Publications

2017

2017 Alfaro J, 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 (in press)
2017 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 (in press)
2017 Bayani J, Yao CQ, Quintayo MA, Yan F, Haider S, D’Costa A, Brookes CL, van de Velde CJ, Hasenburg A, Kieback DG, Markopoulos C, Dirix L, Seynaeve C, Re D, Boutros PC, Bartlett JM
“Molecular stratification of early breast cancer identifies drug targets to drive stratified medicine”
NPJ Breast Cancer (in press)
2017 Shiah YJ, Fraser M , Bristow RG, Boutros PC
“Comparison of Pre-processing Methods for Infinium HumanMethylation450 BeadChip Array”
Bioinformatics (in press) (PMID: 28605401)
2017 Chüeh AC, Liew MS, Russell PA, Walkiewicz M, Jayachandran A, Starmans MH, 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 (in press)
2017 Chua ML, Lo W, Pintilie M, Murgic J, Lalonde E, Mahamud O, Gopalan A, Kweldam CF, van Leenders GJ, Verhoef EI, Hoogland AM, Livingstone J, Bhandari V, Berlin A, Dal Pra A, Meng A, Zhang J, Orain M, Picard V, Honvington 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 Sub-pathologies”
European Urology (in press)
2017 Ghasemi F, Black M, Vizeacoumar F, Pinto N, Ruicci KM, Son Huu Le CC, 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 (in press) (PMID: 28488581)
2017 Feldcamp LA, Boutros PC, Raymond R, Fletcher PJ, Nobrega JN, Wong AHC
“Pdxdc1 modulates pre-pulse inhibition of acoustic startle in the mouse”
Translational Psychiatry 7(5):e1125 (PMID: 28485732)
2017 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 (in press)
2017 Albuquerque MA, Grande BM, Ritch EJ , Jessa S, Krzywinski M, Grewal JK, Shah SP, Boutros PC, Morin RD
"Enhancing Knowledge Discovery from Cancer Genomics Data with Galaxy”
Gigascience 6(5):1-13 (PMID: 28327945)
2017 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 S2352-3964(17)30081-30086 (PMID: 28286059)
2017 Thapa B, Salcedo A, Lin X, Walkeiwicz 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 17:30124-30127 (PMID: 28257959)
2017 Keller A, Gerkin RC, Guan Y, Panwar B, Dhurandhar A, Turu G, Szalai B, Mainland J, Ihara Y, Yu W, Wolfinger R, Vens C, Schietgat L, De Grave K, Norel R, DREAM Olfaction Consortium, Stolovitzky G, Cecchi G, Vosshall LB, Meyer P
"Personalized predictions of human odour perceptual attributes from chemical features”
Science 355(6327):820-826 (PMID: 28219971)
2017 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 M, 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
“Epigenomic and Genomic Correlates of Aggression in Curable Prostate Cancer”
Nature 541(7637):359-364 (PMID: 28068672)
2017 Taylor RA, Fraser M, Livingstone J, Espiritu SM, Thorne H, Huang V, Lo W, Shiah YJ, Yamaguchi TN, Ania 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 8(113671):1-10 (PMID: 28067867)

