Korbinian Strimmer

Structured Abstract (2008)

Abstract Background False discovery rate (FDR) methods play an important role in analyzing high-dimensional data. There are two types of FDR, tail area-based FDR and local FDR, as well as numerous...

Oxford Ox Ps, Korbinian Strimmer, Korbinian Strimmer

Evolutionary trees provide a natural way for hierarchical classification of DNA sequences. It is now being recognised that incorporating phylogenetic information is important in sequence search and...

email: strimmer @ stat.uni-muenchen.de (2008)

Copyright Heiko, A. Schmidt, Korbinian Strimmer, Arndt Von Haeseler, K. Strimmer, M. Vingron, ...

Remarks: • A bug has been fixed, which tended to produce less resolved trees. Hence, versions prior to 5.2 should not be used anymore! • Some menus have been extended. Hence, the order of some...

Identifying periodically expressed transcripts in microarray time series data (2008)

Wichert, Sofia, Fokianos, Konstantinos, Strimmer, Korbinian

fdrtool: a versatile R package for estimating local and tail area-based false discovery rates (2008)

BMC Bioinformatics BioMed Central Methodology article (2008)

Summary: False discovery rate (FDR) methodologies are essential in the study of high-dimensional genomic and proteomic data. The R package ‘fdrtool’ facilitates such analyses by offering a...

Korbinian Strimmer

which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Background: False discovery rate (FDR) methods play an important role in...

approach (2007)

Bmc Bioinformatics, Korbinian Strimmer, Korbinian Strimmer

Modeling gene expression measurement error: a quasi-likelihood

From correlation to causation networks: a simple approximate learning algorithm and its application to high-dimensional plant gene expression data (2007)

Learning causal networks from systems biology time course data: an effective model selection procedure for the vector autoregressive process (2007)

Abstract Background The use of correlation networks is widespread in the analysis of gene expression and proteomics data, even though it is known that correlations not only confound direct and...

Accurate Ranking of Differentially Expressed Genes by a Distribution-Free Shrinkage Approach (2007)

Abstract Background Causal networks based on the vector autoregressive (VAR) process are a promising statistical tool for modeling regulatory interactions in a cell. However, learning these networks...

Accurate Ranking of Differentially Expressed Genes by a Distribution-Free Shrinkage Approach (2007)

High-dimensional case-control analysis is encountered in many different settings in genomics. In order to rank genes accordingly, many different scores have been proposed, ranging from ad hoc...

Accurate Ranking of Differentially Expressed Genes by a Distribution-Free Shrinkage Approach (2007)

High-dimensional case-control analysis is encountered in many different settings in genomics. In order to rank genes accordingly, many different scores have been proposed, ranging from ad hoc...

Accurate Ranking of Differentially Expressed Genes by a Distribution-Free Shrinkage Approach (2007)

High-dimensional case-control analysis is encountered in many different settings in genomics. In order to rank genes accordingly, many different scores have been proposed, ranging from ad hoc...

Partial least squares: A versatile tool for the analysis of high-dimensional genomic data (2007)

High-dimensional case-control analysis is encountered in many different settings in genomics. In order to rank genes accordingly, many different scores have been proposed, ranging from ad hoc...

Korbinian Strimmer, Anne-laure Boulesteix, Anne-laure Boulesteix

Partial Least Squares (PLS) is a highly efficient statistical regression technique that is well suited for the analysis of high-dimensional genomic data. In this paper we review the theory and...

Partial least squares: A versatile tool for the analysis of high-dimensional genomic data (2007)

Korbinian Strimmer, Anne-laure Boulesteix, Anne-laure Boulesteix

Partial Least Squares (PLS) is a highly efficient statistical regression technique that is well suited for the analysis of high-dimensional genomic data. In this paper we review the theory and...

Short title: Partial Least Squares for Genomics Analyses (2006)

Anne-laure Boulesteix, Korbinian Strimmer, Anne-laure Boulesteix

Partial Least Squares (PLS) is an efficient statistical reqression technique that is highly suited for the analysis of genomic and proteomic data. In this paper we re-view both the theory underlying...

The matrix cookbook (2006)

Kaare Brandt Petersen, Michael Syskind Pedersen, Jan Larsen, Korbinian Strimmer, Lars Christiansen, Kai Hansen, ...

