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For: Rychel K, Sastry AV, Palsson BO. Machine learning uncovers independently regulated modules in the Bacillus subtilis transcriptome. Nat Commun 2020;11:6338. [PMID: 33311500 DOI: 10.1038/s41467-020-20153-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 10/29/2020] [Indexed: 12/24/2022]  Open
Number Cited by Other Article(s)
1
Zhang Y, Zhao J, Sun X, Zheng Y, Chen T, Wang Z. Leveraging independent component analysis to unravel transcriptional regulatory networks: A critical review and future directions. Biotechnol Adv 2025;78:108479. [PMID: 39577573 DOI: 10.1016/j.biotechadv.2024.108479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2024] [Revised: 11/11/2024] [Accepted: 11/14/2024] [Indexed: 11/24/2024]
2
Novak JK, Gardner JG. Current models in bacterial hemicellulase-encoding gene regulation. Appl Microbiol Biotechnol 2024;108:39. [PMID: 38175245 PMCID: PMC10766802 DOI: 10.1007/s00253-023-12977-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024]
3
Catoiu EA, Krishnan J, Li G, Lou XA, Rychel K, Yuan Y, Bajpe H, Patel A, Choe D, Shin J, Burrows J, Phaneuf PV, Zielinski DC, Palsson BO. iModulonDB 2.0: dynamic tools to facilitate knowledge-mining and user-enabled analyses of curated transcriptomic datasets. Nucleic Acids Res 2024:gkae1009. [PMID: 39494532 DOI: 10.1093/nar/gkae1009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2024] [Revised: 10/04/2024] [Accepted: 10/22/2024] [Indexed: 11/05/2024]  Open
4
Bi X, Cheng Y, Lv X, Liu Y, Li J, Du G, Chen J, Liu L. A Multi-Omics, Machine Learning-Aware, Genome-Wide Metabolic Model of Bacillus Subtilis Refines the Gene Expression and Cell Growth Prediction. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024;11:e2408705. [PMID: 39287062 PMCID: PMC11558093 DOI: 10.1002/advs.202408705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Indexed: 09/19/2024]
5
Shin J, Zielinski D, Palsson B. Modulating bacterial function utilizing A knowledge base of transcriptional regulatory modules. Nucleic Acids Res 2024;52:11362-11377. [PMID: 39193902 PMCID: PMC11472167 DOI: 10.1093/nar/gkae742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 07/29/2024] [Accepted: 08/19/2024] [Indexed: 08/29/2024]  Open
6
Sastry AV, Yuan Y, Poudel S, Rychel K, Yoo R, Lamoureux CR, Li G, Burrows JT, Chauhan S, Haiman ZB, Al Bulushi T, Seif Y, Palsson BO, Zielinski DC. iModulonMiner and PyModulon: Software for unsupervised mining of gene expression compendia. PLoS Comput Biol 2024;20:e1012546. [PMID: 39441835 PMCID: PMC11534266 DOI: 10.1371/journal.pcbi.1012546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 11/04/2024] [Accepted: 10/09/2024] [Indexed: 10/25/2024]  Open
7
Yuan Y, Al Bulushi T, Sastry AV, Sancar C, Szubin R, Golden SS, Palsson BO. Machine learning reveals the transcriptional regulatory network and circadian dynamics of Synechococcus elongatus PCC 7942. Proc Natl Acad Sci U S A 2024;121:e2410492121. [PMID: 39269777 PMCID: PMC11420160 DOI: 10.1073/pnas.2410492121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Accepted: 08/05/2024] [Indexed: 09/15/2024]  Open
8
Patel A, McGrosso D, Hefner Y, Campeau A, Sastry AV, Maurya S, Rychel K, Gonzalez DJ, Palsson BO. Proteome allocation is linked to transcriptional regulation through a modularized transcriptome. Nat Commun 2024;15:5234. [PMID: 38898010 PMCID: PMC11187210 DOI: 10.1038/s41467-024-49231-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/28/2024] [Indexed: 06/21/2024]  Open
9
Wu S, Zhou H, Chen D, Lu Y, Li Y, Qiao J. Multi-omic analysis tools for microbial metabolites prediction. Brief Bioinform 2024;25:bbae264. [PMID: 38859767 PMCID: PMC11165163 DOI: 10.1093/bib/bbae264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 05/08/2024] [Indexed: 06/12/2024]  Open
10
Menon ND, Poudel S, Sastry AV, Rychel K, Szubin R, Dillon N, Tsunemoto H, Hirose Y, Nair BG, Kumar GB, Palsson BO, Nizet V. Independent component analysis reveals 49 independently modulated gene sets within the global transcriptional regulatory architecture of multidrug-resistant Acinetobacter baumannii. mSystems 2024;9:e0060623. [PMID: 38189271 PMCID: PMC10878099 DOI: 10.1128/msystems.00606-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 11/29/2023] [Indexed: 01/09/2024]  Open
