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For: Lassmann T. Kalign 3: multiple sequence alignment of large data sets. Bioinformatics 2019;36:btz795. [PMID: 31665271 PMCID: PMC7703769 DOI: 10.1093/bioinformatics/btz795] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/12/2019] [Accepted: 10/14/2019] [Indexed: 11/13/2022]  Open
Number Cited by Other Article(s)
1
Rakesh S, Behera K, Krishnan A. Unveiling the structural and functional implications of uncharacterized NSPs and variations in the molecular toolkit across arteriviruses. NAR Genom Bioinform 2025;7:lqaf035. [PMID: 40213365 PMCID: PMC11983283 DOI: 10.1093/nargab/lqaf035] [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: 11/16/2024] [Revised: 02/16/2025] [Accepted: 03/18/2025] [Indexed: 04/15/2025]  Open
2
Bandeira PT, Chaves CR, Monteiro Torres PH, de Souza W. Immunolocalization and 3D modeling of three unique proteins belonging to the costa of Tritrichomonas foetus. Parasitol Res 2025;124:30. [PMID: 40053153 PMCID: PMC11889022 DOI: 10.1007/s00436-025-08466-4] [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: 09/27/2024] [Accepted: 02/10/2025] [Indexed: 03/10/2025]
3
Gillani M, Pollastri G. Impact of Alignments on the Accuracy of Protein Subcellular Localization Predictions. Proteins 2025;93:745-759. [PMID: 39575640 PMCID: PMC11809130 DOI: 10.1002/prot.26767] [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: 07/02/2024] [Revised: 10/01/2024] [Accepted: 11/01/2024] [Indexed: 02/11/2025]
4
Zaychikova M, Malakhova M, Bespiatykh D, Kornienko M, Klimina K, Strokach A, Gorodnichev R, German A, Fursov M, Bagrov D, Vnukova A, Gracheva A, Kazyulina A, Shleeva M, Shitikov E. Vic9 mycobacteriophage: the first subcluster B2 phage isolated in Russia. Front Microbiol 2025;15:1513081. [PMID: 39877753 PMCID: PMC11772480 DOI: 10.3389/fmicb.2024.1513081] [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: 10/17/2024] [Accepted: 12/12/2024] [Indexed: 01/31/2025]  Open
5
Gao S, Zhang Y, Bush SJ, Wang B, Yang X, Ye K. Centromere Landscapes Resolved from Hundreds of Human Genomes. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024;22:qzae071. [PMID: 39423139 DOI: 10.1093/gpbjnl/qzae071] [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: 07/18/2024] [Revised: 08/27/2024] [Accepted: 09/20/2024] [Indexed: 10/21/2024]
6
Cheng J, Jia Y, Hill C, He T, Wang K, Guo G, Shabala S, Zhou M, Han Y, Li C. Diversity of Gibberellin 2-oxidase genes in the barley genome offers opportunities for genetic improvement. J Adv Res 2024;66:105-118. [PMID: 38199453 PMCID: PMC11674783 DOI: 10.1016/j.jare.2023.12.021] [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: 05/27/2023] [Revised: 12/26/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024]  Open
7
Zhai Y, Zhou T, Wei Y, Zou Q, Wang Y. ReAlign-N: an integrated realignment approach for multiple nucleic acid sequence alignment, combining global and local realignments. NAR Genom Bioinform 2024;6:lqae170. [PMID: 39703429 PMCID: PMC11655299 DOI: 10.1093/nargab/lqae170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Revised: 10/05/2024] [Accepted: 11/19/2024] [Indexed: 12/21/2024]  Open
8
Cinquin O. Steering veridical large language model analyses by correcting and enriching generated database queries: first steps toward ChatGPT bioinformatics. Brief Bioinform 2024;26:bbaf045. [PMID: 39910777 PMCID: PMC11798674 DOI: 10.1093/bib/bbaf045] [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: 10/01/2024] [Revised: 01/09/2025] [Accepted: 01/20/2025] [Indexed: 02/07/2025]  Open
