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Anyimadu EA, Engelbart JM, Semprini J, Kahl A, Trentz C, Buatti JM, Casavant TL, Charlton ME, Canahuate G. Racial Disparities in Cancer Guideline-Concordant Treatment Using Surveillance, Epidemiology, and End Results Data for Patients With NSCLC. JTO Clin Res Rep 2025;6:100747. [PMID: 39758596 PMCID: PMC11699381 DOI: 10.1016/j.jtocrr.2024.100747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/05/2024] [Accepted: 10/12/2024] [Indexed: 01/07/2025]  Open
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Corrigan RA, Thiel AC, Lynn JR, Casavant TL, Ren P, Ponder JW, Schnieders MJ. A generalized Kirkwood implicit solvent for the polarizable AMOEBA protein model. J Chem Phys 2023;159:054102. [PMID: 37526158 PMCID: PMC10396400 DOI: 10.1063/5.0158914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/17/2023] [Indexed: 08/02/2023]  Open
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Tollefson MR, Gogal RA, Weaver AM, Schaefer AM, Marini RJ, Azaiez H, Kolbe DL, Wang D, Weaver AE, Casavant TL, Braun TA, Smith RJH, Schnieders MJ. Assessing variants of uncertain significance implicated in hearing loss using a comprehensive deafness proteome. Hum Genet 2023;142:819-834. [PMID: 37086329 PMCID: PMC10182131 DOI: 10.1007/s00439-023-02559-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/11/2023] [Indexed: 04/23/2023]
4
Tollefson MR, Gogal RA, Weaver AM, Schaefer AM, Marini RJ, Azaiez H, Kolbe DL, Wang D, Weaver AE, Casavant TL, Braun TA, Smith RJH, Schnieders M. Assessing Variants of Uncertain Significance Implicated in Hearing Loss Using a Comprehensive Deafness Proteome. RESEARCH SQUARE 2023:rs.3.rs-2508462. [PMID: 36778238 PMCID: PMC9915777 DOI: 10.21203/rs.3.rs-2508462/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Thorpe RK, Walls WD, Corrigan R, Schaefer A, Wang K, Huygen P, Casavant TL, Smith RJH. AudioGene: refining the natural history of KCNQ4, GSDME, WFS1, and COCH-associated hearing loss. Hum Genet 2022;141:877-887. [PMID: 35038006 PMCID: PMC9092196 DOI: 10.1007/s00439-021-02424-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 12/20/2021] [Indexed: 12/24/2022]
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Corrigan RA, Qi G, Thiel AC, Lynn JR, Walker BD, Casavant TL, Lagardere L, Piquemal JP, Ponder JW, Ren P, Schnieders MJ. Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field. J Chem Theory Comput 2021;17:2323-2341. [PMID: 33769814 DOI: 10.1021/acs.jctc.0c01286] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Walls WD, Moteki H, Thomas TR, Nishio SY, Yoshimura H, Iwasa Y, Frees KL, Nishimura CJ, Azaiez H, Booth KT, Marini RJ, Kolbe DL, Weaver AM, Schaefer AM, Wang K, Braun TA, Usami SI, Barr-Gillespie PG, Richardson GP, Smith RJ, Casavant TL. A comparative analysis of genetic hearing loss phenotypes in European/American and Japanese populations. Hum Genet 2020;139:1315-1323. [PMID: 32382995 DOI: 10.1007/s00439-020-02174-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 04/29/2020] [Indexed: 01/04/2023]
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Tollefson MR, Litman JM, Qi G, O'Connell CE, Wipfler MJ, Marini RJ, Bernabe HV, Tollefson WTA, Braun TA, Casavant TL, Smith RJH, Schnieders MJ. Structural Insights into Hearing Loss Genetics from Polarizable Protein Repacking. Biophys J 2019;117:602-612. [PMID: 31327459 DOI: 10.1016/j.bpj.2019.06.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 06/10/2019] [Accepted: 06/25/2019] [Indexed: 12/21/2022]  Open
