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Mark T. Ebbert, Ph.D. - Publications

Affiliations: 
2014 Biology Brigham Young University, Provo, UT, United States 
Area:
Alzheimer's disease genetics
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18/39 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Ebbert MT, Wadsworth ME, Staley LA, Hoyt KL, Pickett B, Miller J, Duce J, Kauwe JS, Ridge PG. Evaluating the necessity of PCR duplicate removal from next-generation sequencing data and a comparison of approaches. Bmc Bioinformatics. 17: 239. PMID 27454357 DOI: 10.1186/S12859-016-1097-3  0.65
2016 Bodily PM, Fujimoto MS, Page JT, Clement MJ, Ebbert MT, Ridge PG. A novel approach for multi-SNP GWAS and its application in Alzheimer's disease. Bmc Bioinformatics. 17: 268. PMID 27453991 DOI: 10.1186/S12859-016-1093-7  0.652
2016 Ebbert MT, Staley LA, Parker J, Parker S, Bailey M, Ridge PG, Goate AM, Kauwe JS. Variants in CCL16 are associated with blood plasma and cerebrospinal fluid CCL16 protein levels. Bmc Genomics. 17: 437. PMID 27357396 DOI: 10.1186/S12864-016-2788-X  0.683
2016 Staley LA, Ebbert MT, Bunker D, Bailey M, Ridge PG, Goate AM, Kauwe JS. Variants in ACPP are associated with cerebrospinal fluid Prostatic Acid Phosphatase levels. Bmc Genomics. 17: 439. PMID 27357282 DOI: 10.1186/S12864-016-2787-Y  0.663
2016 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. 17: 438. PMID 27357204 DOI: 10.1186/S12864-016-2786-Z  0.615
2016 Staley LA, Ebbert MT, Parker S, Bailey M, Ridge PG, Goate AM, Kauwe JS. Genome-wide association study of prolactin levels in blood plasma and cerebrospinal fluid. Bmc Genomics. 17: 436. PMID 27357110 DOI: 10.1186/S12864-016-2785-0  0.672
2016 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 (Oxford, England). PMID 27170037 DOI: 10.1093/Bioinformatics/Btw298  0.566
2016 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 POST-CONTRACTION IN SKELETAL MUSCLE. Journal of Applied Physiology (Bethesda, Md. : 1985). jap.00727.2015. PMID 26796753 DOI: 10.1152/Japplphysiol.00727.2015  0.449
2015 Ebbert MT, Boehme KL, Wadsworth ME, Staley LA, Mukherjee S, Crane PK, Ridge PG, Kauwe JS. Interaction between variants in CLU and MS4A4E modulates Alzheimer's disease risk. Alzheimer's & Dementia : the Journal of the Alzheimer's Association. PMID 26449541 DOI: 10.1016/J.Jalz.2015.08.163  0.679
2015 Ebbert MT, Ridge PG, Kauwe JS. Bridging the Gap between Statistical and Biological Epistasis in Alzheimer's Disease. Biomed Research International. 2015: 870123. PMID 26075270 DOI: 10.1155/2015/870123  0.703
2015 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. Neurobiology of Aging. 36: 547.e1-3. PMID 25260850 DOI: 10.1016/J.Neurobiolaging.2014.08.022  0.676
2014 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. 15: S12. PMID 25080132 DOI: 10.1186/1471-2105-15-S7-S12  0.678
2014 Cruchaga C, Ebbert MT, Kauwe JS. Genetic discoveries in AD using CSF amyloid and tau. Current Genetic Medicine Reports. 2: 23-29. PMID 24729949 DOI: 10.1007/S40142-014-0031-0  0.557
2014 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. Biological Psychiatry. 75: 732-7. PMID 23954108 DOI: 10.1016/J.Biopsych.2013.07.008  0.702
2013 Ridge PG, Ebbert MT, Kauwe JS. Genetics of Alzheimer's disease. Biomed Research International. 2013: 254954. PMID 23984328 DOI: 10.1155/2013/254954  0.706
2013 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. Neurobiology of Aging. 34: 2889.e11-3. PMID 23855982 DOI: 10.1016/J.Neurobiolaging.2013.06.004  0.587
2013 Gonzalez J, Schmutz C, Kauwe J, Munger C, Perkes A, Gustin A, Ebbert M, Norton M, Tschanz J, Munger R, Corcoran C. Assessment of TREM2 R47H in a population-based sample: The Cache County Study Alzheimers & Dementia. 9. DOI: 10.1016/J.Jalz.2013.05.1088  0.531
2013 Ebbert M, Ridge P, Wilson A, Sharp A, Bailey M, Norton M, Tschanz J, Munger R, Corcoran C, Kauwe J. P3-005: Population-based analysis of late-onset Alzheimer's disease risk alleles identifies candidate gene-gene interactions Alzheimer's & Dementia. 9: P551-P551. DOI: 10.1016/J.Jalz.2013.05.1074  0.713
Low-probability matches (unlikely to be authored by this person)
2010 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. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 16: 5222-32. PMID 20837693 DOI: 10.1158/1078-0432.Ccr-10-1282  0.272
2012 Sweeney C, Bernard PS, Factor R, Shakespear K, Kwan ML, Habel LA, Stijleman IJ, Davis CA, Ebbert M, Kushi LH, Caan BJ. Abstract 1670: Molecular subtypes from PAM50 in a breast cancer cohort: differences by patient characteristic, reproducibility Cancer Research. 72: 1670-1670. DOI: 10.1158/1538-7445.Am2012-1670  0.252
2007 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 (Oxford, England). 23: 2648-9. PMID 17686799 DOI: 10.1093/Bioinformatics/Btm389  0.246
