ROCR: visualizing classifier performance in R
UNLABELLED ROCR is a package for evaluating and visualizing the performance of scoring classifiers in the statistical language R. It features over 25 performance measures that can be freely combined…
Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
Two novel algorithms that improve GO group scoring using the underlying GO graph topology are presented and it is shown that both methods eliminate local dependencies between GO terms and point to relevant areas in the GO graph that remain undetected with state-of-the-art algorithms for scoring functional terms.
A fast flexible docking method using an incremental construction algorithm.
This work presents an automatic method for docking organic ligands into protein binding sites that combines an appropriate model of the physico-chemical properties of the docked molecules with efficient methods for sampling the conformational space of the ligand.
Computing topological parameters of biological networks
- Y. Assenov, F. Ramírez, Sven-Eric Schelhorn, Thomas Lengauer, M. Albrecht
- Computer ScienceBioinform.
- 15 January 2008
The versatile Cytoscape plugin NetworkAnalyzer computes and displays a comprehensive set of topological parameters, which includes the number of nodes, edges, and connected components, the network diameter, radius, density, centralization, heterogeneity, and clustering coefficient, and the characteristic path length.
A new measure for functional similarity of gene products based on Gene Ontology
- A. Schlicker, F. S. Domingues, J. Rahnenführer, Thomas Lengauer
- BiologyBMC Bioinformatics
- 15 June 2006
A new method for comparing sets of GO terms and for assessing the functional similarity of gene products and a proposed map of the functional space provides a new global view on the functional relationships between gene products or protein families.
A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1
Data suggest that the underlying biological process may be specific to Crohn disease, and that marker rs2241880, a coding SNP (T300A), carries virtually all the disease risk exerted by the ATG16L1 locus.
Combinatorial algorithms for integrated circuit layout
- Thomas Lengauer
- EducationApplicable theory in computer science
- 7 September 1990
This paper will concern you to try reading combinatorial algorithms for integrated circuit layout as one of the reading material to finish quickly.
A fast algorithm for finding dominators in a flowgraph
A fast algorithm for finding dominators in a flowgraph is presented, which beat the straightforward algorithm and the bit vector algorithm on all but the smallest graphs tested.
Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment.
Comprehensive Analysis of DNA Methylation Data with RnBeads
- Y. Assenov, F. Müller, P. Lutsik, J. Walter, Thomas Lengauer, C. Bock
- BiologyNature Methods
- 11 September 2014
RnBeads is a software tool for large-scale analysis and interpretation of DNA methylation data, providing a user-friendly analysis workflow that yields detailed hypertext reports…