Finding disease specific alterations in the co-expression of genes. - Dennis Kostka; Rainer Spang (ISMB/ECCB (Supplement of Bioinformatics), 2004)

A physical model for tiling array analysis. - Ho-Ryun Chung; Dennis Kostka; Martin Vingron (ISMB/ECCB (Supplement of Bioinformatics), 2007)

Nested effects models for high-dimensional phenotyping screens. - Florian Markowetz; Dennis Kostka; Olga G. Troyanskaya; Rainer Spang (ISMB/ECCB (Supplement of Bioinformatics), 2007)

Methodology for exploring and communicating molecular characteristics of disease (Methodik zum Erkennen und zur Kommunikation molekularer Krankheitssignaturen) - Dennis Kostka (2007)

Analyzing gene perturbation screens with nested effects models in R and bioconductor. - Holger Fröhlich; Tim Beißbarth; Achim Tresch; Dennis Kostka; Juby Jacob; Rainer Spang; Florian Markowetz (Bioinform., 2008)

Detecting hierarchical structure in molecular characteristics of disease using transitive approximations of directed graphs. - Juby Jacob; Marcel Jentsch; Dennis Kostka; Stefan Bentink; Rainer Spang (Bioinform., 2008)

Microarray Based Diagnosis Profits from Better Documentation of Gene Expression Signatures. - Dennis Kostka; Rainer Spang (PLoS Comput. Biol., 2008)

Modeling DNA methylation dynamics with approaches from phylogenetics. - John A. Capra; Dennis Kostka (Bioinform., 2014)

Integrating Diverse Datasets Improves Developmental Enhancer Prediction. - Genevieve D. Erwin; Nir Oksenberg; Rebecca M. Truty; Dennis Kostka; Karl K. Murphy; Nadav Ahituv; Katherine S. Pollard; John A. Capra (PLoS Comput. Biol., 2014)

Random forest based similarity learning for single cell RNA sequencing data. - Maziyar Baran Pouyan; Dennis Kostka (Bioinform., 2018)

Large-scale inference of competing endogenous RNA networks with sparse partial correlation. - Markus List; Azim Dehghani Amirabad; Dennis Kostka; Marcel H. Schulz (Bioinform., 2019)

scds: computational annotation of doublets in single-cell RNA sequencing data. - Abha S. Bais; Dennis Kostka (Bioinform., 2020)

Non-negative Independent Factor Analysis disentangles discrete and continuous sources of variation in scRNA-seq data. - Weiguang Mao; Maziyar Baran Pouyan; Dennis Kostka; Maria Chikina (Bioinform., 2022)

An intrinsically interpretable neural network architecture for sequence-to-function learning. - Ali Tugrul Balci; Mark Maher Ebeid; Panayiotis V. Benos; Dennis Kostka; Maria Chikina (Bioinform., 2023)

Vaeda computationally annotates doublets in single-cell RNA sequencing data. - Hannah Schriever; Dennis Kostka (Bioinform., 2023)

aenmd: annotating escape from nonsense-mediated decay for transcripts with protein-truncating variants. - Jonathan Klonowski; Qianqian Liang; Zeynep H. Coban Akdemir; Cecilia Lo; Dennis Kostka (Bioinform., 2023)