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For: Bairoch A, Apweiler R. The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999. Nucleic Acids Res 1999;27:49-54. [PMID: 9847139 PMCID: PMC148094 DOI: 10.1093/nar/27.1.49] [Citation(s) in RCA: 331] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
Number Cited by Other Article(s)
1
Chen H, Zhong S, Liu Z, Hu Z, Wang C, Zhou Y, Xu N, Zhao F, Li D, Hu Y. Microbiome-metabolomic insights into the systemic regulation in Fangxian Huangjiu fermentation. Food Chem 2025;481:143980. [PMID: 40154057 DOI: 10.1016/j.foodchem.2025.143980] [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: 01/04/2025] [Revised: 03/04/2025] [Accepted: 03/19/2025] [Indexed: 04/01/2025]
2
Wu H, Yang W, Dong G, Hu Q, Li D, Liu J. Construction of the super pan-genome for the genus Actinidia reveals structural variations linked to phenotypic diversity. HORTICULTURE RESEARCH 2025;12:uhaf067. [PMID: 40303430 PMCID: PMC12038230 DOI: 10.1093/hr/uhaf067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2024] [Accepted: 02/23/2025] [Indexed: 05/02/2025]
3
Liao S, Zhang Z, Yang C, Gardner EM, Peng Y, Xiong Y, Dai S, Deng Y. A chromosome-level genome assembly of Ficus benjamina, a fig tree with great ecological and ornamental value. Sci Data 2025;12:824. [PMID: 40393990 PMCID: PMC12092655 DOI: 10.1038/s41597-025-05155-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2024] [Accepted: 05/08/2025] [Indexed: 05/22/2025]  Open
4
Dong WY, Huang TY, Zhao SY, Zhang J, Lei Y, Huang J, Zhou ZS, Lu YB. Chromosome-level genome assembly of the parasitoid wasp Aenasius arizonensis. Sci Data 2025;12:809. [PMID: 40382346 PMCID: PMC12085690 DOI: 10.1038/s41597-025-05020-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2024] [Accepted: 04/14/2025] [Indexed: 05/20/2025]  Open
5
Usman S, Xu D, Ma J, Sheoran N, Okoye CO, Guo X. Comparative Genomics Reveals the Molecular Mechanisms of a Newly Isolated Pediococcus cellicola zy165 Strain and Its Adaptation in Corn Silage. Biochem Genet 2025:10.1007/s10528-025-11114-2. [PMID: 40327195 DOI: 10.1007/s10528-025-11114-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2024] [Accepted: 04/20/2025] [Indexed: 05/07/2025]
6
Wang J, Chen J, Hu Y, Song C, Li X, Qian Y, Deng L. DeepMFFGO: A Protein Function Prediction Method for Large-Scale Multifeature Fusion. J Chem Inf Model 2025;65:3841-3853. [PMID: 40116538 DOI: 10.1021/acs.jcim.5c00062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2025]
7
Ma L, Zeng X, Wang J, Xiong H, Yu Y, Liu H, Yang QY, Yang R, Yang X. Telomere-to-telomere gapless genome assembly of Triplophysa yaopeizhii. Sci Data 2025;12:597. [PMID: 40210914 PMCID: PMC11985934 DOI: 10.1038/s41597-025-04943-8] [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: 01/15/2025] [Accepted: 04/01/2025] [Indexed: 04/12/2025]  Open
8
Huang W, Xiang J, Ding Y, Liu W, Fang N, Xiong Y, Dai S, Yu H. A high-quality chromosome-level genome assembly of Antiaris toxicaria. BMC Genom Data 2025;26:21. [PMID: 40128643 PMCID: PMC11934813 DOI: 10.1186/s12863-025-01309-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2024] [Accepted: 03/10/2025] [Indexed: 03/26/2025]  Open
9
Cao J, Tong Y, Xiao Z, Chen H, Liu Z. Chromosome-level genome assembly of Jaguar guapote (Parachromis manguensis) by massive parallel sequencing. Sci Data 2025;12:411. [PMID: 40064893 PMCID: PMC11894119 DOI: 10.1038/s41597-025-04752-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2024] [Accepted: 03/04/2025] [Indexed: 03/14/2025]  Open
10
Liu S, Zheng N, Wang J, Zhao S. Nitrogen metabolism of the highly ureolytic bacterium Proteus penneri S99 isolated from the rumen. BMC Microbiol 2025;25:104. [PMID: 40021987 PMCID: PMC11869435 DOI: 10.1186/s12866-025-03808-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Accepted: 02/05/2025] [Indexed: 03/03/2025]  Open
11