9
Zhou Y, Song L, Li H. Full-resolution HLA and KIR gene annotations for human genome assemblies. Genome Res 2024;34:1931-1941. [PMID: 38839374 PMCID: PMC11610593 DOI: 10.1101/gr.278985.124] [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: 01/12/2024] [Accepted: 05/22/2024] [Indexed: 06/07/2024]
10
Khamespanah E, Asad S, Vanak Z, Mehrshad M. Niche-Aware Metagenomic Screening for Enzyme Methioninase Illuminates Its Contribution to Metabolic Syntrophy. MICROBIAL ECOLOGY 2024;87:141. [PMID: 39546027 PMCID: PMC11568061 DOI: 10.1007/s00248-024-02458-0] [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: 06/16/2024] [Accepted: 11/01/2024] [Indexed: 11/17/2024]
11
Horvath M, Schrofel A, Kowalska K, Sabo J, Vlasak J, Nourisanami F, Sobol M, Pinkas D, Knapp K, Koupilova N, Novacek J, Veverka V, Lansky Z, Rozbesky D. Structural basis of MICAL autoinhibition. Nat Commun 2024;15:9810. [PMID: 39532862 PMCID: PMC11557892 DOI: 10.1038/s41467-024-54131-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 11/01/2024] [Indexed: 11/16/2024]  Open
12
Bolognini D, Halgren A, Lou RN, Raveane A, Rocha JL, Guarracino A, Soranzo N, Chin CS, Garrison E, Sudmant PH. Recurrent evolution and selection shape structural diversity at the amylase locus. Nature 2024;634:617-625. [PMID: 39232174 PMCID: PMC11485256 DOI: 10.1038/s41586-024-07911-1] [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: 11/29/2023] [Accepted: 08/06/2024] [Indexed: 09/06/2024]
13
Qin Z, Yuan B, Qu G, Sun Z. Rational enzyme design by reducing the number of hotspots and library size. Chem Commun (Camb) 2024;60:10451-10463. [PMID: 39210728 DOI: 10.1039/d4cc01394h] [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: 09/04/2024]
14
Santoni D. An entropy-based study on the mutational landscape of SARS-CoV-2 in USA: Comparing different variants and revealing co-mutational behavior of proteins. Gene 2024;922:148556. [PMID: 38754568 DOI: 10.1016/j.gene.2024.148556] [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: 02/21/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 05/18/2024]
15
Becker F, Stanke M. learnMSA2: deep protein multiple alignments with large language and hidden Markov models. Bioinformatics 2024;40:ii79-ii86. [PMID: 39230690 PMCID: PMC11373405 DOI: 10.1093/bioinformatics/btae381] [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] [Indexed: 09/05/2024]  Open
16
Camargo AP, Roux S, Schulz F, Babinski M, Xu Y, Hu B, Chain PSG, Nayfach S, Kyrpides NC. Identification of mobile genetic elements with geNomad. Nat Biotechnol 2024;42:1303-1312. [PMID: 37735266 PMCID: PMC11324519 DOI: 10.1038/s41587-023-01953-y] [Citation(s) in RCA: 207] [Impact Index Per Article: 207.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 08/17/2023] [Indexed: 09/23/2023]
17
Birtles D, Guiyab L, Abbas W, Lee J. Positive residues of the SARS-CoV-2 fusion domain are key contributors to the initiation of membrane fusion. J Biol Chem 2024;300:107564. [PMID: 39002677 PMCID: PMC11357847 DOI: 10.1016/j.jbc.2024.107564] [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: 05/09/2024] [Revised: 06/25/2024] [Accepted: 07/09/2024] [Indexed: 07/15/2024]  Open
18
Tan Y, Scornet AL, Yap MNF, Zhang D. Machine learning-based classification reveals distinct clusters of non-coding genomic allelic variations associated with Erm-mediated antibiotic resistance. mSystems 2024;9:e0043024. [PMID: 38953319 PMCID: PMC11264731 DOI: 10.1128/msystems.00430-24] [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: 03/25/2024] [Accepted: 06/05/2024] [Indexed: 07/04/2024]  Open
