Haralick’s Texture Features Computed by GPUs for Biological Applications (2009)
Guillermo Marcus, Nathalie Harder, Apichat Suratanee, Karl Rohr, Rainer König, Reinhard Männer
Abstract—This paper presents an approach to speedup the computation of co-occurrence matrices and Haralick texture features, as used for analyzing microscopy images of cells, by general-purpose...
Dittami, Simon M, Scornet, Delphine, Petit, Jean-Louis, Ségurens, Béatrice, Da Silva, Corinne, Corre, Erwan, ...
Abstract Background Brown algae (Phaeophyceae) are phylogenetically distant from red and green algae and an important component of the coastal ecosystem. They have developed unique mechanisms that...
Dittami, Simon, Scornet, Delphine, Petit, Jean-Louis, Ségurens, Béatrice, Da Silva, Corinne, Corre, Erwan, ...
Background: Brown algae (Phaeophyceae) are phylogenetically distant from red and green algae and an important component of the coastal ecosystem. They have developed unique mechanisms that allow them...
Westermann, Frank, Muth, Daniel, Benner, Axel, Bauer, Tobias, Henrich, Kai-Oliver, Oberthuer, André, ...
Abstract Background Amplified MYCN oncogene resulting in deregulated MYCN transcriptional activity is observed in 20% of neuroblastomas and identifies a highly aggressive subtype. In MYCN single-copy...
Plaimas, Kitiporn, Mallm, Jan-Phillip, Oswald, Marcus, Svara, Fabian, Sourjik, Victor, Eils, Roland, ...
Abstract Background Computational identification of new drug targets is a major goal of pharmaceutical bioinformatics. Results This paper presents a machine learning strategy to study and validate...
Gunnar Schramm, Marcus Oswald, Hanna Seitz, Sebastian Sager, Marc Zapatka, Gerhard Reinelt, ...
Pattern recognition of gene expression data on biochemical networks with simple
conditional experiments with a (2008)
Rainer König, Danila Baldessari, Nicolas Pollet, Christof Niehrs, Dr. Rainer König
of gene expression ratios for cDNA microarrays in multi-
FULL PAPER Refined Genetic Algorithm Simulations to Model Proteins (2007)
Genome and sequencing projects are yielding an exponentially growing amount of protein sequence data [1,2]. To understand their structure and function, protein modelling efforts have become an...
Schramm, Gunnar, Zapatka, Marc, Eils, Roland, König, Rainer
Abstract Background Biochemical investigations over the last decades have elucidated an increasingly complete image of the cellular metabolism. To derive a systems view for the regulation of the...
Klopocki, Eva, Schulze, Harald, Strauß, Gabriele, Ott, Claus-Eric, Hall, Judith, Trotier, Fabienne, ...
Thrombocytopenia–absent radius (TAR) syndrome is characterized by hypomegakaryocytic thrombocytopenia and bilateral radial aplasia in the presence of both thumbs. Other frequent associations are...
GOPET: A tool for automated predictions of Gene Ontology terms (2006)
Vinayagam, Arunachalam, Del Val, Coral, Schubert, Falk, Eils, Roland, Glatting, Karl-Heinz, Suhai, Sándor, ...
Abstract Background Vast progress in sequencing projects has called for annotation on a large scale. A Number of methods have been developed to address this challenging task. These methods, however,...
König, Rainer, Schramm, Gunnar, Oswald, Marcus, Seitz, Hanna, Sager, Sebastian, Zapatka, Marc, ...
Abstract Background Microarray technology produces gene expression data on a genomic scale for an endless variety of organisms and conditions. However, this vast amount of information needs to be...
Oberthuer, André, Berthold, Frank, Warnat, Patrick, Hero, Barbara, Kahlert, Yvonne, Spitz, Rüdiger, ...
PURPOSE: To develop a gene expression–based classifier for neuroblastoma patients that reliably predicts courses of the disease. PATIENTS AND METHODS: Two hundred fifty-one neuroblastoma specimens...
Rainer König, Gunnar Schramm, Marcus Oswald, Hanna Seitz, Sebastian Sager, Marc Zapatka, ...
Discovering functional gene expression patterns in the metabolic
Bmc Bioinformatics, Gunnar Schramm, Marc Zapatka, Rainer König, Biomed Central, Rainer König
Using gene expression data and network topology to detect substantial pathways, clusters and switches during oxygen
Arunachalam Vinayagam, Coral Del Val, Falk Schubert, Heinz Glatting, Sándor Suhai, Rainer König, ...
© 2006Vinayagam et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Applying Support Vector Machines for Gene ontology based gene function prediction (2004)
Vinayagam, Arunachalam, König, Rainer, Moormann, Jutta, Schubert, Falk, Eils, Roland, Glatting, Karl-Heinz, ...
Abstract Background The current progress in sequencing projects calls for rapid, reliable and accurate function assignments of gene products. A variety of methods has been designed to annotate...
Introduction. Gene expression profiling on a large scale has emerged from specialised groups to mainstream laboratories in modern medical and biological research within a few years time (Shoemaker...