Wang W, Kyrkou I, Bojer MS, Kalloubi D, Kali AJ, Alena-Rodriguez M, Leisner JJ, Fulaz S, Ingmer H. Characterization of agr-like Loci in Lactiplantibacillus plantarum and L. paraplantarum and Their Role in Quorum Sensing and Virulence Inhibition of Staphylococcus aureus. Probiotics Antimicrob Proteins 2025:10.1007/s12602-025-10476-8. [PMID: 39966225 DOI: 10.1007/s12602-025-10476-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2025] [Indexed: 02/20/2025]
12
Bian Q, Shen Z, Gao J, Shen L, Lu Y, Zhang Q, Chen R, Xu D, Liu T, Che J, Lu Y, Dong X. PPI-CoAttNet: A Web Server for Protein-Protein Interaction Tasks Using a Coattention Model. J Chem Inf Model 2025;65:461-471. [PMID: 39761551 DOI: 10.1021/acs.jcim.4c01365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2025]
13
Wang MY, Zhang BL, Liang QQ, Lian XM, Zhang K, Yang QE, Yang WK. Chromosome-level genome assembly, annotation, and population genomic resource of argali (Ovis ammon). Sci Data 2025;12:57. [PMID: 39799149 PMCID: PMC11724849 DOI: 10.1038/s41597-025-04400-6] [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: 07/19/2024] [Accepted: 01/02/2025] [Indexed: 01/15/2025]  Open
14
Cao C, Miao J, Xie Q, Sun J, Cheng H, Zhang Z, Wu F, Liu S, Ye X, Gong H, Zhang Z, Wang Q, Pan Y, Wang Z. A near telomere-to-telomere genome assembly of the Jinhua pig: enabling more accurate genetic research. Gigascience 2025;14:giaf048. [PMID: 40372724 PMCID: PMC12080228 DOI: 10.1093/gigascience/giaf048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2024] [Revised: 01/29/2025] [Accepted: 03/31/2025] [Indexed: 05/16/2025]  Open
15
Cao M, Ding Z, Wang X, Guo S, Kang Y, Hu L, Zhang B, Pei J, Ma Y, Guo X. Full-length transcriptome sequencing of the longissimus dorsi muscle of yak and cattle-yak using nanopore technology. Int J Biol Macromol 2025;284:138071. [PMID: 39603298 DOI: 10.1016/j.ijbiomac.2024.138071] [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: 09/09/2024] [Revised: 11/13/2024] [Accepted: 11/23/2024] [Indexed: 11/29/2024]
16
Wang Y, Yang Y, Wu Y, Liu Y, Li Q, Liu C, Jiang Z, Jiang W, Chen F, Mu X. Chromosome-level genome assembly of the ratmouth barbel, Ptychidio jordani. Sci Data 2024;11:1435. [PMID: 39725708 DOI: 10.1038/s41597-024-04331-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Accepted: 12/18/2024] [Indexed: 12/28/2024]  Open
17
Wu J, Liu Y, Zhu Y, Yu DJ. Improving Antifreeze Proteins Prediction With Protein Language Models and Hybrid Feature Extraction Networks. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024;21:2349-2358. [PMID: 39316498 DOI: 10.1109/tcbb.2024.3467261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2024]
18
Feng J, Zhang W, Chen C, Liang Y, Li T, Wu Y, Liu H, Wu J, Lin W, Li J, He Y, He J, Luan A. The pineapple reference genome: Telomere-to-telomere assembly, manually curated annotation, and comparative analysis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024;66:2208-2225. [PMID: 39109967 DOI: 10.1111/jipb.13748] [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: 12/21/2023] [Revised: 06/27/2024] [Accepted: 07/03/2024] [Indexed: 10/19/2024]
19
Wu L, Gu S, Wen P, Wu L, Li L, Guo S, Ding S. Chromosome-level genome assembly and annotation of the Spinibarbus caldwelli. Sci Data 2024;11:933. [PMID: 39198473 PMCID: PMC11358287 DOI: 10.1038/s41597-024-03796-x] [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: 05/24/2024] [Accepted: 08/19/2024] [Indexed: 09/01/2024]  Open
20
Tadesse BT, Gu L, Solem C, Mijakovic I, Jers C. The Probiotic Enterococcus Lactis SF68 as a Potential Food Fermentation Microorganism for Safe Food Production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024;72:18089-18099. [PMID: 39102436 DOI: 10.1021/acs.jafc.4c03644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/07/2024]
21