19
Madeira F, Madhusoodanan N, Lee J, Eusebi A, Niewielska A, Tivey ARN, Lopez R, Butcher S. The EMBL-EBI Job Dispatcher sequence analysis tools framework in 2024. Nucleic Acids Res 2024;52:W521-W525. [PMID: 38597606 PMCID: PMC11223882 DOI: 10.1093/nar/gkae241] [Citation(s) in RCA: 321] [Impact Index Per Article: 321.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/29/2024] [Accepted: 03/26/2024] [Indexed: 04/11/2024]  Open
20
Ravi J, Anantharaman V, Chen SZ, Brenner EP, Datta P, Aravind L, Gennaro ML. The phage shock protein (PSP) envelope stress response: discovery of novel partners and evolutionary history. mSystems 2024;9:e0084723. [PMID: 38809013 PMCID: PMC11237479 DOI: 10.1128/msystems.00847-23] [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: 08/28/2023] [Accepted: 03/20/2024] [Indexed: 05/30/2024]  Open
21
Bai G, Zeng X, Zhang L, Wang Y, Ma B. Computational investigation of the inhibitory interaction of IRF3 and SARS-CoV-2 accessory protein ORF3b. Biochem Biophys Res Commun 2024;712-713:149945. [PMID: 38640732 DOI: 10.1016/j.bbrc.2024.149945] [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: 03/30/2024] [Accepted: 04/14/2024] [Indexed: 04/21/2024]
22
Bolognini D, Halgren A, Lou RN, Raveane A, Rocha JL, Guarracino A, Soranzo N, Chin J, Garrison E, Sudmant PH. Global diversity, recurrent evolution, and recent selection on amylase structural haplotypes in humans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.07.579378. [PMID: 38370750 PMCID: PMC10871346 DOI: 10.1101/2024.02.07.579378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
23
Li W, Miller D, Liu X, Tosi L, Chkaiban L, Mei H, Hung PH, Parekkadan B, Sherlock G, Levy S. Arrayed in vivo barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries. Nucleic Acids Res 2024;52:e47. [PMID: 38709890 PMCID: PMC11162764 DOI: 10.1093/nar/gkae332] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 02/23/2024] [Accepted: 04/16/2024] [Indexed: 05/08/2024]  Open
24
Zhao Q, Bertolli S, Park YJ, Tan Y, Cutler KJ, Srinivas P, Asfahl KL, Fonesca-García C, Gallagher LA, Li Y, Wang Y, Coleman-Derr D, DiMaio F, Zhang D, Peterson SB, Veesler D, Mougous JD. Streptomyces umbrella toxin particles block hyphal growth of competing species. Nature 2024;629:165-173. [PMID: 38632398 PMCID: PMC11062931 DOI: 10.1038/s41586-024-07298-z] [Citation(s) in RCA: 4] [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: 12/05/2023] [Accepted: 03/11/2024] [Indexed: 04/19/2024]
25
Ng CL, Lim TS, Choong YS. Application of Computational Techniques in Antibody Fc-Fused Molecule Design for Therapeutics. Mol Biotechnol 2024;66:568-581. [PMID: 37742298 DOI: 10.1007/s12033-023-00885-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 08/23/2023] [Indexed: 09/26/2023]
26
Zhai Y, Chao J, Wang Y, Zhang P, Tang F, Zou Q. TPMA: A two pointers meta-alignment tool to ensemble different multiple nucleic acid sequence alignments. PLoS Comput Biol 2024;20:e1011988. [PMID: 38557416 PMCID: PMC11008887 DOI: 10.1371/journal.pcbi.1011988] [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: 11/28/2023] [Revised: 04/11/2024] [Accepted: 03/11/2024] [Indexed: 04/04/2024]  Open
27
