How to understand the cell by breaking it: network analysis of gene perturbation screens (2009)
Modern high-throughput gene perturbation screens are key technologies at the forefront of genetic research. Combined with rich phenotypic descriptors they enable researchers to observe detailed...
SMP BIOINFORMATICS BIOINFORMATICS – WHAT THE DATA REALLY MEAN (2009)
Elena Reiffel, Stefanie Scheid, Florian Markowetz, Stefan Bentink
Clinic, 26 young scientists are sitting engrossed in their work at computer terminals. In four days the participants are to learn as much as possible about the statistical analysis of DNA microarray...
Florian Markowetz, Lutz Edler, Martin Vingron
Abstract: Knowledge of the three-dimensional structure of a protein is essential for describing and understanding its function. Today, a large number of known protein sequences faces a small number...
Florian Markowetz, Jacques Bloch, Rainer Spang
Motivation: Cellular signaling pathways, which are not modulated on a transcriptional level, cannot be directly deduced from expression profiling experiments. The situation changes, when external...
Florian Markowetz, From Rnai Data, Boutros Et Al, Dev Cell
group headed by Michael Boutros at DKFZ Heidelberg. Genome-wide RNAi screens in Drosophila systematically probe loss-of-phenotypes in cell-based assays. (Boutros et al., Science, Feb 2004)
Edoardo M. Airoldi, Florian Markowetz, David M. Blei, Olga G. Troyanskaya
discovery of signaling pathways from an ensemble of
Pleiotropic hierarchies from high-dimensional phenotyping by (2008)
Florian Markowetz, Juby Jacob, Stefan Bentink, Rainer Spang
RNA interference
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...
→ Optimal Separating Hyperplanes, SVM (2008)
Two roads to classification Given: patient profiles already diagnosed by an expert. Task: infer a general rule to diagnose new patients. Basically, there are two ways to solve the task 1. model class...
Florian Markowetz, Max Planck, Different Covs
Two roads to classification 1. model class probabilities
Computational Inference of Cellular Pathways (2008)
Coexpression hints to • coregulation • gene function If genes show the same expression profiles they follow the same regulatory regimes [4, 10]. Florian Markowetz, Computational Inference of...
Structure Learning in Nested Effects Models (2008)
Tresch, Achim, Markowetz, Florian
Nested Effects Models (NEMs) are a class of graphical models introduced to analyze the results of gene perturbation screens. NEMs explore noisy subset relations between the high-dimensional outputs...
Structure Learning in Nested Effects Models (2008)
Tresch, Achim, Markowetz, Florian
Nested Effects Models (NEMs) are a class of graphical models introduced to analyze the results of gene perturbation screens. NEMs explore noisy subset relations between the high-dimensional outputs...
Structure Learning in Nested Effects Models (2008)
Tresch, Achim, Markowetz, Florian
Nested Effects Models (NEMs) are a class of graphical models introduced to analyze the results of gene perturbation screens. NEMs explore noisy subset relations between the high-dimensional outputs...
Structure Learning in Nested Effects Models (2008)
Tresch, Achim, Markowetz, Florian
Nested Effects Models (NEMs) are a class of graphical models introduced to analyze the results of gene perturbation screens. NEMs explore noisy subset relations between the high-dimensional outputs...
Max-Planck-Institute for Molecular Genetics Computational Molecular Biology (2007)
Florian Markowetz, Martin Vingron
Knowledge of the three-dimensional structure of a protein is essential for describing and understanding its function. Today, a large number of known protein sequences faces a small number of identied...
Florian Markowetz, Martin Vingron
Abstract: Knowledge of the three-dimensional structure of a protein is essential for describing and understanding its function. Today, a large number of known protein sequences faces a small number...
on Theoretical and Experimental Analysis of Discrete Algorithms). URL (2007)
This is a collection of references about learning regulatory networks with an emphasis an bayesian network models. It contains articles from biology and bioinformatics, as well as theoretical...
Florian Markowetz, Rainer Spang
gene regulation networks from passive observations and active interventions
Florian Markowetz, Rainer Spang
gene regulation networks from passive observations and active interventions
Florian Markowetz, Betreuer Prof, Dr. E. Mammen, Mathematische Fakultat Der, Jorge Luis Borges
under the supervision of Prof. Dr. Enno Mammen. I wish to thank him for his help and advice. The research was carried out at the Department of Theoretical Bioinformatics (TBI) at the German Cancer...
Florian Markowetz, Anja Von Heydebreck
convert into numerical values standard experiment gene 1 14,243 12,154 gene 2 5,323 27,152 gene 3 10,300
Florian Markowetz, Anja Von Heydebreck
ISIS is a class discovery method for microarray data described by Heydebreck et al. (2001). The objective is to discover biologically relevant structures in the gene expression proles of dierent...
Florian Markowetz, Anja Von Heydebreck
What is ISIS? ISIS is a class discovery method for microarray data described by Heydebreck et al. (2001). The objective is to discover biologically relevant structures in the gene expression proles...
