Todd E. Scheetz, MS, PhD

Portrait
The Roy J. Carver, Jr. Chair in Bioinformatics and Computational Biology
Professor of Ophthalmology and Visual Sciences
Professor of Biomedical Engineering (BME)

Contact Information

Primary Office: 5015 SC
Iowa City, IA 52242
319-335-6054

Education

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

Education/Training Program Affiliations

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

Center, Program and Institute Affiliations

Center for Bioinformatics and Computational Biology, Holden Comprehensive Cancer Center, Institute for Vision Research, Iowa Institute for Biomedical Imaging, Iowa Institute of Human Genetics., John and Marcia Carver Nonprofit Genetic Testing Laboratory

Research Summary

I am a trained bioinformaticist and geneticist. A major focus of my lab is the utilization and analysis of next-generation sequencing technology. We have identified two novel disease-causing genes to date, and are currently pursing validation in several additional families. I have a broad background in bioinformatics, with specific training and expertise in genetics and genomics. My PhD research focused on the large-scale gene discovery and mapping project in rat. Since then, my research projects have focused on genome-scale analysis of sequences and expression data

Publications

DeLuca, A. P., Alward, W. L., Liebmann, J., Ritch, R., Kawase, K., Kwon, Y. H., Robin, A. L., Stone, E. M., Scheetz, T. E. & Fingert, J. H. (2017). Genomic Organization of TBK1 Copy Number Variations in Glaucoma Patients. Journal of glaucoma, 26(12), 1063-1067. PMID: 28984711.

Morris, S. M., Davison, J., Carter, K. T., O'Leary, R. M., Trobridge, P., Knoblaugh, S. E., Myeroff, L. L., Markowitz, S. D., Brett, B. T., Scheetz, T. E., Dupuy, A. J., Starr, T. K. & Grady, W. M. (2017). Transposon mutagenesis identifies candidate genes that cooperate with loss of transforming growth factor-beta signaling in mouse intestinal neoplasms. International journal of cancer, 140(4), 853-863. PMID: 27790711.

Chirco, K. R., Lewis, C. J., Scheetz, T. E., Johnston, R. M., Tucker, B. A., Stone, E. M., Fingert, J. H. & Mullins, R. F. (In Press). Evaluation of sFLT1 protein levels in human eyes with the FLT1 rs9943922 polymorphism. Ophthalmic genetics. PMID: 28949775.

Simpson, A., Avdic, A., Roos, B. R., DeLuca, A., Miller, K., Schnieders, M. J., Scheetz, T. E., Alward, W. L. & Fingert, J. H. (2017). LADD syndrome with glaucoma is caused by a novel gene. Molecular vision, 23, 179-184. PMID: 28400699.

Stone, E. M., Andorf, J. L., Whitmore, S. S., DeLuca, A. P., Giacalone, J. C., Streb, L. M., Braun, T. A., Mullins, R. F., Scheetz, T. E., Sheffield, V. C. & Tucker, B. A. (2017). Clinically Focused Molecular Investigation of 1000 Consecutive Families with Inherited Retinal Disease. Ophthalmology, 124(9), 1314-1331. PMID: 28559085.

Hedberg-Buenz, A., Christopher, M. A., Lewis, C. J., Fernandes, K. A., Dutca, L. M., Wang, K., Scheetz, T. E., Abràmoff, M. D., Libby, R. T., Garvin, M. K. & Anderson, M. G. (2016). Quantitative measurement of retinal ganglion cell populations via histology-based random forest classification. Experimental eye research, 146, 370-85. PMID: 26474494.

Kuehn, M. H., Lipsett, K. A., Menotti-Raymond, M., Whitmore, S. S., Scheetz, T. E., David, V. A., O'Brien, S. J., Zhao, Z., Jens, J. K., Snella, E. M., Ellinwood, N. M. & McLellan, G. J. (2016). A Mutation in LTBP2 Causes Congenital Glaucoma in Domestic Cats (Felis catus). PLoS One, 11(5), e0154412. PMID: 27149523.

Hedberg-Buenz, A., Christopher, M. A., Lewis, C. J., Meyer, K. J., Rudd, D. S., Dutca, L. M., Wang, K., Garvin, M. K., Scheetz, T. E., Abràmoff, M. D., Harper, M. M. & Anderson, M. G. (2016). RetFM-J, an ImageJ-based module for automated counting and quantifying features of nuclei in retinal whole-mounts. Experimental eye research, 146, 386-92. PMID: 26283021.

Small, K. W., DeLuca, A. P., Whitmore, S. S., Rosenberg, T., Silva-Garcia, R., Udar, N., Puech, B., Garcia, C. A., Rice, T. A., Fishman, G. A., Héon, E., Folk, J. C., Streb, L. M., Haas, C. M., Wiley, L. A., Scheetz, T. E., Fingert, J. H., Mullins, R. F., Tucker, B. A. & Stone, E. M. (2016). North Carolina Macular Dystrophy Is Caused by Dysregulation of the Retinal Transcription Factor PRDM13. Ophthalmology, 123(1), 9-18. PMID: 26507665.

Zeng, S., Whitmore, S. S., Sohn, E. H., Riker, M. J., Wiley, L. A., Scheetz, T. E., Stone, E. M., Tucker, B. A. & Mullins, R. F. (2016). Molecular response of chorioretinal endothelial cells to complement injury: implications for macular degeneration. The Journal of pathology, 238(3), 446-56. PMID: 26564985.

Priest, J. R., Osoegawa, K., Mohammed, N., Nanda, V., Kundu, R., Schultz, K., Lammer, E. J., Girirajan, S., Scheetz, T., Waggott, D., Haddad, F., Reddy, S., Bernstein, D., Burns, T., Steimle, J. D., Yang, X. H., Moskowitz, I. P., Hurles, M., Lifton, R. P., Nickerson, D., Bamshad, M., Eichler, E. E., Mital, S., Sheffield, V., Quertermous, T., Gelb, B. D., Portman, M. & Ashley, E. A. (2016). De Novo and Rare Variants at Multiple Loci Support the Oligogenic Origins of Atrioventricular Septal Heart Defects. PLoS genetics, 12(4), e1005963. PMID: 27058611.

