Education and Training

Awards and Honors

• 1st Place, DREAM AML Prognosis Challenge Sub-Challenge 3: Overall Survival Time, 2014.
• 2018 Bernard and Francine Dorval Prize, Canadian Cancer Society, 2018.
• PRECARN Fellowship, Institute for Robotics and Intelligent Systems, 2004.
• Ontario Graduate Scholarship (declined), The Government of Ontario, 2006-2007.
• Travel Award, Canadian Cancer Society, 2007.
• Invitrogen Canada Young Investigator Silver Award, Invitrogen Canada, Inc., 2006.
• Student Presenter Award, 25th International Symposium on Halogenated Environmental Organic Pollutants and POPs, 2005.
• Second Place, Biochemistry Presentation, Southwestern Ontario Undergraduate Conference, 2003.
• CCSRI Junior Investigator Grant Panel Travel Award, Canadian Cancer Society Research Institute, 2010.
• Young Alumni Award, University of Waterloo, Faculty of Science, 2015.
• Excellence in Postdoctoral Mentoring Award, University of California, Los Angeles, 2023.
• Fellow, BioVision.Nxt, 2007.
• First Place CIHR Next Generation Award, Canadian Institutes for Health Research / BioContact-Québec, 2006.
• Travel Award, International Society for Computational Biology Student Council, 2008.
• CIHR Strategic Training Fellowship Alumni Award, Excellence in Radiation Research for the 21st Century CIHR STIHR, 2006-2008.
• First Prize, Poster Presentations, 15th International Symposium on Microsomes and Drug Oxidations; Mainz, Germany, 2004.
• Travel Award, National Cancer Institute of Canada, 2007.
• Abstract Winner, UHN Research Day 2006, 2006.
• 1st Place, DREAM AML Prognosis Challenge Sub-Challenge 2: Remission Duration, 2014.
• Travel Award, BioConductor Workshop 2008, 2008.
• First Place, Overall, National Undergraduate Chemistry Conference, 2003.
• Travel Award, Prostate Cancer Canada, 2013.
• Travel Award, Canadian Institutes for Health Research / BioContact-Québec, 2006.
• CGS Postgraduate Fellowship, Natural Sciences and Engineering Research Council, 2006-2009.
• Travel Award, National Undergraduate Chemistry Conference, 2003.
• First Place Oral Presentation, Department of Medical Biophysics Harold Johns Memorial Prize, 2008.
• Collaboration Exploration and Development Award, Prostate Cancer Canada, 2012.
• CIHR Strategic Training Fellowship (2007 declined), Excellence in Radiation Research for the 21st Century CIHR STIHR, 2005-2007.
• Travel Award, The 17th International Conference on Intelligent Systems for Molecular Biology, 2009.
• Reviewer of the Month, European Urology, 2018.
• Best Presentation Award, CIHR EIRR21st Research Day, 2005.
• Top 25 Peer Reviewer, Journal of the National Cancer Institute, 2019-2020.
• Work-Term Report Award, Dow Canada Environmental Chemistry, 2001.
• Travel Award (declined), The 11th International Meeting of the Microarray and Gene Expression Data Society, 2008.
• Early Career Excellence in Graduate Teaching and Mentorship, Faculty of Medicine Graduate Teaching Award, University of Toronto, 2016.
• Outstanding Mentorship Award, BIG Summer Research Program, University of California, Los Angeles, 2023.
• Dean’s List & Bregman’s Scholar, Rotman School of Management, University of Toronto, 2016.
• Dean’s Honour List, University of Waterloo, Faculty of Science, 2002.

Publications

1. 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.. Journal of proteome research, 2024.
2. 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 genomics, 2024.
3. 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 reports, 2024.
4. Patel Y, Zhu C, Yamaguchi TN, Bugh YZ, Tian M, Holmes A, Fitz-Gibbon ST, Boutros PC. NFTest: Automated testing of nextflow pipelines.. Bioinformatics (Oxford, England), 2024.
5. Patel Y, Beshlikyan A, Jordan M, Kim G, Holmes A, Yamaguchi TN, Boutros PC. PipeVal: light-weight extensible tool for file validation.. Bioinformatics (Oxford, England), 2024.
6. Steinberg PL, Liu LY, Neiman-Golden A, Patel Y, Boutros PC. Quantifying the seed sensitivity of cancer subclonal reconstruction algorithms.. bioRxiv : the preprint server for biology, 2024.
7. 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 : the preprint server for health sciences, 2024.
8. 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.. Current treatment options in oncology, 2024.
9. 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.
10. 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.
11. 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.. International journal of radiation oncology, biology, physics, 2023.
12. 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, 2023.
13. 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.. Nature cell biology, 2023.
