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Items: 1 to 50 of 373

1.

neoepiscope improves neoepitope prediction with multi-variant phasing.

Wood MA, Nguyen A, Struck A, Ellrott K, Nellore A, Thompson RF.

Bioinformatics. 2019 Aug 19. pii: btz653. doi: 10.1093/bioinformatics/btz653. [Epub ahead of print]

PMID:
31424527
2.

Clinical Documentation and Patient Care Using Artificial Intelligence in Radiation Oncology.

Luh JY, Thompson RF, Lin S.

J Am Coll Radiol. 2019 Jun 22. pii: S1546-1440(19)30696-9. doi: 10.1016/j.jacr.2019.05.044. [Epub ahead of print]

PMID:
31238022
3.

Enhancing Career Paths for Tomorrow's Radiation Oncologists.

Vapiwala N, Thomas CR Jr, Grover S, Yap ML, Mitin T, Shulman LN, Gospodarowicz MK, Longo J, Petereit DG, Ennis RD, Hayman JA, Rodin D, Buchsbaum JC, Vikram B, Abdel-Wahab M, Epstein AH, Okunieff P, Goldwein J, Kupelian P, Weidhaas JB, Tucker MA, Boice JD Jr, Fuller CD, Thompson RF, Trister AD, Formenti SC, Barcellos-Hoff MH, Jones J, Dharmarajan KV, Zietman AL, Coleman CN.

Int J Radiat Oncol Biol Phys. 2019 Sep 1;105(1):52-63. doi: 10.1016/j.ijrobp.2019.05.025. Epub 2019 May 22. Review. No abstract available.

PMID:
31128144
4.

The Potential and Pitfalls of Crowdsourced Algorithm Development in Radiation Oncology.

Elhalawani H, Fuller CD, Thompson RF.

JAMA Oncol. 2019 May 1;5(5):662-663. doi: 10.1001/jamaoncol.2019.0157. No abstract available.

PMID:
30998812
5.

Directed Assembly of Homopentameric Cholera Toxin B-Subunit Proteins into Higher-Order Structures Using Coiled-Coil Appendages.

Ross JF, Wildsmith GC, Johnson M, Hurdiss DL, Hollingsworth K, Thompson RF, Mosayebi M, Trinh CH, Paci E, Pearson AR, Webb ME, Turnbull WB.

J Am Chem Soc. 2019 Apr 3;141(13):5211-5219. doi: 10.1021/jacs.8b11480. Epub 2019 Mar 21.

6.

Career Enrichment Opportunities at the Scientific Frontier in Radiation Oncology.

Thompson RF, Fuller CD, Berman AT, Aneja S, Thomas CR Jr.

JCO Clin Cancer Inform. 2019 Feb;3:1-4. doi: 10.1200/CCI.18.00126. No abstract available.

7.

Collection, pre-processing and on-the-fly analysis of data for high-resolution, single-particle cryo-electron microscopy.

Thompson RF, Iadanza MG, Hesketh EL, Rawson S, Ranson NA.

Nat Protoc. 2019 Jan;14(1):100-118. doi: 10.1038/s41596-018-0084-8.

8.

Artificial Intelligence in Radiation Oncology Imaging.

Thompson RF, Valdes G, Fuller CD, Carpenter CM, Morin O, Aneja S, Lindsay WD, Aerts HJWL, Agrimson B, Deville C Jr, Rosenthal SA, Yu JB, Thomas CR Jr.

Int J Radiat Oncol Biol Phys. 2018 Nov 15;102(4):1159-1161. doi: 10.1016/j.ijrobp.2018.05.070. Epub 2018 Oct 18. No abstract available.

PMID:
30353870
9.

The Future of Artificial Intelligence in Radiation Oncology.

Thompson RF, Valdes G, Fuller CD, Carpenter CM, Morin O, Aneja S, Lindsay WD, Aerts HJWL, Agrimson B, Deville C, Rosenthal SA, Yu JB, Thomas CR Jr.

