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A deep learning approach to automate refinement of somatic variant calling from cancer sequencing data.

Ainscough BJ, Barnell EK, Ronning P, Campbell KM, Wagner AH, Fehniger TA, Dunn GP, Uppaluri R, Govindan R, Rohan TE, Griffith M, Mardis ER, Swamidass SJ, Griffith OL.

Nat Genet. 2018 Nov 5. doi: 10.1038/s41588-018-0257-y. [Epub ahead of print]


The geo-spatial distribution of childhood diarrheal disease in West Africa, 2008-2013: A covariate-adjusted cluster analysis.

Dunn G, Johnson GD.

Spat Spatiotemporal Epidemiol. 2018 Aug;26:127-141. doi: 10.1016/j.sste.2018.06.005. Epub 2018 Jun 19.


The benefit of minocycline on negative symptoms of schizophrenia in patients with recent-onset psychosis (BeneMin): a randomised, double-blind, placebo-controlled trial.

Deakin B, Suckling J, Barnes TRE, Byrne K, Chaudhry IB, Dazzan P, Drake RJ, Giordano A, Husain N, Jones PB, Joyce E, Knox E, Krynicki C, Lawrie SM, Lewis S, Lisiecka-Ford DM, Nikkheslat N, Pariante CM, Smallman R, Watson A, Williams SCR, Upthegrove R, Dunn G; BeneMin Study team.

Lancet Psychiatry. 2018 Nov;5(11):885-894. doi: 10.1016/S2215-0366(18)30345-6. Epub 2018 Oct 12. Erratum in: Lancet Psychiatry. 2018 Nov 1;:.


Developing a foot ulcer risk model: what is needed to do this in a real-world primary care setting?

Heald A, Lunt M, Rutter MK, Anderson SG, Cortes G, Edmonds M, Jude E, Boulton A, Dunn G.

Diabet Med. 2018 Oct 15. doi: 10.1111/dme.13837. [Epub ahead of print]


Perinatal Nutrition and Programmed Risk for Neuropsychiatric Disorders: A Focus on Animal Models.

DeCapo M, Thompson JR, Dunn G, Sullivan EL.

Biol Psychiatry. 2018 Aug 23. pii: S0006-3223(18)31778-5. doi: 10.1016/j.biopsych.2018.08.006. [Epub ahead of print] Review.


Feeding Rates in the Swordtail Fish Xiphophorus multilineatus: A Model System for Genetic Variation in Nutritional Programming.

Morris MR, Friebertshauser RJ, Zupi M, Liotta MN, Dunn G, Kleinas N, Rios-Cardenas O.

Zebrafish. 2018 Oct;15(5):484-491. doi: 10.1089/zeb.2018.1624. Epub 2018 Aug 23.


Cognitive Behavioral Therapy for antipsychotic-free schizophrenia spectrum disorders: Does therapy dose influence outcome?

Spencer HM, McMenamin M, Emsley R, Turkington D, Dunn G, Morrison AP, Brabban A, Hutton P, Dudley R.

Schizophr Res. 2018 Jul 12. pii: S0920-9964(18)30433-X. doi: 10.1016/j.schres.2018.07.016. [Epub ahead of print]


Stereotactic radiosurgery and immunotherapy in melanoma brain metastases: Patterns of care and treatment outcomes.

Gabani P, Fischer-Valuck BW, Johanns TM, Hernandez-Aya LF, Keller JW, Rich KM, Kim AH, Dunn GP, Robinson CG, Chicoine MR, Huang J, Abraham CD.

Radiother Oncol. 2018 Aug;128(2):266-273. doi: 10.1016/j.radonc.2018.06.017. Epub 2018 Jun 27.


The COMMAND trial of cognitive therapy for harmful compliance with command hallucinations (CTCH): a qualitative study of acceptability and tolerability in the UK.

Birchwood M, Mohan L, Meaden A, Tarrier N, Lewis S, Wykes T, Davies LM, Dunn G, Peters E, Michail M.

BMJ Open. 2018 Jun 15;8(6):e021657. doi: 10.1136/bmjopen-2018-021657.


Focused Ultrasound-enabled Brain Tumor Liquid Biopsy.

Zhu L, Cheng G, Ye D, Nazeri A, Yue Y, Liu W, Wang X, Dunn GP, Petti AA, Leuthardt EC, Chen H.

Sci Rep. 2018 Apr 26;8(1):6553. doi: 10.1038/s41598-018-24516-7.