What is this? These pages are a collection of facts (identities, approximations, inequalities, relations,...) about matrices and matters relating to them. It is collected in this form for the...

The matrix cookbook (2006)

Kaare Brandt Petersen, Michael Syskind Pedersen, Suggestions Bill Baxter, Brian Templeton, Christian Rishøj, L. Theobald, ...

What is this? These pages are a collection of facts (identities, approximations, inequalities, relations,...) about matrices and matters relating to them. It is collected in this form for the...

A Shrinkage Approach to Large-Scale Covariance Matrix Estimation and Implications for Functional Genomics (2005)

A Shrinkage Approach to Large-Scale Covariance Matrix Estimation and Implications for Functional Genomics (2005)

Inferring large-scale covariance matrices from sparse genomic data is an ubiquitous problem in bioinformatics. Clearly, the widely used standard covariance and correlation estimators are ill-suited...

A Shrinkage Approach to Large-Scale Covariance Matrix Estimation and Implications for Functional Genomics (2005)

Inferring large-scale covariance matrices from sparse genomic data is an ubiquitous problem in bioinformatics. Clearly, the widely used standard covariance and correlation estimators are ill-suited...

A Shrinkage Approach to Large-Scale Covariance Matrix Estimation and Implications for Functional Genomics (2005)

Inferring large-scale covariance matrices from sparse genomic data is an ubiquitous problem in bioinformatics. Clearly, the widely used standard covariance and correlation estimators are ill-suited...

Predicting transcription factor activities from combined analysis of microarray and ChIP data: a partial least squares approach (2005)

Inferring large-scale covariance matrices from sparse genomic data is an ubiquitous problem in bioinformatics. Clearly, the widely used standard covariance and correlation estimators are ill-suited...

Inference of demographic history from genealogical trees using reversible jump Markov chain Monte Carlo (2005)

Abstract Background The study of the network between transcription factors and their targets is important for understanding the complex regulatory mechanisms in a cell. Unfortunately, with standard...

Opgen-Rhein, Rainer, Fahrmeir, Ludwig, Strimmer, Korbinian

Abstract Background Coalescent theory is a general framework to model genetic variation in a population. Specifically, it allows inference about population parameters from sampled DNA sequences....

Predicting Transcription Factor Activities from Combined Analysis of Microarray and ChIP Data: A Partial Least Squares Approach (2005)

Partial Least Squares: A Versatile Tool for the Analysis of High-Dimensional Genomic Data (2005)

The study of the network between transcription factors and their targets is important for understanding the complex regulatory mechanisms in a cell. However, due to post-translational modifications...

Learning Large-Scale Graphical Gaussian Models from Genomic Data (2005)

Partial Least Squares (PLS) is a highly efficient statistical regression technique that is well suited for the analysis of high-dimensional genomic data. In this paper we review the theory and...

Juliane Schäfer, Korbinian Strimmer

The inference and modeling of network-like structures in genomic data is of prime importance in systems biology. Complex stochastic associations and interdependencies can very generally be described...

An empirical Bayes approach to inferring large-scale gene association networks (2005)

Schäfer, Juliane, Strimmer, Korbinian

Motivation: Genetic networks are often described statistically using graphical models (e.g. Bayesian networks). However, inferring the network structure offers a serious challenge in microarray...

TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics (2004)

Jobb, Gangolf, Von Haeseler, Arndt, Strimmer, Korbinian

Abstract Background Most analysis programs for inferring molecular phylogenies are difficult to use, in particular for researchers with little programming experience. Results TREEFINDER is an...

A brief introduction to the Phylogenetic Analysis Library version 1.5 (2004)

Matthew Goode, Korbinian Strimmer, Alexei Drummond, Allen Rodrigo

TREEFINDER: A Powerful graphical . . . (2004)

Arndt Von Haeseler, Arndt Von Haeseler, Korbinian Strimmer

Background: Most analysis programs for inferring molecular phylogenies are di#cult to use, in particular for researchers with little programming experience.

APE: Analyses of Phylogenetics and Evolution in R language (2004)

Paradis, Emmanuel, Claude, Julien, Strimmer, Korbinian

Summary: Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics. APE provides both utility functions for reading and...

