Integrating multiple 'omics' analysis for microbial biology: application and methodologies

W Zhang, F Li, L Nie - Microbiology, 2010 - microbiologyresearch.org
Recent advances in various 'omics' technologies enable quantitative monitoring of the
abundance of various biological molecules in a high-throughput manner, and thus allow …

The state of the art in the analysis of two-dimensional gel electrophoresis images

M Berth, FM Moser, M Kolbe, J Bernhardt - Applied microbiology and …, 2007 - Springer
Software-based image analysis is a crucial step in the biological interpretation of two-
dimensional gel electrophoresis experiments. Recent significant advances in image …

Addressing accuracy and precision issues in iTRAQ quantitation

NA Karp, W Huber, PG Sadowski, PD Charles… - Molecular & Cellular …, 2010 - ASBMB
iTRAQ (isobaric tags for relative or absolute quantitation) is a mass spectrometry technology
that allows quantitative comparison of protein abundance by measuring peak intensities of …

Multidimensional separations-based shotgun proteomics

ML Fournier, JM Gilmore, SA Martin-Brown… - Chemical …, 2007 - ACS Publications
The proteome refers to the collection of proteins in a given biological organism or system
under a particular set of environmental conditions. The study of proteins, referred to as …

2DE: the phoenix of proteomics

BM Oliveira, JR Coorssen, D Martins-de-Souza - Journal of proteomics, 2014 - Elsevier
Given the rapid developments in mass spectrometry (MS) in terms of sensitivity, mass
accuracy, and throughput, some have suggested that two-dimensional gel electrophoresis …

Chitosan enhances rice seedling growth via gene expression network between nucleus and chloroplast

N Chamnanmanoontham, W Pongprayoon… - Plant Growth …, 2015 - Springer
Chitosan, a partially deacetylated form of the natural and biodegradable biopolymer chitin,
has been used as plant growth promoter in agriculture. The aim of this work was to …

Comparison of detergent‐based sample preparation workflows for LTQ‐Orbitrap analysis of the Escherichia coli proteome

A Tanca, G Biosa, D Pagnozzi, MF Addis… - Proteomics, 2013 - Wiley Online Library
This work presents a comparative evaluation of several detergent‐based sample
preparation workflows for the MS‐based analysis of bacterial proteomes, performed using …

An integrated proteomics and transcriptomics reference data set provides new insights into the Bradyrhizobium japonicum bacteroid metabolism in soybean root …

N Delmotte, CH Ahrens, C Knief, E Qeli, M Koch… - …, 2010 - Wiley Online Library
Bradyrhizobium japonicum, a gram‐negative soil bacterium that establishes an N2‐fixing
symbiosis with its legume host soybean (Glycine max), has been used as a symbiosis model …

Prediction and validation of novel SigB regulon members in Bacillus subtilis and regulon structure comparison to Bacillales members

KYC Yeak, J Boekhorst, M Wels, T Abee… - BMC microbiology, 2023 - Springer
Abstract Background Sigma factor B (SigB) is the central regulator of the general stress
response in Bacillus subtilis and regulates a group of genes in response to various …

Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) Applied to Quantitative Proteomics of Bacillus subtilis

B Soufi, C Kumar, F Gnad, M Mann… - Journal of proteome …, 2010 - ACS Publications
We applied stable isotope labeling by amino acids in cell culture (SILAC) to large-scale
quantitative proteomics analyses of the model bacterium Bacillus subtilis in two …