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TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing
TREE-PUZZLE is a program package for quartet-based maximum-likelihood phylogenetic analysis that provides methods for reconstruction, comparison, and testing of trees and models on DNA as well as protein sequences to reduce waiting time for larger datasets.
A gene expression map of Arabidopsis thaliana development
Examining the expression patterns of large gene families, it is found that they are often more similar than would be expected by chance, indicating that many gene families have been co-opted for specific developmental processes.
Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels
A software package named Oases designed to heuristically assemble RNA-seq reads in the absence of a reference genome, across a broad spectrum of expression values and in presence of alternative isoforms is presented.
Minimum information about a microarray experiment (MIAME)—toward standards for microarray data
The ultimate goal of this work is to establish a standard for recording and reporting microarray-based gene expression data, which will in turn facilitate the establishment of databases and public repositories and enable the development of data analysis tools.
Comprehensive genomic profiles of small cell lung cancer
This first comprehensive study of somatic genome alterations in SCLC uncovers several key biological processes and identifies candidate therapeutic targets in this highly lethal form of cancer.
Variance stabilization applied to microarray data calibration and to the quantification of differential expression
A statistical model for microarray gene expression data that comprises data calibration, the quantifying of differential expression, and the quantification of measurement error is introduced, and a difference statistic Deltah whose variance is approximately constant along the whole intensity range is derived.
IntAct: an open source molecular interaction database
IntAct provides an open source database and toolkit for the storage, presentation and analysis of protein interactions, and allows exploring interaction networks in the context of the GO annotations of the interacting proteins.
Ontologizer 2.0 - a multifunctional tool for GO term enrichment analysis and data exploration
The Ontologizer allows users to visualize data as a graph including all significantly overrepresented GO terms and to explore the data by linking GO terms to all genes/proteins annotated to the term and by linking individual terms to child terms.
A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome
A global survey of messenger RNA splicing events identified 94,241 splice junctions and showed that exon skipping is the most prevalent form of alternative splicing.
Histone modification levels are predictive for gene expression
- R. Karlic, Ho-Ryun Chung, Julia A. Lasserre, K. Vlahovicek, M. Vingron
- BiologyProceedings of the National Academy of Sciences
- 1 February 2010
It is found that histone modification levels and gene expression are very well correlated, and it is shown that only a small number of histone modifications are necessary to accurately predict gene expression.