Publications by authors named "Dennis Kostka"

34Publications

Deletion of hypoxia-responsive microRNA-210 results in a sex-specific decrease in nephron number.

FASEB J 2020 Apr 5;34(4):5782-5799. Epub 2020 Mar 5.

Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.

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http://dx.doi.org/10.1096/fj.201902767RDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7136145PMC
April 2020

Large-scale inference of competing endogenous RNA networks with sparse partial correlation.

Bioinformatics 2019 07;35(14):i596-i604

Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btz314DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6612827PMC
July 2019

scds: computational annotation of doublets in single-cell RNA sequencing data.

Bioinformatics 2020 02;36(4):1150-1158

Department of Developmental Biology, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz698DOI Listing
February 2020

Genome-wide enhancer annotations differ significantly in genomic distribution, evolution, and function.

BMC Genomics 2019 Jun 20;20(1):511. Epub 2019 Jun 20.

Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, 37235, USA.

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http://dx.doi.org/10.1186/s12864-019-5779-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6585034PMC
June 2019

Von Hippel-Lindau Acts as a Metabolic Switch Controlling Nephron Progenitor Differentiation.

J Am Soc Nephrol 2019 07 29;30(7):1192-1205. Epub 2019 May 29.

Rangos Research Center, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania;

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http://dx.doi.org/10.1681/ASN.2018111170DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6622426PMC
July 2019

Loss of results in dysregulation of in nephron progenitors.

Am J Physiol Renal Physiol 2019 05 6;316(5):F993-F1005. Epub 2019 Mar 6.

Rangos Research Center, UPMC Children's Hospital of Pittsburgh , Pittsburgh, Pennsylvania.

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http://dx.doi.org/10.1152/ajprenal.00450.2018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6580251PMC
May 2019

Small non-coding RNA expression in mouse nephrogenic mesenchymal progenitors.

Sci Data 2018 11 13;5:180218. Epub 2018 Nov 13.

Rangos Research Center, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA.

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http://www.nature.com/articles/sdata2018218
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http://dx.doi.org/10.1038/sdata.2018.218DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6233257PMC
November 2018

Random forest based similarity learning for single cell RNA sequencing data.

Bioinformatics 2018 07;34(13):i79-i88

Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA.

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http://dx.doi.org/10.1093/bioinformatics/bty260DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6022547PMC
July 2018

DAF-16 and TCER-1 Facilitate Adaptation to Germline Loss by Restoring Lipid Homeostasis and Repressing Reproductive Physiology in C. elegans.

PLoS Genet 2016 Feb 10;12(2):e1005788. Epub 2016 Feb 10.

Department of Pediatrics, Rangos Research Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1005788DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4749232PMC
February 2016

motifDiverge: a model for assessing the statistical significance of gene regulatory motif divergence between two DNA sequences.

Stat Interface 2015;8(4):463-476

Gladstone Institutes, Institute for Human Genetics, Division of Biostatistics, University of California, 1650 Owens Street, San Francisco, CA 94158, USA.

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http://www.intlpress.com/site/pub/pages/journals/items/sii/c
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http://dx.doi.org/10.4310/SII.2015.v8.n4.a6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4689439PMC
January 2015

Gibbon genome and the fast karyotype evolution of small apes.

Nature 2014 Sep;513(7517):195-201

Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1038/nature13679DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4249732PMC
September 2014

Modeling DNA methylation dynamics with approaches from phylogenetics.

Bioinformatics 2014 Sep;30(17):i408-14

Center for Human Genetics Research, Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37232, Departments of Developmental Biology and Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA 15201, USA Center for Human Genetics Research, Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37232, Departments of Developmental Biology and Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA 15201, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu445DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4147898PMC
September 2014

Integrating diverse datasets improves developmental enhancer prediction.

PLoS Comput Biol 2014 Jun 26;10(6):e1003677. Epub 2014 Jun 26.

Center for Human Genetics Research and Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1003677DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4072507PMC
June 2014

MicroRNA-17~92 is required for nephrogenesis and renal function.

J Am Soc Nephrol 2014 Jul 7;25(7):1440-52. Epub 2014 Feb 7.

Division of Nephrology, Department of Pediatrics,

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http://dx.doi.org/10.1681/ASN.2013040390DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073423PMC
July 2014

A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes.

PLoS Genet 2013 15;9(8):e1003684. Epub 2013 Aug 15.

