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Current Genomics

Editor-in-Chief

ISSN (Print): 1389-2029
ISSN (Online): 1875-5488

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Perspective

Towards an Analytical Biology

Author(s): Max H. Garzon* and Fredy A. Coloradodo

Volume 25, Issue 2, 2024

Published on: 10 January, 2024

Page: [65 - 68] Pages: 4

DOI: 10.2174/0113892029283759231227075715

Price: $65

Abstract

This article draws a perspective on the increasingly unavoidable question of whether steps can be taken in genomics and biology at large to move them more rapidly towards more analytical and deductive biology, akin to similar developments that occurred in other natural sciences, such as physics and chemistry, centuries ago. It provides a summary of recent advances in other relevant sciences in the last 3 decades that are likely to pull it in that direction in the next decade or so, as well as what methods and tools will make it possible.

« Previous Next »
[1]
Liu, E.T. Systems biology, integrative biology, predictive biology. Cell, 2005, 121(4), 505-506.
[http://dx.doi.org/10.1016/j.cell.2005.04.021] [PMID: 15907463]
[2]
De Queiroz, K.; Delimitation, S. Species concepts and species delimitation. Syst. Biol., 2007, 56(6), 879-886.
[http://dx.doi.org/10.1080/10635150701701083] [PMID: 18027281]
[3]
Mayden, R.L. A hierarchy of species concepts: The denouement in the saga of the species problem. In: Species: The units of diversity; Claridge, M.F.; Dawah, H.A.; Wilson, M.R., Eds.; Chapman & Hall, 1997; pp. 381-423.
[4]
de Queiroz, K. Different species problems and their resolution. BioEssays, 2005, 27(12), 1263-1269.
[http://dx.doi.org/10.1002/bies.20325] [PMID: 16299765]
[5]
Mendel, G. Experiments on plant hybridization. Negotiations of the natural research association in Brno, 1866; pp. 3-47.
[6]
Watson, J.D.; Crick, F.H.C. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature, 1953, 171(4356), 737-738.
[http://dx.doi.org/10.1038/171737a0] [PMID: 13054692]
[7]
Karsenti, E. Self-organization in cell biology: A brief history. Nat. Rev. Mol. Cell Biol., 2008, 9(3), 255-262.
[http://dx.doi.org/10.1038/nrm2357] [PMID: 18292780]
[8]
Lander, E.S.; Linton, L.M.; Birren, B.; Nusbaum, C.; Zody, M.C.; Baldwin, J.; Devon, K.; Dewar, K.; Doyle, M.; FitzHugh, W.; Funke, R.; Gage, D.; Harris, K.; Heaford, A.; Howland, J.; Kann, L.; Lehoczky, J.; LeVine, R.; McEwan, P.; McKernan, K.; Meldrim, J.; Mesirov, J.P.; Miranda, C.; Morris, W.; Naylor, J.; Raymond, C.; Rosetti, M.; Santos, R.; Sheridan, A.; Sougnez, C.; Stange-Thomann, N.; Stojanovic, N.; Subramanian, A.; Wyman, D.; Rogers, J.; Sulston, J.; Ainscough, R.; Beck, S.; Bentley, D.; Burton, J.; Clee, C.; Carter, N.; Coulson, A.; Deadman, R.; Deloukas, P.; Dunham, A.; Dunham, I.; Durbin, R.; French, L.; Grafham, D.; Gregory, S.; Hubbard, T.; Humphray, S.; Hunt, A.; Jones, M.; Lloyd, C.; McMurray, A.; Matthews, L.; Mercer, S.; Milne, S.; Mullikin, J.C.; Mungall, A.; Plumb, R.; Ross, M.; Shownkeen, R.; Sims, S.; Waterston, R.H.; Wilson, R.K.; Hillier, L.W.; McPherson, J.D.; Marra, M.A.; Mardis, E.R.; Fulton, L.A.; Chinwalla, A.T.; Pepin, K.H.; Gish, W.R.; Chissoe, S.L.; Wendl, M.C.; Delehaunty, K.D.; Miner, T.L.; Delehaunty, A.; Kramer, J.B.; Cook, L.L.; Fulton, R.S.; Johnson, D.L.; Minx, P.J.; Clifton, S.W.; Hawkins, T.; Branscomb, E.; Predki, P.; Richardson, P.; Wenning, S.; Slezak, T.; Doggett, N.; Cheng, J.F.; Olsen, A.; Lucas, S.; Elkin, C.; Uberbacher, E.; Frazier, M.; Gibbs, R.A.; Muzny, D.M.; Scherer, S.E.; Bouck, J.B.; Sodergren, E.J.; Worley, K.C.; Rives, C.M.; Gorrell, J.H.; Metzker, M.L.; Naylor, S.L.; Kucherlapati, R.S.; Nelson, D.L.; Weinstock, G.M.; Sakaki, Y.; Fujiyama, A.; Hattori, M.; Yada, T.; Toyoda, A.; Itoh, T.; Kawagoe, C.; Watanabe, H.; Totoki, Y.; Taylor, T.; Weissenbach, J.; Heilig, R.; Saurin, W.; Artiguenave, F.; Brottier, P.; Bruls, T.; Pelletier, E.; Robert, C.; Wincker, P.; Rosenthal, A.; Platzer, M.; Nyakatura, G.; Taudien, S.; Rump, A.; Smith, D.R.; Doucette-Stamm, L.; Rubenfield, M.; Weinstock, K.; Lee, H.M.; Dubois, J.A.; Yang, H.; Yu, J.; Wang, J.; Huang, G.; Gu, J.; Hood, L.; Rowen, L.; Madan, A.; Qin, S.; Davis, R.W.; Federspiel, N.A.; Abola, A.P.; Proctor, M.J.; Roe, B.A.; Chen, F.; Pan, H.; Ramser, J.; Lehrach, H.; Reinhardt, R.; McCombie, W.R.; de la Bastide, M.; Dedhia, N.; Blöcker, H.; Hornischer, K.; Nordsiek, G.; Agarwala, R.; Aravind, L.; Bailey, J.A.; Bateman, A.; Batzoglou, S.; Birney, E.; Bork, P.; Brown, D.G.; Burge, C.B.; Cerutti, L.; Chen, H-C.; Church, D.; Clamp, M.; Copley, R.R.; Doerks, T.; Eddy, S.R.; Eichler, E.E.; Furey, T.S.; Galagan, J.; Gilbert, J.G.R.; Harmon, C.; Hayashizaki, Y.; Haussler, D.; Hermjakob, H.; Hokamp, K.; Jang, W.; Johnson, L.S.; Jones, T.A.; Kasif, S.; Kaspryzk, A.; Kennedy, S.; Kent, W.J.; Kitts, P.; Koonin, E.V.; Korf, I.; Kulp, D.; Lancet, D.; Lowe, T.M.; McLysaght, A.; Mikkelsen, T.; Moran, J.V.; Mulder, N.; Pollara, V.J.; Ponting, C.P.; Schuler, G.; Schultz, J.; Slater, G.; Smit, A.F.A.; Stupka, E.; Szustakowki, J.; Thierry-Mieg, D.; Thierry-Mieg, J.; Wagner, L.; Wallis, J.; Wheeler, R.; Williams, A.; Wolf, Y.I.; Wolfe, K.H.; Yang, S-P.; Yeh, R-F.; Collins, F.; Guyer, M.S.; Peterson, J.; Felsenfeld, A.; Wetterstrand, K.A.; Myers, R.M.; Schmutz, J.; Dickson, M.; Grimwood, J.; Cox, D.R.; Olson, M.V.; Kaul, R.; Raymond, C.; Shimizu, N.; Kawasaki, K.; Minoshima, S.; Evans, G.A.; Athanasiou, M.; Schultz, R.; Patrinos, A.; Morgan, M.J.; de Jong, P.; Catanese, J.J.; Osoegawa, K.; Shizuya, H.; Choi, S.; Chen, Y.J.; Szustakowki, J. Initial sequencing and analysis of the human genome. Nature, 2001, 409(6822), 860-921.
[http://dx.doi.org/10.1038/35057062] [PMID: 11237011]
[9]
Stace, C.A. Cytology and cytogenetics as a fundamental taxonomic resource for the 20th and 21st centuries. Taxon, 2000, 49(3), 451-477.
[http://dx.doi.org/10.2307/1224344]
[10]
Guerra, M. Chromosome numbers in plant cytotaxonomy: Concepts and implications. Cytogenet. Genome Res., 2008, 120(3-4), 339-350.
[http://dx.doi.org/10.1159/000121083] [PMID: 18504363]
[11]
Schaeffer, S.W.; Bhutkar, A.; McAllister, B.F.; Matsuda, M.; Matzkin, L.M.; O’Grady, P.M.; Rohde, C.; Valente, V.L.S.; Aguadé, M.; Anderson, W.W.; Edwards, K.; Garcia, A.C.L.; Goodman, J.; Hartigan, J.; Kataoka, E.; Lapoint, R.T.; Lozovsky, E.R.; Machado, C.A.; Noor, M.A.F.; Papaceit, M.; Reed, L.K.; Richards, S.; Rieger, T.T.; Russo, S.M.; Sato, H.; Segarra, C.; Smith, D.R.; Smith, T.F.; Strelets, V.; Tobari, Y.N.; Tomimura, Y.; Wasserman, M.; Watts, T.; Wilson, R.; Yoshida, K.; Markow, T.A.; Gelbart, W.M.; Kaufman, T.C. Polytene chromosomal maps of 11 Drosophila species: The order of genomic scaffolds inferred from genetic and physical maps. Genetics, 2008, 179(3), 1601-1655.
