Constraint-based models predict metabolic and associated cellular functions
The prediction of cellular function from a genotype is a fundamental goal in biology. For
metabolism, constraint-based modelling methods systematize biochemical, genetic and …
metabolism, constraint-based modelling methods systematize biochemical, genetic and …
Bacterial transcription terminators: the RNA 3′-end chronicles
JM Peters, AD Vangeloff, R Landick - Journal of molecular biology, 2011 - Elsevier
The process of transcription termination is essential to proper expression of bacterial genes
and, in many cases, to the regulation of bacterial gene expression. Two types of bacterial …
and, in many cases, to the regulation of bacterial gene expression. Two types of bacterial …
RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond
S Gama-Castro, H Salgado… - Nucleic acids …, 2016 - academic.oup.com
Abstract RegulonDB (http://regulondb. ccg. unam. mx) is one of the most useful and
important resources on bacterial gene regulation, as it integrates the scattered scientific …
important resources on bacterial gene regulation, as it integrates the scattered scientific …
Wisdom of crowds for robust gene network inference
Reconstructing gene regulatory networks from high-throughput data is a long-standing
challenge. Through the Dialogue on Reverse Engineering Assessment and Methods …
challenge. Through the Dialogue on Reverse Engineering Assessment and Methods …
Evaluating methods of inferring gene regulatory networks highlights their lack of performance for single cell gene expression data
Background A fundamental fact in biology states that genes do not operate in isolation, and
yet, methods that infer regulatory networks for single cell gene expression data have been …
yet, methods that infer regulatory networks for single cell gene expression data have been …
Computational analysis of bacterial RNA-Seq data
R McClure, D Balasubramanian, Y Sun… - Nucleic acids …, 2013 - academic.oup.com
Recent advances in high-throughput RNA sequencing (RNA-seq) have enabled
tremendous leaps forward in our understanding of bacterial transcriptomes. However …
tremendous leaps forward in our understanding of bacterial transcriptomes. However …
Lag phase is a distinct growth phase that prepares bacteria for exponential growth and involves transient metal accumulation
MD Rolfe, CJ Rice, S Lucchini, C Pin… - Journal of …, 2012 - Am Soc Microbiol
Lag phase represents the earliest and most poorly understood stage of the bacterial growth
cycle. We developed a reproducible experimental system and conducted functional genomic …
cycle. We developed a reproducible experimental system and conducted functional genomic …
Characterization of 582 natural and synthetic terminators and quantification of their design constraints
Large genetic engineering projects require more cistrons and consequently more strong and
reliable transcriptional terminators. We have measured the strengths of a library of …
reliable transcriptional terminators. We have measured the strengths of a library of …
GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods
Motivation: Over the last decade, numerous methods have been developed for inference of
regulatory networks from gene expression data. However, accurate and systematic …
regulatory networks from gene expression data. However, accurate and systematic …
TIGRESS: trustful inference of gene regulation using stability selection
Background Inferring the structure of gene regulatory networks (GRN) from a collection of
gene expression data has many potential applications, from the elucidation of complex …
gene expression data has many potential applications, from the elucidation of complex …