14. 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 reports, 2023.
15. 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 oncology, 2023.
16. Lavery JA, Boutros PC, Scott JM, Tammela T, Moskowitz CS, Jones LW. Pan-Cancer Analysis of Postdiagnosis Exercise and Mortality.. Journal of clinical oncology : official journal of the American Society of Clinical Oncology, 2023.
17. 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 : the preprint server for biology, 2023.
18. 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 : the preprint server for biology, 2023.
19. 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 neuropathologica, 2023.
20. 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.. Nature communications, 2023.
21. 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.
22. 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, 2023.
23. 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.. The Journal of urology, 2023.
24. 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 neuropathologica, 2023.
25. 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.. Journal of the National Cancer Institute, 2023.
26. 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.. European urology oncology, 2023.
27. 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.
28. 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 research, 2023.
29. 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.
30. Dreval K, Boutros PC, Morin RD. Minimal information for reporting a genomics experiment.. Blood, 2022.
31. Bhandari V, Li CH, Bristow RG, Boutros PC, PCAWG Consortium. Author Correction: Divergent mutational processes distinguish hypoxic and normoxic tumours.. Nature communications, 2022.
32. 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.. Nature communications, 2022.
33. 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 discovery, 2022.
34. 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.
35. 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. Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative.. PLoS genetics, 2022.
36. Sjöström M, Zhao SG, Levy S, Zhang M, Ning Y, Shrestha R, Lundberg A, Herberts C, Foye A, Aggarwal R, Hua JT, Li H, Bergamaschi A, Maurice-Dror C, Maheshwari A, Chen S, Ng SWS, Ye W, Petricca J, Fraser M, Chesner L, Perry MD, Moreno-Rodriguez T, Chen WS, Alumkal JJ, Chou J, Morgans AK, Beer TM, Thomas GV, Gleave M, Lloyd P, Phillips T, McCarthy E, Haffner MC, Zoubeidi A, Annala M, Reiter RE, Rettig MB, Witte ON, Fong L, Bose R, Huang FW, Luo J, Bjartell A, Lang JM, Mahajan NP, Lara PN, Evans CP, Tran PT, Posadas EM, He C, Cui XL, Huang J, Zwart W, Gilbert LA, Maher CA, Boutros PC, Chi KN, Ashworth A, Small EJ, He HH, Wyatt AW, Quigley DA, Feng FY. The 5-Hydroxymethylcytosine Landscape of Prostate Cancer.. Cancer research, 2022.
37. 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 neuropathologica, 2022.
38. 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.. International journal of radiation oncology, biology, physics, 2022.
39. 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.
40. 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.
41. 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 and prostatic diseases, 2022.
42. 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, 2022.
43. 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 epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology, 2022.
44. 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.. Nature biotechnology, 2022.
45. 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 epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology, 2022.
46. 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.. Journal of hematology & oncology, 2022.
47. 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.. Nature communications, 2022.
48. 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.. The Journal of laryngology and otology, 2022.
49. 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 genomics and bioinformatics, 2022.
50. 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, England), 2022.
51. 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 oncology, 2022.
52. 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.. Journal of otolaryngology - head & neck surgery = Le Journal d'oto-rhino-laryngologie et de chirurgie cervico-faciale, 2022.
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54. 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.. Journal of extracellular vesicles, 2022.
55. Li CH, Haider S, Boutros PC. Age influences on the molecular presentation of tumours.. Nature communications, 2022.
56. 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 reports, 2021.
57. 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 network open, 2021.
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59. Livingstone J, Shiah YJ, Yamaguchi TN, Heisler LE, Huang V, Lesurf R, Gebo T, Carlin B, Eng S, Drysdale E, Green J, van der Kwast T, Bristow RG, Fraser M, Boutros PC. The telomere length landscape of prostate cancer.. Nature communications, 2021.
60. 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.. Canadian journal of kidney health and disease, 2021.
61. Ma TM, Roy S, Wu X, Mantz C, Fuller D, Miszczyk L, Napieralska A, Namysl-Kaletka A, Bagshaw HP, Buyyounouski MK, Glicksman R, Loblaw DA, Katz A, Upadhyaya SK, Nickols N, Steinberg ML, Philipson R, Aghdam N, Suy S, Pepin A, Collins SP, Boutros P, Rettig MB, Calais J, Wang M, Zaorsky N, Kishan AU. Refining the definition of biochemical failure in the era of stereotactic body radiation therapy for prostate cancer: The Phoenix definition and beyond.. Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology, 2021.
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63. 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, 2021.
64. Zhu C, Boutros PC. Sex Differences in Cancer Genomes: Much Learned, More Unknown.. Endocrinology, 2021.
65. 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.. Nature communications, 2021.
