Thomas L. Casavant, BS, MS, PhD

Portrait
Roy J. Carver, Jr. Chair in Bioinformatics and Computational Biology
Professor and Director of the UI Center for Bioinformatics and Computational Biology and the ECE Parallel Processing Laboratory
Professor of Ophthalmology and Visual Sciences
Professor of Electrical and Computer Engineering (ECE)
Professor of Biomedical Engineering (BME)

Contact Information

Department
319-335-5632

Iowa City, IA 52242
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Office
314 CC
Iowa City, IA 52242
319-335-5953

Primary Office
5316 SC
319-335-5953

Education

BS, Computer Science, University of Iowa
MS, Electrical and Computer Engineering, University of Iowa
PhD, Electrical and Computer Engineering, University of Iowa

Education/Training Program Affiliations

Interdisciplinary Graduate Program in Genetics, Interdisciplinary Graduate Program in Informatics, Interdisciplinary Graduate Program in Neuroscience, Interdisciplinary Graduate Program in Translational Biomedicine

Research Summary

My research interests span the areas of computational aspects of genomics, molecular biology, and human genetics, as well as high performance computing systems, software and networks. For the first 15 years of my research career, I have been engaged in research and development efforts in high performance computing systems [1] and software [2]. Since 1994, I have become increasingly involved in applying computational and networking techniques to problems of genomics and human genetics. These collaborative efforts with several other members of the Genetics Ph.D. Program faculty at Iowa (E. Stone, V. Sheffield, M.B. Soares, and V. Vieland) have included identification of genome loci linked to rare and common diseases such as macular degeneration, autism [3], and hypertension and obesity. GenoMap [4], a web-based system to gather and analyse pedigree, genotype, and phenotype data, was developed at Iowa to assist clinicians, molecular biologists, and geneticists in cooperating to gather and analyze data sets to help identify disease-causing gene candidates. Large-scale cDNA sequencing and mapping projects [5] have (as of April 2000) contributed over 50, 000 novel ESTs (Expressed Sequence Tags) to the public databases in Rat, Mouse, Human and other species (http://genome.uiowa.edu). These efforts are being expanded to now include the large scale identification and sequencing of the Mammalian Gene Collection of all full-length human mRNAs.

Publications

Taylor, K. R., Booth, K. T., Azaiez, H., Sloan, C. M., Kolbe, D. L., Glanz, E. N., Shearer, A. E., DeLuca, A. P., Anand, V. N., Hildebrand, M. S., Simpson, A. C., Eppsteiner, R. W., Scheetz, T. E., Braun, T. A., Huygen, P. L., Smith, R. J. & Casavant, T. L. (2016). Audioprofile Surfaces: The 21st Century Audiogram. Annals of otology, rhinology, and laryngology, 125(5), 361-368. PMID: 26530094.

Goodman, C. W., Major, H. J., Walls, W. D., Sheffield, V. C., Casavant, T. L. & Darbro, B. W. (2015). CNV-ROC: A cost effective, computer-aided analytical performance evaluator of chromosomal microarrays. Journal of biomedical informatics, 54, 106-113. PMID: 25595567.

Scheetz, T. E., Fingert, J. H., Wang, K., Kuehn, M. H., Knudtson, K. L., Alward, W. L., Boldt, H. C., Russell, S. R., Folk, J. C., Casavant, T. L., Braun, T. A., Clark, A. F., Stone, E. M. & Sheffield, V. C. (2013). A genome-wide association study for primary open angle glaucoma and macular degeneration reveals novel Loci. PLoS One, 8(3), e58657. PMID: 23536807.00.

Shearer, A. E., Black-Ziegelbein, E. A., Hildebrand, M. S., Eppsteiner, R. W., Ravi, H., Joshi, S., Guiffre, A. C., Sloan, C. M., Happe, S., Howard, S. D., Novak, B., Deluca, A. P., Taylor, K. R., Scheetz, T. E., Braun, T. A., Casavant, T. L., Kimberling, W. J., Leproust, E. M. & Smith, R. J. (2013). Advancing genetic testing for deafness with genomic technology. J Med Genet, 50(9), 627-634. PMID: 23804846.00.

