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Items: 39

1.

Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight.

Ebbert MTW, Jensen TD, Jansen-West K, Sens JP, Reddy JS, Ridge PG, Kauwe JSK, Belzil V, Pregent L, Carrasquillo MM, Keene D, Larson E, Crane P, Asmann YW, Ertekin-Taner N, Younkin SG, Ross OA, Rademakers R, Petrucelli L, Fryer JD.

Genome Biol. 2019 May 20;20(1):97. doi: 10.1186/s13059-019-1707-2.

2.

Common DNA Variants Accurately Rank an Individual of Extreme Height.

Sexton CE, Ebbert MTW, Miller RH, Ferrel M, Tschanz JAT, Corcoran CD; Alzheimer's Disease Neuroimaging Initiative , Ridge PG, Kauwe JSK.

Int J Genomics. 2018 Sep 4;2018:5121540. doi: 10.1155/2018/5121540. eCollection 2018.

3.

Long-read sequencing across the C9orf72 'GGGGCC' repeat expansion: implications for clinical use and genetic discovery efforts in human disease.

Ebbert MTW, Farrugia SL, Sens JP, Jansen-West K, Gendron TF, Prudencio M, McLaughlin IJ, Bowman B, Seetin M, DeJesus-Hernandez M, Jackson J, Brown PH, Dickson DW, van Blitterswijk M, Rademakers R, Petrucelli L, Fryer JD.

Mol Neurodegener. 2018 Aug 21;13(1):46. doi: 10.1186/s13024-018-0274-4.

4.

Microglial translational profiling reveals a convergent APOE pathway from aging, amyloid, and tau.

Kang SS, Ebbert MTW, Baker KE, Cook C, Wang X, Sens JP, Kocher JP, Petrucelli L, Fryer JD.

J Exp Med. 2018 Sep 3;215(9):2235-2245. doi: 10.1084/jem.20180653. Epub 2018 Aug 6.

5.

Poly(GR) impairs protein translation and stress granule dynamics in C9orf72-associated frontotemporal dementia and amyotrophic lateral sclerosis.

Zhang YJ, Gendron TF, Ebbert MTW, O'Raw AD, Yue M, Jansen-West K, Zhang X, Prudencio M, Chew J, Cook CN, Daughrity LM, Tong J, Song Y, Pickles SR, Castanedes-Casey M, Kurti A, Rademakers R, Oskarsson B, Dickson DW, Hu W, Gitler AD, Fryer JD, Petrucelli L.

Nat Med. 2018 Aug;24(8):1136-1142. doi: 10.1038/s41591-018-0071-1. Epub 2018 Jun 25.

6.

Corticobasal degeneration with TDP-43 pathology presenting with progressive supranuclear palsy syndrome: a distinct clinicopathologic subtype.

Koga S, Kouri N, Walton RL, Ebbert MTW, Josephs KA, Litvan I, Graff-Radford N, Ahlskog JE, Uitti RJ, van Gerpen JA, Boeve BF, Parks A, Ross OA, Dickson DW.

Acta Neuropathol. 2018 Sep;136(3):389-404. doi: 10.1007/s00401-018-1878-z. Epub 2018 Jun 20.

7.

An Epigenetic Spin to ALS and FTD.

Ebbert MTW, Lank RJ, Belzil VV.

Adv Neurobiol. 2018;20:1-29. doi: 10.1007/978-3-319-89689-2_1. Review.

PMID:
29916014
8.

Correction to: Linkage, whole genome sequence, and biological data implicate variants in RAB10 in Alzheimer's disease resilience.

Ridge PG, Karch CM, Hsu S, Arano I, Teerlink CC, Ebbert MTW, Murcia JDG, Farnham JM, Damato AR, Allen M, Wang X, Harari O, Fernandez VM, Guerreiro R, Bras J, Hardy J, Munger R, Norton M, Sassi C, Singleton A, Younkin SG, Dickson DW, Golde TE, Price ND, Ertekin-Taner N, Cruchaga C, Goate AM, Corcoran C, Tschanz J, Cannon-Albright LA, Kauwe JSK; Alzheimer’s Disease Neuroimaging Initiative.

Genome Med. 2018 Jan 12;10(1):4. doi: 10.1186/s13073-018-0516-7.

9.

Linkage, whole genome sequence, and biological data implicate variants in RAB10 in Alzheimer's disease resilience.

