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Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments
We present a novel technique for identifying differentially expressed genes that does not originate from a sophisticated statistical model but rather from an analysis of biological reasoning. Expand
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antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters
We present the third version of antiSMASH, a web server and stand-alone tool for the automatic genomic identification and analysis of biosynthetic gene clusters, which has undergone major improvements. Expand
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antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification
We present the thoroughly updated antiSMASH version 4, which adds several novel features, including prediction of gene cluster boundaries using 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 a domain-level alignment tool for comparative analysis of trans-AT polyketide synthase assembly line architectures. Expand
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RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis
We present a new meta-analysis tool to detect differentially expressed genes by integrating multiple array datasets from various experimental platforms/settings across laboratories. Expand
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antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences
We present antiSMASH (antibiotics & Secondary Metabolite Analysis Shell), the first comprehensive pipeline capable of identifying biosynthetic loci covering the whole range of known secondary metabolite compound classes (polyketides, non-ribosomal peptides, terpenes, aminoglycosides and aminocoumarins). Expand
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The Potassium-Dependent Transcriptome of Arabidopsis Reveals a Prominent Role of Jasmonic Acid in Nutrient Signaling1[w]
Full genome microarrays were used to assess transcriptional responses of Arabidopsis seedlings to changing external supply of the essential macronutrient potassium (K+). Rank product statistics andExpand
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antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers
We present the highly improved antiSMASH 2.0 release, available at http://antismash.secondarymetabolites.org/. Expand
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Detecting Sequence Homology at the Gene Cluster Level with MultiGeneBlast
The genes encoding many biomolecular systems and pathways are genomically organized in operons or gene clusters. With MultiGeneBlast, we provide a user-friendly and effective tool to perform homologyExpand
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What is Systems Biology?
  • R. Breitling
  • Computer Science, Medicine
  • Front. Physiology
  • 22 March 2010
Systems biology is increasingly popular, but to many biologists it remains unclear what this new discipline actually encompasses. Expand
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GeneRank: Using search engine technology for the analysis of microarray experiments
GeneRank is an intuitive modification of PageRank that maintains many of its mathematical properties. Expand
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