Ophthalmology And Visual Sciences

Todd E. Scheetz, MS, PhD

Portrait

Associate Professor of Ophthalmology and Visual Sciences
Associate Professor of Biomedical Engineering

Contact Information

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

Email: todd-scheetz@uiowa.edu

Education

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

Education/Training Program Affiliations

Biosciences Graduate Program
Interdisciplinary Graduate Program in Genetics
Interdisciplinary Graduate Program in Informatics
Interdisciplinary Graduate Program in Neuroscience

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

Center, Program and Institute Affiliations

Center for Bioinformatics and Computational Biology
Holden Comprehensive Cancer Center
Iowa Initiative in Human Genetics
Iowa Institute for Biomedical Imaging
John and Marcia Carver Nonprofit Genetic Testing Laboratory
Stephen A. Wynn Institute for Vision Research

All Publications

Brownstein C, 71 Intervening authors , Scheetz T, et al .  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.  2014. 15(3):R53.
[PubMed]

Christopher M, Tang L, Fingert J, Scheetz T, Abramoff M.  Automated discovery of structural features of the optic nerve head on the basis of image and genetic data.  Proc SPIE.  2014. 9035:90350S.

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

Shearer A, Black-Ziegelbein E, Hildebrand M, Eppsteiner R, Ravi H, Joshi S, Guiffre A, Sloan C, Happe S, Howard S, Novak B, Deluca A, Taylor K, Scheetz T, Braun T, Casavant T, Kimberling W, Leproust E, Smith R.  Advancing genetic testing for deafness with genomic technology.  J Med Genet.  2013. 50(9):627-34.
[PubMed]

Whitmore S, Braun T, Skeie J, Haas C, Sohn E, Stone E, Scheetz T, Mullins R.  Altered gene expression in dry age-related macular degeneration suggests early loss of choroidal endothelial cells.  Mol Vis.  2013. 19:2274-97.
[PubMed]

Taylor K, Deluca A, Shearer A, Hildebrand M, Black-Ziegelbein E, Anand V, Sloan C, Eppsteiner R, Scheetz T, Huygen P, Smith R, Braun T, Casavant T.  AudioGene: Predicting Hearing Loss Genotypes from Phenotypes to Guide Genetic Screening.  Hum Mutat.  2013. 34(4):539-45.
[PubMed]

Novak C, Christopher M, Tang L, Fingert J, Scheetz T, Abramoff M, Alyward S.  Changes in quantitative 3D shape features of the optic nerve head associated with age.  2013. 8670:86700O.

Nannapaneni K, Ben-Shahar Y, Keen H, Welsh M, Casavant T, Scheetz T.  Computational identification of operon-like transcriptional loci in eukaryotes.  Comput Biol Med.  2013. 43(6):738-43.
[PubMed]

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

Wagner A, Anand N, Wang W, Chatterton J, Sun D, Shepard A, Jacobson N, Pang I, Deluca A, Casavant T, Scheetz T, Mullins R, Braun T, Clark A.  Exon-level expression profiling of ocular tissues.  Exp Eye Res.  2013. 111:105-11.
[PubMed]

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

Hu Q, Garvin M, Christopher M, Xu X, Scheetz T, Abramoff M.  Optimal filter approach for the detection of vessel bifurcations in color fundus images.  2013. 8669:art. no. 866920.

Wagner A, Taylor K, Deluca A, Casavant T, Mullins R, Stone E, Scheetz T, Braun T.  Prioritization of Retinal Disease Genes: An Integrative Approach.  Hum Mutat.  2013. 34(6):853-9.
[PubMed]

Christopher M, Scheetz T, Mullins R, Abràmoff M.  Selection of phototransduction genes in Homo sapiens.  Invest Ophthalmol Vis Sci.  2013. 54(8):5489-96.
[PubMed]

Stone E, Mullins R, Tucker B, Wagner A, Braun T, Scheetz T.  Alternative splicing of exon 12 in the male germ cell associated kinase gene (MAK) results in a cone-specific isoform.  2012 May. 