Duan M, Yang S, Li X, Tang X, Cheng Y, Luo J, Wang J, Song H, Wang Q, Zhu GX. Chromosome-level genome assembly and annotation of the Rhabdophis nuchalis (Hubei keelback). Sci Data 2024;11:850. [PMID: 39117633 PMCID: PMC11310211 DOI: 10.1038/s41597-024-03708-z] [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: 05/23/2024] [Accepted: 07/30/2024] [Indexed: 08/10/2024]  Open
22
Li M, Chen C, Wang H, Qin H, Hou S, Yang X, Jian J, Gao P, Liu M, Mu Z. Telomere-to-telomere genome assembly of sorghum. Sci Data 2024;11:835. [PMID: 39095379 PMCID: PMC11297213 DOI: 10.1038/s41597-024-03664-8] [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: 11/28/2023] [Accepted: 07/19/2024] [Indexed: 08/04/2024]  Open
23
Xiong L, Yu H, Zeng K, Li Y, Wei Y, Li H, Ji X. Whole genome analysis of Pseudomonas mandelii SW-3 and the insights into low-temperature adaptation. Folia Microbiol (Praha) 2024;69:775-787. [PMID: 38051419 DOI: 10.1007/s12223-023-01117-0] [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: 04/14/2023] [Accepted: 11/14/2023] [Indexed: 12/07/2023]
24
Huang X, Hu X, Liu Q, Xie Z, Tan S, Qin X, Chen T, Wu W, Saud S, Nawaz T, El-Kahtany K, Fahad S, Yi K. Full-length agave transcriptome reveals candidate glycosyltransferase genes involved in hemicellulose biosynthesis. Int J Biol Macromol 2024;274:133508. [PMID: 38944067 DOI: 10.1016/j.ijbiomac.2024.133508] [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: 01/27/2024] [Revised: 06/07/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
25
You X, Fang Q, Chen C, Cao J, Fu S, Zhang T, Wang S, He X, He J, Zhou Y, Wang B, Wang L, Wang Z, Sun T, Yang X, Te R, Jian J, Zhou H, Dai Y, Liu Y. A near complete genome assembly of the East Friesian sheep genome. Sci Data 2024;11:762. [PMID: 38992134 PMCID: PMC11239650 DOI: 10.1038/s41597-024-03581-w] [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: 11/10/2023] [Accepted: 06/27/2024] [Indexed: 07/13/2024]  Open
26
Ahmed MH, Samia NSN, Singh G, Gupta V, Mishal MFM, Hossain A, Suman KH, Raza A, Dutta AK, Labony MA, Sultana J, Faysal EH, Alnasser SM, Alam P, Azam F. An immuno-informatics approach for annotation of hypothetical proteins and multi-epitope vaccine designed against the Mpox virus. J Biomol Struct Dyn 2024;42:5288-5307. [PMID: 37519185 DOI: 10.1080/07391102.2023.2239921] [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: 04/02/2023] [Accepted: 06/09/2023] [Indexed: 08/01/2023]
27
Niu Y, Fan X, Yang Y, Li J, Lian J, Wang L, Zhang Y, Tang Y, Tang Z. Haplotype-resolved assembly of a pig genome using single-sperm sequencing. Commun Biol 2024;7:738. [PMID: 38890535 PMCID: PMC11189477 DOI: 10.1038/s42003-024-06397-x] [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: 10/07/2023] [Accepted: 05/29/2024] [Indexed: 06/20/2024]  Open
28
Bavadi M, Zhu Z, Zhang B. Evaluation of surfactant-aided polycyclic aromatic hydrocarbon biodegradation by molecular docking and molecular dynamic simulation in the marine environment. CHEMOSPHERE 2024;358:142171. [PMID: 38714247 DOI: 10.1016/j.chemosphere.2024.142171] [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: 08/02/2023] [Revised: 03/27/2024] [Accepted: 04/26/2024] [Indexed: 05/09/2024]
29
Huang W, Ding Y, Fan S, Liu W, Chen H, Segar S, Compton SG, Yu H. A high-quality chromosome-level genome assembly of Ficus hirta. Sci Data 2024;11:526. [PMID: 38778063 PMCID: PMC11111794 DOI: 10.1038/s41597-024-03376-z] [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: 11/30/2023] [Accepted: 05/14/2024] [Indexed: 05/25/2024]  Open
30
Chu H, Liu T. Comprehensive Research on Druggable Proteins: From PSSM to Pre-Trained Language Models. Int J Mol Sci 2024;25:4507. [PMID: 38674091 PMCID: PMC11049818 DOI: 10.3390/ijms25084507] [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: 03/21/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024]  Open
31
