Paul Boutros*

Paul Boutros, Ph.D., M.B.A., is a cancer data scientist and professor in the departments of human genetics and urology at the David Geffen School of Medicine at UCLA. He currently serves as director of the UCLA Jonsson Comprehensive Cancer Center’s Cancer Data Science program, Associate Director of cancer informatics at the UCLA Institute for Precision Health, and is a member of the Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research. The research in Boutros’ laboratory lies at the intersection of clinical, molecular and imaging data. He focuses on how these diverse pieces of information can be linked to personalize therapy for cancer patients. By applying techniques from modern data science strategies, particularly machine-learning, he creates biomarkers to help ensure therapies are selected that maximize cure and minimize morbidities. His work sometimes centers on specific tumor types, particularly prostate and sarcoma, but often includes others in conjunction to identify general and tumor-type specific features of cancer. Some of his recent studies focus on how cancers develop differently based on the sex, age or ancestric features of the patient. Boutros has published over 300 peer-reviewed papers, and in his leadership roles as professor in the departments of human genetics and urology, he is currently working to support personalizing therapy for cancer by developing novel statistical methodologies. He leads the ICGC-TCGA DREAM Somatic Mutation Calling Challenge that is setting global standards for analyzing cancer genomic data, and drives programs in cancer genomics, data science and biomarker translation.

Websites:

UCLA Institute of Urologic Oncology

Research Interests:

Cancer, Machine Learning, Cloud Computing, Genomics, Sequencing, Molecular, Computational Biology, Proteomics, Computational Algorithms, Statistical Pipelines, Bioinformatics, Big Data, Data Analysis,

Publications:

Agrawal R, Al-Hiyari S, Hugh-White R, Hromas R, Patel Y, Williamson EA, Mootor MFE, Gonzalez A, Fu J, Haas R, Jordan M, Wickes BL, Mohammed G, Tian M, Doris MJ, Jobin C, Wernke KM, Pan Y, Yamaguchi TN, Herzon SB, Boutros PC, Liss MA. Colibactin Exerts Androgen-dependent and -independent Effects on Prostate Cancer. Eur Urol Oncol. 2024 Nov 14. view on PubMed

Wang S, Zeng Y, Zhu L, Zhang M, Zhou L, Yang W, Luo W, Wang L, Liu Y, Zhu H, Xu X, Su P, Zhang X, Ahmed M, Chen W, Chen M, Chen S, Slobodyanyuk M, Xie Z, Guan J, Zhang W, Khan AA, Sakashita S, Liu N, Pham NA, Boutros PC, Ke Z, Moran MF, Cai Z, Cheng C, Yu J, Tsao MS, He HH. The N6-methyladenosine Epitranscriptomic Landscape of Lung Adenocarcinoma. Cancer Discov. 2024 Nov 01; 14(11):2279-2299. view on PubMed

Liss MA, Zeltser N, Zheng Y, Lopez C, Liu M, Patel Y, Yamaguchi TN, Eng SE, Tian M, Semmes OJ, Lin DW, Brooks JD, Wei JT, Klein EA, Tewari AK, Mosquera JM, Khani F, Robinson BD, Aasad M, Troyer DA, Kagan J, Sanda MG, Thompson IM, Boutros PC, Leach RJ. Upgrading of Grade Group 1 Prostate Cancer at Prostatectomy: Germline Risk Factors in a Prospective Cohort. Cancer Epidemiol Biomarkers Prev. 2024 Nov 01; 33(11):1500-1511. view on PubMed

Underwood WP, Michalski MG, Lee CP, Fickera GA, Chun SS, Eng SE, Liu LY, Tsai BL, Moskowitz CS, Lavery JA, Van Zee KJ, Gardner GJ, Mueller JJ, Dang CT, Ehdaie B, Laudone VP, Eastham JA, Scott JM, Boutros PC, Jones LW. A digital, decentralized trial of exercise therapy in patients with cancer. NPJ Digit Med. 2024 Oct 28; 7(1):304. view on PubMed

Houlahan KE, Bihie M, Contreras JG, Fulop DJ, Lopez G, Huang HH, Van Loo P, Curtis C, Boutros PC, Huang KL. Deletions Rate-Limit Breast and Ovarian Cancer Initiation. bioRxiv. 2024 Oct 21. view on PubMed

Fox NS, Tian M, Markowitz AL, Haider S, Li CH, Boutros PC. iSubGen generates integrative disease subtypes by pairwise similarity assessment. Cell Rep Methods. 2024 Oct 18; 100884. view on PubMed

Bliss JW, Underwood WP, Carlson AM, Scott JM, Daly R, Li BT, Drilon A, Stetson P, Boutros PC, Jones LW. Case report: dynamic personalized physiological monitoring in lung cancer using wearable data. Front Oncol. 2024; 14:1420888. view on PubMed

Al Shihabi A, Tebon PJ, Nguyen HTL, Chantharasamee J, Sartini S, Davarifar A, Jensen AY, Diaz-Infante M, Cox H, Gonzalez AE, Norris S, Sperry J, Nakashima J, Tavanaie N, Winata H, Fitz-Gibbon ST, Yamaguchi TN, Jeong JH, Dry S, Singh AS, Chmielowski B, Crompton JG, Kalbasi AK, Eilber FC, Hornicek F, Bernthal NM, Nelson SD, Boutros PC, Federman NC, Yanagawa J, Soragni A. The landscape of drug sensitivity and resistance in sarcoma. Cell Stem Cell. 2024 Oct 03; 31(10):1524-1542.e4. view on PubMed

Weiner AB, Agrawal R, Wang NK, Sonni I, Li EV, Arbet J, Zhang JJH, Proudfoot JA, Hong BH, Davicioni E, Kane N, Valle LF, Kishan AU, Pra AD, Ghadjar P, Sweeney CJ, Nickols NG, Karnes RJ, Shen J, Rettig MB, Czernin J, Ross AE, Lee Kiang Chua M, Schaeffer EM, Calais J, Boutros PC, Reiter RE. Molecular Hallmarks of Prostate-specific Membrane Antigen in Treatment-naïve Prostate Cancer. Eur Urol. 2024 Sep 17. view on PubMed

Zhu C, Liu LY, Ha A, Yamaguchi TN, Zhu H, Hugh-White R, Livingstone J, Patel Y, Kislinger T, Boutros PC. moPepGen: Rapid and Comprehensive Identification of Non-canonical Peptides. bioRxiv. 2024 Sep 13. view on PubMed

Patel Y, Zhu C, Yamaguchi TN, Wang NK, Wiltsie N, Gonzalez AE, Winata HK, Zeltser N, Pan Y, Mootor MFE, Sanders T, Kandoth C, Fitz-Gibbon ST, Livingstone J, Liu LY, Carlin B, Holmes A, Oh J, Sahrmann J, Tao S, Eng S, Hugh-White R, Pashminehazar K, Park A, Beshlikyan A, Jordan M, Wu S, Tian M, Arbet J, Neilsen B, Bugh YZ, Kim G, Salmingo J, Zhang W, Haas R, Anand A, Hwang E, Neiman-Golden A, Steinberg P, Zhao W, Anand P, Tsai BL, Boutros PC. Metapipeline-DNA: A Comprehensive Germline & Somatic Genomics Nextflow Pipeline. bioRxiv. 2024 Sep 07. view on PubMed

Jones LW, Moskowitz CS, Lee CP, Fickera GA, Chun SS, Michalski MG, Stoeckel K, Underwood WP, Lavery JA, Bhanot U, Linkov I, Dang CT, Ehdaie B, Laudone VP, Eastham JA, Collins A, Sheerin PT, Liu LY, Eng SE, Boutros PC. Neoadjuvant Exercise Therapy in Prostate Cancer: A Phase 1, Decentralized Nonrandomized ControlledTrial. JAMA Oncol. 2024 Sep 01; 10(9):1187-1194. view on PubMed

Haas R, Frame G, Khan S, Neilsen BK, Hong BH, Yeo CPX, Yamaguchi TN, Ong EHW, Zhao W, Carlin B, Yeo ELL, Tan KM, Bugh YZ, Zhu C, Hugh-White R, Livingstone J, Poon DJJ, Chu PL, Patel Y, Tao S, Ignatchenko V, Kurganovs NJ, Higgins GS, Downes MR, Loblaw A, Vesprini D, Kishan AU, Chua MLK, Kislinger T, Boutros PC, Liu SK. The Proteogenomics of Prostate Cancer Radioresistance. Cancer Res Commun. 2024 Sep 01; 4(9):2463-2479. view on PubMed

Haas R, Patel Y, Liu LY, Huang RR, Weiner A, Yamaguchi TN, Agrawal R, Boutros PC, Reiter RE. Divergent Evolution in Bilateral Prostate Cancer: a Case Study. medRxiv. 2024 Aug 23. view on PubMed

Frame G, Leong H, Haas R, Huang X, Wright J, Emmenegger U, Downes M, Boutros PC, Kislinger T, Liu SK. Targeting PLOD2 suppresses invasion and metastatic potential in radiorecurrent prostate cancer. BJC Rep. 2024; 2(1):60. view on PubMed

Afiaz A, Ivanov AA, Chamberlin J, Hanauer D, Savonen CL, Goldman MJ, Morgan M, Reich M, Getka A, Holmes A, Pati S, Knight D, Boutros PC, Bakas S, Caporaso JG, Del Fiol G, Hochheiser H, Haas B, Schloss PD, Eddy JA, Albrecht J, Fedorov A, Waldron L, Hoffman AM, Bradshaw RL, Leek JT, Wright C. Best practices to evaluate the impact of biomedical research software-metric collection beyond citations. Bioinformatics. 2024 08 02; 40(8). view on PubMed

Tohi Y, Sahrmann JM, Arbet J, Kato T, Lee LS, Peacock M, Ginsburg K, Pavlovich C, Carroll P, Bangma CH, Sugimoto M, Boutros PC, Global Action Plan Prostate Cancer Active Surveillance (GAP3) Consortium. De-escalation of Monitoring in Active Surveillance for Prostate Cancer: Results from the GAP3 Consortium. Eur Urol Oncol. 2024 Jul 31. view on PubMed

Lin I, Wei A, Gebo TA, Boutros PC, Flanagan M, Kucine N, Cunniff C, Arboleda VA, Chang VY. Increased frequency of clonal hematopoiesis of indeterminate potential in Bloom syndrome probands and carriers. Haematologica. 2024 Jul 25. view on PubMed

Nikitas J, Subramanian K, Gozal NB, Ricaurte-Fajardo A, Li E, Proudfoot JA, Davicioni E, Marciscano AE, Osborne JR, Barbieri CE, Armstrong WR, Smith CP, Valle LF, Steinberg ML, Boutros PC, Nickols NG, Rettig MB, Reiter R, Weiner AB, Calais J, Czernin J, Ross AE, Kim EH, Nagar H, Kishan AU. Transcriptomic Profiling of Primary Prostate Cancers and Nonlocalized Disease on Prostate-Specific Membrane Antigen Positron Emission Tomography/Computed Tomography: A Multicenter Retrospective Study. JCO Precis Oncol. 2024 Jul; 8:e2400161. view on PubMed

Khoo A, Govindarajan M, Qiu Z, Liu LY, Ignatchenko V, Waas M, Macklin A, Keszei A, Neu S, Main BP, Yang L, Lance RS, Downes MR, Semmes OJ, Vesprini D, Liu SK, Nyalwidhe JO, Boutros PC, Kislinger T. Prostate cancer reshapes the secreted and extracellular vesicle urinary proteomes. Nat Commun. 2024 Jun 13; 15(1):5069. view on PubMed

Salcedo A, Tarabichi M, Buchanan A, Espiritu SMG, Zhang H, Zhu K, Ou Yang TH, Leshchiner I, Anastassiou D, Guan Y, Jang GH, Mootor MFE, Haase K, Deshwar AG, Zou W, Umar I, Dentro S, Wintersinger JA, Chiotti K, Demeulemeester J, Jolly C, Sycza L, Ko M, PCAWG Evolution and Heterogeneity Working Group, SMC-Het Participants, Wedge DC, Morris QD, Ellrott K, Van Loo P, Boutros PC. Crowd-sourced benchmarking of single-sample tumor subclonal reconstruction. Nat Biotechnol. 2024 Jun 11. view on PubMed

Nguyen HTL, Kohl E, Bade J, Eng SE, Tosevska A, Al Shihabi A, Tebon PJ, Hong JJ, Dry S, Boutros PC, Panossian A, Gosline SJC, Soragni A. A platform for rapid patient-derived cutaneous neurofibroma organoid establishment and screening. Cell Rep Methods. 2024 May 20; 4(5):100772. view on PubMed

Ha A, Khoo A, Ignatchenko V, Khan S, Waas M, Vesprini D, Liu SK, Nyalwidhe JO, Semmes OJ, Boutros PC, Kislinger T. Comprehensive Prostate Fluid-Based Spectral Libraries for Enhanced Protein Detection in Urine. J Proteome Res. 2024 May 03; 23(5):1768-1778. view on PubMed

Woodcock DJ, Sahli A, Teslo R, Bhandari V, Gruber AJ, Ziubroniewicz A, Gundem G, Xu Y, Butler A, Anokian E, Pope BJ, Jung CH, Tarabichi M, Dentro SC, Farmery JHR, CRUK ICGC Prostate Group, Van Loo P, Warren AY, Gnanapragasam V, Hamdy FC, Bova GS, Foster CS, Neal DE, Lu YJ, Kote-Jarai Z, Fraser M, Bristow RG, Boutros PC, Costello AJ, Corcoran NM, Hovens CM, Massie CE, Lynch AG, Brewer DS, Eeles RA, Cooper CS, Wedge DC. Genomic evolution shapes prostate cancer disease type. Cell Genom. 2024 Mar 13; 4(3):100511. view on PubMed

Zeng PYF, Prokopec SD, Lai SY, Pinto N, Chan-Seng-Yue MA, Clifton-Bligh R, Williams MD, Howlett CJ, Plantinga P, Cecchini MJ, Lam AK, Siddiqui I, Wang J, Sun RX, Watson JD, Korah R, Carling T, Agrawal N, Cipriani N, Ball D, Nelkin B, Rooper LM, Bishop JA, Garnis C, Berean K, Nicolson NG, Weinberger P, Henderson YC, Lalansingh CM, Tian M, Yamaguchi TN, Livingstone J, Salcedo A, Patel K, Vizeacoumar F, Datti A, Xi L, Nikiforov YE, Smallridge R, Copland JA, Marlow LA, Hyrcza MD, Delbridge L, Sidhu S, Sywak M, Robinson B, Fung K, Ghasemi F, Kwan K, MacNeil SD, Mendez A, Palma DA, Khan MI, Shaikh M, Ruicci KM, Wehrli B, Winquist E, Yoo J, Mymryk JS, Rocco JW, Wheeler D, Scherer S, Giordano TJ, Barrett JW, Faquin WC, Gill AJ, Clayman G, Boutros PC, Nichols AC. The genomic and evolutionary landscapes of anaplastic thyroid carcinoma. Cell Rep. 2024 Mar 26; 43(3):113826. view on PubMed

Steinberg PL, Liu LY, Neiman-Golden A, Patel Y, Boutros PC. Quantifying the seed sensitivity of cancer subclonal reconstruction algorithms. bioRxiv. 2024 Feb 08. view on PubMed

Lin I, Wei A, Gebo TA, Boutros PC, Flanagan M, Kucine N, Cunniff C, Arboleda VA, Chang VY. Increased Frequency of Clonal Hematopoiesis of Indeterminate Potential in Bloom Syndrome Probands and Carriers. medRxiv. 2024 Feb 06. view on PubMed

Patel Y, Zhu C, Yamaguchi TN, Bugh YZ, Tian M, Holmes A, Fitz-Gibbon ST, Boutros PC. NFTest: automated testing of Nextflow pipelines. Bioinformatics. 2024 02 01; 40(2). view on PubMed

Patel Y, Beshlikyan A, Jordan M, Kim G, Holmes A, Yamaguchi TN, Boutros PC. PipeVal: light-weight extensible tool for file validation. Bioinformatics. 2024 02 01; 40(2). view on PubMed

Weiner AB, Agrawal R, Valle LF, Sonni I, Kishan AU, Rettig MB, Raman SS, Calais J, Boutros PC, Reiter RE. Impact of PSMA PET on Prostate Cancer Management. Curr Treat Options Oncol. 2024 02; 25(2):191-205. view on PubMed

Mathur R, Wang Q, Schupp PG, Nikolic A, Hilz S, Hong C, Grishanina NR, Kwok D, Stevers NO, Jin Q, Youngblood MW, Stasiak LA, Hou Y, Wang J, Yamaguchi TN, Lafontaine M, Shai A, Smirnov IV, Solomon DA, Chang SM, Hervey-Jumper SL, Berger MS, Lupo JM, Okada H, Phillips JJ, Boutros PC, Gallo M, Oldham MC, Yue F, Costello JF. Glioblastoma evolution and heterogeneity from a 3D whole-tumor perspective. Cell. 2024 01 18; 187(2):446-463.e16. view on PubMed

Lavery JA, Boutros PC, Knight D, Tammela T, Moskowitz CS, Jones LW. Association of exercise with pan-cancer incidence and overall survival. Cancer Cell. 2024 02 12; 42(2):169-171. view on PubMed

Nikitas J, Ong WL, Carrier N, Romero T, Millar J, Steinberg ML, Rettig MB, Boutros PC, Reiter R, Nickols NG, Valle L, McGuire SE, Spratt DE, Souhami L, Roy S, Martin JM, Joseph D, Nabid A, Kishan AU. Prostate-Specific Antigen Response to Androgen Deprivation Therapy in the Neoadjuvant Setting for High-Risk Prostate Adenocarcinoma (PIRANHA): Pooled Analysis of Two Randomized Clinical Trials. Int J Radiat Oncol Biol Phys. 2024 Jul 01; 119(3):826-831. view on PubMed

Kim HAJ, Zeng PYF, Cecchini M, Shaikh MH, Laxague F, Deng X, Jarycki L, Ryan SEB, Dawson A, Liu MH, Palma DA, Patel K, Mundi N, Barrett JW, Mymryk JS, Boutros PC, Nichols AC. HPV-negative head and neck cancers with adverse pathological features carry specific molecular changes that are associated with survival. Head Neck. 2024 02; 46(2):353-366. view on PubMed

Giafaglione JM, Crowell PD, Delcourt AML, Hashimoto T, Ha SM, Atmakuri A, Nunley NM, Dang RMA, Tian M, Diaz JA, Tika E, Payne MC, Burkhart DL, Li D, Navone NM, Corey E, Nelson PS, Lin NYC, Blanpain C, Ellis L, Boutros PC, Goldstein AS. Prostate lineage-specific metabolism governs luminal differentiation and response to antiandrogen treatment. Nat Cell Biol. 2023 Dec; 25(12):1821-1832. view on PubMed

Crowell PD, Giafaglione JM, Jones AE, Nunley NM, Hashimoto T, Delcourt AML, Petcherski A, Agrawal R, Bernard MJ, Diaz JA, Heering KY, Huang RR, Low JY, Matulionis N, Navone NM, Ye H, Zoubeidi A, Christofk HR, Rettig MB, Reiter RE, Haffner MC, Boutros PC, Shirihai OS, Divakaruni AS, Goldstein AS. MYC is a regulator of androgen receptor inhibition-induced metabolic requirements in prostate cancer. Cell Rep. 2023 10 31; 42(10):113221. view on PubMed

Shaikh MH, Dawson A, Prokopec SD, Barrett JW, Y F Zeng P, Khan MI, Ryan SEB, Cecchini M, Palma DA, Mymryk JS, Boutros PC, Nichols AC. Loss of LRP1B expression drives acquired chemo and radio-resistance in HPV-positive head and neck cancer. Oral Oncol. 2023 11; 146:106580. view on PubMed

Lavery JA, Boutros PC, Scott JM, Tammela T, Moskowitz CS, Jones LW. Pan-Cancer Analysis of Postdiagnosis Exercise and Mortality. J Clin Oncol. 2023 Nov 10; 41(32):4982-4992. view on PubMed

Al Shihabi A, Tebon PJ, Nguyen HTL, Chantharasamee J, Sartini S, Davarifar A, Jensen AY, Diaz-Infante M, Cox H, Gonzalez AE, Swearingen S, Tavanaie N, Dry S, Singh A, Chmielowski B, Crompton JG, Kalbasi A, Eilber FC, Hornicek F, Bernthal N, Nelson SD, Boutros PC, Federman N, Yanagawa J, Soragni A. The landscape of drug sensitivity and resistance in sarcoma. bioRxiv. 2023 Aug 08. view on PubMed

