Paul Christopher Boutros

Title(s)Professor, Human Genetics
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    Title(s)Professor, Urology

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    University of Waterloo , CanadaB.Sc.2004Chemistry
    University of Toronto , CanadaPhD2008Medical Biophysics
    University of Toronto , CanadaExecutive MBA2016Business Administration
    Institute of Genetics, Canadian Institutes of Health Research, Canada2017Sex and Gender in Biomedical Research Workshop
    Howard Hughes Medical Institute, USA2022Mentorship Skills Development Course
    Rotman School of Management, University of Toronto, Canada2017Rotman-UHN Leadership Training Program
    University of California, Los Angeles, USA2021Advanced Faculty Mentoring Training
    Collapse Awards and Honors
    University of California, Los Angeles2023Excellence in Postdoctoral Mentoring Award
    University of California, Los Angeles2023Outstanding Mentorship Award, BIG Summer Research Program
    Journal of the National Cancer Institute2019  - 2020Top 25 Peer Reviewer
    Canadian Cancer Society20182018 Bernard and Francine Dorval Prize
    European Urology2018Reviewer of the Month
    Rotman School of Management, University of Toronto2016Dean’s List & Bregman’s Scholar
    Faculty of Medicine Graduate Teaching Award, University of Toronto2016Early Career Excellence in Graduate Teaching and Mentorship
    University of Waterloo, Faculty of Science2015Young Alumni Award
    DREAM AML Prognosis Challenge Sub-Challenge 2: Remission Duration20141st Place
    DREAM AML Prognosis Challenge Sub-Challenge 3: Overall Survival Time20141st Place
    Prostate Cancer Canada2013Travel Award
    Prostate Cancer Canada2012Collaboration Exploration and Development Award
    Canadian Cancer Society Research Institute2010CCSRI Junior Investigator Grant Panel Travel Award
    The 17th International Conference on Intelligent Systems for Molecular Biology2009Travel Award
    The 11th International Meeting of the Microarray and Gene Expression Data Society2008Travel Award (declined)
    Department of Medical Biophysics Harold Johns Memorial Prize2008First Place Oral Presentation
    BioConductor Workshop 20082008Travel Award
    International Society for Computational Biology Student Council2008Travel Award
    National Cancer Institute of Canada2007Travel Award
    Canadian Cancer Society2007Travel Award
    UHN Research Day 20062006Abstract Winner
    Canadian Institutes for Health Research / BioContact-Québec2006First Place CIHR Next Generation Award
    Canadian Institutes for Health Research / BioContact-Québec2006Travel Award
    Invitrogen Canada, Inc.2006Invitrogen Canada Young Investigator Silver Award
    Natural Sciences and Engineering Research Council2006  - 2009CGS Postgraduate Fellowship
    Excellence in Radiation Research for the 21st Century CIHR STIHR2006  - 2008CIHR Strategic Training Fellowship Alumni Award
    The Government of Ontario2006  - 2007Ontario Graduate Scholarship (declined)
    25th International Symposium on Halogenated Environmental Organic Pollutants and POPs2005Student Presenter Award
    CIHR EIRR21st Research Day2005Best Presentation Award
    Excellence in Radiation Research for the 21st Century CIHR STIHR2005  - 2007CIHR Strategic Training Fellowship (2007 declined)
    Institute for Robotics and Intelligent Systems2004PRECARN Fellowship
    15th International Symposium on Microsomes and Drug Oxidations; Mainz, Germany2004First Prize, Poster Presentations
    National Undergraduate Chemistry Conference2003First Place, Overall
    National Undergraduate Chemistry Conference2003Travel Award
    Southwestern Ontario Undergraduate Conference2003Second Place, Biochemistry Presentation
    University of Waterloo, Faculty of Science2002Dean’s Honour List
    Dow Canada Environmental Chemistry2001Work-Term Report Award

    Collapse Overview 
    Collapse Overview
    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.

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    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Comprehensive Prostate Fluid-Based Spectral Libraries for Enhanced Protein Detection in Urine. J Proteome Res. 2024 Apr 05. Ha A, Khoo A, Ignatchenko V, Khan S, Waas M, Vesprini D, Liu SK, Nyalwidhe JO, Semmes OJ, Boutros PC, Kislinger T. PMID: 38580319.
      View in: PubMed   Mentions:    Fields:    
    2. moPepGen: Rapid and Comprehensive Proteoform Identification. bioRxiv. 2024 Mar 31. Zhu C, Liu LY, Yamaguchi TN, Zhu H, Hugh-White R, Livingstone J, Patel Y, Kislinger T, Boutros PC. PMID: 38585946; PMCID: PMC10996593.
      View in: PubMed   Mentions:
    3. Genomic evolution shapes prostate cancer disease type. Cell Genom. 2024 Mar 13; 4(3):100511. 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. PMID: 38428419; PMCID: PMC10943594.
      View in: PubMed   Mentions: Translation:Humans
    4. The genomic and evolutionary landscapes of anaplastic thyroid carcinoma. Cell Rep. 2024 Mar 26; 43(3):113826. 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. PMID: 38412093.
      View in: PubMed   Mentions:    Fields:    
    5. Quantifying the seed sensitivity of cancer subclonal reconstruction algorithms. bioRxiv. 2024 Feb 08. Steinberg PL, Liu LY, Neiman-Golden A, Patel Y, Boutros PC. PMID: 38370678; PMCID: PMC10871259.
