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SEPATH: benchmarking the search for pathogens in human tissue whole genome sequence data leads to template pipelines.

Gihawi A, Rallapalli G, Hurst R, Cooper CS, Leggett RM, Brewer DS.

Genome Biol. 2019 Oct 22;20(1):208. doi: 10.1186/s13059-019-1819-8.


Assessment and validation of a screening questionnaire for the diagnosis of pediatric bladder and bowel dysfunction.

Anwar T, Cooper CS, Lockwood G, Ferguson KJ, Barlow PB, Storm DW.

J Pediatr Urol. 2019 Jul 27. pii: S1477-5131(19)30227-X. doi: 10.1016/j.jpurol.2019.07.016. [Epub ahead of print]


A Four-Group Urine Risk Classifier for Predicting Outcome in Prostate Cancer Patients.

Connell SP, Hanna M, McCarthy F, Hurst R, Webb M, Curley H, Walker H, Mills R, Ball RY, Sanda MG, Pellegrini KL, Patil D, Perry AS, Schalken J, Pandha H, Whitaker H, Dennis N, Stuttle C, Mills IG, Guldvik I; Movember GAP1 Urine Biomarker Consortium, Parker C, Brewer DS, Cooper CS, Clark J.

BJU Int. 2019 May 20. doi: 10.1111/bju.14811. [Epub ahead of print]


Transcriptional changes in prostate of men on active surveillance after a 12-mo glucoraphanin-rich broccoli intervention-results from the Effect of Sulforaphane on prostate CAncer PrEvention (ESCAPE) randomized controlled trial.

Traka MH, Melchini A, Coode-Bate J, Al Kadhi O, Saha S, Defernez M, Troncoso-Rey P, Kibblewhite H, O'Neill CM, Bernuzzi F, Mythen L, Hughes J, Needs PW, Dainty JR, Savva GM, Mills RD, Ball RY, Cooper CS, Mithen RF.

Am J Clin Nutr. 2019 Apr 1;109(4):1133-1144. doi: 10.1093/ajcn/nqz012.


Putting students at the center: moving beyond time-variable one-size-fits-all medical education to true individualization.

Schwinn DA, Cooper CS, Robillard JE.

Adv Med Educ Pract. 2019 Feb 28;10:109-112. doi: 10.2147/AMEP.S187946. eCollection 2019.


epiCaPture: A Urine DNA Methylation Test for Early Detection of Aggressive Prostate Cancer.

O'Reilly E, Tuzova AV, Walsh AL, Russell NM, O'Brien O, Kelly S, Dhomhnallain ON, DeBarra L, Dale CM, Brugman R, Clarke G, Schmidt O, O'Meachair S, Patil D, Pellegrini KL, Fleshner N, Garcia J, Zhao F, Finn S, Mills R, Hanna MY, Hurst R, McEvoy E, Gallagher WM, Manecksha RP, Cooper CS, Brewer DS, Bapat B, Sanda MG, Clark J, Perry AS.

JCO Precis Oncol. 2019;2019. doi: 10.1200/PO.18.00134. Epub 2019 Jan 14.


New trends in voiding cystourethrography and vesicoureteral reflux: Who, when and how?

Arlen AM, Cooper CS.

Int J Urol. 2019 Apr;26(4):440-445. doi: 10.1111/iju.13915. Epub 2019 Feb 14. Review.


Predictors of becoming overweight among pediatric patients at risk for urinary tract infections.

Gaither TW, Cooper CS, Kornberg Z, Baskin LS, Copp HL.

J Pediatr Urol. 2019 Feb;15(1):61.e1-61.e6. doi: 10.1016/j.jpurol.2018.09.002. Epub 2018 Sep 18.


Continuous Antibiotic Prophylaxis in Pediatric Urology.

Storm DW, Braga LH, Cooper CS.

Urol Clin North Am. 2018 Nov;45(4):525-538. doi: 10.1016/j.ucl.2018.06.001. Epub 2018 Sep 7. Review.


Impact of continuous low-dose antibiotic prophylaxis on growth in children with vesicoureteral reflux.

