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Items: 1 to 50 of 67

1.

Structural Insights into Hearing Loss Genetics from Polarizable Protein Repacking.

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.

Biophys J. 2019 Aug 6;117(3):602-612. doi: 10.1016/j.bpj.2019.06.030. Epub 2019 Jul 3.

PMID:
31327459
2.

Machine learning with the TCGA-HNSC dataset: improving usability by addressing inconsistency, sparsity, and high-dimensionality.

Rendleman MC, Buatti JM, Braun TA, Smith BJ, Nwakama C, Beichel RR, Brown B, Casavant TL.

BMC Bioinformatics. 2019 Jun 17;20(1):339. doi: 10.1186/s12859-019-2929-8.

3.

Whole-gene sequencing investigation of SAT1 in attempted suicide.

Monson ET, de Klerk K, Gaynor SC, Wagner AH, Breen ME, Parsons M, Casavant TL, Zandi PP, Potash JB, Willour VL.

Am J Med Genet B Neuropsychiatr Genet. 2016 Sep;171(6):888-95. doi: 10.1002/ajmg.b.32462. Epub 2016 May 27.

4.

Audioprofile Surfaces: The 21st Century Audiogram.

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 PL, Smith RJ, Casavant TL.

Ann Otol Rhinol Laryngol. 2016 May;125(5):361-8. doi: 10.1177/0003489415614863. Epub 2015 Nov 3.

5.

CNV-ROC: A cost effective, computer-aided analytical performance evaluator of chromosomal microarrays.

Goodman CW, Major HJ, Walls WD, Sheffield VC, Casavant TL, Darbro BW.

J Biomed Inform. 2015 Apr;54:106-13. doi: 10.1016/j.jbi.2015.01.001. Epub 2015 Jan 13.

6.

Utilizing ethnic-specific differences in minor allele frequency to recategorize reported pathogenic deafness variants.

Shearer AE, Eppsteiner RW, Booth KT, Ephraim SS, Gurrola J 2nd, Simpson A, Black-Ziegelbein EA, Joshi S, Ravi H, Giuffre AC, Happe S, Hildebrand MS, Azaiez H, Bayazit YA, Erdal ME, Lopez-Escamez JA, Gazquez I, Tamayo ML, Gelvez NY, Leal GL, Jalas C, Ekstein J, Yang T, Usami S, Kahrizi K, Bazazzadegan N, Najmabadi H, Scheetz TE, Braun TA, Casavant TL, LeProust EM, Smith RJ.

Am J Hum Genet. 2014 Oct 2;95(4):445-53. doi: 10.1016/j.ajhg.2014.09.001. Epub 2014 Sep 25.

7.

Cordova: web-based management of genetic variation data.

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 RJ, Braun TA.

Bioinformatics. 2014 Dec 1;30(23):3438-9. doi: 10.1093/bioinformatics/btu539. Epub 2014 Aug 14.

8.

Advancing genetic testing for deafness with genomic technology.

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 RJ.

J Med Genet. 2013 Sep;50(9):627-34. doi: 10.1136/jmedgenet-2013-101749. Epub 2013 Jun 26.

9.

Computational identification of operon-like transcriptional loci in eukaryotes.

Nannapaneni K, Ben-Shahar Y, Keen HL, Welsh MJ, Casavant TL, Scheetz TE.

Comput Biol Med. 2013 Jul;43(6):738-43. doi: 10.1016/j.compbiomed.2013.03.004. Epub 2013 Mar 28.

PMID:
23668349
10.

A genome-wide association study for primary open angle glaucoma and macular degeneration reveals novel Loci.

Scheetz TE, Fingert JH, Wang K, Kuehn MH, Knudtson KL, Alward WL, Boldt HC, Russell SR, Folk JC, Casavant TL, Braun TA, Clark AF, Stone EM, Sheffield VC.

PLoS One. 2013;8(3):e58657. doi: 10.1371/journal.pone.0058657. Epub 2013 Mar 11.

11.

Prioritization of retinal disease genes: an integrative approach.

Wagner AH, Taylor KR, DeLuca AP, Casavant TL, Mullins RF, Stone EM, Scheetz TE, Braun TA.