      View in: PubMed   Mentions:
    6. Increased Frequency of Clonal Hematopoiesis of Indeterminate Potential in Bloom Syndrome Probands and Carriers. medRxiv. 2024 Feb 06. Lin I, Wei A, Gebo TA, Boutros PC, Flanagan M, Kucine N, Cunniff C, Arboleda VA, Chang VY. PMID: 38370823; PMCID: PMC10871368.
      View in: PubMed   Mentions:
    7. PipeVal: light-weight extensible tool for file validation. Bioinformatics. 2024 02 01; 40(2). Patel Y, Beshlikyan A, Jordan M, Kim G, Holmes A, Yamaguchi TN, Boutros PC. PMID: 38341658; PMCID: PMC10893582.
      View in: PubMed   Mentions: 1     Fields:    
    8. NFTest: automated testing of Nextflow pipelines. Bioinformatics. 2024 02 01; 40(2). Patel Y, Zhu C, Yamaguchi TN, Bugh YZ, Tian M, Holmes A, Fitz-Gibbon ST, Boutros PC. PMID: 38341660; PMCID: PMC10881102.
      View in: PubMed   Mentions: 1     Fields:    
    9. Impact of PSMA PET on Prostate Cancer Management. Curr Treat Options Oncol. 2024 Feb; 25(2):191-205. Weiner AB, Agrawal R, Valle LF, Sonni I, Kishan AU, Rettig MB, Raman SS, Calais J, Boutros PC, Reiter RE. PMID: 38270802.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    10. Glioblastoma evolution and heterogeneity from a 3D whole-tumor perspective. Cell. 2024 01 18; 187(2):446-463.e16. 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. PMID: 38242087; PMCID: PMC10832360.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    11. Association of exercise with pan-cancer incidence and overall survival. Cancer Cell. 2024 02 12; 42(2):169-171. Lavery JA, Boutros PC, Knight D, Tammela T, Moskowitz CS, Jones LW. PMID: 38181796.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    12. 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. 2023 Dec 25. 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. PMID: 38151191.
      View in: PubMed   Mentions:    Fields:    
    13. HPV-negative head and neck cancers with adverse pathological features carry specific molecular changes that are associated with survival. Head Neck. 2024 Feb; 46(2):353-366. 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. PMID: 38059331.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    14. Prostate lineage-specific metabolism governs luminal differentiation and response to antiandrogen treatment. Nat Cell Biol. 2023 Dec; 25(12):1821-1832. 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. PMID: 38049604; PMCID: PMC10709144.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    15. MYC is a regulator of androgen receptor inhibition-induced metabolic requirements in prostate cancer. Cell Rep. 2023 10 31; 42(10):113221. 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. PMID: 37815914.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    16. Loss of LRP1B expression drives acquired chemo and radio-resistance in HPV-positive head and neck cancer. Oral Oncol. 2023 11; 146:106580. 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. PMID: 37778229.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    17. Pan-Cancer Analysis of Postdiagnosis Exercise and Mortality. J Clin Oncol. 2023 Nov 10; 41(32):4982-4992. Lavery JA, Boutros PC, Scott JM, Tammela T, Moskowitz CS, Jones LW. PMID: 37651670.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    18. The landscape of drug sensitivity and resistance in sarcoma. bioRxiv. 2023 Aug 08. 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. PMID: 37292676; PMCID: PMC10245988.
      View in: PubMed   Mentions:
    19. Prostate Cancer Reshapes the Secreted and Extracellular Vesicle Urinary Proteomes. bioRxiv. 2023 Jul 25. 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. PMID: 37546794; PMCID: PMC10402038.
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    20. Correction: Increased mRNA expression of CDKN2A is a transcriptomic marker of clinically aggressive meningiomas. Acta Neuropathol. 2023 Jul; 146(1):171-172. 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. PMID: 37171636; PMCID: PMC10261159.
      View in: PubMed   Mentions:    Fields:    
    21. Drug screening at single-organoid resolution via bioprinting and interferometry. Nat Commun. 2023 06 06; 14(1):3168. 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. PMID: 37280220; PMCID: PMC10244450.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    22. Evaluation of software impact designed for biomedical research: Are we measuring what's meaningful? ArXiv. 2023 Jun 05. 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. PMID: 37332562; PMCID: PMC10274942.
      View in: PubMed   Mentions:
    23. 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). Gamallat Y, Choudhry M, Li Q, Rokne JG, Alhajj R, Abdelsalam R, Ghosh S, Arbet J, Boutros PC, Bismar TA. PMID: 37345203; PMCID: PMC10216025.
      View in: PubMed   Mentions:
    24. Multimodal Biomarkers That Predict the Presence of Gleason Pattern 4: Potential Impact for Active Surveillance. J Urol. 2023 08; 210(2):257-271. 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. PMID: 37126232.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    25. Increased mRNA expression of CDKN2A is a transcriptomic marker of clinically aggressive meningiomas. Acta Neuropathol. 2023 07; 146(1):145-162. 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. PMID: 37093270; PMCID: PMC10261216.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    26. A polygenic two-hit hypothesis for prostate cancer. J Natl Cancer Inst. 2023 04 11; 115(4):468-472. 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. PMID: 36610996; PMCID: PMC10086625.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    27. 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. 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. PMID: 36870853.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    28. Fumarate Hydratase Variants and Their Association With Paraganglioma/Pheochromocytoma. Urology. 2023 Jun; 176:106-114. 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. PMID: 36773955.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    29. 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. Chan TW, Dodson JP, Arbet J, Boutros PC, Xiao X. PMID: 36449563; PMCID: PMC9898195.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    30. Author Correction: The evolutionary history of 2,658 cancers. Nature. 2023 Feb; 614(7948):E42. 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. PMID: 36697833; PMCID: PMC9931577.
