Publications

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    ☆ = Authors contributed equally
    ✉ = Co-corresponding Authors

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    Preprints:

  • An intrinsically interpretable neural network architecture for sequence to function learning. AT Balci, MM Ebeid, PV Benos, D Kostka✉, and M Chikina✉. Preprint (bioRxiv) 2023 . ( doi )

  • The perils of interaction prediction. W Mao, D Kostka, M Chikina Preprint (bioRxiv) 2018. ( doi )

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

    Peer reviewed:

  • Vaeda computationally annotates doublets in single-cell RNA sequencing data. H Schriever and D Kostka Bioinformatics 2023 39(1). ( doi )

  • Single-cell transcriptomic analysis identifies murine heart molecular features at embryonic and neonatal stages. W Feng, A Bais, H He, C Rios, S Jiang, J Xu, C Chang, D Kostka, and G Li. Nature Communications 2022 13(1). ( doi )

  • Computational profiling of hiPSC-derived heart organoids reveals chamber defects associated with NKX2-5 deficiency W Feng☆, H Schriever☆, S Jiang, A Bais, H Wu, D Kostka✉, and G Li✉ Communications Biology 2022 5(1). ( doi )

  • Non-negative Independent Factor Analysis for single cell RNA-seq W Mao, MB Pouyan, D Kostka, M Chikina Bioinformatics 2022 . ( doi )

  • Uncompensated mitochondrial oxidative stress underlies heart failure in an iPSC-derived model of congenital heart disease X Xu, K Jin, AS Bais, W Zhu, H Yagi, TN Feinstein, PK Nguyen, JD Criscione, X Liu, G Beutner, KB Karunakaran, KS Rao, H He, P Adams, CK Kuo, D Kostka, GS Pryhuber, S Shiva, MK Ganapathiraju, GA Porter, JI Lin, B Aronow, and CW Lo Cell Stem Cell 2022 (Online ahead of print). ( doi )

  • Chromatin accessibility and microRNA expression in nephron progenitor cells during kidney development A Clugston , A Bodnar , D Cerqueria , YL Pua, A Lawler, K Boggs, A Pfenning, J Ho✉, D Kostka✉. Genomics 2022 114(1):278-291. ( doi  )

  • Single cell RNA sequencing reveals differential cell cycle activity in key cell populations during nephrogenesis AS Bais☆ , DM Cerqueria☆ , AS Clugston☆ , J Ho✉, D Kostka✉ Scientific Reports 2021, 11, 22434. ( doi )

  • Apoptosis of hematopoietic progenitor-derived adipose tissue–resident macrophages contributes to insulin resistance after myocardial infarction. SB Vasamsetti, E Coppin, X Zhang, J Florentin, S Koul, M Götberg, AS Clugston, F Thoma, J Sembrat, GC Bullock, D Kostka, CM St. Croix, A Chattopadhyay, Mauricio Rojas, SR Mulukutla, P Dutta. Science Translational Medicine 2020, 12(533):eaaw0638. ( doi )

  • Deletion of hypoxia-responsive microRNA-210 results in a sex-specific decrease in nephron number. SL Hemker, DM Cerqueira, AJ Bodnar, KR Cargill, AC Clugston, MJ Anslow, S Sims-Lucas, D Kostka, J Ho. The FASEB Journal 2020, 34(4):5782-5799. ( doi )

  • scds: Computational Annotation of Doublets in Single Cell RNA Sequencing Data. AS Bais and D Kostka. Bioinformatics 2020, 36(4):1150–1158. ( doi )

  • Follistatin-like 1 Attenuation Causes Spontaneous Smoke-Resistant Pulmonary Emphysema M Henkel, J Partyka, AD Gregory, E Forno, MH Cho, T Eddens, AR Tout, N Salamacha, W Horne, KS Rao, Y Wu, JF Alcorn, D Kostka, R Hirsch, JC Celedón, SD Shapiro, JK Kolls, BT Campfield. Am J Respir Crit Care Med. 2019, 201(8):934-945. ( doi )

  • Control of cytokinesis by β-adrenergic receptors indicates an approach for regulating cardiomyocyte endowment. H Liu, CH Zhang, N Ammanamanchi, S Suresh, C Lewarchik, K Rao, GM Uys, L Han, M Abrial, D Yimlamai, B Ganapathy, C Guillermier, N Chen, M Khaladkar, J Spaethling, JH Eberwine, J Kim, S Walsh, S Choudhury, K Little, K Francis, M Sharma, M Viegas, AS Bais, D Kostka, J Ding, Z Bar-Joseph, Y Wu, ML Steinhauser, B Kühn. Sciene Translational Medicine 2019, 11(21):eaaw6419 ( doi )

  • Large-scale inference of competing endogeneous RNA networks with sparse partial correlation. M List, AD Amirabad, D Kostka, 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 )

  • Von Hippel-Lindau Acts as a Metabolic Switch Controlling Nephron Progenitor Differentiation. K Cargill, SL Hemker, A Clugston, A Murali, E Mukherjee, J Liu, D Bushnell, AJ Bodnar, Z Saifudeen, J Ho, CM Bates, D Kostka, ES Goetzman and S Sims-Lucas. J Am Soc Nephrol 2019, 30(7):1192-1205. ( doi )

  • Loss of miR-17~92 results in dysregulation of Cftr in nephron progenitors. YL Phua, KH Chen, SL Hemker, AK Marrone, AJ Bodnar, X Liu, A Clugston, D Kostka, MB Butterworth and J Ho. Am J Physiol Renal Physiol 2019, 316(5):F993-F1005. ( doi )

  • Small non-coding RNA expression in developing mouse nephron progenitor cells. YL Phua☆, A Clugston☆, KH Chen, D Kostka✉, J Ho✉. Scientific Data 2018, Article number: 180218. ( doi )

  • Random forest based similarity learning for single cell RNA sequencing data. MB Pouyan and D 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 )

  • 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 )

  • MicroRNA-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 )