Scott Dudek

Scott Dudek

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Scott Dudek

Scott Dudek

Publications by authors named "Scott Dudek"

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Integration of genetic and functional genomics data to uncover chemotherapeutic induced cytotoxicity.

Pharmacogenomics J 2019 04 25;19(2):178-190. Epub 2018 May 25.

Bioinformatics and Genomics program, Pennsylvania State University, University Park, Pennsylvania, USA.

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http://dx.doi.org/10.1038/s41397-018-0024-6DOI Listing
April 2019

A simulation study investigating power estimates in phenome-wide association studies.

BMC Bioinformatics 2018 04 4;19(1):120. Epub 2018 Apr 4.

Department of Genetics and Institute for Biomedical Informatics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.

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http://dx.doi.org/10.1186/s12859-018-2135-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5885318PMC
April 2018

Collective feature selection to identify crucial epistatic variants.

BioData Min 2018 19;11. Epub 2018 Apr 19.

1Biomedical and Translational Bioinformatics Institute, Geisinger Health System, 100 N Academy Avenue, Danville, PA 17822 USA.

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http://dx.doi.org/10.1186/s13040-018-0168-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5907720PMC
April 2018

INTEGRATING CLINICAL LABORATORY MEASURES AND ICD-9 CODE DIAGNOSES IN PHENOME-WIDE ASSOCIATION STUDIES.

Pac Symp Biocomput 2016 ;21:168-79

Biomedical and Translational Informatics, Geisinger Health System, Danville, PA, USA3Center for Systems Genomics, The Pennsylvania State University, University Park, PA, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4718547PMC
October 2016

Pathway analysis by randomization incorporating structure-PARIS: an update.

Bioinformatics 2016 08 7;32(15):2361-3. Epub 2016 Mar 7.

Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4965631PMC
August 2016

Identification of genetic interaction networks via an evolutionary algorithm evolved Bayesian network.

BioData Min 2016 10;9:18. Epub 2016 May 10.

Center for Systems Genomics, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA ; Biomedical & Translational Informatics, Geisinger Health System, Danville, Pennsylvania USA.

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http://dx.doi.org/10.1186/s13040-016-0094-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4862166PMC
May 2016

Binning somatic mutations based on biological knowledge for predicting survival: an application in renal cell carcinoma.

Pac Symp Biocomput 2015 :96-107

Center for Systems Genomics, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299944PMC
April 2016

Predicting censored survival data based on the interactions between meta-dimensional omics data in breast cancer.

J Biomed Inform 2015 Aug 3;56:220-8. Epub 2015 Jun 3.

Center for Systems Genomics, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA; Geisinger Health System, Danville, PA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jbi.2015.05.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4550096PMC
August 2015

Knowledge-driven genomic interactions: an application in ovarian cancer.

BioData Min 2014 9;7:20. Epub 2014 Sep 9.

Department of Biochemistry and Molecular Biology, Center for Systems Genomics, Pennsylvania State University, University Park, Pennsylvania, USA.

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http://dx.doi.org/10.1186/1756-0381-7-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4161273PMC
September 2014

Environment-wide association study (EWAS) for type 2 diabetes in the Marshfield Personalized Medicine Research Project Biobank.

Pac Symp Biocomput 2014 :200-11

Center for Systems Genomics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 512 Wartik Lab, University Park, PA 16802, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4037237PMC
August 2014

ATHENA: the analysis tool for heritable and environmental network associations.

Bioinformatics 2014 Mar 21;30(5):698-705. Epub 2013 Oct 21.

Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, USA and Department of Biochemistry and Molecular Biology, Center for Systems Genomics, Pennsylvania State University, University Park, PA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt572DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3933870PMC
March 2014

ATHENA: Identifying interactions between different levels of genomic data associated with cancer clinical outcomes using grammatical evolution neural network.

BioData Min 2013 Dec 20;6(1):23. Epub 2013 Dec 20.

Center for Systems Genomics, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park PA, USA.

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http://dx.doi.org/10.1186/1756-0381-6-23DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3912499PMC
December 2013

Finding unique filter sets in PLATO: a precursor to efficient interaction analysis in GWAS data.

Pac Symp Biocomput 2010 :315-26

Center for Human Genetics Research, Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN 37232, United States.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2903053PMC
November 2013

Visual integration of results from a large DNA biobank (BioVU) using synthesis-view.

Pac Symp Biocomput 2011 :265-75

Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University, 507D Light Hall, Nashville, TN 37205, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3065108PMC
November 2013

Visualizing genomic information across chromosomes with PhenoGram.

BioData Min 2013 Oct 16;6(1):18. Epub 2013 Oct 16.

Center for Systems Genomics, Department of Biochemistry and Molecular Biology, Eberly College of Science, The Huck Institutes of the Life Sciences, The Pennsylvania State University, 512 Wartik Laboratory, University Park, PA 16802, USA.

