Detalhe da pesquisa
1.
A multi-scale expression and regulation knowledge base for Escherichia coli.
Nucleic Acids Res
; 51(19): 10176-10193, 2023 10 27.
Artigo
em Inglês
| MEDLINE | ID: mdl-37713610
2.
Machine learning from Pseudomonas aeruginosa transcriptomes identifies independently modulated sets of genes associated with known transcriptional regulators.
Nucleic Acids Res
; 50(7): 3658-3672, 2022 04 22.
Artigo
em Inglês
| MEDLINE | ID: mdl-35357493
3.
Advanced transcriptomic analysis reveals the role of efflux pumps and media composition in antibiotic responses of Pseudomonas aeruginosa.
Nucleic Acids Res
; 50(17): 9675-9688, 2022 09 23.
Artigo
em Inglês
| MEDLINE | ID: mdl-36095122
4.
iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning.
Nucleic Acids Res
; 49(D1): D112-D120, 2021 01 08.
Artigo
em Inglês
| MEDLINE | ID: mdl-33045728
5.
Revealing 29 sets of independently modulated genes in Staphylococcus aureus, their regulators, and role in key physiological response.
Proc Natl Acad Sci U S A
; 117(29): 17228-17239, 2020 07 21.
Artigo
em Inglês
| MEDLINE | ID: mdl-32616573
6.
Membrane transporter identification and modulation via adaptive laboratory evolution.
Metab Eng
; 72: 376-390, 2022 07.
Artigo
em Inglês
| MEDLINE | ID: mdl-35598887
7.
Machine-learning from Pseudomonas putida KT2440 transcriptomes reveals its transcriptional regulatory network.
Metab Eng
; 72: 297-310, 2022 07.
Artigo
em Inglês
| MEDLINE | ID: mdl-35489688
8.
Independent component analysis recovers consistent regulatory signals from disparate datasets.
PLoS Comput Biol
; 17(2): e1008647, 2021 02.
Artigo
em Inglês
| MEDLINE | ID: mdl-33529205
9.
The Bitome: digitized genomic features reveal fundamental genome organization.
Nucleic Acids Res
; 48(18): 10157-10163, 2020 10 09.
Artigo
em Inglês
| MEDLINE | ID: mdl-32976587
10.
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
em Inglês
| MEDLINE | ID: mdl-31767748
11.
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
em Inglês
| MEDLINE | ID: mdl-31270234
12.
Optimal dimensionality selection for independent component analysis of transcriptomic data.
BMC Bioinformatics
; 22(1): 584, 2021 Dec 08.
Artigo
em Inglês
| MEDLINE | ID: mdl-34879815
13.
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
em Inglês
| MEDLINE | ID: mdl-31651953
14.
Adaptive laboratory evolution of Escherichia coli under acid stress.
Microbiology (Reading)
; 166(2): 141-148, 2020 02.
Artigo
em Inglês
| MEDLINE | ID: mdl-31625833
15.
Independent component analysis of E. coli's transcriptome reveals the cellular processes that respond to heterologous gene expression.
Metab Eng
; 61: 360-368, 2020 09.
Artigo
em Inglês
| MEDLINE | ID: mdl-32710928
16.
BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data.
PLoS Comput Biol
; 15(4): e1006971, 2019 04.
Artigo
em Inglês
| MEDLINE | ID: mdl-31009451
17.
Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655.
Nucleic Acids Res
; 46(20): 10682-10696, 2018 11 16.
Artigo
em Inglês
| MEDLINE | ID: mdl-30137486
18.
Independent component analysis reveals 49 independently modulated gene sets within the global transcriptional regulatory architecture of multidrug-resistant Acinetobacter baumannii.
mSystems
; 9(2): e0060623, 2024 Feb 20.
Artigo
em Inglês
| MEDLINE | ID: mdl-38189271
19.
Machine learning uncovers the Pseudomonas syringae transcriptome in microbial communities and during infection.
mSystems
; 8(5): e0043723, 2023 Oct 26.
Artigo
em Inglês
| MEDLINE | ID: mdl-37638727
20.
Proteome allocation is linked to transcriptional regulation through a modularized transcriptome.
bioRxiv
; 2023 Feb 21.
Artigo
em Inglês
| MEDLINE | ID: mdl-36865326