Resistance-promoting effects of ependymoma treatment revealed through genomic analysis of multiple recurrences in a single patient.

Miller CA, Dahiya S, Li T, Fulton RS, Smyth MD, Dunn GP, Rubin JB, Mardis ER.

Cold Spring Harb Mol Case Stud. 2018 Apr 2;4(2). pii: a002444. doi: 10.1101/mcs.a002444. Print 2018 Apr.


T-Cell Exhaustion Signatures Vary with Tumor Type and Are Severe in Glioblastoma.

Woroniecka K, Chongsathidkiet P, Rhodin K, Kemeny H, Dechant C, Farber SH, Elsamadicy AA, Cui X, Koyama S, Jackson C, Hansen LJ, Johanns TM, Sanchez-Perez L, Chandramohan V, Yu YA, Bigner DD, Giles A, Healy P, Dranoff G, Weinhold KJ, Dunn GP, Fecci PE.

Clin Cancer Res. 2018 Sep 1;24(17):4175-4186. doi: 10.1158/1078-0432.CCR-17-1846. Epub 2018 Feb 7.


Cancer immunogenomic approach to neoantigen discovery in a checkpoint blockade responsive murine model of oral cavity squamous cell carcinoma.

Zolkind P, Przybylski D, Marjanovic N, Nguyen L, Lin T, Johanns T, Alexandrov A, Zhou L, Allen CT, Miceli AP, Schreiber RD, Artyomov M, Dunn GP, Uppaluri R.

Oncotarget. 2017 Dec 28;9(3):4109-4119. doi: 10.18632/oncotarget.23751. eCollection 2018 Jan 9.


The impact of the Boko Haram insurgency in Northeast Nigeria on childhood wasting: a double-difference study.

Dunn G.

Confl Health. 2018 Jan 24;12:6. doi: 10.1186/s13031-018-0136-2. eCollection 2018.


Echocardiography Core Laboratory Reproducibility of Cardiac Safety Assessments in Cardio-Oncology.

Khouri MG, Ky B, Dunn G, Plappert T, Englefield V, Rabineau D, Yow E, Barnhart HX, St John Sutton M, Douglas PS.

J Am Soc Echocardiogr. 2018 Mar;31(3):361-371.e3. doi: 10.1016/j.echo.2017.11.018. Epub 2018 Feb 2.


Consumption of NADPH for 2-HG Synthesis Increases Pentose Phosphate Pathway Flux and Sensitizes Cells to Oxidative Stress.

Gelman SJ, Naser F, Mahieu NG, McKenzie LD, Dunn GP, Chheda MG, Patti GJ.

Cell Rep. 2018 Jan 9;22(2):512-522. doi: 10.1016/j.celrep.2017.12.050.


Delivery of cognitive-behaviour therapy for psychosis: a service user preference trial.

Haddock G, Berry K, Davies G, Dunn G, Harris K, Hartley S, Holland F, Kelly J, Law H, Morrison AP, Mulligan J, Neil ST, Pitt L, Rivers Z, Taylor CDJ, Wass R, Welford M, Woodward S, Barrowclough C.

J Ment Health. 2018 Aug;27(4):336-344. doi: 10.1080/09638237.2017.1417549. Epub 2017 Dec 22.


Social deprivation modifies the association between incident foot ulceration and mortality in type 1 and type 2 diabetes: a longitudinal study of a primary-care cohort.

Anderson SG, Shoo H, Saluja S, Anderson CD, Khan A, Livingston M, Jude EB, Lunt M, Dunn G, Heald AH.

Diabetologia. 2018 Apr;61(4):959-967. doi: 10.1007/s00125-017-4522-x. Epub 2017 Dec 21.


Erratum: Genomic landscape of high-grade meningiomas.

Bi WL, Greenwald NF, Abedalthagafi M, Wala J, Gibson WJ, Agarwalla PK, Horowitz P, Schumacher SE, Esaulova E, Mei Y, Chevalier A, A Ducar M, Thorner AR, van Hummelen P, O Stemmer-Rachamimov A, Artyomov M, Al-Mefty O, Dunn GP, Santagata S, Dunn IF, Beroukhim R.

NPJ Genom Med. 2017 Sep 4;2:26. doi: 10.1038/s41525-017-0023-6. eCollection 2017.


Biological and therapeutic implications of multisector sequencing in newly diagnosed glioblastoma.

