Detalhe da pesquisa
1.
StressME: Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses.
PLoS Comput Biol
; 20(2): e1011865, 2024 Feb.
Artigo
Inglês
| MEDLINE | ID: mdl-38346086
2.
Novel context-specific genome-scale modelling explores the potential of triacylglycerol production by Chlamydomonas reinhardtii.
Microb Cell Fact
; 22(1): 13, 2023 Jan 17.
Artigo
Inglês
| MEDLINE | ID: mdl-36650525
3.
Metabolic and genetic basis for auxotrophies in Gram-negative species.
Proc Natl Acad Sci U S A
; 117(11): 6264-6273, 2020 03 17.
Artigo
Inglês
| MEDLINE | ID: mdl-32132208
4.
Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth.
PLoS Comput Biol
; 17(6): e1007817, 2021 06.
Artigo
Inglês
| MEDLINE | ID: mdl-34161321
5.
Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration.
Proc Natl Acad Sci U S A
; 116(50): 25287-25292, 2019 12 10.
Artigo
Inglês
| MEDLINE | ID: mdl-31767748
6.
Cellular responses to reactive oxygen species are predicted from molecular mechanisms.
Proc Natl Acad Sci U S A
; 116(28): 14368-14373, 2019 07 09.
Artigo
Inglês
| MEDLINE | ID: mdl-31270234
7.
OxyR Is a Convergent Target for Mutations Acquired during Adaptation to Oxidative Stress-Prone Metabolic States.
Mol Biol Evol
; 37(3): 660-667, 2020 03 01.
Artigo
Inglês
| MEDLINE | ID: mdl-31651953
8.
Synthesizing Systems Biology Knowledge from Omics Using Genome-Scale Models.
Proteomics
; 20(17-18): e1900282, 2020 09.
Artigo
Inglês
| MEDLINE | ID: mdl-32579720
9.
Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes.
BMC Bioinformatics
; 21(1): 162, 2020 Apr 29.
Artigo
Inglês
| MEDLINE | ID: mdl-32349661
10.
Visualizing metabolic network dynamics through time-series metabolomic data.
BMC Bioinformatics
; 21(1): 130, 2020 Apr 03.
Artigo
Inglês
| MEDLINE | ID: mdl-32245365
11.
Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli.
PLoS Comput Biol
; 15(12): e1007525, 2019 12.
Artigo
Inglês
| MEDLINE | ID: mdl-31809503
12.
BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data.
PLoS Comput Biol
; 15(4): e1006971, 2019 04.
Artigo
Inglês
| MEDLINE | ID: mdl-31009451
13.
Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655.
Nucleic Acids Res
; 46(20): 10682-10696, 2018 11 16.
Artigo
Inglês
| MEDLINE | ID: mdl-30137486
14.
Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation.
Proc Natl Acad Sci U S A
; 114(43): 11548-11553, 2017 10 24.
Artigo
Inglês
| MEDLINE | ID: mdl-29073085
15.
Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities.
Proc Natl Acad Sci U S A
; 114(38): 10286-10291, 2017 09 19.
Artigo
Inglês
| MEDLINE | ID: mdl-28874552
16.
COBRAme: A computational framework for genome-scale models of metabolism and gene expression.
PLoS Comput Biol
; 14(7): e1006302, 2018 07.
Artigo
Inglês
| MEDLINE | ID: mdl-29975681
17.
Quantitative time-course metabolomics in human red blood cells reveal the temperature dependence of human metabolic networks.
J Biol Chem
; 292(48): 19556-19564, 2017 12 01.
Artigo
Inglês
| MEDLINE | ID: mdl-29030425
18.
Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells.
PLoS Comput Biol
; 13(3): e1005424, 2017 03.
Artigo
Inglês
| MEDLINE | ID: mdl-28264007
19.
Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data.
Proc Natl Acad Sci U S A
; 112(34): 10810-5, 2015 Aug 25.
Artigo
Inglês
| MEDLINE | ID: mdl-26261351
20.
solveME: fast and reliable solution of nonlinear ME models.
BMC Bioinformatics
; 17(1): 391, 2016 Sep 22.
Artigo
Inglês
| MEDLINE | ID: mdl-27659412