Detalhe da pesquisa
1.
A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action.
Cell
; 177(6): 1649-1661.e9, 2019 05 30.
Artigo
em Inglês
| MEDLINE | ID: mdl-31080069
2.
Using Genome-scale Models to Predict Biological Capabilities.
Cell
; 161(5): 971-987, 2015 May 21.
Artigo
em Inglês
| MEDLINE | ID: mdl-26000478
3.
Redefining fundamental concepts of transcription initiation in bacteria.
Nat Rev Genet
; 21(11): 699-714, 2020 11.
Artigo
em Inglês
| MEDLINE | ID: mdl-32665585
4.
BGCFlow: systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets.
Nucleic Acids Res
; 2024 Apr 30.
Artigo
em Inglês
| MEDLINE | ID: mdl-38686794
5.
Metabolic homeostasis and growth in abiotic cells.
Proc Natl Acad Sci U S A
; 120(19): e2300687120, 2023 05 09.
Artigo
em Inglês
| MEDLINE | ID: mdl-37126695
6.
Whole-genome sequences from wild-type and laboratory-evolved strains define the alleleome and establish its hallmarks.
Proc Natl Acad Sci U S A
; 120(15): e2218835120, 2023 04 11.
Artigo
em Inglês
| MEDLINE | ID: mdl-37011218
7.
Deep-learning optimized DEOCSU suite provides an iterable pipeline for accurate ChIP-exo peak calling.
Brief Bioinform
; 24(2)2023 03 19.
Artigo
em Inglês
| MEDLINE | ID: mdl-36702751
8.
StressME: Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses.
PLoS Comput Biol
; 20(2): e1011865, 2024 Feb.
Artigo
em Inglês
| MEDLINE | ID: mdl-38346086
9.
Inferred regulons are consistent with regulator binding sequences in E. coli.
PLoS Comput Biol
; 20(1): e1011824, 2024 Jan.
Artigo
em Inglês
| MEDLINE | ID: mdl-38252668
10.
The Escherichia coli Fur pan-regulon has few conserved but many unique regulatory targets.
Nucleic Acids Res
; 51(8): 3618-3630, 2023 05 08.
Artigo
em Inglês
| MEDLINE | ID: mdl-37026477
11.
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
12.
An unexpected role for leucyl aminopeptidase in UV tolerance revealed by a genome-wide fitness assessment in a model cyanobacterium.
Proc Natl Acad Sci U S A
; 119(45): e2211789119, 2022 Nov 08.
Artigo
em Inglês
| MEDLINE | ID: mdl-36322730
13.
Adaptive laboratory evolution and independent component analysis disentangle complex vancomycin adaptation trajectories.
Proc Natl Acad Sci U S A
; 119(30): e2118262119, 2022 07 26.
Artigo
em Inglês
| MEDLINE | ID: mdl-35858453
14.
Systems biology approach to functionally assess the Clostridioides difficile pangenome reveals genetic diversity with discriminatory power.
Proc Natl Acad Sci U S A
; 119(18): e2119396119, 2022 05 03.
Artigo
em Inglês
| MEDLINE | ID: mdl-35476524
15.
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
16.
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
17.
proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms.
Nucleic Acids Res
; 50(D1): D1077-D1084, 2022 01 07.
Artigo
em Inglês
| MEDLINE | ID: mdl-34791440
18.
CRISPR-aided genome engineering for secondary metabolite biosynthesis in Streptomyces.
J Ind Microbiol Biotechnol
; 512024 Jan 09.
Artigo
em Inglês
| MEDLINE | ID: mdl-38439699
19.
DeepTFactor: A deep learning-based tool for the prediction of transcription factors.
Proc Natl Acad Sci U S A
; 118(2)2021 01 12.
Artigo
em Inglês
| MEDLINE | ID: mdl-33372147
20.
Integration of physiologically relevant photosynthetic energy flows into whole genome models of light-driven metabolism.
Plant J
; 112(3): 603-621, 2022 11.
Artigo
em Inglês
| MEDLINE | ID: mdl-36053127