Publications

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    ☆ = co-first authors
    ✉ = co-corresponding authors

    Preprints:

  • Small non-coding RNA expression in developing mouse nephron progenitor cells. Yu Leng Phua☆, Andrew Clugston☆, Kevin Hong Chen, Dennis Kostka✉, Jacqueline Ho✉ Preprint (bioRxiv) 2018. ( doi )

  • Random forest based similarity learning for single cell RNA sequencing data. M Baran Pouyan and Dennis Kostka Preprint (bioRxiv) 2018. ( doi )

  • Genome-wide Enhancer Maps Differ Significantly in Genomic Distribution, Evolution, and Function. ML Benton, SC Talipineni, D Kostka✉, JA Capra✉ Preprint (bioRxiv) 2017. ( doi )

  • Developmental loci harbor clusters of accelerated regions that evolved independently in ape lineages. D Kostka, AK Holloway, KS Pollard Preprint (bioRxiv) 2017. ( doi )

  • Modeling Enhancer-Promoter Interactions with Attention-Based Neural Networks. W Mao, D Kostka, M Chikina Preprint (bioRxiv) 2017. ( doi )


    Peer reviewed:

  • 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 )

  • DAF-16 and TCER-1 Facilitate Adaptation to Germline Loss by Restoring Lipid Homeostasis and Repressing Reproductive Physiology in C. elegans. FRG Amrit, EM Steenkiste, R Ratnappan, SW Chen, TB McClendon, D Kostka, J Yanowithz, CP Olsen, A Ghazi PLoS Genetics 2016, 12(2) e1005788. ( 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 )

  • Gibbon genome and the fast karyotype evolution of small apes. L Carbone et al. (93 authors) Nature 2014, 513, 195-201. ( doi )

  • Integrating diverse datasets improves developmental enhancer prediction. GD Erwin, N Oksenberg, RM Truty, D Kostka, N Ahituv, K Murphy, KS Pollard and JA Capra PLoS Computational Biology 2014, 10 (26) , e1003677. ( doi )

  • miR-17~92 is Required for Nephrogenesis and Renal Function. AK Marrone, DB Stolz, SI Bastacky, D Kostka, A Bodnar and J Ho Journal of the American Society of Nephrology (JASN) 2014, 25 (3). ( doi )

  • A Model-Based Analysis of GC-Biased Gene Conversion in the Human and Chimpanzee Genomes. JA Capra, MJ Hubisz, D Kostka, KS Pollard and A Siepel PLoS Genetics 2013, 9 (8), e1003684. ( 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 )

  • A High-Resolution Map of Human Evolutionary Constraint Using 29 Mammals K Lindblad-Toh et al. (68 authors) Nature 2011, 478, 476-482. ( 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 )

  • The Importance of Being Cis: Evolution of Orthologous Fish and Mammalian Enhancer Activity D Ritter, Q Li, D Kostka, KS Pollard, S Guo and JH Chuang Molecular Biology and Evolution 2010, 27, 2322-2332. ( doi )

  • Analyzing Gene Perturbation Screens With Nested Effects Models in R and Bioconductor H Fröhlich, T Beißbarth, A Tresch, D Kostka, J Jacob, R Spang and F Markowetz Bioinformatics 2008, 24, 2549-2550. ( doi )

  • Regulatory networks define phenotypic classes of human stem cell lines FJ Mueller, L Laurent, D Kostka, I Ulitsky, R Williams, C Lu, MS Rao, R Shamir, PH Schwartz, NO Schmidt and JF Loring Nature, 2008, 455, 401-105. ( doi )

  • Computational diagnostics with gene expression profiles C Lottaz, D Kostka , F Markowetz and R Spang Methods Mol Biol, 2008, 453, 281-296. ( doi )

  • Detecting Hierarchical Structure in Molecular Characteristics of Disease Using Transitive Approximations of Directed Graphs J Jacob, M Jentsch, D Kostka and R Spang, Bioinformatics 2008, 24, 995-1001. ( 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 )

  • Nested Effects Models for High-Dimensional Phenotyping Screens F Markowetz, D Kostka, O Troyanskaya and R Spang, Bioinformatics 2007, 23, i305-i312. ( doi )

  • A physical model for tiling array analysis HR Chung, D Kostka and M Vingron, Bioinformatics 2007, 23, i80-i86. ( doi )

  • Patient classification C Lottaz, D Kostka and R Spang. In Bioinformatics - From Genomes to Therapies, T. Lengauer (Ed), Wiley-VCH 2007.

  • Expression of Late Cell Cycle Genes and an Increased Proliferative Capacity Characterize Very Early Relapse of Childhood Acute Lymphoblastic Leukemia R Kirschner-Schwabe, C Lottaz, J Tödling, P Rhein, L Karawajew, C Eckert, A von Stackelberg, U Ungethüm, D Kostka, AE Kulozik, WD Ludwig, G Henze, R Spang, C Hagemeier and K Seeger, Clinical Cancer Research 2006, 2(15), 4553-61. ( doi )

  • Traces of Molecular Disease Mechanisms on Microarrays D Kostka, C Lottaz and R Spang In Statistische Methoden in der empirischen Forschung (ISSN 1615-4177), J. Kaufmann (Hrsg.) Schering AG (Berlin) 2005, 231-236.

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