237 related articles for article (PubMed ID: 28874552)
1. Global transcriptional regulatory network for
Fang X; Sastry A; Mih N; Kim D; Tan J; Yurkovich JT; Lloyd CJ; Gao Y; Yang L; Palsson BO
Proc Natl Acad Sci U S A; 2017 Sep; 114(38):10286-10291. PubMed ID: 28874552
[TBL] [Abstract][Full Text] [Related]
2. Interplay between network structures, regulatory modes and sensing mechanisms of transcription factors in the transcriptional regulatory network of E. coli.
Balaji S; Babu MM; Aravind L
J Mol Biol; 2007 Sep; 372(4):1108-1122. PubMed ID: 17706247
[TBL] [Abstract][Full Text] [Related]
3. The Escherichia coli transcriptome mostly consists of independently regulated modules.
Sastry AV; Gao Y; Szubin R; Hefner Y; Xu S; Kim D; Choudhary KS; Yang L; King ZA; Palsson BO
Nat Commun; 2019 Dec; 10(1):5536. PubMed ID: 31797920
[TBL] [Abstract][Full Text] [Related]
4. An integrated approach to reconstructing genome-scale transcriptional regulatory networks.
Imam S; Noguera DR; Donohue TJ
PLoS Comput Biol; 2015 Feb; 11(2):e1004103. PubMed ID: 25723545
[TBL] [Abstract][Full Text] [Related]
5. Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach.
Ma HW; Buer J; Zeng AP
BMC Bioinformatics; 2004 Dec; 5():199. PubMed ID: 15603590
[TBL] [Abstract][Full Text] [Related]
6. Analysis of the hierarchical structure of the B. subtilis transcriptional regulatory network.
Kumar S; Vendruscolo M; Singh A; Kumar D; Samal A
Mol Biosyst; 2015 Mar; 11(3):930-41. PubMed ID: 25599335
[TBL] [Abstract][Full Text] [Related]
7. Predicting transcriptional regulatory interactions with artificial neural networks applied to E. coli multidrug resistance efflux pumps.
Veiga DF; Vicente FF; Nicolás MF; Vasconcelos AT
BMC Microbiol; 2008 Jun; 8():101. PubMed ID: 18565227
[TBL] [Abstract][Full Text] [Related]
8. Transcriptional regulatory networks via gene ontology and expression data.
Tuncay K; Ensman L; Sun J; Haidar AA; Stanley F; Trelinski M; Ortoleva P
In Silico Biol; 2007; 7(1):21-34. PubMed ID: 17688426
[TBL] [Abstract][Full Text] [Related]
9. Machine Learning of All Mycobacterium tuberculosis H37Rv RNA-seq Data Reveals a Structured Interplay between Metabolism, Stress Response, and Infection.
Yoo R; Rychel K; Poudel S; Al-Bulushi T; Yuan Y; Chauhan S; Lamoureux C; Palsson BO; Sastry A
mSphere; 2022 Apr; 7(2):e0003322. PubMed ID: 35306876
[TBL] [Abstract][Full Text] [Related]
10. Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data.
Zhang Y; Xuan J; de los Reyes BG; Clarke R; Ressom HW
BMC Bioinformatics; 2008 Apr; 9():203. PubMed ID: 18426580
[TBL] [Abstract][Full Text] [Related]
11. Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells.
Miraldi ER; Pokrovskii M; Watters A; Castro DM; De Veaux N; Hall JA; Lee JY; Ciofani M; Madar A; Carriero N; Littman DR; Bonneau R
Genome Res; 2019 Mar; 29(3):449-463. PubMed ID: 30696696
[TBL] [Abstract][Full Text] [Related]
12. An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs.
Ma HW; Kumar B; Ditges U; Gunzer F; Buer J; Zeng AP
Nucleic Acids Res; 2004; 32(22):6643-9. PubMed ID: 15604458
[TBL] [Abstract][Full Text] [Related]
13. A link partition approach for finding overlapping functional modules in the transcriptional regulatory network.
Zou Q; Liu F; Hou T; Jiang Y; Mo R
Biomed Mater Eng; 2014; 24(6):3719-27. PubMed ID: 25227087
[TBL] [Abstract][Full Text] [Related]
14. Reconstructing genome-wide regulatory network of E. coli using transcriptome data and predicted transcription factor activities.
Fu Y; Jarboe LR; Dickerson JA
BMC Bioinformatics; 2011 Jun; 12():233. PubMed ID: 21668997
[TBL] [Abstract][Full Text] [Related]
15. Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655.
Gao Y; Yurkovich JT; Seo SW; Kabimoldayev I; Dräger A; Chen K; Sastry AV; Fang X; Mih N; Yang L; Eichner J; Cho BK; Kim D; Palsson BO
Nucleic Acids Res; 2018 Nov; 46(20):10682-10696. PubMed ID: 30137486
[TBL] [Abstract][Full Text] [Related]
16. Deciphering transcriptional regulations coordinating the response to environmental changes.
Acuña V; Aravena A; Guziolowski C; Eveillard D; Siegel A; Maass A
BMC Bioinformatics; 2016 Jan; 17():35. PubMed ID: 26772805
[TBL] [Abstract][Full Text] [Related]
17. Inferring the regulatory interaction models of transcription factors in transcriptional regulatory networks.
Awad S; Panchy N; Ng SK; Chen J
J Bioinform Comput Biol; 2012 Oct; 10(5):1250012. PubMed ID: 22849367
[TBL] [Abstract][Full Text] [Related]
18. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles.
Faith JJ; Hayete B; Thaden JT; Mogno I; Wierzbowski J; Cottarel G; Kasif S; Collins JJ; Gardner TS
PLoS Biol; 2007 Jan; 5(1):e8. PubMed ID: 17214507
[TBL] [Abstract][Full Text] [Related]
19. A Systems Biology Approach To Disentangle the Direct and Indirect Effects of Global Transcription Factors on Gene Expression in Escherichia coli.
Iyer MS; Pal A; Venkatesh KV
Microbiol Spectr; 2023 Feb; 11(2):e0210122. PubMed ID: 36749045
[TBL] [Abstract][Full Text] [Related]
20. Machine-learning from Pseudomonas putida KT2440 transcriptomes reveals its transcriptional regulatory network.
Lim HG; Rychel K; Sastry AV; Bentley GJ; Mueller J; Schindel HS; Larsen PE; Laible PD; Guss AM; Niu W; Johnson CW; Beckham GT; Feist AM; Palsson BO
Metab Eng; 2022 Jul; 72():297-310. PubMed ID: 35489688
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