Whitmore S, Braun T, Scheetz T, Stone E, Mullins R.  ARMS2 A69S associated alternative splicing and differential gene expression in RPE/choroid suggest an early role for vascular loss in AMD.  2012 May. 

Wagner A, DeLuca A, Thole D, Casavant T, Stone E, Mullins R, Braun T, Scheetz T.  RNA-seq and identifying retin-specific exons.  2012 May. 

Tucker B, Anfinson K, Andorf J, Streb L, Scheetz T, Mullins R, Stone E.  Targeting human MAK mutant iPCSs for in vitro gene replacement.  2012 May. 

Burnight E, Staber J, Korsakov P, Li X, Brett B, Scheetz T, Craig N, McCray Jr P.  A Hyperactive Transposase Promotes Persistent Gene Transfer of a piggyBac DNA Transposon.  Molecular Therapy Nucleic acids.  2012. 1:e50.
[PubMed]

Fingert J, Roos B, Solivan-Timpe F, Miller K, Oetting T, Wang K, Kwon Y, Scheetz T, Stone E, Alward W.  Analysis of ASB10 variants in open angle glaucoma.  Hum Mol Genet.  2012. 21(20):4543-8.
[PubMed]

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

Eppsteiner R, Shearer A, HIldebrand M, Deluca A, Ji H, Dunn C, Black-Ziegelbein E, Casavant T, Braun T, Scheetz T, Scherer S, Hansen M, Gantz B, Smith R.  Prediction of cochlear implant performance by genetic mutation: The spiral ganglion hypothesis.  Hear Res.  2012. 29(1-2):51-8.
[PubMed]

Huang Y, Hernandez F, Gu B, Stockdale K, Nanapaneni K, Scheetz T, Behlke M, Peek A, Bair T, Giangrande P, McNamara 2nd J.  RNA Aptamer-Based Functional Ligands of the Neurotrophin Receptor, TrkB.  Mol Pharmacol.  2012. 82(4):623-35.
[PubMed]

Morcuende J, Stevens J, Scheetz T, de Fatima Bonaldoc M, Casavant T, Otero J, Soares M.  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.

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

Christopher M, Moga D, Russell S, Folk J, Scheetz T, Abramoff M.  Validation of tablet-based evaluation of color fundus images.  Retina.  2012. 32(8):1629-35.
[PubMed]

Scheetz T, DeLuca A, Braun T, Streb L, Affatigato L, Sheffield V, Stone E.  The importance of variation databases in interpretation of exome sequencing.  American Society for Human Genetics.  2011 October. 

Folk J, Abramoff M, Orien J, Christopher M, Scheetz T, Mullins R, Russell S, Boldt H, Schindler E, Mahajan V, Stone E.  Automated quantification of genotype-phenotype correlation in ARMS2-associated age related macular degeneration.  2011 May. 

McGrail M, Hatler J, Kuang X, Liao H, Nannapaneni K, Watt K, Uhl J, Largaespada D, Vollbrecht E, Scheetz T, Dupuy A, Hostetter J, Essner J.  Somatic mutagenesis with a Sleeping Beauty transposon system leads to solid tumor formation in zebrafish.  PLoS One.  2011 April 21. 6(4):e18826.
[Link]

Fingert J, Robin A, Stone J, Roos B, Davis L, Scheetz T, Bennett S, Wassink T, Kwon Y, Alward A, Mullins R, Sheffield V, Stone E.  Copy number variations on chromosome 12q14 in patients with normal tension glaucoma.  Hum Mol Genet.  2011 April 19. 20(12):2482-94.
[PubMed]

Zheng J, Miller K, Yang T, Hildebrand M, Shearer A, DeLuca A, Scheetz T, Drummond J, Scherer S, Legan P, Goodyear R, Richardson G, Cheatham M, Smith R, Dallos P.  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.  2011 March 8. 108(10):4218-23.
[Link]

 .  AudioGene: Computer-based prediction of genetic factors involved in non-syndromic hearing impairment.  IEEE Computer Society.  2011. 

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

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

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

Davis L, Meyer K, Schindler E, Beck J, Rudd D, Grunstad A, Scheetz T, Braun T, Fingert J, Kwon W, Folk J, Russell S, Wassink T, Sheffield V, Stone E.  Copy Number Variations (CNVs) and Primary Open Angle Glaucoma (POAG).  Invest Ophthalmol Vis Sci.  2011. 

