Research Topics
Genomes and Genes | Todd E ScheetzSummaryAffiliation: University of Iowa Country: USA Publications
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Detail Information
Publications
Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genesEduardo R Macagno
Division of Biological Sciences, University of California, San Diego, CA, USA
BMC Genomics 11:407. 2010..To begin to address this problem, we constructed whole embryo and adult central nervous system (CNS) EST libraries and created a clustered sequence database of the Hirudo transcriptome that is available to the scientific community...
ESTprep: preprocessing cDNA sequence readsTodd E Scheetz
Center for Bioinformatics and Computational Biology, The University of Iowa, Iowa City, IA 52242, USA
Bioinformatics 19:1318-24. 2003..These errors further complicate the automated identification of EST-related sequencing. A tool is required to prepare the data prior to advanced annotation processing and submission to public databases...- High-throughput gene discovery in the ratTodd E Scheetz
Center for Bioinformatics and Computational Biology, The University of Iowa, Iowa City, Iowa 52242, USA
Genome Res 14:733-41. 2004..Complete information, including radiation hybrid mapping data, is also maintained locally at http://genome.uiowa.edu/clcg.html. All of the sequences described in this article have been submitted to the dbEST division of the NCBI... - Insights into a dinoflagellate genome through expressed sequence tag analysisJeremiah D Hackett
Department of Biological Sciences and Roy J, Carver Center for Comparative Genomics, University of Iowa, Iowa City, IA 52242, USA
BMC Genomics 6:80. 2005..Previous analyses of these data have clarified plastid origin and here we study the gene content, annotate the ESTs, and analyze the genes that are putatively involved in DNA packaging... - Prediction of cochlear implant performance by genetic mutation: the spiral ganglion hypothesisRobert W Eppsteiner
Department of Otolaryngology Head and Neck Surgery, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA
Hear Res 292:51-8. 2012..As a corollary, we hypothesize that because genetic testing can identify sites of cochlear pathology, it may be useful in predicting CI performance... - 1274 full-open reading frames of transcripts expressed in the developing mouse nervous systemMaria F Bonaldo
Department of Pediatrics, The University of Iowa, Iowa City, Iowa 52242, USA
Genome Res 14:2053-63. 2004..Importantly, we identified transcripts, among the 1274 full-ORF sequences, that are exclusively or predominantly expressed in brain and eye tissues, many of which encode yet uncharacterized proteins... - Regulation of gene expression in the mammalian eye and its relevance to eye diseaseTodd E Scheetz
Departments of Ophthalmology and Biomedical Engineering, Howard Hughes Medical Institute, University of Iowa, Iowa City, IA 52242, USA
Proc Natl Acad Sci U S A 103:14429-34. 2006..These data and analytical approaches can be used to facilitate the discovery of additional genes and regulatory elements involved in human eye disease... - Genome-wide identification of pseudogenes capable of disease-causing gene conversionJared M Bischof
Coordinated Laboratory for Computational Genomics, The University of Iowa, Iowa City, Iowa 52240, USA
Hum Mutat 27:545-52. 2006..All results and tools produced by this study are available for download at: http://genome.uiowa.edu/pseudogenes... - Cell of origin strongly influences genetic selection in a mouse model of T-ALLKatherine E Berquam-Vrieze
Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA, USA
Blood 118:4646-56. 2011..These findings have broad implications for the genetic analysis of human cancers as well as the production of mouse models of cancer... 