Khoo A, Govindarajan M, Qiu Z, Liu LY, Ignatchenko V, Waas M, Macklin A, Keszei A, Main BP, Yang L, Lance RS, Downes MR, Semmes OJ, Vesprini D, Liu SK, Nyalwidhe JO, Boutros PC, Kislinger T. Prostate Cancer Reshapes the Secreted and Extracellular Vesicle Urinary Proteomes. bioRxiv. 2023 Jul 25. view on PubMed

Wang JZ, Patil V, Liu J, Dogan H, Tabatabai G, Yefet LS, Behling F, Hoffman E, Bunda S, Yakubov R, Kaloti R, Brandner S, Gao A, Cohen-Gadol A, Barnholtz-Sloan J, Skardelly M, Tatagiba M, Raleigh DR, Sahm F, Boutros PC, Aldape K, International Consortium on Meningiomas (ICOM), Nassiri F, Zadeh G. Correction: Increased mRNA expression of CDKN2A is a transcriptomic marker of clinically aggressive meningiomas. Acta Neuropathol. 2023 Jul; 146(1):171-172. view on PubMed

Tebon PJ, Wang B, Markowitz AL, Davarifar A, Tsai BL, Krawczuk P, Gonzalez AE, Sartini S, Murray GF, Nguyen HTL, Tavanaie N, Nguyen TL, Boutros PC, Teitell MA, Soragni A. Drug screening at single-organoid resolution via bioprinting and interferometry. Nat Commun. 2023 06 06; 14(1):3168. view on PubMed

Afiaz A, Ivanov AA, Chamberlin J, Hanauer D, Savonen CL, Goldman MJ, Morgan M, Reich M, Getka A, Holmes A, Pati S, Knight D, Boutros PC, Bakas S, Caporaso JG, Del Fiol G, Hochheiser H, Haas B, Schloss PD, Eddy JA, Albrecht J, Fedorov A, Waldron L, Hoffman AM, Bradshaw RL, Leek JT, Wright C. Evaluation of software impact designed for biomedical research: Are we measuring what's meaningful? ArXiv. 2023 Jun 05. view on PubMed

Gamallat Y, Choudhry M, Li Q, Rokne JG, Alhajj R, Abdelsalam R, Ghosh S, Arbet J, Boutros PC, Bismar TA. Serrate RNA Effector Molecule (SRRT) Is Associated with Prostate Cancer Progression and Is a Predictor of Poor Prognosis in Lethal Prostate Cancer. Cancers (Basel). 2023 May 22; 15(10). view on PubMed

Berman DM, Lee AY, Lesurf R, Patel PG, Ebrahimizadeh W, Bayani J, Lee LA, Boufaied N, Selvarajah S, Jamaspishvili T, Guérard KP, Dion D, Kawashima A, Clarke GM, How N, Jackson CL, Scarlata E, Siddiqui K, Okello JBA, Aprikian AG, Moussa M, Finelli A, Chin J, Brimo F, Bauman G, Loblaw A, Venkateswaran V, Buttyan R, Chevalier S, Thomson A, Park PC, Siemens DR, Lapointe J, Boutros PC, Bartlett JMS. Multimodal Biomarkers That Predict the Presence of Gleason Pattern 4: Potential Impact for Active Surveillance. J Urol. 2023 08; 210(2):257-271. view on PubMed

Wang JZ, Patil V, Liu J, Dogan H, Tabatabai G, Yefet LS, Behling F, Hoffman E, Bunda S, Yakubov R, Kaloti R, Brandner S, Gao A, Cohen-Gadol A, Barnholtz-Sloan J, Skardelly M, Tatagiba M, Raleigh DR, Sahm F, Boutros PC, Aldape K, International Consortium on Meningiomas (ICOM), Nassiri F, Zadeh G. Increased mRNA expression of CDKN2A is a transcriptomic marker of clinically aggressive meningiomas. Acta Neuropathol. 2023 07; 146(1):145-162. view on PubMed

Houlahan KE, Livingstone J, Fox NS, Kurganovs N, Zhu H, Sietsma Penington J, Jung CH, Yamaguchi TN, Heisler LE, Jovelin R, Costello AJ, Pope BJ, Kishan AU, Corcoran NM, Bristow RG, Waszak SM, Weischenfeldt J, He HH, Hung RJ, Hovens CM, Boutros PC. A polygenic two-hit hypothesis for prostate cancer. J Natl Cancer Inst. 2023 04 11; 115(4):468-472. view on PubMed

Smith CP, Proudfoot JA, Boutros PC, Reiter RE, Valle L, Rettig MB, Nickols NG, Feng FY, Nguyen PL, Nagar H, Spratt DE, Attard G, Weiner A, Weidhaas JB, Calais J, Ma TM, Davicioni E, Xiang M, Kishan AU. Transcriptomic Heterogeneity in High-risk Prostate Cancer and Implications for Extraprostatic Disease at Presentation on Prostate-specific Membrane Antigen Positron Emission Tomography. Eur Urol Oncol. 2023 04; 6(2):224-227. view on PubMed

Zavoshi S, Lu E, Boutros PC, Zhang L, Harari A, Hatchell KE, Nielsen SM, Esplin ED, Ouyang K, Nykamp K, Wilde B, Christofk H, Shuch B. Fumarate Hydratase Variants and Their Association With Paraganglioma/Pheochromocytoma. Urology. 2023 06; 176:106-114. view on PubMed

Chan TW, Dodson JP, Arbet J, Boutros PC, Xiao X. Single-Cell Analysis in Lung Adenocarcinoma Implicates RNA Editing in Cancer Innate Immunity and Patient Prognosis. Cancer Res. 2023 02 03; 83(3):374-385. view on PubMed

Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vázquez-García I, Haase K, Jerman L, Sengupta S, Macintyre G, Malikic S, Donmez N, Livitz DG, Cmero M, Demeulemeester J, Schumacher S, Fan Y, Yao X, Lee J, Schlesner M, Boutros PC, Bowtell DD, Zhu H, Getz G, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Markowetz F, Mustonen V, Yuan K, Wang W, Morris QD, PCAWG Evolution & Heterogeneity Working Group, Spellman PT, Wedge DC, Van Loo P, PCAWG Consortium. Author Correction: The evolutionary history of 2,658 cancers. Nature. 2023 Feb; 614(7948):E42. view on PubMed

Dreval K, Boutros PC, Morin RD. Minimal information for reporting a genomics experiment. Blood. 2022 12 15; 140(24):2549-2555. view on PubMed

Bhandari V, Li CH, Bristow RG, Boutros PC, PCAWG Consortium. Author Correction: Divergent mutational processes distinguish hypoxic and normoxic tumours. Nat Commun. 2022 Dec 08; 13(1):7569. view on PubMed

Paczkowska M, Barenboim J, Sintupisut N, Fox NS, Zhu H, Abd-Rabbo D, Mee MW, Boutros PC, PCAWG Drivers and Functional Interpretation Working Group, Reimand J, PCAWG Consortium. Author Correction: Integrative pathway enrichment analysis of multivariate omics data. Nat Commun. 2022 Dec 08; 13(1):7570. view on PubMed

Yuan J, Houlahan KE, Ramanand SG, Lee S, Baek G, Yang Y, Chen Y, Strand DW, Zhang MQ, Boutros PC, Mani RS. Prostate Cancer Transcriptomic Regulation by the Interplay of Germline Risk Alleles, Somatic Mutations, and 3D Genomic Architecture. Cancer Discov. 2022 12 02; 12(12):2838-2855. view on PubMed

Zeng PYF, Cecchini MJ, Barrett JW, Shammas-Toma M, De Cecco L, Serafini MS, Cavalieri S, Licitra L, Hoebers F, Brakenhoff RH, Leemans CR, Scheckenbach K, Poli T, Wang X, Liu X, Laxague F, Prisman E, Poh C, Bose P, Dort JC, Shaikh MH, Ryan SEB, Dawson A, Khan MI, Howlett CJ, Stecho W, Plantinga P, Daniela da Silva S, Hier M, Khan H, MacNeil D, Mendez A, Yoo J, Fung K, Lang P, Winquist E, Palma DA, Ziai H, Amelio AL, Li SS, Boutros PC, Mymryk JS, Nichols AC. Immune-based classification of HPV-associated oropharyngeal cancer with implications for biomarker-driven treatment de-intensification. EBioMedicine. 2022 Dec; 86:104373. view on PubMed

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Tatari N, Khan S, Livingstone J, Zhai K, Mckenna D, Ignatchenko V, Chokshi C, Gwynne WD, Singh M, Revill S, Mikolajewicz N, Zhu C, Chan J, Hawkins C, Lu JQ, Provias JP, Ask K, Morrissy S, Brown S, Weiss T, Weller M, Han H, Greenspoon JN, Moffat J, Venugopal C, Boutros PC, Singh SK, Kislinger T. The proteomic landscape of glioblastoma recurrence reveals novel and targetable immunoregulatory drivers. Acta Neuropathol. 2022 12; 144(6):1127-1142. view on PubMed

Patel SA, Ma TM, Wong JK, Stish BJ, Dess RT, Pilar A, Reddy C, Wedde TB, Lilleby WA, Fiano R, Merrick GS, Stock RG, Demanes DJ, Moran BJ, Tran PT, Krauss DJ, Abu-Isa EI, Pisansky TM, Choo CR, Song DY, Greco S, Deville C, DeWeese TL, Tilki D, Ciezki JP, Karnes RJ, Nickols NG, Rettig MB, Feng FY, Berlin A, Tward JD, Davis BJ, Reiter RE, Boutros PC, Romero T, Horwitz EM, Tendulkar RD, Steinberg ML, Spratt DE, Xiang M, Kishan AU. External Beam Radiation Therapy With or Without Brachytherapy Boost in Men With Very-High-Risk Prostate Cancer: A Large Multicenter International Consortium Analysis. Int J Radiat Oncol Biol Phys. 2023 03 01; 115(3):645-653. view on PubMed

Jung CH, Boutros PC, Park DJ, Corcoran NM, Pope BJ, Hovens CM. Perish and publish: Dynamics of biomedical publications by deceased authors. PLoS One. 2022; 17(9):e0273783. view on PubMed

Ueno D, Vasquez JC, Sule A, Liang J, van Doorn J, Sundaram R, Friedman S, Caliliw R, Ohtake S, Bao X, Li J, Ye H, Boyd K, Huang RR, Dodson J, Boutros P, Bindra RS, Shuch B. Targeting Krebs-cycle-deficient renal cell carcinoma with Poly ADP-ribose polymerase inhibitors and low-dose alkylating chemotherapy. Oncotarget. 2022; 13:1054-1067. view on PubMed

Eng SE, Basasie B, Lam A, John Semmes O, Troyer DA, Clarke GD, Sunnapwar AG, Leach RJ, Johnson-Pais TL, Sokoll LJ, Chan DW, Tosoian JJ, Siddiqui J, Chinnaiyan AM, Thompson IM, Boutros PC, Liss MA. Prospective comparison of restriction spectrum imaging and non-invasive biomarkers to predict upgrading on active surveillance prostate biopsy. Prostate Cancer Prostatic Dis. 2024 Mar; 27(1):65-72. view on PubMed

Marenghi C, Qiu Z, Helleman J, Nieboer D, Rubio-Briones J, Carroll PR, Lee LS, Valdagni R, Boutros PC, Nicolai N, Movember Foundation’s Global Action Plan Prostate Cancer Active Surveillance (GAP3) Consortium. Adverse Pathological Findings at Radical Prostatectomy following Active Surveillance: Results from the Movember GAP3 Cohort. Cancers (Basel). 2022 07 22; 14(15). view on PubMed

Wang X, Jordahl KM, Zhu C, Livingstone J, Rhie SK, Wright JL, Grady WM, Boutros PC, Stanford JL, Dai JY. Methylation Subtypes of Primary Prostate Cancer Predict Poor Prognosis. Cancer Epidemiol Biomarkers Prev. 2022 07 01; 31(7):1473-1482. view on PubMed

Cao S, Wang JR, Ji S, Yang P, Dai Y, Guo S, Montierth MD, Shen JP, Zhao X, Chen J, Lee JJ, Guerrero PA, Spetsieris N, Engedal N, Taavitsainen S, Yu K, Livingstone J, Bhandari V, Hubert SM, Daw NC, Futreal PA, Efstathiou E, Lim B, Viale A, Zhang J, Nykter M, Czerniak BA, Brown PH, Swanton C, Msaouel P, Maitra A, Kopetz S, Campbell P, Speed TP, Boutros PC, Zhu H, Urbanucci A, Demeulemeester J, Van Loo P, Wang W. Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression. Nat Biotechnol. 2022 11; 40(11):1624-1633. view on PubMed

Bliss JW, Lavery JA, Underwood WP, Chun SS, Fickera GA, Lee CP, Corcoran S, Maloy MA, Polubriaginof FC, Kelly DW, Scott JM, Boutros PC, Moskowitz CS, Jones LW. Impact of Exercise on Susceptibility and Severity of COVID-19 in Patients with Cancer: A Retrospective Study. Cancer Epidemiol Biomarkers Prev. 2022 05 04; 31(5):1036-1042. view on PubMed

Khoo A, Liu LY, Sadun TY, Salmasi A, Pooli A, Felker E, Houlahan KE, Ignatchenko V, Raman SS, Sisk AE, Reiter RE, Boutros PC, Kislinger T. Prostate cancer multiparametric magnetic resonance imaging visibility is a tumor-intrinsic phenomena. J Hematol Oncol. 2022 05 03; 15(1):48. view on PubMed

Wedge ME, Jennings VA, Crupi MJF, Poutou J, Jamieson T, Pelin A, Pugliese G, de Souza CT, Petryk J, Laight BJ, Boileau M, Taha Z, Alluqmani N, McKay HE, Pikor L, Khan ST, Azad T, Rezaei R, Austin B, He X, Mansfield D, Rose E, Brown EEF, Crawford N, Alkayyal A, Surendran A, Singaravelu R, Roy DG, Migneco G, McSweeney B, Cottee ML, Jacobus EJ, Keller BA, Yamaguchi TN, Boutros PC, Geoffrion M, Rayner KJ, Chatterjee A, Auer RC, Diallo JS, Gibbings D, tenOever BR, Melcher A, Bell JC, Ilkow CS. Virally programmed extracellular vesicles sensitize cancer cells to oncolytic virus and small molecule therapy. Nat Commun. 2022 04 07; 13(1):1898. view on PubMed

Patel KB, Prokopec S, Barrett JW, Mymryk JS, Boutros PC, Nichols AC. Establishment of four head and neck squamous cell carcinoma cell lines: importance of reference DNA for accurate genomic characterisation. J Laryngol Otol. 2023 Mar; 137(3):301-307. view on PubMed

Latorre P, Böttcher R, Nadal-Ribelles M, Li CH, Solé C, Martínez-Cebrián G, Boutros PC, Posas F, de Nadal E. Data-driven identification of inherent features of eukaryotic stress-responsive genes. NAR Genom Bioinform. 2022 Mar; 4(1):lqac018. view on PubMed

Muñoz-Grajales C, Prokopec SD, Johnson SR, Touma Z, Ahmad Z, Bonilla D, Hiraki L, Bookman A, Boutros PC, Chruscinski A, Wither J. Serological abnormalities that predict progression to systemic autoimmune rheumatic diseases in antinuclear antibody-positive individuals. Rheumatology (Oxford). 2022 03 02; 61(3):1092-1105. view on PubMed

Kishan AU, Steigler A, Denham JW, Zapatero A, Guerrero A, Joseph D, Maldonado X, Wong JK, Stish BJ, Dess RT, Pilar A, Reddy C, Wedde TB, Lilleby WA, Fiano R, Merrick GS, Stock RG, Demanes DJ, Moran BJ, Tran PT, Martin S, Martinez-Monge R, Krauss DJ, Abu-Isa EI, Pisansky TM, Choo CR, Song DY, Greco S, Deville C, McNutt T, DeWeese TL, Ross AE, Ciezki JP, Tilki D, Karnes RJ, Tosoian JJ, Nickols NG, Bhat P, Shabsovich D, Juarez JE, Jiang T, Ma TM, Xiang M, Philipson R, Chang A, Kupelian PA, Rettig MB, Feng FY, Berlin A, Tward JD, Davis BJ, Reiter RE, Steinberg ML, Elashoff D, Boutros PC, Horwitz EM, Tendulkar RD, Spratt DE, Romero T. Interplay Between Duration of Androgen Deprivation Therapy and External Beam Radiotherapy With or Without a Brachytherapy Boost for Optimal Treatment of High-risk Prostate Cancer: A Patient-Level Data Analysis of 3 Cohorts. JAMA Oncol. 2022 Mar 01; 8(3):e216871. view on PubMed

Pinto N, Ruicci KM, Khan MI, Shaikh MH, Zeng YFP, Yoo J, Fung K, MacNeil SD, Mendez A, Mymryk JS, Barrett JW, Boutros PC, Nichols AC. Introduction and expression of PIK3CAE545K in a papillary thyroid cancer BRAFV600E cell line leads to a dedifferentiated aggressive phenotype. J Otolaryngol Head Neck Surg. 2022 Feb 22; 51(1):7. view on PubMed

Kim HAJ, Zeng PYF, Sorgini A, Shaikh MH, Khan H, MacNeil D, Khan MI, Mendez A, Yoo J, Fung K, Lang P, Palma DA, Mymryk JS, Barrett JW, Patel KB, Boutros PC, Nichols AC. Tumor molecular differences associated with outcome disparities of Black patients with head and neck cancer. Head Neck. 2022 05; 44(5):1124-1135. view on PubMed

Correll VL, Otto JJ, Risi CM, Main BP, Boutros PC, Kislinger T, Galkin VE, Nyalwidhe JO, Semmes OJ, Yang L. Optimization of small extracellular vesicle isolation from expressed prostatic secretions in urine for in-depth proteomic analysis. J Extracell Vesicles. 2022 02; 11(2):e12184. view on PubMed

Li CH, Haider S, Boutros PC. Age influences on the molecular presentation of tumours. Nat Commun. 2022 01 11; 13(1):208. view on PubMed

Nesterenko PA, McLaughlin J, Tsai BL, Burton Sojo G, Cheng D, Zhao D, Mao Z, Bangayan NJ, Obusan MB, Su Y, Ng RH, Chour W, Xie J, Li YR, Lee D, Noguchi M, Carmona C, Phillips JW, Kim JT, Yang L, Heath JR, Boutros PC, Witte ON. HLA-A∗02:01 restricted T cell receptors against the highly conserved SARS-CoV-2 polymerase cross-react with human coronaviruses. Cell Rep. 2021 12 28; 37(13):110167. view on PubMed

Ma TM, Romero T, Nickols NG, Rettig MB, Garraway IP, Roach M, Michalski JM, Pisansky TM, Lee WR, Jones CU, Rosenthal SA, Wang C, Hartman H, Nguyen PL, Feng FY, Boutros PC, Saigal C, Chamie K, Jackson WC, Morgan TM, Mehra R, Salami SS, Vince R, Schaeffer EM, Mahal BA, Dess RT, Steinberg ML, Elashoff D, Sandler HM, Spratt DE, Kishan AU. Comparison of Response to Definitive Radiotherapy for Localized Prostate Cancer in Black and White Men: A Meta-analysis. JAMA Netw Open. 2021 12 01; 4(12):e2139769. view on PubMed

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Jain A, Huang R, Lee J, Jawa N, Lim YJ, Guron M, Abish S, Boutros PC, Brudno M, Carleton B, Cuvelier GDE, Gunaratnam L, Ho C, Adeli K, Kuruvilla S, Lajoie G, Liu G, Nathan PC, Rod Rassekh S, Rieder M, Waikar SS, Welch SA, Weir MA, Winquist E, Wishart DS, Zorzi AP, Blydt-Hansen T, Zappitelli M, Urquhart B. A Canadian Study of Cisplatin Metabolomics and Nephrotoxicity (ACCENT): A Clinical Research Protocol. Can J Kidney Health Dis. 2021; 8:20543581211057708. view on PubMed