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

Tucker B, Scheetz T, Mullins R, Deluca A, Hoffmann J, Johnston R, Jacobson S, Sheffield V, Stone E.  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.  2011. 108(34):E569-76.
[PubMed]

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

Ramachandran S, Clarke L, Scheetz T, Amaral M, McCray P.  Microarray mRNA expression profiling to study cystic fibrosis.  Methods Mol Biol.  2011. 742:193-212.
[Link]

Brett B, Berquam-Vrieze K, Nannapaneni K, Huang J, Scheetz T, Dupuy A.  Novel molecular and computational methods improve the accuracy of insertion site analysis in Sleeping Beauty-induced tumors.  PLoS One.  2011. 6(9):e24668.
[Link]

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

 .  Sequencing and disease variation detection tools and techniques.  IEEE Computer Society.  2011. 

Walters J, Bair T, Braun T, Scheetz T, Robinson J, Casavant T.  Validation of computational prediction of horizontal gene transfer events-XenoCluster.  Journal of Supercomputing.  2011. 57(2):141-50.

Pezzulo A, Starner T, Scheetz T, Traver G, Tilley A, Harvey B, Crystal R, McCray P, Zabner J.  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.  2011 January. 300(1):L25-31.
[Link]

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

Shearer A, DeLuca A, Hildebrand M, Taylor K, Gurrola J, Scherer S, Scheetz T, Smith R.  Comprehensive genetic testing for hereditary hearing loss using massively parallel sequencing.  Proc Natl Acad Sci U S A.  2010 December 7. 107(49):21104-9.
[Link]

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

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

Macagno E, Gaasterland T, Edsall L, Bafna V, Soares M, Scheetz T, Casavant T, Da Silva C, Wincker P, Tasiemski A, Salzet M.  Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes.  BMC Genomics.  2010. 11(1):407.
[PubMed]

Wier A, Nyholm S, Mandel M, Massengo-Tiassé  R, Schaefer A, Koroleva I, Splinter-Bondurant S, Brown B, Manzella L, Snir E, Almabrazi H, Scheetz T, Bonaldo Mde F, Casavant T, Soares M, Cronan J, Reed J, Ruby E, McFall-Ngai M.  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.  2010. 107(5):2259-2264.
[PubMed]

Winder A, Wohlford-Lenane C, Scheetz T, Nardy B, Manzel L, Look D, McCray P.  Differential effects of cytokines and corticosteroids on toll-like receptor 2 expression and activity in human airway epithelia.  Respir Res.  2009 October 16. 10:96.
[Link]

Scheetz T, Cribben K, Casavant T, Braun T, Fingert J, Stone E, Sheffield V.  A computational system to facilitate efficient discovery of disease genes.  American Society for Human Genetics.  2009 October. 

Braun T, DeLuca A, Anand N, Bogaard J, Casavant T, Faga B, Grundstad J, Scheetz T, Sheffield V, Stone E.  Automated Sequence Analysis Pipeline (ASAP) for Genetic Testing.  2009 May. 

Scheetz T, Braun T, Smith R, Walls W, Faga B, Folk J, Sheffield V, Casavant T, Stone E.  CPS: A collaborative phenotype system.  2009 May. 

Fingert J, Roos B, Alward W, Kwon Y, Sheffield V, Stone E, Scheetz T.  Identification of genetic risk factors for pigment dispersion syndrome.  2009 May. 

Fischer A, Goss K, Scheetz T, Wohlford-Lenane C, Snyder J, McCray P.  Differential gene expression in human conducting airway surface epithelia and submucosal glands.  Am J Respir Cell Mol Biol.  2009 February. 40(2):189-99.
[Link]

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

Winder A, Wohlford-Lenane C, Scheetz T, Nardy B, Manzel L, Look D, McCray Jr P.  Differential effects of cytokines and corticosteroids on Toll-like receptor 2 expression and activity in human airway epithelia.  Respir Res.  2009. 10(1):96.