Taylor, K. R., Deluca, A. P., Shearer, A. E., Hildebrand, M. S., Black-Ziegelbein, E. A., Anand, V. N., Sloan, C., Eppsteiner, R. W., Scheetz, T. E., Huygen, P. L., Smith, R. J., Braun, T. A. & Casavant, T. L. (2013). AudioGene: predicting hearing loss genotypes from phenotypes to guide genetic screening. Human Mutation, 34(4), 539-545.

Nannapaneni, K., Ben-Shahar, Y., Keen, H. L., Welsh, M. J., Casavant, T. L. & Scheetz, T. E. (2013). Computational identification of operon-like transcriptional loci in eukaryotes. Comput Biol Med, 43(6), 738-743. PMID: 23668349.00.

Wagner, A. H., Anand, V. N., Wang, W. H., Chatterton, J. E., Sun, D., Shepard, A. R., Jacobson, N., Pang, I., Deluca, A. P., Casavant, T. L., Scheetz, T. E., Mullins, R. F., Braun, T. A. & Clark, A. F. (2013). Exon-level expression profiling of ocular tissues. Exp Eye Res, 111, 105-111. PMID: 23500522.00.

Wagner, A. H., Taylor, K. R., Deluca, A. P., Casavant, T. L., Mullins, R. F., Stone, E. M., Scheetz, T. E. & Braun, T. A. (2013). Prioritization of retinal disease genes: an integrative approach. Hum Mutat, 34(6), 853-859. PMID: 23508994.00.

Cai, J., Keen, H. L., Sigmund, C. D. & Casavant, T. L. (2012). Coex-Rank: An approach incorporating co-expression information for combined analysis of microarray data. J Integr Bioinform, 9(1), 208.

Levy, M. A., Freymann, J. B., Kirby, J. S., Fedorov, A., Fennessy, F. M., Eschrich, S. A., Berglund, A. E., Fenstermacher, D. A., Tan, Y., Guo, X., Casavant, T. L., Brown, B. J., Braun, T. A., Dekker, A., Roelofs, E., Mountz, J. M., Boada, F., Laymon, C., Oborski, M. & Rubin, D. L. (2012). Informatics methods to enable sharing of quantitative imaging research data. Magn Reson Imaging, 30(9), 1249-1256. PMID: 22770688.00.

Eppsteiner, R. W., Shearer, A. E., Hildebrand, M. S., Deluca, A. P., Ji, H., Dunn, C. C., Black-Ziegelbein, E. A., Casavant, T. L., Braun, T. A., Scheetz, T. E., Scherer, S. E., Hansen, M. R., Gantz, B. J. & Smith, R. J. (2012). Prediction of cochlear implant performance by genetic mutation: the spiral ganglion hypothesis. Hear Res, 292(1-2), 51-58. PMID: 22975204.00.

Malchenko, S., Seftor, E. A., Nikolsky, Y., Hasegawa, S. L., Kuo, S., Stevens, J. W., Poyarkov, S., Nikolskaya, T., Kucaba, T., Wang, M., Abdulkawy, H., Casavant, T., Morcuende, J., Buckwalter, J., Hohl, R., Deyoung, B., Kernstine, K., Bonaldo Mde, F., Hendrix, M. J., Soares, M. B. & Soares, V. M. (2012). Putative multifunctional signature of lung metastases in dedifferentiated chondrosarcoma. Sarcoma, 2012, 820254.

Morcuende, J. A., Stevens, J. W., Scheetz, T. E., de Fatima Bonaldoc, M., Casavant, T. L., Otero, J. E. & Soares, M. B. (2012). Swarm rat chondrosarcoma cells as an in vivo model: lung colonization and effects of tissue environment on tumor growth. Iowa Orthop J, 32, 46-53. PMID: 23576921.00.