Hum Mutat. 2013 Jun;34(6):853-9. doi: 10.1002/humu.22317. Epub 2013 Apr 12.

12.

Exon-level expression profiling of ocular tissues.

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.

Exp Eye Res. 2013 Jun;111:105-11. doi: 10.1016/j.exer.2013.03.004. Epub 2013 Mar 14.

13.

AudioGene: predicting hearing loss genotypes from phenotypes to guide genetic screening.

Taylor KR, Deluca AP, Shearer AE, Hildebrand MS, Black-Ziegelbein EA, Anand VN, Sloan CM, Eppsteiner RW, Scheetz TE, Huygen PL, Smith RJ, Braun TA, Casavant TL.

Hum Mutat. 2013 Apr;34(4):539-45. doi: 10.1002/humu.22268. Epub 2013 Feb 19.

14.

Prediction of cochlear implant performance by genetic mutation: the spiral ganglion hypothesis.

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 RJ.

Hear Res. 2012 Oct;292(1-2):51-8. doi: 10.1016/j.heares.2012.08.007. Epub 2012 Aug 28.

15.

Coex-Rank: An approach incorporating co-expression information for combined analysis of microarray data.

Cai J, Keen HL, Sigmund CD, Casavant TL.

J Integr Bioinform. 2012 Jul 30;9(1):208. doi: 10.2390/biecoll-jib-2012-208.

16.

Using the phenome and genome to improve genetic diagnosis for deafness.

Eppsteiner RW, Shearer AE, Hildebrand MS, Taylor KR, Deluca AP, Scherer S, Huygen P, Scheetz TE, Braun TA, Casavant TL, Smith RJ.

Otolaryngol Head Neck Surg. 2012 Nov;147(5):975-7. doi: 10.1177/0194599812454271. Epub 2012 Jul 11. No abstract available.

17.

Informatics methods to enable sharing of quantitative imaging research data.

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.

Magn Reson Imaging. 2012 Nov;30(9):1249-56. doi: 10.1016/j.mri.2012.04.007. Epub 2012 Jul 6.

18.

Swarm rat chondrosarcoma cells as an in vivo model: lung colonization and effects of tissue environment on tumor growth.

Morcuende JA, Stevens JW, Scheetz TE, de Fatima Bonaldoc M, Casavant TL, Otero JE, Soares MB.

Iowa Orthop J. 2012;32:46-53.

19.

DFNA8/12 caused by TECTA mutations is the most identified subtype of nonsyndromic autosomal dominant hearing loss.

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 PL, Kremer H, Van Camp G, Moreno F, Casavant TL, Smith RJ, Moreno-Pelayo MA.

Hum Mutat. 2011 Jul;32(7):825-34. doi: 10.1002/humu.21512. Epub 2011 Jun 7.

20.

Image-based biomarkers in clinical practice.

Bayouth JE, Casavant TL, Graham MM, Sonka M, Muruganandham M, Buatti JM.

Semin Radiat Oncol. 2011 Apr;21(2):157-66. doi: 10.1016/j.semradonc.2010.11.003. Review.

21.

Microenvironment alters epigenetic and gene expression profiles in Swarm rat chondrosarcoma tumors.

Hamm CA, Stevens JW, Xie H, Vanin EF, Morcuende JA, Abdulkawy H, Seftor EA, Sredni ST, Bischof JM, Wang D, Malchenko S, Bonaldo Mde F, Casavant TL, Hendrix MJ, Soares MB.

BMC Cancer. 2010 Sep 1;10:471. doi: 10.1186/1471-2407-10-471.

22.

Transcriptional patterns in both host and bacterium underlie a daily rhythm of anatomical and metabolic change in a beneficial symbiosis.

Wier AM, Nyholm SV, Mandel MJ, Massengo-Tiassé RP, Schaefer AL, Koroleva I, Splinter-Bondurant S, Brown B, Manzella L, Snir E, Almabrazi H, Scheetz TE, Bonaldo Mde F, Casavant TL, Soares MB, Cronan JE, Reed JL, Ruby EG, McFall-Ngai MJ.