Loktev A, Zhang Q, Beck J, Searby C, Scheetz T, Bazan J, Slusarski D, Sheffield V, Jackson P, Nachury M.  A BBSome subunit links ciliogenesis, microtubule stability, and acetylation.  Dev Cell.  2008 December. 15(6):854-65.
[Link]

DeLuca A, Wilder-Tack D, Stone N, Taylor K, Bogaard J, Scheetz T, Casavant T, Sheffield V, Stone E, Braun T.  Automated Sequence Analysis Pipeline (ASAP) for Clinical Genetic Testing.  American Society for Human Genetics.  2008 October. 

Cribben K, Braun T, Fingert J, Sheffield V, Stone E, Casavant T, Scheetz T.  Prioritization of Candidate genes for retinitis pigmentosa.  American Society for Human Genetics.  2008 October. 

Kalari K, Casavant T, Scheetz T.  A knowledge-based approach to predict intragenic deletions or duplications.  Bioinformatics.  2008 September 15. 24(18):1975-9.
[Link]

Fischer A, Goss K, Scheetz T, Wohlford-Lenane C, Snyder J, McCray Jr P.  Differential Gene Expression in Human Conducting Airway Surface Epithelia and Submucosal Glands.  Am J Respir Cell Mol Biol.  2008 August 14. 

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

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

Ben-Shahar Y, Nannapaneni K, Casavant T, Scheetz T, Welsh M.  Eukaryotic operon-like transcription of functionally related genes in Drosophila.  Proc Natl Acad Sci U S A.  2007 January 2. 104(1):222-7.
[Link]

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

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

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

Chun C, Scheetz T, Bonaldo M, Brown B, Clemens A, Crookes-Goodson W, Crouch K, DeMartini T, Eyestone M, Goodson M, Janssens B, Kimbell J, Koropatnick T, Kucaba T, Smith C, Stewart J, Tong D, Troll J, Webster S, Winhall-Rice J, Yap C, Casavant T, McFall-Ngai M, Soares M.  An Annotated cDNA Library of Juvenile Euprymna scolopes with and without Colonization by the Symbiont Vibrio fischeri.  BMC Genomics.  2006. 7:154.

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

Kalari K, Casavant M, Bair T, Keen H, Comeron J, Casavant T, Scheetz T.  First exons and introns--a survey of GC content and gene structure in the human genome.  In Silico Biol.  2006. 6(3):237-42.
[Link]

Bischoff J, Chiang A, Scheetz T, Stone E, Casavant T, Sheffield T, Braun T.  Genome-Wide Identification of Pseudogenes Capable of Disease-Causing Gene Conversion.  Hum Mutat.  2006. 27(6):542-552.

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

Kang Y, Moressi C, Scheetz T, Xie L, Tran D, Casavant T, Ak P, Benham C, Davidson B, McCray Jr P.  Integration Site Choice of a Feline Immunodeficiency Virus Vector.  J Virol.  2006. 80(17):8820-8823.

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

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

Kim K, Scheetz T, Swiderski R, Philp A, Casavant T, Huang J, Stone E, Sheffield V.  eQTL mapping in the mammalian eye.  American Society for Human Genetics.  2005 October. 

Kalari K, Braun T, Stone E, Sheffield V, Casavant T, Scheetz T.  Computational approach to elucidate the gene rearrangement mechanism: applications in prioritizing deletion/duplication candidate regions within a gene.  2005 September. 

Ritchison J, Braun T, Casavant T, Scheetz T.  Intrval: A public repository for genetic intervals.  2005 September. 

Starner T, Scheetz T, Brown B, Apicella M, McCray Jr P.  Analysis of airway epithelial gene expression patterns from non-typeable Homo sapiens influenzae biofilm stimulation.  2005 June. 

Stone E, Scheetz T, Casavant T, Soares M.  Gene Discovery in the Human Visual System.  2005 May. 

Scheetz T, Trivedi N, Pedretti K, Braun T, Casavant T.  Gene transcript clustering: a comparison of parallel approaches.  Future Generation Computer Systems.  2005. 21(5):731-735.

