Using graph theory to analyze biological networks

GA Pavlopoulos, M Secrier, CN Moschopoulos… - BioData mining, 2011 - Springer
Understanding complex systems often requires a bottom-up analysis towards a systems
biology approach. The need to investigate a system, not only as individual components but …

Reconstruction of biochemical networks in microorganisms

AM Feist, MJ Herrgård, I Thiele, JL Reed… - Nature Reviews …, 2009 - nature.com
Abstract Systems analysis of metabolic and growth functions in microbial organisms is
rapidly developing and maturing. Such studies are enabled by reconstruction, at the …

Gene co-expression analysis for functional classification and gene–disease predictions

S Van Dam, U Vosa, A van der Graaf… - Briefings in …, 2018 - academic.oup.com
Gene co-expression networks can be used to associate genes of unknown function with
biological processes, to prioritize candidate disease genes or to discern transcriptional …

Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles

JJ Faith, B Hayete, JT Thaden, I Mogno… - PLoS …, 2007 - journals.plos.org
Machine learning approaches offer the potential to systematically identify transcriptional
regulatory interactions from a compendium of microarray expression profiles. However …

Transcription factor-based biosensors in biotechnology: current state and future prospects

R Mahr, J Frunzke - Applied microbiology and biotechnology, 2016 - Springer
Living organisms have evolved a plethora of sensing systems for the intra-and extracellular
detection of small molecules, ions or physical parameters. Several recent studies have …

A bagging SVM to learn from positive and unlabeled examples

F Mordelet, JP Vert - Pattern Recognition Letters, 2014 - Elsevier
We consider the problem of learning a binary classifier from a training set of positive and
unlabeled examples, both in the inductive and in the transductive setting. This problem …

Mistranslation of membrane proteins and two-component system activation trigger antibiotic-mediated cell death

MA Kohanski, DJ Dwyer, J Wierzbowski, G Cottarel… - Cell, 2008 - cell.com
Aminoglycoside antibiotics, such as gentamicin and kanamycin, directly target the ribosome,
yet the mechanisms by which these bactericidal drugs induce cell death are not fully …

Gyrase inhibitors induce an oxidative damage cellular death pathway in Escherichia coli

DJ Dwyer, MA Kohanski, B Hayete… - Molecular systems …, 2007 - embopress.org
Modulation of bacterial chromosomal supercoiling is a function of DNA gyrase‐catalyzed
strand breakage and rejoining. This reaction is exploited by both antibiotic and proteic …

Graph theory and networks in biology

O Mason, M Verwoerd - IET systems biology, 2007 - IET
A survey of the use of graph theoretical techniques in Biology is presented. In particular,
recent work on identifying and modelling the structure of bio-molecular networks is …

What are DNA sequence motifs?

P D'haeseleer - Nature biotechnology, 2006 - nature.com
Sequence motifs are becoming increasingly important in the analysis of gene regulation.
How do we define sequence motifs, and why should we use sequence logos instead of …