Bibliography and comments on notable books and papers


List of books and papers I found relevant to amateur research, or previous studies.

These are mostly references from our upcoming research paper - I hope to add some notes and explanations on their content soon.

Abeles AL. P1 plasmid replication. Purification and DNA-binding activity of the replication protein RepA. Journal of Biological Chemistry. 1986 Mar 15;261(8):3548-55.

Art III. On the Connexions of the Physical Sciences. By Mrs. Somerville. In: London: The Quarterly Review v51; 1834. pp.54-59 Or Whewell W. On the Connexion of the Physical Sciences: By Mrs. Somerville. 1834.

Beccati, A., Gerken, J., Quast, C. et al. SILVA tree viewer: interactive web browsing of the SILVA phylogenetic guide trees. BMC Bioinformatics18, 433 (2017). DOI: 10.1186/s12859-017-1841-3

Bollivar DW, Bernardoni B, Bockman MR, Miller BM, Russell DA, Delesalle VA, Krukonis GP, Hatfull GF, Cross MR, Szewczyk MM, Eppurath A. Complete genome sequences of five bacteriophages that infect Rhodobacter capsulatus. Genome Announc.. 2016 Jun 30;4(3):e00051-16. DOI: 10.1128/genomeA.00051-16

Copeland A, Zeytun A, Yassawong M, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Han C, Tapia R, Goodwin LA. Complete genome sequence of the orange-red pigmented, radioresistant Deinococcus proteolyticus type strain (MRP T). Standards in genomic sciences. 2012 Mar 1;6(2):240-50. DOI: 10.4056/sigs.2756060

Dallinger WH. I. On the life-history of a minute septic organisms with an account of experiments made to determine its thermal death point. Proceedings of the Royal Society of London. 1878 Dec 31;27(185-189):332-50. DOI: 10.1098/rspl.1878.0055

Darling AC, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome research. 2004 Jul 1;14(7):1394-403. DOI: 10.1101/gr.2289704.

d'Herelle F, Smith GH. The bacteriophage, its role in immunity. Williams & Wilkins; 1922.

Druery CT, Bateson W. Experiments in plant hybridization. Journal of the Royal Horticultural Society. 1901;26:1-32.

Dueholm MS, Albertsen M, D'Imperio S, Tale VP, Lewis D, Nielsen PH, Nielsen JL. Complete genome of Rhodococcus pyridinivorans SB3094, a methyl-ethyl-ketone-degrading bacterium used for bioaugmentation. Genome Announc.. 2014 Jun 26;2(3):e00525-14. DOI: 10.1128/genomeA.00525-14

Emmert EA. Biosafety guidelines for handling microorganisms in the teaching laboratory: development and rationale. Journal of Microbiology & Biology Education: JMBE. 2013;14(1):78. DOI: 10.1128/jmbe.v14i1.531

George S, Pankhurst L, Hubbard A, Votintseva A, Stoesser N, Sheppard AE, Mathers A, Norris R, Navickaite I, Eaton C, Iqbal Z. Resolving plasmid structures in Enterobacteriaceae using the MinION nanopore sequencer: assessment of MinION and MinION/Illumina hybrid data assembly approaches. Microbial genomics. 2017 Aug;3(8). DOI: 10.1099/mgen.0.000118

Gregor Mendel Mendel, J.G. (1866). "Versuche über Pflanzenhybriden", Verhandlungen des naturforschenden Vereines in Brünn, Bd. IV für das Jahr, 1865, Abhandlungen: 3–47.

Hug, L., Baker, B., Anantharaman, K. et al. A new view of the tree of life. Nat Microbiol1, 16048 (2016). DOI: 10.1038/nmicrobiol.2016.48

Kohler RE. Lords of the fly: Drosophila genetics and the experimental life. University of Chicago Press; 1994 May 2. p. 134

Krisko A, Radman M. Biology of extreme radiation resistance: the way of Deinococcus radiodurans. Cold Spring Harbor perspectives in biology. 2013 Jul 1;5(7):a012765. DOI:10.1101/cshperspect.a012765

Kumar S, Stecher G, Suleski M, Hedges SB. TimeTree: a resource for timelines, timetrees, and divergence times. Molecular biology and evolution. 2017 Jul 1;34(7):1812-9. DOI: 10.1093/molbev/msx116

Lee MD. GToTree: a user-friendly workflow for phylogenomics. Bioinformatics. 2019 Oct 15;35(20):4162-4. DOI: 10.1093/bioinformatics/btz188

Leeuwenhoeck V, Observations A. communicated to the publisher by Mr. Antony van Leeuwenhoeck, in a Dutch letter of the 9th of Octob. 1676. Here English’d: concerning little animals by him observed in rain-well-sea-and snow-water; as also in water wherein pepper had lain infused. Phil. Trans.;12(821831):1677. DOI: 10.1098/rstl.1677.0003

Lewis NF. Studies on a radio-resistant coccus isolated from Bombay duck (Harpodon nehereus). Microbiology. 1971 Apr 1;66(1):29-35. DOI: 10.1099/00221287-66-1-29

Makarova KS, Omelchenko MV, Gaidamakova EK, Matrosova VY, Vasilenko A, Zhai M, et al. (2007) Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks. PLoS ONE 2(9): e955. DOI: 10.1371/journal.pone.0000955

Ma Y, Paulsen IT, Palenik B. Analysis of two marine metagenomes reveals the diversity of plasmids in oceanic environments. Environmental microbiology. 2012 Feb;14(2):453-66. DOI: 10.1111/j.1462-2920.2011.02633.x

Rainey FA, Nobre MF, Schumann P, Stackebrandt ER, DA COSTA MS. Phylogenetic diversity of the deinococci as determined by 16S ribosomal DNA sequence comparison. International Journal of Systematic and Evolutionary Microbiology. 1997 Apr 1;47(2):510-4. DOI: 10.1099/00207713-47-2-510

Rubin GM. FlyBook: a preface. Genetics. 2015 Oct 1;201(2):343

Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014 Jul 15;30(14):2068-9. DOI: 10.1093/bioinformatics/btu153

Summers WC. Felix d'Herelle and the origins of molecular biology. Yale University Press; 1999 May.

Wick RR, Judd LM, Gorrie CL, Holt KE (2017) Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 13(6): e1005595. DOI: 10.1371/journal.pcbi.1005595

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