      View in: PubMed   Mentions: 1     Fields:    
    31. Minimal information for reporting a genomics experiment. Blood. 2022 12 15; 140(24):2549-2555. Dreval K, Boutros PC, Morin RD. PMID: 36219881; PMCID: PMC10653092.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    32. Author Correction: Divergent mutational processes distinguish hypoxic and normoxic tumours. Nat Commun. 2022 Dec 08; 13(1):7569. Bhandari V, Li CH, Bristow RG, Boutros PC, PCAWG Consortium. PMID: 36481612.
      View in: PubMed   Mentions:    Fields:    
    33. Author Correction: Integrative pathway enrichment analysis of multivariate omics data. Nat Commun. 2022 Dec 08; 13(1):7570. 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. PMID: 36481658.
      View in: PubMed   Mentions:    Fields:    
    34. 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. Yuan J, Houlahan KE, Ramanand SG, Lee S, Baek G, Yang Y, Chen Y, Strand DW, Zhang MQ, Boutros PC, Mani RS. PMID: 36108240; PMCID: PMC9722594.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    35. Immune-based classification of HPV-associated oropharyngeal cancer with implications for biomarker-driven treatment de-intensification. EBioMedicine. 2022 Dec; 86:104373. 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. PMID: 36442320; PMCID: PMC9706534.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    36. Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative. PLoS Genet. 2022 11; 18(11):e1010367. Butler-Laporte G, Povysil G, Kosmicki JA, Cirulli ET, Drivas T, Furini S, Saad C, Schmidt A, Olszewski P, Korotko U, Quinodoz M, Çelik E, Kundu K, Walter K, Jung J, Stockwell AD, Sloofman LG, Jordan DM, Thompson RC, Del Valle D, Simons N, Cheng E, Sebra R, Schadt EE, Kim-Schulze S, Gnjatic S, Merad M, Buxbaum JD, Beckmann ND, Charney AW, Przychodzen B, Chang T, Pottinger TD, Shang N, Brand F, Fava F, Mari F, Chwialkowska K, Niemira M, Pula S, Baillie JK, Stuckey A, Salas A, Bello X, Pardo-Seco J, Gómez-Carballa A, Rivero-Calle I, Martinón-Torres F, Ganna A, Karczewski KJ, Veerapen K, Bourgey M, Bourque G, Eveleigh RJ, Forgetta V, Morrison D, Langlais D, Lathrop M, Mooser V, Nakanishi T, Frithiof R, Hultström M, Lipcsey M, Marincevic-Zuniga Y, Nordlund J, Schiabor Barrett KM, Lee W, Bolze A, White S, Riffle S, Tanudjaja F, Sandoval E, Neveux I, Dabe S, Casadei N, Motameny S, Alaamery M, Massadeh S, Aljawini N, Almutairi MS, Arabi YM, Alqahtani SA, Al Harthi FS, Almutairi A, Alqubaishi F, Alotaibi S, Binowayn A, Alsolm EA, El Bardisy H, Fawzy M, Cai F, Soranzo N, Butterworth A, COVID-19 Host Genetics Initiative, DeCOI Host Genetics Group, GEN-COVID Multicenter Study (Italy), Mount Sinai Clinical Intelligence Center, GEN-COVID consortium (Spain), GenOMICC Consortium, Japan COVID-19 Task Force, Regeneron Genetics Center, Geschwind DH, Arteaga S, Stephens A, Butte MJ, Boutros PC, Yamaguchi TN, Tao S, Eng S, Sanders T, Tung PJ, Broudy ME, Pan Y, Gonzalez A, Chavan N, Johnson R, Pasaniuc B, Yaspan B, Smieszek S, Rivolta C, Bibert S, Bochud PY, Dabrowski M, Zawadzki P, Sypniewski M, Kaja E, Chariyavilaskul P, Nilaratanakul V, Hirankarn N, Shotelersuk V, Pongpanich M, Phokaew C, Chetruengchai W, Tokunaga K, Sugiyama M, Kawai Y, Hasegawa T, Naito T, Namkoong H, Edahiro R, Kimura A, Ogawa S, Kanai T, Fukunaga K, Okada Y, Imoto S, Miyano S, Mangul S, Abedalthagafi MS, Zeberg H, Grzymski JJ, Washington NL, Ossowski S, Ludwig KU, Schulte EC, Riess O, Moniuszko M, Kwasniewski M, Mbarek H, Ismail SI, Verma A, Goldstein DB, Kiryluk K, Renieri A, Ferreira MAR, Richards JB. PMID: 36327219; PMCID: PMC9632827.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansCells
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    228. 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. Watson JD, Prokopec SD, Smith AB, Okey AB, Pohjanvirta R, Boutros PC. PMID: 27136898; PMCID: PMC5225275.
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    229. PD-L1 and Tumor Infiltrating Lymphocytes as Prognostic Markers in Resected NSCLC. PLoS One. 2016; 11(4):e0153954. Ameratunga M, Asadi K, Lin X, Walkiewicz M, Murone C, Knight S, Mitchell P, Boutros P, John T. PMID: 27104612; PMCID: PMC4841565.