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Lu E, Hatchell KE, Nielsen SM, Esplin ED, Ouyang K, Nykamp K, Zavoshi S, Li S, Zhang L, Wilde BR, Christofk HR, Boutros PC, Shuch B. Fumarate hydratase variant prevalence and manifestations among individuals receiving germline testing. Cancer. 2022 02 15; 128(4):675-684. view on PubMed

Zhu C, Boutros PC. Sex Differences in Cancer Genomes: Much Learned, More Unknown. Endocrinology. 2021 11 01; 162(11). view on PubMed

Fraser M, Livingstone J, Wrana JL, Finelli A, He HH, van der Kwast T, Zlotta AR, Bristow RG, Boutros PC. Somatic driver mutation prevalence in 1844 prostate cancers identifies ZNRF3 loss as a predictor of metastatic relapse. Nat Commun. 2021 10 29; 12(1):6248. view on PubMed

Kim HAJ, Shaikh MH, Lee M, Zeng PYF, Sorgini A, Akintola T, Deng X, Jarycki L, Khan H, MacNeil D, Khan MI, Mendez A, Yoo J, Fung K, Lang P, Palma DA, Patel K, Mymryk JS, Barrett JW, Boutros PC, Morris LGT, Nichols AC. 3p Arm Loss and Survival in Head and Neck Cancer: An Analysis of TCGA Dataset. Cancers (Basel). 2021 Oct 22; 13(21). view on PubMed

Hawley JR, Zhou S, Arlidge C, Grillo G, Kron KJ, Hugh-White R, van der Kwast TH, Fraser M, Boutros PC, Bristow RG, Lupien M. Reorganization of the 3D Genome Pinpoints Noncoding Drivers of Primary Prostate Tumors. Cancer Res. 2021 12 01; 81(23):5833-5848. view on PubMed

Khoo A, Liu LY, Nyalwidhe JO, Semmes OJ, Vesprini D, Downes MR, Boutros PC, Liu SK, Kislinger T. Proteomic discovery of non-invasive biomarkers of localized prostate cancer using mass spectrometry. Nat Rev Urol. 2021 12; 18(12):707-724. view on PubMed

Nassiri F, Liu J, Patil V, Mamatjan Y, Wang JZ, Hugh-White R, Macklin AM, Khan S, Singh O, Karimi S, Corona RI, Liu LY, Chen CY, Chakravarthy A, Wei Q, Mehani B, Suppiah S, Gao A, Workewych AM, Tabatabai G, Boutros PC, Bader GD, de Carvalho DD, Kislinger T, Aldape K, Zadeh G. A clinically applicable integrative molecular classification of meningiomas. Nature. 2021 09; 597(7874):119-125. view on PubMed

Pollan SG, Teng PC, Jan YJ, Livingstone J, Huang C, Kim M, Mariscal J, Rodriguez M, Chen JF, You S, DiVizio D, Boutros PC, Chan KS, Rasorenova O, Cress A, Spassov D, Moasser M, Posadas EM, Freedland SJ, Freeman MR, Zheng JJ, Knudsen BS. Loss of CDCP1 triggers FAK activation in detached prostate cancer cells. Am J Clin Exp Urol. 2021; 9(4):350-366. view on PubMed

Bartlett JMS, Bayani J, Kornaga E, Xu K, Pond GR, Piper T, Mallon E, Yao CQ, Boutros PC, Hasenburg A, Dunn JA, Markopoulos C, Dirix L, Seynaeve C, van de Velde CJH, Stein RC, Rea D. Comparative survival analysis of multiparametric tests-when molecular tests disagree-A TEAM Pathology study. NPJ Breast Cancer. 2021 Jul 08; 7(1):90. view on PubMed

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Kurganovs N, Wang H, Huang X, Ignatchenko V, Macklin A, Khan S, Downes MR, Boutros PC, Liu SK, Kislinger T. A proteomic investigation of isogenic radiation resistant prostate cancer cell lines. Proteomics Clin Appl. 2021 Sep; 15(5):e2100037. view on PubMed

Creason A, Haan D, Dang K, Chiotti KE, Inkman M, Lamb A, Yu T, Hu Y, Norman TC, Buchanan A, van Baren MJ, Spangler R, Rollins MR, Spellman PT, Rozanov D, Zhang J, Maher CA, Caloian C, Watson JD, Uhrig S, Haas BJ, Jain M, Akeson M, Ahsen ME, SMC-RNA Challenge Participants, Stolovitzky G, Guinney J, Boutros PC, Stuart JM, Ellrott K. A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery. Cell Syst. 2021 08 18; 12(8):827-838.e5. view on PubMed

Walker SR, Abdelsalam R, Ghosh S, Livingstone J, Palanisamy N, Boutros PC, Yip SM, Lees-Miller SP, Bismar TA. Decreased ATM Protein Expression Is Substantiated with PTEN Loss in Defining Aggressive Phenotype of Prostate Cancer Associated with Lethal Disease. Eur Urol Open Sci. 2021 Jul; 29:93-101. view on PubMed

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Freeland J, Crowell PD, Giafaglione JM, Boutros PC, Goldstein AS. Aging of the progenitor cells that initiate prostate cancer. Cancer Lett. 2021 09 01; 515:28-35. view on PubMed

Albawardi A, Livingstone J, Almarzooqi S, Palanisamy N, Houlahan KE, Awwad AAA, Abdelsalam RA, Boutros PC, Bismar TA. Copy Number Profiles of Prostate Cancer in Men of Middle Eastern Ancestry. Cancers (Basel). 2021 May 14; 13(10). view on PubMed

Philipson RG, Romero T, Wong JK, Stish BJ, Dess RT, Spratt DE, Pilar A, Reddy C, Wedde TB, Lilleby WA, Fiano R, Merrick GS, Stock RG, Demanes DJ, Moran BJ, Braccioforte M, Tran PT, Martin S, Martinez-Monge R, Krauss DJ, Abu-Isa EI, Valle L, Chong N, Pisansky TM, Choo CR, Song DY, Greco S, Deville C, McNutt T, DeWeese TL, Ross AE, Ciezki JP, Tilki D, Karnes RJ, Klein EA, Tosoian JJ, Boutros PC, Nickols NG, Bhat P, Shabsovich D, Juarez JE, Kupelian PA, Rettig MB, Berlin A, Tward JD, Davis BJ, Reiter RE, Steinberg ML, Elashoff D, Horwitz EM, Tendulkar RD, Kishan AU. Patterns of Clinical Progression in Radiorecurrent High-risk Prostate Cancer. Eur Urol. 2021 08; 80(2):142-146. view on PubMed

Jain P, Dvorkin-Gheva A, Mollen E, Malbeteau L, Xie M, Jessa F, Dhavarasa P, Chung S, Brown KR, Jang GH, Vora P, Notta F, Moffat J, Hedley D, Boutros PC, Wouters BG, Koritzinsky M. NOX4 links metabolic regulation in pancreatic cancer to endoplasmic reticulum redox vulnerability and dependence on PRDX4. Sci Adv. 2021 05; 7(19). view on PubMed

Dentro SC, Leshchiner I, Haase K, Tarabichi M, Wintersinger J, Deshwar AG, Yu K, Rubanova Y, Macintyre G, Demeulemeester J, Vázquez-García I, Kleinheinz K, Livitz DG, Malikic S, Donmez N, Sengupta S, Anur P, Jolly C, Cmero M, Rosebrock D, Schumacher SE, Fan Y, Fittall M, Drews RM, Yao X, Watkins TBK, Lee J, Schlesner M, Zhu H, Adams DJ, McGranahan N, Swanton C, Getz G, Boutros PC, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Martincorena I, Markowetz F, Mustonen V, Yuan K, Gerstung M, Spellman PT, Wang W, Morris QD, Wedge DC, Van Loo P, PCAWG Evolution and Heterogeneity Working Group and the PCAWG Consortium. Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes. Cell. 2021 04 15; 184(8):2239-2254.e39. view on PubMed

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Degeling K, Pereira-Salgado A, Corcoran NM, Boutros PC, Kuhn P, IJzerman MJ. Health Economic Evidence for Liquid- and Tissue-based Molecular Tests that Inform Decisions on Prostate Biopsies and Treatment of Localised Prostate Cancer: A Systematic Review. Eur Urol Open Sci. 2021 May; 27:77-87. view on PubMed

Ahmed M, Soares F, Xia JH, Yang Y, Li J, Guo H, Su P, Tian Y, Lee HJ, Wang M, Akhtar N, Houlahan KE, Bosch A, Zhou S, Mazrooei P, Hua JT, Chen S, Petricca J, Zeng Y, Davies A, Fraser M, Quigley DA, Feng FY, Boutros PC, Lupien M, Zoubeidi A, Wang L, Walsh MJ, Wang T, Ren S, Wei GH, He HH. CRISPRi screens reveal a DNA methylation-mediated 3D genome dependent causal mechanism in prostate cancer. Nat Commun. 2021 03 19; 12(1):1781. view on PubMed

Kim HAJ, Zeng PYF, Shaikh MH, Mundi N, Ghasemi F, Di Gravio E, Khan H, MacNeil D, Khan MI, Patel K, Mendez A, Yoo J, Fung K, Lang P, Palma DA, Mymryk JS, Barrett JW, Boutros PC, Nichols AC. All HPV-negative head and neck cancers are not the same: Analysis of the TCGA dataset reveals that anatomical sites have distinct mutation, transcriptome, hypoxia, and tumor microenvironment profiles. Oral Oncol. 2021 05; 116:105260. view on PubMed

Chen S, Zhu G, Yang Y, Wang F, Xiao YT, Zhang N, Bian X, Zhu Y, Yu Y, Liu F, Dong K, Mariscal J, Liu Y, Soares F, Loo Yau H, Zhang B, Chen W, Wang C, Chen D, Guo Q, Yi Z, Liu M, Fraser M, De Carvalho DD, Boutros PC, Di Vizio D, Jiang Z, van der Kwast T, Berlin A, Wu S, Wang J, He HH, Ren S. Single-cell analysis reveals transcriptomic remodellings in distinct cell types that contribute to human prostate cancer progression. Nat Cell Biol. 2021 01; 23(1):87-98. view on PubMed

Casanova-Salas I, Athie A, Boutros PC, Del Re M, Miyamoto DT, Pienta KJ, Posadas EM, Sowalsky AG, Stenzl A, Wyatt AW, Mateo J. Quantitative and Qualitative Analysis of Blood-based Liquid Biopsies to Inform Clinical Decision-making in Prostate Cancer. Eur Urol. 2021 06; 79(6):762-771. view on PubMed

Deek MP, Van der Eecken K, Phillips R, Parikh NR, Isaacsson Velho P, Lotan TL, Kishan AU, Maurer T, GAP6 Consortium, Boutros PC, Hovens C, Abramowtiz M, Pollack A, Desai N, Stish B, Feng FY, Eisenberger M, Carducci M, Pienta KJ, Markowski M, Paller CJ, Antonarakis ES, Berlin A, Ost P, Tran PT. The Mutational Landscape of Metastatic Castration-sensitive Prostate Cancer: The Spectrum Theory Revisited. Eur Urol. 2021 11; 80(5):632-640. view on PubMed

Tarabichi M, Salcedo A, Deshwar AG, Ni Leathlobhair M, Wintersinger J, Wedge DC, Van Loo P, Morris QD, Boutros PC. A practical guide to cancer subclonal reconstruction from DNA sequencing. Nat Methods. 2021 02; 18(2):144-155. view on PubMed

Sorgini A, Kim HAJ, Zeng PYF, Shaikh MH, Mundi N, Ghasemi F, Di Gravio E, Khan H, MacNeil D, Khan MI, Mendez A, Yoo J, Fung K, Lang P, Palma DA, Mymryk JS, Barrett JW, Patel KB, Boutros PC, Nichols AC. Analysis of the TCGA Dataset Reveals that Subsites of Laryngeal Squamous Cell Carcinoma are Molecularly Distinct. Cancers (Basel). 2020 Dec 31; 13(1). view on PubMed

Liu LY, Bhandari V, Salcedo A, Espiritu SMG, Morris QD, Kislinger T, Boutros PC. Quantifying the influence of mutation detection on tumour subclonal reconstruction. Nat Commun. 2020 12 07; 11(1):6247. view on PubMed

Vittrant B, Bergeron A, Molina OE, Leclercq M, Légaré XP, Hovington H, Picard V, Martin-Magniette ML, Livingstone J, Boutros PC, Collins C, Fradet Y, Droit A. Immune-focused multi-omics analysis of prostate cancer: leukocyte Ig-Like receptors are associated with disease progression. Oncoimmunology. 2020 12 01; 9(1):1851950. view on PubMed

Zook JM, Hansen NF, Olson ND, Chapman L, Mullikin JC, Xiao C, Sherry S, Koren S, Phillippy AM, Boutros PC, Sahraeian SME, Huang V, Rouette A, Alexander N, Mason CE, Hajirasouliha I, Ricketts C, Lee J, Tearle R, Fiddes IT, Barrio AM, Wala J, Carroll A, Ghaffari N, Rodriguez OL, Bashir A, Jackman S, Farrell JJ, Wenger AM, Alkan C, Soylev A, Schatz MC, Garg S, Church G, Marschall T, Chen K, Fan X, English AC, Rosenfeld JA, Zhou W, Mills RE, Sage JM, Davis JR, Kaiser MD, Oliver JS, Catalano AP, Chaisson MJP, Spies N, Sedlazeck FJ, Salit M. Author Correction: A robust benchmark for detection of germline large deletions and insertions. Nat Biotechnol. 2020 Nov; 38(11):1357. view on PubMed

Ruicci KM, Meens J, Plantinga P, Stecho W, Pinto N, Yoo J, Fung K, MacNeil D, Mymryk JS, Barrett JW, Howlett CJ, Boutros PC, Ailles L, Nichols AC. TAM family receptors in conjunction with MAPK signalling are involved in acquired resistance to PI3Kα inhibition in head and neck squamous cell carcinoma. J Exp Clin Cancer Res. 2020 Oct 15; 39(1):217. view on PubMed

Levin-Epstein RG, Jiang NY, Wang X, Upadhyaya SK, Collins SP, Suy S, Aghdam N, Mantz C, Katz AJ, Miszczyk L, Napieralska A, Namysl-Kaletka A, Prionas N, Bagshaw H, Buyyounouski MK, Cao M, Agazaryan N, Dang A, Yuan Y, Kupelian PA, Zaorsky NG, Spratt DE, Mohamad O, Feng FY, Mahal BA, Boutros PC, Kishan AU, Juarez J, Shabsovich D, Jiang T, Kahlon S, Patel A, Patel J, Nickols NG, Steinberg ML, Fuller DB, Kishan AU. Dose-response with stereotactic body radiotherapy for prostate cancer: A multi-institutional analysis of prostate-specific antigen kinetics and biochemical control. Radiother Oncol. 2021 01; 154:207-213. view on PubMed

Pinto N, Prokopec SD, Ghasemi F, Meens J, Ruicci KM, Khan IM, Mundi N, Patel K, Han MW, Yoo J, Fung K, MacNeil D, Mymryk JS, Datti A, Barrett JW, Boutros PC, Ailles L, Nichols AC. Flavopiridol causes cell cycle inhibition and demonstrates anti-cancer activity in anaplastic thyroid cancer models. PLoS One. 2020; 15(9):e0239315. view on PubMed

McGillivray PD, Ueno D, Pooli A, Mendhiratta N, Syed JS, Nguyen KA, Schulam PG, Humphrey PA, Adeniran AJ, Boutros PC, Shuch B. Distinguishing Benign Renal Tumors with an Oncocytic Gene Expression (ONEX) Classifier. Eur Urol. 2021 01; 79(1):107-111. view on PubMed

Haider S, Tyekucheva S, Prandi D, Fox NS, Ahn J, Xu AW, Pantazi A, Park PJ, Laird PW, Sander C, Wang W, Demichelis F, Loda M, Boutros PC, Cancer Genome Atlas Research Network. Systematic Assessment of Tumor Purity and Its Clinical Implications. JCO Precis Oncol. 2020; 4. view on PubMed

Bartlett JMS, Bayani J, Kornaga EN, Danaher P, Crozier C, Piper T, Yao CQ, Dunn JA, Boutros PC, Stein RC, OPTIMA Trial Management Group. Computational approaches to support comparative analysis of multiparametric tests: Modelling versus Training. PLoS One. 2020; 15(9):e0238593. view on PubMed

Li CH, Prokopec SD, Sun RX, Yousif F, Schmitz N, PCAWG Tumour Subtypes and Clinical Translation, Boutros PC, PCAWG Consortium. Sex differences in oncogenic mutational processes. Nat Commun. 2020 08 28; 11(1):4330. view on PubMed

Grosset AA, Dallaire F, Nguyen T, Birlea M, Wong J, Daoust F, Roy N, Kougioumoutzakis A, Azzi F, Aubertin K, Kadoury S, Latour M, Albadine R, Prendeville S, Boutros P, Fraser M, Bristow RG, van der Kwast T, Orain M, Brisson H, Benzerdjeb N, Hovington H, Bergeron A, Fradet Y, Têtu B, Saad F, Leblond F, Trudel D. Identification of intraductal carcinoma of the prostate on tissue specimens using Raman micro-spectroscopy: A diagnostic accuracy case-control study with multicohort validation. PLoS Med. 2020 08; 17(8):e1003281. view on PubMed

Ramanand SG, Chen Y, Yuan J, Daescu K, Lambros MB, Houlahan KE, Carreira S, Yuan W, Baek G, Sharp A, Paschalis A, Kanchwala M, Gao Y, Aslam A, Safdar N, Zhan X, Raj GV, Xing C, Boutros PC, de Bono J, Zhang MQ, Mani RS. The landscape of RNA polymerase II-associated chromatin interactions in prostate cancer. J Clin Invest. 2020 08 03; 130(8):3987-4005. view on PubMed

Yang M, Petralia F, Li Z, Li H, Ma W, Song X, Kim S, Lee H, Yu H, Lee B, Bae S, Heo E, Kaczmarczyk J, Stepniak P, Warchol M, Yu T, Calinawan AP, Boutros PC, Payne SH, Reva B, NCI-CPTAC-DREAM Consortium, Boja E, Rodriguez H, Stolovitzky G, Guan Y, Kang J, Wang P, Fenyö D, Saez-Rodriguez J. Community Assessment of the Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics. Cell Syst. 2020 08 26; 11(2):186-195.e9. view on PubMed

Zhao SG, Chen WS, Li H, Foye A, Zhang M, Sjöström M, Aggarwal R, Playdle D, Liao A, Alumkal JJ, Das R, Chou J, Hua JT, Barnard TJ, Bailey AM, Chow ED, Perry MD, Dang HX, Yang R, Moussavi-Baygi R, Zhang L, Alshalalfa M, Laura Chang S, Houlahan KE, Shiah YJ, Beer TM, Thomas G, Chi KN, Gleave M, Zoubeidi A, Reiter RE, Rettig MB, Witte O, Yvonne Kim M, Fong L, Spratt DE, Morgan TM, Bose R, Huang FW, Li H, Chesner L, Shenoy T, Goodarzi H, Asangani IA, Sandhu S, Lang JM, Mahajan NP, Lara PN, Evans CP, Febbo P, Batzoglou S, Knudsen KE, He HH, Huang J, Zwart W, Costello JF, Luo J, Tomlins SA, Wyatt AW, Dehm SM, Ashworth A, Gilbert LA, Boutros PC, Farh K, Chinnaiyan AM, Maher CA, Small EJ, Quigley DA, Feng FY. The DNA methylation landscape of advanced prostate cancer. Nat Genet. 2020 08; 52(8):778-789. view on PubMed

Otto JJ, Correll VL, Engstroem HA, Hitefield NL, Main BP, Albracht B, Johnson-Pais T, Yang LF, Liss M, Boutros PC, Kislinger T, Leach RJ, Semmes OJ, Nyalwidhe JO. Targeted Mass Spectrometry of a Clinically Relevant PSA Variant from Post-DRE Urines for Quantitation and Genotype Determination. Proteomics Clin Appl. 2020 11; 14(6):e2000012. view on PubMed

Brastianos HC, Murgic J, Salcedo A, Chua MLK, Meng A, Fraser M, Brundage M, Fleshner NE, van der Kwast T, Bristow RG, Boutros PC, Berlin A. Determining the Impact of Spatial Heterogeneity on Genomic Prognostic Biomarkers for Localized Prostate Cancer. Eur Urol Oncol. 2022 06; 5(3):362-365. view on PubMed