Goodson M, Kojadinovic M, Troll J, Scheetz T, Casavant T, Soares M, McFall-Ngai M.  Identifying Components of the NF-κB Pathway in the Beneficial Euprymna scolopes-Vibrio fischeri Light Organ Symbiosis.  Applied and Environmental Microbiology.  2005. 71(11):6934-6946.

Hackett J, Scheetz T, Yoon H, Soares M, Bonaldo M, Casavant T, Bhattacharya D.  Insights into a dinoflagellate genome through expressed sequence tag analysis.  BMC Genomics.  2005. 6:80.

Shrout J, Scheetz T, Casavant T, Parkin G.  Isolation and characterization of autotrophic, hydrogen-utilizing, perchlorate-reducing bacteria.  Applied Microbial and Cell Physiology.  2005. 67:261-268.

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

Walters J, Casavant T, Robinson J, Bair T, Braun T, Scheetz T.  XenoCluster: A Grid Computing Approach to Finding Ancient Evolutionary Genetic Anomalies.  Lecture Notes in Computer Science.  2005. 3603:355.

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

Scheetz T, Almabrazi H, Mokrzycki B, Braun T, Soares M, Casavant T.  High-throughput assessment of regulation in alternative transcriptional processing.  2004 September. 

Scheetz T, Casavant T.  Informatics for Efficient EST-Based Gene Discovery in Normalized and Subtracted cDNA Libraries.  World Scientific Press.  2004 May. 

Hackett J, Yoon H, Soares M, Bonaldo M, Casavant T, Scheetz T, Nosenko T, Bhattacharya D.  Migration of the plastid genome to the nucleus in a peridinin dinoflagellate.  Curr Biol.  2004 February 3. 14(3):213-8.
[Link]

Bonaldo M, Bair T, Scheetz T, Snir E, Akabogu I, Bair J, Berger B, Crouch K, Davis A, Eyestone M, Keppel C, Kucaba T, Lebeck M, Lin J, DeMelo A, Rehman J, Reiter R, Schaefer K, Smith C, Tack D, Trout K, Sheffield V, Lin J, Casavant T, Soares M.  1,274 Full-open reading frames of transcripts expressed in the developing mouse nervous system.  Genome Research.  2004. 14(10B):2053-2063.

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

Keen H, Ryan M, Beyer A, Mathur S, Scheetz T, Gackle B, Faraci F, Casavant T, Sigmund C.  Gene expression profiling of potential PPARg target genes in mouse aorta.  Physiological Genomics.  2004. 18(1):33-42.

Kwitek A, Gullings-Handley J, Yu J, Carlos D, Orlebeke K, Nie J, Eckert J, Lemke A, Andrae J, Bromberg S, Pasko D, Chen D, Scheetz T, Casavant T, Soares M, Sheffield V, Tonellato P, Jacob H.  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.  2004. 14:750-757.

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

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

Scheetz T, Trivedi N, Roberts C, Pedretti K, Robinson N, Birkett C, Gavin A, Robinson J, Sheffield V, Soares M, Casavant T.  ESTPrep: A Software System for Preprocessing cDNA Sequence Reads.  Bioinformatics.  2003. 19:1318-1324.

Braun T, Scheetz T, Webster G, Clark A, Stone E, Sheffield V, Casavant T.  Identifying candidate disease genes with high-performance computing.  Journal of Supercomputing.  2003. 26:7-24.

Strausberg R, Feingold E, Grouse L, Derge J, Klausner R, Collins F, Wagner L, Shenmen C, Schuler G, Altschul S, Zeeberg B, Buetow K, Schaefer C, Bhat N, Hopkins R, Jordan H, Moore T, Max S, Wang J, Hsieh F, Diatchenko L, Marusina K, Farmer A, Rubin G, Hong L, Stapleton M, Soares M, Bonaldo M, Casavant T, Scheetz T, Brownstein M, Usdin T, Toshiyuki S, Carninci P, Prange C, Raha S, Loquellano N, Peters G, Abramson R, Mullahy S, Bosak S, McEwan P, McKernan K, Malek J, Gunaratne P, Richards S, Worley K, Hale S, Garcia A, Gay L, Hulyk S, Villalon D, Muzny D, Sodergren E, Lu X, Gibbs R, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madan A, Young A, Shevchenko Y, Bouffard G, Blakesley R, Touchman J, Green E, Dickson M, Rodriguez A, Grimwood J, Schmutz J, Myers R, Butterfield Y, Krzywinski M, Skalska U, Smailus D, Schnerch A, Schein J, Jones S, Marra M.  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.  2002 December 24. 99(26):16899-903.
[Link]