Ridge PG, Karch CM, Hsu S, Arano I, Teerlink CC, Ebbert MTW, Gonzalez Murcia JD, Farnham JM, Damato AR, Allen M, Wang X, Harari O, Fernandez VM, Guerreiro R, Bras J, Hardy J, Munger R, Norton M, Sassi C, Singleton A, Younkin SG, Dickson DW, Golde TE, Price ND, Ertekin-Taner N, Cruchaga C, Goate AM, Corcoran C, Tschanz J, Cannon-Albright LA, Kauwe JSK; Alzheimer’s Disease Neuroimaging Initiative.

Genome Med. 2017 Nov 29;9(1):100. doi: 10.1186/s13073-017-0486-1. Erratum in: Genome Med. 2018 Jan 12;10 (1):4.

10.

Conserved DNA methylation combined with differential frontal cortex and cerebellar expression distinguishes C9orf72-associated and sporadic ALS, and implicates SERPINA1 in disease.

Ebbert MTW, Ross CA, Pregent LJ, Lank RJ, Zhang C, Katzman RB, Jansen-West K, Song Y, da Rocha EL, Palmucci C, Desaro P, Robertson AE, Caputo AM, Dickson DW, Boylan KB, Rademakers R, Ordog T, Li H, Belzil VV.

Acta Neuropathol. 2017 Nov;134(5):715-728. doi: 10.1007/s00401-017-1760-4. Epub 2017 Aug 14.

11.

Repetitive element transcripts are elevated in the brain of C9orf72 ALS/FTLD patients.

Prudencio M, Gonzales PK, Cook CN, Gendron TF, Daughrity LM, Song Y, Ebbert MTW, van Blitterswijk M, Zhang YJ, Jansen-West K, Baker MC, DeTure M, Rademakers R, Boylan KB, Dickson DW, Petrucelli L, Link CD.

Hum Mol Genet. 2017 Sep 1;26(17):3421-3431. doi: 10.1093/hmg/ddx233.

12.

Evaluation of the Abbott RealTime HCV genotype II plus RUO (PLUS) assay with reference to core and NS5B sequencing.

Mallory MA, Lucic D, Ebbert MT, Cloherty GA, Toolsie D, Hillyard DR.

J Clin Virol. 2017 May;90:26-31. doi: 10.1016/j.jcv.2017.03.007. Epub 2017 Mar 9.

PMID:
28324789
13.

Evaluating the necessity of PCR duplicate removal from next-generation sequencing data and a comparison of approaches.

Ebbert MT, Wadsworth ME, Staley LA, Hoyt KL, Pickett B, Miller J, Duce J; Alzheimer’s Disease Neuroimaging Initiative, Kauwe JS, Ridge PG.

BMC Bioinformatics. 2016 Jul 25;17 Suppl 7:239. doi: 10.1186/s12859-016-1097-3.

14.

A novel approach for multi-SNP GWAS and its application in Alzheimer's disease.

Bodily PM, Fujimoto MS, Page JT, Clement MJ, Ebbert MT, Ridge PG; Alzheimer’s Disease Neuroimaging Initiative.

BMC Bioinformatics. 2016 Jul 25;17 Suppl 7:268. doi: 10.1186/s12859-016-1093-7.

15.

Variants in CCL16 are associated with blood plasma and cerebrospinal fluid CCL16 protein levels.

Ebbert MT, Staley LA, Parker J, Parker S, Bailey M; Alzheimer’s Disease Neuroimaging Initiative, Ridge PG, Goate AM, Kauwe JS.

BMC Genomics. 2016 Jun 29;17 Suppl 3:437. doi: 10.1186/s12864-016-2788-x.

16.

Variants in ACPP are associated with cerebrospinal fluid Prostatic Acid Phosphatase levels.

Staley LA, Ebbert MT, Bunker D, Bailey M; Alzheimer’s Disease Neuroimaging Initiative, Ridge PG, Goate AM, Kauwe JS.

BMC Genomics. 2016 Jun 29;17 Suppl 3:439. doi: 10.1186/s12864-016-2787-y.

17.

Presenilin E318G variant and Alzheimer's disease risk: the Cache County study.

Hippen AA, Ebbert MT, Norton MC, Tschanz JT, Munger RG, Corcoran CD, Kauwe JS.

BMC Genomics. 2016 Jun 29;17 Suppl 3:438. doi: 10.1186/s12864-016-2786-z.

18.

Genome-wide association study of prolactin levels in blood plasma and cerebrospinal fluid.

Staley LA, Ebbert MT, Parker S, Bailey M; Alzheimer’s Disease Neuroimaging Initiative, Ridge PG, Goate AM, Kauwe JS.

BMC Genomics. 2016 Jun 29;17 Suppl 3:436. doi: 10.1186/s12864-016-2785-0.

19.

SA-SSR: a suffix array-based algorithm for exhaustive and efficient SSR discovery in large genetic sequences.