Zook JM, Hansen NF, Olson ND, Chapman L, Mullikin JC, Xiao C, Sherry S, Koren S, Phillippy AM, Boutros PC, Sahraeian SME, Huang V, Rouette A, Alexander N, Mason CE, Hajirasouliha I, Ricketts C, Lee J, Tearle R, Fiddes IT, Barrio AM, Wala J, Carroll A, Ghaffari N, Rodriguez OL, Bashir A, Jackman S, Farrell JJ, Wenger AM, Alkan C, Soylev A, Schatz MC, Garg S, Church G, Marschall T, Chen K, Fan X, English AC, Rosenfeld JA, Zhou W, Mills RE, Sage JM, Davis JR, Kaiser MD, Oliver JS, Catalano AP, Chaisson MJP, Spies N, Sedlazeck FJ, Salit M. A robust benchmark for detection of germline large deletions and insertions. Nat Biotechnol. 2020 11; 38(11):1347-1355. view on PubMed

Kishan AU, Romero T, Alshalalfa M, Liu Y, Tran PT, Nickols NG, Ye H, Sajed D, Rettig MB, Reiter RE, Garraway IP, Spratt DE, Freedland SJ, Zhao X, Li Z, Deek M, Livingstone J, Mahal BA, Nguyen PL, Feng FY, Den RB, Schaeffer EM, Lotan TL, Karnes RJ, Klein EA, Ross AE, Grogan T, Davicioni E, Elashoff D, Boutros PC, Weidhaas JB. Transcriptomic Heterogeneity of Gleason Grade Group 5 Prostate Cancer. Eur Urol. 2020 09; 78(3):327-332. view on PubMed

Prokopec SD, Viluksela M, Miettinen HM, Boutros PC, Pohjanvirta R. Transgenerational epigenetic and transcriptomic effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin exposure in rat. Arch Toxicol. 2020 05; 94(5):1613-1624. view on PubMed

Hoey C, Jeyapala R, Boutros PC, Bapat B, Liu SK. Urinary biomarkers in prostate cancer: to the miRnome and beyond. Transl Androl Urol. 2020 Apr; 9(2):843-845. view on PubMed

Syed JS, Brito J, Pooli A, Boutros PC, Shuch B. Transcriptomics in RCC. Urol Oncol. 2020 10; 38(10):742-754. view on PubMed

Mundi N, Ghasemi F, Zeng PYF, Prokopec SD, Patel K, Kim HAJ, Di Gravio E, MacNeil D, Khan MI, Han MW, Shaikh M, Mendez A, Yoo J, Fung K, Gameiro SF, Palma DA, Mymryk JS, Barrett JW, Boutros PC, Nichols AC. Sex disparities in head & neck cancer driver genes: An analysis of the TCGA dataset. Oral Oncol. 2020 05; 104:104614. view on PubMed

Jeon J, Olkhov-Mitsel E, Xie H, Yao CQ, Zhao F, Jahangiri S, Cuizon C, Scarcello S, Jeyapala R, Watson JD, Fraser M, Ray J, Commisso K, Loblaw A, Fleshner NE, Bristow RG, Downes M, Vesprini D, Liu S, Bapat B, Boutros PC. Temporal Stability and Prognostic Biomarker Potential of the Prostate Cancer Urine miRNA Transcriptome. J Natl Cancer Inst. 2020 03 01; 112(3):247-255. view on PubMed

Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vázquez-García I, Haase K, Jerman L, Sengupta S, Macintyre G, Malikic S, Donmez N, Livitz DG, Cmero M, Demeulemeester J, Schumacher S, Fan Y, Yao X, Lee J, Schlesner M, Boutros PC, Bowtell DD, Zhu H, Getz G, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Markowetz F, Mustonen V, Yuan K, Wang W, Morris QD, PCAWG Evolution & Heterogeneity Working Group, Spellman PT, Wedge DC, Van Loo P, PCAWG Consortium. The evolutionary history of 2,658 cancers. Nature. 2020 02; 578(7793):122-128. view on PubMed

Bhandari V, Li CH, Bristow RG, Boutros PC, PCAWG Consortium. Divergent mutational processes distinguish hypoxic and normoxic tumours. Nat Commun. 2020 02 05; 11(1):737. view on PubMed

Paczkowska M, Barenboim J, Sintupisut N, Fox NS, Zhu H, Abd-Rabbo D, Mee MW, Boutros PC, PCAWG Drivers and Functional Interpretation Working Group, Reimand J, PCAWG Consortium. Integrative pathway enrichment analysis of multivariate omics data. Nat Commun. 2020 02 05; 11(1):735. view on PubMed

Zhou S, Hawley JR, Soares F, Grillo G, Teng M, Madani Tonekaboni SA, Hua JT, Kron KJ, Mazrooei P, Ahmed M, Arlidge C, Yun HY, Livingstone J, Huang V, Yamaguchi TN, Espiritu SMG, Zhu Y, Severson TM, Murison A, Cameron S, Zwart W, van der Kwast T, Pugh TJ, Fraser M, Boutros PC, Bristow RG, He HH, Lupien M. Noncoding mutations target cis-regulatory elements of the FOXA1 plexus in prostate cancer. Nat Commun. 2020 01 23; 11(1):441. view on PubMed

Zhu H, Uusküla-Reimand L, Isaev K, Wadi L, Alizada A, Shuai S, Huang V, Aduluso-Nwaobasi D, Paczkowska M, Abd-Rabbo D, Ocsenas O, Liang M, Thompson JD, Li Y, Ruan L, Krassowski M, Dzneladze I, Simpson JT, Lupien M, Stein LD, Boutros PC, Wilson MD, Reimand J. Candidate Cancer Driver Mutations in Distal Regulatory Elements and Long-Range Chromatin Interaction Networks. Mol Cell. 2020 03 19; 77(6):1307-1321.e10. view on PubMed

Salcedo A, Tarabichi M, Espiritu SMG, Deshwar AG, David M, Wilson NM, Dentro S, Wintersinger JA, Liu LY, Ko M, Sivanandan S, Zhang H, Zhu K, Ou Yang TH, Chilton JM, Buchanan A, Lalansingh CM, P'ng C, Anghel CV, Umar I, Lo B, Zou W, DREAM SMC-Het Participants, Simpson JT, Stuart JM, Anastassiou D, Guan Y, Ewing AD, Ellrott K, Wedge DC, Morris Q, Van Loo P, Boutros PC. A community effort to create standards for evaluating tumor subclonal reconstruction. Nat Biotechnol. 2020 01; 38(1):97-107. view on PubMed

Lin X, Boutros PC. Optimization and expansion of non-negative matrix factorization. BMC Bioinformatics. 2020 Jan 06; 21(1):7. view on PubMed

Ray J, Haughey C, Hoey C, Jeon J, Murphy R, Dura-Perez L, McCabe N, Downes M, Jain S, Boutros PC, Mills IG, Liu SK. miR-191 promotes radiation resistance of prostate cancer through interaction with RXRA. Cancer Lett. 2020 03 31; 473:107-117. view on PubMed

Black M, Ghasemi F, Sun RX, Stecho W, Datti A, Meens J, Pinto N, Ruicci KM, Khan MI, Han MW, Shaikh M, Yoo J, Fung K, MacNeil D, Palma DA, Winquist E, Howlett CJ, Mymryk JS, Ailles L, Boutros PC, Barrett JW, Nichols AC. Spleen tyrosine kinase expression is correlated with human papillomavirus in head and neck cancer. Oral Oncol. 2020 02; 101:104529. view on PubMed

Guarischi-Sousa R, Monteiro JS, Alecrim LC, Michaloski JS, Cardeal LB, Ferreira EN, Carraro DM, Nunes DN, Dias-Neto E, Reimand J, Boutros PC, Setubal JC, Giordano RJ. A transcriptome-based signature of pathological angiogenesis predicts breast cancer patient survival. PLoS Genet. 2019 12; 15(12):e1008482. view on PubMed

Mundi N, Prokopec SD, Ghasemi F, Warner A, Patel K, MacNeil D, Howlett C, Stecho W, Plantinga P, Pinto N, Ruicci KM, Khan MI, Han MW, Yoo J, Fung K, Sahovaler A, Palma DA, Winquist E, Mymryk JS, Barrett JW, Boutros PC, Nichols AC. Genomic and human papillomavirus profiling of an oral cancer cohort identifies TP53 as a predictor of overall survival. Cancers Head Neck. 2019; 4:5. view on PubMed

Bayani J, Kornaga EN, Crozier C, Jang GH, Bathurst L, Kalatskaya I, Trinh QM, Yao CQ, Livingstone J, Boutros PC, Spears M, McPherson JD, Stein LD, Rea D, Bartlett JMS. Identification of Distinct Prognostic Groups: Implications for Patient Selection to Targeted Therapies Among Anti-Endocrine Therapy-Resistant Early Breast Cancers. JCO Precis Oncol. 2019 Dec; 3:1-13. view on PubMed

van Dessel LF, van Riet J, Smits M, Zhu Y, Hamberg P, van der Heijden MS, Bergman AM, van Oort IM, de Wit R, Voest EE, Steeghs N, Yamaguchi TN, Livingstone J, Boutros PC, Martens JWM, Sleijfer S, Cuppen E, Zwart W, van de Werken HJG, Mehra N, Lolkema MP. The genomic landscape of metastatic castration-resistant prostate cancers reveals multiple distinct genotypes with potential clinical impact. Nat Commun. 2019 11 20; 10(1):5251. view on PubMed

Mazrooei P, Kron KJ, Zhu Y, Zhou S, Grillo G, Mehdi T, Ahmed M, Severson TM, Guilhamon P, Armstrong NS, Huang V, Yamaguchi TN, Fraser M, van der Kwast T, Boutros PC, He HH, Bergman AM, Bristow RG, Zwart W, Lupien M. Cistrome Partitioning Reveals Convergence of Somatic Mutations and Risk Variants on Master Transcription Regulators in Primary Prostate Tumors. Cancer Cell. 2019 12 09; 36(6):674-689.e6. view on PubMed

Kishan AU, Chu FI, King CR, Seiferheld W, Spratt DE, Tran P, Wang X, Pugh SE, Sandler KA, Bolla M, Maingon P, De Reijke T, Nickols NG, Rettig M, Drakaki A, Liu ST, Reiter RE, Chang AJ, Feng FY, Sajed D, Nguyen PL, Kupelian PA, Steinberg ML, Boutros PC, Elashoff D, Collette L, Sandler HM. Local Failure and Survival After Definitive Radiotherapy for Aggressive Prostate Cancer: An Individual Patient-level Meta-analysis of Six Randomized Trials. Eur Urol. 2020 02; 77(2):201-208. view on PubMed

Houlahan KE, Shiah YJ, Gusev A, Yuan J, Ahmed M, Shetty A, Ramanand SG, Yao CQ, Bell C, O'Connor E, Huang V, Fraser M, Heisler LE, Livingstone J, Yamaguchi TN, Rouette A, Foucal A, Espiritu SMG, Sinha A, Sam M, Timms L, Johns J, Wong A, Murison A, Orain M, Picard V, Hovington H, Bergeron A, Lacombe L, Lupien M, Fradet Y, Têtu B, McPherson JD, Pasaniuc B, Kislinger T, Chua MLK, Pomerantz MM, van der Kwast T, Freedman ML, Mani RS, He HH, Bristow RG, Boutros PC. Genome-wide germline correlates of the epigenetic landscape of prostate cancer. Nat Med. 2019 10; 25(10):1615-1626. view on PubMed

Almaani S, Prokopec SD, Zhang J, Yu L, Avila-Casado C, Wither J, Scholey JW, Alberton V, Malvar A, Parikh SV, Boutros PC, Rovin BH, Reich HN. Rethinking Lupus Nephritis Classification on a Molecular Level. J Clin Med. 2019 Sep 23; 8(10). view on PubMed

Prokopec SD, Lu A, Lee SCS, Yao CQ, Sun RX, Watson JD, Soliymani R, de Borja R, Wong A, Sam M, Zuzarte P, McPherson JD, Okey AB, Pohjanvirta R, Boutros PC. Comparative toxicoproteogenomics of mouse and rat liver identifies TCDD-resistance genes. Arch Toxicol. 2019 10; 93(10):2961-2978. view on PubMed

Ellrott K, Buchanan A, Creason A, Mason M, Schaffter T, Hoff B, Eddy J, Chilton JM, Yu T, Stuart JM, Saez-Rodriguez J, Stolovitzky G, Boutros PC, Guinney J. Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges. Genome Biol. 2019 09 10; 20(1):195. view on PubMed

Patel PG, Wessel T, Kawashima A, Okello JBA, Jamaspishvili T, Guérard KP, Lee L, Lee AY, How NE, Dion D, Scarlata E, Jackson CL, Boursalie S, Sack T, Dunn R, Moussa M, Mackie/ K, Ellis A, Marra E, Chin J, Siddiqui K, Hetou K, Pickard LA, Arthur-Hayward V, Bauman G, Chevalier S, Brimo F, Boutros PC, Lapointe PhD J, Bartlett JMS, Gooding RJ, Berman DM. A three-gene DNA methylation biomarker accurately classifies early stage prostate cancer. Prostate. 2019 10; 79(14):1705-1714. view on PubMed

Villaseñor-Altamirano AB, Watson JD, Prokopec SD, Yao CQ, Boutros PC, Pohjanvirta R, Valdés-Flores J, Elizondo G. 2,3,7,8-Tetrachlorodibenzo-p-dioxin modifies alternative splicing in mouse liver. PLoS One. 2019; 14(8):e0219747. view on PubMed

Lourenco C, Kalkat M, Houlahan KE, De Melo J, Longo J, Done SJ, Boutros PC, Penn LZ. Modelling the MYC-driven normal-to-tumour switch in breast cancer. Dis Model Mech. 2019 07 26; 12(7). view on PubMed

Fox NS, Haider S, Harris AL, Boutros PC. Landscape of transcriptomic interactions between breast cancer and its microenvironment. Nat Commun. 2019 07 15; 10(1):3116. view on PubMed

Ray J, Hoey C, Huang X, Jeon J, Taeb S, Downes MR, Boutros PC, Liu SK. MicroRNA‑198 suppresses prostate tumorigenesis by targeting MIB1. Oncol Rep. 2019 Sep; 42(3):1047-1056. view on PubMed

Krusche P, Trigg L, Boutros PC, Mason CE, De La Vega FM, Moore BL, Gonzalez-Porta M, Eberle MA, Tezak Z, Lababidi S, Truty R, Asimenos G, Funke B, Fleharty M, Chapman BA, Salit M, Zook JM, Global Alliance for Genomics and Health Benchmarking Team. Author Correction: Best practices for benchmarking germline small-variant calls in human genomes. Nat Biotechnol. 2019 05; 37(5):567. view on PubMed

Taylor RA, Fraser M, Rebello RJ, Boutros PC, Murphy DG, Bristow RG, Risbridger GP. The influence of BRCA2 mutation on localized prostate cancer. Nat Rev Urol. 2019 05; 16(5):281-290. view on PubMed

Joshi PA, Waterhouse PD, Kasaian K, Fang H, Gulyaeva O, Sul HS, Boutros PC, Khokha R. PDGFRα+ stromal adipocyte progenitors transition into epithelial cells during lobulo-alveologenesis in the murine mammary gland. Nat Commun. 2019 04 15; 10(1):1760. view on PubMed

Mesci A, Lucien F, Huang X, Wang EH, Shin D, Meringer M, Hoey C, Ray J, Boutros PC, Leong HS, Liu SK. RSPO3 is a prognostic biomarker and mediator of invasiveness in prostate cancer. J Transl Med. 2019 04 15; 17(1):125. view on PubMed

Rivalland G, Mitchell P, Murone C, Asadi K, Morey AL, Starmans M, Boutros PC, Walkiewicz M, Solomon B, Wright G, Knight S, John T. Mesenchyme to epithelial transition protein expression, gene copy number and clinical outcome in a large non-small cell lung cancer surgical cohort. Transl Lung Cancer Res. 2019 Apr; 8(2):167-175. view on PubMed

Denis RGP, Busi F, Castel J, Morel C, Zhang W, Bui LC, Sugamori KS, Prokopec SD, Boutros PC, Grant DM, Rodrigues-Lima F, Luquet S, Dupret JM. A readout of metabolic efficiency in arylamine N-acetyltransferase-deficient mice reveals minor energy metabolism changes. FEBS Lett. 2019 04; 593(8):831-841. view on PubMed

Prokopec SD, Pohjanvirta R, Mahiout S, Pettersson L, Boutros PC. Transcriptomic Impact of IMA-08401, a Novel AHR Agonist Resembling Laquinimod, on Rat Liver. Int J Mol Sci. 2019 Mar 19; 20(6). view on PubMed

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Krusche P, Trigg L, Boutros PC, Mason CE, De La Vega FM, Moore BL, Gonzalez-Porta M, Eberle MA, Tezak Z, Lababidi S, Truty R, Asimenos G, Funke B, Fleharty M, Chapman BA, Salit M, Zook JM, Global Alliance for Genomics and Health Benchmarking Team. Best practices for benchmarking germline small-variant calls in human genomes. Nat Biotechnol. 2019 05; 37(5):555-560. view on PubMed

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Houlahan KE, Salmasi A, Sadun TY, Pooli A, Felker ER, Livingstone J, Huang V, Raman SS, Ahuja P, Sisk AE, Boutros PC, Reiter RE. Molecular Hallmarks of Multiparametric Magnetic Resonance Imaging Visibility in Prostate Cancer. Eur Urol. 2019 07; 76(1):18-23. view on PubMed

P'ng C, Green J, Chong LC, Waggott D, Prokopec SD, Shamsi M, Nguyen F, Mak DYF, Lam F, Albuquerque MA, Wu Y, Jung EH, Starmans MHW, Chan-Seng-Yue MA, Yao CQ, Liang B, Lalonde E, Haider S, Simone NA, Sendorek D, Chu KC, Moon NC, Fox NS, Grzadkowski MR, Harding NJ, Fung C, Murdoch AR, Houlahan KE, Wang J, Garcia DR, de Borja R, Sun RX, Lin X, Chen GM, Lu A, Shiah YJ, Zia A, Kearns R, Boutros PC. BPG: Seamless, automated and interactive visualization of scientific data. BMC Bioinformatics. 2019 Jan 21; 20(1):42. view on PubMed

Guo H, Ci X, Ahmed M, Hua JT, Soares F, Lin D, Puca L, Vosoughi A, Xue H, Li E, Su P, Chen S, Nguyen T, Liang Y, Zhang Y, Xu X, Xu J, Sheahan AV, Ba-Alawi W, Zhang S, Mahamud O, Vellanki RN, Gleave M, Bristow RG, Haibe-Kains B, Poirier JT, Rudin CM, Tsao MS, Wouters BG, Fazli L, Feng FY, Ellis L, van der Kwast T, Berlin A, Koritzinsky M, Boutros PC, Zoubeidi A, Beltran H, Wang Y, He HH. ONECUT2 is a driver of neuroendocrine prostate cancer. Nat Commun. 2019 01 17; 10(1):278. view on PubMed

Bhandari V, Hoey C, Liu LY, Lalonde E, Ray J, Livingstone J, Lesurf R, Shiah YJ, Vujcic T, Huang X, Espiritu SMG, Heisler LE, Yousif F, Huang V, Yamaguchi TN, Yao CQ, Sabelnykova VY, Fraser M, Chua MLK, van der Kwast T, Liu SK, Boutros PC, Bristow RG. Molecular landmarks of tumor hypoxia across cancer types. Nat Genet. 2019 02; 51(2):308-318. view on PubMed

Fraser M, Koontz B, Emmenegger U, De Meerleer G, Khoo V, Feng F, Corcoran NM, Hovens CM, Tran PT, Ost P, Boutros PC, GAP6 Consortium. What Is Oligometastatic Prostate Cancer? Eur Urol Focus. 2019 03; 5(2):159-161. view on PubMed

Ghasemi F, Prokopec SD, MacNeil D, Mundi N, Gameiro SF, Howlett C, Stecho W, Plantinga P, Pinto N, Ruicci KM, Khan MI, Yoo J, Fung K, Sahovaler A, Palma DA, Winquist E, Mymryk JS, Barrett JW, Boutros PC, Nichols AC. Mutational analysis of head and neck squamous cell carcinoma stratified by smoking status. JCI Insight. 2019 Jan 10; 4(1). view on PubMed