Guidos PJ, Arlen AM, Leong T, Bonnett MA, Cooper CS.

J Pediatr Urol. 2018 Aug;14(4):325.e1-325.e7. doi: 10.1016/j.jpurol.2018.07.007. Epub 2018 Jul 23.


ORIF versus arthroplasty for open proximal humerus fractures: Nationwide Inpatient Sample data between 1998 and 2013.

Dixit A, Cautela FS, Cooper CS, Beyer GA, Messina JC, Mait JE, Shah NV, Diebo BG, Paulino CB, Urban WP.

J Orthop Traumatol. 2018 Aug 22;19(1):12. doi: 10.1186/s10195-018-0503-1.


The implications of fellowship expansion on future pediatric urologist surgical volumes.

Groth TW, See WA, Ramsay S, Cooper CS, Kryger JV.

J Pediatr Urol. 2018 Jun;14(3):246-250. doi: 10.1016/j.jpurol.2017.10.013. Epub 2017 Nov 27.


Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets.

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.

Nat Genet. 2018 May;50(5):682-692. doi: 10.1038/s41588-018-0086-z. Epub 2018 Apr 16.


Risk Factors for the Development of Bladder and Bowel Dysfunction.

Gaither TW, Cooper CS, Kornberg Z, Baskin LS, Copp HL.

Pediatrics. 2018 Jan;141(1). pii: e20172797. doi: 10.1542/peds.2017-2797.


The Institutional Review Board.

Caldamone AA, Cooper CS.

J Pediatr Urol. 2017 Dec;13(6):557-558. doi: 10.1016/j.jpurol.2017.10.006. Epub 2017 Oct 27. No abstract available.


Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data.

Camacho N, Van Loo P, Edwards S, Kay JD, Matthews L, Haase K, Clark J, Dennis N, Thomas S, Kremeyer B, Zamora J, Butler AP, Gundem G, Merson S, Luxton H, Hawkins S, Ghori M, Marsden L, Lambert A, Karaszi K, Pelvender G, Massie CE, Kote-Jarai Z, Raine K, Jones D, Howat WJ, Hazell S, Livni N, Fisher C, Ogden C, Kumar P, Thompson A, Nicol D, Mayer E, Dudderidge T, Yu Y, Zhang H, Shah NC, Gnanapragasam VJ; CRUK-ICGC Prostate Group, Isaacs W, Visakorpi T, Hamdy F, Berney D, Verrill C, Warren AY, Wedge DC, Lynch AG, Foster CS, Lu YJ, Bova GS, Whitaker HC, McDermott U, Neal DE, Eeles R, Cooper CS, Brewer DS.

PLoS Genet. 2017 Sep 25;13(9):e1007001. doi: 10.1371/journal.pgen.1007001. eCollection 2017 Sep.


DESNT: A Poor Prognosis Category of Human Prostate Cancer.

Luca BA, Brewer DS, Edwards DR, Edwards S, Whitaker HC, Merson S, Dennis N, Cooper RA, Hazell S, Warren AY; CancerMap Group, Eeles R, Lynch AG, Ross-Adams H, Lamb AD, Neal DE, Sethia K, Mills RD, Ball RY, Curley H, Clark J, Moulton V, Cooper CS.

Eur Urol Focus. 2018 Dec;4(6):842-850. doi: 10.1016/j.euf.2017.01.016. Epub 2017 Mar 6.


The Iowa Voiding Improvement Partnership experience: Early observations with a collaborative pediatric uro-psychologic clinic.

Bonnett KM, Fuller LL, Cooper CS, Arlen AM, Storm DW.

J Pediatr Urol. 2017 Aug;13(4):391.e1-391.e6. doi: 10.1016/j.jpurol.2017.05.024. Epub 2017 Jul 1.


Identification of FBXL4 as a Metastasis Associated Gene in Prostate Cancer.

Stankiewicz E, Mao X, Mangham DC, Xu L, Yeste-Velasco M, Fisher G, North B, Chaplin T, Young B, Wang Y, Kaur Bansal J, Kudahetti S, Spencer L, Foster CS, Møller H, Scardino P, Oliver RT, Shamash J, Cuzick J, Cooper CS, Berney DM, Lu YJ.

