Annotation-Driven Class Discovery User’s Guide to the Bioconductor package adSplit (2009)
Max Planck, Claudio Lottaz, Joern Toedling, Rainer Spang
Nr. 2005/02 This is the vignette of the Bioconductor compliant packege adSplit. We describe our implementation of annotation- driven clustering for microarray gene expression profiling studies.
Estimation of Local False Discovery Rates User’s Guide to the Bioconductor Package (2009)
Max Planck, Stefanie Scheid, Rainer Spang
Nr. 2004/01 This is the vignette of the Bioconductor compliant package twilight. We describe our implementation of a stochastic search algorithm to estimate the local false discovery rate. In...
Similarities of Ordered Gene Lists User’s Guide to the Bioconductor Package (2009)
Max Planck, Stefanie Scheid, Claudio Lottaz, Xinan Yang, Rainer Spang
Nr. 2006/01 This is the vignette of the Bioconductor compliant package OrderedList. We describe the methods and functions to explore the similarity between two lists of ordered genes. Contents
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...
Pleiotropic hierarchies from high-dimensional phenotyping by (2008)
Florian Markowetz, Juby Jacob, Stefan Bentink, Rainer Spang
RNA interference
Similarities of Ordered Gene Lists User’s Guide to the Bioconductor Package (2008)
Max Planck, Stefanie Scheid, Claudio Lottaz, Xinan Yang, Rainer Spang
Nr. 2006/01 This is the vignette of the Bioconductor compliant package OrderedList. We describe the methods and functions to explore the similarity between two lists of ordered genes. Contents
BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btm322 (2008)
Gene Expression, Claudio Lottaz, Joern Toedling, Rainer Spang
Annotation-based distance measures for patient subgroup discovery in clinical microarray studies
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...
Similarities of Ordered Gene Lists User’s Guide to the Bioconductor Package (2008)
Max Planck, Stefanie Scheid, Claudio Lottaz, Xinan Yang, Rainer Spang
Nr. 2006/01 This is the vignette of the Bioconductor compliant package OrderedList. We describe the methods and functions to explore the similarity between two lists of ordered genes. Contents
Claudio Lottaz, Joern Toedling, Rainer Spang
Motivation: Clustering algorithms are widely used in the analysis of microarray data. In clinical studies, they are often applied to find groups of co-regulated genes. Clustering, however, can also...
BIOINFORMATICS APPLICATIONS NOTE (2008)
Gene Expression, Claudio Lottaz, Xinan Yang, Stefanie Scheid, Rainer Spang
OrderedList—a bioconductor package for detecting similarity in ordered gene lists
Burns C. Blaxall, Ph. D, Rainer Spang, Ph. D, Howard A. Rockman, Walter J. Koch, ...
Copyright (c) 2003 by the American Physiological Society. Numerous murine models of heart failure (HF) have been described, many of which develop progressive deterioration of cardiac function. We...
Claudio Lottaz, Julie Floch, Renate Kirschner, Christian Hagemeier, Rainer Spang
Dataset: 327 cases of acute lymphoblastic leukemia (ALL), various translocation types Hybridised on HG-U95Av2 (12625 probe-sets) [Yeoh et al., 2002]. StAM analysis to detect MLL based on the...
1 Design of a clinical microarray chip (2008)
Keywords: microarray, medical diagnostics, chip design, clinical trials, sequential methods 1 Introduction For microarray based diagnosis only a small number of genes is really substantial. In a...
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...
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...
Rheinischen Friedrich-Wilhelms-Universitat Bonn (2007)
Mathematisch-naturwissenschaftlichen Fakultat, Rainer Spang
On the significance of local similarities between pairs of amino acid sequences Dissertation zur
Stefanie Scheid, Rainer Spang, Microarray Experiments
Measurement of abundance of mRNA transcripts in given tissue. Simultaneously, for up to 20 000 genes. Question: Which genes are dierentially expressed (\induced ") if we compare two classes...
Kurt Hornik, Friedrich Leisch, Achim Zeileis (eds, Stefanie Scheid, Rainer Spang
The distribution of scores for differential gene expression observed in microarray experiments give rise to the assumption that the underlying score distributions of induced and non-induced genes...
