Genome Biology

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Comparing protein abundance and mRNA expression levels on a genomic scale

Dov Greenbaum, Christopher Colangelo, Kenneth Williams* and Mark Gerstein*

Genome Biology 2003, 4:117 doi:10.1186/gb-2003-4-9-117

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BioMed Central: 22 citations

Research article   Open Access Highly Accessed

Gender effect on neurodegeneration and myelin markers in an animal model for multiple sclerosis.

Alessandro Massella, Giulia D'Intino, Mercedes Fernandez, Sandra Sivilia, Luca Lorenzini, Silvia Giatti, Roberto C Melcangi, Laura Calza, Luciana Giardino BMC Neuroscience 2012, 13:12 (24 January 2012)

Research article   Open Access

Genome-wide differential gene expression in immortalized DF-1 chicken embryo fibroblast cell line

Byung-Whi Kong, Jeong Yoon Lee, Walter G Bottje, Kentu Lassiter, Jonghyuk Lee, Douglas N Foster BMC Genomics 2011, 12:571 (23 November 2011)

Proceedings   Open Access

Bayesian non-negative factor analysis for reconstructing transcription factor mediated regulatory networks

Jia Meng, Jianqiu (Michelle) Zhang, Yidong Chen, Yufei Huang Proteome Science 2011, 9(Suppl 1):S9 (14 October 2011)

Research   Open Access

Multi-membership gene regulation in pathway based microarray analysis

Stelios P Pavlidis, Annette M Payne, Stephen M Swift Algorithms for Molecular Biology 2011, 6:22 (22 September 2011)

Methodology article   Open Access

Identifier mapping performance for integrating transcriptomics and proteomics experimental results

Roger S Day, Kevin K McDade, Uma R Chandran, Alex Lisovich, Thomas P Conrads, Brian L Hood, VS Kolli, David Kirchner, Traci Litzi, G Maxwell BMC Bioinformatics 2011, 12:213 (27 May 2011)

Research article   Open Access

Dissecting the fission yeast regulatory network reveals phase-specific control elements of its cell cycle

Pierre R Bushel, Nicholas A Heard, Roee Gutman, Liwen Liu, Shyamal D Peddada, Saumyadipta Pyne BMC Systems Biology 2009, 3:93 (16 September 2009)

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Correlations between RNA and protein expression profiles in 23 human cell lines

Marcus Gry, Rebecca Rimini, Sara Strömberg, Anna Asplund, Fredrik Pontén, Mathias Uhlén, Peter Nilsson BMC Genomics 2009, 10:365 (7 August 2009)

Methodology article   Open Access Highly Accessed

A new multitest correction (SGoF) that increases its statistical power when increasing the number of tests

Antonio Carvajal-Rodríguez, Jacobo de Uña-Alvarez, Emilio Rolán-Alvarez BMC Bioinformatics 2009, 10:209 (8 July 2009)

Software   Open Access

A score system for quality evaluation of RNA sequence tags: an improvement for gene expression profiling

Daniel G Pinheiro, Pedro AF Galante, Sandro J de Souza, Marco A Zago, Wilson A Silva BMC Bioinformatics 2009, 10:170 (6 June 2009)

Research article   Open Access Highly Accessed

CD133+ adult human retinal cells remain undifferentiated in Leukaemia Inhibitory Factor (LIF)

Debra A Carter, Andrew D Dick, Eric J Mayer BMC Ophthalmology 2009, 9:1 (23 February 2009)

The adult human retina possess a population of cells positive for the CD133 stem cell marker, these proliferate after exposure to leukaemia inhibitory factor and have a phenotypic profile suggestive of progenitor cell status

Research   Open Access Highly Accessed

Quantitative protein expression profiling reveals extensive post-transcriptional regulation and post-translational modifications in schizont-stage malaria parasites

Bernardo J Foth, Neng Zhang, Sachel Mok, Peter R Preiser, Zbynek Bozdech Genome Biology 2008, 9:R177 (17 December 2008)

A quantitative time-course analysis of protein abundance for Plasmodium falciparum schizonts using two-dimensional differential gel electrophoresis reveals significant post-transcriptional regulation.

