Mediaboss Marketing

Fish, F. E. Transitions from drag-based to lift-based propulsion in mammalian swimming. Am. Zool. 36, 628641 (1996).

Article Google Scholar

Ashley-Ross, M. A., Hsieh, S. T., Gibb, A. C. & Blob, R. W. Vertebrate land invasions-past, present, and future: An introduction to the symposium. Integr. Comp. Biol. 53, 192196 (2013).

Article PubMed Google Scholar

Zimmer, C. At the Waters Edge: Fish with Fingers, Whales with Legs, and How Life Came Ashore but Then Went Back to Sea (Simon and Schuster, 2014).

Google Scholar

Ruiz-Herrera, A. & Robinson, T. J. Chromosomal instability in Afrotheria: Fragile sites, evolutionary breakpoints and phylogenetic inference from genome sequence assemblies. BMC Evol. Biol. 7, 199 (2007).

Article PubMed PubMed Central Google Scholar

Dececchi, T. A. & Larsson, H. C. E. Body and limb size dissociation at the origin of birds: Uncoupling allometric constraints across a macroevolutionary transition. Evolution 67, 27412752 (2013).

Article PubMed Google Scholar

Behrens, M., Di Pizio, A., Redel, U., Meyerhof, W. & Korsching, S. I. At the Root of T2R Gene Evolution: Recognition Profiles of Coelacanth and Zebrafish Bitter Receptors. Genome Biol Evol 13, evaa264 (2021).

Hannisdal, B. & Peters, S. E. Phanerozoic Earth system evolution and marine biodiversity. Science 334, 11211124 (2011).

Article ADS CAS PubMed Google Scholar

Mayhew, P. J., Bell, M. A., Benton, T. G. & McGowan, A. J. Biodiversity tracks temperature over time. Proc. Natl. Acad. Sci. U. S. A. 109, 1514115145 (2012).

Article ADS CAS PubMed PubMed Central Google Scholar

Doyle, J. J. & Egan, A. N. Dating the origins of polyploidy events. New Phytol. 186, 7385 (2010).

Article PubMed Google Scholar

Clark, J. W. & Donoghue, P. C. J. Whole-genome duplication and plant macroevolution. Trends Plant Sci. 23, 933945 (2018).

Article CAS PubMed Google Scholar

Clark, J. W., Puttick, M. N. & Donoghue, P. C. J. Origin of horsetails and the role of whole-genome duplication in plant macroevolution. Proc. Biol. Sci. 286, 20191662 (2019).

PubMed PubMed Central Google Scholar

Guo, B., Wagner, A. & He, S. Duplicated gene evolution following wholegenome duplication in teleost Fish. Gene Duplic. 27, 36 (2011).

Google Scholar

Schwager, E. E. et al. The house spider genome reveals an ancient whole-genome duplication during arachnid evolution. BMC Biol. 15, 62 (2017).

Article PubMed PubMed Central Google Scholar

Fan, Z. et al. A chromosome-level genome of the spider Trichonephila antipodiana reveals the genetic basis of its polyphagy and evidence of an ancient whole-genome duplication event. Gigascience 10, giab016. https://doi.org/10.1093/gigascience/giab016 (2021).

Article CAS PubMed PubMed Central Google Scholar

Baumholtz, A. I., Gupta, I. R. & Ryan, A. K. Claudins in morphogenesis: Forming an epithelial tube. Tissue Barriers 5, e1361899 (2017).

Article PubMed PubMed Central Google Scholar

Hughes, G. M. et al. The birth and death of olfactory receptor gene families in mammalian niche adaptation. Mol. Biol. Evol. 35, 13901406 (2018).

Article CAS PubMed PubMed Central Google Scholar

Ground tit genome reveals avian adaptation to living at high altitudes in the Tibetan plateau | Nature Communications. https://www.nature.com/articles/ncomms3071.