Sequence Database Search Alignments Using Jumping (2007)
Rainer Spang, Marc Rehmsmeier, Jens Stoye
We describe a new algorithm for amino acid sequence classification and the detection of remote homologues. The algorithm is based on the dynamic programming principle and evaluates the fit of a...
Rheinischen Friedrich-Wilhelms-Universitit Bonn (2007)
Mathematisch-naturwissenschaftlichen Fakultit, Rainer Spang
the significance of local between pgirs of amino acid sequences
Limits of hornology detection by pairwise (2007)
Rainer Spang, Martin Vingron, Deutsches Krebsforschungszentrum, Theoretische Bioinformatik, Im Neuenheimer Feld
sequence comparison
Computational Diagnostics Group (2007)
Claudio Lottaz, Stefan Bentink, Rainer Spang
From a machine learning point of view, classification of gene expression patterns is a very particular task. Typically, training data consists of few samples (small number of experiments) but...
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
A False Discovery Rate approach to (2007)
separate the score distributions of induced and non-induced genes
Constantin Bannert, Marc Rehmsmeier, Rainer Spang, Jens Stoye
We present an algorithm for amino acid sequence classification and the detection of remote homologues. The rationale is to exploit vertical and horizontal information of a multiple alignment in a...
Mike Westy, Joseph R Nevins, Jeffrey R Marks, Rainer Spang, Harry Zuzan
Summary. Statistical modelling and inference problems in which sample sizes are substantially smaller than the number of available and potentially interesting predictors (explanatory variables)...
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...
Lottaz, Claudio, Toedling, Joern, Spang, Rainer
Motivation: Clustering algorithms are widely used in the analysis of microarray data. In clinical studies, they are often applied to find groups of co-regulated genes. Clustering, however, can also...
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...
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...
Selecting normalization genes for small diagnostic microarrays (2006)
Abstract Background Normalization of gene expression microarrays carrying thousands of genes is based on assumptions that do not hold for diagnostic microarrays carrying only few genes. Thus,...
Toedling, Joern, Rhein, Peter, Ratei, Richard, Karawajew, Leonid, Spang, Rainer
Abstract Background Identification of minor cell populations, e.g. leukemic blasts within blood samples, has become increasingly important in therapeutic disease monitoring. Modern flow cytometers...
A Biologic Definition of Burkitt's Lymphoma from Transcriptional and Genomic Profiling (2006)
Hummel, Michael, Bentink, Stefan, Berger, Hilmar, Klapper, Wolfram, Wessendorf, Swen, Barth, Thomas F.E., ...
Background: The distinction between Burkitt's lymphoma and diffuse large-B-cell lymphoma is unclear. We used transcriptional and genomic profiling to define Burkitt's lymphoma more precisely and to...
BMC Bioinformatics BioMed Central (2006)
Joern Toedling, Peter Rhein, Richard Ratei, Leonid Karawajew, Rainer Spang
2Research article Automated in-silico detection of cell populations in flow cytometry readouts and its application to leukemia disease monitoring
Statistics for Biological Networks (2006)
Florian Markowetz, Rainer Spang, Transcriptional Regulation
reconstructed from secondary effects of RNAi
OrderedList--a bioconductor package for detecting similarity in ordered gene lists (2006)
Lottaz, Claudio, Yang, Xinan, Scheid, Stefanie, Spang, Rainer
Summary: OrderedList is a Bioconductor compliant package for meta-analysis based on ordered gene lists like those resulting from differential gene expression analysis. Our package quantifies the...
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Background: Normalization of gene expression microarrays carrying thousands...
stam – a Bioconductor compliant R package for structured analysis of microarray data (2005)
Lottaz, Claudio, Spang, Rainer
Abstract Background Genome wide microarray studies have the potential to unveil novel disease entities. Clinically homogeneous groups of patients can have diverse gene expression profiles. The...
Early diagnostic marker panel determination for microarray based clinical studies (2005)
Jaeger,Jochen, Weichenhan,Dieter, Ivandic,Boris, Spang,Rainer
We present a novel, cost efficient two-phase design for predictive clinical gene expression studies: early marker panel determination (EMPD). In Phase-1, genome-wide microarrays are used only for a...