Identifying periodically expressed transcripts in microarray time series data (2004)

Wichert, Sofia, Fokianos, Konstantinos, Strimmer, Korbinian

Motivation: Microarray experiments are now routinely used to collect large-scale time series data, for example to monitor gene expression during the cell cycle. Statistical analysis of this data...

An empirical bayes approach to inferring large-scale gene association networks (2004)

Schäfer, Juliane, Strimmer, Korbinian

Motivation: Genetic networks are often described statistically by graphical models (e.g. Bayesian networks). However, inferring the network structure offers a serious challenge in microarray analysis...

An empirical bayes approach to inferring large-scale gene association networks (2004)

Schäfer, Juliane, Strimmer, Korbinian

Motivation: Genetic networks are often described statistically by graphical models (e.g. Bayesian networks). However, inferring the network structure offers a serious challenge in microarray analysis...

A novel exploratory method for visual recombination detection (2003)

Strimmer, Korbinian, Forslund, Kristoffer, Holland, Barbara, Moulton, Vincent

Abstract A versatile visual approach for detecting recombination and identifying recombination breakpoints within a sequence alignment is presented. The method is based on two novel diagrams - the...

Modeling gene expression measurement error: a quasi-likelihood approach (2003)

Nucleotide substitution models (2003)

Abstract Background Using suitable error models for gene expression measurements is essential in the statistical analysis of microarray data. However, the true probabilistic model underlying gene...

Phylogeny inference based on maximum-likelihood methods with Tree-Puzzle (2003)

Von Haeseler, Arndt, Strimmer, Korbinian

A CART-based approach to discover emerging patterns in microarray data (2003)

Boulesteix, Anne-Laure, Tutz, Gerhard, Strimmer, Korbinian

Motivation: Cancer diagnosis using gene expression profiles requires supervised learning and gene selection methods. Of the many suggested approaches, the method of emerging patterns (EPs) has the...

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing (2002)

Schmidt,Heiko A., Strimmer,Korbinian, Vingron,Martin, Von Haeseler,Arndt

Summary: TREE-PUZZLE is a program package for quartet-based maximum-likelihood phylogenetic analysis (formerly PUZZLE, Strimmer and von Haeseler, Mol. Biol. Evol. , 13, 964–969, 1996) that provides...

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing (2002)

Schmidt, Heiko A., Strimmer, Korbinian, Vingron, Martin, Von Haeseler, Arndt

Summary: TREE-PUZZLE is a program package for quartet-based maximum-likelihood phylogenetic analysis (formerly PUZZLE, Strimmer and von Haeseler, Mol. Biol. Evol. , 13, 964-969, 1996) that provides...

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing (2002)

Schmidt, Heiko A., Strimmer, Korbinian, Vingron, Martin, Von Haeseler, Arndt

Summary: TREE-PUZZLE is a program package for quartet-based maximum-likelihood phylogenetic analysis (formerly PUZZLE, Strimmer and von Haeseler, Mol. Biol. Evol. , 13, 964–969, 1996) that provides...

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing (2002)

Schmidt, Heiko A., Strimmer, Korbinian, Vingron, Martin, Von Haeseler, Arndt

Summary: TREE-PUZZLE is a program package for quartet-based maximum-likelihood phylogenetic analysis (formerly PUZZLE, Strimmer and von Haeseler, Mol. Biol. Evol. , 13, 964–969, 1996) that provides...

PAL: an object-oriented programming library for molecular evolution and phylogenetics (2001)

Drummond, Alexei, Strimmer, Korbinian

Summary: Phylogenetic Analysis Library (PAL) is a collection of Java classes for use in molecular evolution and phylogenetics. PAL provides a modular environment for the rapid construction of both...

PAL: an object-oriented programming library for molecular evolution and phylogenetics (2001)

Drummond, Alexei, Strimmer, Korbinian

Summary: Phylogenetic Analysis Library (PAL) is a collection of Java classes for use in molecular evolution and phylogenetics. PAL provides a modular environment for the rapid construction of both...

Exploring the Demographic History of DNA Sequences Using the Generalized Skyline Plot (2001)

Strimmer, Korbinian, Pybus, Oliver G.

We present an intuitive visual framework, the generalized skyline plot, to explore the demographic history of sampled DNA sequences. This approach is based on a genealogy inferred from the sequences...