Mahlokozera T, Vellimana AK, Li T, Mao DD, Zohny ZS, Kim DH, Tran DD, Marcus DS, Fouke SJ, Campian JL, Dunn GP, Miller CA, Kim AH.

Neuro Oncol. 2018 Mar 27;20(4):472-483. doi: 10.1093/neuonc/nox232.


Novel Mitochondria-Targeting Peptide in Heart Failure Treatment: A Randomized, Placebo-Controlled Trial of Elamipretide.

Daubert MA, Yow E, Dunn G, Marchev S, Barnhart H, Douglas PS, O'Connor C, Goldstein S, Udelson JE, Sabbah HN.

Circ Heart Fail. 2017 Dec;10(12). pii: e004389. doi: 10.1161/CIRCHEARTFAILURE.117.004389.


Distant intracranial failure in melanoma brain metastases treated with stereotactic radiosurgery in the era of immunotherapy and targeted agents.

Acharya S, Mahmood M, Mullen D, Yang D, Tsien CI, Huang J, Perkins SM, Rich K, Chicoine M, Leuthardt E, Dowling J, Dunn G, Keller J, Robinson CG, Abraham C.

Adv Radiat Oncol. 2017 Aug 12;2(4):572-580. doi: 10.1016/j.adro.2017.07.003. eCollection 2017 Oct-Dec.


The COMMAND trial of cognitive therapy to prevent harmful compliance with command hallucinations: predictors of outcome and mediators of change.

Birchwood M, Dunn G, Meaden A, Tarrier N, Lewis S, Wykes T, Davies L, Michail M, Peters E.

Psychol Med. 2018 Sep;48(12):1966-1974. doi: 10.1017/S0033291717003488. Epub 2017 Dec 5.


Management of intracranial melanomas in the era of precision medicine.

Young GJ, Bi WL, Wu WW, Johanns TM, Dunn GP, Dunn IF.

Oncotarget. 2017 Jul 13;8(51):89326-89347. doi: 10.18632/oncotarget.19223. eCollection 2017 Oct 24. Review.


Effect of initiating drug treatment on the risk of drug-related poisoning death and acquisitive crime among offending heroin users.

Pierce M, Bird SM, Hickman M, Marsden J, Dunn G, Seddon T, Millar T.

Int J Drug Policy. 2018 Jan;51:42-51. doi: 10.1016/j.drugpo.2017.09.017. Epub 2017 Nov 20.


Direct puncture Onyx embolization of a large calvarial metastasis with intracranial extension: Case report.

Zhou MH, Dunn GP, Osbun JW, Cross DT 3rd, Moran CJ, Dacey RG Jr, Kansagra AP.

Interv Neuroradiol. 2018 Apr;24(2):220-224. doi: 10.1177/1591019917740353. Epub 2017 Nov 9.


Fabrication of Subnanometer-Precision Nanopores in Hexagonal Boron Nitride.

Gilbert SM, Dunn G, Azizi A, Pham T, Shevitski B, Dimitrov E, Liu S, Aloni S, Zettl A.

Sci Rep. 2017 Nov 8;7(1):15096. doi: 10.1038/s41598-017-12684-x.


SlowMo, a digital therapy targeting reasoning in paranoia, versus treatment as usual in the treatment of people who fear harm from others: study protocol for a randomised controlled trial.

Garety PA, Ward T, Freeman D, Fowler D, Emsley R, Dunn G, Kuipers E, Bebbington P, Waller H, Greenwood K, Rus-Calafell M, McGourty A, Hardy A.

Trials. 2017 Nov 2;18(1):510. doi: 10.1186/s13063-017-2242-7.


Comprehensive Analysis of Hypermutation in Human Cancer.

Campbell BB, Light N, Fabrizio D, Zatzman M, Fuligni F, de Borja R, Davidson S, Edwards M, Elvin JA, Hodel KP, Zahurancik WJ, Suo Z, Lipman T, Wimmer K, Kratz CP, Bowers DC, Laetsch TW, Dunn GP, Johanns TM, Grimmer MR, Smirnov IV, Larouche V, Samuel D, Bronsema A, Osborn M, Stearns D, Raman P, Cole KA, Storm PB, Yalon M, Opocher E, Mason G, Thomas GA, Sabel M, George B, Ziegler DS, Lindhorst S, Issai VM, Constantini S, Toledano H, Elhasid R, Farah R, Dvir R, Dirks P, Huang A, Galati MA, Chung J, Ramaswamy V, Irwin MS, Aronson M, Durno C, Taylor MD, Rechavi G, Maris JM, Bouffet E, Hawkins C, Costello JF, Meyn MS, Pursell ZF, Malkin D, Tabori U, Shlien A.

