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Items: 1 to 50 of 74

1.

Genomes from bacteria associated with the canine oral cavity: A test case for automated genome-based taxonomic assignment.

Coil DA, Jospin G, Darling AE, Wallis C, Davis IJ, Harris S, Eisen JA, Holcombe LJ, O'Flynn C.

PLoS One. 2019 Jun 10;14(6):e0214354. doi: 10.1371/journal.pone.0214354. eCollection 2019.

2.

Casein Kinase II Phosphorylation of Spt6 Enforces Transcriptional Fidelity by Maintaining Spn1-Spt6 Interaction.

Dronamraju R, Kerschner JL, Peck SA, Hepperla AJ, Adams AT, Hughes KD, Aslam S, Yoblinski AR, Davis IJ, Mosley AL, Strahl BD.

Cell Rep. 2018 Dec 18;25(12):3476-3489.e5. doi: 10.1016/j.celrep.2018.11.089.

3.

PBRM1 bromodomains variably influence nucleosome interactions and cellular function.

Slaughter MJ, Shanle EK, McFadden AW, Hollis ES, Suttle LE, Strahl BD, Davis IJ.

J Biol Chem. 2018 Aug 31;293(35):13592-13603. doi: 10.1074/jbc.RA118.003381. Epub 2018 Jul 9.

PMID:
29986887
4.

Spt6 Association with RNA Polymerase II Directs mRNA Turnover During Transcription.

Dronamraju R, Hepperla AJ, Shibata Y, Adams AT, Magnuson T, Davis IJ, Strahl BD.

Mol Cell. 2018 Jun 21;70(6):1054-1066.e4. doi: 10.1016/j.molcel.2018.05.020.

5.

CHD4 and the NuRD complex directly control cardiac sarcomere formation.

Wilczewski CM, Hepperla AJ, Shimbo T, Wasson L, Robbe ZL, Davis IJ, Wade PA, Conlon FL.

Proc Natl Acad Sci U S A. 2018 Jun 26;115(26):6727-6732. doi: 10.1073/pnas.1722219115. Epub 2018 Jun 11.

6.

SETD2 Haploinsufficiency for Microtubule Methylation Is an Early Driver of Genomic Instability in Renal Cell Carcinoma.

Chiang YC, Park IY, Terzo EA, Tripathi DN, Mason FM, Fahey CC, Karki M, Shuster CB, Sohn BH, Chowdhury P, Powell RT, Ohi R, Tsai YS, de Cubas AA, Khan A, Davis IJ, Strahl BD, Parker JS, Dere R, Walker CL, Rathmell WK.

Cancer Res. 2018 Jun 15;78(12):3135-3146. doi: 10.1158/0008-5472.CAN-17-3460. Epub 2018 May 3.

7.

Cavitation Enhancement Increases the Efficiency and Consistency of Chromatin Fragmentation from Fixed Cells for Downstream Quantitative Applications.

Chiarella AM, Quimby AL, Mehrab-Mohseni M, Velasco B, Kasoji SK, Davis IJ, Dayton PA, Hathaway NA, Pattenden SG.

Biochemistry. 2018 May 15;57(19):2756-2761. doi: 10.1021/acs.biochem.8b00075. Epub 2018 Apr 25.

8.

H3K36 Methylation Regulates Nutrient Stress Response in Saccharomyces cerevisiae by Enforcing Transcriptional Fidelity.

McDaniel SL, Hepperla AJ, Huang J, Dronamraju R, Adams AT, Kulkarni VG, Davis IJ, Strahl BD.

Cell Rep. 2017 Jun 13;19(11):2371-2382. doi: 10.1016/j.celrep.2017.05.057.

9.

Assessment of dental plaque coverage by Quantitative Light-induced Fluorescence (QLF) in domestic short-haired cats.

Marshall-Jones ZV, Wallis CV, Allsopp JM, Colyer A, Davis IJ, Holcombe LJ.

Res Vet Sci. 2017 Apr;111:99-107. doi: 10.1016/j.rvsc.2017.02.005. Epub 2017 Feb 10.

10.