66. 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, 2021.
67. 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 research, 2021.
68. 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.. Nature reviews. Urology, 2021.
69. 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.
70. 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.. American journal of clinical and experimental urology, 2021.
71. 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.
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73. 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. Clinical applications, 2021.
74. 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 systems, 2021.
75. 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.. European urology open science, 2021.
76. Riaz N, Sherman E, Pei X, Schöder H, Grkovski M, Paudyal R, Katabi N, Selenica P, Yamaguchi TN, Ma D, Lee SK, Shah R, Kumar R, Kuo F, Ratnakumar A, Aleynick N, Brown D, Zhang Z, Hatzoglou V, Liu LY, Salcedo A, Tsai CJ, McBride S, Morris LGT, Boyle J, Singh B, Higginson DS, Damerla RR, Paula ADC, Price K, Moore EJ, Garcia JJ, Foote R, Ho A, Wong RJ, Chan TA, Powell SN, Boutros PC, Humm JL, Shukla-Dave A, Pfister D, Reis-Filho JS, Lee N. Precision Radiotherapy: Reduction in Radiation for Oropharyngeal Cancer in the 30 ROC Trial.. Journal of the National Cancer Institute, 2021.
77. Freeland J, Crowell PD, Giafaglione JM, Boutros PC, Goldstein AS. Aging of the progenitor cells that initiate prostate cancer.. Cancer letters, 2021.
78. 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, 2021.
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81. 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.
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83. 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.. European urology open science, 2021.
84. 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.. Nature communications, 2021.
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87. 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.. European urology, 2021.
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97. 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.. European urology, 2020.
98. 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 precision oncology, 2020.
99. 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.
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101. 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 medicine, 2020.
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105. 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. Clinical applications, 2020.
106. 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.. European urology oncology, 2020.
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109. 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.. Archives of toxicology, 2020.
110. Hoey C, Jeyapala R, Boutros PC, Bapat B, Liu SK. Urinary biomarkers in prostate cancer: to the miRnome and beyond.. Translational andrology and urology, 2020.
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113. 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.. Journal of the National Cancer Institute, 2020.
114. 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.
115. Bhandari V, Li CH, Bristow RG, Boutros PC, PCAWG Consortium. Divergent mutational processes distinguish hypoxic and normoxic tumours.. Nature communications, 2020.
116. 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.. Nature communications, 2020.
117. 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.. Nature communications, 2020.
118. 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.. Molecular cell, 2020.
119. 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.. Nature biotechnology, 2020.
120. Lin X, Boutros PC. Optimization and expansion of non-negative matrix factorization.. BMC bioinformatics, 2020.
121. 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 letters, 2019.
122. 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 oncology, 2019.
123. 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 genetics, 2019.
124. 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 of the head & neck, 2019.
125. 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 precision oncology, 2019.
126. 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.. Nature communications, 2019.
127. 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.
128. 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.. European urology, 2019.
129. 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.. Nature medicine, 2019.
130. 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.. Journal of clinical medicine, 2019.
131. 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.. Archives of toxicology, 2019.
132. 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 biology, 2019.
133. 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.. The Prostate, 2019.
134. 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.
135. 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.. Disease models & mechanisms, 2019.
136. Fox NS, Haider S, Harris AL, Boutros PC. Landscape of transcriptomic interactions between breast cancer and its microenvironment.. Nature communications, 2019.
137. Ray J, Hoey C, Huang X, Jeon J, Taeb S, Downes MR, Boutros PC, Liu SK. MicroRNA‑198 suppresses prostate tumorigenesis by targeting MIB1.. Oncology reports, 2019.
138. 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.. Nature biotechnology, 2019.
139. Taylor RA, Fraser M, Rebello RJ, Boutros PC, Murphy DG, Bristow RG, Risbridger GP. The influence of BRCA2 mutation on localized prostate cancer.. Nature reviews. Urology, 2019.
140. 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.. Nature communications, 2019.
141. 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.. Journal of translational medicine, 2019.
142. 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.. Translational lung cancer research, 2019.
143. 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 letters, 2019.
144. Prokopec SD, Pohjanvirta R, Mahiout S, Pettersson L, Boutros PC. Transcriptomic Impact of IMA-08401, a Novel AHR Agonist Resembling Laquinimod, on Rat Liver.. International journal of molecular sciences, 2019.
145. Sinha A, Huang V, Livingstone J, Wang J, Fox NS, Kurganovs N, Ignatchenko V, Fritsch K, Donmez N, Heisler LE, Shiah YJ, Yao CQ, Alfaro JA, Volik S, Lapuk A, Fraser M, Kron K, Murison A, Lupien M, Sahinalp C, Collins CC, Tetu B, Masoomian M, Berman DM, van der Kwast T, Bristow RG, Kislinger T, Boutros PC. The Proteogenomic Landscape of Curable Prostate Cancer.. Cancer cell, 2019.