Zarei, K., Scheetz, T. E., Christopher, M., Miller, K., Hedberg-Buenz, A., Tandon, A., Anderson, M. G., Fingert, J. H. & Abràmoff, M. D. (2016). Automated Axon Counting in Rodent Optic Nerve Sections with AxonJ. Scientific reports, 6, 26559. PMID: 27226405.

DeLuca, A. P., Whitmore, S. S., Barnes, J., Sharma, T. P., Westfall, T. A., Scott, C. A., Weed, M. C., Wiley, J. S., Wiley, L. A., Johnston, R. M., Schnieders, M. J., Lentz, S. R., Tucker, B. A., Mullins, R. F., Scheetz, T. E., Stone, E. M. & Slusarski, D. C. (2016). Hypomorphic mutations in TRNT1 cause retinitis pigmentosa with erythrocytic microcytosis. Human molecular genetics, 25(1), 44-56. PMID: 26494905.

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. The Annals of otology, rhinology, and laryngology, 125(5), 361-8. PMID: 26530094.

Scheetz, T. E., Roos, B. R., Solivan-Timpe, F., Miller, K., DeLuca, A. P., Stone, E. M., Kwon, Y. H., Alward, W. L., Wang, K. & Fingert, J. H. (2016). SQSTM1 Mutations and Glaucoma. PloS one, 11(6), e0156001. PMID: 27275741.

Scheetz, T. E., Faga, B., Ortega, L., Roos, B. R., Gordon, M. O., Kass, M. A., Wang, K. & Fingert, J. H. (2016). Glaucoma Risk Alleles in the Ocular Hypertension Treatment Study. Ophthalmology, 123(12), 2527-2536. PMID: 27707548.

Gaynor, S. C., Breen, M. E., Monson, E. T., de Klerk, K., Parsons, M., DeLuca, A. P., Scheetz, T. E., Zandi, P. P., Potash, J. B. & Willour, V. L. (2016). A targeted sequencing study of glutamatergic candidate genes in suicide attempters with bipolar disorder. American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics, 171(8), 1080-1087. PMID: 27480506.

Zarei, K., Scheetz, T. E., Christopher, M., Miller, K., Hedberg-Buenz, A., Tandon, A., Anderson, M. G., Fingert, J. H. & Abràmoff, M. D. (2016). Corrigendum: Automated Axon Counting in Rodent Optic Nerve Sections with AxonJ. Scientific reports, 6, 34124. PMID: 27759018.

Kuehn, M. H., Lipsett, K. A., Menotti-Raymond, M., Whitmore, S. S., Scheetz, T. E., David, V. A., O'Brien, S. J., Zhao, Z., Jens, J. K., Snella, E. M., Ellinwood, N. M. & McLellan, G. J. (2016). Correction: A Mutation in LTBP2 Causes Congenital Glaucoma in Domestic Cats (Felis catus). PloS one, 11(8), e0161517. PMID: 27537365.

Fingert, J. H., Robin, A. L., Scheetz, T. E., Kwon, Y. H., Liebmann, J. M., Ritch, R. & Alward, W. L. (2016). Tank-Binding Kinase 1 (TBK1) Gene and Open-Angle Glaucomas (An American Ophthalmological Society Thesis). Transactions of the American Ophthalmological Society, 114, T6. PMID: 27881886.

Reish, O., Aspit, L., Zouella, A., Roth, Y., Polak-Charcon, S., Baboushkin, T., Benyamini, L., Scheetz, T. E., Mussaffi, H., Sheffield, V. C. & Parvari, R. (2016). A Homozygous Nme7 Mutation Is Associated with Situs Inversus Totalis. Human mutation, 37(8), 727-31. PMID: 27060491.

Ephraim, S. S., Anand, N., DeLuca, A. P., Taylor, K. R., Kolbe, D. L., Simpson, A. C., Azaiez, H., Sloan, C. M., Shearer, A. E., Hallier, A. R., Casavant, T. L., Scheetz, T. E., Smith, R. J. & Braun, T. A. (2014). Cordova: Web-based management of genetic variation data. Bioinformatics. PMID: 25123904.

Shearer, A. E., Eppsteiner, R. W., Booth, K. T., Ephraim, S. S., Gurrola, J., Simpson, A., Black-Ziegelbein, E. A., Joshi, S., Ravi, H., Gluffre, A. C., Happe, S., Hildebrand, M. S., Azaiez, H., Bayazit, Y. A., Erdal, M. E., Lopex-Escamez, J. A., Gazquez, I., Tamayo, M. L., Gelvez, N. Y., Leal, G. L., Jalas, C., Ekstein, J., Yang, T., Usami, S., Kahrizi, K., Bazazzadegan, N., Najmabadi, H., Scheetz, T. E., Braun, T. A., Casavant, T. L., LeProust, E. M. & Smith, R. (2014). Utilizing Ethnic-Specific Differences in Minor Allele Frequency to Recategorize Reported Pathogenic Deafness Variants. The American Journal of Human Genetics. PMID: 25262649.

Brownstein, C. A., 71 Intervening authors, Scheetz, T. E. & et al (2014). An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge. Genome Biology, 15(3), R53. PMID: 24667040.

Christopher, M., Tang, L., Fingert, J. H., Scheetz, T. E. & Abramoff, M. D. (2014). Automated discovery of structural features of the optic nerve head on the basis of image and genetic data. Proc SPIE, 9035, 90350S. DOI: 10.1117/12.2043798.

Novak, C. L., Christopher, M., Tang, L., Fingert, J. H., Scheetz, T. E., Abramoff, M. D. & Alyward, S. (2013). Changes in quantitative 3D shape features of the optic nerve head associated with age. DOI: doi: 10.1117/12.2006908.

Taylor, K. R., Deluca, A. P., Shearer, A. E., Hildebrand, M. S., Black-Ziegelbein, E. A., Anand, V. N., Sloan, C. M., 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. Hum Mutat, 34(4), 539-45. PMID: 23280582.

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), 738-43. PMID: 23668349.

Muhammad, E., Reish, O., Ohno, Y., Scheetz, T., Deluca, A., Searby, C., Regev, M., Benyamini, L., Fellig, Y., Kihara, A., Sheffield, V. C. & Parvari, R. (2013). Congenital myopathy is caused by mutation of HACD1. Hum Mol Genet, 22(25), 5229-36. PMID: 23933735.