Microarray mRNA expression profiling to study cystic fibrosisShyam Ramachandran
Interdisciplinary Program in Genetics, Department of Pediatrics, University of Iowa, Iowa City, IA, USA
Methods Mol Biol 742:193-212. 2011..We also outline novel strategies for experimental design and data analysis, and describe some powerful gene and pathway discovery tools...- IDOCS: intelligent distributed ontology consensus system--the use of machine learning in retinal drusen phenotypingGeorge Thomas
Department of Computer Science, University of Iowa, Iowa City, Iowa, USA
Invest Ophthalmol Vis Sci 48:2278-84. 2007..To use the power of knowledge acquisition and machine learning in the development of a collaborative computer classification system based on the features of age-related macular degeneration (AMD)... - Computational quantification of complex fundus phenotypes in age-related macular degeneration and Stargardt diseaseGwenole Quellec
Department of Ophthalmology and Visual Sciences, University of Iowa Hospitals and Clinics, Iowa City, Iowa, USA
Invest Ophthalmol Vis Sci 52:2976-81. 2011.... - A genome-wide association study for primary open angle glaucoma and macular degeneration reveals novel LociTodd E Scheetz
Department of Ophthalmology and Visual Sciences, The University of Iowa, Iowa City, Iowa, United States of America
PLoS ONE 8:e58657. 2013..However, several yielded putative associations requiring validation. Our data suggest that POAG is more genetically complex than AMD, with no common risk alleles of large effect... - 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 pigmentosaBudd A Tucker
Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
Proc Natl Acad Sci U S A 108:E569-76. 2011.... - Association of a novel mutation in the retinol dehydrogenase 12 (RDH12) gene with autosomal dominant retinitis pigmentosaJohn H Fingert
Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
Arch Ophthalmol 126:1301-7. 2008..To identify the gene causing retinitis pigmentosa (RP) in an autosomal dominant pedigree... - Homozygosity mapping with SNP arrays identifies TRIM32, an E3 ubiquitin ligase, as a Bardet-Biedl syndrome gene (BBS11)Annie P Chiang
Department of Electrical Engineering, University of Iowa, Iowa City, IA 52242, USA
Proc Natl Acad Sci U S A 103:6287-92. 2006.... - Transcript annotation prioritization and screening system (TrAPSS) for mutation screeningBrian M O'Leary
Coordinated Laboratory for Computational Genomics, University of Iowa, Iowa City, IA 52242, USA
J Bioinform Comput Biol 5:1155-72. 2007..g. conserved protein functional domains) so as to prioritize candidate genes... - Differential gene expression in human conducting airway surface epithelia and submucosal glandsAnthony J Fischer
Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA
Am J Respir Cell Mol Biol 40:189-99. 2009..This study illustrates the power of LCM in defining the roles of specific anatomic features in airway biology and may be useful in examining how disease states alter transcriptional programs in the conducting airways... - Integration site choice of a feline immunodeficiency virus vectorYubin Kang
Program in Gene Therapy, Department of Pediatrics, University of Iowa, Iowa City, 52242, 52242, USA
J Virol 80:8820-3. 2006..FIV integration preferences are more similar to those of primate lentiviruses and distinct from those of Moloney murine leukemia virus, avian sarcoma leukosis virus, and foamy virus... - Copy number variations on chromosome 12q14 in patients with normal tension glaucomaJohn H Fingert
Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
Hum Mol Genet 20:2482-94. 2011..However, animal studies will be necessary to rule out a role for the other duplicated or neighboring genes... - Large-scale gene discovery in human airway epithelia reveals novel transcriptsTodd E Scheetz
Department of Pediatrics, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA
Physiol Genomics 17:69-77. 2004..This UniGene set should be useful for studies of pulmonary diseases involving the airway epithelium including cystic fibrosis, respiratory infections and asthma. It also provides a reagent for large-scale expression profiling... - AudioGene: predicting hearing loss genotypes from phenotypes to guide genetic screeningKyle R Taylor
Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA, USA
Hum Mutat 34:539-45. 2013..As personalized genomic medicine becomes more common, AudioGene will be increasingly useful as a phenotypic filter to assess pathogenicity of variants identified by massively parallel sequencing... - Analysis of ASB10 variants in open angle glaucomaJohn H Fingert
Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
Hum Mol Genet 21:4543-8. 2012..These data suggest that non-synonymous mutations in ASB10 do not cause Mendelian forms of POAG... - Novel molecular and computational methods improve the accuracy of insertion site analysis in Sleeping Beauty-induced tumorsBenjamin T Brett
Center for Bioinformatics and Computational Biology, Roy J and Lucille A Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
PLoS ONE 6:e24668. 2011..Overall, this method will facilitate ongoing efforts to decipher the genetic complexity of the human cancer genome by providing more accurate comparative information from Sleeping Beauty models of cancer... - A knowledge-based approach to predict intragenic deletions or duplicationsKrishna R Kalari