Recombination Analysis Using Directed Graphical Models (2001)

Strimmer, Korbinian, Wiuf, Carsten, Moulton, Vincent

Likelihood Analysis of Phylogenetic Networks Using Directed Graphical Models (2000)

Strimmer, Korbinian, Moulton, Vincent

A method for computing the likelihood of a set of sequences assuming a phylogenetic network as an evolutionary hypothesis is presented. The approach applies directed graphical models to sequence...

A Simple Scheme for Mining Approximate Evolutionary Trees From Large Scale Data Sets (1999)

Korbinian Strimmer, Korbinian Strimmer

Introduction Statistical methods for reconstructing the evolutionary history of a set of DNA sequences are well developed (Nei, 1996; Felsenstein, 1988). However, in face of the growing amount of...

Likelihood-mapping: A simple method to visualize phylogenetic content of a sequence alignment (1997)

Strimmer, Korbinian, Haeseler, Arndt Von

Accuracy of Neighbor Joining for n-Taxon Trees (1996)

Likelihood-mapping: A simple method to visualize phylogenetic content of a sequence alignment

A Monte Carlo approach was used to estimate the accuracy of a given tree reconstruction method for any number of taxa. In this procedure, we sampled randomly over all possible bifurcating trees...

Modeling gene expression measurement error: a quasi-likelihood approach

We introduce a graphical method, likelihood-mapping, to visualize the phylogenetic content of a set of aligned sequences. The method is based on an analysis of the maximum likelihoods for the three...

A novel exploratory method for visual recombination detection

Strimmer, Korbinian, Forslund, Kristoffer, Holland, Barbara, Moulton, Vincent

A versatile visual approach for detecting recombination and identifying recombination breakpoints within a sequence alignment is presented.

TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics

Jobb, Gangolf, Von Haeseler, Arndt, Strimmer, Korbinian

Inference of demographic history from genealogical trees using reversible jump Markov chain Monte Carlo

Opgen-Rhein, Rainer, Fahrmeir, Ludwig, Strimmer, Korbinian

Predicting transcription factor activities from combined analysis of microarray and ChIP data: a partial least squares approach

Likelihood-mapping: A simple method to visualize phylogenetic content of a sequence alignment

Modeling gene expression measurement error: a quasi-likelihood approach

We introduce a graphical method, likelihood-mapping, to visualize the phylogenetic content of a set of aligned sequences. The method is based on an analysis of the maximum likelihoods for the three...

A novel exploratory method for visual recombination detection

Strimmer, Korbinian, Forslund, Kristoffer, Holland, Barbara, Moulton, Vincent

A versatile visual approach for detecting recombination and identifying recombination breakpoints within a sequence alignment is presented.

TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics

Jobb, Gangolf, Von Haeseler, Arndt, Strimmer, Korbinian

Inference of demographic history from genealogical trees using reversible jump Markov chain Monte Carlo

Opgen-Rhein, Rainer, Fahrmeir, Ludwig, Strimmer, Korbinian

Predicting transcription factor activities from combined analysis of microarray and ChIP data: a partial least squares approach

Inferring confidence sets of possibly misspecified gene trees.

Strimmer, Korbinian, Rambaut, Andrew

The problem of inferring confidence sets of gene trees is discussed without assuming that the substitution model or the branching pattern of any of the investigated trees is correct. In this case,...

Learning causal networks from systems biology time course data: an effective model selection procedure for the vector autoregressive process

From correlation to causation networks: a simple approximate learning algorithm and its application to high-dimensional plant gene expression data

Comments on: Augmenting the bootstrap to analyze high dimensional genomic data

Korbinian Strimmer

Accurate Ranking of Differentially Expressed Genes by a Distribution-Free Shrinkage Approach

Rainer Opgen-Rhein, Korbinian Strimmer

High-dimensional case-control analysis is encountered in many different settings in genomics. In order to rank genes accordingly, many different scores have been proposed, ranging from ad hoc...

A Shrinkage Approach to Large-Scale Covariance Matrix Estimation and Implications for Functional Genomics

Juliane Schäfer, Korbinian Strimmer

Inferring large-scale covariance matrices from sparse genomic data is an ubiquitous problem in bioinformatics. Clearly, the widely used standard covariance and correlation estimators are ill-suited...

A unified approach to false discovery rate estimation