A whole-cell computational model predicts phenotype from genotype (Q24622101)

23 June 2017

A whole-cell computational model predicts phenotype from genotype (English)

1 reference

2,3-dipalmitoyl-S-glycerylcysteine

23 June 2017

1 reference

1-myristoyl-2-oleoylglycerol

61842

1 reference

6'-amino-1,3'-bis(2-deoxy-beta-D-erythro-pentofuranosyl)-5'-hydroxy-5-methyl-3,4-dihydro[4,4'-bipyrimidine]-2,2'(1H,3'H)-dione

75582

1 reference

2'-deoxy-5-(4,5-dihydroxypentyl)uridine

132160

1 reference

5-carboxy-2'-deoxyuridine

132191

1 reference

5,6-dihydroxy-2'-deoxyuridine 5'-monophosphate

102485

1 reference

8,5'-cyclo-2'-deoxyadenosine

132190

1 reference

5-O-phosphono-2-deoxyribosyl-(3->5)-2-deoxyribose

131825

1 reference

1 reference

1,2-ditetradec-7-enoyl-sn-glycero-3-cytidine 5'-diphosphate

76403

1 reference

2'-deoxy-5,6-dihydroxy-5,6-dihydrocytidine 5'-monophosphate

103990

1 reference

2,3-dideoxy-beta-D-ribose 5-phosphate

132165

1 reference

5-carboxymethylaminomethyl-2-thiouridine 5'-monophosphate

132170

1 reference

2-deoxy-D-glucose 6-phosphate

115218

1 reference

2'-deoxy-5,6-dihydroxy-5,6-dihydrocytidine

16043

1 reference

1 reference

1 reference

2'-deoxy-5-(4,5-dihydroxypentyl)uridine 5'-monophosphate

115240

1 reference

6-(4,5-diamino-2-oxo-5,6-dihydro-1H-pyrimidin-6-yl)-1,3-diazabicyclo[2.2.0]hex-4-en-2-one

132193

1 reference

5-O-phosphono-2-deoxyribosyl-(3->5)-2,3-dideoxyribose

116226

1 reference

1,2-Didodecanoyl-sn-glycero-3-cytidine 5'-diphosphate

132204

1 reference

1 reference

1 reference

4,5-Diamino-1,4a,4b,8,8a,8b-hexahydrocyclobuta[1,2-d:4,3-d']dipyrimidine-2,7-dione

131824

1 reference

8,5'-cyclo-2'-deoxyguanosine monophosphate

116510

1 reference

1,3'-bis(2-deoxy-beta-D-erythro-pentofuranosyl)-6-(5,6-diamino-2-oxo-2,3,4,5-tetrahydropyrimidin-4-yl)-1,3-diazabicyclo[2.2.0]hex-4-en-2-one

131829

1 reference

2'-deoxyinosine-5'-monophosphate

132158

1 reference

5-Amino-5-methyl-6-{2-oxo-1,3-diazabicyclo[2.2.0]hex-4-en-6-yl}-1,3-diazinane-2,4-dione

28806

1 reference

5-(4,5-dihydroxypentyl)uracil

116315

1 reference

2'-deoxycytidine-thymidine dimer

132195

1 reference

deoxycytidine diphosphate

116810

1 reference

5-carboxy-2'-deoxyuridine 5'-monophosphate

28846

1 reference

1,2-dioctadecanoyl-sn-glycero-3-cytidine 5'-diphosphate

102517

1 reference

8-aza-2'-deoxyadenosine 5'-monophosphate

104121

1 reference

1,2-Ditetradecanoyl-sn-glycero-3-cytidine 5'-diphosphate

102466

1 reference

tetrahexadecanoyl cardiolipin

103211

1 reference

5',6'-diamino-1,3'-bis(2-deoxy-beta-D-erythro-pentofuranosyl)-4',5'-dihydro[4,4'-bipyrimidine]-2,2'(1H,3'H)-dione

104586

1 reference

4-(5,6-diamino-2-oxo-4,5-dihydro-3H-pyrimidin-4-yl)-1H-pyrimidin-2-one

131835

1 reference

1 reference

1 reference

1 reference

102328

2'-deoxycytidine dimer

1 reference

5',6'-diamino-1,3'-bis(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-4',5'-dihydro[4,4'-bipyrimidine]-2,2'(1H,3'H)-dione

116736

1 reference

1 reference

1 reference

1 reference

1,3'-bis(2-deoxy-beta-D-erythro-pentofuranosyl)-5-amino-5-methyl-6-{2-oxo-1,3-diazabicyclo[2.2.0]hex-4-en-6-yl}-1,3-diazinane-2,4-dione

116916

1 reference

N(6)-carbamoylmethyl-2'-deoxyadenosine 5'-monophosphate

132159

1 reference

8,5'-cyclo-2'-deoxyadenosine monophosphate

103067

1 reference

1 reference

5-carboxymethylaminomethyl-2-thiouridine

132197

1 reference

1,2-di-[(9Z)-hexadecenoyl]glycerol

64336

1 reference

tetraoctadec-11-enoyl cardiolipin

131830

1 reference

N(6)-carbamoylmethyladenine

105685

1 reference

6-azathymidine 5'-monophosphate

102525

1 reference

1,2-dihexadec-9-enoyl-sn-glycero-3-cytidine 5'-diphosphate

102257

1 reference

thymidine 5'-monophosphate dimer

104012

1 reference

6'-amino-1,3'-bis(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-5'-hydroxy-5-methyl-3,4-dihydro[4,4'-bipyrimidine]-2,2'(1H,3'H)-dione