146. 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.. Nature biotechnology, 2019.
147. Chen S, Huang V, Xu X, Livingstone J, Soares F, Jeon J, Zeng Y, Hua JT, Petricca J, Guo H, Wang M, Yousif F, Zhang Y, Donmez N, Ahmed M, Volik S, Lapuk A, Chua MLK, Heisler LE, Foucal A, Fox NS, Fraser M, Bhandari V, Shiah YJ, Guan J, Li J, Orain M, Picard V, Hovington H, Bergeron A, Lacombe L, Fradet Y, Têtu B, Liu S, Feng F, Wu X, Shao YW, Komor MA, Sahinalp C, Collins C, Hoogstrate Y, de Jong M, Fijneman RJA, Fei T, Jenster G, van der Kwast T, Bristow RG, Boutros PC, He HH. Widespread and Functional RNA Circularization in Localized Prostate Cancer.. Cell, 2019.
148. 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.. European urology, 2019.
149. 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.
150. 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.. Nature communications, 2019.
151. 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.. Nature genetics, 2019.
152. 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?. European urology focus, 2019.
153. 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.
154. 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.. International journal of cancer, 2018.
155. 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.
156. 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.
157. 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.. Nature communications, 2018.
158. 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.. Molecular cell, 2018.
159. 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 biology, 2018.
160. 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.
161. 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.
162. Li CH, Haider S, Shiah YJ, Thai K, Boutros PC. Sex Differences in Cancer Driver Genes and Biomarkers.. Cancer research, 2018.
163. 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.
164. Gong IY, Fox NS, Huang V, Boutros PC. Prediction of early breast cancer patient survival using ensembles of hypoxia signatures.. PloS one, 2018.
165. 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.. International journal of radiation oncology, biology, physics, 2018.
166. 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.. Nature communications, 2018.
167. Boutros PC. The Promise and Perils of Sequencing Individual Prostate Cancer Nuclei.. European urology, 2018.
168. Hua JT, Ahmed M, Guo H, Zhang Y, Chen S, Soares F, Lu J, Zhou S, Wang M, Li H, Larson NB, McDonnell SK, Patel PS, Liang Y, Yao CQ, van der Kwast T, Lupien M, Feng FY, Zoubeidi A, Tsao MS, Thibodeau SN, Boutros PC, He HH. Risk SNP-Mediated Promoter-Enhancer Switching Drives Prostate Cancer through lncRNA PCAT19.. Cell, 2018.
169. 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.. The Journal of cell biology, 2018.
170. 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.. Molecular oncology, 2018.
171. 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.
172. 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.
173. Encinas G, Sabelnykova VY, de Lyra EC, Hirata Katayama ML, Maistro S, de Vasconcellos Valle PWM, de Lima Pereira GF, Rodrigues LM, de Menezes Pacheco Serio PA, de Gouvêa ACRC, Geyer FC, Basso RA, Pasini FS, Del Pilar Esteves Diz M, Brentani MM, Guedes Sampaio Góes JC, Chammas R, Boutros PC, Koike Folgueira MAA. Somatic mutations in early onset luminal breast cancer.. Oncotarget, 2018.
174. Yang L, Roberts D, Takhar M, Erho N, Bibby BAS, Thiruthaneeswaran N, Bhandari V, Cheng WC, Haider S, McCorry AMB, McArt D, Jain S, Alshalalfa M, Ross A, Schaffer E, Den RB, Jeffrey Karnes R, Klein E, Hoskin PJ, Freedland SJ, Lamb AD, Neal DE, Buffa FM, Bristow RG, Boutros PC, Davicioni E, Choudhury A, West CML. Development and Validation of a 28-gene Hypoxia-related Prognostic Signature for Localized Prostate Cancer.. EBioMedicine, 2018.
175. Espiritu SMG, Liu LY, Rubanova Y, Bhandari V, Holgersen EM, Szyca LM, Fox NS, Chua MLK, Yamaguchi TN, Heisler LE, Livingstone J, Wintersinger J, Yousif F, Lalonde E, Rouette A, Salcedo A, Houlahan KE, Li CH, Huang V, Fraser M, van der Kwast T, Morris QD, Bristow RG, Boutros PC. The Evolutionary Landscape of Localized Prostate Cancers Drives Clinical Aggression.. Cell, 2018.