Proc Natl Acad Sci U S A. 2010 Feb 2;107(5):2259-64. doi: 10.1073/pnas.0909712107. Epub 2010 Jan 19.

23.

Bioinformatic analysis of gene sets regulated by ligand-activated and dominant-negative peroxisome proliferator-activated receptor gamma in mouse aorta.

Keen HL, Halabi CM, Beyer AM, de Lange WJ, Liu X, Maeda N, Faraci FM, Casavant TL, Sigmund CD.

Arterioscler Thromb Vasc Biol. 2010 Mar;30(3):518-25. doi: 10.1161/ATVBAHA.109.200733. Epub 2009 Dec 17.

24.

A contemporary review of AudioGene audioprofiling: a machine-based candidate gene prediction tool for autosomal dominant nonsyndromic hearing loss.

Hildebrand MS, DeLuca AP, Taylor KR, Hoskinson DP, Hur IA, Tack D, McMordie SJ, Huygen PL, Casavant TL, Smith RJ.

Laryngoscope. 2009 Nov;119(11):2211-5. doi: 10.1002/lary.20664. Review. No abstract available.

25.

Mutation in the COCH gene is associated with superior semicircular canal dehiscence.

Hildebrand MS, Tack D, Deluca A, Hur IA, Van Rybroek JM, McMordie SJ, Muilenburg A, Hoskinson DP, Van Camp G, Pensak ML, Storper IS, Huygen PL, Casavant TL, Smith RJ.

Am J Med Genet A. 2009 Feb;149A(2):280-5. doi: 10.1002/ajmg.a.32618. No abstract available.

26.

Multi-granularity Parallel Computing in a Genome-Scale Molecular Evolution Application.

Walters JD, Bair TB, Braun TA, Scheetz TE, Robinson JP, Casavant TL.

J Supercomput. 2009 Jan 1;5698:49-59.

27.

Audioprofile-directed screening identifies novel mutations in KCNQ4 causing hearing loss at the DFNA2 locus.

Hildebrand MS, Tack D, McMordie SJ, DeLuca A, Hur IA, Nishimura C, Huygen P, Casavant TL, Smith RJ.

Genet Med. 2008 Nov;10(11):797-804. doi: 10.1097/GIM.0b013e318187e106.

28.

Effects of colonization, luminescence, and autoinducer on host transcription during development of the squid-vibrio association.

Chun CK, Troll JV, Koroleva I, Brown B, Manzella L, Snir E, Almabrazi H, Scheetz TE, Bonaldo Mde F, Casavant TL, Soares MB, Ruby EG, McFall-Ngai MJ.

Proc Natl Acad Sci U S A. 2008 Aug 12;105(32):11323-8. doi: 10.1073/pnas.0802369105. Epub 2008 Aug 5.

29.

A knowledge-based approach to predict intragenic deletions or duplications.

Kalari KR, Casavant TL, Scheetz TE.

Bioinformatics. 2008 Sep 15;24(18):1975-9. doi: 10.1093/bioinformatics/btn370. Epub 2008 Jul 21.

PMID:
18647756
30.

Transcript annotation prioritization and screening system (TrAPSS) for mutation screening.

O'Leary BM, Davis SG, Smith MF, Brown B, Kemp MB, Almabrazi H, Grundstad JA, Burns T, Leontiev V, Andorf J, Clark AF, Sheffield VC, Casavant TL, Scheetz TE, Stone EM, Braun TA.

J Bioinform Comput Biol. 2007 Dec;5(6):1155-72.

PMID:
18172923
31.

IDOCS: intelligent distributed ontology consensus system--the use of machine learning in retinal drusen phenotyping.

Thomas G, Grassi MA, Lee JR, Edwards AO, Gorin MB, Klein R, Casavant TL, Scheetz TE, Stone EM, Williams AB.

Invest Ophthalmol Vis Sci. 2007 May;48(5):2278-84.

PMID:
17460291
32.

Eukaryotic operon-like transcription of functionally related genes in Drosophila.

Ben-Shahar Y, Nannapaneni K, Casavant TL, Scheetz TE, Welsh MJ.