2016

2016 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, Linden J, Lensu S, Okey AB, Pohjanvirta R, Boutros PC
“Compendium of TCDD-mediated transcriptomic response datasets in mammalian model systems”
BMC Genomics 18(1):78 (PMID: 28086803)
2016 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 11(1):14 (PMID: 27999613)
2016 Fatouhi 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 PC, Liu SK
“Long non-coding RNA urethelia carcinoma associated 1 (UCA1) mediates radiation response in prostate cancer”
Oncotarget 8(3):4668-4689 (PMID: 27902466)
2016 Chong Z, Gao M, Ruan J, Zhou W, Fan X, Ding L, Lee A, Boutros PC, Chen J, Chen T, Chen K
“novoBreak: glocal assembly for breakpoint detection in cancer genomes”
Nature Methods 14(1):65-67 (PMID: 27892959)
2016 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 (PMID: 27862626)
2016 Lalonde E, Alkallas R, Chua ML, 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 tumours”
European Urology (PMID: 27815082)
2016 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 (PMID: 27750381)
2016 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 and Therapy 18(1):218 (PMID: 27716443)
2016 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 17(1):401 (PMID: 27716034)
2016 David M, Dursi J, Yao D, Boutros PC, Simpson JD
“Nanocall: An Open Source Basecaller for Oxford Nanopore Sequencing Data”
Bioinformatics (in press) (PMID: 27614348)
2016 Huang BF, Boutros PC
“The Parameter Sensitivity of Random Forests”
BMC Bioinformatics 7(1):331 (PMID: 27586051)
2016 Guo H, Ahmed M, Zhang F, Yao CQ, Li S, Liang Y, Hua J, Sun Y, Langstein J, Poon C, Bailey SD, Desai K, Fei T, Li Q, Sendorek DH, Fraser M, Prensner JR, Pugh T, Pomerantz M, Bristow RG, Lupien M, Feng FY, Boutros PC, Freedman M, Walsh MJ, He HH
“Modulation of long noncoding RNAs by risk SNPs underlying genetic predispositions to prostate cancer”
Nature Genetics (in press) (PMID: 27526323)
2016 Masella AP, Lalansingh CM, Sivasundaram P, Fraser M, Bristow RG, Boutros PC
“BAMQL: A query language for extracting reads from BAM files”
BMC Bioinformatics 17:305 (PMID: 27516195)
2016 Noren DP, Long B, Norel R, Rrhissorrakrai K, Hess K, Hu W, Bisberg A, Schultz A, Engquist E, Liu L, Lin X, Chen GM, Xie H, Hunter GAM, Boutros PC, Stepanov O, DREAM 9 AML OPC Consortium, Norman T, Friend SH, Stolovitzky G, Kornblau G, Qutub AA
“A Crowd Sourcing Approach to Developing and Assessing Prediction Algorithms for AML Prognosis”
PLoS Computational Biology 12(6):e1004890 (PMID: 27351836)
2016 Kim Y, Jeon J, Mejia S, Yao CQ, Ignathchenko V, Nyalwidhe J, Gramolini AO, Lance RS, Troyer DA, Drake RR, Boutros PC, Semmes OJ, Kislinger TK
“Targeted proteomics identifies liquid-biopsy signatures for extracapsular prostate cancer”
Nature Communications 7:11906 (PMID: 27350604)