Ruicci KM, Meens J, Sun RX, Rizzo G, Pinto N, Yoo J, Fung K, MacNeil D, Mymryk JS, Barrett JW, Boutros PC, Ailles L, Nichols AC. A controlled trial of HNSCC patient-derived xenografts reveals broad efficacy of PI3Kα inhibition in controlling tumor growth. Int J Cancer. 2019 10 15; 145(8):2100-2106. view on PubMed

Gerhauser C, Favero F, Risch T, Simon R, Feuerbach L, Assenov Y, Heckmann D, Sidiropoulos N, Waszak SM, Hübschmann D, Urbanucci A, Girma EG, Kuryshev V, Klimczak LJ, Saini N, Stütz AM, Weichenhan D, Böttcher LM, Toth R, Hendriksen JD, Koop C, Lutsik P, Matzk S, Warnatz HJ, Amstislavskiy V, Feuerstein C, Raeder B, Bogatyrova O, Schmitz EM, Hube-Magg C, Kluth M, Huland H, Graefen M, Lawerenz C, Henry GH, Yamaguchi TN, Malewska A, Meiners J, Schilling D, Reisinger E, Eils R, Schlesner M, Strand DW, Bristow RG, Boutros PC, von Kalle C, Gordenin D, Sültmann H, Brors B, Sauter G, Plass C, Yaspo ML, Korbel JO, Schlomm T, Weischenfeldt J. Molecular Evolution of Early-Onset Prostate Cancer Identifies Molecular Risk Markers and Clinical Trajectories. Cancer Cell. 2018 12 10; 34(6):996-1011.e8. view on PubMed

Pinto N, Prokopec SD, Vizeacoumar F, Searle K, Lowerison M, Ruicci KM, Yoo J, Fung K, MacNeil D, Lacefield JC, Leong HS, Mymryk JS, Barrett JW, Datti A, Boutros PC, Nichols AC. Lestaurtinib is a potent inhibitor of anaplastic thyroid cancer cell line models. PLoS One. 2018; 13(11):e0207152. view on PubMed

Haider S, Yao CQ, Sabine VS, Grzadkowski M, Stimper V, Starmans MHW, Wang J, Nguyen F, Moon NC, Lin X, Drake C, Crozier CA, Brookes CL, van de Velde CJH, Hasenburg A, Kieback DG, Markopoulos CJ, Dirix LY, Seynaeve C, Rea DW, Kasprzyk A, Lambin P, Lio' P, Bartlett JMS, Boutros PC. Pathway-based subnetworks enable cross-disease biomarker discovery. Nat Commun. 2018 11 12; 9(1):4746. view on PubMed

Kalkat M, Resetca D, Lourenco C, Chan PK, Wei Y, Shiah YJ, Vitkin N, Tong Y, Sunnerhagen M, Done SJ, Boutros PC, Raught B, Penn LZ. MYC Protein Interactome Profiling Reveals Functionally Distinct Regions that Cooperate to Drive Tumorigenesis. Mol Cell. 2018 12 06; 72(5):836-848.e7. view on PubMed

Lee AY, Ewing AD, Ellrott K, Hu Y, Houlahan KE, Bare JC, Espiritu SMG, Huang V, Dang K, Chong Z, Caloian C, Yamaguchi TN, ICGC-TCGA DREAM Somatic Mutation Calling Challenge Participants, Kellen MR, Chen K, Norman TC, Friend SH, Guinney J, Stolovitzky G, Haussler D, Margolin AA, Stuart JM, Boutros PC. Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection. Genome Biol. 2018 11 06; 19(1):188. view on PubMed

Grzadkowski MR, Sendorek DH, P'ng C, Huang V, Boutros PC. A comparative study of survival models for breast cancer prognostication revisited: the benefits of multi-gene models. BMC Bioinformatics. 2018 Nov 03; 19(1):400. view on PubMed

Tu WB, Shiah YJ, Lourenco C, Mullen PJ, Dingar D, Redel C, Tamachi A, Ba-Alawi W, Aman A, Al-Awar R, Cescon DW, Haibe-Kains B, Arrowsmith CH, Raught B, Boutros PC, Penn LZ. MYC Interacts with the G9a Histone Methyltransferase to Drive Transcriptional Repression and Tumorigenesis. Cancer Cell. 2018 10 08; 34(4):579-595.e8. view on PubMed

Li CH, Haider S, Shiah YJ, Thai K, Boutros PC. Sex Differences in Cancer Driver Genes and Biomarkers. Cancer Res. 2018 10 01; 78(19):5527-5537. view on PubMed

Cooper CI, Yao D, Sendorek DH, Yamaguchi TN, P'ng C, Houlahan KE, Caloian C, Fraser M, SMC-DNA Challenge Participants, Ellrott K, Margolin AA, Bristow RG, Stuart JM, Boutros PC. Valection: design optimization for validation and verification studies. BMC Bioinformatics. 2018 Sep 25; 19(1):339. view on PubMed

Gong IY, Fox NS, Huang V, Boutros PC. Prediction of early breast cancer patient survival using ensembles of hypoxia signatures. PLoS One. 2018; 13(9):e0204123. view on PubMed

Berlin A, Murgic J, Hosni A, Pintilie M, Salcedo A, Fraser M, Kamel-Reid S, Zhang J, Wang Q, Ch'ng C, Deheshi S, Davicioni E, van der Kwast T, Boutros PC, Bristow RG, Chua MLK. Genomic Classifier for Guiding Treatment of Intermediate-Risk Prostate Cancers to Dose-Escalated Image Guided Radiation Therapy Without Hormone Therapy. Int J Radiat Oncol Biol Phys. 2019 01 01; 103(1):84-91. view on PubMed

Dingar D, Tu WB, Resetca D, Lourenco C, Tamachi A, De Melo J, Houlahan KE, Kalkat M, Chan PK, Boutros PC, Raught B, Penn LZ. MYC dephosphorylation by the PP1/PNUTS phosphatase complex regulates chromatin binding and protein stability. Nat Commun. 2018 08 29; 9(1):3502. view on PubMed

Boutros PC. The Promise and Perils of Sequencing Individual Prostate Cancer Nuclei. Eur Urol. 2018 11; 74(5):560-561. view on PubMed

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Casey AE, Sinha A, Singhania R, Livingstone J, Waterhouse P, Tharmapalan P, Cruickshank J, Shehata M, Drysdale E, Fang H, Kim H, Isserlin R, Bailey S, Medina T, Deblois G, Shiah YJ, Barsyte-Lovejoy D, Hofer S, Bader G, Lupien M, Arrowsmith C, Knapp S, De Carvalho D, Berman H, Boutros PC, Kislinger T, Khokha R. Mammary molecular portraits reveal lineage-specific features and progenitor cell vulnerabilities. J Cell Biol. 2018 08 06; 217(8):2951-2974. view on PubMed

Hoey C, Ray J, Jeon J, Huang X, Taeb S, Ylanko J, Andrews DW, Boutros PC, Liu SK. miRNA-106a and prostate cancer radioresistance: a novel role for LITAF in ATM regulation. Mol Oncol. 2018 08; 12(8):1324-1341. view on PubMed

Ghasemi F, Black M, Sun RX, Vizeacoumar F, Pinto N, Ruicci KM, Yoo J, Fung K, MacNeil D, Palma DA, Winquist E, Mymryk JS, Ailles LA, Datti A, Barrett JW, Boutros PC, Nichols AC. High-throughput testing in head and neck squamous cell carcinoma identifies agents with preferential activity in human papillomavirus-positive or negative cell lines. Oncotarget. 2018 May 25; 9(40):26064-26071. view on PubMed

Wither JE, Prokopec SD, Noamani B, Chang NH, Bonilla D, Touma Z, Avila-Casado C, Reich HN, Scholey J, Fortin PR, Boutros PC, Landolt-Marticorena C. Identification of a neutrophil-related gene expression signature that is enriched in adult systemic lupus erythematosus patients with active nephritis: Clinical/pathologic associations and etiologic mechanisms. PLoS One. 2018; 13(5):e0196117. view on PubMed

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Chong T, Sarac A, Yao CQ, Liao L, Lyttle N, Boutros PC, Bartlett JMS, Spears M. Deregulation of the spindle assembly checkpoint is associated with paclitaxel resistance in ovarian cancer. J Ovarian Res. 2018 Apr 04; 11(1):27. view on PubMed

Hopkins JF, Denroche RE, Aguiar JA, Notta F, Connor AA, Wilson JM, Stein LD, Gallinger S, Boutros PC. Mutations in Mitochondrial DNA From Pancreatic Ductal Adenocarcinomas Associate With Survival Times of Patients and Accumulate as Tumors Progress. Gastroenterology. 2018 05; 154(6):1620-1624.e5. view on PubMed

Sendorek DH, Lalonde E, Yao CQ, Sabelnykova VY, Bristow RG, Boutros PC. NanoStringNormCNV: pre-processing of NanoString CNV data. Bioinformatics. 2018 03 15; 34(6):1034-1036. view on PubMed

Sendorek DH, Caloian C, Ellrott K, Bare JC, Yamaguchi TN, Ewing AD, Houlahan KE, Norman TC, Margolin AA, Stuart JM, Boutros PC. Germline contamination and leakage in whole genome somatic single nucleotide variant detection. BMC Bioinformatics. 2018 01 31; 19(1):28. view on PubMed

Böttcher R, Kweldam CF, Livingstone J, Lalonde E, Yamaguchi TN, Huang V, Yousif F, Fraser M, Bristow RG, van der Kwast T, Boutros PC, Jenster G, van Leenders GJLH. Cribriform and intraductal prostate cancer are associated with increased genomic instability and distinct genomic alterations. BMC Cancer. 2018 01 02; 18(1):8. view on PubMed

Fraser M, Boutros PC, Bristow RG. A Partner in Crime: Tumor-associated Stroma and Metastatic Prostate Cancer. Eur Urol. 2018 04; 73(4):533-534. view on PubMed

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Li M, Kouzmina E, McCusker M, Rodin D, Boutros PC, Paige CJ, Rodin G. Cytokines and depression in cancer patients and caregivers. Neuropsychiatr Dis Treat. 2017; 13:2903-2911. view on PubMed

Abdalla M, Tran-Thanh D, Moreno J, Iakovlev V, Nair R, Kanwar N, Abdalla M, Lee JPY, Kwan JYY, Cawthorn TR, Warren K, Arneson N, Wang DY, Fox NS, Youngson BJ, Miller NA, Easson AM, McCready D, Leong WL, Boutros PC, Done SJ. Mapping genomic and transcriptomic alterations spatially in epithelial cells adjacent to human breast carcinoma. Nat Commun. 2017 11 01; 8(1):1245. view on PubMed

Shiah YJ, Fraser M, Bristow RG, Boutros PC. Comparison of pre-processing methods for Infinium HumanMethylation450 BeadChip array. Bioinformatics. 2017 Oct 15; 33(20):3151-3157. view on PubMed

Hopkins JF, Sabelnykova VY, Weischenfeldt J, Simon R, Aguiar JA, Alkallas R, Heisler LE, Zhang J, Watson JD, Chua MLK, Fraser M, Favero F, Lawerenz C, Plass C, Sauter G, McPherson JD, van der Kwast T, Korbel J, Schlomm T, Bristow RG, Boutros PC. Mitochondrial mutations drive prostate cancer aggression. Nat Commun. 2017 09 22; 8(1):656. view on PubMed

Liang Y, Ahmed M, Guo H, Soares F, Hua JT, Gao S, Lu C, Poon C, Han W, Langstein J, Ekram MB, Li B, Davicioni E, Takhar M, Erho N, Karnes RJ, Chadwick D, van der Kwast T, Boutros PC, Arrowsmith CH, Feng FY, Joshua AM, Zoubeidi A, Cai C, He HH. LSD1-Mediated Epigenetic Reprogramming Drives CENPE Expression and Prostate Cancer Progression. Cancer Res. 2017 10 15; 77(20):5479-5490. view on PubMed

Kron KJ, Murison A, Zhou S, Huang V, Yamaguchi TN, Shiah YJ, Fraser M, van der Kwast T, Boutros PC, Bristow RG, Lupien M. TMPRSS2-ERG fusion co-opts master transcription factors and activates NOTCH signaling in primary prostate cancer. Nat Genet. 2017 Sep; 49(9):1336-1345. view on PubMed

Alfaro JA, Ignatchenko A, Ignatchenko V, Sinha A, Boutros PC, Kislinger T. Detecting protein variants by mass spectrometry: a comprehensive study in cancer cell-lines. Genome Med. 2017 07 18; 9(1):62. view on PubMed

Taghiyar MJ, Rosner J, Grewal D, Grande BM, Aniba R, Grewal J, Boutros PC, Morin RD, Bashashati A, Shah SP. Kronos: a workflow assembler for genome analytics and informatics. Gigascience. 2017 07 01; 6(7):1-10. view on PubMed

Chüeh AC, Liew MS, Russell PA, Walkiewicz M, Jayachandran A, Starmans MHW, Boutros PC, Wright G, Barnett SA, Mariadason JM, John T. Promoter hypomethylation of NY-ESO-1, association with clinicopathological features and PD-L1 expression in non-small cell lung cancer. Oncotarget. 2017 Sep 26; 8(43):74036-74048. view on PubMed

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Feldcamp LA, Boutros PC, Raymond R, Fletcher PJ, Nobrega JN, Wong AHC. Pdxdc1 modulates prepulse inhibition of acoustic startle in the mouse. Transl Psychiatry. 2017 05 09; 7(5):e1125. view on PubMed

Albuquerque MA, Grande BM, Ritch EJ, Pararajalingam P, Jessa S, Krzywinski M, Grewal JK, Shah SP, Boutros PC, Morin RD. Enhancing knowledge discovery from cancer genomics data with Galaxy. Gigascience. 2017 05 01; 6(5):1-13. view on PubMed

Ghasemi F, Black M, Vizeacoumar F, Pinto N, Ruicci KM, Le CCSH, Lowerison MR, Leong HS, Yoo J, Fung K, MacNeil D, Palma DA, Winquist E, Mymryk JS, Boutros PC, Datti A, Barrett JW, Nichols AC. Repurposing Albendazole: new potential as a chemotherapeutic agent with preferential activity against HPV-negative head and neck squamous cell cancer. Oncotarget. 2017 Sep 22; 8(42):71512-71519. view on PubMed

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Dunning MJ, Vowler SL, Lalonde E, Ross-Adams H, Boutros P, Mills IG, Lynch AG, Lamb AD. Mining Human Prostate Cancer Datasets: The "camcAPP" Shiny App. EBioMedicine. 2017 Mar; 17:5-6. view on PubMed

Thapa B, Salcedo A, Lin X, Walkiewicz M, Murone C, Ameratunga M, Asadi K, Deb S, Barnett SA, Knight S, Mitchell P, Watkins DN, Boutros PC, John T. The Immune Microenvironment, Genome-wide Copy Number Aberrations, and Survival in Mesothelioma. J Thorac Oncol. 2017 05; 12(5):850-859. view on PubMed

Bayani J, Yao CQ, Quintayo MA, Yan F, Haider S, D'Costa A, Brookes CL, van de Velde CJH, Hasenburg A, Kieback DG, Markopoulos C, Dirix L, Seynaeve C, Rea D, Boutros PC, Bartlett JMS. Molecular stratification of early breast cancer identifies drug targets to drive stratified medicine. NPJ Breast Cancer. 2017; 3:3. view on PubMed

Fotouhi Ghiam A, Taeb S, Huang X, Huang V, Ray J, Scarcello S, Hoey C, Jahangiri S, Fokas E, Loblaw A, Bristow RG, Vesprini D, Boutros P, Liu SK. Long non-coding RNA urothelial carcinoma associated 1 (UCA1) mediates radiation response in prostate cancer. Oncotarget. 2017 Jan 17; 8(3):4668-4689. view on PubMed

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Haider S, Waggott D, Lalonde E, Fung C, Liu FF, Boutros PC. Erratum to: A bedr way of genomic interval processing. Source Code Biol Med. 2017; 12:1. view on PubMed

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Li M, Kouzmina E, McCusker M, Rodin D, Boutros PC, Paige CJ, Rodin G. Pro- and anti-inflammatory cytokine associations with major depression in cancer patients. Psychooncology. 2017 Dec; 26(12):2149-2156. view on PubMed

Chong Z, Ruan J, Gao M, Zhou W, Chen T, Fan X, Ding L, Lee AY, Boutros P, Chen J, Chen K. novoBreak: local assembly for breakpoint detection in cancer genomes. Nat Methods. 2017 01; 14(1):65-67. view on PubMed

Wang D, Pham NA, Tong J, Sakashita S, Allo G, Kim L, Yanagawa N, Raghavan V, Wei Y, To C, Trinh QM, Starmans MH, Chan-Seng-Yue MA, Chadwick D, Li L, Zhu CQ, Liu N, Li M, Lee S, Ignatchenko V, Strumpf D, Taylor P, Moghal N, Liu G, Boutros PC, Kislinger T, Pintilie M, Jurisica I, Shepherd FA, McPherson JD, Muthuswamy L, Moran MF, Tsao MS. Molecular heterogeneity of non-small cell lung carcinoma patient-derived xenografts closely reflect their primary tumors. Int J Cancer. 2017 Feb 01; 140(3):662-673. view on PubMed

Lalonde E, Alkallas R, Chua MLK, Fraser M, Haider S, Meng A, Zheng J, Yao CQ, Picard V, Orain M, Hovington H, Murgic J, Berlin A, Lacombe L, Bergeron A, Fradet Y, Têtu B, Lindberg J, Egevad L, Grönberg H, Ross-Adams H, Lamb AD, Halim S, Dunning MJ, Neal DE, Pintilie M, van der Kwast T, Bristow RG, Boutros PC. Translating a Prognostic DNA Genomic Classifier into the Clinic: Retrospective Validation in 563 Localized Prostate Tumors. Eur Urol. 2017 07; 72(1):22-31. view on PubMed

Landolt-Marticorena C, Prokopec SD, Morrison S, Noamani B, Bonilla D, Reich H, Scholey J, Avila-Casado C, Fortin PR, Boutros PC, Wither J. A discrete cluster of urinary biomarkers discriminates between active systemic lupus erythematosus patients with and without glomerulonephritis. Arthritis Res Ther. 2016 10 04; 18(1):218. view on PubMed

Lam F, Lalansingh CM, Babaran HE, Wang Z, Prokopec SD, Fox NS, Boutros PC. VennDiagramWeb: a web application for the generation of highly customizable Venn and Euler diagrams. BMC Bioinformatics. 2016 Oct 03; 17(1):401. view on PubMed

David M, Dursi LJ, Yao D, Boutros PC, Simpson JT. Nanocall: an open source basecaller for Oxford Nanopore sequencing data. Bioinformatics. 2017 01 01; 33(1):49-55. view on PubMed

Huang BF, Boutros PC. The parameter sensitivity of random forests. BMC Bioinformatics. 2016 Sep 01; 17(1):331. view on PubMed

Guo H, Ahmed M, Zhang F, Yao CQ, Li S, Liang Y, Hua J, Soares F, Sun Y, Langstein J, Li Y, Poon C, Bailey SD, Desai K, Fei T, Li Q, Sendorek DH, Fraser M, Prensner JR, Pugh TJ, Pomerantz M, Bristow RG, Lupien M, Feng FY, Boutros PC, Freedman ML, Walsh MJ, He HH. Modulation of long noncoding RNAs by risk SNPs underlying genetic predispositions to prostate cancer. Nat Genet. 2016 10; 48(10):1142-50. view on PubMed

Masella AP, Lalansingh CM, Sivasundaram P, Fraser M, Bristow RG, Boutros PC. BAMQL: a query language for extracting reads from BAM files. BMC Bioinformatics. 2016 Aug 11; 17:305. view on PubMed

Spears M, Lyttle N, D'Costa A, Chen BE, Yao CQ, Boutros PC, Burnell M, Levine MN, O'Brien P, Shepherd L, Bartlett JM. A four gene signature of chromosome instability (CIN4) predicts for benefit from taxanes in the NCIC-CTG MA21 clinical trial. Oncotarget. 2016 Aug 02; 7(31):49099-49106. view on PubMed

Noren DP, Long BL, Norel R, Rrhissorrakrai K, Hess K, Hu CW, Bisberg AJ, Schultz A, Engquist E, Liu L, Lin X, Chen GM, Xie H, Hunter GA, Boutros PC, Stepanov O, DREAM 9 AML-OPC Consortium, Norman T, Friend SH, Stolovitzky G, Kornblau S, Qutub AA. A Crowdsourcing Approach to Developing and Assessing Prediction Algorithms for AML Prognosis. PLoS Comput Biol. 2016 06; 12(6):e1004890. view on PubMed