Proc Natl Acad Sci U S A. 2007 Jan 2;104(1):222-7. Epub 2006 Dec 26.

33.

Regulation of gene expression in the mammalian eye and its relevance to eye disease.

Scheetz TE, Kim KY, Swiderski RE, Philp AR, Braun TA, Knudtson KL, Dorrance AM, DiBona GF, Huang J, Casavant TL, Sheffield VC, Stone EM.

Proc Natl Acad Sci U S A. 2006 Sep 26;103(39):14429-34. Epub 2006 Sep 18.

34.

First exons and introns--a survey of GC content and gene structure in the human genome.

Kalari KR, Casavant M, Bair TB, Keen HL, Comeron JM, Casavant TL, Scheetz TE.

In Silico Biol. 2006;6(3):237-42.

PMID:
16922687
35.

Integration site choice of a feline immunodeficiency virus vector.

Kang Y, Moressi CJ, Scheetz TE, Xie L, Tran DT, Casavant TL, Ak P, Benham CJ, Davidson BL, McCray PB Jr.

J Virol. 2006 Sep;80(17):8820-3.

36.

Analysis of ESTs from Lutzomyia longipalpis sand flies and their contribution toward understanding the insect-parasite relationship.

Dillon RJ, Ivens AC, Churcher C, Holroyd N, Quail MA, Rogers ME, Soares MB, Bonaldo MF, Casavant TL, Lehane MJ, Bates PA.

Genomics. 2006 Dec;88(6):831-840. doi: 10.1016/j.ygeno.2006.06.011. Epub 2006 Aug 1.

37.

An annotated cDNA library of juvenile Euprymna scolopes with and without colonization by the symbiont Vibrio fischeri.

Chun CK, Scheetz TE, Bonaldo Mde F, Brown B, Clemens A, Crookes-Goodson WJ, Crouch K, DeMartini T, Eyestone M, Goodson MS, Janssens B, Kimbell JL, Koropatnick TA, Kucaba T, Smith C, Stewart JJ, Tong D, Troll JV, Webster S, Winhall-Rice J, Yap C, Casavant TL, McFall-Ngai MJ, Soares MB.

BMC Genomics. 2006 Jun 16;7:154.

38.

Genome-wide identification of pseudogenes capable of disease-causing gene conversion.

Bischof JM, Chiang AP, Scheetz TE, Stone EM, Casavant TL, Sheffield VC, Braun TA.

Hum Mutat. 2006 Jun;27(6):545-52.

PMID:
16671097
39.

Protein expression in a transformed trabecular meshwork cell line: proteome analysis.

Steely HT, Dillow GW, Bian L, Grundstad J, Braun TA, Casavant TL, McCartney MD, Clark AF.

Mol Vis. 2006 Apr 18;12:372-83.

40.

Homozygosity mapping with SNP arrays identifies TRIM32, an E3 ubiquitin ligase, as a Bardet-Biedl syndrome gene (BBS11).

Chiang AP, Beck JS, Yen HJ, Tayeh MK, Scheetz TE, Swiderski RE, Nishimura DY, Braun TA, Kim KY, Huang J, Elbedour K, Carmi R, Slusarski DC, Casavant TL, Stone EM, Sheffield VC.

Proc Natl Acad Sci U S A. 2006 Apr 18;103(16):6287-92. Epub 2006 Apr 10.

41.

Prioritizing regions of candidate genes for efficient mutation screening.

Braun TA, Shankar SP, Davis S, O'Leary B, Scheetz TE, Clark AF, Sheffield VC, Casavant TL, Stone EM.

Hum Mutat. 2006 Feb;27(2):195-200.

PMID:
16395665
42.

Identifying components of the NF-kappaB pathway in the beneficial Euprymna scolopes-Vibrio fischeri light organ symbiosis.

Goodson MS, Kojadinovic M, Troll JV, Scheetz TE, Casavant TL, Soares MB, McFall-Ngai MJ.

Appl Environ Microbiol. 2005 Nov;71(11):6934-46.

43.

Genetic characterization of commonly used glioma cell lines in the rat animal model system.