Early Diagnostic Marker Panel Determination for Microarray Based Clinical Studies (2005)
Jaeger, Jochen, Weichenhan, Dieter, Ivandic, Boris, Spang, Rainer
We present a novel, cost efficient two-phase design for predictive clinical gene expression studies: early marker panel determination (EMPD). In Phase-1, genome-wide microarrays are used only for a...
Early Diagnostic Marker Panel Determination for Microarray Based Clinical Studies (2005)
Jaeger, Jochen, Weichenhan, Dieter, Ivandic, Boris, Spang, Rainer
We present a novel, cost efficient two-phase design for predictive clinical gene expression studies: early marker panel determination (EMPD). In Phase-1, genome-wide microarrays are used only for a...
Early Diagnostic Marker Panel Determination for Microarray Based Clinical Studies (2005)
Jaeger, Jochen, Weichenhan, Dieter, Ivandic, Boris, Spang, Rainer
We present a novel, cost efficient two-phase design for predictive clinical gene expression studies: early marker panel determination (EMPD). In Phase-1, genome-wide microarrays are used only for a...
Early Diagnostic Marker Panel Determination for Microarray Based Clinical Studies (2005)
Jaeger, Jochen, Weichenhan, Dieter, Ivandic, Boris, Spang, Rainer
We present a novel, cost efficient two-phase design for predictive clinical gene expression studies: early marker panel determination (EMPD). In Phase-1, genome-wide microarrays are used only for a...
Motivation: Today, the characterization of clinical phenotypes by gene-expression patterns is widely used in clinical research. If the investigated phenotype is complex from the molecular point of...
Early diagnostic marker panel determination for microarray based clinical studies (2005)
Jaeger, Jochen, Weichenhan, Dieter, Ivandic, Boris, Spang, Rainer
We present a novel, cost efficient two-phase design for predictive clinical gene expression studies: early marker panel determination (EMPD). In Phase-1, genome-wide microarrays are used only for a...
stam - a Bioconductor compliant R package for structured analysis of microarray data (2005)
Lottaz, Claudio, Spang, Rainer
Genome wide microarray studies have the potential to unveil novel disease entities. Clinically homogeneous groups of patients can have diverse gene expression profiles. The definition of novel...
Lottaz, Claudio, Spang, Rainer
Motivation: Today, the characterization of clinical phenotypes by gene-expression patterns is widely used in clinical research. If the investigated phenotype is complex from the molecular point of...
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...
twilight; a Bioconductor package for estimating the local false discovery rate (2005)
Scheid, Stefanie, Spang, Rainer
Summary: twilight is a Bioconductor compatible package for analysing the statistical significance of differentially expressed genes. It is based on the concept of the local false discovery rate...
Detecting common gene expression patterns in multiple cancer outcome entities (2005)
Yang, Xinan, Bentink, Stefan, Spang, Rainer
Most oncological microarray studies focus on molecular distinctions in different cancer entities. Recently, researchers started using microarrays for investigating molecular commonalities of multiple...
Bmc Bioinformatics, Claudio Lottaz, Rainer Spang
Software stam – a Bioconductor compliant R package for structured analysis of microarray data
Probabilistic Soft Interventions in Conditional Gaussian Networks (2005)
Florian Markowetz Steen, Steffen Grossmann, Rainer Spang
We introduce a general concept of probabilistic interventions in Bayesian networks.
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...
Lottaz, Claudio, Spang, Rainer
Motivation: Today, the characterization of clinical phenotypes by gene-expression patterns is widely used in clinical research. If the investigated phenotype is complex from the molecular point of...
twilight; a Bioconductor package for estimating the local false discovery rate (2005)
Scheid, Stefanie, Spang, Rainer
Summary: twilight is a Bioconductor compatible package for analysing the statistical significance of differentially expressed genes. It is based on the concept of the local false discovery rate...
Lottaz, Claudio, Spang, Rainer
Motivation: Today, the characterization of clinical phenotypes by gene expression patterns is widely used in clinical research. If the investigated phenotype is complex from the molecular point of...
TWILIGHT - a Bioconductor package for estimating the local false discovery rate (2005)
Scheid, Stefanie, Spang, Rainer
Summary: TWILIGHT is a Bioconductor compatible package for analysing the statistical significance of differentially expressed genes. It is based on the concept of the local false discovery rate, a...
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...
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...