Structure Learning in Nested Effects Models (2007)
Tresch, Achim, Markowetz, Florian
Nested Effects Models (NEMs) are a class of graphical models introduced to analyze the results of gene perturbation screens. NEMs explore noisy subset relations between the high-dimensional outputs...
Inferring cellular networks – a review (2007)
Markowetz, Florian, Spang, Rainer
Abstract In this review we give an overview of computational and statistical methods to reconstruct cellular networks. Although this area of research is vast and fast developing, we show that most...
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...
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...
Inferring cellular networks – a review. (2007)
Markowetz, Florian, Spang, Rainer
In this review we give an overview of computational and statistical methods to reconstruct cellular networks. Although this area of research is vast and fast developing, we show that most currently...
Basic research: What role plays gene A in disease B? • differentialy expressed genes • co-expressed genes • research about populations • aims for increased general knowledge Clinical routine:...
— Molecular Diagnosis — Tumor classification by SVM and PAM (2007)
Abstract. This tutorial refers to the practical session on day five of the course on microarray at Oslo University.. The topic is Molecular Diagnosis. You will learn how to apply Nearest Shrunken...
Florian Markowetz, Sachiyo Aburatani, Kosuke Tashiro, Christopher J Savoie, Mayumi Nishizawa, Kaori Hayashi, ...
This is a collection of references on learning regulatory and signaling networks. It contains articles from biology and bioinformatics, as well as theoretical background in mathematics and computer...
BMC Bioinformatics Review Inferring cellular networks – a review (2007)
Florian Markowetz, Rainer Spang
In this review we give an overview of computational and statistical methods to reconstruct cellular networks. Although this area of research is vast and fast developing, we show that most currently...
am Fachbereich Mathematik und Informatik (2006)
Florian Markowetz, Viola Gesellchen, Britta Koch, Stefanie Scheid, Stefan Bentink, Stefan Haas
Acknowledgements This work was carried out in the Computational Diagnostics
Statistics for Biological Networks (2006)
Florian Markowetz, Rainer Spang, Transcriptional Regulation
reconstructed from secondary effects of RNAi
Non-transcriptional pathway features reconstructed from secondary effects of RNA interference (2005)
Markowetz, Florian, Bloch, Jacques, Spang, Rainer
Motivation: Cellular signaling pathways, which are not modulated on a transcriptional level, cannot be directly deduced from expression profiling experiments. The situation changes, when external...
Probabilistic soft interventions in Conditional Gaussian networks (2005)
Markowetz, Florian, Grossmann, Steffen, Spang, Rainer
We introduce a general concept of probabilistic interventions in Bayesian networks. This generalizes deterministic interventions, which fix nodes to certain states. We propose “pushing” variables...
Molecular diagnosis: classification, model selection, and performance evaluation (2005)
Markowetz, Florian, Spang, Rainer
OBJECTIVES: We discuss supervised classification techniques applied to medical diagnosis based on gene expression profiles. Our focus lies on strategies of adaptive model selection to avoid...
Supervised learning In the first part, I introduced molecular diagnosis as a problem of classification in high dimensions. From given patient expression profiles and labels, we derive a classifier to...
Florian Markowetz, Microarray Data
Personalized medicine Which disease has the patient? Which treatment should he get? Will he develop side-effects? These questions 1. refer to individuals, 2. address predictive problems, 3. directly...
Berlin Center for Genome Based Bioinformatics (2005)
High-throughput assays probe cells at a genome-wide scale. Very prominent: microarrays measure mRNA transcript quantitites. Need to use probabilistic models, which account for • measurement noise,...
Clustering by coexpression (2005)
Florian Markowetz, Modelling Networks
High-throughput assays can probe cells at a genome-wide scale. Very prominent: microarrays that measure mRNA transcript quantitites. Need to use probabilistic models, which account for •...
Non-transcriptional pathway features reconstructed from secondary effects of RNA interference (2005)
Markowetz, Florian, Bloch, Jacques, Spang, Rainer
Motivation: Cellular signaling pathways, which are not modulated on a transcriptional level, cannot be directly deduced from expression profiling experiments. The situation changes, when external...
Non-transcriptional pathway features reconstructed from secondary effects of RNA interference (2005)
Markowetz, Florian, Bloch, Jacques, Spang, Rainer
Motivation: Cellular signaling pathways, which are not modulated on a transcriptional level, cannot be directly deduced from expression profiling experiments. The situation changes, when external...
Berlin Center for Genome Based Bioinformatics (2004)
Florian Markowetz, Rainer Spang, Max Planck
Project in collaboration with the Signaling and Functional Genomics group headed by Michael Boutros at DKFZ Heidelberg. Genome-wide RNA interference screens in Drosophila systematically probe...