Int J Radiat Oncol Biol Phys. 2018 Oct 1;102(2):247-248. doi: 10.1016/j.ijrobp.2018.05.072. Epub 2018 Jun 6. No abstract available.

PMID:
30191856
10.

Artificial intelligence in radiation oncology: A specialty-wide disruptive transformation?

Thompson RF, Valdes G, Fuller CD, Carpenter CM, Morin O, Aneja S, Lindsay WD, Aerts HJWL, Agrimson B, Deville C Jr, Rosenthal SA, Yu JB, Thomas CR Jr.

Radiother Oncol. 2018 Dec;129(3):421-426. doi: 10.1016/j.radonc.2018.05.030. Epub 2018 Jun 12. Review.

PMID:
29907338
11.

Approaches to altering particle distributions in cryo-electron microscopy sample preparation.

Drulyte I, Johnson RM, Hesketh EL, Hurdiss DL, Scarff CA, Porav SA, Ranson NA, Muench SP, Thompson RF.

Acta Crystallogr D Struct Biol. 2018 Jun 1;74(Pt 6):560-571. doi: 10.1107/S2059798318006496. Epub 2018 May 18. Review.

12.

Population-level distribution and putative immunogenicity of cancer neoepitopes.

Wood MA, Paralkar M, Paralkar MP, Nguyen A, Struck AJ, Ellrott K, Margolin A, Nellore A, Thompson RF.

BMC Cancer. 2018 Apr 13;18(1):414. doi: 10.1186/s12885-018-4325-6.

13.

Variations on Negative Stain Electron Microscopy Methods: Tools for Tackling Challenging Systems.

Scarff CA, Fuller MJG, Thompson RF, Iadaza MG.

J Vis Exp. 2018 Feb 6;(132). doi: 10.3791/57199.

14.

Precision Oncology and Genomically Guided Radiation Therapy: A Report From the American Society for Radiation Oncology/American Association of Physicists in Medicine/National Cancer Institute Precision Medicine Conference.

Hall WA, Bergom C, Thompson RF, Baschnagel AM, Vijayakumar S, Willers H, Li XA, Schultz CJ, Wilson GD, West CML, Capala J, Coleman CN, Torres-Roca JF, Weidhaas J, Feng FY.

Int J Radiat Oncol Biol Phys. 2018 Jun 1;101(2):274-284. doi: 10.1016/j.ijrobp.2017.05.044. Epub 2017 Jun 9.

PMID:
28964588
15.

HBV RNA pre-genome encodes specific motifs that mediate interactions with the viral core protein that promote nucleocapsid assembly.

Patel N, White SJ, Thompson RF, Bingham R, WeiƟ EU, Maskell DP, Zlotnick A, Dykeman E, Tuma R, Twarock R, Ranson NA, Stockley PG.

Nat Microbiol. 2017 Jun 19;2:17098. doi: 10.1038/nmicrobiol.2017.98.

16.

The structures of a naturally empty cowpea mosaic virus particle and its genome-containing counterpart by cryo-electron microscopy.

Hesketh EL, Meshcheriakova Y, Thompson RF, Lomonossoff GP, Ranson NA.

Sci Rep. 2017 Apr 3;7(1):539. doi: 10.1038/s41598-017-00533-w.

17.

New Structural Insights into the Genome and Minor Capsid Proteins of BK Polyomavirus using Cryo-Electron Microscopy.

Hurdiss DL, Morgan EL, Thompson RF, Prescott EL, Panou MM, Macdonald A, Ranson NA.

Structure. 2016 Apr 5;24(4):528-536. doi: 10.1016/j.str.2016.02.008. Epub 2016 Mar 17.

18.

An introduction to sample preparation and imaging by cryo-electron microscopy for structural biology.

Thompson RF, Walker M, Siebert CA, Muench SP, Ranson NA.

Methods. 2016 May 1;100:3-15. doi: 10.1016/j.ymeth.2016.02.017. Epub 2016 Feb 28.