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http://dx.doi.org/10.1186/1756-0381-6-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4015356PMC
October 2013

Visually integrating and exploring high throughput Phenome-Wide Association Study (PheWAS) results using PheWAS-View.

BioData Min 2012 Jun 8;5(1). Epub 2012 Jun 8.

Center for Systems Genomics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, Eberly College of Science, The Huck Institutes of the Life Sciences, University Park, PA, USA.

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http://biodatamining.biomedcentral.com/articles/10.1186/1756
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http://dx.doi.org/10.1186/1756-0381-5-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3476448PMC
June 2012

Synthesis-View: visualization and interpretation of SNP association results for multi-cohort, multi-phenotype data and meta-analysis.

BioData Min 2010 Dec 16;3:10. Epub 2010 Dec 16.

Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville TN, USA.

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http://dx.doi.org/10.1186/1756-0381-3-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3012023PMC
December 2010

ATHENA: A knowledge-based hybrid backpropagation-grammatical evolution neural network algorithm for discovering epistasis among quantitative trait Loci.

BioData Min 2010 Sep 27;3(1). Epub 2010 Sep 27.

Center for Human Genetics Research, Departments of Molecular Physiology & Biophysics and Biomedical Informatics, Vanderbilt University, Nashville, TN, USA.

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http://dx.doi.org/10.1186/1756-0381-3-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2955681PMC
September 2010

A cross-validation procedure for general pedigrees and matched odds ratio fitness metric implemented for the multifactor dimensionality reduction pedigree disequilibrium test.

Genet Epidemiol 2010 Feb;34(2):194-9

Center for Genetic Epidemiology and Statistical Genetics, Miami Institute for Human Genomics, University of Miami Miller School of Medicine, Florida, USA.

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http://dx.doi.org/10.1002/gepi.20447DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2811750PMC
February 2010

Visualizing SNP statistics in the context of linkage disequilibrium using LD-Plus.

Bioinformatics 2010 Feb 3;26(4):578-9. Epub 2010 Feb 3.

Department of Molecular Physiology, Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
Publisher Site
http://dx.doi.org/10.1093/bioinformatics/btp678DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2820673PMC
February 2010

A general framework for formal tests of interaction after exhaustive search methods with applications to MDR and MDR-PDT.

PLoS One 2010 Feb 23;5(2):e9363. Epub 2010 Feb 23.

Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0009363PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2826406PMC
February 2010

Biofilter: a knowledge-integration system for the multi-locus analysis of genome-wide association studies.

Pac Symp Biocomput 2009 :368-79

Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37232, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2859610PMC
March 2009

Comparison of approaches for machine-learning optimization of neural networks for detecting gene-gene interactions in genetic epidemiology.

Genet Epidemiol 2008 May;32(4):325-40

Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA.

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http://dx.doi.org/10.1002/gepi.20307DOI Listing
May 2008

Alternative contingency table measures improve the power and detection of multifactor dimensionality reduction.

BMC Bioinformatics 2008 May 16;9:238. Epub 2008 May 16.

Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, Tennessee, USA.

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http://dx.doi.org/10.1186/1471-2105-9-238DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2412877PMC
May 2008

Data simulation software for whole-genome association and other studies in human genetics.

Pac Symp Biocomput 2006 :499-510

Center for Human Genetics Research, Vanderbilt University, 519 Light Hall, Nashville, TN 37232, USA.

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January 2007

Parallel multifactor dimensionality reduction: a tool for the large-scale analysis of gene-gene interactions.

Bioinformatics 2006 Sep 29;22(17):2173-4. Epub 2006 Jun 29.

Center for Human Genetics Research, Vanderbilt University, Nashville, TN, USA.

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http://dx.doi.org/10.1093/bioinformatics/btl347DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4939609PMC
September 2006

Drosophila CLOCK is constitutively expressed in circadian oscillator and non-oscillator cells.

J Biol Rhythms 2006 Apr;21(2):93-103

Department of Biology and Biochemistry, University of Houston, Houston, TX, USA.

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http://dx.doi.org/10.1177/0748730405283697DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1435446PMC
April 2006

Exploratory visual analysis of pharmacogenomic results.

Pac Symp Biocomput 2005 :296-307

Computational Genetics Laboratory, Department of Genetics, Dartmouth Medical School, Lebanon, NH 03756, USA.

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April 2005

VRILLE feeds back to control circadian transcription of Clock in the Drosophila circadian oscillator.

Neuron 2003 Jan;37(2):249-61

Department of Biology and Biochemistry, University of Houston, 369 Science and Research Bldg 2, Houston, TX 77204, USA.

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http://dx.doi.org/10.1016/s0896-6273(03)00002-3DOI Listing
January 2003