Publications

1. Udine E, Finch NA, DeJesus-Hernandez M, Jackson JL, Baker MC, Saravanaperumal SA, Wieben E, Ebbert MTW, Shah J, Petrucelli L, Rademakers R, Oskarsson B, van Blitterswijk M. Targeted long-read sequencing to quantify methylation of the C9orf72 repeat expansion. Mol Neurodegener. 2024 Dec 21; 19 (1):99
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2. Aguzzoli Heberle B, Brandon JA, Page ML, Nations KA, Dikobe KI, White BJ, Gordon LA, Fox GA, Wadsworth ME, Doyle PH, Williams BA, Fox EJ, Shantaraman A, Ryten M, Goodwin S, Ghiban E, Wappel R, Mavruk-Eskipehlivan S, Miller JB, Seyfried NT, Nelson PT, Fryer JD, Ebbert MTW. Mapping medically relevant RNA isoform diversity in the aged human frontal cortex with deep long-read RNA-seq. Nat Biotechnol. 2024 May 22 [Epub ahead of print]
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3. Page ML, Vance EL, Cloward ME, Ringger E, Dayton L, Ebbert MTW, Miller JB, Kauwe JSK, Alzheimer's Disease Neuroimaging Initiative. The Polygenic Risk Score Knowledge Base offers a centralized online repository for calculating and contextualizing polygenic risk scores. Commun Biol. 2022 Sep 2; 5 (1):899 Epub 2022 Sept 02
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4. Cadiz MP, Jensen TD, Sens JP, Zhu K, Song WM, Zhang B, Ebbert M, Chang R, Fryer JD. Culture shock: microglial heterogeneity, activation, and disrupted single-cell microglial networks in vitro. Mol Neurodegener. 2022 Mar 28; 17 (1):26
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5. DeJesus-Hernandez M, Aleff RA, Jackson JL, Finch NA, Baker MC, Gendron TF, Murray ME, McLaughlin IJ, Harting JR, Graff-Radford NR, Oskarsson B, Knopman DS, Josephs KA, Boeve BF, Petersen RC, Fryer JD, Petrucelli L, Dickson DW, Rademakers R, Ebbert MTW, Wieben ED, van Blitterswijk M. Long-read targeted sequencing uncovers clinicopathological associations for C9orf72-linked diseases. Brain. 2021 May 7; 144 (4):1082-1088
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6. 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. Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight. Genome Biol. 2019 May 20; 20 (1):97
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7. Kang SS, Ebbert MTW, Baker KE, Cook C, Wang X, Sens JP, Kocher JP, Petrucelli L, Fryer JD. Microglial translational profiling reveals a convergent APOE pathway from aging, amyloid, and tau. J Exp Med. 2018 Sep 3; 215 (9):2235-2245 Epub 2018 Aug 06
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8. 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. Corticobasal degeneration with TDP-43 pathology presenting with progressive supranuclear palsy syndrome: a distinct clinicopathologic subtype. Acta Neuropathol. 2018 Sep; 136 (3):389-404 Epub 2018 June 20
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9. 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. Long-read sequencing across the C9orf72 'GGGGCC' repeat expansion: implications for clinical use and genetic discovery efforts in human disease. Mol Neurodegener. 2018 Aug 21; 13 (1):46
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10. 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. Poly(GR) impairs protein translation and stress granule dynamics in C9orf72-associated frontotemporal dementia and amyotrophic lateral sclerosis. Nat Med. 2018 Aug; 24 (8):1136-1142 Epub 2018 June 25
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11. Sexton CE, Ebbert MTW, Miller RH, Ferrel M, Tschanz JAT, Corcoran CD, Ridge PG, Kauwe JSK, Alzheimer's Disease Neuroimaging Initiative. Common DNA Variants Accurately Rank an Individual of Extreme Height. Int J Genomics. 2018; 2018:5121540 Epub 2018 Sept 04
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12. 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. Linkage, whole genome sequence, and biological data implicate variants in RAB10 in Alzheimer's disease resilience. Genome Med. 2017 Nov 29; 9 (1):100
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13. 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. Conserved DNA methylation combined with differential frontal cortex and cerebellar expression distinguishes C9orf72-associated and sporadic ALS, and implicates SERPINA1 in disease. Acta Neuropathol. 2017 Nov; 134(5):715-728. Epub 2017 Aug 14.