Scheetz T, Bair T, Tack D, Kucaba T, Bonaldo M, Sheffield V, Soares M, Casavant T.  Implementation and evaluation of EST-based novelty assessment techniques.  2002 May. 

Scheetz T, Bartlett J, Walters J, Shutte B, Casavant T, McCray Jr P.  Genomics-based Approaches to Gene Discovery in Innate Immunity.  Immunological Reviews.  2002. 190:137-145.

Morcuende J, Huang X, Stevens J, Kucaba T, Brown B, Abudlkawy H, Scheetz T, Malchenko S, Bonaldo F, Casavant T, Soares B.  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.  2002. 22:28-34.

Trivedi N, Bischof J, Davis S, Pedretti K, Scheetz T, Braun T, Roberts C, Robinson N, Sheffield V, Soares M, Casavant T.  Parallel Creation of Non-redundant Gene Indices from Partial mRNA Transcripts.  Future Generation Computer Systems.  2002. 18(6):863-870.

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

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

Braun T, Scheetz T, Mykytyn K, Nishimura D, Casavant T, Sheffield V.  Applying computational methods to search genomic sequence to identify candidate disease genes and novel sequence characteristics.  American Journal of Human Genetics.  2001 October. 69(4):221 Suppl 1.

Scheetz T, Raymond M, McClain A, Soares M, Casavant T, Sheffield V.  Integration of rat, mouse and human EST and comparative maps.  American Journal of Human Genetics.  2001 October. 69(4):1583 Suupl. 1.

Scheetz T, Raymond M, Nishimura D, McClain A, Roberts C, Birkett C, Gardiner J, Zhang J, Butters N, Sun C, Kwitek-Black A, Jacob H, Casavant T, Soares M, Sheffield V.  Generation of a high-density rat EST map.  Genome Res.  2001 March. 11(3):497-502.
[Link]

Pedretti K, Casavant T, Scheetz T, Roberts C, Braun T, Robinson N.  A Parallel Expressed Sequence Tag (EST) Clustering Program.  Lecture Notes in Computer Science.  2001. 2127:490-497.

Casavant T, Braun T, Kaliannan S, Scheetz T, Munn K, Birkett C.  A parallel/distributed architecture for hierarchically heterogeneous web-based cooperative applications.  Future Generation Computer Systems.  2001. 17(6):783-793.

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, Scheetz T, Sheffield V, Casavant T, Soares M.  Current status of the University of Iowa Mammalian Gene Discovery Program.  Cytogenetics and Cell Genetics.  2001. 92(1-2):46.

Braun R, Pedretti K, Casavant T, Scheetz T, Birkett C, Roberts C.  Parallelization of local BLAST service on workstation clusters.  Future Generation Computer Systems.  2001. 17(6):745-754.

Scheetz T, Casavant T, Soares M, Sheffield V.  Creation of a rat EST placement, and rat-human and rat-mouse comparative maps.  2000 November. 

Dimopoulos G, Casavant T, Chang S, Scheetz T, Roberts C, Donohue M, Schultz J, Benes V, Bork P, Ansorge W, Soares M, Kafatos F.  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.  2000 June 6. 97(12):6619-24.
[Link]

Shastri M, Scheetz T, Nishimura D, Cornier A, Cox G, Fulton A, Stone E, Sheffield V.  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.  1999 October. 65(4 (SUPPL. S)):2525.

Scheetz T, Raymond M, Zhang J, McClain A, Roberts C, Nishimura D, Casavant T, Soares M, Sheffield V.  High-density EST map of the rat.  American Journal of Human Genetics.  1999 October. 65(4 (Suppl S)):2370.