Garmaeva S, Sinha T, Gulyaeva A, Kuzub N, Spreckels JE, Andreu-Sánchez S, Gacesa R, Vich Vila A, Brushett S, Kruk M, Dekens J, Sikkema J, Kuipers F, Shkoporov AN, Hill C, Scherjon S, Wijmenga C, Fu J, Kurilshikov A, Zhernakova A. Transmission and dynamics of mother-infant gut viruses during pregnancy and early life. Nat Commun 2024;15:1945. [PMID: 38431663 PMCID: PMC10908809 DOI: 10.1038/s41467-024-45257-4] [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: 08/15/2023] [Accepted: 01/16/2024] [Indexed: 03/05/2024]  Open
28
Fogarty EC, Schechter MS, Lolans K, Sheahan ML, Veseli I, Moore RM, Kiefl E, Moody T, Rice PA, Yu MK, Mimee M, Chang EB, Ruscheweyh HJ, Sunagawa S, Mclellan SL, Willis AD, Comstock LE, Eren AM. A cryptic plasmid is among the most numerous genetic elements in the human gut. Cell 2024;187:1206-1222.e16. [PMID: 38428395 PMCID: PMC10973873 DOI: 10.1016/j.cell.2024.01.039] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 10/03/2023] [Accepted: 01/25/2024] [Indexed: 03/03/2024]
29
Currie MJ, Davies JS, Scalise M, Gulati A, Wright JD, Newton-Vesty MC, Abeysekera GS, Subramanian R, Wahlgren WY, Friemann R, Allison JR, Mace PD, Griffin MDW, Demeler B, Wakatsuki S, Drew D, Indiveri C, Dobson RCJ, North RA. Structural and biophysical analysis of a Haemophilus influenzae tripartite ATP-independent periplasmic (TRAP) transporter. eLife 2024;12:RP92307. [PMID: 38349818 PMCID: PMC10942642 DOI: 10.7554/elife.92307] [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] [Indexed: 02/15/2024]  Open
30
Chopy M, Cavallini-Speisser Q, Chambrier P, Morel P, Just J, Hugouvieux V, Rodrigues Bento S, Zubieta C, Vandenbussche M, Monniaux M. Cell layer-specific expression of the homeotic MADS-box transcription factor PhDEF contributes to modular petal morphogenesis in petunia. THE PLANT CELL 2024;36:324-345. [PMID: 37804091 PMCID: PMC10827313 DOI: 10.1093/plcell/koad258] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/31/2023] [Accepted: 09/18/2023] [Indexed: 10/08/2023]
31
Xiao B, Rey-lglesia A, Yuan J, Hu J, Song S, Hou Y, Chen X, Germonpré M, Bao L, Wang S, Taogetongqimuge, Valentinovna LL, Lister AM, Lai X, Sheng G. Relationships of Late Pleistocene giant deer as revealed by Sinomegaceros mitogenomes from East Asia. iScience 2023;26:108406. [PMID: 38047074 PMCID: PMC10690636 DOI: 10.1016/j.isci.2023.108406] [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: 07/26/2023] [Revised: 09/26/2023] [Accepted: 11/03/2023] [Indexed: 12/05/2023]  Open
32
Scott CJR, Leadbeater DR, Oates NC, James SR, Newling K, Li Y, McGregor NGS, Bird S, Bruce NC. Whole genome structural predictions reveal hidden diversity in putative oxidative enzymes of the lignocellulose-degrading ascomycete Parascedosporium putredinis NO1. Microbiol Spectr 2023;11:e0103523. [PMID: 37811978 PMCID: PMC10714830 DOI: 10.1128/spectrum.01035-23] [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: 03/31/2023] [Accepted: 08/22/2023] [Indexed: 10/10/2023]  Open
33
Liu Y, Yuan H, Zhang Q, Wang Z, Xiong S, Wen N, Zhang Y. Multiple sequence alignment based on deep reinforcement learning with self-attention and positional encoding. Bioinformatics 2023;39:btad636. [PMID: 37856335 PMCID: PMC10628385 DOI: 10.1093/bioinformatics/btad636] [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: 09/20/2022] [Revised: 07/24/2023] [Accepted: 10/17/2023] [Indexed: 10/21/2023]  Open
34
Van Doren SR, Scott BS, Koppisetti RK. SARS-CoV-2 fusion peptide sculpting of a membrane with insertion of charged and polar groups. Structure 2023;31:1184-1199.e3. [PMID: 37625399 PMCID: PMC10592393 DOI: 10.1016/j.str.2023.07.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 07/10/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023]
