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Resolving the full spectrum of human genome variation using Linked-Reads.

Marks P, Garcia S, Barrio AM, Belhocine K, Bernate J, Bharadwaj R, Bjornson K, Catalanotti C, Delaney J, Fehr A, Fiddes IT, Galvin B, Heaton H, Herschleb J, Hindson C, Holt E, Jabara CB, Jett S, Keivanfar N, Kyriazopoulou-Panagiotopoulou S, Lek M, Lin B, Lowe A, Mahamdallie S, Maheshwari S, Makarewicz T, Marshall J, Meschi F, O'Keefe CJ, Ordonez H, Patel P, Price A, Royall A, Ruark E, Seal S, Schnall-Levin M, Shah P, Stafford D, Williams S, Wu I, Xu AW, Rahman N, MacArthur D, Church DM.

Genome Res. 2019 Mar 20. doi: 10.1101/gr.234443.118. [Epub ahead of print]


The impact of variant histological differentiation on extranodal extension and survival in node positive bladder cancer treated with radical cystectomy.

Marks P, Gild P, Soave A, Janisch F, Minner S, Engel O, Vetterlein MW, Shariat SF, Sauter G, Dahlem R, Fisch M, Rink M.

Surg Oncol. 2019 Mar;28:208-213. doi: 10.1016/j.suronc.2019.01.008. Epub 2019 Jan 30.


Prospective analysis of artificial urinary sphincter AMS 800 implantation after buccal mucosa graft urethroplasty.

Maurer V, Marks P, Dahlem R, Rosenbaum C, Meyer CP, Riechardt S, Fisch M, Ludwig T.

World J Urol. 2019 Jan 17. doi: 10.1007/s00345-019-02631-y. [Epub ahead of print]


Urothelial Carcinoma in Bladder Diverticula: A Multicenter Analysis of Characteristics and Clinical Outcomes.

Voskuilen CS, Seiler R, Rink M, Poyet C, Noon AP, Roghmann F, Necchi A, Aziz A, Lavollé A, Young MJ, Marks P, Saba K, van Rhijn BWG, Fransen van de Putte EE, Ablat J, Black PC, Sosnowski R, Dobruch J, Kumar P, Jallad S, Catto JWF, Xylinas E, Hendricksen K; Young Academic Urologists’ Working Group on Urothelial Carcinoma of the European Association of Urology.

Eur Urol Focus. 2018 Dec 14. pii: S2405-4569(18)30382-1. doi: 10.1016/j.euf.2018.12.002. [Epub ahead of print]


Paritaprevir, ritonavir, ombitasvir, and dasabuvir with and without ribavirin in people with HCV genotype 1 and recent injecting drug use or receiving opioid substitution therapy.

Grebely J, Conway B, Cunningham EB, Fraser C, Moriggia A, Gane E, Stedman C, Cooper C, Castro E, Schmid P, Petoumenos K, Hajarizadeh B, Marks P, Erratt A, Dalgard O, Lacombe K, Feld JJ, Bruneau J, Daulouede JP, Powis J, Bruggmann P, Matthews GV, Kronborg I, Shaw D, Dunlop A, Hellard M, Applegate TL, Crawford S, Dore GJ; D3FEAT Study Group.

Int J Drug Policy. 2018 Dec;62:94-103. doi: 10.1016/j.drugpo.2018.10.004. Epub 2018 Oct 29.


Adherence to sofosbuvir and velpatasvir among people with chronic HCV infection and recent injection drug use: The SIMPLIFY study.

Cunningham EB, Amin J, Feld JJ, Bruneau J, Dalgard O, Powis J, Hellard M, Cooper C, Read P, Conway B, Dunlop AJ, Norton B, Litwin AH, Hajarizadeh B, Thurnheer MC, Dillon JF, Weltman M, Shaw D, Bruggmann P, Gane E, Fraser C, Marks P, Applegate TL, Quiene S, Siriragavan S, Matthews GV, Dore GJ, Grebely J; SIMPLIFY study group.

Int J Drug Policy. 2018 Dec;62:14-23. doi: 10.1016/j.drugpo.2018.08.013. Epub 2018 Oct 22.