Research article   Open Access

A quantitative estimation of the global translational activity in logarithmically growing yeast cells

Tobias von der Haar BMC Systems Biology 2008, 2:87 (16 October 2008)

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Correlation of mRNA and protein levels: Cell type-specific gene expression of cluster designation antigens in the prostate

Laura E Pascal, Lawrence D True, David S Campbell, Eric W Deutsch, Michael Risk, Ilsa M Coleman, Lillian J Eichner, Peter S Nelson, Alvin Y Liu BMC Genomics 2008, 9:246 (23 May 2008)

Research   Open Access Highly Accessed

Common gene expression strategies revealed by genome-wide analysis in yeast

José García-Martínez, Fernando González-Candelas, José E Pérez-Ortín Genome Biology 2007, 8:R222 (19 October 2007)

A comprehensive analysis of six variables characterizing gene expression in yeast, including transcription and translation, mRNA and protein amounts, reveals a general tendency for levels of mRNA and protein to be harmonized, and for functionally related genes to have similar values for these variables.

Research   Open Access Highly Accessed

Dynamic cumulative activity of transcription factors as a mechanism of quantitative gene regulation

Feng He, Jan Buer, An-Ping Zeng, Rudi Balling Genome Biology 2007, 8:R181 (4 September 2007)

By combining information on the yeast transcription network and high-resolution time-series data with a series of factors, support is provided for the concept that dynamic cumulative regulation is a major principle of quantitative transcriptional control.

Software   Open Access

PARE: A tool for comparing protein abundance and mRNA expression data

Eric Z Yu, Anne Burba, Mark Gerstein BMC Bioinformatics 2007, 8:309 (24 August 2007)

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Growth control of the eukaryote cell: a systems biology study in yeast

Juan I Castrillo, Leo A Zeef, David C Hoyle, Nianshu Zhang, Andrew Hayes, David CJ Gardner, Michael J Cornell, June Petty, Luke Hakes, Leanne Wardleworth, Bharat Rash, Marie Brown, Warwick B Dunn, David Broadhurst, Kerry O'Donoghue, Svenja S Hester, Tom PJ Dunkley, Sarah R Hart, Neil Swainston, Peter Li, Simon J Gaskell, Norman W Paton, Kathryn S Lilley, Douglas B Kell, Stephen G Oliver Journal of Biology 2007, 6:4 (30 April 2007)

The first comprehensive systems biology study on growth rate control in yeast integrates information from the transcriptome, proteome and metabolome to reveal how cell growth underlies key cellular and development processes.

Research   Open Access

Integration of metabolite with transcript and enzyme activity profiling during diurnal cycles in Arabidopsis rosettes

Yves Gibon, Bjoern Usadel, Oliver E Blaesing, Beate Kamlage, Melanie Hoehne, Richard Trethewey, Mark Stitt Genome Biology 2006, 7:R76 (17 August 2006)

An analysis of the temporal dynamics of metabolite and transcript levels, as well as enzyme activity, of 137 metabolites during diurnal cycles in Arabidopsis leaves

Methodology article   Open Access

Causal inference of regulator-target pairs by gene mapping of expression phenotypes

David C Kulp, Manjunatha Jagalur BMC Genomics 2006, 7:125 (24 May 2006)

Methodology article   Open Access

Improved tagging strategy for protein identification in mammalian cells

Agnieszka Bialkowska, Xian-Yang Zhang, Jakob Reiser BMC Genomics 2005, 6:113 (4 September 2005)

Full-length endogenous proteins can be expressed as green fluorescent fusion proteins from their own promoters using a lentivirus vector that displays several improvements over its retrovirus predecessors.

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The synovial proteome: analysis of fibroblast-like synoviocytes

Kumar Dasuri, Mihaela Antonovici, Keding Chen, Ken Wong, Kenneth Standing, Werner Ens, Hani El-Gabalawy, John A Wilkins Arthritis Res Ther 2004, 6:R161-R168 (16 February 2004)

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Scratching the (T cell) surface

Joerg Ermann, Chan D Chung, C Garrison Fathman Genome Biology 2003, 5:202 (11 December 2003)

Using a genome-scale approach to study transcription levels in a human CD8+ T-cell clone, a recent study has suggested that the repertoire of molecules on the surface of T cells is close to being completely characterized.