Cell. 2017 Nov 16;171(5):1042-1056.e10. doi: 10.1016/j.cell.2017.09.048. Epub 2017 Oct 19.


Osteoglycin promotes meningioma development through downregulation of NF2 and activation of mTOR signaling.

Mei Y, Du Z, Hu C, Greenwald NF, Abedalthagafi M, Agar NYR, Dunn GP, Bi WL, Santagata S, Dunn IF.

Cell Commun Signal. 2017 Sep 18;15(1):34. doi: 10.1186/s12964-017-0189-7.


Modeling Bivariate Change in Individual Differences: Prospective Associations Between Personality and Life Satisfaction.

Hounkpatin HO, Boyce CJ, Dunn G, Wood AM.

J Pers Soc Psychol. 2017 Sep 18. doi: 10.1037/pspp0000161. [Epub ahead of print]


Targeting Neoantigens in Glioblastoma: An Overview of Cancer Immunogenomics and Translational Implications.

Johanns TM, Bowman-Kirigin JA, Liu C, Dunn GP.

Neurosurgery. 2017 Sep 1;64(CN_suppl_1):165-176. doi: 10.1093/neuros/nyx321. No abstract available.


Insights into the link between drug use and criminality: Lifetime offending of criminally-active opiate users.

Pierce M, Hayhurst K, Bird SM, Hickman M, Seddon T, Dunn G, Millar T.

Drug Alcohol Depend. 2017 Oct 1;179:309-316. doi: 10.1016/j.drugalcdep.2017.07.024. Epub 2017 Aug 16.


CHOICE: Choosing Health Options In Chronic Care Emergencies.

Guthrie E, Afzal C, Blakeley C, Blakemore A, Byford R, Camacho E, Chan T, Chew-Graham C, Davies L, de Lusignan S, Dickens C, Drinkwater J, Dunn G, Hunter C, Joy M, Kapur N, Langer S, Lovell K, Macklin J, Mackway-Jones K, Ntais D, Salmon P, Tomenson B, Watson J.

Southampton (UK): NIHR Journals Library; 2017 Jul.


Genomic landscape of high-grade meningiomas.

Bi WL, Greenwald NF, Abedalthagafi M, Wala J, Gibson WJ, Agarwalla PK, Horowitz P, Schumacher SE, Esaulova E, Mei Y, Chevalier A, Ducar M, Thorner AR, van Hummelen P, Stemmer-Rachamimov A, Artyomov M, Al-Mefty O, Dunn GP, Santagata S, Dunn IF, Beroukhim R.

NPJ Genom Med. 2017;2. pii: 15. doi: 10.1038/s41525-017-0014-7. Epub 2017 Apr 26. Erratum in: NPJ Genom Med. 2017 Sep 4;2:26.


Free ammonia offers algal crop protection from predators in dairy wastewater and ammonium-rich media.

Thomas PK, Dunn GP, Passero M, Feris KP.

Bioresour Technol. 2017 Nov;243:724-730. doi: 10.1016/j.biortech.2017.07.008. Epub 2017 Jul 5.


Genomic profile of human meningioma cell lines.

Mei Y, Bi WL, Greenwald NF, Agar NY, Beroukhim R, Dunn GP, Dunn IF.

PLoS One. 2017 May 26;12(5):e0178322. doi: 10.1371/journal.pone.0178322. eCollection 2017.


Applied Cancer Immunogenomics: Leveraging Neoantigen Discovery in Glioblastoma.

Johanns TM, Dunn GP.

Cancer J. 2017 Mar/Apr;23(2):125-130. doi: 10.1097/PPO.0000000000000247. Review.


Confounding in longitudinal studies in addiction treatment research.

Pierce M, Dunn G, Millar T.

Addict Res Theory. 2017 May 4;25(3):236-242. doi: 10.1080/16066359.2016.1247812. Epub 2016 Dec 22.


Randomised controlled trial of ketamine augmentation of electroconvulsive therapy to improve neuropsychological and clinical outcomes in depression (Ketamine-ECT study).