Sci Rep. 2017 Jul 11;7(1):5124. doi: 10.1038/s41598-017-05209-z.


Distal Ureteral Diameter Ratio is Predictive of Breakthrough Febrile Urinary Tract Infection.

Arlen AM, Leong T, Guidos PJ, Alexander SE, Cooper CS.

J Urol. 2017 Dec;198(6):1418-1423. doi: 10.1016/j.juro.2017.06.095. Epub 2017 Jul 8.


Fat, demented and stupid: An unrecognized legacy of pediatric urology?

Cooper CS.

J Pediatr Urol. 2017 Aug;13(4):341-344. doi: 10.1016/j.jpurol.2017.04.027. Epub 2017 Jun 17. Review.


Role of body mass index in school-aged children with lower urinary tract dysfunction: Does weight classification predict treatment outcome?

Arlen AM, Cooper CS, Leong T.

J Pediatr Urol. 2017 Oct;13(5):454.e1-454.e5. doi: 10.1016/j.jpurol.2017.03.033. Epub 2017 Apr 25.


Development of the certificate of added qualification in pediatric urology in the U.S.

Cooper CS, Caldamone AA.

Can Urol Assoc J. 2017 Jan-Feb;11(1-2):10-11. doi: 10.5489/cuaj.4417. No abstract available.


Detection of prostate cancer-specific transcripts in extracellular vesicles isolated from post-DRE urine.

Pellegrini KL, Patil D, Douglas KJS, Lee G, Wehrmeyer K, Torlak M, Clark J, Cooper CS, Moreno CS, Sanda MG.

Prostate. 2017 Jun;77(9):990-999. doi: 10.1002/pros.23355. Epub 2017 Apr 17.


Hospital-acquired Urinary Tract Infections in Neonatal ICU Patients: Is Voiding Cystourethrogram Necessary?

Asghar AM, Leong T, Cooper CS, Arlen AM.

Urology. 2017 Jul;105:163-166. doi: 10.1016/j.urology.2017.04.002. Epub 2017 Apr 10.


Corrigendum to "Integration of Copy Number and Transcriptomics Provides Risk Stratification in Prostate Cancer: A Discovery and Validation Cohort Study" [EBioMedicine 2 (9) (2015) 1133-1144].

Ross-Adams H, Lamb AD, Dunning MJ, Halim S, Lindberg J, Massie CM, Egevad LA, Russell R, Ramos-Montoya A, Vowler SL, Sharma NL, Kay J, Whitaker H, Clark J, Hurst R, Gnanapragasam VJ, Shah NC, Warren AY, Cooper CS, Lynch AG, Stark R, Mills IG, Grönberg H, Neal DE; CamCaP Study Group.

EBioMedicine. 2017 Mar;17:238. doi: 10.1016/j.ebiom.2017.03.010. Epub 2017 Mar 8. No abstract available.


The Need for Improved Detection of Urinary Tract Infections in Young Children.

Bunting-Early TE, Shaikh N, Woo L, Cooper CS, Figueroa TE.

Front Pediatr. 2017 Feb 21;5:24. doi: 10.3389/fped.2017.00024. eCollection 2017.


Validation of the ureteral diameter ratio for predicting early spontaneous resolution of primary vesicoureteral reflux.

Arlen AM, Kirsch AJ, Leong T, Cooper CS.

J Pediatr Urol. 2017 Aug;13(4):383.e1-383.e6. doi: 10.1016/j.jpurol.2017.01.012. Epub 2017 Feb 14.


Time to resolution: A prospective evaluation from the Society for Fetal Urology hydronephrosis registry.

Zee RS, Herndon CDA, Cooper CS, Kim C, McKenna PH, Khoury A, Herbst KW.

J Pediatr Urol. 2017 Jun;13(3):316.e1-316.e5. doi: 10.1016/j.jpurol.2016.12.012. Epub 2017 Jan 19.


Inter-rater reliability of distal ureteral diameter ratio compared to grade of VUR.