2016 Macdonald JM, Boutros PC
“Log::ProgramInfo: A Perl module to collect and log data for bioinformatics pipelines”
Source Code for Biology and Medicine 11:9 (PMID: 27347003)
2016 Bhandari V, Boutros PC
“Comparing continuous and discrete analyses of breast cancer survival information”
Genomics 108(2):78-83 (PMID: 27311755)
2016 Stojanova A, Tu, WB ,Chan PK, Ponzielli R, Kotlyar M, Boutros PC, Khosravi F, Jurisica I, Raught B, Penn LZ
“Myc interaction with the tumour suppressive SWI/SNF complex member INI1 regulates transcription and cellular transformation”
Cell Cycle 15(13):1693-705 (PMID: 27267444)
2016 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 42:173-180 (PMID: 27173062)
2016 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 (in press) (PMID: 27136898)
2016 Ameratunga M, Asadi K, Lin X, Walkiewicz M, Murone C, Knight S, Mitchell P, Boutros PC , John T
“PD-L1 and Tumor infiltrating lymphocytes as prognostic markers in resected NSCLC”
PLoS One 11(4):e0153954 (PMID: 27104612)
2016 Spears M, Lyttle N, D’Costa A, Chen BE, Yao CQ, Boutros PC , Burnell B, Levine MN, O’Brien P, Shepherd L, Barlett JM
“A four gene signature of chromosome instability (CIN4) predicts for benefit from taxanes in the NCIC-CTG MA21 clinical trial”
Oncotarget 7(31):49099-49106 (PMID: 27056899)
2016 Gagliano SA, Ptak C, Mak DY, Shamsi M, Oh G, Knight J, Boutros PC , Petronis A
“Allele-skewed DNA modification in the brain: relevance to schizophrenia GWAS”
American Journal of Human Genetics 98(5):956-962 (PMID: 27087318)
2016 Allen GI, Amoroso N, Anghel C, Balagurusamy V, Bare CJ, Beaton D, Bellotti D, Bennett DA, Boehme K, Boutros PC, Caberlotto L, Caloian C, Campbell F, Neto EC, Chang Y-C, Chen B, Chen C-Y, Chien T-Y, 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 M-Y, Huang C, Hwang J, Ibrahim J, Inglese P, 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, Lyappan A, Ma M, Malhotra A, Mangravite LM, Maxwell TJ, Merrill E, Nagorski J, Namasivayam A, Narayan M, Naz M, Newhouse SJ, Norman TC, Nurtdinov RN, Oyang R-J, 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 Y-A, 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 12(6):645-53 (PMID: 27079753)
2016 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 14(1):67 (PMID: 26952093)
2016 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 JMS, Spears M
“Downregulation of histone H2A and H2B pathways is associated with anthracycline sensitivity in breast cancer”
Breast Cancer Research 18(1):16 (PMID: 26852132)
2016 Boutros PC, Fraser M, van der Kwast T, Bristow RG
“Clonality of localized and metastatic prostate cancer”
Current Opinion in Urology 26(3):219-24 (PMID: 26885716)
2016 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 108(8) (PMID: 27245079)

