Dennis Kostka, Ph.D.

  • Associate Professor

Research Interests

How do different organs and tissues arise? What are the genetic and epigenetic mechanisms that drive this development? To address these questions we design statistical methods and algorithms and apply them to large-scale, genome-wide data. Ultimately, our goal is to generate, test, and confirm hypotheses that are relevant to human health. 

Representative Publications

scds: Computational Annotation of Doublets in Single Cell RNA Sequencing Data. AS Bais and D Kostka Bioinformatics 2019, epub ahead of print ( doi )

Large-scale inference of competing endogeneous RNA networks with sparse partial correlation. M List, AD Amirabad, D Kostka and M Schulz. Bioinformatics 2019, 35(14):i596-i604 ( doi )

Genome-wide Enhancer Maps Differ Significantly in Genomic Distribution, Evolution, and Function. ML Benton, SC Talipineni, D Kostka, JA Capra. BMC Genomics 2019, 20(1):511. ( doi )

Small non-coding RNA expression in developing mouse nephron progenitor cells. Yu Leng Phua, Andrew Clugston, Kevin Hong Chen, Dennis Kostka, Jacqueline Ho. Scientific Data 2018, Article number: 180218. ( doi )

Random forest based similarity learning for single cell RNA sequencing data. M Baran Pouyan and Dennis Kostka. Bioinformatics >2018, 34(13):i79-i88. ( doi )

Developmental loci harbor clusters of accelerated regions that evolved independently in ape lineages D Kostka, AK Holloway, KS Pollard. Molecular Biology and Evolution 2018, 35(8):2034-2045. ( doi )

The complex genetics of hypoplastic left heart syndrome. X Liu, H Yagi, S Saeed, AS Bais, GC Gabriel, Z Chen, KA Peterson, Y Li, MC Schwartz, WT Reynolds, M Saydmohammed, B Gibbs, Y Wu, W Devine, B Chatterjee, NT Klena, D Kostka, KL de Mesy Bentley, MK Ganapathiraju, P Dexheimer, L Leatherbury, O Khalifa, A Bhagat, M Zahid, W Pu, S Watkins, P Grossfeld, S Murray, GA Porter Jr, M Tsang, LJ Martin, DW Benson, BJ Aronow, CW Lo. Nature Genetics 2017, 49(7):1152-1159. ( doi )

motifDiverge: a model for assessing the statistical significance of gene regulatory motif divergence between two DNA sequences. D Kostka, T Friedrich, AK Holloway, KS Pollard. Statistics and Its Interface 2015, 8(4): 463–476. ( doi )

Modeling DNA methylation dynamics with approaches from phylogenetics. JA Capra and D Kostka. Bioinformatics 2014, 30 (17), i408-i414. ( doi )

The Role of GC-Biased Gene Conversion in Shaping the Fastest Evolving Regions of the Human Genome D Kostka, MJ Hubisz, A Siepel and KS Pollard. Molecular Biology and Evolution 2012, 29, 1047-1057. ( doi )

Non-coding sequences near duplicated genes evolve rapidly D Kostka, MW Hahn and KS Pollard. Genome Biology and Evolution 2010, 2, 518-33. ( doi )

Microarray Based Diagnosis Profits from Better Documentation of Gene Expression Signatures D Kostka and R Spang. PLoS Computational Biology 2008, Feb 15, e22. ( doi )

Finding Disease Specific Alterations in the Coexpression of Genes D Kostka and R Spang. Bioinformatics 2004, 20, i194-i199. ( doi )