Kim Y, Jeon J, Mejia S, Yao CQ, Ignatchenko V, Nyalwidhe JO, Gramolini AO, Lance RS, Troyer DA, Drake RR, Boutros PC, Semmes OJ, Kislinger T. Targeted proteomics identifies liquid-biopsy signatures for extracapsular prostate cancer. Nat Commun. 2016 06 28; 7:11906. view on PubMed

Macdonald JM, Boutros PC. Log::ProgramInfo: A Perl module to collect and log data for bioinformatics pipelines. Source Code Biol Med. 2016; 11:9. view on PubMed

Bhandari V, Boutros PC. Comparing continuous and discrete analyses of breast cancer survival information. Genomics. 2016 08; 108(2):78-83. view on PubMed

Stojanova A, Tu WB, Ponzielli R, Kotlyar M, Chan PK, Boutros PC, Khosravi F, Jurisica I, Raught B, Penn LZ. MYC interaction with the tumor suppressive SWI/SNF complex member INI1 regulates transcription and cellular transformation. Cell Cycle. 2016 07 02; 15(13):1693-705. view on PubMed

Chia PL, Gedye C, Boutros PC, Wheatley-Price P, John T. Current and Evolving Methods to Visualize Biological Data in Cancer Research. J Natl Cancer Inst. 2016 08; 108(8). view on PubMed

Azad AK, Bairati I, Qiu X, Girgis H, Cheng L, Waggott D, Cheng D, Mirshams M, Ho J, Fortin A, Vigneault E, Huang SH, O'Sullivan B, Waldron J, Boutros PC, Goldstein D, Meyer F, Xu W, Liu G. A genome-wide association study of non-HPV-related head and neck squamous cell carcinoma identifies prognostic genetic sequence variants in the MAP-kinase and hormone pathways. Cancer Epidemiol. 2016 06; 42:173-80. view on PubMed

Boutros PC, Fraser M, van der Kwast T, Bristow RG. Clonality of localized and metastatic prostate cancer. Curr Opin Urol. 2016 May; 26(3):219-24. view on PubMed

Watson JD, Prokopec SD, Smith AB, Okey AB, Pohjanvirta R, Boutros PC. 2,3,7,8 Tetrachlorodibenzo-p-dioxin-induced RNA abundance changes identify Ackr3, Col18a1, Cyb5a and Glud1 as candidate mediators of toxicity. Arch Toxicol. 2017 Jan; 91(1):325-338. view on PubMed

Ameratunga M, Asadi K, Lin X, Walkiewicz M, Murone C, Knight S, Mitchell P, Boutros P, John T. PD-L1 and Tumor Infiltrating Lymphocytes as Prognostic Markers in Resected NSCLC. PLoS One. 2016; 11(4):e0153954. view on PubMed

Gagliano SA, Ptak C, Mak DYF, Shamsi M, Oh G, Knight J, Boutros PC, Petronis A. Allele-Skewed DNA Modification in the Brain: Relevance to a Schizophrenia GWAS. Am J Hum Genet. 2016 May 05; 98(5):956-962. view on PubMed

Allen GI, Amoroso N, Anghel C, Balagurusamy V, Bare CJ, Beaton D, Bellotti R, Bennett DA, Boehme KL, Boutros PC, Caberlotto L, Caloian C, Campbell F, Chaibub Neto E, Chang YC, Chen B, Chen CY, Chien TY, Clark T, Das S, Davatzikos C, Deng J, Dillenberger D, Dobson RJ, Dong Q, Doshi J, Duma D, Errico R, Erus G, Everett E, Fardo DW, Friend SH, Fröhlich H, Gan J, St George-Hyslop P, Ghosh SS, Glaab E, Green RC, Guan Y, Hong MY, Huang C, Hwang J, Ibrahim J, Inglese P, Iyappan A, Jiang Q, Katsumata Y, Kauwe JS, Klein A, Kong D, Krause R, Lalonde E, Lauria M, Lee E, Lin X, Liu Z, Livingstone J, Logsdon BA, Lovestone S, Ma TW, Malhotra A, Mangravite LM, Maxwell TJ, Merrill E, Nagorski J, Namasivayam A, Narayan M, Naz M, Newhouse SJ, Norman TC, Nurtdinov RN, Oyang YJ, Pawitan Y, Peng S, Peters MA, Piccolo SR, Praveen P, Priami C, Sabelnykova VY, Senger P, Shen X, Simmons A, Sotiras A, Stolovitzky G, Tangaro S, Tateo A, Tung YA, Tustison NJ, Varol E, Vradenburg G, Weiner MW, Xiao G, Xie L, Xie Y, Xu J, Yang H, Zhan X, Zhou Y, Zhu F, Zhu H, Zhu S, Alzheimer's Disease Neuroimaging Initiative. Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease. Alzheimers Dement. 2016 06; 12(6):645-53. view on PubMed

Babichev Y, Kabaroff L, Datti A, Uehling D, Isaac M, Al-Awar R, Prakesch M, Sun RX, Boutros PC, Venier R, Dickson BC, Gladdy RA. PI3K/AKT/mTOR inhibition in combination with doxorubicin is an effective therapy for leiomyosarcoma. J Transl Med. 2016 Mar 08; 14:67. view on PubMed

Braunstein M, Liao L, Lyttle N, Lobo N, Taylor KJ, Krzyzanowski PM, Kalatskaya I, Yao CQ, Stein LD, Boutros PC, Twelves CJ, Marcellus R, Bartlett JM, Spears M. Downregulation of histone H2A and H2B pathways is associated with anthracycline sensitivity in breast cancer. Breast Cancer Res. 2016 Feb 06; 18(1):16. view on PubMed

Alioto TS, Buchhalter I, Derdak S, Hutter B, Eldridge MD, Hovig E, Heisler LE, Beck TA, Simpson JT, Tonon L, Sertier AS, Patch AM, Jäger N, Ginsbach P, Drews R, Paramasivam N, Kabbe R, Chotewutmontri S, Diessl N, Previti C, Schmidt S, Brors B, Feuerbach L, Heinold M, Gröbner S, Korshunov A, Tarpey PS, Butler AP, Hinton J, Jones D, Menzies A, Raine K, Shepherd R, Stebbings L, Teague JW, Ribeca P, Giner FC, Beltran S, Raineri E, Dabad M, Heath SC, Gut M, Denroche RE, Harding NJ, Yamaguchi TN, Fujimoto A, Nakagawa H, Quesada V, Valdés-Mas R, Nakken S, Vodák D, Bower L, Lynch AG, Anderson CL, Waddell N, Pearson JV, Grimmond SM, Peto M, Spellman P, He M, Kandoth C, Lee S, Zhang J, Létourneau L, Ma S, Seth S, Torrents D, Xi L, Wheeler DA, López-Otín C, Campo E, Campbell PJ, Boutros PC, Puente XS, Gerhard DS, Pfister SM, McPherson JD, Hudson TJ, Schlesner M, Lichter P, Eils R, Jones DT, Gut IG. A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing. Nat Commun. 2015 Dec 09; 6:10001. view on PubMed

Spears M, Yousif F, Lyttle N, Boutros PC, Munro AF, Twelves C, Pritchard KI, Levine MN, Shepherd L, Bartlett JM. A four gene signature predicts benefit from anthracyclines: evidence from the BR9601 and MA.5 clinical trials. Oncotarget. 2015 Oct 13; 6(31):31693-701. view on PubMed

Boutros PC. The path to routine use of genomic biomarkers in the cancer clinic. Genome Res. 2015 Oct; 25(10):1508-13. view on PubMed

Huang X, Taeb S, Jahangiri S, Korpela E, Cadonic I, Yu N, Krylov SN, Fokas E, Boutros PC, Liu SK. miR-620 promotes tumor radioresistance by targeting 15-hydroxyprostaglandin dehydrogenase (HPGD). Oncotarget. 2015 Sep 08; 6(26):22439-51. view on PubMed

Lee J, Prokopec SD, Watson JD, Sun RX, Pohjanvirta R, Boutros PC. Male and female mice show significant differences in hepatic transcriptomic response to 2,3,7,8-tetrachlorodibenzo-p-dioxin. BMC Genomics. 2015 Aug 20; 16:625. view on PubMed

Houlahan KE, Prokopec SD, Sun RX, Moffat ID, Lindén J, Lensu S, Okey AB, Pohjanvirta R, Boutros PC. Transcriptional profiling of rat white adipose tissue response to 2,3,7,8-tetrachlorodibenzo-ρ-dioxin. Toxicol Appl Pharmacol. 2015 Oct 15; 288(2):223-31. view on PubMed

Creixell P, Reimand J, Haider S, Wu G, Shibata T, Vazquez M, Mustonen V, Gonzalez-Perez A, Pearson J, Sander C, Raphael BJ, Marks DS, Ouellette BFF, Valencia A, Bader GD, Boutros PC, Stuart JM, Linding R, Lopez-Bigas N, Stein LD, Mutation Consequences and Pathway Analysis Working Group of the International Cancer Genome Consorti. Pathway and network analysis of cancer genomes. Nat Methods. 2015 Jul; 12(7):615-621. view on PubMed

Cooper CS, Eeles R, Wedge DC, Van Loo P, Gundem G, Alexandrov LB, Kremeyer B, Butler A, Lynch AG, Camacho N, Massie CE, Kay J, Luxton HJ, Edwards S, Kote-Jarai Z, Dennis N, Merson S, Leongamornlert D, Zamora J, Corbishley C, Thomas S, Nik-Zainal S, Ramakrishna M, O'Meara S, Matthews L, Clark J, Hurst R, Mithen R, Bristow RG, Boutros PC, Fraser M, Cooke S, Raine K, Jones D, Menzies A, Stebbings L, Hinton J, Teague J, McLaren S, Mudie L, Hardy C, Anderson E, Joseph O, Goody V, Robinson B, Maddison M, Gamble S, Greenman C, Berney D, Hazell S, Livni N, ICGC Prostate Group, Fisher C, Ogden C, Kumar P, Thompson A, Woodhouse C, Nicol D, Mayer E, Dudderidge T, Shah NC, Gnanapragasam V, Voet T, Campbell P, Futreal A, Easton D, Warren AY, Foster CS, Stratton MR, Whitaker HC, McDermott U, Brewer DS, Neal DE. Corrigendum: analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue. Nat Genet. 2015 Jun; 47(6):689. view on PubMed

Boutros PC, Fraser M, Harding NJ, de Borja R, Trudel D, Lalonde E, Meng A, Hennings-Yeomans PH, McPherson A, Sabelnykova VY, Zia A, Fox NS, Livingstone J, Shiah YJ, Wang J, Beck TA, Have CL, Chong T, Sam M, Johns J, Timms L, Buchner N, Wong A, Watson JD, Simmons TT, P'ng C, Zafarana G, Nguyen F, Luo X, Chu KC, Prokopec SD, Sykes J, Dal Pra A, Berlin A, Brown A, Chan-Seng-Yue MA, Yousif F, Denroche RE, Chong LC, Chen GM, Jung E, Fung C, Starmans MH, Chen H, Govind SK, Hawley J, D'Costa A, Pintilie M, Waggott D, Hach F, Lambin P, Muthuswamy LB, Cooper C, Eeles R, Neal D, Tetu B, Sahinalp C, Stein LD, Fleshner N, Shah SP, Collins CC, Hudson TJ, McPherson JD, van der Kwast T, Bristow RG. Spatial genomic heterogeneity within localized, multifocal prostate cancer. Nat Genet. 2015 Jul; 47(7):736-45. view on PubMed

Ewing AD, Houlahan KE, Hu Y, Ellrott K, Caloian C, Yamaguchi TN, Bare JC, P'ng C, Waggott D, Sabelnykova VY, ICGC-TCGA DREAM Somatic Mutation Calling Challenge participants, Kellen MR, Norman TC, Haussler D, Friend SH, Stolovitzky G, Margolin AA, Stuart JM, Boutros PC. Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection. Nat Methods. 2015 Jul; 12(7):623-30. view on PubMed

Anghel CV, Quon G, Haider S, Nguyen F, Deshwar AG, Morris QD, Boutros PC. ISOpureR: an R implementation of a computational purification algorithm of mixed tumour profiles. BMC Bioinformatics. 2015 May 14; 16:156. view on PubMed

Starmans MH, Boutros PC. Biomarkers and subtypes of cancer. Aging (Albany NY). 2015 May; 7(5):280-1. view on PubMed

Reich HN, Sabelnykova VY, Boutros PC. Matching Kidneys and Urines: Establishing Noninvasive Surrogates of Intrarenal Events in Primary Glomerulonephritis. Semin Nephrol. 2015 May; 35(3):256-65. view on PubMed

How C, Pintilie M, Bruce JP, Hui AB, Clarke BA, Wong P, Yin S, Yan R, Waggott D, Boutros PC, Fyles A, Hedley DW, Hill RP, Milosevic M, Liu FF. Developing a prognostic micro-RNA signature for human cervical carcinoma. PLoS One. 2015; 10(4):e0123946. view on PubMed

Dodbiba L, Teichman J, Fleet A, Thai H, Starmans MH, Navab R, Chen Z, Girgis H, Eng L, Espin-Garcia O, Shen X, Bandarchi B, Schwock J, Tsao MS, El-Zimaity H, Der SD, Xu W, Bristow RG, Darling GE, Boutros PC, Ailles LE, Liu G. Appropriateness of using patient-derived xenograft models for pharmacologic evaluation of novel therapies for esophageal/gastro-esophageal junction cancers. PLoS One. 2015; 10(3):e0121872. view on PubMed

Cooper CS, Eeles R, Wedge DC, Van Loo P, Gundem G, Alexandrov LB, Kremeyer B, Butler A, Lynch AG, Camacho N, Massie CE, Kay J, Luxton HJ, Edwards S, Kote-Jarai Z, Dennis N, Merson S, Leongamornlert D, Zamora J, Corbishley C, Thomas S, Nik-Zainal S, O'Meara S, Matthews L, Clark J, Hurst R, Mithen R, Bristow RG, Boutros PC, Fraser M, Cooke S, Raine K, Jones D, Menzies A, Stebbings L, Hinton J, Teague J, McLaren S, Mudie L, Hardy C, Anderson E, Joseph O, Goody V, Robinson B, Maddison M, Gamble S, Greenman C, Berney D, Hazell S, Livni N, ICGC Prostate Group, Fisher C, Ogden C, Kumar P, Thompson A, Woodhouse C, Nicol D, Mayer E, Dudderidge T, Shah NC, Gnanapragasam V, Voet T, Campbell P, Futreal A, Easton D, Warren AY, Foster CS, Stratton MR, Whitaker HC, McDermott U, Brewer DS, Neal DE. Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue. Nat Genet. 2015 Apr; 47(4):367-372. view on PubMed

Bruce JP, Hui AB, Shi W, Perez-Ordonez B, Weinreb I, Xu W, Haibe-Kains B, Waggott DM, Boutros PC, O'Sullivan B, Waldron J, Huang SH, Chen EX, Gilbert R, Liu FF. Identification of a microRNA signature associated with risk of distant metastasis in nasopharyngeal carcinoma. Oncotarget. 2015 Feb 28; 6(6):4537-50. view on PubMed

Prokopec SD, Watson JD, Lee J, Pohjanvirta R, Boutros PC. Sex-related differences in murine hepatic transcriptional and proteomic responses to TCDD. Toxicol Appl Pharmacol. 2015 Apr 15; 284(2):188-96. view on PubMed

Shiah YJ, Tharmapalan P, Casey AE, Joshi PA, McKee TD, Jackson HW, Beristain AG, Chan-Seng-Yue MA, Bader GD, Lydon JP, Waterhouse PD, Boutros PC, Khokha R. A Progesterone-CXCR4 Axis Controls Mammary Progenitor Cell Fate in the Adult Gland. Stem Cell Reports. 2015 Mar 10; 4(3):313-322. view on PubMed

Ignatchenko V, Ignatchenko A, Sinha A, Boutros PC, Kislinger T. VennDIS: a JavaFX-based Venn and Euler diagram software to generate publication quality figures. Proteomics. 2015 Apr; 15(7):1239-44. view on PubMed

Starmans MH, Pintilie M, Chan-Seng-Yue M, Moon NC, Haider S, Nguyen F, Lau SK, Liu N, Kasprzyk A, Wouters BG, Der SD, Shepherd FA, Jurisica I, Penn LZ, Tsao MS, Lambin P, Boutros PC. Integrating RAS status into prognostic signatures for adenocarcinomas of the lung. Clin Cancer Res. 2015 Mar 15; 21(6):1477-86. view on PubMed

van Gisbergen MW, Voets AM, Starmans MH, de Coo IF, Yadak R, Hoffmann RF, Boutros PC, Smeets HJ, Dubois L, Lambin P. How do changes in the mtDNA and mitochondrial dysfunction influence cancer and cancer therapy? Challenges, opportunities and models. Mutat Res Rev Mutat Res. 2015 Apr-Jun; 764:16-30. view on PubMed

Houlahan KE, Prokopec SD, Moffat ID, Lindén J, Lensu S, Okey AB, Pohjanvirta R, Boutros PC. Transcriptional profiling of rat hypothalamus response to 2,3,7,8-tetrachlorodibenzo-ρ-dioxin. Toxicology. 2015 Feb 03; 328:93-101. view on PubMed

Sun RX, Chong LC, Simmons TT, Houlahan KE, Prokopec SD, Watson JD, Moffat ID, Lensu S, Lindén J, P'ng C, Okey AB, Pohjanvirta R, Boutros PC. Cross-species transcriptomic analysis elucidates constitutive aryl hydrocarbon receptor activity. BMC Genomics. 2014 Dec 03; 15:1053. view on PubMed

Berlin A, Lalonde E, Sykes J, Zafarana G, Chu KC, Ramnarine VR, Ishkanian A, Sendorek DH, Pasic I, Lam WL, Jurisica I, van der Kwast T, Milosevic M, Boutros PC, Bristow RG. NBN gain is predictive for adverse outcome following image-guided radiotherapy for localized prostate cancer. Oncotarget. 2014 Nov 30; 5(22):11081-90. view on PubMed

Nichols AC, Black M, Yoo J, Pinto N, Fernandes A, Haibe-Kains B, Boutros PC, Barrett JW. Exploiting high-throughput cell line drug screening studies to identify candidate therapeutic agents in head and neck cancer. BMC Pharmacol Toxicol. 2014 Nov 27; 15:66. view on PubMed

Lalonde E, Ishkanian AS, Sykes J, Fraser M, Ross-Adams H, Erho N, Dunning MJ, Halim S, Lamb AD, Moon NC, Zafarana G, Warren AY, Meng X, Thoms J, Grzadkowski MR, Berlin A, Have CL, Ramnarine VR, Yao CQ, Malloff CA, Lam LL, Xie H, Harding NJ, Mak DYF, Chu KC, Chong LC, Sendorek DH, P'ng C, Collins CC, Squire JA, Jurisica I, Cooper C, Eeles R, Pintilie M, Dal Pra A, Davicioni E, Lam WL, Milosevic M, Neal DE, van der Kwast T, Boutros PC, Bristow RG. Tumour genomic and microenvironmental heterogeneity for integrated prediction of 5-year biochemical recurrence of prostate cancer: a retrospective cohort study. Lancet Oncol. 2014 Dec; 15(13):1521-1532. view on PubMed

Alfaro JA, Sinha A, Kislinger T, Boutros PC. Onco-proteogenomics: cancer proteomics joins forces with genomics. Nat Methods. 2014 Nov; 11(11):1107-13. view on PubMed

van den Beucken T, Koch E, Chu K, Rupaimoole R, Prickaerts P, Adriaens M, Voncken JW, Harris AL, Buffa FM, Haider S, Starmans MHW, Yao CQ, Ivan M, Ivan C, Pecot CV, Boutros PC, Sood AK, Koritzinsky M, Wouters BG. Hypoxia promotes stem cell phenotypes and poor prognosis through epigenetic regulation of DICER. Nat Commun. 2014 Oct 29; 5:5203. view on PubMed

Prokopec SD, Watson JD, Pohjanvirta R, Boutros PC. Identification of reference proteins for Western blot analyses in mouse model systems of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) toxicity. PLoS One. 2014; 9(10):e110730. view on PubMed