Wagner, A. H., Anand, N., Wang, W. H., Chatterton, J. E., Sun, D., Shepard, A., Jacobson, N., Pang, I. H., Deluca, A., Casavant, T. L., Scheetz, T. E., Mullins, R., Braun, T. A. & Clark, A. F. (2013). Exon-level expression profiling of ocular tissues. Exp Eye Res, 111, 105-11. PMID: 23500522.

Whitmore, S. S., Braun, T. A., Skeie, J. M., Haas, C. M., Sohn, E. H., Stone, E. M., Scheetz, T. E. & Mullins, R. F. (2013). Altered gene expression in dry age-related macular degeneration suggests early loss of choroidal endothelial cells. Mol Vis, 19, 2274-97. PMID: 24265543.

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.

Riordan, J. D., Keng, V. W., Tschida, B. R., Scheetz, T. E., Bell, J. B., Podertz-Pedersen, K. M., Moser, C. D., Copeland, N. G., Jenkins, N. A., Roberts, L. R., Largaespada, D. A. & Dupuy, A. J. (2013). Identification of rtl1, a retrotransposon-derived imprinted gene, as a novel driver of hepatocarcinogenesis. PLoS Genetics, 9(4), e1003441. PMID: 23593033.

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), 853-9. PMID: 23508994.

Christopher, M., Scheetz, T. E., Mullins, R. F. & Abràmoff, M. D. (2013). Selection of phototransduction genes in Homo sapiens. Invest Ophthalmol Vis Sci, 54(8), 5489-96. PMID: 23868983.

Hu, Q., Garvin, M. K., Christopher, M. A., Xu, X., Scheetz, T. E. & Abramoff, M. D. (2013). Optimal filter approach for the detection of vessel bifurcations in color fundus images. DOI: doi: 10.1117/12.2007088.

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), 627-34. PMID: 23804846.

Mann, K. M., Ward, J. M., Yew, C. C., Kovochich, A., Dawson, D. W., Black, M. A., Brett, B. T., Scheetz, T. E., Dupuy, A. J., Chang, D. K., Biankin, A. V., Waddell, N., Kassahn, K. S., Grimmond, S. M., Rust, A. G., Adams, D. G., Jenkins, N. A. & Copeland, N. G. (2012). Sleeping Beauty mutagenesis reveals cooperating mutations and pathways in pancreatic adenocarcinoma. (Vols. 109). (16), pp. 5934-5941. Proc Natl Acad Sci U S A. DOI: 10.1073/pnas.1202490109.

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. The Iowa Orthopaedic Journal, 32, 46-53. PMID: 23576921.

Eppsteiner, R. W., Shearer, A. E., Hildebrand, M. S., Taylor, K. R., Deluca, A. P., Scherer, S., Huygen, P., Scheetz, T. E., Braun, T. A., Casavant, T. L. & Smith, R. J. (2012). Using the Phenome and Genome to Improve Genetic Diagnosis for Deafness. Otolaryngol Head Neck Surg, 147(5), 975-7. PMID: 22785243.

Huang, Y. Z., Hernandez, F. J., Gu, B., Stockdale, K. R., Nanapaneni, K., Scheetz, T. E., Behlke, M. A., Peek, A. S., Bair, T., Giangrande, P. H. & McNamara 2nd, J. O. (2012). RNA Aptamer-Based Functional Ligands of the Neurotrophin Receptor, TrkB. Mol Pharmacol, 82(4), 623-35. PMID: 22752556.

Christopher, M., Moga, D. C., Russell, S. R., Folk, J. C., Scheetz, T. & Abramoff, M. D. (2012). Validation of tablet-based evaluation of color fundus images. Retina, 32(8), 1629-35. PMID: 22495326.

Burnight, E. R., Staber, J. M., Korsakov, P., Li, X., Brett, B. T., Scheetz, T. E., Craig, N. L. & McCray Jr, P. B. (2012). A Hyperactive Transposase Promotes Persistent Gene Transfer of a piggyBac DNA Transposon. Molecular Therapy Nucleic acids, 1, e50. PMID: 23344650.

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, 29(1-2), 51-8. PMID: 22975204.

Fingert, J. H., Roos, B. R., Solivan-Timpe, F., Miller, K. A., Oetting, T. A., Wang, K., Kwon, Y. H., Scheetz, T. E., Stone, E. M. & Alward, W. L. (2012). Analysis of ASB10 variants in open angle glaucoma. Hum Mol Genet, 21(20), 4543-8. PMID: 22798626.

Wu, X., Northcott, P. A., Dubuc, A., Dupuy, A. J., Shih, D. J., Witt, H., Croul, S., Bouffet, E., Fults, D. W., Eberhart, C. G., Garzia, L., Van Meter, T., Zagzag, D., Jabado, N., Schwartzentruber, J., Majewski, J., Scheetz, T. E., Pfister, S. M., Korshunov, A., Li, X. N., Scherer, S. W., Cho, Y. J., Akagi, K., MacDonald, T. J., Koster, J., McCabe, M. G., Sarver, A. L., Collins, V. P., Weiss, W. A., Largaespada, D. A., Collier, L. S. & Taylor, M. D. (2012). Clonal selection drives genetic divergence of metastatic medulloblastoma [letter]. Nature, 482(7386), 529-33. PMID: 22343890.

Quellec, G., Russell, S. R., Scheetz, T. E., Stone, E. M. & Abràmoff, M. D. (2011). Computational Quantification of Complex Fundus Phenotypes in Age-Related Macular Degeneration and Stargardt Disease. Invest Ophthalmol Vis Sci, 52(6), 2976-2981. PMID: 21310908.

Davis, L. K., Meyer, K. J., Schindler, E. I., Beck, J. S., Rudd, D. S., Grundstad, A. J., Scheetz, T. E., Braun, T. A., Fingert, J. H., Alward, W. L., Kwon, Y. H., Folk, J. C., Russell, S. R., Wassink, T. H., Sheffield, V. C. & Stone, E. M. (2011). Copy number variations and primary open-angle glaucoma. Invest Ophthalmol Vis Sci, 52(10), 7122-33. PMID: 21310917.