Hildebrand, M. S., Morin, M., Meyer, N. C., Mayo, F., Modamio-Hoybjor, S., Mencia, A., Olavarrieta, L., Morales-Angulo, C., Nishimura, C. J., Workman, H., Deluca, A. P., del Castillo, I., Taylor, K. R., Tompkins, B., Goodman, C. W., Schrauwen, I., Wesemael, M. V., Lachlan, K., Schearer, A. E., Braun, T. A., Huygen, P. L., Kremer, H., Van Camp, G., Moreno, F., Casavant, T. L., Smith, R. J. & Moreno-Pelayo, M. A. (2011). DFNA8/12 caused by TECTA mutations is the most identified subtype of nonsyndromic autosomal dominant hearing loss. Hum Mutat, 32(7), 825-834. PMID: 21520338.00.

Bayouth, J. E., Casavant, T. L., Graham, M. M., Sonka, M., Muruganandham, M. & Buatti, J. M. (2011). Image-based biomarkers in clinical practice. Semin Radiat Oncol, 21(2), 157-166. PMID: 21356483.00.

Keen, H. L., Halabi, C. M., Beyer, A. M., de Lange, W. J., Liu, X., Maeda, N., Faraci, F. M., Casavant, T. L. & Sigmund, C. D. (2010). Bioinformatic analysis of gene sets regulated by ligand-activated and dominant-negative peroxisome proliferator-activated receptor gamma in mouse aorta. Arterioscler Thromb Vasc Biol, 30(3), 518-25. PMID: 20018933.

Wier, A. M., Nyholm, S. V., Mandel, M. J., Massengo-Tiassé, R. P., Schaefer, A. L., Koroleva, I., Splinter-Bondurant, S., Brown, B., Manzella, L., Snir, E., Almabrazi, H., Scheetz, T. E., Bonaldo, M. d., Casavant, T. L., Soares, M. B., Cronan, J. E., Reed, J. L., Ruby, E. G. & McFall-Ngai, M. J. (2010). Transcriptional patterns in both host and bacterium underlie a daily rhythm of anatomical and metabolic change in a beneficial symbiosis. Proc Natl Acad Sci U S A, 107(5), 2259-64. PMID: 20133870.

Macagno, E. R., Gaasterland, T., Edsall, L., Bafna, V., Soares, M. B., Scheetz, T. E., Casavant, T. L., Da Silva, C., Wincker, P., Tasiemski, A. & Salzet, M. (2010). Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes. BMC Genomics, 11, 407. PMID: 20579359.

Hamm, C. A., Stevens, J. W., Xie, H., Vanin, E. F., Morcuende, J. A., Abdulkawy, H., Seftor, E. A., Sredni, S. T., Bischof, J. M., Wang, D., Malchenko, S., Bonaldo Mde, F., Casavant, T. L., Hendrix, M. J. & Soares, M. B. (2010). Microenvironment alters epigenetic and gene expression profiles in Swarm rat chondrosarcoma tumors. BMC Cancer, 10, 471. PMID: 20809981.00.

Hildebrand, M. S., Tack, D., Deluca, A., Hur, I. A., Van Rybroek, J. M., McMordie, S. J., Muilenburg, A., Hoskinson, D. P., Van Camp, G., Pensak, M. L., Storper, I. S., Huygen, P. L., Casavant, T. L. & Smith, R. J. (2009). Mutation in the COCH gene is associated with superior semicircular canal dehiscence. American journal of medical genetics. Part A, 149A(2), 280-285. PMID: 19161137.

Chun, C. K., Troll, J. V., Koroleva, I., Brown, B., Manzella, L., Snir, E., Almabrazi, H., Scheetz, T. E., Bonaldo, M. d., Casavant, T. L., Soares, M. B., Ruby, E. G. & McFall-Ngai, M. J. (2008). Effects of colonization, luminescence, and autoinducer on host transcription during development of the squid-vibrio association. Proc Natl Acad Sci U S A, 105(32), 11323-8. PMID: 18682555.

O'Leary, B. M., Davis, S. G., Smith, M. F., Brown, B., Kemp, M. B., Almabrazi, H., Grundstad, J. A., Burns, T., Leontiev, V., Andorf, J., Clark, A. F., Sheffield, V. C., Casavant, T. L., Scheetz, T. E., Stone, E. M. & Braun, T. A. (2007). Transcript annotation prioritization and screening system (TrAPSS) for mutation screening. Journal of bioinformatics and computational biology, 5(6), 1155-1172. PMID: 18172923.

