Page 144 - Read Online

Wottrich et al. Microbiome Res Rep 2024;3:27 https://dx.doi.org/10.20517/mrr.2023.42 Page 17 of 17

2007;23:673-9. DOI PubMed PMC
31. Besemer J, Borodovsky M. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res
2005;33:W451-4. DOI PubMed PMC
32. Lawrence JG. DNA Master. 2007. Available from: http://cobamide2.bio.pitt.edu/computer.htm. [Last accessed on 16 Apr 2024].
33. Jordan TC, Burnett SH, Carson S, et al. A broadly implementable research course in phage discovery and genomics for first-year
undergraduate students. mBio 2014;5:e01051-13. DOI PubMed PMC
34. Cresawn SG, Bogel M, Day N, Jacobs-Sera D, Hendrix RW, Hatfull GF. Phamerator: a bioinformatic tool for comparative
bacteriophage genomics. BMC Bioinformatics 2011;12:395. DOI PubMed PMC
35. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990;215:403-10. DOI
PubMed
36. Söding J, Biegert A, Lupas AN. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids
Res 2005;33:W244-8. DOI PubMed PMC
37. Marchler-Bauer A, Derbyshire MK, Gonzales NR, et al. CDD: NCBI’s conserved domain database. Nucleic Acids Res 2015;43:D222-
6. DOI PubMed PMC
38. Russell DA, Hatfull GF. PhagesDB: the actinobacteriophage database. Bioinformatics 2017;33:784-6. DOI PubMed PMC
39. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and
improved distance functions. BMC Bioinformatics 2013;14:60. DOI PubMed PMC
40. Meier-Kolthoff JP, Göker M. VICTOR: genome-based phylogeny and classification of prokaryotic viruses. Bioinformatics
2017;33:3396-404. DOI PubMed PMC
41. Lefort V, Desper R, Gascuel O. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol
Biol Evol 2015;32:2798-800. DOI PubMed PMC
42. Farris JS. Estimating phylogenetic trees from distance matrices. Am Nat 1972;106:645-68. Available from: http://www.jstor.org/stable/
2459725. [Last accessed on 16 Apr 2024]
43. Letunic I, Bork P. Interactive tree of life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res
2021;49:W293-6. DOI PubMed PMC
44. Mitchell A, Chang HY, Daugherty L, et al. The InterPro protein families database: the classification resource after 15 years. Nucleic
Acids Res 2015;43:D213-21. DOI PubMed PMC
45. Bailey TJ, Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst
Mol Biol 1994;2:28-36. PubMed
46. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol
2016;33:1870-4. DOI PubMed PMC
47. Källberg M, Wang H, Wang S, et al. Template-based protein structure modeling using the RaptorX web server. Nature Protoc
2012;7:1511-22. DOI PubMed PMC
48. Jumper J, Evans R, Pritzel A, et al. Highly accurate protein structure prediction with AlphaFold. Nature 2021;596:583-9. DOI
PubMed PMC
49. Holm L, Laiho A, Törönen P, Salgado M. DALI shines a light on remote homologs: one hundred discoveries. Protein Sci
2023;32:e4519. DOI PubMed PMC
50. Jurrus E, Engel D, Star K, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 2018;27:112-28. DOI
PubMed PMC
51. Zhang Y, Skolnick J. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 2005;33:2302-9.
DOI PubMed PMC
52. ImageJ. Image processing and analysis in Java. Available from: https://imagej.nih.gov/ij/. [Last accessed on 16 Apr 2024].
53. Hewetson A, Khan NH, Dominguez MJ, et al. Maturation of the functional mouse CRES amyloid from globular form. Proc Natl Acad
Sci U S A 2020;117:16363-72. DOI PubMed PMC
54. Whelly S, Johnson S, Powell J, Borchardt C, Hastert MC, Cornwall GA. Nonpathological extracellular amyloid is present during
normal epididymal sperm maturation. PLoS One 2012;7:e36394. DOI PubMed PMC
55. Wu X, Zhao Y, Sun L, et al. Crystal structure of CagV, the Helicobacter pylori homologue of the T4SS protein VirB8. FEBS J
2019;286:4294-309. DOI PubMed
56. Singer ZS, Ambrose PM, Danino T, Rice CM. Quantitative measurements of early alphaviral replication dynamics in single cells
reveals the basis for superinfection exclusion. Cell Syst 2021;12:210-9.e3. DOI PubMed PMC
57. Biggs KRH, Bailes CL, Scott L, Wichman HA, Schwartz EJ. Ecological approach to understanding superinfection inhibition in
bacteriophage. Viruses 2021;13:1389. DOI PubMed PMC
58. Carvalho C, Ren R, Han J, Qu F. Natural selection, intracellular bottlenecks of virus populations, and viral superinfection exclusion.
Annu Rev Virol 2022;9:121-37. DOI PubMed
59. Redman M, King A, Watson C, King D. What is CRISPR/Cas9? Arch Dis Child Educ Pract Ed 2016;101:213-5. DOI PubMed PMC
60. Cobian N, Garlet A, Hidalgo-Cantabrana C, Barrangou R. Comparative genomic analyses and CRISPR-Cas characterization of
Cutibacterium acnes provide insights into genetic diversity and typing applications. Front Microbiol 2021;12:758749. DOI PubMed
PMC
61. Kermani AA. A guide to membrane protein X-ray crystallography. FEBS J 2021;288:5788-804. DOI PubMed
62. Marinelli LJ, Hatfull GF, Piuri M. Recombineering: a powerful tool for modification of bacteriophage genomes. Bacteriophage
2012;2:5-14. DOI PubMed PMC
63. Knödlseder N, Nevot G, Fábrega MJ, et al. Engineering selectivity of Cutibacterium acnes phages by epigenetic imprinting. PLoS
Pathog 2022;18:e1010420. DOI PubMed PMC