2013 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, et al. A phase II study of UCN-01 in combination with irinotecan in patients with metastatic triple negative breast cancer. Breast Cancer Research and Treatment. 137: 483-92. PMID 23242585 DOI: 10.1007/S10549-012-2378-9  0.237
2009 Carey L, O'Shaughnessy J, Hoadley K, Khambata-Ford S, Horak C, Xu L, Awad M, Brickman D, Muller S, Donato J, Asmar L, Stiljeman I, Ebbert M, Bernard P, Perou C. Potential Predictive Markers of Benefit from Cetuximab in Metastatic Breast Cancer: An Analysis of Two Randomized Phase 2 Trials. Cancer Research. 69: 2014-2014. DOI: 10.1158/0008-5472.Sabcs-09-2014  0.21
2007 Ebbert MT, Beckstead WA, O'Connor TD, Clement MJ, McClellan DA. Pharmacogenomics: analysing SNPs in the CYP2D6 gene using amino acid properties. International Journal of Bioinformatics Research and Applications. 3: 471-9. PMID 18048313 DOI: 10.1504/Ijbra.2007.015415  0.181
2011 Ebbert MT, Bastien RR, Boucher KM, Martín 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. Journal of Clinical Bioinformatics. 1: 37. PMID 22196354 DOI: 10.1186/2043-9113-1-37  0.164
2022 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. Molecular Neurodegeneration. 17: 26. PMID 35346293 DOI: 10.1186/s13024-022-00531-1  0.136
2012 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®) and the PAM50 breast cancer intrinsic Classifierâ„¢ in early-stage estrogen receptor-positive breast cancer. The Oncologist. 17: 492-8. PMID 22418568 DOI: 10.1634/theoncologist.2012-0007  0.134
2014 Sweeney C, Bernard PS, Factor RE, Kwan ML, Habel LA, Quesenberry CP, 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 Epidemiology, Biomarkers & Prevention : a Publication of the American Association For Cancer Research, Cosponsored by the American Society of Preventive Oncology. 23: 714-24. PMID 24521995 DOI: 10.1158/1055-9965.Epi-13-1023  0.125
2012 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, et al. PAM50 breast cancer subtyping by RT-qPCR and concordance with standard clinical molecular markers. Bmc Medical Genomics. 5: 44. PMID 23035882 DOI: 10.1186/1755-8794-5-44  0.117
2012 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, et al. Responsiveness of intrinsic subtypes to adjuvant anthracycline substitution in the NCIC.CTG MA.5 randomized trial. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 18: 2402-12. PMID 22351696 DOI: 10.1158/1078-0432.Ccr-11-2956  0.109
2011 Bastien RR, Ebbert MT, Boucher KM, Kelly CM, Wang B, Iwamoto T, Krishnamurthy S, Pusztai L, Bernard PS. Using the PAM50 breast cancer intrinsic classifier to assess risk in ER+ breast cancers: A direct comparison to Oncotype DX. Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology. 29: 503. PMID 28021372 DOI: 10.1200/jco.2011.29.15_suppl.503  0.107
2013 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, et al. PAM50 proliferation score as a predictor of weekly paclitaxel benefit in breast cancer. Breast Cancer Research and Treatment. 138: 457-66. PMID 23423445 DOI: 10.1007/S10549-013-2416-2  0.093
2013 Ebbert MT, Mallory MA, Wilson AR, Dooley SK, Hillyard DR. Application of a new informatics tool for contamination screening in the HIV sequencing laboratory. Journal of Clinical Virology : the Official Publication of the Pan American Society For Clinical Virology. 57: 249-53. PMID 23583427 DOI: 10.1016/j.jcv.2013.03.013  0.093
2011 Bernard PS, Davis C, Munarriz B, Stijleman IJ, Ruiz-Borrego M, Ebbert MT, Rodriguez-Lescure A, Bastien RR, Crespo C, Perou CM, Rodriguez C, Aranda FI, Furió V, Alvarez I, Seguí MA, et al. Determining agreement between immunohistochemistry and RT-qPCR for standard biomarkers in breast cancer: Validation on GEICAM 9906 clinical trial. Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology. 29: 611. PMID 28020639 DOI: 10.1200/Jco.2011.29.15_Suppl.611  0.087
2011 Ebbert MT, Bastien RR, Rowe LR, Miller PA, Anderson D, Boucher KM, Pappas LM, Fauron C, Lyons BW, Dowell T, Wall DE, Barley L, Bernard PS. PAM50 breast cancer intrinsic classifier: Clinical validation of a multianalyte laboratory developed test. Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology. 29: 10597. PMID 28022017 DOI: 10.1200/jco.2011.29.15_suppl.10597  0.085
2017 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. Journal of Clinical Virology : the Official Publication of the Pan American Society For Clinical Virology. 90: 26-31. PMID 28324789 DOI: 10.1016/j.jcv.2017.03.007  0.076
2012 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. The American Journal of Pathology. 180: 839-47. PMID 22138580 DOI: 10.1016/j.ajpath.2011.10.020  0.069
2009 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. 4: e5836. PMID 19503808 DOI: 10.1371/Journal.Pone.0005836  0.064
2011 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. Nature Medicine. 17: 1514-20. PMID 22019887 DOI: 10.1038/nm.2454  0.058
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