Swanton AR, Arlen AM, Alexander SE, Kieran K, Storm DW, Cooper CS.

J Pediatr Urol. 2017 Apr;13(2):207.e1-207.e5. doi: 10.1016/j.jpurol.2016.10.021. Epub 2016 Dec 1.


The American Academy of Pediatrics Workforce Survey for the Section on Urology 2015.

Shapiro E, Cooper CS, Greenfield S; American Academy of Pediatrics Section on Urology.

J Pediatr Urol. 2017 Feb;13(1):68-72. doi: 10.1016/j.jpurol.2016.09.002. Epub 2016 Oct 8.


Vesicoureteral Reflux Index: Predicting Primary Vesicoureteral Reflux Resolution in Children Diagnosed after Age 24 Months.

Garcia-Roig M, Ridley DE, McCracken C, Arlen AM, Cooper CS, Kirsch AJ.

J Urol. 2017 Apr;197(4):1150-1157. doi: 10.1016/j.juro.2016.12.008. Epub 2016 Dec 9.


Establishing a standard protocol for the voiding cystourethrography.

Frimberger D, Bauer SB, Cain MP, Greenfield SP, Kirsch AJ, Ramji F, Mercado-Deane MG, Cooper CS.

J Pediatr Urol. 2016 Dec;12(6):362-366. doi: 10.1016/j.jpurol.2016.11.001. Epub 2016 Nov 10.


Bone mineral content and areal density, but not bone area, predict an incident fracture risk: a comparative study in a UK prospective cohort.

Curtis EM, Harvey NC, D'Angelo S, Cooper CS, Ward KA, Taylor P, Pearson G, Cooper C.

Arch Osteoporos. 2016 Dec;11(1):39. Epub 2016 Dec 3.


Establishing a standard protocol for the voiding cystourethrography (VCUG).

Frimberger D, Bauer SB, Cain MP, Greenfield SP, Kirsch AJ, Ramji F, Mercado-Deane MG, Cooper CS.

J Pediatr Urol. 2016 Dec;12(6):361. doi: 10.1016/j.jpurol.2016.11.002. Epub 2016 Nov 12. No abstract available.


The Modern Metabolic Stone Evaluation in Children.

Bevill M, Kattula A, Cooper CS, Storm DW.

Urology. 2017 Mar;101:15-20. doi: 10.1016/j.urology.2016.09.058. Epub 2016 Nov 9.


Prostate cancer risk regions at 8q24 and 17q24 are differentially associated with somatic TMPRSS2:ERG fusion status.

Luedeke M, Rinckleb AE, FitzGerald LM, Geybels MS, Schleutker J, Eeles RA, Teixeira MR, Cannon-Albright L, Ostrander EA, Weikert S, Herkommer K, Wahlfors T, Visakorpi T, Leinonen KA, Tammela TLJ, Cooper CS, Kote-Jarai Z, Edwards S, Goh CL, McCarthy F, Parker C, Flohr P, Paulo P, Jerónimo C, Henrique R, Krause H, Wach S, Lieb V, Rau TT, Vogel W, Kuefer R, Hofer MD, Perner S, Rubin MA, Agarwal AM, Easton DF, Al Olama AA, Benlloch S; PRACTICAL consortium, Hoegel J, Stanford JL, Maier C.

Hum Mol Genet. 2016 Dec 15;25(24):5490-5499. doi: 10.1093/hmg/ddw349.


Prevalence and bother of patient-reported lower urinary tract symptoms in the muscular dystrophies.

Bertrand LA, Askeland EJ, Mathews KD, Erickson BA, Cooper CS.

J Pediatr Urol. 2016 Dec;12(6):398.e1-398.e4. doi: 10.1016/j.jpurol.2016.04.051. Epub 2016 Jul 12.


Urinary tract infections in children with prenatal hydronephrosis: A risk assessment from the Society for Fetal Urology Hydronephrosis Registry.

Zee RS, Herbst KW, Kim C, McKenna PH, Bentley T, Cooper CS, Herndon CD.

J Pediatr Urol. 2016 Aug;12(4):261.e1-7. doi: 10.1016/j.jpurol.2016.04.024. Epub 2016 May 26.