2015

2015 Alioto T, Buchhalter I, Derdak S, Hutter B, Eldridge M, Hovig E, Heisler LE, Beck T, Simpson J, Tonon L, Sertier A-S, Patch A-M, Jäger N, Ginsbach P, Drews R, Paramasivam N, Kabbe R, Chotewutmontri S, Diessl N, Previti C, Schmidt S, Brors B, Feuerbach L, Heinold M, Groebner S, Korshunov A, Tarpey P, Butler A, Hinton J, Jones D, Menzies A, Raine K, Shepherd R, Stebbings L, Teague J, Ribeca P, Castro-Giner F, Beltran S, Raineri E, Dabad M, Heath S, Gut M, Denroche R, Harding NJ, Yamaguchi TN, Fujimoto A, Nakagawa H, Quesada V, Valdés-Mas R, Nakken S, Vodák D, Bower L, Lynch A, Anderson C, Waddell N, Pearson J, Grimmond S, Peto M, Spellman PT, He M, Kandoth C, Lee S, Zhang J, Letourneau L, Ma S, Seth S, Torrents D, Xi L, Wheeler D, Lopez-Otin C, Campo E, Campbell P, Boutros PC, Puente X, Gerhard D, Pfister S, McPherson JD, Hudson TJ, Schlesner M, Lichter P, Eils R, Jones D, Gut I
“A comprehensive assessment of somatic mutation detection in cancer using whole genome sequencing”
Nature Communications 6:10001 (PMID: 26647970)
2015 The Cancer Genome Atlas Research Network
“The molecular taxonomy of primary prostate cancer”
Cell 163(4):1011-1025 (PMID: 26544944)
2015 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 MA5 clinical trials”
Oncotarget 6(31):31693-31701 (PMID: 26372731)
2015 Lee J, Prokopec SD,Watson JD ,Sun RX, Pohjanvirta R, Boutros PC
“Male and female mice show significant differences in hepatic transcriptome response to 2,3,7,8-tetrachlorodibenzo-p-dioxin”
BMC Genomics (PMID: 26290441)
2015 Houlahan KE, Prokopec SD, Sun RX, Moffat ID, Linden J, Lensu S, Okey AB, Pohjanvirta R, Boutros PC
“Transcriptional profiling of raw white adipose tissue response to 2,3,7,8-tetrachlorodibenzo-p-dioxin”
Toxicology and Applied Pharmacology (PMID: 26232522)
2015 Huang X, Taeb S, Jahangiri S, Korpela E, Cadonic I, Yu N, Krylov S, Fokas E, Boutros PC, Liu SK
“miR-620 promotes tumor radioresistance by targeting 15-hydroxyprostaglandin dehydrogenase (HPGD)”
Oncotarget (PMID: 26068950)
2015 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 T, 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 L, 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
“Spatio-genomic heterogeneity within localized, multi-focal prostate cancer”
Nature Genetics (PMID: 26005866)
2015 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 A, Stuart JM, Boutros PC
“Combining accurate tumour genome simulation with crowd-sourcing to benchmark somatic single nucleotide variant detection”
Nature Methods (PMID: 25984700)
2015 Boutros PC
“The path to routine use of genomic biomarkers in the cancer clinic”
Genome Research 25(10):1508-1513 (PMID: 26430161)
2015 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 16:156 (PMID: 25972088)
2015 Reich HN, Sabelnykova VY, Boutros PC
“Matching kidneys and urines: establishing non-invasive surrogates of intra-renal events in primary glomerulonephritis”
Seminars in Nephrology 35(3):256-265 (PMID: 26215863)
2015 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 10(4):e0123946 (PMID: 25880806)
2015 Mutation Consequences and Pathway Analysis Working Group of the International Cancer Genome Consortium
“Pathway and Network Analysis of Cancer Genomes”
Nature Methods 12(7):615-621 (PMID: 26125594)
2015 Dodbiba L, Teichman J, Fleet A, Thai H, Starmans MHW, Navab R, Chena Z, Girgis H, Eng L, Espin-Garcia O, Shen X, Bandarchi B, Schwock J, Tsao M-S, 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 10(3):e0121872 (PMID: 25826681)
2015 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 (PMID: 26041263)
2015 Starmans MH, Boutros PC
“Biomarkers and subtypes of cancer”
Aging (PMID: 26021974)
2015 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 (PMID: 25738365)
2015 Cooper CS, Eeles R, Wedge DC, Van Loo P, Gundem G, Alexandrov LV, Kremeyer B, Butler A, Lynch AG, Edwards S, Camacho N, Massie CE, Kote-Jarai Z, Dennis N, Merson S, Leongamornlert D, Zamora J, Kay J, Luxton HJ, 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, The 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 M, 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 (PMID: 25730763)
2015 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 (PMID: 25703434)
2015 Shiah Y-J, 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 CXCR4 Function in Mammary Progenitors”
Stem Cell Reports (PMID: 25702641)
2015 The Cancer Genome Atlas Research Network
“Comprehensive genomic characterization of head and neck squamous cell carcinomas”
Nature 517(7536):576-82 (PMID: 25631445)
2015 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 (PMID: 25609067)