176. Wedge DC, Gundem G, Mitchell T, Woodcock DJ, Martincorena I, Ghori M, Zamora J, Butler A, Whitaker H, Kote-Jarai Z, Alexandrov LB, Van Loo P, Massie CE, Dentro S, Warren AY, Verrill C, Berney DM, Dennis N, Merson S, Hawkins S, Howat W, Lu YJ, Lambert A, Kay J, Kremeyer B, Karaszi K, Luxton H, Camacho N, Marsden L, Edwards S, Matthews L, Bo V, Leongamornlert D, McLaren S, Ng A, Yu Y, Zhang H, Dadaev T, Thomas S, Easton DF, Ahmed M, Bancroft E, Fisher C, Livni N, Nicol D, Tavaré S, Gill P, Greenman C, Khoo V, Van As N, Kumar P, Ogden C, Cahill D, Thompson A, Mayer E, Rowe E, Dudderidge T, Gnanapragasam V, Shah NC, Raine K, Jones D, Menzies A, Stebbings L, Teague J, Hazell S, Corbishley C, CAMCAP Study Group, de Bono J, Attard G, Isaacs W, Visakorpi T, Fraser M, Boutros PC, Bristow RG, Workman P, Sander C, TCGA Consortium, Hamdy FC, Futreal A, McDermott U, Al-Lazikani B, Lynch AG, Bova GS, Foster CS, Brewer DS, Neal DE, Cooper CS, Eeles RA. Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets.. Nature genetics, 2018.
177. Huang KL, Mashl RJ, Wu Y, Ritter DI, Wang J, Oh C, Paczkowska M, Reynolds S, Wyczalkowski MA, Oak N, Scott AD, Krassowski M, Cherniack AD, Houlahan KE, Jayasinghe R, Wang LB, Zhou DC, Liu D, Cao S, Kim YW, Koire A, McMichael JF, Hucthagowder V, Kim TB, Hahn A, Wang C, McLellan MD, Al-Mulla F, Johnson KJ, Cancer Genome Atlas Research Network, Lichtarge O, Boutros PC, Raphael B, Lazar AJ, Zhang W, Wendl MC, Govindan R, Jain S, Wheeler D, Kulkarni S, Dipersio JF, Reimand J, Meric-Bernstam F, Chen K, Shmulevich I, Plon SE, Chen F, Ding L. Pathogenic Germline Variants in 10,389 Adult Cancers.. Cell, 2018.
178. 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.. Journal of ovarian research, 2018.
179. 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.
180. Sendorek DH, Lalonde E, Yao CQ, Sabelnykova VY, Bristow RG, Boutros PC. NanoStringNormCNV: pre-processing of NanoString CNV data.. Bioinformatics (Oxford, England), 2018.
181. 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.
182. 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.
183. Fraser M, Boutros PC, Bristow RG. A Partner in Crime: Tumor-associated Stroma and Metastatic Prostate Cancer.. European urology, 2017.
184. Briollais L, Bristow RG, Boutros PC, PRACTICAL consortium, Zlotta AR. Response.. Journal of the National Cancer Institute, 2017.
185. Li M, Kouzmina E, McCusker M, Rodin D, Boutros PC, Paige CJ, Rodin G. Cytokines and depression in cancer patients and caregivers.. Neuropsychiatric disease and treatment, 2017.
186. 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.. Nature communications, 2017.
187. Shiah YJ, Fraser M, Bristow RG, Boutros PC. Comparison of pre-processing methods for Infinium HumanMethylation450 BeadChip array.. Bioinformatics (Oxford, England), 2017.
188. 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.. Nature communications, 2017.
189. 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 research, 2017.
190. 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.. Nature genetics, 2017.
191. 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 medicine, 2017.
192. 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.
193. 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.
194. Chua MLK, Lo W, Pintilie M, Murgic J, Lalonde E, Bhandari V, Mahamud O, Gopalan A, Kweldam CF, van Leenders GJLH, Verhoef EI, Hoogland AM, Livingstone J, Berlin A, Dal Pra A, Meng A, Zhang J, Orain M, Picard V, Hovington H, Bergeron A, Lacombe L, Fradet Y, Têtu B, Reuter VE, Fleshner N, Fraser M, Boutros PC, van der Kwast TH, Bristow RG. A Prostate Cancer "Nimbosus": Genomic Instability and SChLAP1 Dysregulation Underpin Aggression of Intraductal and Cribriform Subpathologies.. European urology, 2017.
195. Feldcamp LA, Boutros PC, Raymond R, Fletcher PJ, Nobrega JN, Wong AHC. Pdxdc1 modulates prepulse inhibition of acoustic startle in the mouse.. Translational psychiatry, 2017.
196. 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.
197. 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.
