(Q31116249)

29 June 2017

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title

Integrative analysis of transcriptomic and proteomic data: challenges, solutions and applications (English)

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29 June 2017

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Lei Nie

1

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29 June 2017

Gang Wu

2

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29 June 2017

David E Culley

3

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29 June 2017

Johannes C M Scholten

4

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29 June 2017

Weiwen Zhang

5

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29 June 2017

1 April 2007

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Critical Reviews in Biotechnology

29 June 2017

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29 June 2017

27

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29 June 2017

2

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29 June 2017

63-75

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Mass spectrometry-based proteomics

29 June 2017

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Integrative analysis of genome-scale data by using pseudoinverse projection predicts novel correlation between DNA replication and RNA transcription

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Quantifying reproducibility for differential proteomics: noise analysis for protein liquid chromatography-mass spectrometry of human serum.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

A comparison of selected mRNA and protein abundances in human liver

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Codon bias evolution in Drosophila. Population genetics of mutation-selection drift

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

The iron-regulated transcriptome and proteome of Neisseria meningitidis serogroup C.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Osteopontin regulation by inorganic phosphate is ERK1/2-, protein kinase C-, and proteasome-dependent

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Growth rate-optimised tRNA abundance and codon usage.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Post-transcriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

LSimpute: accurate estimation of missing values in microarray data with least squares methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Automatic poisson peak harvesting for high throughput protein identification

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Absolute quantification strategies in proteomics based on mass spectrometry.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Bacterial proteomics and its role in antibacterial drug discovery

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Sequence analysis suggests that tetra-nucleotides signal the termination of protein synthesis in eukaryotes

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Discordant protein and mRNA expression in lung adenocarcinomas

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

A combined proteome and microarray investigation of inorganic phosphate-induced pre-osteoblast cells.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Integrating gene and protein expression data: pattern analysis and profile mining

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Differences in codon bias cannot explain differences in translational power among microbes

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Codon choice and potential complementarity between mRNA downstream of the initiation codon and bases 1471 –1480 in 16S ribosomal RNA affects expression ofglnS

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

A sampling of the yeast proteome

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Changes in the protein expression of yeast as a function of carbon source

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Global analysis of protein expression in yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Why is transcription coupled to translation in bacteria?

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Analysis of mRNA expression and protein abundance data: an approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Comparing protein abundance and mRNA expression levels on a genomic scale

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Correlation between protein and mRNA abundance in yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Integrated transcriptome and proteome data: the challenges ahead

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Interplay of transcriptomics and proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Global analysis of gene expression in yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Integrated genomic and proteomic analyses of a systematically perturbed metabolic network

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Effects of rare codon clusters on high-level expression of heterologous proteins in Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Missing value estimation for DNA microarray gene expression data: local least squares imputation

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Global analyses of transcriptomes and proteomes of a parent strain and an L-threonine-overproducing mutant strain

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Transcriptional regulatory networks in Saccharomyces cerevisiae

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Hierarchy of sequence-dependent features associated with prokaryotic translation

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Gene expression analyzed by high-resolution state array analysis and quantitative proteomics: response of yeast to mating pheromone

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Integrating global proteomic and genomic expression profiles generated from islet alpha cells: opportunities and challenges to deriving reliable biological inferences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Prokaryotic translation: the interactive pathway leading to initiation

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Insights into the relation between mRNA and protein expression patterns: I. Theoretical considerations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

An algorithmic framework for genome-wide modeling and analysis of translation networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Identification of a gene causing human cytochrome c oxidase deficiency by integrative genomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Microarray and EST database estimates of mRNA expression levels differ: the protein length versus expression curve for C. elegans

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Correlation of mRNA expression and protein abundance affected by multiple sequence features related to translational efficiency in Desulfovibrio vulgaris: a quantitative analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Integrated analysis of transcriptomic and proteomic data of Desulfovibrio vulgaris: zero-inflated Poisson regression models to predict abundance of undetected proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Discrimination models using variance-stabilizing transformation of metabolomic NMR data

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Comparative proteome analysis of Staphylococcus aureus biofilm and planktonic cells and correlation with transcriptome profiling

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Proteomics strategies for protein identification

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Uses and pitfalls of microarrays for studying transcriptional regulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Translation in Bacillus subtilis: roles and trends of initiation and termination, insights from a genome analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Bacterial translational control at atomic resolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Correlation of proteomic and transcriptomic profiles of Staphylococcus aureus during the post-exponential phase of growth.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Exploring glycopeptide-resistance in Staphylococcus aureus: a combined proteomics and transcriptomics approach for the identification of resistance-related markers.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

RNA expression analysis using a 30 base pair resolution Escherichia coli genome array

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Codon usage and genome evolution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Codon bias at the 3'-side of the initiation codon is correlated with translation initiation efficiency in Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Integrated genomic and proteomic analyses of gene expression in Mammalian cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Improving missing value estimation in microarray data with gene ontology

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Missing value estimation methods for DNA microarrays

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

The influence of ribosome-binding-site elements on translational efficiency in Bacillus subtilis and Escherichia coli in vivo

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Proteome and transcriptome analysis of retinoic acid-induced differentiation of human acute promyelocytic leukemia cells, NB4.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Guidelines for the next 10 years of proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Assessment of metals in reconstituted metallothioneins by electrospray mass spectrometry.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

Global transcriptomic analysis of Desulfovibrio vulgaris on different electron donors.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

A proteomic view ofDesulfovibrio vulgaris metabolism as determined by liquid chromatography coupled with tandem mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07388550701334212

10.1080/07388550701334212

21 January 2018

Identifiers

DOI

1 reference

29 June 2017

1 reference