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    230. Allele-Skewed DNA Modification in the Brain: Relevance to a Schizophrenia GWAS. Am J Hum Genet. 2016 May 05; 98(5):956-962. Gagliano SA, Ptak C, Mak DYF, Shamsi M, Oh G, Knight J, Boutros PC, Petronis A. PMID: 27087318; PMCID: PMC4863558.
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    231. Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease. Alzheimers Dement. 2016 06; 12(6):645-53. 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. PMID: 27079753; PMCID: PMC5474755.
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    232. PI3K/AKT/mTOR inhibition in combination with doxorubicin is an effective therapy for leiomyosarcoma. J Transl Med. 2016 Mar 08; 14:67. 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. PMID: 26952093; PMCID: PMC4782390.
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    233. Downregulation of histone H2A and H2B pathways is associated with anthracycline sensitivity in breast cancer. Breast Cancer Res. 2016 Feb 06; 18(1):16. 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. PMID: 26852132; PMCID: PMC4744406.
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    234. A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing. Nat Commun. 2015 Dec 09; 6:10001. 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. PMID: 26647970; PMCID: PMC4682041.
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    235. 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. Spears M, Yousif F, Lyttle N, Boutros PC, Munro AF, Twelves C, Pritchard KI, Levine MN, Shepherd L, Bartlett JM. PMID: 26372731; PMCID: PMC4741633.
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    236. The path to routine use of genomic biomarkers in the cancer clinic. Genome Res. 2015 Oct; 25(10):1508-13. Boutros PC. PMID: 26430161; PMCID: PMC4579336.
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    237. miR-620 promotes tumor radioresistance by targeting 15-hydroxyprostaglandin dehydrogenase (HPGD). Oncotarget. 2015 Sep 08; 6(26):22439-51. Huang X, Taeb S, Jahangiri S, Korpela E, Cadonic I, Yu N, Krylov SN, Fokas E, Boutros PC, Liu SK. PMID: 26068950; PMCID: PMC4673174.
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    238. 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. Lee J, Prokopec SD, Watson JD, Sun RX, Pohjanvirta R, Boutros PC. PMID: 26290441; PMCID: PMC4546048.
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    239. 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. Houlahan KE, Prokopec SD, Sun RX, Moffat ID, Lindén J, Lensu S, Okey AB, Pohjanvirta R, Boutros PC. PMID: 26232522.
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    240. Pathway and network analysis of cancer genomes. Nat Methods. 2015 Jul; 12(7):615-621. 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. PMID: 26125594; PMCID: PMC4717906.
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    241. 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. 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. PMID: 26018901.
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    242. Spatial genomic heterogeneity within localized, multifocal prostate cancer. Nat Genet. 2015 Jul; 47(7):736-45. 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. PMID: 26005866.
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    243. Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection. Nat Methods. 2015 Jul; 12(7):623-30. 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. PMID: 25984700; PMCID: PMC4856034.
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    244. ISOpureR: an R implementation of a computational purification algorithm of mixed tumour profiles. BMC Bioinformatics. 2015 May 14; 16:156. Anghel CV, Quon G, Haider S, Nguyen F, Deshwar AG, Morris QD, Boutros PC. PMID: 25972088; PMCID: PMC4429941.
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    245. Biomarkers and subtypes of cancer. Aging (Albany NY). 2015 May; 7(5):280-1. Starmans MH, Boutros PC. PMID: 26021974; PMCID: PMC4468304.
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    246. Matching Kidneys and Urines: Establishing Noninvasive Surrogates of Intrarenal Events in Primary Glomerulonephritis. Semin Nephrol. 2015 May; 35(3):256-65. Reich HN, Sabelnykova VY, Boutros PC. PMID: 26215863.
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    247. Developing a prognostic micro-RNA signature for human cervical carcinoma. PLoS One. 2015; 10(4):e0123946. 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. PMID: 25880806; PMCID: PMC4399941.
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    248. 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. 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. PMID: 25826681; PMCID: PMC4380353.
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    249. 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. 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. PMID: 25730763; PMCID: PMC4380509.
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    251. Sex-related differences in murine hepatic transcriptional and proteomic responses to TCDD. Toxicol Appl Pharmacol. 2015 Apr 15; 284(2):188-96. Prokopec SD, Watson JD, Lee J, Pohjanvirta R, Boutros PC. PMID: 25703434.
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    254. Integrating RAS status into prognostic signatures for adenocarcinomas of the lung. Clin Cancer Res. 2015 Mar 15; 21(6):1477-86. 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. PMID: 25609067.
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    255. 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. van Gisbergen MW, Voets AM, Starmans MH, de Coo IF, Yadak R, Hoffmann RF, Boutros PC, Smeets HJ, Dubois L, Lambin P. PMID: 26041263.
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    263. 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. Prokopec SD, Watson JD, Pohjanvirta R, Boutros PC. PMID: 25329058; PMCID: PMC4201576.
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    277. 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. Hoeben BA, Starmans MH, Leijenaar RT, Dubois LJ, van der Kogel AJ, Kaanders JH, Boutros PC, Lambin P, Bussink J. PMID: 24571588; PMCID: PMC3940254.