Evaluating Guideline Adherence for T1 Bladder Cancer Treatment and Surveillance: A Retrospective German Multicenter Observation.

Vetterlein MW, Gild P, Marks P, Roschinski J, Doh O, Höppner W, Wagner W, Isbarn H, Büscheck F, Sauter G, Dahlem R, Soave A, Fisch M, Rink M.

Urol Int. 2018;101(3):285-292. doi: 10.1159/000493369. Epub 2018 Sep 20.


MetaHCR: a web-enabled metagenome data management system for hydrocarbon resources.

Marks PC, Bigler M, Alsop EB, Vigneron A, Lomans BP, De Paula R, Geissler B, Tsesmetzis N.

Database (Oxford). 2018 Jan 1;2018:1-10. doi: 10.1093/database/bay087.


Bulk phase behavior of lithium imide-metal nitride ammonia decomposition catalysts.

Makepeace JW, Wood TJ, Marks PL, Smith RI, Murray CA, David WIF.

Phys Chem Chem Phys. 2018 Sep 12;20(35):22689-22697. doi: 10.1039/c8cp02824a.


Evaluation of a Hepatitis C Virus Core Antigen Assay in Plasma and Dried Blood Spot Samples.

Lamoury FMJ, Hajarizadeh B, Soker A, Martinez D, Quek C, Cunningham P, Catlett B, Cloherty G, Marks P, Amin J, Grebely J, Dore GJ, Applegate TL.

J Mol Diagn. 2018 Sep;20(5):621-627. doi: 10.1016/j.jmoldx.2018.05.010. Epub 2018 Jun 26.


Germline pathogenic variants in PALB2 and other cancer-predisposing genes in families with hereditary diffuse gastric cancer without CDH1 mutation: a whole-exome sequencing study.

Fewings E, Larionov A, Redman J, Goldgraben MA, Scarth J, Richardson S, Brewer C, Davidson R, Ellis I, Evans DG, Halliday D, Izatt L, Marks P, McConnell V, Verbist L, Mayes R, Clark GR, Hadfield J, Chin SF, Teixeira MR, Giger OT, Hardwick R, di Pietro M, O'Donovan M, Pharoah P, Caldas C, Fitzgerald RC, Tischkowitz M.

Lancet Gastroenterol Hepatol. 2018 Jul;3(7):489-498. doi: 10.1016/S2468-1253(18)30079-7. Epub 2018 Apr 27.


Shortened therapy of eight weeks with paritaprevir/ritonavir/ombitasvir and dasabuvir is highly effective in people with recent HCV genotype 1 infection.

Martinello M, Bhagani S, Gane E, Orkin C, Cooke G, Dore GJ, Petoumenos K, Applegate TL, Tu E, Marks P, Pagani N, Grebely J, Nelson M, Matthews GV.

J Viral Hepat. 2018 Oct;25(10):1180-1188. doi: 10.1111/jvh.12917. Epub 2018 May 8.


Evaluation of the Xpert HCV Viral Load Finger-Stick Point-of-Care Assay.

Lamoury FMJ, Bajis S, Hajarizadeh B, Marshall AD, Martinello M, Ivanova E, Catlett B, Mowat Y, Marks P, Amin J, Smith J, Ezard N, Cock V, Hayllar J, Persing DH, Kleman M, Cunningham P, Dore GJ, Applegate TL, Grebely J; LiveRLife Study Group.

J Infect Dis. 2018 May 25;217(12):1889-1896. doi: 10.1093/infdis/jiy114.


Balancing Safety and Innovation for Cell-Based Regenerative Medicine.

Marks P, Gottlieb S.

N Engl J Med. 2018 Mar 8;378(10):954-959. doi: 10.1056/NEJMsr1715626. No abstract available.


Impact of the Ki-67 labeling index and p53 expression status on disease-free survival in pT1 urothelial carcinoma of the bladder.

Vetterlein MW, Roschinski J, Gild P, Marks P, Soave A, Doh O, Isbarn H, Höppner W, Wagner W, Shariat SF, Brausi M, Büscheck F, Sauter G, Fisch M, Rink M.