35
Vafaeie F, Miri Karam Z, Yari A, Safarpour H, Kazemi T, Etesam S, Mohammadpour M, Miri‐Moghaddam E. Clinical and genetic screening in a large Iranian family with Marfan syndrome: A case study. Health Sci Rep 2023;6:e1647. [PMID: 37877128 PMCID: PMC10591539 DOI: 10.1002/hsr2.1647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/13/2023] [Accepted: 10/12/2023] [Indexed: 10/26/2023]  Open
36
Rhie A, Nurk S, Cechova M, Hoyt SJ, Taylor DJ, Altemose N, Hook PW, Koren S, Rautiainen M, Alexandrov IA, Allen J, Asri M, Bzikadze AV, Chen NC, Chin CS, Diekhans M, Flicek P, Formenti G, Fungtammasan A, Garcia Giron C, Garrison E, Gershman A, Gerton JL, Grady PGS, Guarracino A, Haggerty L, Halabian R, Hansen NF, Harris R, Hartley GA, Harvey WT, Haukness M, Heinz J, Hourlier T, Hubley RM, Hunt SE, Hwang S, Jain M, Kesharwani RK, Lewis AP, Li H, Logsdon GA, Lucas JK, Makalowski W, Markovic C, Martin FJ, Mc Cartney AM, McCoy RC, McDaniel J, McNulty BM, Medvedev P, Mikheenko A, Munson KM, Murphy TD, Olsen HE, Olson ND, Paulin LF, Porubsky D, Potapova T, Ryabov F, Salzberg SL, Sauria MEG, Sedlazeck FJ, Shafin K, Shepelev VA, Shumate A, Storer JM, Surapaneni L, Taravella Oill AM, Thibaud-Nissen F, Timp W, Tomaszkiewicz M, Vollger MR, Walenz BP, Watwood AC, Weissensteiner MH, Wenger AM, Wilson MA, Zarate S, Zhu Y, Zook JM, Eichler EE, O'Neill RJ, Schatz MC, Miga KH, Makova KD, Phillippy AM. The complete sequence of a human Y chromosome. Nature 2023;621:344-354. [PMID: 37612512 PMCID: PMC10752217 DOI: 10.1038/s41586-023-06457-y] [Citation(s) in RCA: 183] [Impact Index Per Article: 91.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 07/19/2023] [Indexed: 08/25/2023]
37
Yamasaki S, Zwama M, Yoneda T, Hayashi-Nishino M, Nishino K. Drug resistance and physiological roles of RND multidrug efflux pumps in Salmonella enterica, Escherichia coli and Pseudomonas aeruginosa. MICROBIOLOGY (READING, ENGLAND) 2023;169:001322. [PMID: 37319001 PMCID: PMC10333786 DOI: 10.1099/mic.0.001322] [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: 12/23/2022] [Accepted: 03/18/2023] [Indexed: 06/17/2023]
38
Kandwal S, Fayne D. Genetic conservation across SARS-CoV-2 non-structural proteins - Insights into possible targets for treatment of future viral outbreaks. Virology 2023;581:97-115. [PMID: 36940641 PMCID: PMC9999249 DOI: 10.1016/j.virol.2023.02.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 02/10/2023] [Accepted: 02/20/2023] [Indexed: 03/12/2023]
39
Burroughs A, Aravind L. New biochemistry in the Rhodanese-phosphatase superfamily: emerging roles in diverse metabolic processes, nucleic acid modifications, and biological conflicts. NAR Genom Bioinform 2023;5:lqad029. [PMID: 36968430 PMCID: PMC10034599 DOI: 10.1093/nargab/lqad029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/10/2023] [Accepted: 03/09/2023] [Indexed: 03/25/2023]  Open
40
Jacques F, Bolivar P, Pietras K, Hammarlund EU. Roadmap to the study of gene and protein phylogeny and evolution-A practical guide. PLoS One 2023;18:e0279597. [PMID: 36827278 PMCID: PMC9955684 DOI: 10.1371/journal.pone.0279597] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 12/12/2022] [Indexed: 02/25/2023]  Open
41
Cvrčková F, Bezvoda R. Gaining Insight into Large Gene Families with the Aid of Bioinformatic Tools. Methods Mol Biol 2023;2604:173-191. [PMID: 36773233 DOI: 10.1007/978-1-0716-2867-6_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