Yao CQ, Nguyen F, Haider S, Starmans MH, Lambin P, Boutros PC. The transcriptomic profile of ovarian cancer grading. Cancer Med. 2015 Jan; 4(1):56-64. view on PubMed

Sepiashvili L, Waggott D, Hui A, Shi W, Su S, Ignatchenko A, Ignatchenko V, Laureano M, Huang SH, Xu W, Weinreb I, Waldron J, O'Sullivan B, Irish JC, Boutros PC, Liu FF, Kislinger T. Integrated omic analysis of oropharyngeal carcinomas reveals human papillomavirus (HPV)-dependent regulation of the activator protein 1 (AP-1) pathway. Mol Cell Proteomics. 2014 Dec; 13(12):3572-84. view on PubMed

Weinreb I, Piscuoglio S, Martelotto LG, Waggott D, Ng CK, Perez-Ordonez B, Harding NJ, Alfaro J, Chu KC, Viale A, Fusco N, da Cruz Paula A, Marchio C, Sakr RA, Lim R, Thompson LD, Chiosea SI, Seethala RR, Skalova A, Stelow EB, Fonseca I, Assaad A, How C, Wang J, de Borja R, Chan-Seng-Yue M, Howlett CJ, Nichols AC, Wen YH, Katabi N, Buchner N, Mullen L, Kislinger T, Wouters BG, Liu FF, Norton L, McPherson JD, Rubin BP, Clarke BA, Weigelt B, Boutros PC, Reis-Filho JS. Hotspot activating PRKD1 somatic mutations in polymorphous low-grade adenocarcinomas of the salivary glands. Nat Genet. 2014 Nov; 46(11):1166-9. view on PubMed

Boutros PC, Margolin AA, Stuart JM, Califano A, Stolovitzky G. Toward better benchmarking: challenge-based methods assessment in cancer genomics. Genome Biol. 2014 Sep 17; 15(9):462. view on PubMed

Li T, Prokopec SD, Morrison S, Lou W, Reich H, Gladman D, Urowitz M, Scholey J, Fortin PR, Boutros PC, Wither J, Landolt-Marticorena C. Anti-nucleosome antibodies outperform traditional biomarkers as longitudinal indicators of disease activity in systemic lupus erythematosus. Rheumatology (Oxford). 2015 Mar; 54(3):449-57. view on PubMed

Chong LC, Albuquerque MA, Harding NJ, Caloian C, Chan-Seng-Yue M, de Borja R, Fraser M, Denroche RE, Beck TA, van der Kwast T, Bristow RG, McPherson JD, Boutros PC. SeqControl: process control for DNA sequencing. Nat Methods. 2014 Oct; 11(10):1071-5. view on PubMed

Weinreb I, Zhang L, Tirunagari LM, Sung YS, Chen CL, Perez-Ordonez B, Clarke BA, Skalova A, Chiosea SI, Seethala RR, Waggott D, Boutros PC, How C, Liu FF, Irish JC, Goldstein DP, Gilbert R, Ud Din N, Assaad A, Hornick JL, Thompson LD, Antonescu CR. Novel PRKD gene rearrangements and variant fusions in cribriform adenocarcinoma of salivary gland origin. Genes Chromosomes Cancer. 2014 Oct; 53(10):845-56. view on PubMed

Fox NS, Starmans MH, Haider S, Lambin P, Boutros PC. Ensemble analyses improve signatures of tumour hypoxia and reveal inter-platform differences. BMC Bioinformatics. 2014 Jun 06; 15:170. view on PubMed

Smits KM, Melotte V, Niessen HE, Dubois L, Oberije C, Troost EG, Starmans MH, Boutros PC, Vooijs M, van Engeland M, Lambin P. Epigenetics in radiotherapy: where are we heading? Radiother Oncol. 2014 May; 111(2):168-77. view on PubMed

Coschi CH, Ishak CA, Gallo D, Marshall A, Talluri S, Wang J, Cecchini MJ, Martens AL, Percy V, Welch I, Boutros PC, Brown GW, Dick FA. Haploinsufficiency of an RB-E2F1-Condensin II complex leads to aberrant replication and aneuploidy. Cancer Discov. 2014 Jul; 4(7):840-53. view on PubMed

Real FX, Boutros PC, Malats N. Next-generation sequencing of urologic cancers: next is now. Eur Urol. 2014 Jul; 66(1):4-7. view on PubMed

Boutros PC, Ewing AD, Ellrott K, Norman TC, Dang KK, Hu Y, Kellen MR, Suver C, Bare JC, Stein LD, Spellman PT, Stolovitzky G, Friend SH, Margolin AA, Stuart JM. Global optimization of somatic variant identification in cancer genomes with a global community challenge. Nat Genet. 2014 Apr; 46(4):318-319. view on PubMed

Govind SK, Zia A, Hennings-Yeomans PH, Watson JD, Fraser M, Anghel C, Wyatt AW, van der Kwast T, Collins CC, McPherson JD, Bristow RG, Boutros PC. ShatterProof: operational detection and quantification of chromothripsis. BMC Bioinformatics. 2014 Mar 19; 15:78. view on PubMed

Hoeben BA, Starmans MH, Leijenaar RT, Dubois LJ, van der Kogel AJ, Kaanders JH, Boutros PC, Lambin P, Bussink J. Systematic analysis of 18F-FDG PET and metabolism, proliferation and hypoxia markers for classification of head and neck tumors. BMC Cancer. 2014 Feb 26; 14:130. view on PubMed

Miller JK, Buchner N, Timms L, Tam S, Luo X, Brown AM, Pasternack D, Bristow RG, Fraser M, Boutros PC, McPherson JD. Use of Sequenom sample ID Plus® SNP genotyping in identification of FFPE tumor samples. PLoS One. 2014; 9(2):e88163. view on PubMed

Goard CA, Chan-Seng-Yue M, Mullen PJ, Quiroga AD, Wasylishen AR, Clendening JW, Sendorek DH, Haider S, Lehner R, Boutros PC, Penn LZ. Identifying molecular features that distinguish fluvastatin-sensitive breast tumor cells. Breast Cancer Res Treat. 2014 Jan; 143(2):301-12. view on PubMed

Watson JD, Prokopec SD, Smith AB, Okey AB, Pohjanvirta R, Boutros PC. TCDD dysregulation of 13 AHR-target genes in rat liver. Toxicol Appl Pharmacol. 2014 Feb 01; 274(3):445-54. view on PubMed

Koritzinsky M, Levitin F, van den Beucken T, Rumantir RA, Harding NJ, Chu KC, Boutros PC, Braakman I, Wouters BG. Two phases of disulfide bond formation have differing requirements for oxygen. J Cell Biol. 2013 Nov 25; 203(4):615-27. view on PubMed

Peltekova VD, Lemire M, Qazi AM, Zaidi SH, Trinh QM, Bielecki R, Rogers M, Hodgson L, Wang M, D'Souza DJ, Zandi S, Chong T, Kwan JY, Kozak K, De Borja R, Timms L, Rangrej J, Volar M, Chan-Seng-Yue M, Beck T, Ash C, Lee S, Wang J, Boutros PC, Stein LD, Dick JE, Gryfe R, McPherson JD, Zanke BW, Pollett A, Gallinger S, Hudson TJ. Identification of genes expressed by immune cells of the colon that are regulated by colorectal cancer-associated variants. Int J Cancer. 2014 May 15; 134(10):2330-41. view on PubMed

Liew MS, Sia J, Starmans MH, Tafreshi A, Harris S, Feigen M, White S, Zimet A, Lambin P, Boutros PC, Mitchell P, John T. Comparison of toxicity and outcomes of concurrent radiotherapy with carboplatin/paclitaxel or cisplatin/etoposide in stage III non-small cell lung cancer. Cancer Med. 2013 Dec; 2(6):916-24. view on PubMed

Wasylishen AR, Chan-Seng-Yue M, Bros C, Dingar D, Tu WB, Kalkat M, Chan PK, Mullen PJ, Huang L, Meyer N, Raught B, Boutros PC, Penn LZ. MYC phosphorylation at novel regulatory regions suppresses transforming activity. Cancer Res. 2013 Nov 01; 73(21):6504-15. view on PubMed

Chamankhah M, Eftekharpour E, Karimi-Abdolrezaee S, Boutros PC, San-Marina S, Fehlings MG. Genome-wide gene expression profiling of stress response in a spinal cord clip compression injury model. BMC Genomics. 2013 Aug 28; 14:583. view on PubMed

Dal Pra A, Lalonde E, Sykes J, Warde F, Ishkanian A, Meng A, Maloff C, Srigley J, Joshua AM, Petrovics G, van der Kwast T, Evans A, Milosevic M, Saad F, Collins C, Squire J, Lam W, Bismar TA, Boutros PC, Bristow RG. TMPRSS2-ERG status is not prognostic following prostate cancer radiotherapy: implications for fusion status and DSB repair. Clin Cancer Res. 2013 Sep 15; 19(18):5202-9. view on PubMed

Gonzalez-Perez A, Mustonen V, Reva B, Ritchie GR, Creixell P, Karchin R, Vazquez M, Fink JL, Kassahn KS, Pearson JV, Bader GD, Boutros PC, Muthuswamy L, Ouellette BF, Reimand J, Linding R, Shibata T, Valencia A, Butler A, Dronov S, Flicek P, Shannon NB, Carter H, Ding L, Sander C, Stuart JM, Stein LD, Lopez-Bigas N, International Cancer Genome Consortium Mutation Pathways and Consequences Subgroup of the Bioinforma. Computational approaches to identify functional genetic variants in cancer genomes. Nat Methods. 2013 Aug; 10(8):723-9. view on PubMed

John T, Starmans MH, Chen YT, Russell PA, Barnett SA, White SC, Mitchell PL, Walkiewicz M, Azad A, Lambin P, Tsao MS, Deb S, Altorki N, Wright G, Knight S, Boutros PC, Cebon JS. The role of Cancer-Testis antigens as predictive and prognostic markers in non-small cell lung cancer. PLoS One. 2013; 8(7):e67876. view on PubMed

How C, Hui AB, Alajez NM, Shi W, Boutros PC, Clarke BA, Yan R, Pintilie M, Fyles A, Hedley DW, Hill RP, Milosevic M, Liu FF. MicroRNA-196b regulates the homeobox B7-vascular endothelial growth factor axis in cervical cancer. PLoS One. 2013; 8(7):e67846. view on PubMed

Prokopec SD, Buchner NB, Fox NS, Chong LC, Mak DY, Watson JD, Petronis A, Pohjanvirta R, Boutros PC. Validating reference genes within a mouse model system of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) toxicity. Chem Biol Interact. 2013 Sep 05; 205(1):63-71. view on PubMed

Cherney DZ, Zinman B, Kennedy CR, Moineddin R, Lai V, Yang S, Miller JA, Prokopec SD, Boutros PC, Scholey JW, Reich HN. Long-term hemodynamic and molecular effects persist after discontinued renin-angiotensin system blockade in patients with type 1 diabetes mellitus. Kidney Int. 2013 Dec; 84(6):1246-53. view on PubMed

Cappello P, Blaser H, Gorrini C, Lin DC, Elia AJ, Wakeham A, Haider S, Boutros PC, Mason JM, Miller NA, Youngson B, Done SJ, Mak TW. Role of Nek2 on centrosome duplication and aneuploidy in breast cancer cells. Oncogene. 2014 May 01; 33(18):2375-84. view on PubMed

Ching RW, Ahmed K, Boutros PC, Penn LZ, Bazett-Jones DP. Identifying gene locus associations with promyelocytic leukemia nuclear bodies using immuno-TRAP. J Cell Biol. 2013 Apr 15; 201(2):325-35. view on PubMed

Nichols AC, Chan-Seng-Yue M, Yoo J, Agrawal SK, Starmans MH, Waggott D, Harding NJ, Dowthwaite SA, Palma DA, Fung K, Wehrli B, Macneil SD, Lambin P, Winquist E, Koropatnick J, Mymryk JS, Boutros PC, Barrett JW. A case report and genetic characterization of a massive acinic cell carcinoma of the parotid with delayed distant metastases. Case Rep Oncol Med. 2013; 2013:270362. view on PubMed

Quon G, Haider S, Deshwar AG, Cui A, Boutros PC, Morris Q. Computational purification of individual tumor gene expression profiles leads to significant improvements in prognostic prediction. Genome Med. 2013 Mar 28; 5(3):29. view on PubMed

Rushlow DE, Mol BM, Kennett JY, Yee S, Pajovic S, Thériault BL, Prigoda-Lee NL, Spencer C, Dimaras H, Corson TW, Pang R, Massey C, Godbout R, Jiang Z, Zacksenhaus E, Paton K, Moll AC, Houdayer C, Raizis A, Halliday W, Lam WL, Boutros PC, Lohmann D, Dorsman JC, Gallie BL. Characterisation of retinoblastomas without RB1 mutations: genomic, gene expression, and clinical studies. Lancet Oncol. 2013 Apr; 14(4):327-34. view on PubMed

Lipina TV, Haque FN, McGirr A, Boutros PC, Berger T, Mak TW, Roder JC, Wong AH. Prophylactic valproic acid treatment prevents schizophrenia-related behaviour in Disc1-L100P mutant mice. PLoS One. 2012; 7(12):e51562. view on PubMed

Nichols AC, Chan-Seng-Yue M, Yoo J, Xu W, Dhaliwal S, Basmaji J, Szeto CC, Dowthwaite S, Todorovic B, Starmans MH, Lambin P, Palma DA, Fung K, Franklin JH, Wehrli B, Kwan K, Koropatnick J, Mymryk JS, Boutros P, Barrett JW. A Pilot Study Comparing HPV-Positive and HPV-Negative Head and Neck Squamous Cell Carcinomas by Whole Exome Sequencing. ISRN Oncol. 2012; 2012:809370. view on PubMed

Lambin P, van Stiphout RG, Starmans MH, Rios-Velazquez E, Nalbantov G, Aerts HJ, Roelofs E, van Elmpt W, Boutros PC, Granone P, Valentini V, Begg AC, De Ruysscher D, Dekker A. Predicting outcomes in radiation oncology--multifactorial decision support systems. Nat Rev Clin Oncol. 2013 Jan; 10(1):27-40. view on PubMed

Prokopec SD, Watson JD, Waggott DM, Smith AB, Wu AH, Okey AB, Pohjanvirta R, Boutros PC. Systematic evaluation of medium-throughput mRNA abundance platforms. RNA. 2013 Jan; 19(1):51-62. view on PubMed

Starmans MH, Pintilie M, John T, Der SD, Shepherd FA, Jurisica I, Lambin P, Tsao MS, Boutros PC. Exploiting the noise: improving biomarkers with ensembles of data analysis methodologies. Genome Med. 2012; 4(11):84. view on PubMed

Kim Y, Ignatchenko V, Yao CQ, Kalatskaya I, Nyalwidhe JO, Lance RS, Gramolini AO, Troyer DA, Stein LD, Boutros PC, Medin JA, Semmes OJ, Drake RR, Kislinger T. Identification of differentially expressed proteins in direct expressed prostatic secretions of men with organ-confined versus extracapsular prostate cancer. Mol Cell Proteomics. 2012 Dec; 11(12):1870-84. view on PubMed

Yu M, Lin G, Arshadi N, Kalatskaya I, Xue B, Haider S, Nguyen F, Boutros PC, Elson A, Muthuswamy LB, Tonks NK, Muthuswamy SK. Expression profiling during mammary epithelial cell three-dimensional morphogenesis identifies PTPRO as a novel regulator of morphogenesis and ErbB2-mediated transformation. Mol Cell Biol. 2012 Oct; 32(19):3913-24. view on PubMed

Lapuk AV, Wu C, Wyatt AW, McPherson A, McConeghy BJ, Brahmbhatt S, Mo F, Zoubeidi A, Anderson S, Bell RH, Haegert A, Shukin R, Wang Y, Fazli L, Hurtado-Coll A, Jones EC, Hach F, Hormozdiari F, Hajirasouliha I, Boutros PC, Bristow RG, Zhao Y, Marra MA, Fanjul A, Maher CA, Chinnaiyan AM, Rubin MA, Beltran H, Sahinalp SC, Gleave ME, Volik SV, Collins CC. From sequence to molecular pathology, and a mechanism driving the neuroendocrine phenotype in prostate cancer. J Pathol. 2012 Jul; 227(3):286-97. view on PubMed

Starmans MH, Lieuwes NG, Span PN, Haider S, Dubois L, Nguyen F, van Laarhoven HW, Sweep FC, Wouters BG, Boutros PC, Lambin P. Independent and functional validation of a multi-tumour-type proliferation signature. Br J Cancer. 2012 Jul 24; 107(3):508-15. view on PubMed

Chand D, Song L, deLannoy L, Barsyte-Lovejoy D, Ackloo S, Boutros PC, Evans K, Belsham DD, Lovejoy DA. C-Terminal region of teneurin-1 co-localizes with dystroglycan and modulates cytoskeletal organization through an extracellular signal-regulated kinase-dependent stathmin- and filamin A-mediated mechanism in hippocampal cells. Neuroscience. 2012 Sep 06; 219:255-70. view on PubMed

Cortese R, Kwan A, Lalonde E, Bryzgunova O, Bondar A, Wu Y, Gordevicius J, Park M, Oh G, Kaminsky Z, Tverkuviene J, Laurinavicius A, Jankevicius F, Sendorek DH, Haider S, Wang SC, Jarmalaite S, Laktionov P, Boutros PC, Petronis A. Epigenetic markers of prostate cancer in plasma circulating DNA. Hum Mol Genet. 2012 Aug 15; 21(16):3619-31. view on PubMed

Waggott D, Chu K, Yin S, Wouters BG, Liu FF, Boutros PC. NanoStringNorm: an extensible R package for the pre-processing of NanoString mRNA and miRNA data. Bioinformatics. 2012 Jun 01; 28(11):1546-8. view on PubMed

Luong ML, Hosseini-Moghaddam SM, Singer LG, Chaparro C, Azad S, Lazar N, Boutros PC, Keshavjee S, Rotstein C, Husain S. Risk factors for voriconazole hepatotoxicity at 12 weeks in lung transplant recipients. Am J Transplant. 2012 Jul; 12(7):1929-35. view on PubMed

Wu C, Wyatt AW, Lapuk AV, McPherson A, McConeghy BJ, Bell RH, Anderson S, Haegert A, Brahmbhatt S, Shukin R, Mo F, Li E, Fazli L, Hurtado-Coll A, Jones EC, Butterfield YS, Hach F, Hormozdiari F, Hajirasouliha I, Boutros PC, Bristow RG, Jones SJ, Hirst M, Marra MA, Maher CA, Chinnaiyan AM, Sahinalp SC, Gleave ME, Volik SV, Collins CC. Integrated genome and transcriptome sequencing identifies a novel form of hybrid and aggressive prostate cancer. J Pathol. 2012 May; 227(1):53-61. view on PubMed

Starmans MH, Chu KC, Haider S, Nguyen F, Seigneuric R, Magagnin MG, Koritzinsky M, Kasprzyk A, Boutros PC, Wouters BG, Lambin P. The prognostic value of temporal in vitro and in vivo derived hypoxia gene-expression signatures in breast cancer. Radiother Oncol. 2012 Mar; 102(3):436-43. view on PubMed

Yao CQ, Prokopec SD, Watson JD, Pang R, P'ng C, Chong LC, Harding NJ, Pohjanvirta R, Okey AB, Boutros PC. Inter-strain heterogeneity in rat hepatic transcriptomic responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Toxicol Appl Pharmacol. 2012 Apr 15; 260(2):135-45. view on PubMed

Ng T, Chand D, Song L, Al Chawaf A, Watson JD, Boutros PC, Belsham DD, Lovejoy DA. Identification of a novel brain derived neurotrophic factor (BDNF)-inhibitory factor: regulation of BDNF by teneurin C-terminal associated peptide (TCAP)-1 in immortalized embryonic mouse hypothalamic cells. Regul Pept. 2012 Feb 10; 174(1-3):79-89. view on PubMed

Hakem A, Bohgaki M, Lemmers B, Tai E, Salmena L, Matysiak-Zablocki E, Jung YS, Karaskova J, Kaustov L, Duan S, Madore J, Boutros P, Sheng Y, Chesi M, Bergsagel PL, Perez-Ordonez B, Mes-Masson AM, Penn L, Squire J, Chen X, Jurisica I, Arrowsmith C, Sanchez O, Benchimol S, Hakem R. Role of Pirh2 in mediating the regulation of p53 and c-Myc. PLoS Genet. 2011 Nov; 7(11):e1002360. view on PubMed