Meyer, K. J., Davis, L. K., Schindler, E. I., Beck, J. S., Rudd, D. S., Grundstad, A. J., Scheetz, T. E., Braun, T. A., Fingert, J. H., Alward, W. L., Kwon, Y. H., Folk, J. C., Russell, S. R., Wassink, T. H., Stone, E. M. & Sheffield, V. C. (2011). Genome-wide analysis of copy number variants in age-related macular degeneration. Hum Genet, 129(1), 91-100. PMID: 20981449.

Tucker, B. A., Scheetz, T. E., Mullins, R. F., Deluca, A. P., Hoffmann, J. M., Johnston, R. M., Jacobson, S. G., Sheffield, V. C. & Stone, E. M. (2011). Exome sequencing and analysis of induced pluripotent stem cells identify the cilia-related gene male germ cell-associated kinase (MAK) as a cause of retinitis pigmentosa. Proc Natl Acad Sci USA, 108(34), E569-76. PMID: 21825139.

McGrail, M., Hatler, J. M., Kuang, X., Liao, H. K., Nannapaneni, K., Watt, K. E., Uhl, J. D., Largaespada, D. A., Vollbrecht, E., Scheetz, T. E., Dupuy, A. J., Hostetter, J. M. & Essner, J. J. (2011). Somatic mutagenesis with a Sleeping Beauty transposon system leads to solid tumor formation in zebrafish. PLoS One, 6(4), e18826. PMID: 21533036.

DeLuca, A. P., Wagner, A. H., Taylor, K. R., Faga, B., Thole, D., Sheffield, V. C., Stone, E. M., Casavant, T. L., Scheetz, T. E., Braun, T. A., DeLuca, A. P., Wagner, A. H., Taylor, K. R., Faga, B., Thole, D., Sheffield, V. C., Stone, E. M., Casavant, T. L., Scheetz, T. E., Braun, T. A. (Eds.) (2011). Sequencing and disease variation detection tools and techniques. In 9th ACS/IEEE International Conference on Computer Systems and Applications, AICCSA 2011, December 27, 2011 - December 30, 2011. Sharm El-Sheikh, Egypt: IEEE Computer Society.

Berquam-Vrieze, K. E., Nannanpaneni, K., Brett, B. T., Holmfeldt, L., Ma, J., Zagorodna, O., Jenkins, N. A., Copeland, N. G., Meyerholz, D. K., Knudson, C. M., Mullighan, C. G., Scheetz, T. E. & Dupuy, A. J. (2011). Cell of origin strongly influences genetic selection in mouse models of T-ALL. Blood, 118(17), 4646-56. PMID: 21828136.

Taylor, K. R., DeLuca, A. P., Goodman, C. W., Tompkins, B. W., Scheetz, T. E., Hildebrand, M. S., Huygen, P. L., Smith, R. J., Braun, T. A., Casavant, T. L., Taylor, K. R., DeLuca, A. P., Goodman, C. W., Tompkins, B. W., Scheetz, T. E., Hildebrand, M. S., Huygen, P. L., Smith, R. J., Braun, T. A., Casavant, T. L. (Eds.) (2011). AudioGene: Computer-based prediction of genetic factors involved in non-syndromic hearing impairment. In 9th ACS/IEEE International Conference on Computer Systems and Applications, AICCSA 2011, December 27, 2011 - December 30, 2011. Sharm El-Sheikh, Egypt: IEEE Computer Society.

Quellec, G., Russell, S. R., Seddon, J. M., Reynolds, R., Scheetz, T., Mahajan, V. B., Stone, E. M. & Abramoff, M. D. (2011). Automated discovery and quanitification of image-based complex phenotypes: a twin study of drusen phenotypes in age-related macular degeneration. Invest Ophthalmol Vis Sci, 52(12), 9195-9206. PMID: 22039249.

Stone, E. M., Cideciyan, A. V., Aleman, T. S., Scheetz, T. E., Sumaroka, A., Ehlinger, M. A., Schwartz, S. B., Fishman, G. A., Traboulsi, E. I., Lam, B. L., Fulton, A. B., Mullins, R. F., Sheffield, V. C. & Jacobson, S. G. (2011). Variations in NPHP5 in patients with nonsyndromic leber congenital amaurosis and Senior-Loken syndrome. Arch Ophthalmol, 129(1), 81-7. PMID: 21220633.

Ramachandran, S., Clarke, L. A., Scheetz, T. E., Amaral, M. D. & McCray, P. B. (2011). Microarray mRNA expression profiling to study cystic fibrosis. Methods Mol Biol, 742, 193-212. PMID: 21547734.

Fingert, J. H., Robin, A. l., Stone, J. L., Roos, B. R., Davis, L. K., Scheetz, T. E., Bennett, S. R., Wassink, T. H., Kwon, Y. H., Alward, A. L., Mullins, R. F., Sheffield, V. C. & Stone, E. M. (2011). Copy number variations on chromosome 12q14 in patients with normal tension glaucoma. Hum Mol Genet, 20(12), 2482-94. PMID: 21447600.

Zheng, J., Miller, K. K., Yang, T., Hildebrand, M. S., Shearer, A. E., DeLuca, A. P., Scheetz, T. E., Drummond, J., Scherer, S. E., Legan, P. K., Goodyear, R. J., Richardson, G. P., Cheatham, M. A., Smith, R. J. & Dallos, P. (2011). Carcinoembryonic antigen-related cell adhesion molecule 16 interacts with alpha-tectorin and is mutated in autosomal dominant hearing loss (DFNA4). Proc Natl Acad Sci U S A, 108(10), 4218-23. PMID: 21368133.

Brett, B. T., Berquam-Vrieze, K. E., Nannapaneni, K., Huang, J., Scheetz, T. E. & Dupuy, A. J. (2011). Novel molecular and computational methods improve the accuracy of insertion site analysis in sleeping beauty-induced tumors. PLoS One, 6(9), e24668. PMID: 21931803.

Walters, J. D., Bair, T. B., Braun, T. A., Scheetz, T. E., Robinson, J. P. & Casavant, T. L. (2011). Validation of computational prediction of horizontal gene transfer events-XenoCluster. Journal of Supercomputing, 57(2), 141-50. DOI: 10.1007/s11227-010-0386-2.