Department of Biomedical Engineering, Center for Bioinformatics and Computational Biology, University of Iowa, Iowa, USA
Bioinformatics 24:1975-9. 2008..We have developed a novel computational system, SPeeDD (system to prioritize deletions or duplications) that utilizes machine learning techniques to predict likely candidate regions that delete or duplicate exon(s) within a gene... - CFTR DeltaF508 mutation has minimal effect on the gene expression profile of differentiated human airway epitheliaJoseph Zabner
Department of Internal Medicine, University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa City, IA 52242, USA
Am J Physiol Lung Cell Mol Physiol 289:L545-53. 2005..Overall, the results indicate that CFTR dysfunction has little direct impact on airway epithelial gene expression in samples grown under these conditions... - Differential effects of cytokines and corticosteroids on toll-like receptor 2 expression and activity in human airway epitheliaAudra A Winder
Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
Respir Res 10:96. 2009..The recognition of microbial molecular patterns via toll-like receptors (TLRs) is critical for mucosal defenses... - First exons and introns--a survey of GC content and gene structure in the human genomeKrishna R Kalari
Center for Bioinformatics and Computational Biology, The University of Iowa, Iowa City, IA 52242, USA
In Silico Biol 6:237-42. 2006..This study provides insight into the structure of eukaryotic genes. These results confirm and expand the previously identified regulatory potential of first exons and introns... - Genome-wide analysis of copy number variants in age-related macular degenerationKacie J Meyer
Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA
Hum Genet 129:91-100. 2011..These and other candidate genes highlighted by this study deserve further scrutiny as sources of genetic risk for AMD... - Migration of the plastid genome to the nucleus in a peridinin dinoflagellateJeremiah D Hackett
Department of Biological Sciences and Center for Comparative Genomics, The University of Iowa, Iowa City, IA 52242, USA
Curr Biol 14:213-8. 2004..tamarense. The plastid-targeted genes have red and green algal origins. These results highlight the unique position of dinoflagellates as the champions of plastid gene transfer to the nucleus among photosynthetic eukaryotes... - Variations in NPHP5 in patients with nonsyndromic leber congenital amaurosis and Senior-Loken syndromeEdwin M Stone
Department of Ophthalmology and Visual Sciences, The University of Iowa, 375 Newton Rd, 4111 MERF, Iowa City, IA 52242, USA
Arch Ophthalmol 129:81-7. 2011..To investigate whether mutations in NPHP5 can cause Leber congenital amaurosis (LCA) without early-onset renal disease... - The air-liquid interface and use of primary cell cultures are important to recapitulate the transcriptional profile of in vivo airway epitheliaAlejandro A Pezzulo
Department of Internal Medicine, Univ of Iowa, Iowa City, 52242, USA
Am J Physiol Lung Cell Mol Physiol 300:L25-31. 2011..We describe a high level of similarity between cells of tracheal and bronchial origin within and between different human donors, which suggests a very robust expression profile that is specific to airway cells... - Prioritizing regions of candidate genes for efficient mutation screeningTerry A Braun
Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA
Hum Mutat 27:195-200. 2006..These results suggest that prioritization strategies such as PAR can accelerate disease-gene identification through more efficient use of screening resources... - Eukaryotic operon-like transcription of functionally related genes in DrosophilaYehuda Ben-Shahar
Howard Hughes Medical Institute, and Department of Internal Medicine, Roy J and Lucille A Carver College of Medicine Center for Bioinformatics and Computational Biology, University of Iowa, Iowa City, IA 52242, USA
Proc Natl Acad Sci U S A 104:222-7. 2007..These data reveal eukaryotic operon-like transcription of functionally related genes in Drosophila. The results also suggest that operon-based transcription may be more common in eukaryotes than previously appreciated... - Identification and initial characterization of 6,000 expressed sequenced tags (ESTs) from rat normal-growing cartilage and swarm rat chondrosarcoma cDNA librariesJose A Morcuende
Department of Orthopaedic Surgery, University of Iowa, Iowa City 52242, USA
Iowa Orthop J 22:28-34. 2002..It suggests that the biochemical characterization of growing cartilage and chondrosarcoma reported to date has only begun to describe the complexity of these tissues... - A comprehensive nonredundant expressed sequence tag collection for the developing Rattus norvegicus heartJennifer J S Laffin
Department of Pediatrics and Interdepartmental Genetics Graduate Program, The University of Iowa, Iowa City, Iowa 52242, USA
Physiol Genomics 17:245-52. 2004..It is anticipated that such EST and cDNA clone resources will prove invaluable to gene expression studies aimed at the understanding of the molecular mechanisms underlying heart septation defects... - Complement factor H polymorphism p.Tyr402His and cuticular DrusenMichael A Grassi
Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, USA
Arch Ophthalmol 125:93-7. 2007..To determine the histidine frequency in patients with the cuticular drusen phenotype of age-related macular degeneration (AMD)... - Comprehensive genetic testing for hereditary hearing loss using massively parallel sequencingA Eliot Shearer