19.

Mechanisms of assembly and genome packaging in an RNA virus revealed by high-resolution cryo-EM.

Hesketh EL, Meshcheriakova Y, Dent KC, Saxena P, Thompson RF, Cockburn JJ, Lomonossoff GP, Ranson NA.

Nat Commun. 2015 Dec 10;6:10113. doi: 10.1038/ncomms10113.

20.

A Resident's Perspective on Global Health Rotations in Radiation Oncology.

Thompson RF, Grover S.

Int J Radiat Oncol Biol Phys. 2015 Dec 1;93(5):1165-6. doi: 10.1016/j.ijrobp.2015.08.002. Epub 2015 Nov 11. No abstract available.

PMID:
26581156
21.

Development and evaluation of a standardized method and atlas for contouring primary and permanent dentition.

Fang P, Batra S, Hollander AB, Lin A, Hill-Kayser CE, Levin LM, Mupparapu M, Thompson RF.

Dentomaxillofac Radiol. 2015;44(7):20150034. doi: 10.1259/dmfr.20150034. Epub 2015 Mar 26.

22.

Pencil-beam scanning proton therapy for anal cancer: a dosimetric comparison with intensity-modulated radiotherapy.

Ojerholm E, Kirk ML, Thompson RF, Zhai H, Metz JM, Both S, Ben-Josef E, Plastaras JP.

Acta Oncol. 2015;54(8):1209-17. doi: 10.3109/0284186X.2014.1002570. Epub 2015 Mar 3.

PMID:
25734796
23.

Localization and characterization of an essential associative memory trace in the mammalian brain.

Poulos AM, Thompson RF.

Brain Res. 2015 Sep 24;1621:252-9. doi: 10.1016/j.brainres.2014.10.068. Epub 2014 Nov 6.

PMID:
25449891
24.

A dosimetric comparison of proton and photon therapy in unresectable cancers of the head of pancreas.

Thompson RF, Mayekar SU, Zhai H, Both S, Apisarnthanarax S, Metz JM, Plastaras JP, Ben-Josef E.

Med Phys. 2014 Aug;41(8):081711. doi: 10.1118/1.4887797.

PMID:
25086521
25.

Radiotherapy and the tumor microenvironment: mutual influence and clinical implications.

Thompson RF, Maity A.

Adv Exp Med Biol. 2014;772:147-65. doi: 10.1007/978-1-4614-5915-6_7. Review.

PMID:
24272358
26.

Evidence of plasticity in the pontocerebellar conditioned stimulus pathway during classical conditioning of the eyeblink response in the rabbit.

Tracy JA, Thompson JK, Krupa DJ, Thompson RF.

Behav Neurosci. 2013 Oct;127(5):676-89. doi: 10.1037/a0033979.

PMID:
24128357
27.

An essential memory trace found.

Thompson RF.

Behav Neurosci. 2013 Oct;127(5):669-75. doi: 10.1037/a0033978.

PMID:
24128356
28.

Cognitive abnormalities and hippocampal alterations in monoamine oxidase A and B knockout mice.

Singh C, Bortolato M, Bali N, Godar SC, Scott AL, Chen K, Thompson RF, Shih JC.

Proc Natl Acad Sci U S A. 2013 Jul 30;110(31):12816-21. doi: 10.1073/pnas.1308037110. Epub 2013 Jul 15.

29.

Dose to the developing dentition during therapeutic irradiation: organ at risk determination and clinical implications.

Thompson RF, Schneider RA, Albertini F, Lomax AJ, Ares C, Goitein G, Hug EB.

Int J Radiat Oncol Biol Phys. 2013 May 1;86(1):108-13. doi: 10.1016/j.ijrobp.2012.11.041. Epub 2013 Jan 16.

PMID:
23332385
30.

Prolonging the postcomplex spike pause speeds eyeblink conditioning.

Maiz J, Karakossian MH, Pakaprot N, Robleto K, Thompson RF, Otis TS.

