Publications by authors named "Thomas L Casavant"

59Publications

Structural Insights into Hearing Loss Genetics from Polarizable Protein Repacking.

Biophys J 2019 08 3;117(3):602-612. Epub 2019 Jul 3.

Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa; Department of Biochemistry, University of Iowa, Iowa City, Iowa. Electronic address:

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August 2019

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

BMC Bioinformatics 2019 Jun 17;20(1):339. Epub 2019 Jun 17.

Department of Electrical and Computer Engineering, Center for Bioinformatics and Computational Biology, University of Iowa, 5017 Seamans Center, Iowa City, IA, 52242, USA.

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June 2019

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

BMC Bioinformatics 2019 Jun 17;20(1):339. Epub 2019 Jun 17.

Department of Electrical and Computer Engineering, Center for Bioinformatics and Computational Biology, University of Iowa, 5017 Seamans Center, Iowa City, IA, 52242, USA.

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June 2019

Audioprofile Surfaces: The 21st Century Audiogram.

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

Department of Electrical and Computer Engineering, University of Iowa, Iowa City, Iowa, USA Center for Bioinformatics and Computational Biology, University of Iowa, Iowa City, Iowa, USA Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa, USA.

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May 2016

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

J Biomed Inform 2015 Apr 13;54:106-13. Epub 2015 Jan 13.

Department of Pediatrics, The University of Iowa, United States. Electronic address:

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April 2015

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

Am J Hum Genet 2014 Oct 25;95(4):445-53. Epub 2014 Sep 25.

Molecular Otolaryngology & Renal Research Labs, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA; Interdepartmental PhD Program in Genetics, University of Iowa, Iowa City, IA 52242, USA; Department of Molecular Physiology & Biophysics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA. Electronic address:

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October 2014

Cordova: web-based management of genetic variation data.

Bioinformatics 2014 Dec 14;30(23):3438-9. Epub 2014 Aug 14.

Department of Biomedical Engineering, Department of Ophthalmology and Visual Sciences, Department of Electrical and Computer Engineering, Department of Otolaryngology-Head & Neck Surgery, Carver College of Medicine, Department of Molecular Physiology & Biophysics, Carver College of Medicine, Interdisciplinary Graduate Program in Genetics and Iowa Institute for Human Genetics, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA.

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December 2014

Advancing genetic testing for deafness with genomic technology.

J Med Genet 2013 Sep 26;50(9):627-34. Epub 2013 Jun 26.

Department of Otolaryngology-Head and Neck Surgery, Molecular Otolaryngology & Renal Research Labs, University of Iowa Hospitals and Clinics, Iowa City, Iowa, USA.

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September 2013

Computational identification of operon-like transcriptional loci in eukaryotes.

Comput Biol Med 2013 Jul 28;43(6):738-43. Epub 2013 Mar 28.

Center for Bioinformatics and Computational Biology, University of Iowa, Iowa City, IA 52242, USA.

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July 2013

Prioritization of retinal disease genes: an integrative approach.

Hum Mutat 2013 Jun 12;34(6):853-9. Epub 2013 Apr 12.

Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA.

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June 2013

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

J Integr Bioinform 2012 Jul 30;9(1):208. Epub 2012 Jul 30.

Genetics Department, Albert Einstein College of Medicine, New York, New York 10461, USA.

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July 2012

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

Otolaryngol Head Neck Surg 2012 Nov 11;147(5):975-7. Epub 2012 Jul 11.

Department of Otolaryngology-Head and Neck Surgery, University of Iowa Hospitals and Clinics, Iowa City, IA, USA.

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November 2012

Informatics methods to enable sharing of quantitative imaging research data.

Magn Reson Imaging 2012 Nov 6;30(9):1249-56. Epub 2012 Jul 6.

Department of Biomedical Informatics and Medicine, Division of Hematology and Oncology, Vanderbilt University School of Medicine, Nashville, TN 37232-6838, USA.

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November 2012

Image-based biomarkers in clinical practice.

Semin Radiat Oncol 2011 Apr;21(2):157-66

Department of Radiation Oncology, University of Iowa, Iowa City, IA 52242, USA.

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April 2011

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

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

Department of Internal Medicine and Department of Molecular Physiology and Biophysics, 3181B Medical Education and Biomedical Research Facility, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.

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March 2010

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

J Supercomput 2009 Jan;5698:49-59

Coordinated Laboratory for Computational Genomics, University of Iowa, Iowa City, IA 52242 USA.

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January 2009

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

Bioinformatics 2008 Sep 21;24(18):1975-9. Epub 2008 Jul 21.

Department of Biomedical Engineering, Center for Bioinformatics and Computational Biology, University of Iowa, Iowa, USA.

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September 2008

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

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

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.

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January 2007

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

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

Departments of Ophthalmology and Biomedical Engineering, Howard Hughes Medical Institute, University of Iowa, Iowa City, IA 52242, USA.

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September 2006

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

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

Center for Bioinformatics and Computational Biology, The University of Iowa, Iowa City, IA 52242, USA.

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February 2007

Integration site choice of a feline immunodeficiency virus vector.

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

Program in Gene Therapy, Department of Pediatrics, University of Iowa, Iowa City, 52242, 52242, USA.

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September 2006

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

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

Coordinated Laboratory for Computational Genomics, The University of Iowa, Iowa City, Iowa 52240, USA.

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June 2006

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

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

Department of Medical Microbiology and Immunology, University of Wisconsin, 1300 University Ave., Madison, WI 53706, USA.

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November 2005

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

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

Department of Neurosurgery, University of Iowa Hospitals, Iowa City, Iowa 52242, USA.

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October 2005

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

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

Department of Internal Medicine, University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, IA 52242, USA.

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October 2005

Insights into a dinoflagellate genome through expressed sequence tag analysis.

BMC Genomics 2005 May 29;6:80. Epub 2005 May 29.

Department of Biological Sciences and Roy J, Carver Center for Comparative Genomics, University of Iowa, Iowa City, IA 52242, USA.

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May 2005

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

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

Department of Civil and Environmental Engineering, The University of Iowa, Iowa City, IA 52242, USA.

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April 2005

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

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

Center for Macular Degeneration, University of Iowa, Carver College of Medicine, Iowa City 52242, USA.

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July 2004

Gene expression profiling of potential PPARgamma target genes in mouse aorta.

Physiol Genomics 2004 Jun 17;18(1):33-42. Epub 2004 Jun 17.

Department of Internal Medicine, University of Iowa College of Medicine, Iowa City, Iowa 52242, USA.

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June 2004

Migration of the plastid genome to the nucleus in a peridinin dinoflagellate.

Curr Biol 2004 Feb;14(3):213-8

Department of Biological Sciences and Center for Comparative Genomics, The University of Iowa, Iowa City, IA 52242, USA.

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February 2004

Large-scale gene discovery in human airway epithelia reveals novel transcripts.

Physiol Genomics 2004 Mar 12;17(1):69-77. Epub 2004 Mar 12.

Department of Pediatrics, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA.

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March 2004

Genomics-based approaches to gene discovery in innate immunity.

Immunol Rev 2002 Dec;190:137-45

Department of Pediatrics, The University of Iowa, Iowa City, IA 52242, USA.

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December 2002