SETting the Stage for Cancer Development: SETD2 and the Consequences of Lost Methylation.

Fahey CC, Davis IJ.

Cold Spring Harb Perspect Med. 2017 May 1;7(5). pii: a026468. doi: 10.1101/cshperspect.a026468. Review.

11.

Widespread Chromatin Accessibility at Repetitive Elements Links Stem Cells with Human Cancer.

Gomez NC, Hepperla AJ, Dumitru R, Simon JM, Fang F, Davis IJ.

Cell Rep. 2016 Nov 1;17(6):1607-1620. doi: 10.1016/j.celrep.2016.10.011.

12.

Structure/Function Analysis of Recurrent Mutations in SETD2 Protein Reveals a Critical and Conserved Role for a SET Domain Residue in Maintaining Protein Stability and Histone H3 Lys-36 Trimethylation.

Hacker KE, Fahey CC, Shinsky SA, Chiang YJ, DiFiore JV, Jha DK, Vo AH, Shavit JA, Davis IJ, Strahl BD, Rathmell WK.

J Biol Chem. 2016 Sep 30;291(40):21283-21295. Epub 2016 Aug 15.

13.

Dual Chromatin and Cytoskeletal Remodeling by SETD2.

Park IY, Powell RT, Tripathi DN, Dere R, Ho TH, Blasius TL, Chiang YC, Davis IJ, Fahey CC, Hacker KE, Verhey KJ, Bedford MT, Jonasch E, Rathmell WK, Walker CL.

Cell. 2016 Aug 11;166(4):950-962. doi: 10.1016/j.cell.2016.07.005.

14.

Post-transplant lymphoproliferative disorder of the pediatric airway: Presentation and management.

O'Neill AF, Adil EA, Irace AL, Neff L, Davis IJ, Perez-Atayde AR, Voss SD, Weinberg O, Rahbar R.

Int J Pediatr Otorhinolaryngol. 2016 Jul;86:218-23. doi: 10.1016/j.ijporl.2016.04.035. Epub 2016 Apr 30. Review.

PMID:
27260610
15.

International cancer seminars: a focus on kidney cancer.

Scelo G, Hofmann JN, Banks RE, Bigot P, Bhatt RS, Cancel-Tassin G, Chew SK, Creighton CJ, Cussenot O, Davis IJ, Escudier B, Frayling TM, Häggström C, Hildebrandt MA, Holcatova I, Johansson M, Linehan WM, McDermott DF, Nathanson KL, Ogawa S, Perlman EJ, Purdue MP, Stattin P, Swanton C, Vasudev NS, Wu X, Znaor A, Brennan P, Chanock SJ.

Ann Oncol. 2016 Aug;27(8):1382-5. doi: 10.1093/annonc/mdw186. Epub 2016 Apr 29.

16.

Longitudinal quantification of the gingival crevicular fluid proteome during progression from gingivitis to periodontitis in a canine model.

Davis IJ, Jones AW, Creese AJ, Staunton R, Atwal J, Chapple IL, Harris S, Grant MM.

J Clin Periodontol. 2016 Jul;43(7):584-94. doi: 10.1111/jcpe.12548. Epub 2016 May 23.

17.

High-throughput small molecule screen identifies inhibitors of aberrant chromatin accessibility.

Pattenden SG, Simon JM, Wali A, Jayakody CN, Troutman J, McFadden AW, Wooten J, Wood CC, Frye SV, Janzen WP, Davis IJ.

Proc Natl Acad Sci U S A. 2016 Mar 15;113(11):3018-23. doi: 10.1073/pnas.1521827113. Epub 2016 Feb 29.

18.

The Cardiac TBX5 Interactome Reveals a Chromatin Remodeling Network Essential for Cardiac Septation.

Waldron L, Steimle JD, Greco TM, Gomez NC, Dorr KM, Kweon J, Temple B, Yang XH, Wilczewski CM, Davis IJ, Cristea IM, Moskowitz IP, Conlon FL.

Dev Cell. 2016 Feb 8;36(3):262-75. doi: 10.1016/j.devcel.2016.01.009.

19.