Proc Natl Acad Sci U S A. 2012 Oct 9;109(41):16726-30. doi: 10.1073/pnas.1214274109. Epub 2012 Sep 17.

31.

Hypofractionated whole-breast radiation therapy: does breast size matter?

Hannan R, Thompson RF, Chen Y, Bernstein K, Kabarriti R, Skinner W, Chen CC, Landau E, Miller E, Spierer M, Hong L, Kalnicki S.

Int J Radiat Oncol Biol Phys. 2012 Nov 15;84(4):894-901. doi: 10.1016/j.ijrobp.2012.01.093. Epub 2012 Apr 28.

PMID:
22543209
32.

Late-replicating heterochromatin is characterized by decreased cytosine methylation in the human genome.

Suzuki M, Oda M, Ramos MP, Pascual M, Lau K, Stasiek E, Agyiri F, Thompson RF, Glass JL, Jing Q, Sandstrom R, Fazzari MJ, Hansen RS, Stamatoyannopoulos JA, McLellan AS, Greally JM.

Genome Res. 2011 Nov;21(11):1833-40. doi: 10.1101/gr.116509.110. Epub 2011 Sep 28.

33.

Allopregnanolone restores hippocampal-dependent learning and memory and neural progenitor survival in aging 3xTgAD and nonTg mice.

Singh C, Liu L, Wang JM, Irwin RW, Yao J, Chen S, Henry S, Thompson RF, Brinton RD.

Neurobiol Aging. 2012 Aug;33(8):1493-506. doi: 10.1016/j.neurobiolaging.2011.06.008. Epub 2011 Jul 30.

34.

Impaired eyeblink conditioning in 78 kDa-glucose regulated protein (GRP78)/immunoglobulin binding protein (BiP) conditional knockout mice.

Kim S, Wang M, Lee AS, Thompson RF.

Behav Neurosci. 2011 Jun;125(3):404-11. doi: 10.1037/a0023185.

PMID:
21517144
35.

Widespread hypomethylation occurs early and synergizes with gene amplification during esophageal carcinogenesis.

Alvarez H, Opalinska J, Zhou L, Sohal D, Fazzari MJ, Yu Y, Montagna C, Montgomery EA, Canto M, Dunbar KB, Wang J, Roa JC, Mo Y, Bhagat T, Ramesh KH, Cannizzaro L, Mollenhauer J, Thompson RF, Suzuki M, Meltzer SJ, Melnick A, Greally JM, Maitra A, Verma A.

PLoS Genet. 2011 Mar;7(3):e1001356. doi: 10.1371/journal.pgen.1001356. Epub 2011 Mar 31. Erratum in: PLoS Genet. 2011 May;7(5). doi: 10.1371/annotation/8dcded85-a924-40f4-a7ea-56961b87447f. Meltzer, Stephen [corrected to Meltzer, Stephen J].

36.

The cerebellum: a neural system for the study of reinforcement learning.

Swain RA, Kerr AL, Thompson RF.

Front Behav Neurosci. 2011 Mar 3;5:8. doi: 10.3389/fnbeh.2011.00008. eCollection 2011.

37.

DNA methylation changes in murine breast adenocarcinomas allow the identification of candidate genes for human breast carcinogenesis.

Acosta D, Suzuki M, Connolly D, Thompson RF, Fazzari MJ, Greally JM, Montagna C.

Mamm Genome. 2011 Apr;22(3-4):249-59. doi: 10.1007/s00335-011-9318-6. Epub 2011 Mar 4.

PMID:
21373886
38.

c-Fos, Arc, and stargazin expression in rat eyeblink conditioning.

Kim S, Thompson RF.

Behav Neurosci. 2011 Feb;125(1):117-23. doi: 10.1037/a0022328.

PMID:
21319893
39.

Tissue-specific dysregulation of DNA methylation in aging.

Thompson RF, Atzmon G, Gheorghe C, Liang HQ, Lowes C, Greally JM, Barzilai N.