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Rendleman MC, Buatti JM, Braun TA, Smith BJ, Nwakama C, Beichel RR, Brown B, Casavant TL. Machine learning with the TCGA-HNSC dataset: improving usability by addressing inconsistency, sparsity, and high-dimensionality. BMC Bioinformatics 2019;20:339. [PMID: 31208324 PMCID: PMC6580485 DOI: 10.1186/s12859-019-2929-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 06/04/2019] [Indexed: 12/15/2022]  Open
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Monson ET, de Klerk K, Gaynor SC, Wagner AH, Breen ME, Parsons M, Casavant TL, Zandi PP, Potash JB, Willour VL. Whole-gene sequencing investigation of SAT1 in attempted suicide. Am J Med Genet B Neuropsychiatr Genet 2016;171:888-95. [PMID: 27229768 PMCID: PMC5814250 DOI: 10.1002/ajmg.b.32462] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/11/2016] [Indexed: 11/10/2022]
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Taylor KR, Booth KT, Azaiez H, Sloan CM, Kolbe DL, Glanz EN, Shearer AE, DeLuca AP, Anand VN, Hildebrand MS, Simpson AC, Eppsteiner RW, Scheetz TE, Braun TA, Huygen PLM, Smith RJH, Casavant TL. Audioprofile Surfaces: The 21st Century Audiogram. Ann Otol Rhinol Laryngol 2015;125:361-8. [PMID: 26530094 DOI: 10.1177/0003489415614863] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
12
Ephraim SS, Anand N, DeLuca AP, Taylor KR, Kolbe DL, Simpson AC, Azaiez H, Sloan CM, Shearer AE, Hallier AR, Casavant TL, Scheetz TE, Smith RJH, Braun TA. Cordova: web-based management of genetic variation data. Bioinformatics 2014;30:3438-9. [PMID: 25123904 DOI: 10.1093/bioinformatics/btu539] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
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Shearer AE, Black-Ziegelbein EA, Hildebrand MS, Eppsteiner RW, Ravi H, Joshi S, Guiffre AC, Sloan CM, Happe S, Howard SD, Novak B, Deluca AP, Taylor KR, Scheetz TE, Braun TA, Casavant TL, Kimberling WJ, Leproust EM, Smith RJH. Advancing genetic testing for deafness with genomic technology. J Med Genet 2013;50:627-34. [PMID: 23804846 DOI: 10.1136/jmedgenet-2013-101749] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
14
Wagner AH, Taylor KR, DeLuca AP, Casavant TL, Mullins RF, Stone EM, Scheetz TE, Braun TA. Prioritization of retinal disease genes: an integrative approach. Hum Mutat 2013;34:853-9. [PMID: 23508994 DOI: 10.1002/humu.22317] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 03/07/2013] [Indexed: 02/03/2023]
15
Nannapaneni K, Ben-Shahar Y, Keen HL, Welsh MJ, Casavant TL, Scheetz TE. Computational identification of operon-like transcriptional loci in eukaryotes. Comput Biol Med 2013;43:738-43. [PMID: 23668349 DOI: 10.1016/j.compbiomed.2013.03.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 12/12/2012] [Accepted: 03/15/2013] [Indexed: 01/20/2023]
16
Wagner AH, Anand VN, Wang WH, Chatterton JE, Sun D, Shepard AR, Jacobson N, Pang IH, Deluca AP, Casavant TL, Scheetz TE, Mullins RF, Braun TA, Clark AF. Exon-level expression profiling of ocular tissues. Exp Eye Res 2013;111:105-11. [PMID: 23500522 DOI: 10.1016/j.exer.2013.03.004] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 02/06/2013] [Accepted: 03/05/2013] [Indexed: 11/25/2022]
17
Scheetz TE, Fingert JH, Wang K, Kuehn MH, Knudtson KL, Alward WLM, Boldt HC, Russell SR, Folk JC, Casavant TL, Braun TA, Clark AF, Stone EM, Sheffield VC. A genome-wide association study for primary open angle glaucoma and macular degeneration reveals novel Loci. PLoS One 2013;8:e58657. [PMID: 23536807 PMCID: PMC3594156 DOI: 10.1371/journal.pone.0058657] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 02/07/2013] [Indexed: 11/22/2022]  Open