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    278. Use of Sequenom sample ID Plus® SNP genotyping in identification of FFPE tumor samples. PLoS One. 2014; 9(2):e88163. Miller JK, Buchner N, Timms L, Tam S, Luo X, Brown AM, Pasternack D, Bristow RG, Fraser M, Boutros PC, McPherson JD. PMID: 24551080; PMCID: PMC3923782.
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    279. Identifying molecular features that distinguish fluvastatin-sensitive breast tumor cells. Breast Cancer Res Treat. 2014 Jan; 143(2):301-12. Goard CA, Chan-Seng-Yue M, Mullen PJ, Quiroga AD, Wasylishen AR, Clendening JW, Sendorek DH, Haider S, Lehner R, Boutros PC, Penn LZ. PMID: 24337703.
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    280. TCDD dysregulation of 13 AHR-target genes in rat liver. Toxicol Appl Pharmacol. 2014 Feb 01; 274(3):445-54. Watson JD, Prokopec SD, Smith AB, Okey AB, Pohjanvirta R, Boutros PC. PMID: 24355419.
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    281. Two phases of disulfide bond formation have differing requirements for oxygen. J Cell Biol. 2013 Nov 25; 203(4):615-27. Koritzinsky M, Levitin F, van den Beucken T, Rumantir RA, Harding NJ, Chu KC, Boutros PC, Braakman I, Wouters BG. PMID: 24247433; PMCID: PMC3840938.
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    282. 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. 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. PMID: 24154973; PMCID: PMC3949167.
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    283. 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. Liew MS, Sia J, Starmans MH, Tafreshi A, Harris S, Feigen M, White S, Zimet A, Lambin P, Boutros PC, Mitchell P, John T. PMID: 24403265; PMCID: PMC3892396.
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    284. MYC phosphorylation at novel regulatory regions suppresses transforming activity. Cancer Res. 2013 Nov 01; 73(21):6504-15. 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. PMID: 24030976.
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    285. Genome-wide gene expression profiling of stress response in a spinal cord clip compression injury model. BMC Genomics. 2013 Aug 28; 14:583. Chamankhah M, Eftekharpour E, Karimi-Abdolrezaee S, Boutros PC, San-Marina S, Fehlings MG. PMID: 23984903; PMCID: PMC3846681.
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    286. 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. 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. PMID: 23918607.
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    287. Computational approaches to identify functional genetic variants in cancer genomes. Nat Methods. 2013 Aug; 10(8):723-9. 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. PMID: 23900255; PMCID: PMC3919555.
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    288. The role of Cancer-Testis antigens as predictive and prognostic markers in non-small cell lung cancer. PLoS One. 2013; 8(7):e67876. 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. PMID: 23935846; PMCID: PMC3720740.
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    289. MicroRNA-196b regulates the homeobox B7-vascular endothelial growth factor axis in cervical cancer. PLoS One. 2013; 8(7):e67846. 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. PMID: 23861821; PMCID: PMC3701631.
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    290. 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. Prokopec SD, Buchner NB, Fox NS, Chong LC, Mak DY, Watson JD, Petronis A, Pohjanvirta R, Boutros PC. PMID: 23791969.
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    291. 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. Cherney DZ, Zinman B, Kennedy CR, Moineddin R, Lai V, Yang S, Miller JA, Prokopec SD, Boutros PC, Scholey JW, Reich HN. PMID: 23760288.
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    292. Role of Nek2 on centrosome duplication and aneuploidy in breast cancer cells. Oncogene. 2014 May 01; 33(18):2375-84. 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. PMID: 23708664.
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    293. Identifying gene locus associations with promyelocytic leukemia nuclear bodies using immuno-TRAP. J Cell Biol. 2013 Apr 15; 201(2):325-35. Ching RW, Ahmed K, Boutros PC, Penn LZ, Bazett-Jones DP. PMID: 23589495; PMCID: PMC3628506.
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    294. 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. 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. PMID: 23653877; PMCID: PMC3638544.
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    295. Computational purification of individual tumor gene expression profiles leads to significant improvements in prognostic prediction. Genome Med. 2013 Mar 28; 5(3):29. Quon G, Haider S, Deshwar AG, Cui A, Boutros PC, Morris Q. PMID: 23537167; PMCID: PMC3706990.
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    296. Characterisation of retinoblastomas without RB1 mutations: genomic, gene expression, and clinical studies. Lancet Oncol. 2013 Apr; 14(4):327-34. 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. PMID: 23498719.
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    297. Prophylactic valproic acid treatment prevents schizophrenia-related behaviour in Disc1-L100P mutant mice. PLoS One. 2012; 7(12):e51562. Lipina TV, Haque FN, McGirr A, Boutros PC, Berger T, Mak TW, Roder JC, Wong AH. PMID: 23272119; PMCID: PMC3525594.
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    298. A Pilot Study Comparing HPV-Positive and HPV-Negative Head and Neck Squamous Cell Carcinomas by Whole Exome Sequencing. ISRN Oncol. 2012; 2012:809370. 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. PMID: 23304554; PMCID: PMC3530794.
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    299. Predicting outcomes in radiation oncology--multifactorial decision support systems. Nat Rev Clin Oncol. 2013 Jan; 10(1):27-40. 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. PMID: 23165123; PMCID: PMC4555846.
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    300. Systematic evaluation of medium-throughput mRNA abundance platforms. RNA. 2013 Jan; 19(1):51-62. Prokopec SD, Watson JD, Waggott DM, Smith AB, Wu AH, Okey AB, Pohjanvirta R, Boutros PC. PMID: 23169800; PMCID: PMC3527726.