Pezzulo, A. A., Starner, T. D., Scheetz, T. E., Traver, G. L., Tilley, A. E., Harvey, B. G., Crystal, R. G., McCray, P. B. & Zabner, J. (2011). The air-liquid interface and use of primary cell cultures are important to recapitulate the transcriptional profile of in vivo airway epithelia. Am J Physiol Lung Cell Mol Physiol, 300(1), L25-31. PMID: 20971803.

Shearer, A. E., DeLuca, A. P., Hildebrand, M. S., Taylor, K. R., Gurrola, J., Scherer, S., Scheetz, T. E. & Smith, R. J. (2010). Comprehensive genetic testing for hereditary hearing loss using massively parallel sequencing. Proc Natl Acad Sci U S A, 107(49), 21104-9. PMID: 21078986.

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 Mde, F., 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 USA, 107(5), 2259-2264. PMID: 20133870.

Macagno, E. R., Gaasterland, T., Edsall, L., Bafna, V., Soares, M. B., Scheetz, T., Casavant, T., 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(1), 407. PMID: 20579359.

Rosenberg, T., Roos, B., Johnsen, T., Bech, N., Scheetz, T. E., Larsen, M., Stone, E. M. & Fingert, J. H. (2010). Clinical and genetic characterization of a Danish family with North Carolina macular dystrophy. Mol Vis, 16, 2659-68. PMID: 21179233.

Tang, L., Scheetz, T. E., Mackey, D. A., Hewitt, A. W., Fingert, J., Kwon, Y. H., Quellec, G., Reinhardt, J. M. & Abramoff, M. D. (2010). Automated Quantification of Inherited Phenotypes from Color Images: a Twin Study of the Variability of the Optic Nerve Head Shape. Invest Ophthalmol Vis Sci, 51(11), 5870-5877. PMID: 20505201.

Fischer, A. J., Goss, K. L., Scheetz, T. E., Wohlford-Lenane, C. L., Snyder, J. M. & McCray, P. B. (2009). Differential gene expression in human conducting airway surface epithelia and submucosal glands. Am J Respir Cell Mol Biol, 40(2), 189-99. PMID: 18703793.

Dupuy, A. J., Rogers, L. M., Kim, J., Nannapaneni, K., Starr, T. K., Liu, P., Largaespada, D. A., Scheetz, T. E., Jenkins, N. A. & Copeland, N. G. (2009). A modified sleeping beauty transposon system that can be used to model a wide variety of human cancers in mice. Cancer Res, 69(20), 8150-8156. PMID: 19808965.

Winder, A. A., Wohlford-Lenane, C., Scheetz, T. E., Nardy, B. N., Manzel, L. J., Look, D. C. & McCray, P. B. (2009). Differential effects of cytokines and corticosteroids on toll-like receptor 2 expression and activity in human airway epithelia. Respir Res, 10, 96. PMID: 19835594.

Chun, K. C., Troll, J. V., Koroleva, I., Brown, B., Manzella, L., Snir, E., Almabrazi, H., Scheetz, T. E., Bonaldo, M. F., 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 USA, 105(32), 11323-8. PMID: 18682555.

Loktev, A. V., Zhang, Q., Beck, J. S., Searby, C. C., Scheetz, T. E., Bazan, J. F., Slusarski, D. C., Sheffield, V. C., Jackson, P. K. & Nachury, M. V. (2008). A BBSome subunit links ciliogenesis, microtubule stability, and acetylation. Dev Cell, 15(6), 854-65. PMID: 19081074.

Fingert, J. H., Oh, K., Chung, M., Scheetz, T. E., Andorf, J. L., Johnson, R. M., Sheffield, V. C. & Stone, E. M. (2008). Association of a Novel Mutation in the Retinol Dehydrogenase 12 (RDH12) Gene With Autosomal Dominant Retinitis Pigmentosa. Arch Ophthalmol, 126(9), 1301-7. PMID: 18779497.

Kalari, K. R., Casavant, T. L. & Scheetz, T. E. (2008). A knowledge-based approach to predict intragenic deletions or duplications. Bioinformatics, 24(18), 1975-9. PMID: 18647756.

O'Leary, B. M., Davis, S. G., Smith, M. F., Brown, B., Kemp, M. B., Almabrazi, H., Grundstad, A. J., Burns, T., Andorf, J., Leontiev, V., Clark, A. F., Sheffield, V. C., Casavant, T. L., Scheetz, T. E., Stone, E. M. & Braun, T. A. (2007). Transcript Annotation Prioritization Screening System (TrAPSS) for Mutation Screening. Journal of Bioinformatics and Computational Biology, 5(6), 1155-1172. DOI: 10.1142/S0219720007003132.

Thomas, G., Grassi, M. A., Lee, J. R., Edwards, A. O., Gorin, M. B., Klein, R., Casavant, T. L., Scheetz, T. E., Stone, E. M. & Williams, A. B. (2007). IDOCS: Intelligent Distributed Ontology Consensus System – The Use of Machine Learning in Retinal Drusen Phenotyping. Invest Ophthalmol Vis Sci, 48, 2278-2284.

Ben-Shahar, Y., Nannapaneni, K., Casavant, T. L., Scheetz, T. E. & Welsh, M. J. (2007). Eukaryotic operon-like transcription of functionally related genes in Drosophila. Proc Natl Acad Sci U S A, 104(1), 222-7. PMID: 17190802.

Grassi, M. A., Folk, J. C., Scheetz, T. E., Taylor, C. M., Sheffield, V. C. & Stone, E. M. (2007). Complement Factor H Polymorphism p.Tyr402His and Cuticular Drusen. Arch Ophthalmol, 125, 93-97. PMID: 17210858.

Chun, C. K., Scheetz, T. E., Bonaldo, M. F., 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 Biol, 6(3), 237-42. PMID: 16922687.

Scheetz, T. E., Kim, K., Swiderski, R. E., Philp, A. R., Braun, T. A., Knudtson, K. L., Dorrance, A. M., DiBona, G. F., Huang, J., Casavant, T. L., Sheffield, V. C. & Stone, E. M. (2006). Regulation of Gene Expression in the Mammalian Eye and its Relevance to Eye Disease. Proc Natl Acad Sci USA, 103(39), 14429-34. PMID: 16983098.