Subtumoral analysis of PRINT nanoparticle distribution reveals targeting variation based on cellular and particle properties.

Roode LE, Brighton H, Bo T, Perry JL, Parrott MC, Kersey F, Luft JC, Bear JE, DeSimone JM, Davis IJ.

Nanomedicine. 2016 May;12(4):1053-1062. doi: 10.1016/j.nano.2015.12.382. Epub 2016 Jan 7.

20.

A Pyrosequencing Investigation of Differences in the Feline Subgingival Microbiota in Health, Gingivitis and Mild Periodontitis.

Harris S, Croft J, O'Flynn C, Deusch O, Colyer A, Allsopp J, Milella L, Davis IJ.

PLoS One. 2015 Nov 25;10(11):e0136986. doi: 10.1371/journal.pone.0136986. eCollection 2015.

21.

Comparative Genomics of the Genus Porphyromonas Identifies Adaptations for Heme Synthesis within the Prevalent Canine Oral Species Porphyromonas cangingivalis.

O'Flynn C, Deusch O, Darling AE, Eisen JA, Wallis C, Davis IJ, Harris SJ.

Genome Biol Evol. 2015 Nov 13;7(12):3397-413. doi: 10.1093/gbe/evv220.

22.

A Role for Widely Interspaced Zinc Finger (WIZ) in Retention of the G9a Methyltransferase on Chromatin.

Simon JM, Parker JS, Liu F, Rothbart SB, Ait-Si-Ali S, Strahl BD, Jin J, Davis IJ, Mosley AL, Pattenden SG.

J Biol Chem. 2015 Oct 23;290(43):26088-102. doi: 10.1074/jbc.M115.654459. Epub 2015 Sep 3.

23.

Linking germline and somatic variation in Ewing sarcoma.

Gomez NC, Davis IJ.

Nat Genet. 2015 Sep;47(9):964-5. doi: 10.1038/ng.3387.

PMID:
26313223
24.

FOXP1 potentiates Wnt/β-catenin signaling in diffuse large B cell lymphoma.

Walker MP, Stopford CM, Cederlund M, Fang F, Jahn C, Rabinowitz AD, Goldfarb D, Graham DM, Yan F, Deal AM, Fedoriw Y, Richards KL, Davis IJ, Weidinger G, Damania B, Major MB.

Sci Signal. 2015 Feb 3;8(362):ra12. doi: 10.1126/scisignal.2005654.

25.

LKB1 loss in melanoma disrupts directional migration toward extracellular matrix cues.

Chan KT, Asokan SB, King SJ, Bo T, Dubose ES, Liu W, Berginski ME, Simon JM, Davis IJ, Gomez SM, Sharpless NE, Bear JE.

J Cell Biol. 2014 Oct 27;207(2):299-315. doi: 10.1083/jcb.201404067.

26.

BRG1/SMARCA4 inactivation promotes non-small cell lung cancer aggressiveness by altering chromatin organization.

Orvis T, Hepperla A, Walter V, Song S, Simon J, Parker J, Wilkerson MD, Desai N, Major MB, Hayes DN, Davis IJ, Weissman B.

Cancer Res. 2014 Nov 15;74(22):6486-6498. doi: 10.1158/0008-5472.CAN-14-0061. Epub 2014 Aug 12.

27.

The Unculturables: targeted isolation of bacterial species associated with canine periodontal health or disease from dental plaque.

Davis IJ, Bull C, Horsfall A, Morley I, Harris S.

BMC Microbiol. 2014 Aug 1;14:196. doi: 10.1186/1471-2180-14-196.

28.

PTEN deficiency mediates a reciprocal response to IGFI and mTOR inhibition.

Patel M, Gomez NC, McFadden AW, Moats-Staats BM, Wu S, Rojas A, Sapp T, Simon JM, Smith SV, Kaiser-Rogers K, Davis IJ.

Mol Cancer Res. 2014 Nov;12(11):1610-20. doi: 10.1158/1541-7786.MCR-14-0006. Epub 2014 Jul 3.

29.

A chemical tool for in vitro and in vivo precipitation of lysine methyltransferase G9a.