Kang, Y., Moressi, C. J., Scheetz, T. E., Xie, L., Tran, D. T., Casavant, T. L., Ak, P., Benham, C. J., Davidson, B. L. & McCray, P. B. (2006). Integration site choice of a feline immunodeficiency virus vector. J Virol, 80(17), 8820-3. PMID: 16912328.

Bischof, J. M., Chiang, A. P., Scheetz, T. E., Stone, E. M., Casavant, T. L., Sheffield, V. C. & Braun, T. A. (2006). Genome-wide identification of pseudogenes capable of disease-causing gene conversion. Hum Mutat, 27(6), 545-52. PMID: 16671097.

Chun, C. K., Scheetz, T. E., Bonaldo, M. d., Brown, B., Clemens, A., Crookes-Goodson, W. J., Crouch, K., DeMartini, T., Eyestone, M., Goodson, M. S., Janssens, B., Kimbell, J. L., Koropatnick, T. A., Kucaba, T., Smith, C., Stewart, J. J., Tong, D., Troll, J. V., Webster, S., Winhall-Rice, J., Yap, C., Casavant, T. L., McFall-Ngai, M. J. & Soares, M. B. (2006). An annotated cDNA library of juvenile Euprymna scolopes with and without colonization by the symbiont Vibrio fischeri. BMC Genomics, 7, 154. PMID: 16780587.

Kalari, K. R., Casavant, M., Bair, T. B., Keen, H. L., Comeron, J. M., Casavant, T. L. & Scheetz, T. E. (2006). First exons and introns--a survey of GC content and gene structure in the human genome. In silico biology, 6(3), 237-242. PMID: 16922687.

Goodson, M. S., Kojadinovic, M., Troll, J. V., Scheetz, T. E., Casavant, T. L., Soares, M. B. & McFall-Ngai, M. J. (2005). Identifying components of the NF-kappaB pathway in the beneficial Euprymna scolopes-Vibrio fischeri light organ symbiosis. Appl Environ Microbiol, 71(11), 6934-46. PMID: 16269728.

Sibenaller, Z. A., Etame, A. B., Ali, M. M., Barua, M., Braun, T. A., Casavant, T. L. & Ryken, T. C. (2005). Genetic characterization of commonly used glioma cell lines in the rat animal model system. Neurosurgical focus, 19(4), E1. PMID: 16241103.

Zabner, J., Scheetz, T. E., Almabrazi, H. G., Casavant, T. L., Huang, J., Keshavjee, S. & McCray, P. B. (2005). CFTR DeltaF508 mutation has minimal effect on the gene expression profile of differentiated human airway epithelia. Am J Physiol Lung Cell Mol Physiol, 289(4), L545-53. PMID: 15937068.

Shrout, J. D., Scheetz, T. E., Casavant, T. L. & Parkin, G. F. (2005). Isolation and characterization of autotrophic, hydrogen-utilizing, perchlorate-reducing bacteria. Appl Microbiol Biotechnol, 67(2), 261-8. PMID: 15834721.

Hackett, J. D., Scheetz, T. E., Yoon, H. S., Soares, M. B., Bonaldo, M. F., Casavant, T. L. & Bhattacharya, D. (2005). Insights into a dinoflagellate genome through expressed sequence tag analysis. BMC Genomics, 6, 80. PMID: 15921535.

Bonaldo, M. F., Bair, T. B., Scheetz, T. E., Snir, E., Akabogu, I., Bair, J. L., Berger, B., Crouch, K., Davis, A., Eyestone, M. E., Keppel, C., Kucaba, T. A., Lebeck, M., Lin, J. L., de Melo, A. I., Rehmann, J., Reiter, R. S., Schaefer, K., Smith, C., Tack, D., Trout, K., Sheffield, V. C., Lin, J. J., Casavant, T. L. & Soares, M. B. (2004). 1274 full-open reading frames of transcripts expressed in the developing mouse nervous system. Genome Res, 14(10B), 2053-63. PMID: 15489326.