2014

2014 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 (PMID: 25545689)
2014 Houlahan KE, Prokopec SD, Moffat ID, Linden J, Lensu S, Okey AB, Pohjanvirta R, Boutros PC
“Transcriptional Profiling of Rat Hypothalamus Response to 2,3,7,8-tetrachlorodibenzo-ρ-dioxin”
Toxicology 328(C):93-101 (PMID: 25529477)
2014 Sun RX, Chong LC, Simmons TT, Houlahan KE, Prokopec SD, Watson JD, Moffat ID, Lensu S, Linden J, P'ng C, Okey AB, Pohjanvirta R, Boutros PC
“Cross-Species Transcriptomic Analysis Elucidates Constitutive Aryl Hydrocarbon Receptor Activity”
BMC Genomics 15(1):1053 (PMID: 25467400)
2014 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 and Toxicology 15(1):66 (PMID: 25428177)
2014 The Cancer Genome Atlas Research Network
"Comprehensive genomic characterization of head and neck squamous cell carcinomas"
Nature 517(7536):576-82 (PMID: 25631445)
2014 Emilie Lalonde, Adrian S Ishkanian, Jenna Sykes, Michael Fraser, Helen Ross-Adams, Nicholas Erho, Mark J Dunning, Silvia Halim, Alastair D Lamb, Nathalie C Moon, Gaetano Zafarana, Anne Y Warren, Xianyue Meng, John Thoms, Michal R Grzadkowski, Alejandro Berlin, Cherry L Have, Varune R Ramnarine, Cindy Q Yao, Chad A Malloff, Lucia L Lam, Honglei Xie, Nicholas J Harding, Denise YF Mak, Kenneth C Chu, Lauren C Chong, Dorota H Sendorek, Christine P’ng, Colin C Collins, Jeremy A Squire, Igor Jurisica, Colin Cooper, Rosalind Eeles, Melania Pintilie, Alan Dal Pra, Elai Davicioni, Wan L Lam, Michael Milosevic, David E Neal, Theodorus van der Kwast, Paul C Boutros, Robert G Bristow
“Tumour genomic and microenvironmental heterogeneity as integrated predictors for prostate cancer recurrence: a retrospective study"
Lancet Oncology 15(13):1521-1532 (PMID: 25456371)
Univariate prognosis of CNAs in Toronto and MSKCC cohorts
Profiling of 276 genes in 100-loci DNA signature
Clinical and biomarker profiles of Cambridge cohort
Full clinical annotations for the Toronto cohort
Gene by sample CNA matrix for the Toronto and MSKCC cohorts
2014 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 (PMID: 25415046)
2014 Alfaro JA, Sinha A, Kislinger TK, Boutros PC
“Onco-proteogenomics: Cancer Proteomics Joins Forces with Genomics”
Nature Methods 11(11):1107-1113 (PMID: 25357240)
2014 van den Beucken, 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 5:5203 (PMID: 25351418)
2014 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 9(10):e110730 (PMID: 25329058)
2014 Boutros PC, Margolin AA, Stuart JD, Califano A, Stolovitzky G
“Toward Better Benchmarking: Competition-Based Methods Assessment in Cancer Genomics”
Genome Biology 15(9):462 (PMID: 25314947)
2014 Yao CQ, Nguyen F, Haider S, Starmans MHW, Lambin P, Boutros PC
“The Transcriptomic Profile of Ovarian Cancer Grading"
Cancer Medicine (PMID: 25314936)
2014 Parfenov M, Pedamallu CS, Gehlenborg N, Freeman SS, Danilova L, Bristow CA, Lee S, Hadjipanayis AG, Ivanova EV, Wilkerson MD, Protopopov A, Yang L, Seth S, Song X, Tang J, Ren X, Zhang J, Pantazi A, Santoso N, Xu AW, Mahadeshwar H, Wheeler DA, Haddad RI, Jung J, Ojesina AI, Issaeva N, Yarbrough WG, Hayes DN, Grandis JR, El-Naggar AK, Meyerson M, Park PJ, Chin L, Seidman JG, Hammerman PS, Kucherlapati R; The Cancer Genome Atlas Network
“Characterization of HPV and host genome interactions in primary head and neck cancers”
Proceedings of the National Academy of Sciences 111(43): 15544-15549 (PMID: 25313082)
2014 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 HPV-dependent regulation of the AP-1 pathway”
Molecular & Cellular Proteomics (PMID: 25271301)
2014 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 CH, 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 46(11):1166-1169 (PMID: 25240283)
2014 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 (PMID: 25193804)
2014 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 11(10):1071-1075 (PMID: 25173705)
2014 Weinreb I, Zhang L, Tirunagari LM, Sung YS, Chen LC, 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 and Cancer 53(10):845-856 (PMID: 24942367)
2014 Fox NS, Starmans MH, Haider S, Lambin P, Boutros PC
“Ensemble analyses improve signatures of tumour hypoxia and reveal inter-platform differences”
BMC Bioinformatics 15(1):170 (PMID: 24902696)
2014 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 111(2):168-177 (PMID: 24861629)
2014 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 4(7):840-853 (PMID: 24740996)
2014 Real FX, Boutros PC, Malats N
“Next generation sequencing of urologic cancers: Next is Now”
European Urology 14:281-4 (PMID: 24731787)
2014 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 JD
“The Challenge of Identifying Somatic Variants in Cancer Genomes: Global Optimization by a Global Community”
Nature Genetics 46(4):318-319 (PMID: 24675517)
2014 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 15(1):78 (PMID: 24646301)
2014 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 metabolic, proliferation and hypoxia markers for differentiation between head and neck tumors”
BMC Cancer 14(1):130 (PMID: 24571588)
2014 Miller JK, Buchner N, Timms L, Tam S, Luo X, Brown AMK, 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 9(2):e88163 (PMID: 24551080)
2014 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 274(3):445-454 (PMID: 24355419)
2014 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 143(2):301-12 (PMID: 24337703)
2014 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 134(10):2330-2341 (PMID: 24154973)
2014 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 33(18):2375-84 (PMID: 23708664)