42
Bainbridge RE, Rosenbaum JC, Sau P, Carlson AE. Xenopus laevis lack the critical sperm factor PLCζ. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.02.526858. [PMID: 36778253 PMCID: PMC9915601 DOI: 10.1101/2023.02.02.526858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
43
Sanchez-Alonso P, Cobos-Justo E, Avalos-Rangel MA, López-Reyes L, Paniagua-Contreras GL, Vaca-Paniagua F, Anastacio-Marcelino E, López-Ochoa AJ, Pérez Marquez VM, Negrete-Abascal E, Vázquez-Cruz C. A Maverick-like cluster in the genome of a pathogenic, moderately virulent strain of Gallibacterium anatis, ESV200, a transient biofilm producer. Front Microbiol 2023;14:1084766. [PMID: 36778889 PMCID: PMC9909271 DOI: 10.3389/fmicb.2023.1084766] [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: 10/31/2022] [Accepted: 01/06/2023] [Indexed: 01/28/2023]  Open
44
Rodriguez OL, Silver CA, Shields K, Smith ML, Watson CT. Targeted long-read sequencing facilitates phased diploid assembly and genotyping of the human T cell receptor alpha, delta, and beta loci. CELL GENOMICS 2022;2:100228. [PMID: 36778049 PMCID: PMC9903726 DOI: 10.1016/j.xgen.2022.100228] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 08/25/2022] [Accepted: 11/05/2022] [Indexed: 12/02/2022]
45
Maleki E, Akbari Rokn Abadi S, Koohi S. HELIOS: High-speed sequence alignment in optics. PLoS Comput Biol 2022;18:e1010665. [PMID: 36409684 PMCID: PMC9678324 DOI: 10.1371/journal.pcbi.1010665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 10/18/2022] [Indexed: 11/22/2022]  Open
46
Somee MR, Amoozegar MA, Dastgheib SMM, Shavandi M, Maman LG, Bertilsson S, Mehrshad M. Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea. BMC Genomics 2022;23:690. [PMID: 36203131 PMCID: PMC9535955 DOI: 10.1186/s12864-022-08906-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/26/2022] [Indexed: 12/04/2022]  Open
47
Chen PYT, Adak S, Chekan JR, Liscombe DK, Miyanaga A, Bernhardt P, Diethelm S, Fielding EN, George JH, Miles ZD, Murray LAM, Steele TS, Winter JM, Noel JP, Moore BS. Structural Basis of Stereospecific Vanadium-Dependent Haloperoxidase Family Enzymes in Napyradiomycin Biosynthesis. Biochemistry 2022;61:1844-1852. [PMID: 35985031 PMCID: PMC10978243 DOI: 10.1021/acs.biochem.2c00338] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
48
Blaine HC, Burke JT, Ravi J, Stallings CL. DciA Helicase Operators Exhibit Diversity across Bacterial Phyla. J Bacteriol 2022;204:e0016322. [PMID: 35880876 PMCID: PMC9380583 DOI: 10.1128/jb.00163-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/21/2022] [Indexed: 01/28/2023]  Open
49
Hsueh BY, Severin GB, Elg CA, Waldron EJ, Kant A, Wessel AJ, Dover JA, Rhoades CR, Ridenhour BJ, Parent KN, Neiditch MB, Ravi J, Top EM, Waters CM. Phage defence by deaminase-mediated depletion of deoxynucleotides in bacteria. Nat Microbiol 2022;7:1210-1220. [PMID: 35817890 PMCID: PMC9830645 DOI: 10.1038/s41564-022-01162-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 05/24/2022] [Indexed: 02/03/2023]
50
Chao J, Tang F, Xu L. Developments in Algorithms for Sequence Alignment: A Review. Biomolecules 2022;12:biom12040546. [PMID: 35454135 PMCID: PMC9024764 DOI: 10.3390/biom12040546] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/29/2022] [Accepted: 03/31/2022] [Indexed: 01/27/2023]  Open
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