Anderson IM, Blamire A, Branton T, Brigadoi S, Clark R, Downey D, Dunn G, Easton A, Elliott R, Elwell C, Hayden K, Holland F, Karim S, Lowe J, Loo C, Nair R, Oakley T, Prakash A, Sharma PK, Williams SR, McAllister-Williams RH.

Southampton (UK): NIHR Journals Library; 2017 Mar.


Ketamine augmentation of electroconvulsive therapy to improve neuropsychological and clinical outcomes in depression (Ketamine-ECT): a multicentre, double-blind, randomised, parallel-group, superiority trial.

Anderson IM, Blamire A, Branton T, Clark R, Downey D, Dunn G, Easton A, Elliott R, Elwell C, Hayden K, Holland F, Karim S, Loo C, Lowe J, Nair R, Oakley T, Prakash A, Sharma PK, Williams SR, McAllister-Williams RH; Ketamine-ECT Study team.

Lancet Psychiatry. 2017 May;4(5):365-377. doi: 10.1016/S2215-0366(17)30077-9. Epub 2017 Mar 27.


Biomarker and Tumor Responses of Oral Cavity Squamous Cell Carcinoma to Trametinib: A Phase II Neoadjuvant Window-of-Opportunity Clinical Trial.

Uppaluri R, Winkler AE, Lin T, Law JH, Haughey BH, Nussenbaum B, Paniello RC, Rich JT, Diaz JA, Michel LP, Wildes T, Dunn GP, Zolkind P, Kallogjeri D, Piccirillo JF, Dehdashti F, Siegel BA, Chernock RD, Lewis JS Jr, Adkins DR.

Clin Cancer Res. 2017 May 1;23(9):2186-2194. doi: 10.1158/1078-0432.CCR-16-1469. Epub 2016 Nov 9.


Outbreak of Piv-3 in a Neonatal Intensive Care Unit in England.

Dunn GL, Tapson H, Davis J, Gobin M.

Pediatr Infect Dis J. 2017 Mar;36(3):344-345. doi: 10.1097/INF.0000000000001443.


Single-particle mapping of nonequilibrium nanocrystal transformations.

Ye X, Jones MR, Frechette LB, Chen Q, Powers AS, Ercius P, Dunn G, Rotskoff GM, Nguyen SC, Adiga VP, Zettl A, Rabani E, Geissler PL, Alivisatos AP.

Science. 2016 Nov 18;354(6314):874-877.


Immunogenomics of Hypermutated Glioblastoma: A Patient with Germline POLE Deficiency Treated with Checkpoint Blockade Immunotherapy.

Johanns TM, Miller CA, Dorward IG, Tsien C, Chang E, Perry A, Uppaluri R, Ferguson C, Schmidt RE, Dahiya S, Ansstas G, Mardis ER, Dunn GP.

Cancer Discov. 2016 Nov;6(11):1230-1236. Epub 2016 Sep 28.


Endogenous Neoantigen-Specific CD8 T Cells Identified in Two Glioblastoma Models Using a Cancer Immunogenomics Approach.

Johanns TM, Ward JP, Miller CA, Wilson C, Kobayashi DK, Bender D, Fu Y, Alexandrov A, Mardis ER, Artyomov MN, Schreiber RD, Dunn GP.

Cancer Immunol Res. 2016 Dec;4(12):1007-1015. Epub 2016 Oct 31.


Discovery of 8-Membered Ring Sulfonamides as Inhibitors of Oncogenic Mutant Isocitrate Dehydrogenase 1.

Law JM, Stark SC, Liu K, Liang NE, Hussain MM, Leiendecker M, Ito D, Verho O, Stern AM, Johnston SE, Zhang YL, Dunn GP, Shamji AF, Schreiber SL.

ACS Med Chem Lett. 2016 Aug 18;7(10):944-949. eCollection 2016 Oct 13.


Pathways through opiate use and offending: A systematic review.

Hayhurst KP, Pierce M, Hickman M, Seddon T, Dunn G, Keane J, Millar T.

Int J Drug Policy. 2017 Jan;39:1-13. doi: 10.1016/j.drugpo.2016.08.015. Epub 2016 Oct 19. Review.


Neoantigens in immunotherapy and personalized vaccines: Implications for head and neck squamous cell carcinoma.

Zolkind P, Dunn GP, Lin T, Griffith M, Griffith OL, Uppaluri R.

Oral Oncol. 2017 Aug;71:169-176. doi: 10.1016/j.oraloncology.2016.09.010. Epub 2016 Oct 14. Review.

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