2013

2013 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 2(6):916-924 (PMID: 24403265)
2013 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"
Journal of Cell Biology 203(4):615-627 (PMID: 24247433)
2013 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 73(21):6504-6515 (PMID: 24030976)
2013 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 14(1):583 (PMID: 23984903)
2013 Thomas J, Starmans MH, Chen YT, Russell PA, Barnett SA, White SC, Mitchell PL, Walkiewicz M, Azad M, Lambin P, Tsao MS, Deb S, Altorki N, Wright G, Knight S, Boutros PC, Cebon J
“The role of cancer-testis antigens as predictive and prognostic markers in non-small cell lung cancer”
PLoS One 8(7):e67876 (PMID: 23935846)
2013 Dal Pra A, Lalonde E, Sykes J, Warde F, Ishkanian AS, Meng AX, Maloff CA, Srigley J, Joshua A, Petrovics G, van der Kwast T, Evans A, Milosevic M, Saad F, Collins CC, Squire JA, Lam WL, Bismar T, Boutros PC, Bristow RG
“TMPRSS2-ERG Status Is Not Prognostic Following Prostate Cancer Radiotherapy: Implications for Fusion Status and DSB Repair”
Clinical Cancer Research 19(8):5202-5209 (PMID: 23918607)
2013 International Cancer Genome Consortium Mutation Pathways and Consequences Subgroup of the Bioinformatics Analyses Working Group, 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 LF, 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
"Computational approaches to identify functional genetic variants in cancer genomes"
Nature Methods 10(8):732-739 (PMID: 23900255)
2013 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 8(7):e67846 (PMID: 23861821)
2013 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 205(1):63-71 (PMID: 23791969)
2013 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 84(6):1246-1253 (PMID: 23760288)
2013 Nichols AC, Chan-Seng-Yue M, Yoo J, Agrawal S, Starmans MHW, 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 270362:1-7 (PMID: 23653877)
2013 Ching RW, Ahmed K, Boutros PC, Penn LZ, Bazett-Jones DP
“Identifying gene locus associations with promyelocytic leukemia nuclear bodies using immuno-TRAP”
Journal of Cell Biology 201(2):325-35 (PMID: 23589495)
2013 Quon G, Haider S, Deshwar AG, Cui A, Boutros PC, Morris QD
“Computational purification of individual tumor gene expression profiles leads to significant improvements in prognostic prediction”
Genome Medicine 5(3):29 (PMID: 23537167)
2013 Rushlow DE, Mol BM, Kennett JY, Yee S, Pajovic S, Theriault 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 mutations: genomic, gene expression, and clinical studies”
Lancet Oncology 14(4):327-34 (PMID: 23498719)
2013 Prokopec SD, Watson JD, Waggott DM, Smith AB, Wu AH, Okey AB, Pohjanvirta R, Boutros PC
“Systematic Comparison of Medium-Throughput mRNA Abundance Platforms”
RNA 19(1):51-62 (PMID: 23169800)
2013 Lambin P, van Stiphout RGPM, 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 10(1):27-40 (PMID: 23165123)