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    301. Exploiting the noise: improving biomarkers with ensembles of data analysis methodologies. Genome Med. 2012; 4(11):84. Starmans MH, Pintilie M, John T, Der SD, Shepherd FA, Jurisica I, Lambin P, Tsao MS, Boutros PC. PMID: 23146350; PMCID: PMC3580418.
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    302. 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. 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. PMID: 22986220; PMCID: PMC3518113.
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    303. 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. Yu M, Lin G, Arshadi N, Kalatskaya I, Xue B, Haider S, Nguyen F, Boutros PC, Elson A, Muthuswamy LB, Tonks NK, Muthuswamy SK. PMID: 22851698; PMCID: PMC3457532.
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    304. From sequence to molecular pathology, and a mechanism driving the neuroendocrine phenotype in prostate cancer. J Pathol. 2012 Jul; 227(3):286-97. 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. PMID: 22553170; PMCID: PMC3659819.
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    305. Independent and functional validation of a multi-tumour-type proliferation signature. Br J Cancer. 2012 Jul 24; 107(3):508-15. Starmans MH, Lieuwes NG, Span PN, Haider S, Dubois L, Nguyen F, van Laarhoven HW, Sweep FC, Wouters BG, Boutros PC, Lambin P. PMID: 22722312; PMCID: PMC3405210.
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    306. 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. Chand D, Song L, deLannoy L, Barsyte-Lovejoy D, Ackloo S, Boutros PC, Evans K, Belsham DD, Lovejoy DA. PMID: 22698694.
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    307. Epigenetic markers of prostate cancer in plasma circulating DNA. Hum Mol Genet. 2012 Aug 15; 21(16):3619-31. 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. PMID: 22619380.
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    308. NanoStringNorm: an extensible R package for the pre-processing of NanoString mRNA and miRNA data. Bioinformatics. 2012 Jun 01; 28(11):1546-8. Waggott D, Chu K, Yin S, Wouters BG, Liu FF, Boutros PC. PMID: 22513995; PMCID: PMC3356845.
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    309. Risk factors for voriconazole hepatotoxicity at 12 weeks in lung transplant recipients. Am J Transplant. 2012 Jul; 12(7):1929-35. Luong ML, Hosseini-Moghaddam SM, Singer LG, Chaparro C, Azad S, Lazar N, Boutros PC, Keshavjee S, Rotstein C, Husain S. PMID: 22486950.
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    310. Integrated genome and transcriptome sequencing identifies a novel form of hybrid and aggressive prostate cancer. J Pathol. 2012 May; 227(1):53-61. 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. PMID: 22294438; PMCID: PMC3768138.
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    311. 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. Starmans MH, Chu KC, Haider S, Nguyen F, Seigneuric R, Magagnin MG, Koritzinsky M, Kasprzyk A, Boutros PC, Wouters BG, Lambin P. PMID: 22356756.
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    312. 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. Yao CQ, Prokopec SD, Watson JD, Pang R, P'ng C, Chong LC, Harding NJ, Pohjanvirta R, Okey AB, Boutros PC. PMID: 22342509.
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    313. 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. Ng T, Chand D, Song L, Al Chawaf A, Watson JD, Boutros PC, Belsham DD, Lovejoy DA. PMID: 22209827.
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    314. Role of Pirh2 in mediating the regulation of p53 and c-Myc. PLoS Genet. 2011 Nov; 7(11):e1002360. 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. PMID: 22125490; PMCID: PMC3219591.
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    315. Unsupervised detection of genes of influence in lung cancer using biological networks. Bioinformatics. 2011 Nov 15; 27(22):3166-72. Goldenberg A, Mostafavi S, Quon G, Boutros PC, Morris QD. PMID: 21965819.
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    316. mRNA levels in control rat liver display strain-specific, hereditary, and AHR-dependent components. PLoS One. 2011; 6(7):e18337. Boutros PC, Moffat ID, Okey AB, Pohjanvirta R. PMID: 21760882; PMCID: PMC3132743.
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    317. A tree-based approach for motif discovery and sequence classification. Bioinformatics. 2011 Aug 01; 27(15):2054-61. Yan R, Boutros PC, Jurisica I. PMID: 21685048.
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    318. 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. Elschenbroich S, Ignatchenko V, Clarke B, Kalloger SE, Boutros PC, Gramolini AO, Shaw P, Jurisica I, Kislinger T. PMID: 21491939.
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    319. 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. Tan LA, Al Chawaf A, Vaccarino FJ, Boutros PC, Lovejoy DA. PMID: 21411044.
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    320. Molecular markers of injury in kidney biopsy specimens of patients with lupus nephritis. J Mol Diagn. 2011 Mar; 13(2):143-51. Reich HN, Landolt-Marticorena C, Boutros PC, John R, Wither J, Fortin PR, Yang S, Scholey JW, Herzenberg AM. PMID: 21354048; PMCID: PMC3128621.
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    321. VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R. BMC Bioinformatics. 2011 Jan 26; 12:35. Chen H, Boutros PC. PMID: 21269502; PMCID: PMC3041657.
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    322. 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. Boutros PC, Yao CQ, Watson JD, Wu AH, Moffat ID, Prokopec SD, Smith AB, Okey AB, Pohjanvirta R. PMID: 21215274.
