cell histology with epigenetic silencing of the HERG K+ channel. Hum Mol Genet. 2013 Aug 1; 22 (15):3038-47 Epub 2013 Apr 09
    View PubMed
  122. Kandoth C, Schultz N, Cherniack AD, Akbani R, Liu Y, Shen H, Robertson AG, Pashtan I, Shen R, Benz CC, Yau C, Laird PW, Ding L, Zhang W, Mills GB, Kucherlapati R, Mardis ER, Levine DA, Cancer Genome Atlas Research Network, Dowdy SC, Dao L, Gostout B, Wang C. Integrated genomic characterization of endometrial carcinoma. Nature. 2013 May 2; 497 (7447):67-73
    View PubMed
  123. Couch FJ, Wang X, McGuffog L, Lee A, Olswold C, Kuchenbaecker KB, Soucy P, Fredericksen Z, Barrowdale D, Dennis J, Gaudet MM, Dicks E, Kosel M, Healey S, Sinilnikova OM, Lee A, Bacot F, Vincent D, Hogervorst FB, Peock S, Stoppa-Lyonnet D, Jakubowska A, Radice P, Schmutzler RK, Domchek SM, Piedmonte M, Singer CF, Friedman E, Thomassen M, Hansen TV, Neuhausen SL, Szabo CI, Blanco I, Greene MH, Karlan BY, Garber J, Phelan CM, Weitzel JN, Montagna M, Olah E, Andrulis IL, Godwin AK, Yannoukakos D, Goldgar DE, Caldes T, Nevanlinna H, Osorio A, Terry MB, Daly MB, van Rensburg EJ, Hamann U, Ramus SJ, Toland AE, Caligo MA, Olopade OI, Tung N, Claes K, Beattie MS, Southey MC, Imyanitov EN, Tischkowitz M, Janavicius R, John EM, Kwong A, Diez O, Balmana J, Barkardottir RB, Arun BK, Rennert G, Teo SH, Ganz PA, Campbell I, van der Hout AH, van Deurzen CH, Seynaeve C, Gomez Garcia EB, van Leeuwen FE, Meijers-Heijboer HE, Gille JJ, Ausems MG, Blok MJ, Ligtenberg MJ, Rookus MA, Devilee P, Verhoef S, van Os TA, Wijnen JT, Frost D, Ellis S, Fineberg E, Platte R, Evans DG, Izatt L, Eeles RA, Adlard J, Eccles DM, Cook J, Brewer C, Douglas F, Hodgson S, Morrison PJ, Side LE, Donaldson A, Houghton C, Rogers MT, Dorkins H, Eason J, Gregory H, McCann E, Murray A, Calender A, Hardouin A, Berthet P, Delnatte C, Nogues C, Lasset C, Houdayer C, Leroux D, Rouleau E, Prieur F, Damiola F, Sobol H, Coupier I, Venat-Bouvet L, Castera L, Gauthier-Villars M, Leone M, Pujol P, Mazoyer S, Bignon YJ, Zlowocka-Perlowska E, Gronwald J, Lubinski J, Durda K, Jaworska K, Huzarski T, Spurdle AB, Viel A, Peissel B, Bonanni B, Melloni G, Ottini L, Papi L, Varesco L, Tibiletti MG, Peterlongo P, Volorio S, Manoukian S, Pensotti V, Arnold N, Engel C, Deissler H, Gadzicki D, Gehrig A, Kast K, Rhiem K, Meindl A, Niederacher D, Ditsch N, Plendl H, Preisler-Adams S, Engert S, Sutter C, Varon-Mateeva R, Wappenschmidt B, Weber BH, Arver B, Stenmark-Askmalm M, Loman N, Rosenquist R, Einbeigi Z, Nathanson KL, Rebbeck TR, Blank SV, Cohn DE, Rodriguez GC, Small L, Friedlander M, Bae-Jump VL, Fink-Retter A, Rappaport C, Gschwantler-Kaulich D, Pfeiler G, Tea MK, Lindor NM, Kaufman B, Shimon Paluch S, Laitman Y, Skytte AB, Gerdes AM, Pedersen IS, Moeller ST, Kruse TA, Jensen UB, Vijai J, Sarrel K, Robson M, Kauff N, Mulligan AM, Glendon G, Ozcelik H, Ejlertsen B, Nielsen FC, Jonson L, Andersen MK, Ding YC, Steele L, Foretova L, Teule A, Lazaro C, Brunet J, Pujana MA, Mai PL, Loud JT, Walsh C, Lester J, Orsulic S, Narod SA, Herzog J, Sand SR, Tognazzo S, Agata S, Vaszko T, Weaver J, Stavropoulou AV, Buys SS, Romero A, de la Hoya M, Aittomaki K, Muranen TA, Duran M, Chung WK, Lasa A, Dorfling CM, Miron A, Benitez J, Senter L, Huo D, Chan SB, Sokolenko AP, Chiquette J, Tihomirova L, Friebel TM, Agnarsson BA, Lu KH, Lejbkowicz F, James PA, Hall P, Dunning AM, Cunningham J, Cunningham J, Slager SL, Wang C, Hart S, et al, kConFab Investigators//SWE-BRCA//Ontario Cancer Genetics Network//HEBON//EMBRACE//GEMO Study Collaborators//BCFR//CIMBA, Pankratz VS. Genome-wide association study in BRCA1 mutation carriers identifies novel loci associated with breast and ovarian cancer risk. PLoS Genet. 2013; 9 (3):e1003212 Epub 2013 Mar 27