Department of Otolaryngology, Head and Neck Surgery, University of Iowa, Iowa City, IA 52242, USA
Proc Natl Acad Sci U S A 107:21104-9. 2010..Massively parallel sequencing technologies provide sensitivity, specificity, and reproducibility at levels sufficient to perform genetic diagnosis of hearing loss... - Swarm Rat Chondrosarcoma Cells as an in vivo model: Lung Colonization and Effects of Tissue Environment on Tumor GrowthJose A Morcuende
Department of Orthopaedic Surgery and Rehabilitation University of Iowa 200 Hawkins Drive, Iowa City, IA 52242, USA
Iowa Orthop J 32:46-53. 2012..Identifying these interactions will lead to further understanding of chondrosarcoma and contribute to therapeutic targets in the future... - A Hyperactive Transposase Promotes Persistent Gene Transfer of a piggyBac DNA TransposonErin R Burnight
1 Interdisciplinary Graduate Program in Genetics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA 2 Center for Gene Therapy of Cystic Fibrosis and Other Genetic Diseases, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA 3 Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
Mol Ther Nucleic Acids 1:e50. 2012..Molecular Therapy - Nucleic Acids (2012) 1, e50; doi:10.1038/mtna.2012.12; published online 16 October 2012... - Gene expression profiling of potential PPARgamma target genes in mouse aortaHenry L Keen
Department of Internal Medicine, University of Iowa College of Medicine, Iowa City, Iowa 52242, USA
Physiol Genomics 18:33-42. 2004.... - Automated quantification of inherited phenotypes from color images: a twin study of the variability of optic nerve head shapeLi Tang
Department of Ophthalmology and Visual Sciences, University of Iowa Hospitals and Clinics, Iowa City, Iowa 52242, USA
Invest Ophthalmol Vis Sci 51:5870-7. 2010.... - Isolation and characterization of autotrophic, hydrogen-utilizing, perchlorate-reducing bacteriaJoshua D Shrout
Department of Civil and Environmental Engineering, The University of Iowa, Iowa City, IA 52242, USA
Appl Microbiol Biotechnol 67:261-8. 2005..These bacteria used fumarate as an alternate electron acceptor, which is the first report of growth on an organic electron acceptor by perchlorate-reducing bacteria... - A modified sleeping beauty transposon system that can be used to model a wide variety of human cancers in miceAdam J Dupuy
Department of Anatomy and Cell Biology, Center for Bioinformatics, Computational Biology and Biomedical Engineering, Roy J and Lucille A Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA
Cancer Res 69:8150-6. 2009..These novel alleles provide additional tools for the SB system and provide some insight into how this mutagenesis system can be manipulated to model cancer in mice... - Identifying components of the NF-kappaB pathway in the beneficial Euprymna scolopes-Vibrio fischeri light organ symbiosisMichael S Goodson
Department of Medical Microbiology and Immunology, University of Wisconsin, 1300 University Ave, Madison, WI 53706, USA
Appl Environ Microbiol 71:6934-46. 2005..Further investigations should elucidate the role of the Toll/NF-kappaB pathway in the initiation of the beneficial symbiosis between E. scolopes and Vibrio fischeri... - An annotated cDNA library of juvenile Euprymna scolopes with and without colonization by the symbiont Vibrio fischeriCarlene K Chun
Department of Medical Microbiology and Immunology, University of Wisconsin Madison, Madison, WI 53706, USA
BMC Genomics 7:154. 2006..We report here the creation of a juvenile light-organ specific EST database... - The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)Daniela S Gerhard
Genome Res 14:2121-7. 2004..Recently, a rat cDNA component was added to the project, and ongoing frog (Xenopus) and zebrafish (Danio) cDNA projects were expanded to take advantage of the high-throughput MGC pipeline... - High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequenceAnne E Kwitek
Human and Molecular Genetics Center and Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
Genome Res 14:750-7. 2004..This new integrated RH map contains approximately 10 RH-mapped elements per Mb on the genome assembly, enabling the RH maps to serve as a scaffold for a variety of data visualization tools... - Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequencesRobert L Strausberg
National Cancer Institute, Bethessda, MD 20892 2580, USA
Proc Natl Acad Sci U S A 99:16899-903. 2002..All MGC sequences and clones are available without restriction through public databases and clone distribution networks (see http:mgc.nci.nih.gov)... - Ethnic variation in AMD-associated complement factor H polymorphism p.Tyr402HisMichael A Grassi
Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City 52242, USA
Hum Mutat 27:921-5. 2006..This study suggests that there are other yet unidentified genetic factors important in the pathogenesis of AMD that may mitigate the effects of c.1204T>C, p.Tyr402His variant... - PLET1 (C11orf34), a highly expressed and processed novel gene in pig and mouse placenta, is transcribed but poorly spliced in humanShu Hong Zhao
Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA 50011, USA
Genomics 84:114-25. 2004..Our data correct GenomeScan annotation of this region of the human genome and describe functional gene discovery in mammals not recognized in human EST projects...