Pickett BD, Karlinsey SM, Penrod CE, Cormier MJ, Ebbert MT, Shiozawa DK, Whipple CJ, Ridge PG.

Bioinformatics. 2016 Sep 1;32(17):2707-9. doi: 10.1093/bioinformatics/btw298. Epub 2016 May 11.

20.

Liver kinase B1 inhibits the expression of inflammation-related genes postcontraction in skeletal muscle.

Chen T, Moore TM, Ebbert MT, McVey NL, Madsen SR, Hallowell DM, Harris AM, Char RE, Mackay RP, Hancock CR, Hansen JM, Kauwe JS, Thomson DM.

J Appl Physiol (1985). 2016 Apr 15;120(8):876-88. doi: 10.1152/japplphysiol.00727.2015. Epub 2016 Jan 21.

21.

Interaction between variants in CLU and MS4A4E modulates Alzheimer's disease risk.

Ebbert MTW, Boehme KL, Wadsworth ME, Staley LA; Alzheimer's Disease Neuroimaging Initiative; Alzheimer's Disease Genetics Consortium, Mukherjee S, Crane PK, Ridge PG, Kauwe JSK.

Alzheimers Dement. 2016 Feb;12(2):121-129. doi: 10.1016/j.jalz.2015.08.163. Epub 2015 Oct 9.

22.

Bridging the gap between statistical and biological epistasis in Alzheimer's disease.

Ebbert MT, Ridge PG, Kauwe JS.

Biomed Res Int. 2015;2015:870123. doi: 10.1155/2015/870123. Epub 2015 May 17. Review.

23.

Population-based analysis of cholesteryl ester transfer protein identifies association between I405V and cognitive decline: the Cache County Study.

Lythgoe C, Perkes A, Peterson M, Schmutz C, Leary M, Ebbert MT, Ridge PG, Norton MC, Tschanz JT, Munger RG, Corcoran CD, Kauwe JS.

Neurobiol Aging. 2015 Jan;36(1):547.e1-3. doi: 10.1016/j.neurobiolaging.2014.08.022. Epub 2014 Aug 27.

24.

Variant Tool Chest: an improved tool to analyze and manipulate variant call format (VCF) files.

Ebbert MT, Wadsworth ME, Boehme KL, Hoyt KL, Sharp AR, O'Fallon BD, Kauwe JS, Ridge PG.

BMC Bioinformatics. 2014;15 Suppl 7:S12. doi: 10.1186/1471-2105-15-S7-S12. Epub 2014 May 28.

25.

Genetic discoveries in AD using CSF amyloid and tau.

Cruchaga C, Ebbert MT, Kauwe JS.

Curr Genet Med Rep. 2014 Mar 1;2(1):23-29.

26.

Intrinsic subtypes from PAM50 gene expression assay in a population-based breast cancer cohort: differences by age, race, and tumor characteristics.

Sweeney C, Bernard PS, Factor RE, Kwan ML, Habel LA, Quesenberry CP Jr, Shakespear K, Weltzien EK, Stijleman IJ, Davis CA, Ebbert MT, Castillo A, Kushi LH, Caan BJ.

Cancer Epidemiol Biomarkers Prev. 2014 May;23(5):714-24. doi: 10.1158/1055-9965.EPI-13-1023. Epub 2014 Feb 12.

27.

Genetics of Alzheimer's disease.

Ridge PG, Ebbert MT, Kauwe JS.

Biomed Res Int. 2013;2013:254954. doi: 10.1155/2013/254954. Epub 2013 Jul 25. Review.

28.

Population-based analysis of Alzheimer's disease risk alleles implicates genetic interactions.

Ebbert MT, Ridge PG, Wilson AR, Sharp AR, Bailey M, Norton MC, Tschanz JT, Munger RG, Corcoran CD, Kauwe JS.

Biol Psychiatry. 2014 May 1;75(9):732-7. doi: 10.1016/j.biopsych.2013.07.008. Epub 2013 Aug 13.

29.

Assessment of TREM2 rs75932628 association with Alzheimer's disease in a population-based sample: the Cache County Study.

Gonzalez Murcia JD, Schmutz C, Munger C, Perkes A, Gustin A, Peterson M, Ebbert MT, Norton MC, Tschanz JT, Munger RG, Corcoran CD, Kauwe JS.

Neurobiol Aging. 2013 Dec;34(12):2889.e11-3. doi: 10.1016/j.neurobiolaging.2013.06.004. Epub 2013 Jul 12.

30.

Application of a new informatics tool for contamination screening in the HIV sequencing laboratory.

Ebbert MT, Mallory MA, Wilson AR, Dooley SK, Hillyard DR.