Chiang, A. P., Beck, J. S., Yen, H., Tayeh, M. K., Scheetz, T. E., Swiderski, R. E., Nishimura, D. Y., Braun, T. A., Kim, K., Huan, J., Elbedour, K., Carmi, R., Slusarski, D. C., Casavant, T. L., Stone, E. M. & Sheffield, V. C. (2006). Homozygosity mapping with SNP arrays identifies TRIM32, an E3 ubiquitin ligase, as a Bardet-Biedl syndrom gene (BBS11). Proc Natl Acad Sci USA, 103(16), 6287-6298. PMID: 16606853.

Braun, T. A., Shankar, S. P., Davis, S., O'Leary, B., Scheetz, T. E., Sheffield, V. C., Casavant, T. L. & Stone, E. M. (2006). Prioritizing Regions of Candidate Genes for Efficient Mutation Screening. Hum Mutat, 27(2), 195-200. PMID: 16395665.

Bischoff, J. B., Chiang, A. P., Scheetz, T. E., Stone, E. M., Casavant, T. L., Sheffield, T. L. & Braun, T. A. (2006). Genome-Wide Identification of Pseudogenes Capable of Disease-Causing Gene Conversion. Human Mutation, 27(6), 542-552. PMID: 16671097.

Grassi, M. A., Fingert, J. H., Scheetz, T. E., Roos, B. R., Ritch, R., West, S. K., Kawase, K., Shire, A. M., Mullins, R. F. & Stone, E. M. (2006). Ethnic Variation in AMD-Associated Complement Factor H Polymorphism p.Tyr402His. Hum Mutat, 27(9), 921-925. PMID: 16865697.

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 Jr, P. B. (2006). Integration Site Choice of a Feline Immunodeficiency Virus Vector. J Virol, 80(17), 8820-8823. PMID: 16912328.

Zabner, J., Scheetz, T. E., Almabrazi, H. G., Casavant, T. L., Huang, J., Keshavjee, S. & McCray Jr, P. B. (2005). The CFTR ?508 mutation has minimal effect on the gene expression profile of differentiated human airway epithelia. Am J Physiol Lung Cell Mol Physiol, 289(4), L545-L553.

Walters, J. D., Casavant, T. L., Robinson, J. P., Bair, T. B., Braun, T. A. & Scheetz, T. E. (2005). XenoCluster: A Grid Computing Approach to Finding Ancient Evolutionary Genetic Anomalies. Lecture Notes in Computer Science, 3603, 355.

Shrout, J. D., Scheetz, T. E., Casavant, T. L. & Parkin, G. F. (2005). Isolation and characterization of autotrophic, hydrogen-utilizing, perchlorate-reducing bacteria. Applied Microbial and Cell Physiology, 67, 261-268. PMID: 15834721.

Scheetz, T. E., Trivedi, N., Pedretti, K. T., Braun, T. A. & Casavant, T. L. (2005). Gene transcript clustering: a comparison of parallel approaches. Future Generation Computer Systems, 21(5), 731-735. DOI: 10.1016/j.future.2004.05.014.

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-?B Pathway in the Beneficial Euprymna scolopes-Vibrio fischeri Light Organ Symbiosis. Applied and Environmental Microbiology, 71(11), 6934-6946. PMID: 16269728.

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.

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 Research, 14, 750-757. PMID: 15060019.

Laffin, J. J., Scheetz, T. E., Bonaldo, M. F., Reiter, R., Chang, S., Eyestone, M., Abdulkawy, H., Brown, B., Roberts, C., Tack, D., Kucaba, T., Lin, J., Sheffield, V. C., Casavant, T. L. & Soares, M. B. (2004). A comprehensive nonredundant expressed sequence tag collection for the developing Rattus norvegicus heart. Physiological Genomics, 17(2), 245-252. PMID: 14762174.

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 PPARg target genes in mouse aorta. Physiological Genomics, 18(1), 33-42. PMID: 15054141.

Zhao, S., Simmons, D., Cross, J. C., Scheetz, T. E., Casavant, T. L., Soares, M. B. & Tuggle, C. K. (2004). PLET1, A highly expressed and processed novel gene in pig and mouse placenta is transcribed but poorly spliced in human. Genomics, 84, 114-125. PMID: 15203209.

Scheetz, T. E., Casavant, T. L. (2004). Informatics for Efficient EST-Based Gene Discovery in Normalized and Subtracted cDNA Libraries. In The Practical Bioinformatician. World Scientific Press.

Scheetz, T. E., Laffin, J. J., Berger, B., Mackerly, S., Baumes, S. A., Brown II, R., Chang, S., Coco, J., Conklin, J., Crouch, K., Donohue, M., Doonan, G., Estes, C., Eyestone, M., Fishler, K., Gardiner, J., Guo, L., Johnson, B., Keppel, C., Kreger, R., Lebeck, M., Marcelino, R., Miljkovich, V., Perdue, M., Qui, L., Rehmann, J., Reiter, R. S., Rhoads, B., Schaefer, K., Smith, C., Sunjevaric, I., Trout, K., Wu, N., Birkett, C. L., Bischof, J., Gackle, B., Gavin, A., Mokrzycki, B., Moressi, C., O' Leary, B., Pedretti, K., Roberts, C., Smith, M., Tack, D., Trivedi, N., Kucaba, T., Freeman, T., Lin, J., Bonaldo, M. F., Casavant, T. L., Sheffield, V. C. & Soares, M. B. (2004). High-throughput gene discovery in the rat. Genome Research, 14, 733-741. PMID: 15060017.