Scheetz T, Raymond M, Zhang J, McClain A, Roberts C, Nishimura D, Casavant T, Soares M, Sheffield V.  High-density EST map of the rat.  American Journal of Human Genetics.  1999 October. 65(4, Suupl S):2370.

Bonaldo M, Scheetz T, Beck G, Berger B, Birkett C, Brown R, Crouch K, Donahue M, Doonan G, Gardiner J, Guo L, Johnson B, Kinkaid R, Liu K, Miljkovic V, Roberts C, Wu N, Casavant T, Sheffield V, Soares M.  The University of Iowa gene discovery program.  American Journal of Human Genetics.  1999 October. 65(4):1224 Suppl. S.

Scheetz T, Beck G, Birkett C, Black E, Bonaldo M, Braun R, Braun T, Brown R, Crouch K, Donahue M, Doonan G, Gardiner J, Jonson B, Kaliannan S, Kincaid R, Miljokovic V, Munn K, Nishimura D, Pedretti K, Roberts C, Smith C, Stier L, Casavant T, Sheffield V, Soares M,  .  A program for rat gene discovery.  1999 May. 

Scheetz T, Gardiner J, Nishimura D, Roberts C, Birkett C, Raymond M, Butters N, Zhang J, Sun C, McClain A, Staack J, Soares M, Casavant T, Sheffield V.  Development of a rat EST map.  1999 May. 

Scheetz T, Birkett C, Roberts C, Sheffield V, Soares M, Casavant T.  Efficient, exact clustering of ESTs to support serial subtraction of pooled cDNA libraries.  1999 May. 

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

Pedretti K, Casavant T, Braun R, Scheetz T, Birkett C, Roberts C.  Three complementary approaches to parallelization of local BLAST services on workstation clusters.  Lecture Notes in Computer Science.  1999. 1662:271-282.

Soares M, Beck G, Berger B, Birkett C, Black E, Bonaldo M, Braun R, Braun T, Donahue M, Kaliannan S, Kincaid R, Miljokovic V, Munn K, Nishimura D, Pedretti K, Scheetz T, Stier L, Casavant T, Sheffield V.  A program for rat gene discovery and mapping.  1998 May. 

Scheetz T, Birkett C, Braun T, Nishimura D, Sheffield V, Soares M, Casavant T.  Informatics for preparation of EST reads in a mixed-tissue cDNA library setting.  1998 May. 

Scheetz T, Braun T, Munn K, Stone E, Sheffield V, Casavant T.  GenoMap: A distributed system for unifying genotyping and genetic linkage analysis.  Parallel Computing.  1998. 24(9-10):1567-1592.

Munn K, Scheetz T, Casavant T.  Detecting cheating in student programs in the object-oriented paradigm era.  Proceedings of the 59th Annual ASEE North Midwest Section Meeting.  1997. 

Dietz R, Casavant T, Braun T, Scheetz T, Andersland M.  Modeling the impact of Run-Time Uncertainty on Optimal Computational Scheduling Using Feedback.  Proceedings of the International Conference on Parallel Processing.  1997. 

Dietz R, Casavant T, Scheetz T, Braun T, Andersland M.  Using Run-Time Uncertainty to Robustly Schedule Parallel Computation.  Proceedings of the International Conference on Parallel Computing Technologies.  1997. 

Scheetz T, Braun T, Casavant T, Gannon J, Andersland M, Dietz R.  Effectiveness of software trace recovery techniques for current parallel architectures.  Proceedings of the International Conference on High Performance Computing.  1995. 

Scheetz T, Laffin J, Berger B, Mackerly S, Baumes S, 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, Rhoads B, Schaefer K, Smith C, Sunjevaric I, Trout K, Wu N, Birkett C, 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, Casavant T, Sheffield V, Soares M.  High-throughput gene discovery in the rat.  Genome Research.  14:733-741.

Scheetz T, Zabner J, Welsh M, Coco J, Eyestone M, Bonaldo M, Kucaba T, Casavant T, Soares M, McCray Jr P.  Large Scale Gene Discovery in Human Airway Epithelia Reveals Novel Transcripts.  Physiological Genomics.  17:69-77.

Date Last Modified: 06/07/2014 - 21:56:23