11
Tan H, Guo M, Chen J, Wang J, Yu G. HetFCM: functional co-module discovery by heterogeneous network co-clustering. Nucleic Acids Res 2024;52:e16. [PMID: 38088228 PMCID: PMC10853805 DOI: 10.1093/nar/gkad1174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/31/2023] [Accepted: 11/23/2023] [Indexed: 02/10/2024]  Open
12
Walls AW, Rosenthal AZ. Bacterial phenotypic heterogeneity through the lens of single-cell RNA sequencing. Transcription 2024;15:48-62. [PMID: 38532542 DOI: 10.1080/21541264.2024.2334110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 03/19/2024] [Indexed: 03/28/2024]  Open
13
Qiu S, Huang Y, Liang S, Zeng H, Yang A. Systematic elucidation of independently modulated genes in Lactiplantibacillus plantarum reveals a trade-off between secondary and primary metabolism. Microb Biotechnol 2024;17:e14425. [PMID: 38393514 PMCID: PMC10886434 DOI: 10.1111/1751-7915.14425] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 02/02/2024] [Indexed: 02/25/2024]  Open
14
Qiu S, Wan X, Liang Y, Lamoureux CR, Akbari A, Palsson BO, Zielinski DC. Inferred regulons are consistent with regulator binding sequences in E. coli. PLoS Comput Biol 2024;20:e1011824. [PMID: 38252668 PMCID: PMC10833566 DOI: 10.1371/journal.pcbi.1011824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 02/01/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024]  Open
15
Qian J, Wang Y, Hu Z, Shi T, Wang Y, Ye C, Huang H. Bacillus sp. as a microbial cell factory: Advancements and future prospects. Biotechnol Adv 2023;69:108278. [PMID: 37898328 DOI: 10.1016/j.biotechadv.2023.108278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/27/2023] [Accepted: 10/25/2023] [Indexed: 10/30/2023]
16
Miano A, Rychel K, Lezia A, Sastry A, Palsson B, Hasty J. High-resolution temporal profiling of E. coli transcriptional response. Nat Commun 2023;14:7606. [PMID: 37993418 PMCID: PMC10665441 DOI: 10.1038/s41467-023-43173-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 11/02/2023] [Indexed: 11/24/2023]  Open
17
Zhao J, Sun X, Mao Z, Zheng Y, Geng Z, Zhang Y, Ma H, Wang Z. Independent component analysis of Corynebacterium glutamicum transcriptomes reveals its transcriptional regulatory network. Microbiol Res 2023;276:127485. [PMID: 37683565 DOI: 10.1016/j.micres.2023.127485] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023]
18
Lamoureux CR, Decker KT, Sastry AV, Rychel K, Gao Y, McConn J, Zielinski D, Palsson BO. A multi-scale expression and regulation knowledge base for Escherichia coli. Nucleic Acids Res 2023;51:10176-10193. [PMID: 37713610 PMCID: PMC10602906 DOI: 10.1093/nar/gkad750] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/02/2023] [Accepted: 09/05/2023] [Indexed: 09/17/2023]  Open
19
Bajpe H, Rychel K, Lamoureux CR, Sastry AV, Palsson BO. Machine learning uncovers the Pseudomonas syringae transcriptome in microbial communities and during infection. mSystems 2023;8:e0043723. [PMID: 37638727 PMCID: PMC10654099 DOI: 10.1128/msystems.00437-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/19/2023] [Indexed: 08/29/2023]  Open
20
Rychel K, Tan J, Patel A, Lamoureux C, Hefner Y, Szubin R, Johnsen J, Mohamed ETT, Phaneuf PV, Anand A, Olson CA, Park JH, Sastry AV, Yang L, Feist AM, Palsson BO. Laboratory evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance. Cell Rep 2023;42:113105. [PMID: 37713311 PMCID: PMC10591938 DOI: 10.1016/j.celrep.2023.113105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 07/09/2023] [Accepted: 08/23/2023] [Indexed: 09/17/2023]  Open
21
Gao ZP, Gu WC, Li J, Qiu QT, Ma BG. Independent Component Analysis Reveals the Transcriptional Regulatory Modules in Bradyrhizobium diazoefficiens USDA110. Int J Mol Sci 2023;24:12544. [PMID: 37628727 PMCID: PMC10454721 DOI: 10.3390/ijms241612544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/30/2023] [Accepted: 08/05/2023] [Indexed: 08/27/2023]  Open
22