Gerhard, D. S., Wagner, L., Feingold, E. A., Shenmen, C. M., Grouse, L. H., Schuler, G., Klein, S. L., Old, S., Rasooly, R., Good, P., Guyer, M., Peck, A. M., Derge, J. G., Lipman, D., Collins, F. S., Jang, W., Sherry, S., Feolo, M., Misquitta, L., Lee, E., Rotmistrovsky, K., Greenhut, S. F., Schaefer, C. F., Buetow, K., Bonner, T. I., Haussler, D., Kent, J., Kiekhaus, M., Furey, T., Brent, M., Prange, C., Schreiber, K., Shapiro, N., Bhat, N. K., Hopkins, R. F., Hsie, F., Driscoll, T., Soares, M. B., Casavant, T. L., Scheetz, T. E., Brown-stein, M. J., Usdin, T. B., Toshiyuki, S., Carninci, P., Piao, Y., Dudekula, D. B., Ko, M. S., Kawakami, K., Suzuki, Y., Sugano, S., Gruber, C. E., Smith, M. R., Simmons, B., Moore, T., Waterman, R., Johnson, S. L., Ruan, Y., Wei, C. L., Mathavan, S., Gunaratne, P. H., Wu, J., Garcia, A. M., Hulyk, S. W., Fuh, E., Yuan, Y., Sneed, A., Kowis, C., Hodgson, A., Muzny, D. M., McPherson, J., Gibbs, R. A., Fahey, J., Helton, E., Ketteman, M., Madan, A., Rodrigues, S., Sanchez, A., Whiting, M., Madari, A., Young, A. C., Wetherby, K. D., Granite, S. J., Kwong, P. N., Brinkley, C. P., Pearson, R. L., Bouffard, G. G., Blakesly, R. W., Green, E. D., Dickson, M. C., Rodriguez, A. C., Grimwood, J., Schmutz, J., Myers, R. M., Butterfield, Y. S., Griffith, M., Griffith, O. L., Krzywinski, M. I., Liao, N., Morin, R., Morrin, R., Palmquist, D., Petrescu, A. S., Skalska, U., Smailus, D. E., Stott, J. M., Schnerch, A., Schein, J. E., Jones, S. J., Holt, R. A., Baross, A., Marra, M. A., Clifton, S., Makowski, K. A., Bosak, S. & Malek, J. (2004). The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res, 14(10B), 2121-7. PMID: 15489334.

Hackett, J. D., Yoon, H. S., Soares, M. B., Bonaldo, M. F., Casavant, T. L., Scheetz, T. E., Nosenko, T. & Bhattacharya, D. (2004). Migration of the plastid genome to the nucleus in a peridinin dinoflagellate. Curr Biol, 14(3), 213-8. PMID: 14761653.

Scheetz, T. E., Zabner, J., Welsh, M. J., Coco, J., Eyestone, M., Bonaldo, M. F., Kucaba, T., Casavant, T. L., Soares, M. B. & McCray Jr, P. B. (2004). Large Scale Gene Discovery in Human Airway Epithelia Reveals Novel Transcripts. Physiological Genomics, 17, 69-77. PMID: 14701920.

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., DeMelo, A., Rehman, J., Reiter, R. S., Schaefer, K. B., 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 Research, 14(10B), 2053-2063. PMID: 15489326.

Braun, T. A., Scheetz, T. E., Webster, G., Clark, A., Stone, E. M., Sheffield, V. C. & Casavant, T. L. (2003). Identifying candidate disease genes with high-performance computing. Journal of Supercomputing, 26, 7-24. DOI: 10.1023/A:1024417200364.

Tuggle, C. K., Green, J. A., Fitzsimmons, C., Woods, R., Prather, R. S., Malchenko, S., Soares, M. B., Kucaba, T., Crouch, K., Smith, C., Tack, D., Robinson, N., O'Leary, B., Scheetz, T., Casavant, T., Pomp, D., Edeal, J. B., Zhang, Y., Rothschild, M. F., Garwood, K. & Beavis, W. (2003). EST-Based Gene Discovery in Pig: Virtual Expression Patterns and Comparative Mapping to Human. Mammalian Genome, 14, 565-579. PMID: 12925889.

Scheetz, T. E., Trivedi, N., Roberts, C. A., Pedretti, K. T., Robinson, N. L., Birkett, C. L., Gavin, A. J., Robinson, J. P., Sheffield, V. C., Soares, M. B. & Casavant, T. L. (2003). ESTPrep: A Software System for Preprocessing cDNA Sequence Reads. Bioinformatics, 19, 1318-1324. PMID: 12874042.

Gavin, A. J., Scheetz, T. E., Roberts, C. A., O'Leary, B., Braun, T. A., Sheffield, V. C., Soares, M. B., Robinson, J. P. & Casavant, T. L. (2002). Pooled library tissue tags for EST-based gene discovery. Bioinformatics, 18(9), 1162-1166. DOI: 10.1093/bioinformatics/18.9.1162.

Scheetz, T. E., Bartlett, J. A., Walters, J. D., Shutte, B. C., Casavant, T. L. & McCray Jr, P. B. (2002). Genomics-based Approaches to Gene Discovery in Innate Immunity. Immunological Reviews, 190, 137-145. PMID: 12493011.

Trivedi, N., Bischof, J., Davis, S., Pedretti, K., Scheetz, T. E., Braun, T. A., Roberts, C. A., Robinson, N. L., Sheffield, V. C., Soares, M. B. & Casavant, T. L. (2002). Parallel Creation of Non-redundant Gene Indices from Partial mRNA Transcripts. Future Generation Computer Systems, 18(6), 863-870. DOI: 10.1016/S0167-739X(02)00059-6.

Strausberg, R. L., Feingold, E. A., Grouse, L. H., Derge, J. G., Klausner, R. D., Collins, F. S., Wagner, L., Shenmen, C. M., Schuler, G. D., Altschul, S. F., Zeeberg, B., Buetow, K. H., Schaefer, C. F., Bhat, N. K., Hopkins, R. F., Jordan, H., Moore, T., Max, S. I., Wang, J., Hsieh, F., Diatchenko, L., Marusina, K., Farmer, A. A., Rubin, G. M., Hong, L., Stapleton, M., Soares, M. B., Bonaldo, M. F., Casavant, T. L., Scheetz, T. E., Brownstein, M. J., Usdin, T. B., Toshiyuki, S., Carninci, P., Prange, C., Raha, S. S., Loquellano, N. A., Peters, G. J., Abramson, R. D., Mullahy, S. J., Bosak, S. A., McEwan, P. J., McKernan, K. J., Malek, J. A., Gunaratne, P. H., Richards, S., Worley, K. C., Hale, S., Garcia, A. M., Gay, L. J., Hulyk, S. W., Villalon, D. K., Muzny, D. M., Sodergren, E. J., Lu, X., Gibbs, R. A., Fahey, J., Helton, E., Ketteman, M., Madan, A., Rodrigues, S., Sanchez, A., Whiting, M., Madan, A., Young, A. C., Shevchenko, Y., Bouffard, G. G., Blakesley, R. W., Touchman, J. W., Green, E. D., Dickson, M. C., Rodriguez, A. C., Grimwood, J., Schmutz, J., Myers, R. M., Butterfield, Y. S., Krzywinski, M. I., Skalska, U., Smailus, D. E., Schnerch, A., Schein, J. E., Jones, S. J. & Marra, M. A. (2002). Generation and initial analysis of more than 14,000 Non-Redundant, full-length human and mouse cDNA sequences by the NIH Mammalian Gene Collection Program. Proc Natl Acad Sci U S A, 99(26), 16899-903. PMID: 12477932.