J Clin Virol. 2013 Jul;57(3):249-53. doi: 10.1016/j.jcv.2013.03.013. Epub 2013 Apr 11.

PMID:
23583427
31.

PAM50 proliferation score as a predictor of weekly paclitaxel benefit in breast cancer.

Martín M, Prat A, Rodríguez-Lescure A, Caballero R, Ebbert MT, Munárriz B, Ruiz-Borrego M, Bastien RR, Crespo C, Davis C, Rodríguez CA, López-Vega JM, Furió V, García AM, Casas M, Ellis MJ, Berry DA, Pitcher BN, Harris L, Ruiz A, Winer E, Hudis C, Stijleman IJ, Tuck DP, Carrasco E, Perou CM, Bernard PS.

Breast Cancer Res Treat. 2013 Apr;138(2):457-66. doi: 10.1007/s10549-013-2416-2. Epub 2013 Feb 20.

32.

PAM50 breast cancer subtyping by RT-qPCR and concordance with standard clinical molecular markers.

Bastien RR, Rodríguez-Lescure Á, Ebbert MT, Prat A, Munárriz B, Rowe L, Miller P, Ruiz-Borrego M, Anderson D, Lyons B, Álvarez I, Dowell T, Wall D, Seguí MÁ, Barley L, Boucher KM, Alba E, Pappas L, Davis CA, Aranda I, Fauron C, Stijleman IJ, Palacios J, Antón A, Carrasco E, Caballero R, Ellis MJ, Nielsen TO, Perou CM, Astill M, Bernard PS, Martín M.

BMC Med Genomics. 2012 Oct 4;5:44. doi: 10.1186/1755-8794-5-44.

33.

Agreement in risk prediction between the 21-gene recurrence score assay (Oncotype DX®) and the PAM50 breast cancer intrinsic Classifier™ in early-stage estrogen receptor-positive breast cancer.

Kelly CM, Bernard PS, Krishnamurthy S, Wang B, Ebbert MT, Bastien RR, Boucher KM, Young E, Iwamoto T, Pusztai L.

Oncologist. 2012;17(4):492-8. doi: 10.1634/theoncologist.2012-0007. Epub 2012 Mar 14.

34.

Responsiveness of intrinsic subtypes to adjuvant anthracycline substitution in the NCIC.CTG MA.5 randomized trial.

Cheang MC, Voduc KD, Tu D, Jiang S, Leung S, Chia SK, Shepherd LE, Levine MN, Pritchard KI, Davies S, Stijleman IJ, Davis C, Ebbert MT, Parker JS, Ellis MJ, Bernard PS, Perou CM, Nielsen TO.

Clin Cancer Res. 2012 Apr 15;18(8):2402-12. doi: 10.1158/1078-0432.CCR-11-2956. Epub 2012 Feb 20.

35.

Characterization of uncertainty in the classification of multivariate assays: application to PAM50 centroid-based genomic predictors for breast cancer treatment plans.

Ebbert MT, Bastien RR, Boucher KM, Martín M, Carrasco E, Caballero R, Stijleman IJ, Bernard PS, Facelli JC.

J Clin Bioinforma. 2011 Dec 23;1:37. doi: 10.1186/2043-9113-1-37.

36.

TRIM29 functions as a tumor suppressor in nontumorigenic breast cells and invasive ER+ breast cancer.

Liu J, Welm B, Boucher KM, Ebbert MT, Bernard PS.

Am J Pathol. 2012 Feb;180(2):839-47. doi: 10.1016/j.ajpath.2011.10.020. Epub 2011 Dec 2.

37.

Tumor grafts derived from women with breast cancer authentically reflect tumor pathology, growth, metastasis and disease outcomes.

DeRose YS, Wang G, Lin YC, Bernard PS, Buys SS, Ebbert MT, Factor R, Matsen C, Milash BA, Nelson E, Neumayer L, Randall RL, Stijleman IJ, Welm BE, Welm AL.

Nat Med. 2011 Oct 23;17(11):1514-20. doi: 10.1038/nm.2454.

38.

Evolutionary pressure on mitochondrial cytochrome b is consistent with a role of CytbI7T affecting longevity during caloric restriction.

Beckstead WA, Ebbert MT, Rowe MJ, McClellan DA.

PLoS One. 2009 Jun 8;4(6):e5836. doi: 10.1371/journal.pone.0005836.

39.

Pharmacogenomics: analysing SNPs in the CYP2D6 gene using amino acid properties.

Ebbert MT, Beckstead WA, O'Connor TD, Clement MJ, McClellan DA.

Int J Bioinform Res Appl. 2007;3(4):471-9.

PMID:
18048313

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