Yuan S, Sun Y, Chang W, Zhang J, Sang J, Zhao J, Song M, Qiao Y, Zhang C, Zhu M, Tang Y, Lou H. The silkworm (Bombyx mori) gut microbiota is involved in metabolic detoxification by glucosylation of plant toxins. Commun Biol 2023;6:790. [PMID: 37516758 PMCID: PMC10387059 DOI: 10.1038/s42003-023-05150-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 07/17/2023] [Indexed: 07/31/2023]  Open
23
Hirose Y, Poudel S, Sastry AV, Rychel K, Lamoureux CR, Szubin R, Zielinski DC, Lim HG, Menon ND, Bergsten H, Uchiyama S, Hanada T, Kawabata S, Palsson BO, Nizet V. Elucidation of independently modulated genes in Streptococcus pyogenes reveals carbon sources that control its expression of hemolytic toxins. mSystems 2023;8:e0024723. [PMID: 37278526 PMCID: PMC10308926 DOI: 10.1128/msystems.00247-23] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 04/02/2023] [Indexed: 06/07/2023]  Open
24
Shin J, Rychel K, Palsson BO. Systems biology of competency in Vibrio natriegens is revealed by applying novel data analytics to the transcriptome. Cell Rep 2023;42:112619. [PMID: 37285268 DOI: 10.1016/j.celrep.2023.112619] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 04/27/2023] [Accepted: 05/22/2023] [Indexed: 06/09/2023]  Open
25
Charron-Lamoureux V, Haroune L, Pomerleau M, Hall L, Orban F, Leroux J, Rizzi A, Bourassa JS, Fontaine N, d'Astous ÉV, Dauphin-Ducharme P, Legault CY, Bellenger JP, Beauregard PB. Pulcherriminic acid modulates iron availability and protects against oxidative stress during microbial interactions. Nat Commun 2023;14:2536. [PMID: 37137890 PMCID: PMC10156857 DOI: 10.1038/s41467-023-38222-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 04/20/2023] [Indexed: 05/05/2023]  Open
26
Patel A, McGrosso D, Hefner Y, Campeau A, Sastry AV, Maurya S, Rychel K, Gonzalez DJ, Palsson BO. Proteome allocation is linked to transcriptional regulation through a modularized transcriptome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.20.529291. [PMID: 36865326 PMCID: PMC9980150 DOI: 10.1101/2023.02.20.529291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
27
Bi X, Cheng Y, Xu X, Lv X, Liu Y, Li J, Du G, Chen J, Ledesma-Amaro R, Liu L. etiBsu1209: A comprehensive multiscale metabolic model for Bacillus subtilis. Biotechnol Bioeng 2023;120:1623-1639. [PMID: 36788025 DOI: 10.1002/bit.28355] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 12/08/2022] [Accepted: 02/13/2023] [Indexed: 02/16/2023]
28
Predicting stress response and improved protein overproduction in Bacillus subtilis. NPJ Syst Biol Appl 2022;8:50. [PMID: 36575180 PMCID: PMC9794813 DOI: 10.1038/s41540-022-00259-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/07/2022] [Indexed: 12/28/2022]  Open
29
Poudel S, Hefner Y, Szubin R, Sastry A, Gao Y, Nizet V, Palsson BO. Coordination of CcpA and CodY Regulators in Staphylococcus aureus USA300 Strains. mSystems 2022;7:e0048022. [PMID: 36321827 PMCID: PMC9765215 DOI: 10.1128/msystems.00480-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 10/10/2022] [Indexed: 11/07/2022]  Open
30
Rajput A, Tsunemoto H, Sastry AV, Szubin R, Rychel K, Chauhan SM, Pogliano J, Palsson BO. Advanced transcriptomic analysis reveals the role of efflux pumps and media composition in antibiotic responses of Pseudomonas aeruginosa. Nucleic Acids Res 2022;50:9675-9688. [PMID: 36095122 PMCID: PMC9508857 DOI: 10.1093/nar/gkac743] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/06/2022] [Accepted: 09/06/2022] [Indexed: 11/14/2022]  Open
31
Fait A, Seif Y, Mikkelsen K, Poudel S, Wells JM, Palsson BO, Ingmer H. Adaptive laboratory evolution and independent component analysis disentangle complex vancomycin adaptation trajectories. Proc Natl Acad Sci U S A 2022;119:e2118262119. [PMID: 35858453 PMCID: PMC9335240 DOI: 10.1073/pnas.2118262119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 05/11/2022] [Indexed: 11/27/2022]  Open
32
Yang H, Yang J, Liu C, Lv X, Liu L, Li J, Du G, Chen J, Liu Y. High-Level 5-Methyltetrahydrofolate Bioproduction in Bacillus subtilis by Combining Modular Engineering and Transcriptomics-Guided Global Metabolic Regulation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022;70:5849-5859. [PMID: 35521920 DOI: 10.1021/acs.jafc.2c01252] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
33