Berlin Center for Genome Based Bioinformatics (2004)
Florian Markowetz, Rainer Spang, Florian Markowetz, Learning Interventions, Modeling Rnai
Develop novel methodologies to systematically identify novel signaling pathway members and order pathway components into networks. 1. RNAi experiments 2. Computational analysis Figure from (Boutros...
Winter term 03/04 1 — Genetic networks — (2004)
• Microarrays provide a snapshot of gene expression in a cell. Genes are not expressed independently, they regulate each others activity. Goal: Reconstruct the gene regulation network! • We want...
Acetylcysteine for prevention of contrast nephropathy: meta-analysis (2003)
Birck,Rainer, Krzossok,Stefan, Markowetz,Florian, Schnulle,Peter, Van Der Woude,Fokko J., Braun,Claude
Background Contrast nephropathy is associated with increased in-hospital morbidity and mortality and leads to extension of hospital stay in patients with chronic renal insufficiency. Acetylcysteine...
Support vector machines for protein fold class prediction (2003)
Markowetz,Florian, Edler,Lutz, Vingron,Martin
Knowledge of the three-dimensional structure of a protein is essential for describing and understanding its function. Today, a large number of known protein sequences faces a small number of...
Evaluating the effect of perturbations in reconstructing network topologies (2003)
Markowetz,Florian, Spang,Rainer
Many different Bayesian network models have been suggested to reconstruct gene expression networks from microarray data. However, little attention has been payed to the effects of small sample size...
Acetylcysteine for prevention of contrast nephropathy: meta-analysis (2003)
Birck, Rainer, Krzossok, Stefan, Markowetz, Florian, Schnulle, Peter, Van Der Woude, Fokko J., Braun, Claude
Background Contrast nephropathy is associated with increased in-hospital morbidity and mortality and leads to extension of hospital stay in patients with chronic renal insufficiency. Acetylcysteine...
Support vector machines for protein fold class prediction (2003)
Markowetz, Florian, Edler, Lutz, Vingron, Martin
Knowledge of the three-dimensional structure of a protein is essential for describing and understanding its function. Today, a large number of known protein sequences faces a small number of...
Evaluating the effect of perturbations in reconstructing network topologies (2003)
Markowetz, Florian, Spang, Rainer
Many different Bayesian network models have been suggested to reconstruct gene expression networks from microarray data. However, little attention has been payed to the effects of small sample size...
Reconstructing gene regulation networks from passive observations and active interventions (2003)
Florian Markowetz, Rainer Spang
structure learning
Evaluating the effect of perturbations in reconstructing network topologies (2003)
Florian Markowetz, Rainer Spang
Many different Bayesian network models have been suggested to reconstruct gene expression networks from microarray data. However, little attention has been payed to the effects of small sample size...
[Abgabetermin 26.04.2001] Acknowledgements (2003)
Florian Markowetz, Betreuer Prof, Dr. E. Mammen, Mathematische Fakultät Der
This work was written as my diploma thesis in mathematics at the University of Heidelberg under the supervision of Prof. Dr. Enno Mammen. I wish to thank him for his help and advice. The research was...
Proceedings of the 3rd International Workshop (2003)
On Distributed Statistical, Kurt Hornik, Friedrich Leisch, Achim Zeileis (eds, Florian Markowetz, Rainer Spang
Introduction A genetic network is a set of genes in which individual genes influence the activity of other genes. The core task in identifying genetic networks is to distinguish direct from indirect...
Max-Planck-Institute for Molecular Genetics- Computational Molecular Biology- (2003)
Florian Markowetz, Rainer Spang
The effect of perturbations in reconstructing network structure
Class discovery in gene expression data: characterizing splits by support vector machines (2002)
Markowetz,Florian, Von Heydebreck,Anja
We present a variation of ISIS, a class discovery method for microarray data described by Heydebreck et al. (2001). The objective is to discover biologically relevant structures in the gene...
Class discovery in gene expression data: characterizing splits by support vector machines (2002)
Markowetz, Florian, Von Heydebreck, Anja
We present a variation of ISIS, a class discovery method for microarray data described by Heydebreck et al. (2001). The objective is to discover biologically relevant structures in the gene...
[Abgabetermin 26.04.2001] Acknowledgements (2002)
Florian Markowetz, Betreuer Prof, Dr. E. Mammen, Mathematische Fakultät Der
This work was written as my diploma thesis in mathematics at the University of Heidelberg under the supervision of Prof. Dr. Enno Mammen. I wish to thank him for his help and advice. The research was...
Inferring cellular networks – a review
Markowetz, Florian, Spang, Rainer
In this review we give an overview of computational and statistical methods to reconstruct cellular networks. Although this area of research is vast and fast developing, we show that most currently...
Structure Learning in Nested Effects Models
Achim Tresch, Florian Markowetz
Nested Effects Models (NEMs) are a class of graphical models introduced to analyze the results of gene perturbation screens. NEMs explore noisy subset relations between the high-dimensional outputs...