Hydrazine-Free Solution-Deposited CuIn(S,Se)2 Solar Cells by Spray Deposition of Metal Chalcogenides.

Arnou P, van Hest MF, Cooper CS, Malkov AV, Walls JM, Bowers JW.

ACS Appl Mater Interfaces. 2016 May 18;8(19):11893-7. doi: 10.1021/acsami.6b01541. Epub 2016 May 3.


Computer model predicting breakthrough febrile urinary tract infection in children with primary vesicoureteral reflux.

Arlen AM, Alexander SE, Wald M, Cooper CS.

J Pediatr Urol. 2016 Oct;12(5):288.e1-288.e5. doi: 10.1016/j.jpurol.2016.03.005. Epub 2016 Mar 31.


Multi-institutional Study Comparing the Height of Contrast During Performance of Voiding Cystourethrogram in Children.

Frimberger D, Cooper CS, Ramji F, Aston C, Ramadan M, Kieran K, Storm DW, Sato Y, Kropp BP, Palmer B.

Urology. 2016 Jul;93:180-4. doi: 10.1016/j.urology.2016.03.041. Epub 2016 Apr 6.


Management of functional nonretentive fecal incontinence in children: Recommendations from the International Children's Continence Society.

Koppen IJ, von Gontard A, Chase J, Cooper CS, Rittig CS, Bauer SB, Homsy Y, Yang SS, Benninga MA.

J Pediatr Urol. 2016 Feb;12(1):56-64. doi: 10.1016/j.jpurol.2015.09.008. Epub 2015 Oct 21. Review.


Pedicle Reduction Osteotomy in the Upper Cervical Spine: Technique, Case Report and Review of the Literature.

Post N, Naziri Q, Cooper CS, Pivec R, Paulino CB.

Int J Spine Surg. 2015 Oct 27;9:57. doi: 10.14444/2057. eCollection 2015.


Integration of copy number and transcriptomics provides risk stratification in prostate cancer: A discovery and validation cohort study.

Ross-Adams H, Lamb AD, Dunning MJ, Halim S, Lindberg J, Massie CM, Egevad LA, Russell R, Ramos-Montoya A, Vowler SL, Sharma NL, Kay J, Whitaker H, Clark J, Hurst R, Gnanapragasam VJ, Shah NC, Warren AY, Cooper CS, Lynch AG, Stark R, Mills IG, Grönberg H, Neal DE; CamCaP Study Group.

EBioMedicine. 2015 Jul 29;2(9):1133-44. doi: 10.1016/j.ebiom.2015.07.017. eCollection 2015 Sep. Erratum in: EBioMedicine. 2017 Mar;17 :238.


Prostate Single Nucleotide Polymorphism Provides a Crucial Clue to Cancer Aggression in Active Surveillance Patients.

Cooper CS, Clark J, Brewer DS, Edwards DR.

Eur Urol. 2016 Feb;69(2):229-30. doi: 10.1016/j.eururo.2015.09.038. Epub 2015 Oct 9. No abstract available.


Controversies in the Management of Vesicoureteral Reflux.

Arlen AM, Cooper CS.

Curr Urol Rep. 2015 Sep;16(9):64. doi: 10.1007/s11934-015-0538-2. Review.


Utility of the distal ureteral diameter on VCUG for grading VUR.

Cooper CS, Alexander SE, Kieran K, Storm DW.

J Pediatr Urol. 2015 Aug;11(4):183.e1-6. doi: 10.1016/j.jpurol.2015.04.009. Epub 2015 May 19.


Building Data-Driven Pathways From Routinely Collected Hospital Data: A Case Study on Prostate Cancer.

Bettencourt-Silva JH, Clark J, Cooper CS, Mills R, Rayward-Smith VJ, de la Iglesia B.

JMIR Med Inform. 2015 Jul 10;3(3):e26. doi: 10.2196/medinform.4221.


Corrigendum: analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue.

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.

Nat Genet. 2015 Jun;47(6):689. doi: 10.1038/ng0615-689b. No abstract available.

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