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Taylor KR, Deluca AP, Shearer AE, Hildebrand MS, Black-Ziegelbein EA, Anand VN, Sloan CM, Eppsteiner RW, Scheetz TE, Huygen PLM, Smith RJH, Braun TA, Casavant TL. AudioGene: predicting hearing loss genotypes from phenotypes to guide genetic screening. Hum Mutat 2013;34:539-45. [PMID: 23280582 DOI: 10.1002/humu.22268] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 12/18/2012] [Indexed: 12/31/2022]
19
Levy MA, Freymann JB, Kirby JS, Fedorov A, Fennessy FM, Eschrich SA, Berglund AE, Fenstermacher DA, Tan Y, Guo X, Casavant TL, Brown BJ, Braun TA, Dekker A, Roelofs E, Mountz JM, Boada F, Laymon C, Oborski M, Rubin DL. Informatics methods to enable sharing of quantitative imaging research data. Magn Reson Imaging 2012;30:1249-56. [PMID: 22770688 PMCID: PMC3466343 DOI: 10.1016/j.mri.2012.04.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 04/16/2012] [Accepted: 04/18/2012] [Indexed: 10/28/2022]
20
Eppsteiner RW, Shearer AE, Hildebrand MS, Deluca AP, Ji H, Dunn CC, Black-Ziegelbein EA, Casavant TL, Braun TA, Scheetz TE, Scherer SE, Hansen MR, Gantz BJ, Smith RJH. Prediction of cochlear implant performance by genetic mutation: the spiral ganglion hypothesis. Hear Res 2012;292:51-8. [PMID: 22975204 DOI: 10.1016/j.heares.2012.08.007] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2012] [Revised: 08/16/2012] [Accepted: 08/20/2012] [Indexed: 11/29/2022]
21
Eppsteiner RW, Shearer AE, Hildebrand MS, Taylor KR, Deluca AP, Scherer S, Huygen P, Scheetz TE, Braun TA, Casavant TL, Smith RJH. Using the phenome and genome to improve genetic diagnosis for deafness. Otolaryngol Head Neck Surg 2012;147:975-7. [PMID: 22785243 DOI: 10.1177/0194599812454271] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
22
Morcuende JA, Stevens JW, Scheetz TE, de Fatima Bonaldoc M, Casavant TL, Otero JE, Soares MB. Swarm rat chondrosarcoma cells as an in vivo model: lung colonization and effects of tissue environment on tumor growth. THE IOWA ORTHOPAEDIC JOURNAL 2012;32:46-53. [PMID: 23576921 PMCID: PMC3565414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
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Hildebrand MS, Morín M, Meyer NC, Mayo F, Modamio-Hoybjor S, Mencía A, Olavarrieta L, Morales-Angulo C, Nishimura CJ, Workman H, DeLuca AP, del Castillo I, Taylor KR, Tompkins B, Goodman CW, Schrauwen I, Wesemael MV, Lachlan K, Shearer AE, Braun TA, Huygen PLM, Kremer H, Van Camp G, Moreno F, Casavant TL, Smith RJH, Moreno-Pelayo MA. DFNA8/12 caused by TECTA mutations is the most identified subtype of nonsyndromic autosomal dominant hearing loss. Hum Mutat 2011;32:825-34. [PMID: 21520338 DOI: 10.1002/humu.21512] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 03/31/2011] [Indexed: 12/13/2022]
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Bayouth JE, Casavant TL, Graham MM, Sonka M, Muruganandham M, Buatti JM. Image-based biomarkers in clinical practice. Semin Radiat Oncol 2011;21:157-66. [PMID: 21356483 PMCID: PMC4270476 DOI: 10.1016/j.semradonc.2010.11.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
25
Hamm CA, Stevens JW, Xie H, Vanin EF, Morcuende JA, Abdulkawy H, Seftor EA, Sredni ST, Bischof JM, Wang D, Malchenko S, Bonaldo MDF, Casavant TL, Hendrix MJC, Soares MB. Microenvironment alters epigenetic and gene expression profiles in Swarm rat chondrosarcoma tumors. BMC Cancer 2010;10:471. [PMID: 20809981 PMCID: PMC2944175 DOI: 10.1186/1471-2407-10-471] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Accepted: 09/01/2010] [Indexed: 11/10/2022]  Open
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