☆ = Authors contributed equally
✉ = Co-corresponding Authors
Link to Google Scholar
Preprints:
- aenmd: Annotating escape from nonsense-mediated decay for transcripts with protein-truncating variants.
J Klonowski☆, Q Liang☆, ZC Akdemir, C Lo, and D Kostka.
Preprint (bioRxiv) 2023 .
( doi )
- 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 )