Konze KD, Pattenden SG, Liu F, Barsyte-Lovejoy D, Li F, Simon JM, Davis IJ, Vedadi M, Jin J.

ChemMedChem. 2014 Mar;9(3):549-53. doi: 10.1002/cmdc.201300450. Epub 2014 Jan 17.

30.

A cross-sectional survey of bacterial species in plaque from client owned dogs with healthy gingiva, gingivitis or mild periodontitis.

Davis IJ, Wallis C, Deusch O, Colyer A, Milella L, Loman N, Harris S.

PLoS One. 2013 Dec 13;8(12):e83158. doi: 10.1371/journal.pone.0083158. eCollection 2013.

31.

Loss of Arp2/3 induces an NF-κB-dependent, nonautonomous effect on chemotactic signaling.

Wu C, Haynes EM, Asokan SB, Simon JM, Sharpless NE, Baldwin AS, Davis IJ, Johnson GL, Bear JE.

J Cell Biol. 2013 Dec 23;203(6):907-16.

32.

Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects.

Simon JM, Hacker KE, Singh D, Brannon AR, Parker JS, Weiser M, Ho TH, Kuan PF, Jonasch E, Furey TS, Prins JF, Lieb JD, Rathmell WK, Davis IJ.

Genome Res. 2014 Feb;24(2):241-50. doi: 10.1101/gr.158253.113. Epub 2013 Oct 24.

33.

EWS and RE1-Silencing Transcription Factor Inhibit Neuronal Phenotype Development and Oncogenic Transformation in Ewing Sarcoma.

Sankar S, Gomez NC, Bell R, Patel M, Davis IJ, Lessnick SL, Luo W.

Genes Cancer. 2013 May;4(5-6):213-23. doi: 10.1177/1947601913489569.

34.

The open chromatin landscape of Kaposi's sarcoma-associated herpesvirus.

Hilton IB, Simon JM, Lieb JD, Davis IJ, Damania B, Dittmer DP.

J Virol. 2013 Nov;87(21):11831-42. doi: 10.1128/JVI.01685-13. Epub 2013 Aug 28.

35.

Biomarkers in Ewing Sarcoma: The Promise and Challenge of Personalized Medicine. A Report from the Children's Oncology Group.

Shukla N, Schiffman J, Reed D, Davis IJ, Womer RB, Lessnick SL, Lawlor ER; COG Ewing Sarcoma Biology Committee.

Front Oncol. 2013 Jun 6;3:141. doi: 10.3389/fonc.2013.00141. eCollection 2013.

36.

A detailed protocol for formaldehyde-assisted isolation of regulatory elements (FAIRE).

Simon JM, Giresi PG, Davis IJ, Lieb JD.

Curr Protoc Mol Biol. 2013;Chapter 21:Unit21.26. doi: 10.1002/0471142727.mb2126s102.

PMID:
23547014
37.

Valproic acid reduces the tolerability of temsirolimus in children and adolescents with solid tumors.

Coulter DW, Walko C, Patel J, Moats-Staats BM, McFadden A, Smith SV, Khan WA, Bridges AS, Deal AM, Oesterheld J, Davis IJ, Blatt J.

Anticancer Drugs. 2013 Apr;24(4):415-21. doi: 10.1097/CAD.0b013e32835dc7c5.

38.

State of the science: an update on renal cell carcinoma.

Jonasch E, Futreal PA, Davis IJ, Bailey ST, Kim WY, Brugarolas J, Giaccia AJ, Kurban G, Pause A, Frydman J, Zurita AJ, Rini BI, Sharma P, Atkins MB, Walker CL, Rathmell WK.

Mol Cancer Res. 2012 Jul;10(7):859-80. doi: 10.1158/1541-7786.MCR-12-0117. Epub 2012 May 25. Review.

39.

Tivantinib (ARQ 197), a selective inhibitor of MET, in patients with microphthalmia transcription factor-associated tumors: results of a multicenter phase 2 trial.

Wagner AJ, Goldberg JM, Dubois SG, Choy E, Rosen L, Pappo A, Geller J, Judson I, Hogg D, Senzer N, Davis IJ, Chai F, Waghorne C, Schwartz B, Demetri GD.