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14. 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. Repetitive element transcripts are elevated in the brain of C9orf72 ALS/FTLD patients. Hum Mol Genet. 2017 Sep 1; 26 (17):3421-3431
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15. Mallory MA, Lucic D, Ebbert MT, Cloherty GA, Toolsie D, Hillyard DR. Evaluation of the Abbott RealTime HCV genotype II plus RUO (PLUS) assay with reference to core and NS5B sequencing. J Clin Virol. 2017 May; 90:26-31 Epub 2017 Mar 09
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16. Pickett BD, Karlinsey SM, Penrod CE, Cormier MJ, Ebbert MT, Shiozawa DK, Whipple CJ, Ridge PG. SA-SSR: a suffix array-based algorithm for exhaustive and efficient SSR discovery in large genetic sequences. Bioinformatics. 2016 Sep 1; 32 (17):2707-9 Epub 2016 May 11
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17. Bodily PM, Fujimoto MS, Page JT, Clement MJ, Ebbert MT, Ridge PG, Alzheimer's Disease Neuroimaging Initiative. A novel approach for multi-SNP GWAS and its application in Alzheimer's disease. BMC Bioinformatics. 2016 Jul 25; 17 Suppl 7:268 Epub 2016 July 25
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18. Ebbert MT, Wadsworth ME, Staley LA, Hoyt KL, Pickett B, Miller J, Duce J, Kauwe JS, Ridge PG, Alzheimer's Disease Neuroimaging Initiative. Evaluating the necessity of PCR duplicate removal from next-generation sequencing data and a comparison of approaches. BMC Bioinformatics. 2016 Jul 25; 17 Suppl 7:239 Epub 2016 July 25
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19. Staley LA, Ebbert MT, Parker S, Bailey M, Ridge PG, Goate AM, Kauwe JS, Alzheimer's Disease Neuroimaging Initiative. Genome-wide association study of prolactin levels in blood plasma and cerebrospinal fluid. BMC Genomics. 2016 Jun 29; 17 Suppl 3:436 Epub 2016 June 29
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20. Hippen AA, Ebbert MT, Norton MC, Tschanz JT, Munger RG, Corcoran CD, Kauwe JS. Presenilin E318G variant and Alzheimer's disease risk: the Cache County study. BMC Genomics. 2016 Jun 29; 17 Suppl 3:438 Epub 2016 June 29
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21. Staley LA, Ebbert MT, Bunker D, Bailey M, Ridge PG, Goate AM, Kauwe JS, Alzheimer's Disease Neuroimaging Initiative. Variants in ACPP are associated with cerebrospinal fluid Prostatic Acid Phosphatase levels. BMC Genomics. 2016 Jun 29; 17 Suppl 3:439 Epub 2016 June 29
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22. Ebbert MT, Staley LA, Parker J, Parker S, Bailey M, Ridge PG, Goate AM, Kauwe JS, Alzheimer's Disease Neuroimaging Initiative. Variants in CCL16 are associated with blood plasma and cerebrospinal fluid CCL16 protein levels. BMC Genomics. 2016 Jun 29; 17 Suppl 3:437 Epub 2016 June 29
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23. 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. Liver kinase B1 inhibits the expression of inflammation-related genes postcontraction in skeletal muscle. J Appl Physiol (1985). 2016 Apr 15; 120 (8):876-88 Epub 2016 Jan 21
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24. Ebbert MTW, Boehme KL, Wadsworth ME, Staley LA, Mukherjee S, Crane PK, Ridge PG, Kauwe JSK, Alzheimer's Disease Neuroimaging Initiative//Alzheimer's Disease Genetics Consortium. Interaction between variants in CLU and MS4A4E modulates Alzheimer's disease risk. Alzheimers Dement. 2016 Feb; 12 (2):121-129 Epub 2015 Oct 09
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25. Lythgoe C, Perkes A, Peterson M, Schmutz C, Leary M, Ebbert MT, Ridge PG, Norton MC, Tschanz JT, Munger RG, Corcoran CD, Kauwe JS. Population-based analysis of cholesteryl ester transfer protein identifies association between I405V and cognitive decline: the Cache County Study. Neurobiol Aging. 2015 Jan; 36 (1):547.e1-3 Epub 2014 Aug 27
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26. Ebbert MT, Ridge PG, Kauwe JS. Bridging the gap between statistical and biological epistasis in Alzheimer's disease. Biomed Res Int. 2015; 2015:870123 Epub 2015 May 17
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27. Ebbert MT, Ridge PG, Wilson AR, Sharp AR, Bailey M, Norton MC, Tschanz JT, Munger RG, Corcoran CD, Kauwe JS. Population-based analysis of Alzheimer's disease risk alleles implicates genetic interactions. Biol Psychiatry. 2014 May 01; 75 (9):732-7 Epub 2013 Aug 13
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28. 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. Intrinsic subtypes from PAM50 gene expression assay in a population-based breast cancer cohort: differences by age, race, and tumor characteristics. Cancer Epidemiol Biomarkers Prev. 2014 May; 23 (5):714-24 Epub 2014 Feb 12
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29. Cruchaga C, Ebbert MT, Kauwe JS. Genetic discoveries in AD using CSF amyloid and tau. Curr Genet Med Rep. 2014 Mar 01; 2 (1):23-29
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30. Ebbert MT, Wadsworth ME, Boehme KL, Hoyt KL, Sharp AR, O'Fallon BD, Kauwe JS, Ridge PG. Variant Tool Chest: an improved tool to analyze and manipulate variant call format (VCF) files. BMC Bioinformatics. 2014; 15 Suppl 7:S12 Epub 2014 May 28