Transl Androl Urol. 2017 Dec;6(6):1018-1026. doi: 10.21037/tau.2017.11.10.


Sofosbuvir and velpatasvir for hepatitis C virus infection in people with recent injection drug use (SIMPLIFY): an open-label, single-arm, phase 4, multicentre trial.

Grebely J, Dalgard O, Conway B, Cunningham EB, Bruggmann P, Hajarizadeh B, Amin J, Bruneau J, Hellard M, Litwin AH, Marks P, Quiene S, Siriragavan S, Applegate TL, Swan T, Byrne J, Lacalamita M, Dunlop A, Matthews GV, Powis J, Shaw D, Thurnheer MC, Weltman M, Kronborg I, Cooper C, Feld JJ, Fraser C, Dillon JF, Read P, Gane E, Dore GJ; SIMPLIFY Study Group.

Lancet Gastroenterol Hepatol. 2018 Mar;3(3):153-161. doi: 10.1016/S2468-1253(17)30404-1. Epub 2018 Jan 6.


Clinical Development Strategies and Considerations for Zika Vaccine Licensure.

Gruber MF, Farizo KM, Pratt RD, Fink DL, Finn TM, Krause PR, Borio LL, Marks PW.

J Infect Dis. 2017 Dec 16;216(suppl_10):S964-S970. doi: 10.1093/infdis/jix433.


Effect of repeat prostate biopsies on functional outcomes after radical prostatectomy.

Rosenbaum CM, Mandel P, Tennstedt P, Preisser F, Marks P, Chun FK, Graefen M, Tilki D, Salomon G.

Urol Oncol. 2018 Mar;36(3):91.e17-91.e22. doi: 10.1016/j.urolonc.2017.11.016. Epub 2017 Dec 13.


Ultrasound Determination of the Femoral Head-Neck Alpha Angle.

Robinson DJ, Lee S, Marks P, Schneider ME.

Ultrasound Med Biol. 2018 Feb;44(2):495-501. doi: 10.1016/j.ultrasmedbio.2017.10.006. Epub 2017 Nov 29.


Introduction to the Special Issue: 20th-Century Origins and 21st-Century Developments of Peer Nomination Methodology.

Marks PEL.

New Dir Child Adolesc Dev. 2017 Sep;2017(157):7-19. doi: 10.1002/cad.20205.


Methodological Choices in Peer Nomination Research.

Cillessen AHN, Marks PEL.

New Dir Child Adolesc Dev. 2017 Sep;2017(157):21-44. doi: 10.1002/cad.20206. Review.


Safety, tolerability, clinical, and joint structural outcomes of a single intra-articular injection of allogeneic mesenchymal precursor cells in patients following anterior cruciate ligament reconstruction: a controlled double-blind randomised trial.

Wang Y, Shimmin A, Ghosh P, Marks P, Linklater J, Connell D, Hall S, Skerrett D, Itescu S, Cicuttini FM.

Arthritis Res Ther. 2017 Aug 2;19(1):180. doi: 10.1186/s13075-017-1391-0.


Changes in risk behaviours during and following treatment for hepatitis C virus infection among people who inject drugs: The ACTIVATE study.

Midgard H, Hajarizadeh B, Cunningham EB, Conway B, Backmund M, Bruggmann P, Bruneau J, Bourgeois S, Dunlop A, Foster GR, Hellard M, Robaeys G, Thurnheer MC, Weltman M, Amin J, Marks PS, Quiene S, Dore GJ, Dalgard O, Grebely J; ACTIVATE Study Group.

Int J Drug Policy. 2017 Sep;47:230-238. doi: 10.1016/j.drugpo.2017.05.040. Epub 2017 Jun 19.


Efficacy of response-guided directly observed pegylated interferon and self-administered ribavirin for people who inject drugs with hepatitis C virus genotype 2/3 infection: The ACTIVATE study.

Grebely J, Dalgard O, Cunningham EB, Hajarizadeh B, Foster GR, Bruggmann P, Conway B, Backmund M, Robaeys G, Swan T, Amin J, Marks PS, Quiene S, Applegate TL, Weltman M, Shaw D, Dunlop A, Hellard M, Bruneau J, Midgard H, Bourgeois S, Staehelin C, Dore GJ; ACTIVATE Study Group.