Cancer. 2012 Dec 1;118(23):5894-902. doi: 10.1002/cncr.27582. Epub 2012 May 17.

40.

The canine oral microbiome.

Dewhirst FE, Klein EA, Thompson EC, Blanton JM, Chen T, Milella L, Buckley CM, Davis IJ, Bennett ML, Marshall-Jones ZV.

PLoS One. 2012;7(4):e36067. doi: 10.1371/journal.pone.0036067. Epub 2012 Apr 27. Erratum in: PLoS One. 2012;7(6). doi:10.1371/annotation/c2287fc7-c976-4d78-a28f-1d4e024d568f.

41.

Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA.

Simon JM, Giresi PG, Davis IJ, Lieb JD.

Nat Protoc. 2012 Jan 19;7(2):256-67. doi: 10.1038/nprot.2011.444. Erratum in: Nat Protoc. 2014 Feb;9(2):501-3.

42.

Tumor-specific retargeting of an oncogenic transcription factor chimera results in dysregulation of chromatin and transcription.

Patel M, Simon JM, Iglesia MD, Wu SB, McFadden AW, Lieb JD, Davis IJ.

Genome Res. 2012 Feb;22(2):259-70. doi: 10.1101/gr.125666.111. Epub 2011 Nov 15.

43.

Validation of a TFE3 break-apart FISH assay for Xp11.2 translocation renal cell carcinomas.

Mosquera JM, Dal Cin P, Mertz KD, Perner S, Davis IJ, Fisher DE, Rubin MA, Hirsch MS.

Diagn Mol Pathol. 2011 Sep;20(3):129-37. doi: 10.1097/PDM.0b013e31820e9c67.

PMID:
21817901
44.

Unintentional weight loss as the sole indication for colonoscopy is rarely associated with colorectal cancer.

Davis IJ, Marek SJ, Sridhar S, Wilkins T, Chamberlain SM.

J Am Board Fam Med. 2011 Mar-Apr;24(2):218-9. doi: 10.3122/jabfm.2011.02.100166.

45.

Challenges associated with HIV in transgendered patients.

Ogbuokiri JE, Davis Ij.

HIV Clin. 2010 Summer;22(3):12-5. No abstract available.

PMID:
21241047
46.

Aberrant estrogen regulation of PEMT results in choline deficiency-associated liver dysfunction.

Resseguie ME, da Costa KA, Galanko JA, Patel M, Davis IJ, Zeisel SH.

J Biol Chem. 2011 Jan 14;286(2):1649-58. doi: 10.1074/jbc.M110.106922. Epub 2010 Nov 8.

47.

Array comparative hybridisation reveals a high degree of similarity between UK and European clinical isolates of hypervirulent Clostridium difficile.

Marsden GL, Davis IJ, Wright VJ, Sebaihia M, Kuijper EJ, Minton NP.

BMC Genomics. 2010 Jun 21;11:389. doi: 10.1186/1471-2164-11-389.

48.

Regulation of neurotoxin production and sporulation by a Putative agrBD signaling system in proteolytic Clostridium botulinum.

Cooksley CM, Davis IJ, Winzer K, Chan WC, Peck MW, Minton NP.

Appl Environ Microbiol. 2010 Jul;76(13):4448-60. doi: 10.1128/AEM.03038-09. Epub 2010 May 7.

49.

Identification of the receptor tyrosine kinase c-Met and its ligand, hepatocyte growth factor, as therapeutic targets in clear cell sarcoma.

Davis IJ, McFadden AW, Zhang Y, Coxon A, Burgess TL, Wagner AJ, Fisher DE.

Cancer Res. 2010 Jan 15;70(2):639-45. doi: 10.1158/0008-5472.CAN-09-1121. Epub 2010 Jan 12.

50.

Improved ChIP-chip analysis by a mixture model approach.

Sun W, Buck MJ, Patel M, Davis IJ.

BMC Bioinformatics. 2009 Jun 7;10:173. doi: 10.1186/1471-2105-10-173.

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