Goldenberg A, Mostafavi S, Quon G, Boutros PC, Morris QD. Unsupervised detection of genes of influence in lung cancer using biological networks. Bioinformatics. 2011 Nov 15; 27(22):3166-72. view on PubMed

Boutros PC, Moffat ID, Okey AB, Pohjanvirta R. mRNA levels in control rat liver display strain-specific, hereditary, and AHR-dependent components. PLoS One. 2011; 6(7):e18337. view on PubMed

Yan R, Boutros PC, Jurisica I. A tree-based approach for motif discovery and sequence classification. Bioinformatics. 2011 Aug 01; 27(15):2054-61. view on PubMed

Elschenbroich S, Ignatchenko V, Clarke B, Kalloger SE, Boutros PC, Gramolini AO, Shaw P, Jurisica I, Kislinger T. In-depth proteomics of ovarian cancer ascites: combining shotgun proteomics and selected reaction monitoring mass spectrometry. J Proteome Res. 2011 May 06; 10(5):2286-99. view on PubMed

Tan LA, Al Chawaf A, Vaccarino FJ, Boutros PC, Lovejoy DA. Teneurin C-terminal associated peptide (TCAP)-1 modulates dendritic morphology in hippocampal neurons and decreases anxiety-like behaviors in rats. Physiol Behav. 2011 Aug 03; 104(2):199-204. view on PubMed

Reich HN, Landolt-Marticorena C, Boutros PC, John R, Wither J, Fortin PR, Yang S, Scholey JW, Herzenberg AM. Molecular markers of injury in kidney biopsy specimens of patients with lupus nephritis. J Mol Diagn. 2011 Mar; 13(2):143-51. view on PubMed

Chen H, Boutros PC. VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R. BMC Bioinformatics. 2011 Jan 26; 12:35. view on PubMed

Boutros PC, Yao CQ, Watson JD, Wu AH, Moffat ID, Prokopec SD, Smith AB, Okey AB, Pohjanvirta R. Hepatic transcriptomic responses to TCDD in dioxin-sensitive and dioxin-resistant rats during the onset of toxicity. Toxicol Appl Pharmacol. 2011 Mar 01; 251(2):119-29. view on PubMed

Goard CA, Mather RG, Vinepal B, Clendening JW, Martirosyan A, Boutros PC, Sharom FJ, Penn LZ. Differential interactions between statins and P-glycoprotein: implications for exploiting statins as anticancer agents. Int J Cancer. 2010 Dec 15; 127(12):2936-48. view on PubMed

Boutros PC, Pintilie M, John T, Starmans MH, Der SD, Shepherd FA, Tsao MS, Jurisica I. Re: Gene expression-based prognostic signatures in lung cancer: ready for clinical use? J Natl Cancer Inst. 2010 Nov 03; 102(21):1677-8; author reply 1678-9. view on PubMed

Boutros PC. LTR: Linear Cross-Platform Integration of Microarray Data. Cancer Inform. 2010 Aug 27; 9:197-208. view on PubMed

Clendening JW, Pandyra A, Boutros PC, El Ghamrasni S, Khosravi F, Trentin GA, Martirosyan A, Hakem A, Hakem R, Jurisica I, Penn LZ. Dysregulation of the mevalonate pathway promotes transformation. Proc Natl Acad Sci U S A. 2010 Aug 24; 107(34):15051-6. view on PubMed

Wong WW, Boutros PC, Wasylishen AR, Guckert KD, O'Brien EM, Griffiths R, Martirosyan AR, Bros C, Jurisica I, Langler RF, Penn LZ. Characterization of the apoptotic response of human leukemia cells to organosulfur compounds. BMC Cancer. 2010 Jul 02; 10:351. view on PubMed

Tan KP, Wang B, Yang M, Boutros PC, Macaulay J, Xu H, Chuang AI, Kosuge K, Yamamoto M, Takahashi S, Wu AM, Ross DD, Harper PA, Ito S. Aryl hydrocarbon receptor is a transcriptional activator of the human breast cancer resistance protein (BCRP/ABCG2). Mol Pharmacol. 2010 Aug; 78(2):175-85. view on PubMed

Moffat ID, Boutros PC, Chen H, Okey AB, Pohjanvirta R. Aryl hydrocarbon receptor (AHR)-regulated transcriptomic changes in rats sensitive or resistant to major dioxin toxicities. BMC Genomics. 2010 Apr 26; 11:263. view on PubMed

International Cancer Genome Consortium, Hudson TJ, Anderson W, Artez A, Barker AD, Bell C, Bernabé RR, Bhan MK, Calvo F, Eerola I, Gerhard DS, Guttmacher A, Guyer M, Hemsley FM, Jennings JL, Kerr D, Klatt P, Kolar P, Kusada J, Lane DP, Laplace F, Youyong L, Nettekoven G, Ozenberger B, Peterson J, Rao TS, Remacle J, Schafer AJ, Shibata T, Stratton MR, Vockley JG, Watanabe K, Yang H, Yuen MM, Knoppers BM, Bobrow M, Cambon-Thomsen A, Dressler LG, Dyke SO, Joly Y, Kato K, Kennedy KL, Nicolás P, Parker MJ, Rial-Sebbag E, Romeo-Casabona CM, Shaw KM, Wallace S, Wiesner GL, Zeps N, Lichter P, Biankin AV, Chabannon C, Chin L, Clément B, de Alava E, Degos F, Ferguson ML, Geary P, Hayes DN, Hudson TJ, Johns AL, Kasprzyk A, Nakagawa H, Penny R, Piris MA, Sarin R, Scarpa A, Shibata T, van de Vijver M, Futreal PA, Aburatani H, Bayés M, Botwell DD, Campbell PJ, Estivill X, Gerhard DS, Grimmond SM, Gut I, Hirst M, López-Otín C, Majumder P, Marra M, McPherson JD, Nakagawa H, Ning Z, Puente XS, Ruan Y, Shibata T, Stratton MR, Stunnenberg HG, Swerdlow H, Velculescu VE, Wilson RK, Xue HH, Yang L, Spellman PT, Bader GD, Boutros PC, Campbell PJ, Flicek P, Getz G, Guigó R, Guo G, Haussler D, Heath S, Hubbard TJ, Jiang T, Jones SM, Li Q, López-Bigas N, Luo R, Muthuswamy L, Ouellette BF, Pearson JV, Puente XS, Quesada V, Raphael BJ, Sander C, Shibata T, Speed TP, Stein LD, Stuart JM, Teague JW, Totoki Y, Tsunoda T, Valencia A, Wheeler DA, Wu H, Zhao S, Zhou G, Stein LD, Guigó R, Hubbard TJ, Joly Y, Jones SM, Kasprzyk A, Lathrop M, López-Bigas N, Ouellette BF, Spellman PT, Teague JW, Thomas G, Valencia A, Yoshida T, Kennedy KL, Axton M, Dyke SO, Futreal PA, Gerhard DS, Gunter C, Guyer M, Hudson TJ, McPherson JD, Miller LJ, Ozenberger B, Shaw KM, Kasprzyk A, Stein LD, Zhang J, Haider SA, Wang J, Yung CK, Cros A, Cross A, Liang Y, Gnaneshan S, Guberman J, Hsu J, Bobrow M, Chalmers DR, Hasel KW, Joly Y, Kaan TS, Kennedy KL, Knoppers BM, Lowrance WW, Masui T, Nicolás P, Rial-Sebbag E, Rodriguez LL, Vergely C, Yoshida T, Grimmond SM, Biankin AV, Bowtell DD, Cloonan N, deFazio A, Eshleman JR, Etemadmoghadam D, Gardiner BB, Gardiner BA, Kench JG, Scarpa A, Sutherland RL, Tempero MA, Waddell NJ, Wilson PJ, McPherson JD, Gallinger S, Tsao MS, Shaw PA, Petersen GM, Mukhopadhyay D, Chin L, DePinho RA, Thayer S, Muthuswamy L, Shazand K, Beck T, Sam M, Timms L, Ballin V, Lu Y, Ji J, Zhang X, Chen F, Hu X, Zhou G, Yang Q, Tian G, Zhang L, Xing X, Li X, Zhu Z, Yu Y, Yu J, Yang H, Lathrop M, Tost J, Brennan P, Holcatova I, Zaridze D, Brazma A, Egevard L, Prokhortchouk E, Banks RE, Uhlén M, Cambon-Thomsen A, Viksna J, Ponten F, Skryabin K, Stratton MR, Futreal PA, Birney E, Borg A, Børresen-Dale AL, Caldas C, Foekens JA, Martin S, Reis-Filho JS, Richardson AL, Sotiriou C, Stunnenberg HG, Thoms G, van de Vijver M, van't Veer L, Calvo F, Birnbaum D, Blanche H, Boucher P, Boyault S, Chabannon C, Gut I, Masson-Jacquemier JD, Lathrop M, Pauporté I, Pivot X, Vincent-Salomon A, Tabone E, Theillet C, Thomas G, Tost J, Treilleux I, Calvo F, Bioulac-Sage P, Clément B, Decaens T, Degos F, Franco D, Gut I, Gut M, Heath S, Lathrop M, Samuel D, Thomas G, Zucman-Rossi J, Lichter P, Eils R, Brors B, Korbel JO, Korshunov A, Landgraf P, Lehrach H, Pfister S, Radlwimmer B, Reifenberger G, Taylor MD, von Kalle C, Majumder PP, Sarin R, Rao TS, Bhan MK, Scarpa A, Pederzoli P, Lawlor RA, Delledonne M, Bardelli A, Biankin AV, Grimmond SM, Gress T, Klimstra D, Zamboni G, Shibata T, Nakamura Y, Nakagawa H, Kusada J, Tsunoda T, Miyano S, Aburatani H, Kato K, Fujimoto A, Yoshida T, Campo E, López-Otín C, Estivill X, Guigó R, de Sanjosé S, Piris MA, Montserrat E, González-Díaz M, Puente XS, Jares P, Valencia A, Himmelbauer H, Himmelbaue H, Quesada V, Bea S, Stratton MR, Futreal PA, Campbell PJ, Vincent-Salomon A, Richardson AL, Reis-Filho JS, van de Vijver M, Thomas G, Masson-Jacquemier JD, Aparicio S, Borg A, Børresen-Dale AL, Caldas C, Foekens JA, Stunnenberg HG, van't Veer L, et al. International network of cancer genome projects. Nature. 2010 Apr 15; 464(7291):993-8. view on PubMed

Clendening JW, Pandyra A, Li Z, Boutros PC, Martirosyan A, Lehner R, Jurisica I, Trudel S, Penn LZ. Exploiting the mevalonate pathway to distinguish statin-sensitive multiple myeloma. Blood. 2010 Jun 10; 115(23):4787-97. view on PubMed

Li M, Lee KF, Lu Y, Clarke I, Shih D, Eberhart C, Collins VP, Van Meter T, Picard D, Zhou L, Boutros PC, Modena P, Liang ML, Scherer SW, Bouffet E, Rutka JT, Pomeroy SL, Lau CC, Taylor MD, Gajjar A, Dirks PB, Hawkins CE, Huang A. Frequent amplification of a chr19q13.41 microRNA polycistron in aggressive primitive neuroectodermal brain tumors. Cancer Cell. 2009 Dec 08; 16(6):533-46. view on PubMed

Boutros PC, Bielefeld KA, Pohjanvirta R, Harper PA. Dioxin-dependent and dioxin-independent gene batteries: comparison of liver and kidney in AHR-null mice. Toxicol Sci. 2009 Nov; 112(1):245-56. view on PubMed

Labrie V, Fukumura R, Rastogi A, Fick LJ, Wang W, Boutros PC, Kennedy JL, Semeralul MO, Lee FH, Baker GB, Belsham DD, Barger SW, Gondo Y, Wong AH, Roder JC. Serine racemase is associated with schizophrenia susceptibility in humans and in a mouse model. Hum Mol Genet. 2009 Sep 01; 18(17):3227-43. view on PubMed

Hui AB, Shi W, Boutros PC, Miller N, Pintilie M, Fyles T, McCready D, Wong D, Gerster K, Waldron L, Jurisica I, Penn LZ, Liu FF. Robust global micro-RNA profiling with formalin-fixed paraffin-embedded breast cancer tissues. Lab Invest. 2009 May; 89(5):597-606. view on PubMed

Boutros PC, Lau SK, Pintilie M, Liu N, Shepherd FA, Der SD, Tsao MS, Penn LZ, Jurisica I. Prognostic gene signatures for non-small-cell lung cancer. Proc Natl Acad Sci U S A. 2009 Feb 24; 106(8):2824-8. view on PubMed

Ponzielli R, Boutros PC, Katz S, Stojanova A, Hanley AP, Khosravi F, Bros C, Jurisica I, Penn LZ. Optimization of experimental design parameters for high-throughput chromatin immunoprecipitation studies. Nucleic Acids Res. 2008 Dec; 36(21):e144. view on PubMed

Boutros PC, Yan R, Moffat ID, Pohjanvirta R, Okey AB. Transcriptomic responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in liver: comparison of rat and mouse. BMC Genomics. 2008 Sep 16; 9:419. view on PubMed

Celius T, Roblin S, Harper PA, Matthews J, Boutros PC, Pohjanvirta R, Okey AB. Aryl hydrocarbon receptor-dependent induction of flavin-containing monooxygenase mRNAs in mouse liver. Drug Metab Dispos. 2008 Dec; 36(12):2499-505. view on PubMed

Beheshti Zavareh R, Lau KS, Hurren R, Datti A, Ashline DJ, Gronda M, Cheung P, Simpson CD, Liu W, Wasylishen AR, Boutros PC, Shi H, Vengopal A, Jurisica I, Penn LZ, Reinhold VN, Ezzat S, Wrana J, Rose DR, Schachter H, Dennis JW, Schimmer AD. Inhibition of the sodium/potassium ATPase impairs N-glycan expression and function. Cancer Res. 2008 Aug 15; 68(16):6688-97. view on PubMed

Franc MA, Moffat ID, Boutros PC, Tuomisto JT, Tuomisto J, Pohjanvirta R, Okey AB. Patterns of dioxin-altered mRNA expression in livers of dioxin-sensitive versus dioxin-resistant rats. Arch Toxicol. 2008 Nov; 82(11):809-30. view on PubMed

Pohjanvirta R, Boutros PC, Moffat ID, Lindén J, Wendelin D, Okey AB. Genome-wide effects of acute progressive feed restriction in liver and white adipose tissue. Toxicol Appl Pharmacol. 2008 Jul 01; 230(1):41-56. view on PubMed

Joshua AM, Boutros PC. Web-based resources for clinical bioinformatics. Methods Mol Med. 2008; 141:309-29. view on PubMed

Lau SK, Boutros PC, Pintilie M, Blackhall FH, Zhu CQ, Strumpf D, Johnston MR, Darling G, Keshavjee S, Waddell TK, Liu N, Lau D, Penn LZ, Shepherd FA, Jurisica I, Der SD, Tsao MS. Three-gene prognostic classifier for early-stage non small-cell lung cancer. J Clin Oncol. 2007 Dec 10; 25(35):5562-9. view on PubMed

Kim SS, Shago M, Kaustov L, Boutros PC, Clendening JW, Sheng Y, Trentin GA, Barsyte-Lovejoy D, Mao DY, Kay R, Jurisica I, Arrowsmith CH, Penn LZ. CUL7 is a novel antiapoptotic oncogene. Cancer Res. 2007 Oct 15; 67(20):9616-22. view on PubMed

Pacitto SR, Uetrecht JP, Boutros PC, Popovic M. Changes in gene expression induced by tienilic Acid and sulfamethoxazole: testing the danger hypothesis. J Immunotoxicol. 2007 Oct; 4(4):253-66. view on PubMed

Moffat ID, Boutros PC, Celius T, Lindén J, Pohjanvirta R, Okey AB. microRNAs in adult rodent liver are refractory to dioxin treatment. Toxicol Sci. 2007 Oct; 99(2):470-87. view on PubMed

Wong WW, Clendening JW, Martirosyan A, Boutros PC, Bros C, Khosravi F, Jurisica I, Stewart AK, Bergsagel PL, Penn LZ. Determinants of sensitivity to lovastatin-induced apoptosis in multiple myeloma. Mol Cancer Ther. 2007 Jun; 6(6):1886-97. view on PubMed

Semeralul MO, Boutros PC, Likhodi O, Okey AB, Van Tol HH, Wong AH. Microarray analysis of the developing cortex. J Neurobiol. 2006 Dec; 66(14):1646-58. view on PubMed

Bachtiary B, Boutros PC, Pintilie M, Shi W, Bastianutto C, Li JH, Schwock J, Zhang W, Penn LZ, Jurisica I, Fyles A, Liu FF. Gene expression profiling in cervical cancer: an exploration of intratumor heterogeneity. Clin Cancer Res. 2006 Oct 01; 12(19):5632-40. view on PubMed

Barsyte-Lovejoy D, Lau SK, Boutros PC, Khosravi F, Jurisica I, Andrulis IL, Tsao MS, Penn LZ. The c-Myc oncogene directly induces the H19 noncoding RNA by allele-specific binding to potentiate tumorigenesis. Cancer Res. 2006 May 15; 66(10):5330-7. view on PubMed

Pastorelli R, Carpi D, Campagna R, Airoldi L, Pohjanvirta R, Viluksela M, Hakansson H, Boutros PC, Moffat ID, Okey AB, Fanelli R. Differential expression profiling of the hepatic proteome in a rat model of dioxin resistance: correlation with genomic and transcriptomic analyses. Mol Cell Proteomics. 2006 May; 5(5):882-94. view on PubMed

Pohjanvirta R, Niittynen M, Lindén J, Boutros PC, Moffat ID, Okey AB. Evaluation of various housekeeping genes for their applicability for normalization of mRNA expression in dioxin-treated rats. Chem Biol Interact. 2006 Mar 25; 160(2):134-49. view on PubMed

Burgoon LD, Boutros PC, Dere E, Zacharewski TR. dbZach: A MIAME-compliant toxicogenomic supportive relational database. Toxicol Sci. 2006 Apr; 90(2):558-68. view on PubMed

Boutros PC, Okey AB. Unsupervised pattern recognition: an introduction to the whys and wherefores of clustering microarray data. Brief Bioinform. 2005 Dec; 6(4):331-43. view on PubMed

Tijet N, Boutros PC, Moffat ID, Okey AB, Tuomisto J, Pohjanvirta R. Aryl hydrocarbon receptor regulates distinct dioxin-dependent and dioxin-independent gene batteries. Mol Pharmacol. 2006 Jan; 69(1):140-53. view on PubMed

Okey AB, Franc MA, Moffat ID, Tijet N, Boutros PC, Korkalainen M, Tuomisto J, Pohjanvirta R. Toxicological implications of polymorphisms in receptors for xenobiotic chemicals: the case of the aryl hydrocarbon receptor. Toxicol Appl Pharmacol. 2005 Sep 01; 207(2 Suppl):43-51. view on PubMed

Séguin B, Boutros PC, Li X, Okey AB, Uetrecht JP. Gene expression profiling in a model of D-penicillamine-induced autoimmunity in the Brown Norway rat: predictive value of early signs of danger. Chem Res Toxicol. 2005 Aug; 18(8):1193-202. view on PubMed

Okey AB, Boutros PC, Harper PA. Polymorphisms of human nuclear receptors that control expression of drug-metabolizing enzymes. Pharmacogenet Genomics. 2005 Jun; 15(6):371-9. view on PubMed

Heisler LE, Torti D, Boutros PC, Watson J, Chan C, Winegarden N, Takahashi M, Yau P, Huang TH, Farnham PJ, Jurisica I, Woodgett JR, Bremner R, Penn LZ, Der SD. CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome. Nucleic Acids Res. 2005; 33(9):2952-61. view on PubMed

Boutros PC, Moffat ID, Franc MA, Tijet N, Tuomisto J, Pohjanvirta R, Okey AB. Dioxin-responsive AHRE-II gene battery: identification by phylogenetic footprinting. Biochem Biophys Res Commun. 2004 Aug 27; 321(3):707-15. view on PubMed

Boutros PC, Okey AB. PUNS: transcriptomic- and genomic-in silico PCR for enhanced primer design. Bioinformatics. 2004 Oct 12; 20(15):2399-400. view on PubMed