Gladstone Institutes, University of California, San Francisco, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1003684DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3744432PMC
March 2014

The role of GC-biased gene conversion in shaping the fastest evolving regions of the human genome.

Mol Biol Evol 2012 Mar 10;29(3):1047-57. Epub 2011 Nov 10.

Gladstone Institute of Cardiovascular Disease, University of California, San Francisco, USA.

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https://academic.oup.com/mbe/article-lookup/doi/10.1093/molb
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http://dx.doi.org/10.1093/molbev/msr279DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3278478PMC
March 2012

A high-resolution map of human evolutionary constraint using 29 mammals.

Nature 2011 Oct 12;478(7370):476-82. Epub 2011 Oct 12.

Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1038/nature10530DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3207357PMC
October 2011

Noncoding sequences near duplicated genes evolve rapidly.

Genome Biol Evol 2010 29;2:518-33. Epub 2010 Jun 29.

Gladstone Institute for Cardiovascular Disease, Gladstone Institutes, University of California-San Francisco, San Francisco, CA, USA.

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https://academic.oup.com/gbe/article/doi/10.1093/gbe/evq037/
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http://dx.doi.org/10.1093/gbe/evq037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2942038PMC
December 2010

The importance of being cis: evolution of orthologous fish and mammalian enhancer activity.

Mol Biol Evol 2010 Oct 21;27(10):2322-32. Epub 2010 May 21.

Department of Biology, Boston College, Chestnut Hill, Massachusetts, USA.

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https://academic.oup.com/mbe/article-lookup/doi/10.1093/molb
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http://dx.doi.org/10.1093/molbev/msq128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3107594PMC
October 2010

Regulatory networks define phenotypic classes of human stem cell lines.

Nature 2008 Sep 24;455(7211):401-5. Epub 2008 Aug 24.

Center for Regenerative Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.

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http://dx.doi.org/10.1038/nature07213DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2637443PMC
September 2008

Analyzing gene perturbation screens with nested effects models in R and bioconductor.

Bioinformatics 2008 Nov 21;24(21):2549-50. Epub 2008 Aug 21.

German Cancer Research Center, INF 580, 69120 Heidelberg, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btn446DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2732276PMC
November 2008

Computational diagnostics with gene expression profiles.

Methods Mol Biol 2008 ;453:281-96

Max Planck Institute for Molecular Genetics and Berlin Center for Genome-Based Bioinformatics, Berlin, Germany.

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http://dx.doi.org/10.1007/978-1-60327-429-6_15DOI Listing
October 2008

Detecting hierarchical structure in molecular characteristics of disease using transitive approximations of directed graphs.

Bioinformatics 2008 Apr 19;24(7):995-1001. Epub 2008 Feb 19.

Computational Diagnostics Group, Institute of Functional Genomics, University of Regensburg, 93053 Regensburg, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btn056DOI Listing
April 2008

Microarray based diagnosis profits from better documentation of gene expression signatures.

PLoS Comput Biol 2008 Feb;4(2):e22

Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany.

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http://dx.doi.org/10.1371/journal.pcbi.0040022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2242819PMC
February 2008

A physical model for tiling array analysis.

Bioinformatics 2007 Jul;23(13):i80-6

Max-Planck-Institut für molekulare Genetik, Ihnestrasse 63-73, 14195 Berlin, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btm167DOI Listing
July 2007

Nested effects models for high-dimensional phenotyping screens.

Bioinformatics 2007 Jul;23(13):i305-12

Lewis-Sigler Institute for Integrative Genomics and Department of Computer Science, Princeton University, Princeton, NJ, 08544, USA.

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http://dx.doi.org/10.1093/bioinformatics/btm178DOI Listing
July 2007

Expression of late cell cycle genes and an increased proliferative capacity characterize very early relapse of childhood acute lymphoblastic leukemia.

Clin Cancer Res 2006 Aug;12(15):4553-61

Department of Pediatric Oncology/Hematology, HELIOS Klinikum Berlin, Robert-Roessle-Clinic, Laboratory for Functional Genomics, Charité-Universitätsmedizin Berlin, Berlin, Germany.

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http://dx.doi.org/10.1158/1078-0432.CCR-06-0235DOI Listing
August 2006

Finding disease specific alterations in the co-expression of genes.

Bioinformatics 2004 Aug;20 Suppl 1:i194-9

Max Planck Institute for Molecular Genetics, Berlin, Germany.

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http://dx.doi.org/10.1093/bioinformatics/bth909DOI Listing
August 2004