A stochastic downhill search algorithm for estimating the local false discovery rate (2004)
Screening for differential gene expression in microarray studies leads to difficult large-scale multiple testing problems. The local false discovery rate is a statistical concept for quantifying...
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...
A stochastic downhill search algorithm for estimating the local false discovery rate (2004)
Scheid, Stefanie, Spang, Rainer
Screening for differential gene expression in microarray studies leads to difficult large-scale multiple testing problems. The local false discovery rate is a statistical concept for quantifying...
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...
A stochastic downhill search algorithm for estimating the local false discovery rate (2004)
Stefanie Scheid, Stefanie Scheid, Rainer Spang
search algorithm for estimating the local false discovery rate, IEEE Transactions on Computational Biology and Bioinformatics vol. 1, no. 3, p. 98-108. c○2004 IEEE. Personal use of this material is...
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...
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...
Expression profiling of human idiopathic dilated cardiomyopathy (2003)
Grzeskowiak,Rafal, Witt,Henning, Drungowski,Mario, Thermann,Rolf, Hennig,Steffen, Perrot,Andreas, ...
Objective: To investigate the global changes accompanying human dilated cardiomyopathy (DCM) we performed a large-scale expression screen using myocardial biopsies from a group of DCM patients with...
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...
The distribution of scores for differential gene expression observed in microarray experiments give rise to the assumption that the underlying score distributions of induced and non-induced genes...
Expression profiling of human idiopathic dilated cardiomyopathy (2003)
Grzeskowiak, Rafal, Witt, Henning, Drungowski, Mario, Thermann, Rolf, Hennig, Steffen, Perrot, Andreas, ...
Objective: To investigate the global changes accompanying human dilated cardiomyopathy (DCM) we performed a large-scale expression screen using myocardial biopsies from a group of DCM patients with...
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...
Scheid, Stefanie, Spang, Rainer
The distribution of scores for differential gene expression observed in microarray experiments give rise to the assumption that the underlying score distributions of induced and non-induced genes...
Diagnostic signatures from microarrays: a bioinformatics concept for personalized medicine (2003)
Microarrays can be used as diagnostic clinical tools, providing a global overview of gene transcription in diseased tissues. Expression profiles can be easily obtained in a single assay and provide...
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...
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...
Navigating towards Biologically Resolved Diagnoses through Structured Analysis of Microarrays (2003)
Claudio Lottaz, Julie Floch, Renate Kirschner, Christian Hagemeier, Rainer Spang
Introduction Microarray analyses have the potential to increase our understanding of a disease and to provide more detailed diagnoses for individual patients. We propose to structure microarray data...
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...
Assessment of five Microarray Experiments on Gene Expression Profiling of Breast Cancer (2003)
Jrn Tdling Rainer, Rainer Spang
INTRODUCTION Subject: Gene expression profiling of non-hereditary breast cancer Focus on clinically relevant separation of tumor samples into Estrogen-Receptor-positive versus...
Assessment of Five Microarray Experiments on Gene Expression Profiling of Breast Cancer (2003)
Introduction In recent studies gene expression profiling of non-hereditary breast cancer has been increasingly popular. One way of sample differentiation of predominant clinical relevance usually...
Estimating Score Distributions of Induced and Non-Induced Genes (2003)
Stefanie Scheid And, Stefanie Scheid, Rainer Spang
ck) and resulting percentage of induced genes (red), illustration. Classical FDR { Motivated by multiple testing situation in microarray experiments. Genes with scores exceeding extremal threshold...
Estimating the Score Distributions of Induced and Non-Induced Genes in Microarray Experiments (2003)
Introduction. A microarray experiment measures simultaneously the abundance of mRNA for several thousands of genes in a given tissue. With two classes of tissue or state of patient one can search for...
Design of a Clinical Microarray Chip (2003)
Introduction For microarray based diagnosis only a small number of genes is really substantial. In a preprocessing step the majority of the spots can be ltered out and not used any more. If it were...
Max-Planck-Institute for Molecular Genetics- Computational Molecular Biology- (2003)
Florian Markowetz, Rainer Spang
The effect of perturbations in reconstructing network structure
Gene Ontology Driven Classification (2003)
Of Gene Expression, Claudio Lottaz, Stefan Bentink, Renate Kirschner, Christian Hagemeier, Rainer Spang
Introduction From a machine learning point of view, classification of gene expression patterns is a very particular task. Typically, training data consists of few samples (small number of...