2012

2012 Nichols AC, Chan-Seng-Yue M, Yoo J, Xu W, Dhaliwal S, Basmaji J, Szeto CC, Dowthwaite S, Todorovic B, Starmans MHW, 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 809370:1-9 (PMID: 23304554)
2012 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 7(12):e51562 (PMID: 23272119)
2012 Starmans MHW, 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 4(11):84 (PMID: 23146350)
2012 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 11(12):1870-84 (PMID: 22986220)
2012 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 3D morphogenesis identifies PTPRO as a novel regulator of morphogenesis and ErbB2 mediated transformation”
Molecular and Cellular Biology 32(19):3913-24 (PMID: 22851698)
2012 Starmans MHW, Lieuwes NG, Span PN, Haider S, Dubois L, Nguyen F, van Laarhoven HW, Sweep FCGJ, Wouters BG, Boutros PC, Lambin P
“Independent and Functional Validation of a Multi-Tumour-Type Proliferation Signature”
British Journal of Cancer 107(3):508-15 (PMID: 22722312)
2012 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 ERK-dependent stathmin- and filamin A-mediated mechanism in hippocampal cells”
Neuroscience 219:255-70 (PMID: 22698694)
2012 Cortese R, Kwan A, Lalonde ER, Bryzgunova O, Bondar A, Wu Y, Gordevicius J, Park M, Oh G, Kaminsky Z, Tverkuviene J, Laurinavicius A, Jankevicius F, Sendorek DHS, Haider S, Wang S-C, Jarmalaite S, Laktionov P, Boutros PC, Petronis A
“Epigenetic markers of prostate cancer in plasma circulating DNA”
Human Molecular Genetics 21(16):3619-31 (PMID: 22619380)
2012 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, Hajiresouliha 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”
Journal of Pathology 227(3):286-97 (PMID: 22553170)
2012 Waggott D, Chu K, Yin S, Wouters BG, Liu F-F, Boutros PC
“NanoStringNorm: An Extensible R Package For the Pre-Processing of NanoString mRNA and miRNA Data”
Bioinformatics 28(11):1546-1548 (PMID: 22513995)
2012 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 12(7):1929-1935 (PMID: 22486950)
2012 Starmans MHW, 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 102(3):436-443 (PMID: 22356756)
2012 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 & Applied Pharmacology 260(2):135-145 (PMID: 22342509)
2012 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, Collins CC
“Integrated genome and transcriptome sequencing identifies a novel form of hybrid and aggressive prostate cancer”
Journal of Pathology 227(1):53-61 (PMID: 22294438)
2012 Ng T, Chand D, Song L, Watson JD, Boutros PC, Belsham D, Barsyte-Lovejoy D, 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 174(1:3):79-89 (PMID: 22209827)