Zhang W, Yang Y, Hua S, Ruan Q, Li D, Wang L, Wang X, Wen X, Liu X, Meng Z. Chromosome-level genome assembly and annotation of the yellow grouper, Epinephelus awoara. Sci Data 2024;11:151. [PMID: 38296995 PMCID: PMC10830450 DOI: 10.1038/s41597-024-02989-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 01/18/2024] [Indexed: 02/02/2024]  Open
32
Khelghatibana F, Javan-Nikkhah M, Safaie N, Sobhani A, Shams S, Sari E. A reference transcriptome for walnut anthracnose pathogen, Ophiognomonia leptostyla, guides the discovery of candidate virulence genes. Fungal Genet Biol 2023;169:103828. [PMID: 37657751 DOI: 10.1016/j.fgb.2023.103828] [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: 04/12/2023] [Revised: 08/13/2023] [Accepted: 08/28/2023] [Indexed: 09/03/2023]
33
Wei XY, Jia PP, Hu H, Liu L, Li TY, Li YZ, Pei DS. Multi-omics reveal mechanisms underlying chronic kidney disease of unknown etiology (CKDu) pathogenesis using zebrafish. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023;337:122524. [PMID: 37683759 DOI: 10.1016/j.envpol.2023.122524] [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: 07/24/2023] [Revised: 08/24/2023] [Accepted: 09/05/2023] [Indexed: 09/10/2023]
34
Zhao D, Zhang Y, Ren H, Shi Y, Dong D, Li Z, Cui G, Shen Y, Mou Z, Kennelly EJ, Huang L, Ruan J, Chen S, Yu D, Cun Y. Multi-omics analysis reveals the evolutionary origin of diterpenoid alkaloid biosynthesis pathways in Aconitum. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023;65:2320-2335. [PMID: 37688324 DOI: 10.1111/jipb.13565] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/27/2023] [Accepted: 09/07/2023] [Indexed: 09/10/2023]
35
Zhou Y, Zhang X, Tang X, Zhou Y, Ding Y, Liu H. Chromosome-Level Genome Assembly of Protosalanx chinensis and Response to Air Exposure Stress. BIOLOGY 2023;12:1266. [PMID: 37759664 PMCID: PMC10525151 DOI: 10.3390/biology12091266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 09/05/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023]
36
Zhang W, Wang SC, Li Y. Molecular mechanism of thiamine in mitigating drought stress in Chinese wingnut (Pterocarya stenoptera): Insights from transcriptomics. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023;263:115307. [PMID: 37499386 DOI: 10.1016/j.ecoenv.2023.115307] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/21/2023] [Accepted: 07/24/2023] [Indexed: 07/29/2023]
37
Pigoni M, Uzquiano A, Paulsen B, Kedaigle AJ, Yang SM, Symvoulidis P, Adiconis X, Velasco S, Sartore R, Kim K, Tucewicz A, Tropp SY, Tsafou K, Jin X, Barrett L, Chen F, Boyden ES, Regev A, Levin JZ, Arlotta P. Cell-type specific defects in PTEN-mutant cortical organoids converge on abnormal circuit activity. Hum Mol Genet 2023;32:2773-2786. [PMID: 37384417 PMCID: PMC10481103 DOI: 10.1093/hmg/ddad107] [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: 03/31/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/01/2023]  Open
38
Xiong L, Li Y, Yu H, Wei Y, Li H, Ji X. Whole genome analysis and cold adaptation strategies of Pseudomonas sivasensis W-6 isolated from the Napahai plateau wetland. Sci Rep 2023;13:14190. [PMID: 37648730 PMCID: PMC10468529 DOI: 10.1038/s41598-023-41323-x] [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: 01/02/2023] [Accepted: 08/24/2023] [Indexed: 09/01/2023]  Open
39
Seo JJ, Jung SJ, Yang J, Choi DE, Kim VN. Functional viromic screens uncover regulatory RNA elements. Cell 2023:S0092-8674(23)00675-X. [PMID: 37413987 DOI: 10.1016/j.cell.2023.06.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 04/21/2023] [Accepted: 06/10/2023] [Indexed: 07/08/2023]
40
Mou CY, Li Q, Huang ZP, Ke HY, Zhao H, Zhao ZM, Duan YL, Li HD, Xiao Y, Qian ZM, Du J, Zhou J, Zhang L. PacBio single-molecule long-read sequencing provides new insights into the complexity of full-length transcripts in oriental river prawn, macrobrachium nipponense. BMC Genomics 2023;24:340. [PMID: 37340366 DOI: 10.1186/s12864-023-09442-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 06/11/2023] [Indexed: 06/22/2023]  Open