Int J Drug Policy. 2017 Sep;47:177-186. doi: 10.1016/j.drugpo.2017.05.020. Epub 2017 Jun 16.


Adherence to response-guided pegylated interferon and ribavirin for people who inject drugs with hepatitis C virus genotype 2/3 infection: the ACTIVATE study.

Cunningham EB, Hajarizadeh B, Dalgard O, Amin J, Hellard M, Foster GR, Bruggmann P, Conway B, Backmund M, Robaeys G, Swan T, Marks PS, Quiene S, Applegate TL, Weltman M, Shaw D, Dunlop A, Bruneau J, Midgard H, Bourgeois S, Thurnheer MC, Dore GJ, Grebely J; ACTIVATE Study Group.

BMC Infect Dis. 2017 Jun 13;17(1):420. doi: 10.1186/s12879-017-2517-3.


A Randomized Controlled Trial of the Rochester Forensic Assertive Community Treatment Model.

Lamberti JS, Weisman RL, Cerulli C, Williams GC, Jacobowitz DB, Mueser KT, Marks PD, Strawderman RL, Harrington D, Lamberti TA, Caine ED.

Psychiatr Serv. 2017 Oct 1;68(10):1016-1024. doi: 10.1176/ Epub 2017 Jun 1.


Hepatitis C virus core antigen: A simplified treatment monitoring tool, including for post-treatment relapse.

Lamoury FMJ, Soker A, Martinez D, Hajarizadeh B, Cunningham EB, Cunningham P, Bruggmann P, Foster GR, Dalgard O, Backmund M, Conway B, Robaeys G, Swan T, Cloherty G, Marks P, Grebely J, Dore GJ, Applegate TL.

J Clin Virol. 2017 Jul;92:32-38. doi: 10.1016/j.jcv.2017.05.007. Epub 2017 May 11.


Rectus Abdominis Rhabdomyolysis: Report of 2 Cases.

Boyle J, Marks P, Read J.

J Ultrasound Med. 2017 Oct;36(10):2165-2171. doi: 10.1002/jum.14242. Epub 2017 May 15.


Evaluation of the Xpert HCV Viral Load point-of-care assay from venepuncture-collected and finger-stick capillary whole-blood samples: a cohort study.

Grebely J, Lamoury FMJ, Hajarizadeh B, Mowat Y, Marshall AD, Bajis S, Marks P, Amin J, Smith J, Edwards M, Gorton C, Ezard N, Persing D, Kleman M, Cunningham P, Catlett B, Dore GJ, Applegate TL; LiveRLife Study Group.

Lancet Gastroenterol Hepatol. 2017 Jul;2(7):514-520. doi: 10.1016/S2468-1253(17)30075-4. Epub 2017 Apr 22.


Ultrasound Screening for Adverse Local Tissue Reaction after Hip Arthroplasty.

Robinson DJ, Lee S, Marks P, Schneider ME.

Ultrasound Med Biol. 2017 Jul;43(7):1549-1556. doi: 10.1016/j.ultrasmedbio.2017.02.001. Epub 2017 Apr 12.


The Blood Supply and Men Who Have Sex with Men.

Marks PW.

N Engl J Med. 2017 Apr 13;376(15):1486. doi: 10.1056/NEJMc1701828. No abstract available.


Decision making in the face of uncertainty: the challenge of emerging infectious diseases.

Marks PW, Petersen LR.

Transfusion. 2017 Mar;57(3pt2):723-728. doi: 10.1111/trf.14037. No abstract available.


The role of genetic counsellors in genomic healthcare in the United Kingdom: a statement by the Association of Genetic Nurses and Counsellors.

Middleton A, Marks P, Bruce A, Protheroe-Davies LK, King C, Claber O, Houghton C, Giffney C, Macleod R, Dolling C, Kenwrick S, Scotcher D, Hall G, Patch C, Boyes L.

Eur J Hum Genet. 2017 Mar 22;25(6):659-661. doi: 10.1038/ejhg.2017.28. Epub 2017 Mar 22.