Expression profiling of human idiopathic dilated cardiomyopathy (2003)
Grzeskowiak, Rafal, Witt, Henning, Drungowski, Mario, Thermann, Rolf, Hennig, Steffen, Perrot, Andreas, ...
Objective: To investigate the global changes accompanying human dilated cardiomyopathy (DCM) we performed a large-scale expression screen using myocardial biopsies from a group of DCM patients with...
A novel approach to remote homology detection: jumping alignments. (2002)
Spang,Rainer, Rehmsmeier,Marc, Stoye,Jens
We describe a new algorithm for protein classification and the detection of remote homologs. The rationale is to exploit both vertical and horizontal information of a multiple alignment in a...
Prediction and uncertainty in the analysis of gene expression profiles (2002)
Spang,Rainer, Zuzan,Harry, West,Mike, Nevins,Joseph, Blanchette,Carrie, Marks,Jeffrey R.
We have developed a complete statistical model for the analysis of tumor specific gene expression profiles. The approach provides investigators with a global overview on large scale gene expression...
Müller,Tobias, Spang,Rainer, Vingron,Martin
Evolution of proteins is generally modeled as a Markov process acting on each site of the sequence. Replacement frequencies need to be estimated based on sequence alignments. Here we compare three...
Müller, Tobias, Spang, Rainer, Vingron, Martin
Evolution of proteins is generally modeled as a Markov process acting on each site of the sequence. Replacement frequencies need to be estimated based on sequence alignments. Here we compare three...
Prediction and uncertainty in the analysis of gene expression profiles (2002)
Spang, Rainer, Zuzan, Harry, West, Mike, Nevins, Joseph, Blanchette, Carrie, Marks, Jeffrey R.
We have developed a complete statistical model for the analysis of tumor specific gene expression profiles. The approach provides investigators with a global overview on large scale gene expression...
A novel approach to remote homology detection: jumping alignments. (2002)
Spang, Rainer, Rehmsmeier, Marc, Stoye, Jens
We describe a new algorithm for protein classification and the detection of remote homologs. The rationale is to exploit both vertical and horizontal information of a multiple alignment in a...
A novel approach to remote homology detection: jumping alignments (2002)
Rainer Spang, Marc Rehmsmeier, Jens Stoye
We describe a new algorithm for protein classi � cation and the detection of remote homologs. The rationale is to exploit both vertical and horizontal information of a multiple alignment in a...
Müller, Tobias, Spang, Rainer, Vingron, Martin
Evolution of proteins is generally modeled as a Markov process acting on each site of the sequence. Replacement frequencies need to be estimated based on sequence alignments. Here we compare three...
Limits of homology detection by pairwise sequence comparison (2001)
Rainer Spang, Martin Vingron, Deutsches Krebsforschungszentrum, Theoretische Bioinformatik, Im Neuenheimer Feld
Motivation: Noise in database searches resulting from random sequences similarities increases as the databases expand rapidly. The noise problems are not a technical shortcoming of the database...
Concepts for the estimation of amino acid substitution models (2001)
Rainer Spang, Martin Vingron, Deutsches Krebsforschungszentrum
In a simple model, the evolution of proteins can be viewed as the accumulation of amino acid substitutions. Amino acids with similar chemical and physical properties are replaced by each other more...
Limits of homology detection by pairwise sequence comparison (2001)
Spang, Rainer, Vingron, Martin
Motivation: Noise in database searches resulting from random sequence similarities increases as the databases expand rapidly. The noise problems are not a technical shortcoming of the database search...
DNA microarray data analysis and regression modeling for genetic expression profiling (2000)
Mike West, Joseph R Nevins, Jeffrey R Marks, Rainer Spang, Carfie Blanchette, Harry Zuzan
University. We are grateful to Sandfine Dudoit of MSRI for providing precise details of the algorithms used to pre-process the leukemia array expression data. We report on our studies in large-scale...
Sequence database search using jumping alignments (2000)
Rainer Spang, Marc Rehmsmeier, Jens Stoye
We describe a new algorithm for amino acid sequence classi cation and the detection of remote homologues. The rationale is to exploit both vertical and horizontal information of a multiple alignment...
