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Minimal information for studies of extracellular vesicles (MISEV2023): From basic to advanced approaches.
Welsh JA, Goberdhan DCI, O'Driscoll L, Buzas EI, Blenkiron C, Bussolati B, Cai H, Di Vizio D, Driedonks TAP, Erdbrügger U, Falcon-Perez JM, Fu QL, Hill AF, Lenassi M, Lim SK, Mahoney MG, Mohanty S, Möller A, Nieuwland R, Ochiya T, Sahoo S, Torrecilhas AC, Zheng L, Zijlstra A, Abuelreich S, Bagabas R, Bergese P, Bridges EM, Brucale M, Burger D, Carney RP, Cocucci E, Crescitelli R, Hanser E, Harris AL, Haughey NJ, Hendrix A, Ivanov AR, Jovanovic-Talisman T, Kruh-Garcia NA, Ku'ulei-Lyn Faustino V, Kyburz D, Lässer C, Lennon KM, Lötvall J, Maddox AL, Martens-Uzunova ES, Mizenko RR, Newman LA, Ridolfi A, Rohde E, Rojalin T, Rowland A, Saftics A, Sandau US, Saugstad JA, Shekari F, Swift S, Ter-Ovanesyan D, Tosar JP, Useckaite Z, Valle F, Varga Z, van der Pol E, van Herwijnen MJC, Wauben MHM, Wehman AM, Williams S, Zendrini A, Zimmerman AJ; MISEV Consortium; Théry C, Witwer KW. Welsh JA, et al. J Extracell Vesicles. 2024 Feb;13(2):e12404. doi: 10.1002/jev2.12404. J Extracell Vesicles. 2024. PMID: 38326288 Free PMC article.
Xander: employing a novel method for efficient gene-targeted metagenomic assembly.
Wang Q, Fish JA, Gilman M, Sun Y, Brown CT, Tiedje JM, Cole JR. Wang Q, et al. Microbiome. 2015 Aug 5;3:32. doi: 10.1186/s40168-015-0093-6. eCollection 2015. Microbiome. 2015. PMID: 26246894 Free PMC article.
These are used to create a novel combined weighted assembly graph. Xander performs both assembly and annotation concomitantly using information incorporated in this graph. ...This method is implemented as open source software and is available at https://github.com/rdpstaff …
These are used to create a novel combined weighted assembly graph. Xander performs both assembly and annotation concomitantly using i …
Review, Evaluation, and Directions for Gene-Targeted Assembly for Ecological Analyses of Metagenomes.
Guo J, Quensen JF, Sun Y, Wang Q, Brown CT, Cole JR, Tiedje JM. Guo J, et al. Front Genet. 2019 Oct 15;10:957. doi: 10.3389/fgene.2019.00957. eCollection 2019. Front Genet. 2019. PMID: 31749830 Free PMC article.
Here, we review six gene-targeted assemblers with unique algorithms for extracting and/or assembling targeted genes: Xander, MegaGTA, SAT-Assembler, HMM-GRASPx, GenSeed-HMM, and MEGAN. ...Also, Xander and MegaGTA are the only tools that include post-assembly scripts …
Here, we review six gene-targeted assemblers with unique algorithms for extracting and/or assembling targeted genes: Xander, MegaGTA, …
Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity.
Pope WH, Bowman CA, Russell DA, Jacobs-Sera D, Asai DJ, Cresawn SG, Jacobs WR, Hendrix RW, Lawrence JG, Hatfull GF; Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science; Phage Hunters Integrating Research and Education; Mycobacterial Genetics Course. Pope WH, et al. Elife. 2015 Apr 28;4:e06416. doi: 10.7554/eLife.06416. Elife. 2015. PMID: 25919952 Free PMC article.