131821

1 reference

1,3'-bis(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-5-amino-5-methyl-6-{2-oxo-1,3-diazabicyclo[2.2.0]hex-4-en-6-yl}-1,3-diazinane-2,4-dione

132164

1 reference

6'-amino-5'-hydroxy-5-methyl-3,4-dihydro[4,4'-bipyrimidine]-2,2'(1H,5'H)-dione

132163

1 reference

N(6)-carbamoylmethyl-2'-deoxyadenosine

116279

1 reference

CDP-dipalmitoyl-sn-glycerol

102719

1 reference

tetrahexadec-9-enoyl cardiolipin

77358

1 reference

5,6-dihydrothymidine 5'-monophosphate

104873

1 reference

5-amino-4a-methyl-1,4a,4b,8,8a,8b-hexahydrocyclobuta[1,2-d:4,3-d']dipyrimidine-2,4,7(3H)-trione

132172

1 reference

8,5'-cyclo-2'-deoxyguanosine

116698

1 reference

5,6-dihydroxy-2'-deoxyuridine

131828

1 reference

1,3'-bis(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-6-(5,6-diamino-2-oxo-2,3,4,5-tetrahydropyrimidin-4-yl)-1,3-diazabicyclo[2.2.0]hex-4-en-2-one

132189

1 reference

1 reference

1 reference

John I Glass

8

1 reference

ORCID Public Data File 2021

author name string

Jonathan R Karr

1

1 reference

23 June 2017

Jayodita C Sanghvi

2

1 reference

23 June 2017

Derek N Macklin

3

1 reference

23 June 2017

Miriam V Gutschow

4

1 reference

23 June 2017

Jared M Jacobs

5

1 reference

23 June 2017

Benjamin Bolival

6

1 reference

23 June 2017

Nacyra Assad-Garcia

7

1 reference

23 June 2017

Markus W Covert

9

1 reference

23 June 2017

language of work or name

English

0 references

publication date

1 July 2012

1 reference

23 June 2017

1 reference

23 June 2017

150

1 reference

23 June 2017

2

1 reference

23 June 2017

389-401

1 reference

Essential genes of a minimal bacterium

23 June 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413483

The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of 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=3413483

Creation of a bacterial cell controlled by a chemically synthesized genome

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413483

What is flux balance analysis?

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413483

Proteome organization in a genome-reduced bacterium

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413483

Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413483

A genome-scale metabolic reconstruction of Mycoplasma genitalium, iPS189

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413483

Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413483

A genomic regulatory network for development

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413483

The pyruvate dehydrogenase multi-enzyme complex from Gram-negative bacteria

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413483

The Minimal Gene Complement of Mycoplasma genitalium

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413483

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413483

Systems biology: a brief overview

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413483

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=3413483

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011.

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413483

Spatial distribution and diffusive motion of RNA polymerase in live Escherichia coli

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413483

General properties of transcriptional time series in Escherichia coli

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413483

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

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413483

Sequences and consequences

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413483

Protein occupancy landscape of a bacterial genome

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413483

Genome transplantation in bacteria: changing one species to another

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413483

From in vivo to in silico biology and back

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413483

Integrating high-throughput and computational data elucidates bacterial networks

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413483

A modular minimal cell model: purine and pyrimidine transport and metabolism

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413483

Regulation of gene expression in flux balance models of metabolism

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413483

E-CELL: software environment for whole-cell simulation

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413483

Single-molecule imaging of RNA polymerase-DNA interactions in real time

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413483

Repair and transcription. Collision or collusion?

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413483

Energetics of bacterial growth: balance of anabolic and catabolic reactions.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413483

Transcriptome Complexity in a Genome-Reduced Bacterium

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413483

Impact of genome reduction on bacterial metabolism and its regulation.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413483

Stability, flexibility, and dynamic interactions of colliding RNA polymerase II elongation complexes

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413483

Incorporating genome-wide DNA sequence information into a dynamic whole-cell model of Escherichia coli: application to DNA replication

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413483

Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413483

A genomically/chemically complete module for synthesis of lipid membrane in a minimal cell.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413483

Probing gene expression in live cells, one protein molecule at a time.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413483

Robust control of initiation of prokaryotic chromosome replication: essential considerations for a minimal cell.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413483

Suspected utility of enzymes with multiple activities in the small genome Mycoplasma species: the replacement of the missing "household" nucleoside diphosphate kinase gene and activity by glycolytic kinases

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3413483

Malate/lactate dehydrogenase in mollicutes: evidence for a multienzyme protein

28 November 2018

1 reference

12 December 2020

Computer model for glucose-limited growth of a single cell of Escherichia coli B/r-A

1 reference

12 December 2020

Isolation and properties of an H2O-forming NADH oxidase from Streptococcus faecalis

1 reference

12 December 2020

Direct restart of a replication fork stalled by a head-on RNA polymerase

1 reference

12 December 2020

The chemical composition and submicroscopic morphology of Mycoplasma gallisepticum, Avian PPLO 5969

1 reference

12 December 2020

Creating bacterial strains from genomes that have been cloned and engineered in yeast

1 reference

12 December 2020

Transcription profiles of the bacterium Mycoplasma pneumoniae grown at different temperatures

1 reference

Crossref

https://api.crossref.org/works/10.1016%2FJ.CELL.2012.05.044

7 January 2021

inferred from DOI database lookup

Identifiers

DOI

10.1016/J.CELL.2012.05.044

1 reference

OpenCitations bibliographic resource ID

23 June 2017

258831

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1 reference