    View PubMed
  124. Goode EL, DeRycke M, Kalli KR, Oberg AL, Cunningham JM, Maurer MJ, Fridley BL, Armasu SM, Serie DJ, Ramar P, Goergen K, Vierkant RA, Rider DN, Sicotte H, Wang C, Winterhoff B, Phelan CM, Schildkraut JM, Weber RP, Iversen E, Berchuck A, Sutphen R, Birrer MJ, Hampras S, Preus L, Gayther SA, Ramus SJ, Wentzensen N, Yang HP, Garcia-Closas M, Song H, Tyrer J, Pharoah PP, Konecny G, Sellers TA, Ness RB, Sucheston LE, Odunsi K, Hartmann LC, Moysich KB, Knutson KL. Inherited variants in regulatory T cell genes and outcome of ovarian cancer. PLoS One. 2013; 8 (1):e53903 Epub 2013 Jan 30
    View PubMed
  125. Jiang G, Wang C, Zhu Q, Chute CG. A Framework of Knowledge Integration and Discovery for Supporting Pharmacogenomics Target Predication of Adverse Drug Events: A Case Study of Drug-Induced Long QT Syndrome. AMIA Jt Summits Transl Sci Proc. 2013; 2013:88-92 Epub 2013 Mar 18
    View PubMed
  126. Wang C, Ha S, Xuan J, Wang Y, Hoffman E. Computational Analysis of Muscular Dystrophy Sub-types Using A Novel Integrative Scheme. Neurocomputing. 2012 Sep 1; 92:9-17.
    View PubMed
  127. Wang C, Xuan J, Shih IM, Clarke R, Wang Y. Regulatory component analysis: a semi-blind extraction approach to infer gene regulatory networks with imperfect biological knowledge. Signal Processing. 2012 Aug 1; 92(8):1902-15. Epub 2011 Dec 08.
    View PubMed
  128. Gu J, Wang C, Shih IeM, Wang TL, Wang Y, Clarke R, Xuan J. GIST: a Gibbs sampler to identify intracellular signal transduction pathways. Conf Proc IEEE Eng Med Biol Soc. 2011; 2011:2434-7.
    View PubMed
  129. Shih IeM, Chen L, Wang CC, Gu J, Davidson B, Cope L, Kurman RJ, Xuan J, Wang TL. Distinct DNA methylation profiles in ovarian serous neoplasms and their implications in ovarian carcinogenesis. Am J Obstet Gynecol. 2010 Dec; 203(6):584.e1-22. Epub 2010 Oct 20.
    View PubMed
  130. Wang C, Xuan J, Li H, Wang Y, Zhan M, Hoffman EP, Clarke R. Knowledge-guided gene ranking by coordinative component analysis. BMC Bioinformatics. 2010; 11:162. Epub 2010 Mar 30.
    View PubMed
  131. Chen L, Xuan J, Wang C, Wang Y, Shih IeM, Wang TL, Zhang Z, Clarke R, Hoffman EP. Biomarker identification by knowledge-driven multilevel ICA and motif analysis. Int J Data Min Bioinform. 2009; 3(4):365-81.
    View PubMed
  132. Chen L, Xuan J, Wang C, Shih IeM, Wang Y, Zhang Z, Hoffman E, Clarke R. Knowledge-guided multi-scale independent component analysis for biomarker identification. BMC Bioinformatics. 2008; 9:416. Epub 2008 Oct 6.
    View PubMed
  133. Wang C, Xuan J, Chen L, Zhao P, Wang Y, Clarke R, Hoffman E. Motif-directed network component analysis for regulatory network inference. BMC Bioinformatics. 2008; 9 Suppl 1:S21.
    View PubMed
  134. Gong T, Xuan J, Wang C, Li H, Hoffman E, Clarke R, Wang Y. Gene module identification from microarray data using nonnegative independent component analysis. Gene Regul Syst Bio. 2007; 1:349-63. Epub 2008 Jan 15.
    View PubMed