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31. 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. Assessment of TREM2 rs75932628 association with Alzheimer's disease in a population-based sample: the Cache County Study. Neurobiol Aging. 2013 Dec; 34 (12):2889.e11-3 Epub 2013 July 12
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32. Ebbert MT, Mallory MA, Wilson AR, Dooley SK, Hillyard DR. Application of a new informatics tool for contamination screening in the HIV sequencing laboratory. J Clin Virol. 2013 Jul; 57 (3):249-53 Epub 2013 Apr 11
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33. Martin M, Prat A, Rodriguez-Lescure A, Caballero R, Ebbert MT, Munarriz B, Ruiz-Borrego M, Bastien RR, Crespo C, Davis C, Rodriguez CA, Lopez-Vega JM, Furio V, Garcia 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. PAM50 proliferation score as a predictor of weekly paclitaxel benefit in breast cancer. Breast Cancer Res Treat. 2013 Apr; 138 (2):457-66 Epub 2013 Feb 20
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34. Ma CX, Ellis MJ, Petroni GR, Guo Z, Cai SR, Ryan CE, Craig Lockhart A, Naughton MJ, Pluard TJ, Brenin CM, Picus J, Creekmore AN, Mwandoro T, Yarde ER, Reed J, Ebbert M, Bernard PS, Watson M, Doyle LA, Dancey J, Piwnica-Worms H, Fracasso PM. A phase II study of UCN-01 in combination with irinotecan in patients with metastatic triple negative breast cancer. Breast Cancer Res Treat. 2013 Jan; 137 (2):483-92 Epub 2012 Dec 15
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35. Ridge PG, Ebbert MT, Kauwe JS. Genetics of Alzheimer's disease. Biomed Res Int. 2013; 2013:254954 Epub 2013 July 25
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36. Bastien RR, Rodriguez-Lescure A, Ebbert MT, Prat A, Munarriz B, Rowe L, Miller P, Ruiz-Borrego M, Anderson D, Lyons B, Alvarez I, Dowell T, Wall D, Segui MA, Barley L, Boucher KM, Alba E, Pappas L, Davis CA, Aranda I, Fauron C, Stijleman IJ, Palacios J, Anton A, Carrasco E, Caballero R, Ellis MJ, Nielsen TO, Perou CM, Astill M, Bernard PS, Martin M. PAM50 breast cancer subtyping by RT-qPCR and concordance with standard clinical molecular markers. BMC Med Genomics. 2012 Oct 04; 5:44
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37. 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. Responsiveness of intrinsic subtypes to adjuvant anthracycline substitution in the NCIC.CTG MA.5 randomized trial. Clin Cancer Res. 2012 Apr 15; 18 (8):2402-12 Epub 2012 Feb 20
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38. Liu J, Welm B, Boucher KM, Ebbert MT, Bernard PS. TRIM29 functions as a tumor suppressor in nontumorigenic breast cells and invasive ER+ breast cancer. Am J Pathol. 2012 Feb; 180 (2):839-47 Epub 2011 Dec 02
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39. Kelly CM, Bernard PS, Krishnamurthy S, Wang B, Ebbert MT, Bastien RR, Boucher KM, Young E, Iwamoto T, Pusztai L. Agreement in risk prediction between the 21-gene recurrence score assay (Oncotype DX(R)) and the PAM50 breast cancer intrinsic Classifier in early-stage estrogen receptor-positive breast cancer. Oncologist. 2012; 17 (4):492-8 Epub 2012 Mar 14
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40. Ebbert MT, Bastien RR, Boucher KM, Martin M, Carrasco E, Caballero R, Stijleman IJ, Bernard PS, Facelli JC. Characterization of uncertainty in the classification of multivariate assays: application to PAM50 centroid-based genomic predictors for breast cancer treatment plans. J Clin Bioinforma. 2011 Dec 23; 1:37
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41. 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. Tumor grafts derived from women with breast cancer authentically reflect tumor pathology, growth, metastasis and disease outcomes. Nat Med. 2011 Oct 23; 17 (11):1514-20
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42. Nielsen TO, Parker JS, Leung S, Voduc D, Ebbert M, Vickery T, Davies SR, Snider J, Stijleman IJ, Reed J, Cheang MC, Mardis ER, Perou CM, Bernard PS, Ellis MJ. A comparison of PAM50 intrinsic subtyping with immunohistochemistry and clinical prognostic factors in tamoxifen-treated estrogen receptor-positive breast cancer. Clin Cancer Res. 2010 Nov 01; 16 (21):5222-32 Epub 2010 Sept 13
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43. Beckstead WA, Ebbert MT, Rowe MJ, McClellan DA. Evolutionary pressure on mitochondrial cytochrome b is consistent with a role of CytbI7T affecting longevity during caloric restriction. PLoS One. 2009 Jun 08; 4 (6):e5836 Epub 2009 June 08
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44. Carroll H, Beckstead W, O'Connor T, Ebbert M, Clement M, Snell Q, McClellan D. DNA reference alignment benchmarks based on tertiary structure of encoded proteins. Bioinformatics. 2007 Oct 01; 23 (19):2648-9 Epub 2007 Aug 08
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45. Ebbert MT, Beckstead WA, O'Connor TD, Clement MJ, McClellan DA. Pharmacogenomics: analysing SNPs in the CYP2D6 gene using amino acid properties. Int J Bioinform Res Appl. 2007; 3 (4):471-9
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