Sibenaller ZA, Etame AB, Ali MM, Barua M, Braun TA, Casavant TL, Ryken TC.

Neurosurg Focus. 2005 Oct 15;19(4):E1.

PMID:
16241103
44.

CFTR DeltaF508 mutation has minimal effect on the gene expression profile of differentiated human airway epithelia.

Zabner J, Scheetz TE, Almabrazi HG, Casavant TL, Huang J, Keshavjee S, McCray PB Jr.

Am J Physiol Lung Cell Mol Physiol. 2005 Oct;289(4):L545-53. Epub 2005 Jun 3.

45.

Insights into a dinoflagellate genome through expressed sequence tag analysis.

Hackett JD, Scheetz TE, Yoon HS, Soares MB, Bonaldo MF, Casavant TL, Bhattacharya D.

BMC Genomics. 2005 May 29;6:80.

46.

Isolation and characterization of autotrophic, hydrogen-utilizing, perchlorate-reducing bacteria.

Shrout JD, Scheetz TE, Casavant TL, Parkin GF.

Appl Microbiol Biotechnol. 2005 Apr;67(2):261-8. Epub 2004 Sep 4.

PMID:
15834721
47.

The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R, Good P, Guyer M, Peck AM, Derge JG, Lipman D, Collins FS, Jang W, Sherry S, Feolo M, Misquitta L, Lee E, Rotmistrovsky K, Greenhut SF, Schaefer CF, Buetow K, Bonner TI, Haussler D, Kent J, Kiekhaus M, Furey T, Brent M, Prange C, Schreiber K, Shapiro N, Bhat NK, Hopkins RF, Hsie F, Driscoll T, Soares MB, Casavant TL, Scheetz TE, Brown-stein MJ, Usdin TB, Toshiyuki S, Carninci P, Piao Y, Dudekula DB, Ko MS, Kawakami K, Suzuki Y, Sugano S, Gruber CE, Smith MR, Simmons B, Moore T, Waterman R, Johnson SL, Ruan Y, Wei CL, Mathavan S, Gunaratne PH, Wu J, Garcia AM, Hulyk SW, Fuh E, Yuan Y, Sneed A, Kowis C, Hodgson A, Muzny DM, McPherson J, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madari A, Young AC, Wetherby KD, Granite SJ, Kwong PN, Brinkley CP, Pearson RL, Bouffard GG, Blakesly RW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YS, Griffith M, Griffith OL, Krzywinski MI, Liao N, Morin R, Palmquist D, Petrescu AS, Skalska U, Smailus DE, Stott JM, Schnerch A, Schein JE, Jones SJ, Holt RA, Baross A, Marra MA, Clifton S, Makowski KA, Bosak S, Malek J; MGC Project Team.

Genome Res. 2004 Oct;14(10B):2121-7. Erratum in: Genome Res. 2006 Jun;16(6):804. Morrin, Ryan [corrected to Morin, Ryan].

48.

1274 full-open reading frames of transcripts expressed in the developing mouse nervous system.

Bonaldo MF, Bair TB, Scheetz TE, Snir E, Akabogu I, Bair JL, Berger B, Crouch K, Davis A, Eyestone ME, Keppel C, Kucaba TA, Lebeck M, Lin JL, de Melo AI, Rehmann J, Reiter RS, Schaefer K, Smith C, Tack D, Trout K, Sheffield VC, Lin JJ, Casavant TL, Soares MB.

Genome Res. 2004 Oct;14(10B):2053-63.

49.

Missense variations in the fibulin 5 gene and age-related macular degeneration.

Stone EM, Braun TA, Russell SR, Kuehn MH, Lotery AJ, Moore PA, Eastman CG, Casavant TL, Sheffield VC.

N Engl J Med. 2004 Jul 22;351(4):346-53.

50.

PLET1 (C11orf34), a highly expressed and processed novel gene in pig and mouse placenta, is transcribed but poorly spliced in human.

Zhao SH, Simmons DG, Cross JC, Scheetz TE, Casavant TL, Soares MB, Tuggle CK.

Genomics. 2004 Jul;84(1):114-25.

PMID:
15203209

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