198. Briollais L, Ozcelik H, Xu J, Kwiatkowski M, Lalonde E, Sendorek DH, Fleshner NE, Recker F, Kuk C, Olkhov-Mitsel E, Savas S, Hanna S, Juvet T, Hunter GA, Friedlander M, Li H, Chadwick K, Prassas I, Soosaipillai A, Randazzo M, Trachtenberg J, Toi A, Shiah YJ, Fraser M, van der Kwast T, Bristow RG, Bapat B, Diamandis EP, Boutros PC, Zlotta AR. Germline Mutations in the Kallikrein 6 Region and Predisposition for Aggressive Prostate Cancer.. Journal of the National Cancer Institute, 2017.
199. 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.
200. 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.. Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer, 2017.
201. 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.
202. 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.
203. Prokopec SD, Houlahan KE, Sun RX, Watson JD, Yao CQ, Lee J, P'ng C, Pang R, Wu AH, Chong LC, Smith AB, Harding NJ, Moffat ID, Lindén J, Lensu S, Okey AB, Pohjanvirta R, Boutros PC. Compendium of TCDD-mediated transcriptomic response datasets in mammalian model systems.. BMC genomics, 2017.
204. Haider S, Waggott D, Lalonde E, Fung C, Liu FF, Boutros PC. Erratum to: A bedr way of genomic interval processing.. Source code for biology and medicine, 2017.
205. Fraser M, Sabelnykova VY, Yamaguchi TN, Heisler LE, Livingstone J, Huang V, Shiah YJ, Yousif F, Lin X, Masella AP, Fox NS, Xie M, Prokopec SD, Berlin A, Lalonde E, Ahmed M, Trudel D, Luo X, Beck TA, Meng A, Zhang J, D'Costa A, Denroche RE, Kong H, Espiritu SM, Chua ML, Wong A, Chong T, Sam M, Johns J, Timms L, Buchner NB, Orain M, Picard V, Hovington H, Murison A, Kron K, Harding NJ, P'ng C, Houlahan KE, Chu KC, Lo B, Nguyen F, Li CH, Sun RX, de Borja R, Cooper CI, Hopkins JF, Govind SK, Fung C, Waggott D, Green J, Haider S, Chan-Seng-Yue MA, Jung E, Wang Z, Bergeron A, Dal Pra A, Lacombe L, Collins CC, Sahinalp C, Lupien M, Fleshner NE, He HH, Fradet Y, Tetu B, van der Kwast T, McPherson JD, Bristow RG, Boutros PC. Genomic hallmarks of localized, non-indolent prostate cancer.. Nature, 2017.
206. Taylor RA, Fraser M, Livingstone J, Espiritu SM, Thorne H, Huang V, Lo W, Shiah YJ, Yamaguchi TN, Sliwinski A, Horsburgh S, Meng A, Heisler LE, Yu N, Yousif F, Papargiris M, Lawrence MG, Timms L, Murphy DG, Frydenberg M, Hopkins JF, Bolton D, Clouston D, McPherson JD, van der Kwast T, Boutros PC, Risbridger GP, Bristow RG. Germline BRCA2 mutations drive prostate cancers with distinct evolutionary trajectories.. Nature communications, 2017.
207. Haider S, Waggott D, Lalonde E, Fung C, Liu FF, Boutros PC. A bedr way of genomic interval processing.. Source code for biology and medicine, 2016.
208. 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.. Psycho-oncology, 2016.
209. 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.. Nature methods, 2016.
210. 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.. International journal of cancer, 2016.
211. 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.. European urology, 2016.
212. 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 research & therapy, 2016.
213. 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.
214. David M, Dursi LJ, Yao D, Boutros PC, Simpson JT. Nanocall: an open source basecaller for Oxford Nanopore sequencing data.. Bioinformatics (Oxford, England), 2016.
215. Huang BF, Boutros PC. The parameter sensitivity of random forests.. BMC bioinformatics, 2016.
216. 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.. Nature genetics, 2016.
217. 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.
218. 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.
219. 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 computational biology, 2016.
220. 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.. Nature communications, 2016.
221. Macdonald JM, Boutros PC. Log::ProgramInfo: A Perl module to collect and log data for bioinformatics pipelines.. Source code for biology and medicine, 2016.
222. Bhandari V, Boutros PC. Comparing continuous and discrete analyses of breast cancer survival information.. Genomics, 2016.
223. 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 (Georgetown, Tex.), 2016.
224. Chia PL, Gedye C, Boutros PC, Wheatley-Price P, John T. Current and Evolving Methods to Visualize Biological Data in Cancer Research.. Journal of the National Cancer Institute, 2016.
225. 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 epidemiology, 2016.
226. Boutros PC, Fraser M, van der Kwast T, Bristow RG. Clonality of localized and metastatic prostate cancer.. Current opinion in urology, 2016.