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    323. Differential interactions between statins and P-glycoprotein: implications for exploiting statins as anticancer agents. Int J Cancer. 2010 Dec 15; 127(12):2936-48. Goard CA, Mather RG, Vinepal B, Clendening JW, Martirosyan A, Boutros PC, Sharom FJ, Penn LZ. PMID: 21351272.
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    324. 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. Boutros PC, Pintilie M, John T, Starmans MH, Der SD, Shepherd FA, Tsao MS, Jurisica I. PMID: 20921041.
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    325. LTR: Linear Cross-Platform Integration of Microarray Data. Cancer Inform. 2010 Aug 27; 9:197-208. Boutros PC. PMID: 20838609; PMCID: PMC2935818.
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    326. Dysregulation of the mevalonate pathway promotes transformation. Proc Natl Acad Sci U S A. 2010 Aug 24; 107(34):15051-6. Clendening JW, Pandyra A, Boutros PC, El Ghamrasni S, Khosravi F, Trentin GA, Martirosyan A, Hakem A, Hakem R, Jurisica I, Penn LZ. PMID: 20696928; PMCID: PMC2930553.
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    327. Characterization of the apoptotic response of human leukemia cells to organosulfur compounds. BMC Cancer. 2010 Jul 02; 10:351. Wong WW, Boutros PC, Wasylishen AR, Guckert KD, O'Brien EM, Griffiths R, Martirosyan AR, Bros C, Jurisica I, Langler RF, Penn LZ. PMID: 20598143; PMCID: PMC2928001.
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    328. Aryl hydrocarbon receptor is a transcriptional activator of the human breast cancer resistance protein (BCRP/ABCG2). Mol Pharmacol. 2010 Aug; 78(2):175-85. 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. PMID: 20460431.
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    329. Aryl hydrocarbon receptor (AHR)-regulated transcriptomic changes in rats sensitive or resistant to major dioxin toxicities. BMC Genomics. 2010 Apr 26; 11:263. Moffat ID, Boutros PC, Chen H, Okey AB, Pohjanvirta R. PMID: 20420666; PMCID: PMC2881023.
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    330. International network of cancer genome projects. Nature. 2010 Apr 15; 464(7291):993-8. 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, et al. PMID: 20393554; PMCID: PMC2902243.
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    331. Exploiting the mevalonate pathway to distinguish statin-sensitive multiple myeloma. Blood. 2010 Jun 10; 115(23):4787-97. Clendening JW, Pandyra A, Li Z, Boutros PC, Martirosyan A, Lehner R, Jurisica I, Trudel S, Penn LZ. PMID: 20360469.
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    332. Frequent amplification of a chr19q13.41 microRNA polycistron in aggressive primitive neuroectodermal brain tumors. Cancer Cell. 2009 Dec 08; 16(6):533-46. 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. PMID: 19962671; PMCID: PMC3431561.
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    333. Dioxin-dependent and dioxin-independent gene batteries: comparison of liver and kidney in AHR-null mice. Toxicol Sci. 2009 Nov; 112(1):245-56. Boutros PC, Bielefeld KA, Pohjanvirta R, Harper PA. PMID: 19759094; PMCID: PMC2769058.
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    334. Serine racemase is associated with schizophrenia susceptibility in humans and in a mouse model. Hum Mol Genet. 2009 Sep 01; 18(17):3227-43. 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. PMID: 19483194; PMCID: PMC2722985.
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    335. Robust global micro-RNA profiling with formalin-fixed paraffin-embedded breast cancer tissues. Lab Invest. 2009 May; 89(5):597-606. 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. PMID: 19290006.
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    336. Prognostic gene signatures for non-small-cell lung cancer. Proc Natl Acad Sci U S A. 2009 Feb 24; 106(8):2824-8. Boutros PC, Lau SK, Pintilie M, Liu N, Shepherd FA, Der SD, Tsao MS, Penn LZ, Jurisica I. PMID: 19196983; PMCID: PMC2636731.
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    337. Optimization of experimental design parameters for high-throughput chromatin immunoprecipitation studies. Nucleic Acids Res. 2008 Dec; 36(21):e144. Ponzielli R, Boutros PC, Katz S, Stojanova A, Hanley AP, Khosravi F, Bros C, Jurisica I, Penn LZ. PMID: 18940864; PMCID: PMC2588500.
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    338. 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. Boutros PC, Yan R, Moffat ID, Pohjanvirta R, Okey AB. PMID: 18796159; PMCID: PMC2559853.
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    339. Aryl hydrocarbon receptor-dependent induction of flavin-containing monooxygenase mRNAs in mouse liver. Drug Metab Dispos. 2008 Dec; 36(12):2499-505. Celius T, Roblin S, Harper PA, Matthews J, Boutros PC, Pohjanvirta R, Okey AB. PMID: 18765683; PMCID: PMC5003606.
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    340. Inhibition of the sodium/potassium ATPase impairs N-glycan expression and function. Cancer Res. 2008 Aug 15; 68(16):6688-97. 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. PMID: 18701493.
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    341. Patterns of dioxin-altered mRNA expression in livers of dioxin-sensitive versus dioxin-resistant rats. Arch Toxicol. 2008 Nov; 82(11):809-30. Franc MA, Moffat ID, Boutros PC, Tuomisto JT, Tuomisto J, Pohjanvirta R, Okey AB. PMID: 18465118.
