Florian Markowetz, Dennis Kostka, Olga G. Troyanskaya, Rainer Spang
Motivation: In high-dimensional phenotyping screens, a large number of cellular features is observed after perturbing genes by knockouts or RNA interference. Comprehensive analysis of perturbation...
BIOINFORMATICS doi:10.1093/bioinformatics/btm167 A physical model for tiling array analysis (2008)
Ho-ryun Chung, Dennis Kostka, Martin Vingron
Motivation: Chromatin immunoprecipitation (ChIP) is a powerful experimental approach to identify in vivo binding sites of sequencespecific transcription factors (TFs). These experiments are designed...
Microarray Based Diagnosis Profits from Better Documentation of Gene Expression Signatures (2008)
Microarray gene expression signatures hold great promise to improve diagnosis and prognosis of disease. However, current documentation standards of such signatures do not allow for an unambiguous...
Microarray Based Diagnosis Profits from Better Documentation of Gene Expression Signatures (2008)
Microarray gene expression signatures hold great promise to improve diagnosis and prognosis of disease. However, current documentation standards of such signatures do not allow for an unambiguous...
Jacob, Juby, Jentsch, Marcel, Kostka, Dennis, Bentink, Stefan, Spang, Rainer
Motivation: Molecular diagnostics aims at classifying diseases into clinically relevant sub-entities based on molecular characteristics. Typically, the entities are split into subgroups, which might...
Microarray Based Diagnosis Profits from Better Documentation of Gene Expression Signatures (2008)
Microarray gene expression signatures hold great promise to improve diagnosis and prognosis of disease. However, current documentation standards of such signatures do not allow for an unambiguous...
Regulatory networks define phenotypic classes of human stem cell lines (2008)
Müller, Franz-Josef, Laurent, Louise C., Kostka, Dennis, Ulitsky, Igor, Williams, Roy, Lu, Christina, ...
Stem cells are defined as self-renewing cell populations that can differentiate into multiple distinct cell types. However, hundreds of different human cell lines from embryonic, fetal and adult...
Jacob, Juby, Jentsch, Marcel, Kostka, Dennis, Bentink, Stefan, Spang, Rainer
Motivation: Molecular diagnostics aims at classifying diseases into clinically relevant sub-entities based on molecular characteristics. Typically, the entities are split into subgroups, which might...
Analyzing gene perturbation screens with nested effects models in R and bioconductor (2008)
Fröhlich, Holger, Beißbarth, Tim, Tresch, Achim, Kostka, Dennis, Jacob, Juby, Spang, Rainer, ...
Summary: Nested effects models (NEMs) are a class of probabilistic models introduced to analyze the effects of gene perturbation screens visible in high-dimensional phenotypes like microarrays or...
Nested effects models for high-dimensional phenotyping screens (2007)
Markowetz, Florian, Kostka, Dennis, Troyanskaya, Olga G., Spang, Rainer
Motivation: In high-dimensional phenotyping screens, a large number of cellular features is observed after perturbing genes by knockouts or RNA interference. Comprehensive analysis of perturbation...
A physical model for tiling array analysis (2007)
Chung, Ho-Ryun, Kostka, Dennis, Vingron, Martin
Motivation: Chromatin immunoprecipitation (ChIP) is a powerful experimental approach to identify in vivo binding sites of sequence-specific transcription factors (TFs). These experiments are designed...
A physical model for tiling array analysis. (2007)
Chung, Ho-Ryun, Kostka, Dennis, Vingron, Martin
Motivation: Chromatin immunoprecipitation (ChIP) is a powerful experimental approach to identify in vivo binding sites of sequence-specific transcription factors (TFs). These experiments are designed...
Nested effects models for high-dimensional phenotyping screens. (2007)
Markowetz, Florian, Kostka, Dennis, Troyanskaya, Olga G., Soang, Rainer
Motivation: In high-dimensional phenotyping screens, a large number of cellular features is observed after perturbing genes by knockouts or RNA interference. Comprehensive analysis of perturbation...
Traces of molecular disease mechanisms on microarrays (2005)
Dennis Kostka, Claudio Lottaz, Rainer Spang
The main roads of statistical microarray data analysis currently include data normalization, multiple testing, classification models, clustering algorithms and graphical models of transcriptional...
Finding disease specific alterations in the co-expression of genes (2004)
Motivation: Standard analysis routines for microarray data aim at differentially expressed genes. In this paper, we address the complementary problem of detecting sets of differentially co-expressed...
Finding disease specific alterations in the co-expression of genes (2004)
Motivation: Standard analysis routines for microarray data aim at differentially expressed genes. In this paper, we address the complementary problem of detecting sets of differentially co-expressed...
Finding disease specific alterations in the co-expression of genes (2004)
Motivation: Standard analysis routines for microarray data aim at differentially expressed genes. In this paper, we address the complementary problem of detecting sets of differentially co-expressed...
Screening for Gain Or Loss of Co-Regulation in Cancer Specific Expression Profiles (2003)
Introduction Situation: For patients with pediatric acute lymphoblastic leukemia (ALL) chemo--therapy is adapted to a patient's risk of relapse. Certain risk groups that have been defined on a...
Microarray Based Diagnosis Profits from Better Documentation of Gene Expression Signatures
Microarray gene expression signatures hold great promise to improve diagnosis and prognosis of disease. However, current documentation standards of such signatures do not allow for an unambiguous...
Analyzing gene perturbation screens with nested effects models in R and bioconductor
Fröhlich, Holger, Beißbarth, Tim, Tresch, Achim, Kostka, Dennis, Jacob, Juby, Spang, Rainer, ...
Summary: Nested effects models (NEMs) are a class of probabilistic models introduced to analyze the effects of gene perturbation screens visible in high-dimensional phenotypes like microarrays or...