DNA microarray data analysis and regression modeling for genetic expression profiling (2000)
Mike West, Joseph R Nevins, Jerey R Marks, Rainer Spang, Carrie Blanchette, Harry Zuzan
University. We are grateful to Sandrine Dudoit of MSRI for providing precise details of the algorithms used to pre-process the leukemia array expression data. 1 We report on our studies in...
Sequence database search using jumping alignments (2000)
Rainer Spang, Marc Rehmsmeier, Jens Stoye
We describe a new algorithm for amino acid sequence classi cation and the detection of remote homologues. The algorithm is based on the dynamic programming principle and evaluates the t of a...
DNA microarray data analysis and regression modeling for genetic expression profiling (2000)
Mike West, Joseph R Nevins, Jeffrey R Marks, Rainer Spang, Carrie Blanchette, Harry Zuzan
On the significance of local similarities between pairs of amino acid sequences / (1999)
Bonn, University, Diss., 1999 (Nicht für den Austausch).
On the significance of local similarities between pairs of amino acid sequences / (1999)
Zugl.: Bonn, Univ., Diss., 1999.
Statistics of large scale sequence searching (1998)
Rainer Spang, Martin Vingron, Deutsches Krebsforschungszentrum (dkfz, Theorefische Bioinformafik, Im Neuenheimer Feld
Statistics of large scale sequence searching (1998)
Rainer Spang, Martin Vingron, Deutsches Krebsforschungszentrum (dkfz, Theoretische Bioinformatik, Im Neuenheimer Feld
Predicting the clinical status of human breast cancer by using gene expression profiles
West, Mike, Blanchette, Carrie, Dressman, Holly, Huang, Erich, Ishida, Seiichi, Spang, Rainer, ...
Prognostic and predictive factors are indispensable tools in the treatment of patients with neoplastic disease. For the most part, such factors rely on a few specific cell surface, histological, or...
Ishida, Seiichi, Huang, Erich, Zuzan, Harry, Spang, Rainer, Leone, Gustavo, West, Mike, ...
We have used high-density DNA microarrays to provide an analysis of gene regulation during the mammalian cell cycle and the role of E2F in this process. Cell cycle analysis was facilitated by a...
Predicting the clinical status of human breast cancer by using gene expression profiles
West, Mike, Blanchette, Carrie, Dressman, Holly, Huang, Erich, Ishida, Seiichi, Spang, Rainer, ...
Prognostic and predictive factors are indispensable tools in the treatment of patients with neoplastic disease. For the most part, such factors rely on a few specific cell surface, histological, or...
Ishida, Seiichi, Huang, Erich, Zuzan, Harry, Spang, Rainer, Leone, Gustavo, West, Mike, ...
We have used high-density DNA microarrays to provide an analysis of gene regulation during the mammalian cell cycle and the role of E2F in this process. Cell cycle analysis was facilitated by a...
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...
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...
Early Diagnostic Marker Panel Determination for Microarray Based Clinical Studies
Jochen Jaeger, Dieter Weichenhan, Boris Ivandic, Rainer Spang
We present a novel, cost efficient two-phase design for predictive clinical gene expression studies: early marker panel determination (EMPD). In Phase-1, genome-wide microarrays are used only for a...
Hirsch, Burkhard, Hummel, Michael, Bentink, Stefan, Fouladi, Fariba, Spang, Rainer, Zollinger, Raphael, ...
High CD30 expression in classical Hodgkin’s lymphoma and anaplastic large cell lymphoma (ALCL) suggests an important pathogenic role of this cytokine receptor. To test this hypothesis, we...
Anchang, Benedict, Sadeh, Mohammad J., Jacob, Juby, Tresch, Achim, Vlad, Marcel O., Oefner, Peter J., ...
Cellular decision making in differentiation, proliferation, or cell death is mediated by molecular signaling processes, which control the regulation and expression of genes. Vice versa, the...
Kinetic laws, phase–phase expansions, renormalization group, and INR calibration
Vlad, Marcel O., Corlan, Alexandru D., Morán, Federico, Spang, Rainer, Oefner, Peter, Ross, John
We introduce systematic approaches to chemical kinetics based on the use of phase–phase (log–log) representations of the rate equations. For slow processes, we obtain a corrected form of the...
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...