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. Machine-learning from Pseudomonas putida KT2440 transcriptomes reveals its transcriptional regulatory network. Metab Eng 2022;72:297-310. [PMID: 35489688 DOI: 10.1016/j.ymben.2022.04.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/23/2022] [Accepted: 04/23/2022] [Indexed: 11/17/2022]
34
Xavier JB, Monk JM, Poudel S, Norsigian CJ, Sastry AV, Liao C, Bento J, Suchard MA, Arrieta-Ortiz ML, Peterson EJ, Baliga NS, Stoeger T, Ruffin F, Richardson RA, Gao CA, Horvath TD, Haag AM, Wu Q, Savidge T, Yeaman MR. Mathematical models to study the biology of pathogens and the infectious diseases they cause. iScience 2022;25:104079. [PMID: 35359802 PMCID: PMC8961237 DOI: 10.1016/j.isci.2022.104079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]  Open
35
Rajput A, Tsunemoto H, Sastry AV, Szubin R, Rychel K, Sugie J, Pogliano J, Palsson BO. Machine learning from Pseudomonas aeruginosa transcriptomes identifies independently modulated sets of genes associated with known transcriptional regulators. Nucleic Acids Res 2022;50:3658-3672. [PMID: 35357493 PMCID: PMC9023270 DOI: 10.1093/nar/gkac187] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 02/28/2022] [Accepted: 03/29/2022] [Indexed: 12/16/2022]  Open
36
Decker KT, Gao Y, Rychel K, Al Bulushi T, Chauhan S, Kim D, Cho BK, Palsson B. proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms. Nucleic Acids Res 2022;50:D1077-D1084. [PMID: 34791440 PMCID: PMC8728212 DOI: 10.1093/nar/gkab1043] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 10/05/2021] [Accepted: 10/14/2021] [Indexed: 12/03/2022]  Open
37
McConn JL, Lamoureux CR, Poudel S, Palsson BO, Sastry AV. Optimal dimensionality selection for independent component analysis of transcriptomic data. BMC Bioinformatics 2021;22:584. [PMID: 34879815 PMCID: PMC8653613 DOI: 10.1186/s12859-021-04497-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 11/16/2021] [Indexed: 11/23/2022]  Open
38
Chauhan SM, Poudel S, Rychel K, Lamoureux C, Yoo R, Al Bulushi T, Yuan Y, Palsson BO, Sastry AV. Machine Learning Uncovers a Data-Driven Transcriptional Regulatory Network for the Crenarchaeal Thermoacidophile Sulfolobus acidocaldarius. Front Microbiol 2021;12:753521. [PMID: 34777307 PMCID: PMC8578740 DOI: 10.3389/fmicb.2021.753521] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 09/30/2021] [Indexed: 01/24/2023]  Open
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Machine Learning of Bacterial Transcriptomes Reveals Responses Underlying Differential Antibiotic Susceptibility. mSphere 2021;6:e0044321. [PMID: 34431696 PMCID: PMC8386450 DOI: 10.1128/msphere.00443-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
40
Production of proteins and commodity chemicals using engineered Bacillus subtilis platform strain. Essays Biochem 2021;65:173-185. [PMID: 34028523 DOI: 10.1042/ebc20210011] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 05/02/2021] [Accepted: 05/06/2021] [Indexed: 12/19/2022]
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Sastry AV, Hu A, Heckmann D, Poudel S, Kavvas E, Palsson BO. Independent component analysis recovers consistent regulatory signals from disparate datasets. PLoS Comput Biol 2021;17:e1008647. [PMID: 33529205 PMCID: PMC7888660 DOI: 10.1371/journal.pcbi.1008647] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 02/17/2021] [Accepted: 12/18/2020] [Indexed: 01/03/2023]  Open
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Rychel K, Decker K, Sastry AV, Phaneuf PV, Poudel S, Palsson BO. iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning. Nucleic Acids Res 2021;49:D112-D120. [PMID: 33045728 PMCID: PMC7778901 DOI: 10.1093/nar/gkaa810] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/10/2020] [Accepted: 09/15/2020] [Indexed: 12/15/2022]  Open
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Zielinski DC, Patel A, Palsson BO. The Expanding Computational Toolbox for Engineering Microbial Phenotypes at the Genome Scale. Microorganisms 2020;8:E2050. [PMID: 33371386 PMCID: PMC7767376 DOI: 10.3390/microorganisms8122050] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/07/2020] [Accepted: 12/16/2020] [Indexed: 02/06/2023]  Open
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