A Systematic Review and Appraisal of Clinical Practice Guidelines for Musculoskeletal Soft Tissue Injuries and Conditions.

Pincus D, Kuhn JE, Sheth U, Rizzone K, Colbenson K, Dwyer T, Karpinos A, Marks PH, Wasserstein D.

Am J Sports Med. 2017 May;45(6):1458-1464. doi: 10.1177/0363546516667903. Epub 2016 Oct 17. Review.


Transforming Evidence Generation to Support Health and Health Care Decisions.

Califf RM, Robb MA, Bindman AB, Briggs JP, Collins FS, Conway PH, Coster TS, Cunningham FE, De Lew N, DeSalvo KB, Dymek C, Dzau VJ, Fleurence RL, Frank RG, Gaziano JM, Kaufmann P, Lauer M, Marks PW, McGinnis JM, Richards C, Selby JV, Shulkin DJ, Shuren J, Slavitt AM, Smith SR, Washington BV, White PJ, Woodcock J, Woodson J, Sherman RE.

N Engl J Med. 2016 Dec 15;375(24):2395-2400. No abstract available.


Clarifying Stem-Cell Therapy's Benefits and Risks.

Marks PW, Witten CM, Califf RM.

N Engl J Med. 2017 Mar 16;376(11):1007-1009. doi: 10.1056/NEJMp1613723. Epub 2016 Nov 30. No abstract available.


Real-World Evidence - What Is It and What Can It Tell Us?

Sherman RE, Anderson SA, Dal Pan GJ, Gray GW, Gross T, Hunter NL, LaVange L, Marinac-Dabic D, Marks PW, Robb MA, Shuren J, Temple R, Woodcock J, Yue LQ, Califf RM.

N Engl J Med. 2016 Dec 8;375(23):2293-2297. No abstract available.


Female with bladder cancer: what and why is there a difference?

Marks P, Soave A, Shariat SF, Fajkovic H, Fisch M, Rink M.

Transl Androl Urol. 2016 Oct;5(5):668-682. Review.


Sofosbuvir and ribavirin for 6 weeks is not effective among people with recent hepatitis C virus infection: The DARE-C II study.

Martinello M, Gane E, Hellard M, Sasadeusz J, Shaw D, Petoumenos K, Applegate T, Grebely J, Maire L, Marks P, Dore GJ, Matthews GV.

Hepatology. 2016 Dec;64(6):1911-1921. doi: 10.1002/hep.28844. Epub 2016 Oct 27.


Ultrasound-Guided Radiofrequency Denervation of the Medial Calcaneal Nerve.

Counsel PD, Davenport M, Brown A, Ooi CC, Comin J, Marks P, Connell DA.

Clin J Sport Med. 2016 Nov;26(6):465-470.


MIxS-HCR: a MIxS extension defining a minimal information standard for sequence data from environments pertaining to hydrocarbon resources.

Tsesmetzis N, Yilmaz P, Marks PC, Kyrpides NC, Head IM, Lomans BP.

Stand Genomic Sci. 2016 Oct 12;11:78. eCollection 2016.


A Prospective Randomized Clinical Trial in Total Hip Arthroplasty-Comparing Early Results Between the Direct Anterior Approach and the Posterior Approach.

Cheng TE, Wallis JA, Taylor NF, Holden CT, Marks P, Smith CL, Armstrong MS, Singh PJ.

J Arthroplasty. 2017 Mar;32(3):883-890. doi: 10.1016/j.arth.2016.08.027. Epub 2016 Aug 31.


Screening of Blood Donations for Zika Virus Infection - Puerto Rico, April 3-June 11, 2016.

Kuehnert MJ, Basavaraju SV, Moseley RR, Pate LL, Galel SA, Williamson PC, Busch MP, Alsina JO, Climent-Peris C, Marks PW, Epstein JS, Nakhasi HL, Hobson JP, Leiby DA, Akolkar PN, Petersen LR, Rivera-Garcia B.

MMWR Morb Mortal Wkly Rep. 2016 Jun 24;65(24):627-8. doi: 10.15585/mmwr.mm6524e2.


Extensive sequencing of seven human genomes to characterize benchmark reference materials.