Function Prediction, Arunachalam Vinayagam, Rainer König, Jutta Moormann, Falk Schubert, Karl-heinz Glatting, ...
This is an open-access article distributed under the terms of the Creative Commons Attribution License
Gene expression analysis on biochemical networks using the Potts spin model (2004)
Motivation: Microarray technology allows us to profile the expression of a large subset or all genes of a cell. Biochemical research over the last three decades has elucidated an increasingly...
König, Rainer, Baldessari, Danila, Pollet, Nicolas, Niehrs, Christof, Eils, Roland
In a typical gene expression profiling experiment with multiple conditions, a common reference sample is used for co‐hybridization with the samples to yield expression ratios. Differential...
Rainer König, Thomas Dandekar, Rainer Ko Nig, Thomas D
Introduction Solvent entropy has an impact on protein folding and protein interactions as well as protein design. However, the enumeration of the different microstates can become difficult....
König, Rainer, Dandekar, Thomas
Solvent entropy is a force to consider in protein folding and protein design but is difficult to model. It is investigated here in the context of the hp model: Two types of residues, hydrophobic and...
Point mutations throughout the GLI3 gene cause Greig cephalopolysyndactyly syndrome (1999)
Kalff-Suske, Martha, Wild, Anja, Topp, Juliane, Wessling, Martina, Jacobsen, Eva-Maria, Bornholdt, Dorothea, ...
Greig cephalopolysyndactyly syndrome, characterized by craniofacial and limb anomalies (GCPS; MIM 175700), previously has been demonstrated to be associated with translocations as well as point...
Computational methods for the prediction of protein folds (1997)
Thomas Dandekar, Thomas D, Rainer König
Contents 1. Introduction ................................................... 1 2. The protein folding problem ......................................... 2 2.1. The minimum of free energy...
König, Rainer, Baldessari, Danila, Pollet, Nicolas, Niehrs, Christof, Eils, Roland
In a typical gene expression profiling experiment with multiple conditions, a common reference sample is used for co-hybridization with the samples to yield expression ratios. Differential expression...
Applying Support Vector Machines for Gene ontology based gene function prediction
Vinayagam, Arunachalam, König, Rainer, Moormann, Jutta, Schubert, Falk, Eils, Roland, Glatting, Karl-Heinz, ...
Familial Syndromic Esophageal Atresia Maps to 2p23-p24
Celli, Jacopo, Van Beusekom, Ellen, Hennekam, Raoul C. M., Gallardo, M. Esther, De Córdoba, Santiago Rodríguez, ...
Esophageal atresia (EA) is a common life-threatening congenital anomaly that occurs in 1/3,000 newborns. Little is known of the genetic factors that underlie EA. Oculodigitoesophageoduodenal (ODED)...
GOPET: A tool for automated predictions of Gene Ontology terms
Vinayagam, Arunachalam, Del Val, Coral, Schubert, Falk, Eils, Roland, Glatting, Karl-Heinz, Suhai, Sándor, ...
König, Rainer, Baldessari, Danila, Pollet, Nicolas, Niehrs, Christof, Eils, Roland
In a typical gene expression profiling experiment with multiple conditions, a common reference sample is used for co-hybridization with the samples to yield expression ratios. Differential expression...
Applying Support Vector Machines for Gene ontology based gene function prediction
Vinayagam, Arunachalam, König, Rainer, Moormann, Jutta, Schubert, Falk, Eils, Roland, Glatting, Karl-Heinz, ...
Familial Syndromic Esophageal Atresia Maps to 2p23-p24
Celli, Jacopo, Van Beusekom, Ellen, Hennekam, Raoul C. M., Gallardo, M. Esther, De Córdoba, Santiago Rodríguez, ...
Esophageal atresia (EA) is a common life-threatening congenital anomaly that occurs in 1/3,000 newborns. Little is known of the genetic factors that underlie EA. Oculodigitoesophageoduodenal (ODED)...
GOPET: A tool for automated predictions of Gene Ontology terms
Vinayagam, Arunachalam, Del Val, Coral, Schubert, Falk, Eils, Roland, Glatting, Karl-Heinz, Suhai, Sándor, ...
Machine learning based analyses on metabolic networks supports high-throughput knockout screens
Plaimas, Kitiporn, Mallm, Jan-Phillip, Oswald, Marcus, Svara, Fabian, Sourjik, Victor, Eils, Roland, ...
Dittami, Simon M, Scornet, Delphine, Petit, Jean-Louis, Ségurens, Béatrice, Da Silva, Corinne, Corre, Erwan, ...
The brown alga Ectocarpus siliculosus, unlike terrestrial plants, undergoes extensive reprogramming of its transcriptome during the acclimation to mild abiotic stress.
Westermann, Frank, Muth, Daniel, Benner, Axel, Bauer, Tobias, Henrich, Kai-Oliver, Oberthuer, André, ...
Differences in MYCN/c-MYC target gene expression are associated with distinct neuroblastoma subtypes and clinical outcome.