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    342. Genome-wide effects of acute progressive feed restriction in liver and white adipose tissue. Toxicol Appl Pharmacol. 2008 Jul 01; 230(1):41-56. Pohjanvirta R, Boutros PC, Moffat ID, Lindén J, Wendelin D, Okey AB. PMID: 18394668.
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    343. Web-based resources for clinical bioinformatics. Methods Mol Med. 2008; 141:309-29. Joshua AM, Boutros PC. PMID: 18453097.
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    344. Three-gene prognostic classifier for early-stage non small-cell lung cancer. J Clin Oncol. 2007 Dec 10; 25(35):5562-9. 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. PMID: 18065728.
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    345. CUL7 is a novel antiapoptotic oncogene. Cancer Res. 2007 Oct 15; 67(20):9616-22. 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. PMID: 17942889.
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    346. Changes in gene expression induced by tienilic Acid and sulfamethoxazole: testing the danger hypothesis. J Immunotoxicol. 2007 Oct; 4(4):253-66. Pacitto SR, Uetrecht JP, Boutros PC, Popovic M. PMID: 18958736.
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    347. microRNAs in adult rodent liver are refractory to dioxin treatment. Toxicol Sci. 2007 Oct; 99(2):470-87. Moffat ID, Boutros PC, Celius T, Lindén J, Pohjanvirta R, Okey AB. PMID: 17698510.
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    348. Determinants of sensitivity to lovastatin-induced apoptosis in multiple myeloma. Mol Cancer Ther. 2007 Jun; 6(6):1886-97. Wong WW, Clendening JW, Martirosyan A, Boutros PC, Bros C, Khosravi F, Jurisica I, Stewart AK, Bergsagel PL, Penn LZ. PMID: 17575117.
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    349. Microarray analysis of the developing cortex. J Neurobiol. 2006 Dec; 66(14):1646-58. Semeralul MO, Boutros PC, Likhodi O, Okey AB, Van Tol HH, Wong AH. PMID: 17013924.
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    350. Gene expression profiling in cervical cancer: an exploration of intratumor heterogeneity. Clin Cancer Res. 2006 Oct 01; 12(19):5632-40. Bachtiary B, Boutros PC, Pintilie M, Shi W, Bastianutto C, Li JH, Schwock J, Zhang W, Penn LZ, Jurisica I, Fyles A, Liu FF. PMID: 17020965.
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    351. 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. Barsyte-Lovejoy D, Lau SK, Boutros PC, Khosravi F, Jurisica I, Andrulis IL, Tsao MS, Penn LZ. PMID: 16707459.
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    352. 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. Pastorelli R, Carpi D, Campagna R, Airoldi L, Pohjanvirta R, Viluksela M, Hakansson H, Boutros PC, Moffat ID, Okey AB, Fanelli R. PMID: 16497791.
      View in: PubMed   Mentions: 14     Fields:    Translation:AnimalsCells
    353. 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. Pohjanvirta R, Niittynen M, Lindén J, Boutros PC, Moffat ID, Okey AB. PMID: 16466705.
      View in: PubMed   Mentions: 22     Fields:    Translation:Animals
    354. dbZach: A MIAME-compliant toxicogenomic supportive relational database. Toxicol Sci. 2006 Apr; 90(2):558-68. Burgoon LD, Boutros PC, Dere E, Zacharewski TR. PMID: 16403854.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimals
    355. Unsupervised pattern recognition: an introduction to the whys and wherefores of clustering microarray data. Brief Bioinform. 2005 Dec; 6(4):331-43. Boutros PC, Okey AB. PMID: 16420732.
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    356. Aryl hydrocarbon receptor regulates distinct dioxin-dependent and dioxin-independent gene batteries. Mol Pharmacol. 2006 Jan; 69(1):140-53. Tijet N, Boutros PC, Moffat ID, Okey AB, Tuomisto J, Pohjanvirta R. PMID: 16214954.
      View in: PubMed   Mentions: 123     Fields:    Translation:AnimalsCells
    357. 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. Okey AB, Franc MA, Moffat ID, Tijet N, Boutros PC, Korkalainen M, Tuomisto J, Pohjanvirta R. PMID: 15993909.
      View in: PubMed   Mentions: 35     Fields:    Translation:HumansAnimals
    358. 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. Séguin B, Boutros PC, Li X, Okey AB, Uetrecht JP. PMID: 16097792.
      View in: PubMed   Mentions: 2     Fields:    Translation:Animals
    359. Polymorphisms of human nuclear receptors that control expression of drug-metabolizing enzymes. Pharmacogenet Genomics. 2005 Jun; 15(6):371-9. Okey AB, Boutros PC, Harper PA. PMID: 15900209.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    360. 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. 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. PMID: 15911630; PMCID: PMC1137027.
      View in: PubMed   Mentions: 40     Fields:    Translation:HumansCells
    361. Dioxin-responsive AHRE-II gene battery: identification by phylogenetic footprinting. Biochem Biophys Res Commun. 2004 Aug 27; 321(3):707-15. Boutros PC, Moffat ID, Franc MA, Tijet N, Tuomisto J, Pohjanvirta R, Okey AB. PMID: 15358164.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansAnimalsCells
    362. PUNS: transcriptomic- and genomic-in silico PCR for enhanced primer design. Bioinformatics. 2004 Oct 12; 20(15):2399-400. Boutros PC, Okey AB. PMID: 15073008.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
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