227. 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.. Archives of toxicology, 2016.
228. 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.
229. 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.. American journal of human genetics, 2016.
230. 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.. Alzheimer's & dementia : the journal of the Alzheimer's Association, 2016.
231. 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.. Journal of translational medicine, 2016.
232. 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 research : BCR, 2016.
233. 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.. Nature communications, 2015.
234. 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.
235. Boutros PC. The path to routine use of genomic biomarkers in the cancer clinic.. Genome research, 2015.
236. 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.
237. 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.
238. 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.. Toxicology and applied pharmacology, 2015.
239. 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.. Nature methods, 2015.
240. 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.. Nature genetics, 2015.
241. 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.. Nature genetics, 2015.
242. 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.. Nature methods, 2015.
243. 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.
244. Starmans MH, Boutros PC. Biomarkers and subtypes of cancer.. Aging, 2015.
245. Reich HN, Sabelnykova VY, Boutros PC. Matching Kidneys and Urines: Establishing Noninvasive Surrogates of Intrarenal Events in Primary Glomerulonephritis.. Seminars in nephrology, 2015.
246. 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.
247. 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.
248. 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.. Nature genetics, 2015.
249. 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.
250. Prokopec SD, Watson JD, Lee J, Pohjanvirta R, Boutros PC. Sex-related differences in murine hepatic transcriptional and proteomic responses to TCDD.. Toxicology and applied pharmacology, 2015.
251. 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.
252. 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.
253. 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.. Clinical cancer research : an official journal of the American Association for Cancer Research, 2015.
254. 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.. Mutation research. Reviews in mutation research, 2015.
255. 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, 2014.
256. 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.
257. 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.
258. 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 pharmacology & toxicology, 2014.
259. 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.. The Lancet. Oncology, 2014.
260. Alfaro JA, Sinha A, Kislinger T, Boutros PC. Onco-proteogenomics: cancer proteomics joins forces with genomics.. Nature methods, 2014.
261. 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.. Nature communications, 2014.
262. 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.
263. Yao CQ, Nguyen F, Haider S, Starmans MH, Lambin P, Boutros PC. The transcriptomic profile of ovarian cancer grading.. Cancer medicine, 2014.
264. 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.. Molecular & cellular proteomics : MCP, 2014.
265. 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.. Nature genetics, 2014.
266. Boutros PC, Margolin AA, Stuart JM, Califano A, Stolovitzky G. Toward better benchmarking: challenge-based methods assessment in cancer genomics.. Genome biology, 2014.
267. 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, England), 2014.
268. 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.. Nature methods, 2014.
269. 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.
270. 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.
271. 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?. Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology, 2014.
272. 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 discovery, 2014.
273. Real FX, Boutros PC, Malats N. Next-generation sequencing of urologic cancers: next is now.. European urology, 2014.
274. 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.. Nature genetics, 2014.
275. 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.
276. 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.
277. 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.
278. 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 research and treatment, 2013.
279. Watson JD, Prokopec SD, Smith AB, Okey AB, Pohjanvirta R, Boutros PC. TCDD dysregulation of 13 AHR-target genes in rat liver.. Toxicology and applied pharmacology, 2013.
280. 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.. The Journal of cell biology, 2013.
281. 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.. International journal of cancer, 2013.
282. 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 medicine, 2013.
283. 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 research, 2013.
284. 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.
285. 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.. Clinical cancer research : an official journal of the American Association for Cancer Research, 2013.
286. 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.. Nature methods, 2013.
287. 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.
288. 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.
289. 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.. Chemico-biological interactions, 2013.
290. 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 international, 2013.
291. 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, 2013.
292. Ching RW, Ahmed K, Boutros PC, Penn LZ, Bazett-Jones DP. Identifying gene locus associations with promyelocytic leukemia nuclear bodies using immuno-TRAP.. The Journal of cell biology, 2013.
293. 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 reports in oncological medicine, 2013.
294. 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 medicine, 2013.
295. 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.. The Lancet. Oncology, 2013.
296. 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.
297. 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 oncology, 2012.
298. 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.. Nature reviews. Clinical oncology, 2012.
299. 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 (New York, N.Y.), 2012.
300. 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 medicine, 2012.
301. 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.. Molecular & cellular proteomics : MCP, 2012.
302. 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.. Molecular and cellular biology, 2012.
303. 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.. The Journal of pathology, 2012.
304. 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.. British journal of cancer, 2012.
305. 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.
306. 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.. Human molecular genetics, 2012.
307. 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 (Oxford, England), 2012.
308. 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.. American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons, 2012.
309. 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.. The Journal of pathology, 2012.
310. 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.. Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology, 2012.