41
Zhang Z, Xia T, Zhou S, Yang X, Lyu T, Wang L, Fang J, Wang Q, Dou H, Zhang H. High-Quality Chromosome-Level Genome Assembly of the Corsac Fox (Vulpes corsac) Reveals Adaptation to Semiarid and Harsh Environments. Int J Mol Sci 2023;24:ijms24119599. [PMID: 37298549 DOI: 10.3390/ijms24119599] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/24/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023]  Open
42
Wang X, Huang X, Chen L, Xie Z, Tan S, Qin X, Chen T, Huang Y, Xi J, Chen H, Yi K. Transcriptome Sequencing of Agave amaniensis Reveals Shoot-Related Expression Patterns of Expansin A Genes in Agave. PLANTS (BASEL, SWITZERLAND) 2023;12:2020. [PMID: 37653937 PMCID: PMC10222593 DOI: 10.3390/plants12102020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 05/06/2023] [Accepted: 05/17/2023] [Indexed: 09/02/2023]
43
Kashif M, Sang Y, Mo S, Rehman SU, Khan S, Khan MR, He S, Jiang C. Deciphering the biodesulfurization pathway employing marine mangrove Bacillus aryabhattai strain NM1-A2 according to whole genome sequencing and transcriptome analyses. Genomics 2023;115:110635. [PMID: 37150229 DOI: 10.1016/j.ygeno.2023.110635] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 04/22/2023] [Accepted: 05/03/2023] [Indexed: 05/09/2023]
44
Zafar H, Saier MH. Understanding the Relationship of the Human Bacteriome with COVID-19 Severity and Recovery. Cells 2023;12:cells12091213. [PMID: 37174613 PMCID: PMC10177376 DOI: 10.3390/cells12091213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/05/2023] [Accepted: 04/11/2023] [Indexed: 05/15/2023]  Open
45
Wang T, Wang B, Hua X, Tang H, Zhang Z, Gao R, Qi Y, Zhang Q, Wang G, Yu Z, Huang Y, Zhang Z, Mei J, Wang Y, Zhang Y, Li Y, Meng X, Wang Y, Pan H, Chen S, Li Z, Shi H, Liu X, Deng Z, Chen B, Zhang M, Gu L, Wang J, Ming R, Yao W, Zhang J. A complete gap-free diploid genome in Saccharum complex and the genomic footprints of evolution in the highly polyploid Saccharum genus. NATURE PLANTS 2023;9:554-571. [PMID: 36997685 DOI: 10.1038/s41477-023-01378-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 02/21/2023] [Indexed: 06/19/2023]
46
Nguyen R, Sokhansanj BA, Polikar R, Rosen GL. Complet+: a computationally scalable method to improve completeness of large-scale protein sequence clustering. PeerJ 2023;11:e14779. [PMID: 36785708 PMCID: PMC9921987 DOI: 10.7717/peerj.14779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 01/03/2023] [Indexed: 02/10/2023]  Open
47
Han X, Zhang Y, Zhang Q, Ma N, Liu X, Tao W, Lou Z, Zhong C, Deng XW, Li D, He H. Two haplotype-resolved, gap-free genome assemblies for Actinidia latifolia and Actinidia chinensis shed light on the regulatory mechanisms of vitamin C and sucrose metabolism in kiwifruit. MOLECULAR PLANT 2023;16:452-470. [PMID: 36588343 DOI: 10.1016/j.molp.2022.12.022] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
48
Sheng K, Sun Y, Liu M, Cao Y, Han Y, Li C, Muhammad U, Daud MK, Wang W, Li H, Samrana S, Hui Y, Zhu S, Chen J, Zhao T. A reference-grade genome assembly for Gossypium bickii and insights into its genome evolution and formation of pigment glands and gossypol. PLANT COMMUNICATIONS 2023;4:100421. [PMID: 35949167 PMCID: PMC9860168 DOI: 10.1016/j.xplc.2022.100421] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/29/2022] [Accepted: 08/05/2022] [Indexed: 05/31/2023]
49
Chromosome-level genome and population genomics reveal evolutionary characteristics and conservation status of Chinese indigenous geese. Commun Biol 2022;5:1191. [DOI: 10.1038/s42003-022-04125-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 10/18/2022] [Indexed: 11/09/2022]  Open
50
Cui S, Gu Z, Wang W, Tang X, Zhang Q, Mao B, Zhang H, Zhao J. Characterization of peptides available to different bifidobacteria. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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