Aging Cell. 2010 Aug;9(4):506-18. doi: 10.1111/j.1474-9726.2010.00577.x. Epub 2010 May 22.

40.

Regulation of hippocampal synaptic plasticity by estrogen and progesterone.

Foy MR, Baudry M, Akopian GK, Thompson RF.

Vitam Horm. 2010;82:219-39. doi: 10.1016/S0083-6729(10)82012-6. Review.

PMID:
20472141
41.

Involvement of cyclin-dependent kinase-like 2 in cognitive function required for contextual and spatial learning in mice.

Gomi H, Sassa T, Thompson RF, Itohara S.

Front Behav Neurosci. 2010 Apr 19;4:17. doi: 10.3389/fnbeh.2010.00017. eCollection 2010.

42.

Allopregnanolone reverses neurogenic and cognitive deficits in mouse model of Alzheimer's disease.

Wang JM, Singh C, Liu L, Irwin RW, Chen S, Chung EJ, Thompson RF, Brinton RD.

Proc Natl Acad Sci U S A. 2010 Apr 6;107(14):6498-503. doi: 10.1073/pnas.1001422107. Epub 2010 Mar 15. Erratum in: Proc Natl Acad Sci U S A. 2010 Jun 15;107(24):11145.

43.

Experimental intrauterine growth restriction induces alterations in DNA methylation and gene expression in pancreatic islets of rats.

Thompson RF, Fazzari MJ, Niu H, Barzilai N, Simmons RA, Greally JM.

J Biol Chem. 2010 May 14;285(20):15111-8. doi: 10.1074/jbc.M109.095133. Epub 2010 Mar 1.

44.

Extra-cellular signal-regulated kinase 1/2 (ERK1/2) activated in the hippocampal CA1 neurons is critical for retrieval of auditory trace fear memory.

Huang CH, Chiang YW, Liang KC, Thompson RF, Liu IY.

Brain Res. 2010 Apr 22;1326:143-51. doi: 10.1016/j.brainres.2010.02.033. Epub 2010 Feb 24.

PMID:
20188711
45.

Epigenetic basis for fetal origins of age-related disease.

Thompson RF, Einstein FH.

J Womens Health (Larchmt). 2010 Mar;19(3):581-7. doi: 10.1089/jwh.2009.1408.

PMID:
20136551
46.

Cytosine methylation dysregulation in neonates following intrauterine growth restriction.

Einstein F, Thompson RF, Bhagat TD, Fazzari MJ, Verma A, Barzilai N, Greally JM.

PLoS One. 2010 Jan 26;5(1):e8887. doi: 10.1371/journal.pone.0008887.

47.

Differential effects and rates of normal aging in cerebellum and hippocampus.

Woodruff-Pak DS, Foy MR, Akopian GG, Lee KH, Zach J, Nguyen KP, Comalli DM, Kennard JA, Agelan A, Thompson RF.

Proc Natl Acad Sci U S A. 2010 Jan 26;107(4):1624-9. doi: 10.1073/pnas.0914207107. Epub 2010 Jan 8.

48.

Experimental approaches to the study of epigenomic dysregulation in ageing.

Thompson RF, Fazzari MJ, Greally JM.

Exp Gerontol. 2010 Apr;45(4):255-68. doi: 10.1016/j.exger.2009.12.013. Epub 2010 Jan 10. Review.

49.

Eyeblink conditioning leads to fewer synapses in the rabbit cerebellar cortex.

Connor S, Bloomfield J, LeBoutillier JC, Thompson RF, Petit TL, Weeks AC.

Behav Neurosci. 2009 Aug;123(4):856-62. doi: 10.1037/a0016370.

PMID:
19634946
50.

A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry.

Thompson RF, Suzuki M, Lau KW, Greally JM.

Bioinformatics. 2009 Sep 1;25(17):2164-70. doi: 10.1093/bioinformatics/btp382. Epub 2009 Jun 26.

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