311. 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).. Toxicology and applied pharmacology, 2012.
312. 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.. Regulatory peptides, 2011.
313. 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 genetics, 2011.
314. Goldenberg A, Mostafavi S, Quon G, Boutros PC, Morris QD. Unsupervised detection of genes of influence in lung cancer using biological networks.. Bioinformatics (Oxford, England), 2011.
315. 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.
316. Yan R, Boutros PC, Jurisica I. A tree-based approach for motif discovery and sequence classification.. Bioinformatics (Oxford, England), 2011.
317. 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.. Journal of proteome research, 2011.
318. 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.. Physiology & behavior, 2011.
319. 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.. The Journal of molecular diagnostics : JMD, 2011.
320. Chen H, Boutros PC. VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R.. BMC bioinformatics, 2011.
321. 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.. Toxicology and applied pharmacology, 2011.
322. 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.. International journal of cancer, 2010.
323. 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?. Journal of the National Cancer Institute, 2010.
324. Boutros PC. LTR: Linear Cross-Platform Integration of Microarray Data.. Cancer informatics, 2010.
325. 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.. Proceedings of the National Academy of Sciences of the United States of America, 2010.
326. 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.
327. 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).. Molecular pharmacology, 2010.
328. 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.
329. 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.
330. 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.
331. 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.
332. Boutros PC, Bielefeld KA, Pohjanvirta R, Harper PA. Dioxin-dependent and dioxin-independent gene batteries: comparison of liver and kidney in AHR-null mice.. Toxicological sciences : an official journal of the Society of Toxicology, 2009.
333. 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.. Human molecular genetics, 2009.
334. 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.. Laboratory investigation; a journal of technical methods and pathology, 2009.
335. 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.. Proceedings of the National Academy of Sciences of the United States of America, 2009.
336. 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 research, 2008.
337. 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.
338. 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 metabolism and disposition: the biological fate of chemicals, 2008.
339. 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 research, 2008.
340. 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.. Archives of toxicology, 2008.
341. 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.. Toxicology and applied pharmacology, 2008.
342. Joshua AM, Boutros PC. Web-based resources for clinical bioinformatics.. Methods in molecular medicine, 2008.
343. 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.. Journal of clinical oncology : official journal of the American Society of Clinical Oncology, 2007.
344. 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 research, 2007.
345. Pacitto SR, Uetrecht JP, Boutros PC, Popovic M. Changes in gene expression induced by tienilic Acid and sulfamethoxazole: testing the danger hypothesis.. Journal of immunotoxicology, 2007.
346. Moffat ID, Boutros PC, Celius T, Lindén J, Pohjanvirta R, Okey AB. microRNAs in adult rodent liver are refractory to dioxin treatment.. Toxicological sciences : an official journal of the Society of Toxicology, 2007.
347. 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.. Molecular cancer therapeutics, 2007.
348. Semeralul MO, Boutros PC, Likhodi O, Okey AB, Van Tol HH, Wong AH. Microarray analysis of the developing cortex.. Journal of neurobiology, 2006.
349. 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.. Clinical cancer research : an official journal of the American Association for Cancer Research, 2006.
350. 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 research, 2006.
351. 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.. Molecular & cellular proteomics : MCP, 2006.
352. 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.. Chemico-biological interactions, 2006.
353. Burgoon LD, Boutros PC, Dere E, Zacharewski TR. dbZach: A MIAME-compliant toxicogenomic supportive relational database.. Toxicological sciences : an official journal of the Society of Toxicology, 2006.
354. Boutros PC, Okey AB. Unsupervised pattern recognition: an introduction to the whys and wherefores of clustering microarray data.. Briefings in bioinformatics, 2005.
355. Tijet N, Boutros PC, Moffat ID, Okey AB, Tuomisto J, Pohjanvirta R. Aryl hydrocarbon receptor regulates distinct dioxin-dependent and dioxin-independent gene batteries.. Molecular pharmacology, 2005.
356. 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.. Toxicology and applied pharmacology, 2005.
357. 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.. Chemical research in toxicology, 2005.
358. Okey AB, Boutros PC, Harper PA. Polymorphisms of human nuclear receptors that control expression of drug-metabolizing enzymes.. Pharmacogenetics and genomics, 2005.
359. 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 research, 2005.
360. Boutros PC, Moffat ID, Franc MA, Tijet N, Tuomisto J, Pohjanvirta R, Okey AB. Dioxin-responsive AHRE-II gene battery: identification by phylogenetic footprinting.. Biochemical and biophysical research communications, 2004.
361. Boutros PC, Okey AB. PUNS: transcriptomic- and genomic-in silico PCR for enhanced primer design.. Bioinformatics (Oxford, England), 2004.