Zook JM, Catoe D, McDaniel J, Vang L, Spies N, Sidow A, Weng Z, Liu Y, Mason CE, Alexander N, Henaff E, McIntyre AB, Chandramohan D, Chen F, Jaeger E, Moshrefi A, Pham K, Stedman W, Liang T, Saghbini M, Dzakula Z, Hastie A, Cao H, Deikus G, Schadt E, Sebra R, Bashir A, Truty RM, Chang CC, Gulbahce N, Zhao K, Ghosh S, Hyland F, Fu Y, Chaisson M, Xiao C, Trow J, Sherry ST, Zaranek AW, Ball M, Bobe J, Estep P, Church GM, Marks P, Kyriazopoulou-Panagiotopoulou S, Zheng GX, Schnall-Levin M, Ordonez HS, Mudivarti PA, Giorda K, Sheng Y, Rypdal KB, Salit M.

Sci Data. 2016 Jun 7;3:160025. doi: 10.1038/sdata.2016.25.


A hybrid approach for de novo human genome sequence assembly and phasing.

Mostovoy Y, Levy-Sakin M, Lam J, Lam ET, Hastie AR, Marks P, Lee J, Chu C, Lin C, Džakula Ž, Cao H, Schlebusch SA, Giorda K, Schnall-Levin M, Wall JD, Kwok PY.

Nat Methods. 2016 Jul;13(7):587-90. doi: 10.1038/nmeth.3865. Epub 2016 May 9.


Maintaining a Safe Blood Supply in an Era of Emerging Pathogens.

Marks PW, Epstein JS, Borio LL.

J Infect Dis. 2016 Jun 1;213(11):1676-7. doi: 10.1093/infdis/jiw089. Epub 2016 Mar 8.


Quality of Life Assessment After Maxillomandibular Advancement Surgery for Obstructive Sleep Apnea.

Butterfield KJ, Marks PL, McLean L, Newton J.

J Oral Maxillofac Surg. 2016 Jun;74(6):1228-37. doi: 10.1016/j.joms.2016.01.043. Epub 2016 Jan 30.


Haplotyping germline and cancer genomes with high-throughput linked-read sequencing.

Zheng GX, Lau BT, Schnall-Levin M, Jarosz M, Bell JM, Hindson CM, Kyriazopoulou-Panagiotopoulou S, Masquelier DA, Merrill L, Terry JM, Mudivarti PA, Wyatt PW, Bharadwaj R, Makarewicz AJ, Li Y, Belgrader P, Price AD, Lowe AJ, Marks P, Vurens GM, Hardenbol P, Montesclaros L, Luo M, Greenfield L, Wong A, Birch DE, Short SW, Bjornson KP, Patel P, Hopmans ES, Wood C, Kaur S, Lockwood GK, Stafford D, Delaney JP, Wu I, Ordonez HS, Grimes SM, Greer S, Lee JY, Belhocine K, Giorda KM, Heaton WH, McDermott GP, Bent ZW, Meschi F, Kondov NO, Wilson R, Bernate JA, Gauby S, Kindwall A, Bermejo C, Fehr AN, Chan A, Saxonov S, Ness KD, Hindson BJ, Ji HP.

Nat Biotechnol. 2016 Mar;34(3):303-11. doi: 10.1038/nbt.3432. Epub 2016 Feb 1.


Modeling complete removal of risk assessment questions in the USA predicts the risk of HIV exposure in blood recipients could increase despite the use of nucleic acid testing.

Yang H, Anderson SA, Forshee R, Williams A, Epstein JS, Marks PW.

Vox Sang. 2016 May;110(4):324-8. doi: 10.1111/vox.12375. Epub 2016 Jan 14.


Creation of a histone deacetylase 6 inhibitor and its biological effects [corrected].

Lee JH, Yao Y, Mahendran A, Ngo L, Venta-Perez G, Choy ML, Breslow R, Marks PA.

Proc Natl Acad Sci U S A. 2015 Sep 29;112(39):12005-10. doi: 10.1073/pnas.1515882112. Epub 2015 Sep 14. Erratum in: Proc Natl Acad Sci U S A. 2015 Oct 27;112(43):E5899.

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