[http://dx.doi.org/10.1534/genetics.107.086074] [PMID: 18622037]
[12]
Hebert, P.D.N.; Cywinska, A.; Ball, S.L.; deWaard, J.R. Biological identifications through DNA barcodes. Proc. Biol. Sci., 2003, 270(1512), 313-321.
[http://dx.doi.org/10.1098/rspb.2002.2218] [PMID: 12614582]
[13]
Dayrat, B. Towards integrative taxonomy. Biol. J. Linn. Soc. Lond., 2005, 85(3), 407-415.
[http://dx.doi.org/10.1111/j.1095-8312.2005.00503.x]
[14]
Mainali, S.; Garzon, S.M.H.; Colorado, F.A. New Genomic information systems (GenISs): Species delimitation and identification. Bioinformatics and Biomedical Engineering, 8th International Work-Conference, IWBBIO 2020, Granada, SpainMay 6–8, 20202020, pp. 163-174.
[http://dx.doi.org/10.1007/978-3-030-45385-5_15]
[15]
Garzon, M.H.; Minali, S. Deep structure of DNA for genomic analysis. Hum. Mol. Genet., 2022, 31(4), 576-586.
[16]
Mainali, S.; Colorado-Garzon, F.A.; Garzon, M. Foretelling the phenotype of a genomic sequence. IEEE/ACM Trans. Comput. Biol. Bioinformatics, 2020.
[http://dx.doi.org/10.1109/TCBB.2020.2985349] [PMID: 32287003]
[17]
Garzon, M.; Mainali, S.; Chacon, M.F.; Azizzadeh-Roodpish, S. A computational approach to biological pathogenicity. Mol. Genet. Genomics, 2022, 297(6), 1741-1754.
[http://dx.doi.org/10.1007/s00438-022-01951-w] [PMID: 36125534]
[18]
Adler, P.H.; Cheke, R.A.; Post, R.J. Evolution, epidemiology, and population genetics of black flies (Diptera: Simuliidae). Infect. Genet. Evol., 2010, 10(7), 846-865.
[http://dx.doi.org/10.1016/j.meegid.2010.07.003] [PMID: 20624485]
[19]
Colorado-Garzón, F.A.; Adler, P.H.; García, L.F.; Muñoz de Hoyos, P.; Bueno, M.L.; Matta, N.E. Estimating diversity of black flies in the Simulium ignescens and Simulium tunja complexes in Colombia: Chromosomal rearrangements as the core of integrative taxonomy. J. Hered., 2017, 108(1), 12-24.
[http://dx.doi.org/10.1093/jhered/esw063] [PMID: 27974486]
[20]
Konno, N.; Iwasaki, W. Machine learning enables prediction of metabolic system evolution in bacteria. Sci. Adv., 2023, 9(2), eadc9130.
[http://dx.doi.org/10.1126/sciadv.adc9130] [PMID: 36630500]
[21]
Pinto-Ledezma, J.N.; Cavender-Bares, J. Predicting species distributions and community composition using satellite remote sensing predictors. Sci. Rep., 2021, 11(1), 16448.
[http://dx.doi.org/10.1038/s41598-021-96047-7] [PMID: 34385574]
[22]
Smits, P.; Finnegan, S. How predictable is extinction? Forecasting species survival at million-year timescales. Philos. Trans. R. Soc. Lond. B Biol. Sci., 2019, 374(1788), 20190392.
[http://dx.doi.org/10.1098/rstb.2019.0392] [PMID: 31679499]
[23]
Green, Kesten Forecasting global climate change. In: Climate change: The facts; , 2014; pp. 170-186.
[24]
Jinek, M.; Chylinski, K.; Fonfara, I.; Hauer, M.; Doudna, J.A.; Charpentier, E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science, 2012, 337(6096), 816-821.
[http://dx.doi.org/10.1126/science.1225829] [PMID: 22745249]
[25]
Brij Narayan Chakbast. Available from: https://en.wikipedia.org/wiki/Brij_Narayan_Chakbast

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