2011

2011 Hakem A, Bohgaki M, Lemmers B, Tai E, Salmena L, Matysiak-Zablocki E, Jung YS, Karaskova J, Kaustov L, Duan S, Madore J, Boutros PC, Sheng Y, Chesi M, Bergsagel PL, Perez-Ordonez B, Mes-Masson AM, Penn LZ, 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 7(11):e1002360 (PMID: 22125490)
2011 Goldenberg A, Mostafavi S, Quon G, Boutros PC, Morris Q
"Unsupervised detection of genes of influence in lung cancer using biological networks"
Bioinformatics 27(22):3166-3172 (PMID: 21965819)
2011 Boutros PC, Moffat ID, Pohjanvirta R, Okey AB
“mRNA Levels in Control Rat Liver Display Strain-Specific, Hereditary and AHR-Dependent Elements”
PLoS One 6(7):e18337 (PMID: 21760882)
2011 Yan R, Boutros PC, Jurisica I
“A Tree-based Approach to Motif Discovery and Sequence Classification”
Bioinformatics 27(15):2054-61 (PMID: 21685048)
2011 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 10(5):2286-99 (PMID: 21491939)
2011 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 and Behavior 104(2):199-204 (PMID: 21411044)
2011 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”
Journal of Molecular Diagnostics 13(2):143-51 (PMID: 21354048)
2011 Chen H, Boutros PC
“VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R”
BMC Bioinformatics 12(1):35 (PMID: 21269502)
2011 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 & Applied Pharmacology 251(2):119-29 (PMID: 21215274)

2010

2010 Boutros PC, Pintilie M, John T, Starmans HW, 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 102(21):1677-1678 (PMID: 20921041)
2010 Boutros PC
“A Linear Method for Cross-Platform Integration of Microarray Data”
Cancer Informatics 9:197-208 (PMID: 20838609)
2010 Clendening JW, Pandyra A, Boutros PC, Ghamrasni SE, 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 107(34):15051-6 (PMID: 20696928)
2010 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 10(1):351 (PMID: 20598143)
2010 Tan KP, Wang B, Yang MD, Boutros PC, MacAulay J, Xu H, Chuang AI, Kazuhiro K, Yamamoto M, Takahashi S, Wu AM, Harper PA, Ross DD, Ito S
“Aryl Hydrocarbon Receptor (AHR) is A Transcriptional Activator of Human Breast Cancer Resistance Protein (BCRP/ABCG2)”
Molecular Pharmacology 78(2):175-185 (PMID: 20460431)
2010 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 11(1):263 (PMID: 20420666)
2010 “The International Cancer Genome Consortium”
“International network of cancer genome projects”
Nature 464(7291):993-998 (PMID: 20393554)
2010 Clendening JW, Pandyra A, Li Z, Boutros PC, Martirosyan A, Lehner R, Jurisica I, Trudel S, Penn LZ
“Exploiting the mevalonate pathway to identify statin-sensitive multiple myelomas”
Blood 115(23):4787-4797 (PMID: 20360469)
2010 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 127(12):2936-2948 (PMID: 21351272)

2009

2009 Li M, Lee KF, Lu Y, Clarke I, Eberhart C, Collins VP, Van Meter T, Picard D, Zhou L, Boutros PC, Modena P, Liang ML, Scherer SW, Bouffet E, Rutka JT, Pomeroy S, Lau CC, Taylor MD, Gajjar A, Dirks PB, Hawkins CE, Huang A
“Frequent amplification of a chr19q13.41 microRNA polycistron (C19MC) in aggressive primitive neuroectodermal brain tumors”
Cancer Cell 16(6):533-546 (PMID: 19962671)
2009 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 112(1):245-256 (PMID: 19759094)
2009 Labrie V, Fukumura R, Rastogi A, Fick LJ, Wei W, Boutros PC, Kennedy JL, Semeralul MO, Lee FH, Baker GB, Belsham DD, Barger SW, Gondo Y, Wong AHC, Roder JC
“Serine racemase is associated with schizophrenia susceptibility in humans and in a mouse model”
Human Molecular Genetics 18(17):3227-43 (PMID: 19483194)
2009 Hui AH, Shi W, Boutros PC, Miller N, Pintilie M, Fyles T, McCready M, Wong D, Gerster K, Jurisica I, Penn LZ, Liu FF
“Robustness of global micro-RNA profiling using formalin-fixed paraffin-embedded breast cancer tissues”
Laboratory Investigation 89(5):597-606 (PMID: 19290006)
2009 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 106(8):2824-2828 (PMID: 19196983)