Stone, E. M., Braun, T. A., Russell, S. R., Kuehn, M. H., Lotery, A. J., Moore, P. A., Eastman, C. G., Casavant, T. L. & Sheffield, V. C. (2004). Missense variations in the fibulin 5 gene and age-related macular degeneration. N Engl J Med, 351(4), 346-53. PMID: 15269314.

Zhao, S. H., Simmons, D. G., Cross, J. C., Scheetz, T. E., Casavant, T. L., Soares, M. B. & Tuggle, C. K. (2004). PLET1 (C11orf34), a highly expressed and processed novel gene in pig and mouse placenta, is transcribed but poorly spliced in human. Genomics, 84(1), 114-25. PMID: 15203209.

Keen, H. L., Ryan, M. J., Beyer, A., Mathur, S., Scheetz, T. E., Gackle, B. D., Faraci, F. M., Casavant, T. L. & Sigmund, C. D. (2004). Gene expression profiling of potential PPARgamma target genes in mouse aorta. Physiol Genomics, 18(1), 33-42. PMID: 15054141.

Laffin, J. J., Scheetz, T. E., Bonaldo, M. d., Reiter, R. S., Chang, S., Eyestone, M., Abdulkawy, H., Brown, B., Roberts, C., Tack, D., Kucaba, T., Lin, J. J., Sheffield, V. C., Casavant, T. L. & Soares, M. B. (2004). A comprehensive nonredundant expressed sequence tag collection for the developing Rattus norvegicus heart. Physiol Genomics, 17(2), 245-52. PMID: 14762174.

Kwitek, A. E., Gullings-Handley, J., Yu, J., Carlos, D. C., Orlebeke, K., Nie, J., Eckert, J., Lemke, A., Andrae, J. W., Bromberg, S., Pasko, D., Chen, D., Scheetz, T. E., Casavant, T. L., Soares, M. B., Sheffield, V. C., Tonellato, P. J. & Jacob, H. J. (2004). High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence. Genome Res, 14(4), 750-7. PMID: 15060019.

Scheetz, T. E., Zabner, J., Welsh, M. J., Coco, J., Eyestone, M. d., Bonaldo, M., Kucaba, T., Casavant, T. L., Soares, M. B. & McCray, P. B. (2004). Large-scale gene discovery in human airway epithelia reveals novel transcripts. Physiol Genomics, 17(1), 69-77. PMID: 14701920.

Tuggle, C. K., Green, J. A., Fitzsimmons, C., Woods, R., Prather, R. S., Malchenko, S., Soares, B. M., Kucaba, T., Crouch, K., Smith, C., Tack, D., Robinson, N., O'Leary, B., Scheetz, T. E., Casavant, T. L., Pomp, D., Edeal, B. J., Zhang, Y., Rothschild, M. F., Garwood, K. & Beavis, W. (2003). EST-based gene discovery in pig: virtual expression patterns and comparative mapping to human. Mamm Genome, 14(8), 565-79. PMID: 12925889.

Scheetz, T. E., Trivedi, N., Roberts, C. A., Kucaba, T., Berger, B., Robinson, N. L., Birkett, C. L., Gavin, A. J., O'Leary, B., Braun, T. A., Bonaldo, M. F., Robinson, J. P., Sheffield, V. C., Soares, M. B. & Casavant, T. L. (2003). ESTprep: preprocessing cDNA sequence reads. Bioinformatics, 19(11), 1318-24. PMID: 12874042.

Scheetz, T. E., Bartlett, J. A., Walters, J. D., Schutte, B. C., Casavant, T. L. & McCray, P. B. (2002). Genomics-based approaches to gene discovery in innate immunity. Immunol Rev, 190, 137-45. PMID: 12493011.

Morcuende, J. A., Huang, X. D., Stevens, J., Kucaba, T. A., Brown, B., Abdulkawy, H., Scheetz, T. E., Malchenko, S., Bonaldo, F., Casavant, T. L. & Soares, B. (2002). Identification and initial characterization of 6,000 expressed sequenced tags (ESTs) from rat normal-growing cartilage and swarm rat chondrosarcoma cDNA libraries. Iowa Orthop J, 22, 28-34. PMID: 12180607.