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For: Chen Y, He Z, Men Y, Dong G, Hu S, Ying X. MetaLogo: a heterogeneity-aware sequence logo generator and aligner. Brief Bioinform 2022;23:6519790. [PMID: 35108357 PMCID: PMC8921662 DOI: 10.1093/bib/bbab591] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 12/16/2021] [Accepted: 12/22/2021] [Indexed: 11/13/2022]  Open
Number Cited by Other Article(s)
1
Biswas D, Benson S, Matunis A, Gebretsadik G, Wertz A, StPierre BJ, Schacht N, Yan Y, Gebremichael HY, Wong PK, Baughn AD, Medina SH. Lead Informed Artificial Intelligence Mining of Antitubercular Host Defense Peptides. Biomacromolecules 2025;26:3167-3179. [PMID: 40310992 PMCID: PMC12076502 DOI: 10.1021/acs.biomac.5c00244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2025] [Revised: 04/16/2025] [Accepted: 04/18/2025] [Indexed: 05/03/2025]
2
Berdieva M, Kalinina V, Palii O, Skarlato S. Putative MutS2 Homologs in Algae: More Goods in Shopping Bag? J Mol Evol 2024;92:815-833. [PMID: 39365456 DOI: 10.1007/s00239-024-10210-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: 04/12/2024] [Accepted: 09/20/2024] [Indexed: 10/05/2024]
3
Karki BR, Macmillan AC, Vicente-Muñoz S, Greis KD, Romick LE, Cunningham JT. Evolutionary origins and innovations sculpting the mammalian PRPS enzyme complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.01.616059. [PMID: 39411161 PMCID: PMC11476008 DOI: 10.1101/2024.10.01.616059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
4
Wang Z, Peng Y, Li J, Li J, Yuan H, Yang S, Ding X, Xie A, Zhang J, Wang S, Li K, Shi J, Xing G, Shi W, Yan J, Liu J. DeepCBA: A deep learning framework for gene expression prediction in maize based on DNA sequences and chromatin interactions. PLANT COMMUNICATIONS 2024;5:100985. [PMID: 38859587 DOI: 10.1016/j.xplc.2024.100985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/25/2024] [Accepted: 06/05/2024] [Indexed: 06/12/2024]
5
Thagun C, Odahara M, Kodama Y, Numata K. Identification of a highly efficient chloroplast-targeting peptide for plastid engineering. PLoS Biol 2024;22:e3002785. [PMID: 39298532 PMCID: PMC11444414 DOI: 10.1371/journal.pbio.3002785] [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: 12/23/2023] [Revised: 10/01/2024] [Accepted: 08/03/2024] [Indexed: 09/22/2024]  Open
6
Gontijo M, Pereira Teles M, Martins Correia H, Pérez Jorge G, Rodrigues Santos Goes IC, Fasabi Flores AJ, Braz M, de Moraes Ceseti L, Zonzini Ramos P, Rosa e Silva I, Pereira Vidigal PM, Kobarg J, Miguez Couñago R, Alvarez-Martinez CE, Pereira C, Freire CSR, Almeida A, Brocchi M. Combined effect of SAR-endolysin LysKpV475 with polymyxin B and Salmonella bacteriophage phSE-5. MICROBIOLOGY (READING, ENGLAND) 2024;170:001462. [PMID: 38739436 PMCID: PMC11170124 DOI: 10.1099/mic.0.001462] [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: 12/13/2023] [Accepted: 04/26/2024] [Indexed: 05/14/2024]
7
Monzón S, Varona S, Negredo A, Vidal-Freire S, Patiño-Galindo JA, Ferressini-Gerpe N, Zaballos A, Orviz E, Ayerdi O, Muñoz-Gómez A, Delgado-Iribarren A, Estrada V, García C, Molero F, Sánchez-Mora P, Torres M, Vázquez A, Galán JC, Torres I, Causse Del Río M, Merino-Diaz L, López M, Galar A, Cardeñoso L, Gutiérrez A, Loras C, Escribano I, Alvarez-Argüelles ME, Del Río L, Simón M, Meléndez MA, Camacho J, Herrero L, Jiménez P, Navarro-Rico ML, Jado I, Giannetti E, Kuhn JH, Sanchez-Lockhart M, Di Paola N, Kugelman JR, Guerra S, García-Sastre A, Cuesta I, Sánchez-Seco MP, Palacios G. Monkeypox virus genomic accordion strategies. Nat Commun 2024;15:3059. [PMID: 38637500 PMCID: PMC11026394 DOI: 10.1038/s41467-024-46949-7] [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: 09/06/2023] [Accepted: 03/14/2024] [Indexed: 04/20/2024]  Open
8
Xu K, Yu S, Wang K, Tan Y, Zhao X, Liu S, Zhou J, Wang X. AI and Knowledge-Based Method for Rational Design of Escherichia coli Sigma70 Promoters. ACS Synth Biol 2024;13:402-407. [PMID: 38176073 DOI: 10.1021/acssynbio.3c00578] [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] [Indexed: 01/06/2024]
9
Perez LJ, Cloherty GA, Berg MG. Parallel evolution of picobirnaviruses from distinct ancestral origins. Microbiol Spectr 2023;11:e0269323. [PMID: 37888988 PMCID: PMC10714727 DOI: 10.1128/spectrum.02693-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/19/2023] [Indexed: 10/28/2023]  Open
10
Wang X, Xu K, Tan Y, Yu S, Zhao X, Zhou J. Deep Learning-Assisted Design of Novel Promoters in Escherichia coli. ADVANCED GENETICS (HOBOKEN, N.J.) 2023;4:2300184. [PMID: 38099247 PMCID: PMC10716054 DOI: 10.1002/ggn2.202300184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 10/09/2023] [Indexed: 12/17/2023]
11
Yang L, Yang Y, Huang L, Cui X, Liu Y. From single- to multi-omics: future research trends in medicinal plants. Brief Bioinform 2022;24:6840072. [PMID: 36416120 PMCID: PMC9851310 DOI: 10.1093/bib/bbac485] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/25/2022]  Open
12
Cordeiro TFVB, Gontijo MTP, Jorge GP, Brocchi M. EbfC/YbaB: A Widely Distributed Nucleoid-Associated Protein in Prokaryotes. Microorganisms 2022;10:microorganisms10101945. [PMID: 36296221 PMCID: PMC9610160 DOI: 10.3390/microorganisms10101945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/13/2022] [Accepted: 09/20/2022] [Indexed: 11/06/2022]  Open
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