(Q28822192)

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

limma

1 reference

Europe PubMed Central

22 June 2022

https://europepmc.org/article/PMC/5059772

inferred from PubMed Central ID database lookup

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

MOPED 2.5--an integrated multi-omics resource: multi-omics profiling expression database now includes transcriptomics data

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

HMDB 3.0--The Human Metabolome Database in 2013

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

A whole-cell computational model predicts phenotype from genotype

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

Global quantification of mammalian gene expression control

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

BioNumbers--the database of key numbers in molecular and cell biology

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

PubChem: a public information system for analyzing bioactivities of small molecules

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

TopHat: discovering splice junctions with RNA-Seq

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5007486

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

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

PRIDE: a public repository of protein and peptide identifications for the proteomics community

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

Summaries of Affymetrix GeneChip probe level data

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

Trimmomatic: a flexible trimmer for Illumina sequence data

6 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

affy--analysis of Affymetrix GeneChip data at the probe level

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

Gene Ontology Consortium: going forward

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

HTSeq--a Python framework to work with high-throughput sequencing data

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

Activities at the Universal Protein Resource (UniProt)

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

Microarray data normalization and transformation

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

Cross-platform normalization of microarray and RNA-seq data for machine learning applications

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

COLOMBOS v3.0: leveraging gene expression compendia for cross-species analyses

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

An integrative, multi-scale, genome-wide model reveals the phenotypic landscape of Escherichia coli

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

The future of whole-cell modeling

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

A gene ontology inferred from molecular networks

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

Revisiting global gene expression analysis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

Batch effect removal methods for microarray gene expression data integration: a survey

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

In silico method for modelling metabolism and gene product expression at genome scale

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

Insights into the regulation of protein abundance from proteomic and transcriptomic analyses

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

When one and one gives more than two: challenges and opportunities of integrative omics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

Computational and statistical analysis of protein mass spectrometry data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

The challenges of integrating multi-omic data sets

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

Functional genomic study of exogenous n-butanol stress in Escherichia coli

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

Growth rate-dependent global effects on gene expression in bacteria

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

Predicting cellular growth from gene expression signatures

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

A semi-supervised method for predicting transcription factor-gene interactions in Escherichia coli

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

A comparison of background correction methods for two-colour microarrays

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

Functional genomic studies of uropathogenic Escherichia coli and host urothelial cells when intracellular bacterial communities are assembled

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

Multiple high-throughput analyses monitor the response of E. coli to perturbations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

Phylogenetic characterization of virulence and resistance phenotypes of Pseudomonas syringae

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

Open source system for analyzing, validating, and storing protein identification data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

General stress response regulator RpoS in adaptive mutation and amplification in Escherichia coli

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

Regulatory network of Escherichia coli: consistency between literature knowledge and microarray profiles.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

Integrating 'omic' information: a bridge between genomics and systems biology

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

Escherichia coli acid resistance: cAMP receptor protein and a 20 bp cis-acting sequence control pH and stationary phase expression of the gadA and gadBC glutamate decarboxylase genes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

The Kyoto Encyclopedia of Genes and Genomes—KEGG

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

E-CELL: software environment for whole-cell simulation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

Ribosomes as sensors of heat and cold shock in Escherichia coli

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5059772

Identification of Carcass and Meat Quality QTL in an F(2) Duroc × Pietrain Pig Resource Population Using Different Least-Squares Analysis Models

3 June 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS13090

Dependency on medium and temperature of cell size and chemical composition during balanced grown of Salmonella typhimurium

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS13090

A predictive model for transcriptional control of physiology in a free living cell.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS13090

MAGIC: access portal to a cross-platform gene expression compendium for maize.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS13090

Amino acid starvation induced by invasive bacterial pathogens triggers an innate host defense program.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS13090

Indole-3-acetic acid regulates the central metabolic pathways in Escherichia coli.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS13090

Short- and long-term changes in proteome composition and kinetic properties in a culture of Escherichia coli during transition from glucose-excess to glucose-limited growth conditions in continuous culture and vice versa

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS13090

Featured organism: Danio rerio, the zebrafish

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS13090

Generalization of back-propagation to recurrent neural networks

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27713404

12 December 2020

inferred from PubMed ID database lookup

Editorial: ChemSpider--a tool for Natural Products research

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27713404

12 December 2020

inferred from PubMed ID database lookup

1 reference

https://pubmed.ncbi.nlm.nih.gov/27713404

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1038/NCOMMS13090

1 reference

Dimensions Publication ID

3098188

ADS bibcode

2016NatCo...713090K

0 references

1049086693

0 references

3098188

1 reference

1 reference

1 reference