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Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments
antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters
Abstract Microbial secondary metabolism constitutes a rich source of antibiotics, chemotherapeutics, insecticides and other high-value chemicals. Genome mining of gene clusters that encode the…
RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis
- F. Hong, R. Breitling, C. McEntee, B. Wittner, J. Nemhauser, J. Chory
- 15 October 2006
The Bioconductor package RankProd modifies and extends the rank product method proposed by Breitling et al., to integrate multiple microarray studies from different laboratories and/or platforms and accepts pre-processed expression datasets produced from a wide variety of platforms.
antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences
This work presents the first comprehensive pipeline capable of identifying biosynthetic loci covering the whole range of known secondary metabolite compound classes, and integrates or cross-links all previously available secondary-metabolite specific gene analysis methods in one interactive view.
The Potassium-Dependent Transcriptome of Arabidopsis Reveals a Prominent Role of Jasmonic Acid in Nutrient Signaling1[w]
- P. Armengaud, R. Breitling, A. Amtmann
- Environmental Science, BiologyPlant Physiology
- 1 September 2004
A novel role of JA in nutrient signaling and stress management through a variety of physiological processes such as nutrient storage, recycling, and reallocation is highlighted as well as a network of molecular processes underlying plant adaptation to K+ deficiency.
antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers
The highly improved antiSMASH 2.0 now supports input of multiple related sequences simultaneously (multi-FASTA/GenBank/EMBL), which allows the analysis of draft genomes comprising multiple contigs, and direct analysis of protein sequences is now possible.
antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification
The thoroughly updated antiSMASH version 4 is presented, which adds several novel features, including prediction of gene cluster boundaries using the ClusterFinder method or the newly integrated CASSIS algorithm, improved substrate specificity prediction for non-ribosomal peptide synthetase adenylation domains based on the new SANDPUMA algorithm, and several usability features have been updated and improved.
What is Systems Biology?
- R. Breitling
- BiologyFront. Physiology
- 22 March 2010
A brief personal perspective starts by outlining the asthetic qualities that motivate systems biologists, discusses which activities do not belong to the core of systems biology, and concludes by attempting to define systems biology as the research endeavor that aims at providing the scientific foundation for successful synthetic biology.
Detecting Sequence Homology at the Gene Cluster Level with MultiGeneBlast
This work provides a user-friendly and effective tool to perform homology searches with operons or gene clusters as basic units, instead of single genes, to get a better understanding of the function, evolutionary history, and practical applications of such genomic regions.
GeneRank: Using search engine technology for the analysis of microarray experiments
The modification of the PageRank algorithm provides an alternative method of evaluating microarray experimental results which combines prior knowledge about the underlying network and offers an improvement compared to assessing the importance of a gene based on its experimentally observed fold-change alone.