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

Braun, R. C., Pedretti, K. T., Casavant, T. L., Scheetz, T. E., Birkett, C. L. & Roberts, C. A. (2001). Parallelization of local BLAST service on workstation clusters. Future Generation Computer Systems, 17(6), 745-754. DOI: 10.1016/S0167-739X(00)00057-1.

Kucaba, T., Berger, B., Mackerly, S., Marcelino, R., Koroleva, I., Xie, H., Malchenko, S., Kasperski, J., Somani, J., Wu, N., Guo, L., Laffin, J., Chang, S., Sunjevaric, I., Donohue, M., Doonan, G., Brown, R., Smith, C., Johnson, B., Crouch, K., Kinkaid, R., Miljkovic, V., Beck, G., Gardiner, J., Roberts, C., Birkett, C., Liu, K., Bonaldo, M. D., Scheetz, T., Sheffield, V., Casavant, T. & Soares, M. B. (2001). Current status of the University of Iowa Mammalian Gene Discovery Program. Cytogenetics and Cell Genetics, 92(1-2), 46.

Casavant, T. L., Braun, T. A., Kaliannan, S., Scheetz, T. E., Munn, K. J. & Birkett, C. L. (2001). A parallel/distributed architecture for hierarchically heterogeneous web-based cooperative applications. Future Generation Computer Systems, 17(6), 783-793. DOI: 10.1016/S0167-739X(00)00104-7.

Scheetz, T. E., Raymond, M. R., Nishimura, D. Y., McClain, A., Roberts, C., Birkett, C., Gardiner, J., Zhang, J., Butters, N., Sun, C., Kwitek-Black, A., Jacob, H., Casavant, T. L., Soares, M. B. & Sheffield, V. C. (2001). Generation of a high-density rat EST map. Genome Res, 11(3), 497-502. PMID: 11230173.

Kwitek, A. E., Tonellato, P. J., Chen, D., Gullings-Handley, J., Cheng, Y. S., Twigger, S., Scheetz, T. E., Casavant, T. L., Stoll, M., Nobrega, M. A., Shiozawa, M., Soares, M. B., Sheffield, V. C. & Jacob, H. J. (2001). Automated construction of high-density comparative maps between rat, human, and mouse. Genome Research, 11(11), 1935-43. PMID: 11691858.

Pedretti, K., Casavant, T., Scheetz, T., Roberts, C., Braun, T. & Robinson, N. (2001). A Parallel Expressed Sequence Tag (EST) Clustering Program. Lecture Notes in Computer Science, 2127, 490-497. DOI: 10.1007/3-540-44743-1_51.

Dimopoulos, G., Casavant, T. L., Chang, S., Scheetz, T. E., Roberts, C., Donohue, M., Schultz, J., Benes, V., Bork, P., Ansorge, W., Soares, M. B. & Kafatos, F. C. (2000). Anopheles gambiae pilot gene discovery project: identification of mosquito innate immunity genes from expressed sequence tags generated from immune-competent cell lines. Proc Natl Acad Sci U S A, 97(12), 6619-24. PMID: 10841561.

Pedretti, K. T., Casavant, T. L., Braun, R. C., Scheetz, T. E., Birkett, C. L. & Roberts, C. A. (1999). Three complementary approaches to parallelization of local BLAST services on workstation clusters. Lecture Notes in Computer Science, 1662, 271-282. DOI: 10.1007/3-540-48387-X_29.

Shastri, M. D., Scheetz, T. E., Nishimura, D., Cornier, A. S., Cox, G. F., Fulton, A. M., Stone, E. M. & Sheffield, V. C. (1999). Fine mapping of the 11q13 Bardet-Biedl Syndrome 1 (BBS1) locus and use of the rat EST map to identify BBS1 candidate genes. American Journal of Human Genetics, 65(4 (SUPPL. S)), 2525.

Scheetz, T. E., Gardiner, J. M., Nishimura, D. Y., Roberts, C. A., Birkett, C. L., Raymond, M. H., Butters, N. S., Zhang, J. J., Sun, C., McClain, A. M., Staack, J. B., Soares, M. B., Casavant, T. L. & Sheffield, V. C. (1999). Development of a rat EST map.

Braun, T. A., Scheetz, T. E., Casavant, T. L., Munn, K. J., Sheffield, V. C. & Stone, E. M. (1999). A Web-based System for Robust Genotype Gathering and Storage. Proceedings of the Conference on High Performance Networking and Computing.

Scheetz, T. E., Braun, T. A., Munn, K. J., Stone, E. M., Sheffield, V. C. & Casavant, T. L. (1998). GenoMap: A distributed system for unifying genotyping and genetic linkage analysis. Parallel Computing, 24(9-10), 1567-1592. DOI: 10.1016/S0167-8191(98)00072-6.

Dietz, R. D., Casavant, T. L., Scheetz, T. E., Braun, T. A. & Andersland, M. S. (1997). Using Run-Time Uncertainty to Robustly Schedule Parallel Computation. Proceedings of the International Conference on Parallel Computing Technologies, 13-24.

Munn, K. J., Scheetz, T. E. & Casavant, T. L. (1997). Detecting cheating in student programs in the object-oriented paradigm era. Proceedings of the 59th Annual ASEE North Midwest Section Meeting, III.A-2.1—III.A-2.7.

Dietz, R. D., Casavant, T. L., Braun, T. A., Scheetz, T. E. & Andersland, M. S. (1997). Modeling the impact of Run-Time Uncertainty on Optimal Computational Scheduling Using Feedback. Proceedings of the International Conference on Parallel Processing, 481-488.

Scheetz, T. E., Braun, T. A., Casavant, T. L., Gannon, J. A., Andersland, M. S. & Dietz, R. D. (1995). Effectiveness of software trace recovery techniques for current parallel architectures. pp. 509-514. New Delhi, India: Proceedings of the International Conference on High Performance Computing.