Sondhi, Y., Ellis, E. A., Bybee, S. M., Theobald, J. C. & Kawahara, A. Y. Light environment drives evolution of color vision genes in butterflies and moths. Commun. Biol. 4, 177 (2021).

Article CAS PubMed PubMed Central Google Scholar

Timmermans, M. J. T. N., Srivathsan, A., Collins, S., Meier, R. & Vogler, A. P. Mimicry diversification in Papilio dardanus via a genomic inversion in the regulatory region of engrailed-invected. Proc. Biol. Sci. 287, 20200443 (2020).

CAS PubMed PubMed Central Google Scholar

Hayward, A., Cornwallis, C. K. & Jern, P. Pan-vertebrate comparative genomics unmasks retrovirus macroevolution. Proc. Natl. Acad. Sci. U. S. A. 112, 464469 (2015).

Article ADS CAS PubMed Google Scholar

Zhang, G. et al. Comparative genomics reveals insights into avian genome evolution and adaptation. Science 346, 13111320 (2014).

Article ADS CAS PubMed PubMed Central Google Scholar

Li, H. et al. Panoramic insights into microevolution and macroevolution of a prevotella copri-containing lineage in primate guts. Genom. Proteom. Bioinform. 20, 334349 (2022).

Article Google Scholar

Larraaga, P. et al. Machine learning in bioinformatics. Brief. Bioinform. 7, 86112 (2006).

Article PubMed Google Scholar

Leung et al. Machine Learning in Genomic Medicine: A Review of Computational Problems and Data Sets. (2015).

Hroza & Ji. Protein secondary structure prediction by machine learning methods. Bioinformatics 14, 892893 (2005).

Min, S., Lee, B. & Yoon, S. Deep learning in bioinformatics. Brief. Bioinform. 18, 851869 (2017).

PubMed Google Scholar

Li, Y. et al. Deep learning in bioinformatics: Introduction, application, and perspective in the big data era. Methods 166, 421 (2019).

Article CAS PubMed Google Scholar

Wang, W. & Gao, X. Deep learning in bioinformatics. Methods 166, 13 (2019).

Article PubMed Google Scholar

Li, H. et al. Modern deep learning in bioinformatics. J. Mol. Cell Biol. 12, 823827 (2020).

Article PubMed PubMed Central Google Scholar

Berrar, D. & Dubitzky, W. Deep learning in bioinformatics and biomedicine. Brief. Bioinform. 22, 15131514 (2021).

Article PubMed PubMed Central Google Scholar

Attention is all you need Proceedings of the 31st International Conference on Neural Information Processing Systems. https://doi.org/10.5555/3295222.3295349.

Hong, J., Gao, R. & Yang, Y. CrepHAN: Cross-species prediction of enhancers by using hierarchical attention networks. Bioinformatics https://doi.org/10.1093/bioinformatics/btab349 (2021).

Article PubMed PubMed Central Google Scholar

Fergadis, A., Baziotis, C., Pappas, D., Papageorgiou, H. & Potamianos, A. Hierarchical bi-directional attention-based RNNs for supporting document classification on protein-protein interactions affected by genetic mutations. Database (Oxford) https://doi.org/10.1093/database/bay076 (2018).

Article PubMed Google Scholar

Mei, Y. et al. InsectBase 2.0: A comprehensive gene resource for insects. Nucleic Acids Res. 50, D1040D1045 (2022).

Article ADS CAS PubMed Google Scholar

Barber, J. Diel behavior in moths and butterflies: A synthesis of data illuminates the evolution of temporal activity. Organ. Divers. Evol. https://doi.org/10.1007/s13127-017-0350-6 (2018).

Article Google Scholar

Chen, L., Fish, A. E. & Capra, J. A. Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties. PLoS Comput. Biol. 14, e1006484 (2018).

Article ADS PubMed PubMed Central Google Scholar

Mikolov, T., Sutskever, I., Chen, K., Corrado, G. & Dean, J. Distributed Representations of Words and Phrases and their Compositionality. Preprint at http://arxiv.org/abs/1310.4546 (2013).

Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 15471549 (2018).

Article CAS PubMed PubMed Central Google Scholar

Ogueta, M., Hardie, R. C. & Stanewsky, R. Non-canonical phototransduction mediates synchronization of the drosophila melanogaster circadian clock and retinal light responses. Curr. Biol. 28, 1725-1735.e3 (2018).

Article CAS PubMed PubMed Central Google Scholar

Ogueta, M., Hardie, R. C. & Stanewsky, R. Light sampling via throttled visual phototransduction robustly synchronizes the drosophila circadian clock. Curr. Biol. 30, 2551-2563.e3 (2020).

Article CAS PubMed Google Scholar

Curtis, A. M. et al. Histone acetyltransferase-dependent chromatin remodeling and the vascular clock. J. Biol. Chem. 279, 70917097 (2004).

Article CAS PubMed Google Scholar

Cai, Y. D. & Chiu, J. C. Timeless in animal circadian clocks and beyond. FEBS J. 289, 65596575 (2022).

Article CAS PubMed Google Scholar

Zheng, X., Yang, Z., Yue, Z., Alvarez, J. D. & Sehgal, A. FOXO and insulin signaling regulate sensitivity of the circadian clock to oxidative stress. Proc. Natl. Acad. Sci. U. S. A. 104, 1589915904 (2007).

Article ADS CAS PubMed PubMed Central Google Scholar

Saint-Charles, A. et al. Four of the six Drosophila rhodopsin-expressing photoreceptors can mediate circadian entrainment in low light. J. Comp. Neurol. 524, 28282844 (2016).

Article CAS PubMed Google Scholar

Liu, W. et al. Dibutyl phthalate disrupts conserved circadian rhythm in Drosophila and human cells. Sci. Total Environ. 783, 147038 (2021).

Article ADS CAS PubMed Google Scholar

So, W. V. et al. takeout, a novel Drosophila gene under circadian clock transcriptional regulation. Mol. Cell. Biol. 20, 69356944 (2000).

Article CAS PubMed PubMed Central Google Scholar

Yang, Y. & Edery, I. Daywake, an anti-siesta gene linked to a splicing-based thermostat from an adjoining clock gene. Curr. Biol. 29, 1728-1734.e4 (2019).

Article CAS PubMed PubMed Central Google Scholar

Jang, A. R., Moravcevic, K., Saez, L., Young, M. W. & Sehgal, A. Drosophila TIM binds importin 1, and acts as an adapter to transport PER to the nucleus. PLoS Genet. 11, e1004974 (2015).

Article PubMed PubMed Central Google Scholar

Pagel, M., ODonovan, C. & Meade, A. General statistical model shows that macroevolutionary patterns and processes are consistent with Darwinian gradualism. Nat. Commun. 13, 1113 (2022).

Article ADS CAS PubMed PubMed Central Google Scholar

Molecular phylogeny and macroevolution of Chaitophorinae aphids (Insecta: Hemiptera: Aphididae). Systematic Entomology (2021) doi:https://doi.org/10.1111/syen.12531.

Bagchi, B. et al. Sexual conflict drives micro- and macroevolution of sexual dimorphism in immunity. BMC Biol. 19, 114 (2021).

Article PubMed PubMed Central Google Scholar

Alencar, L. R. V. & Quental, T. B. Exploring the drivers of population structure across desert snakes can help to link micro and macroevolution. Mol. Ecol. 28, 45294532 (2019).

Article PubMed Google Scholar

Zou, Q., Xing, P., Wei, L. & Liu, B. Gene2vec: gene subsequence embedding for prediction of mammalian N6-methyladenosine sites from mRNA. RNA 25, 205218 (2019).

Article CAS PubMed PubMed Central Google Scholar

Hoinka, J. & Przytycka, T. M. Embedding gene sets in low-dimensional space. Nat. Mach. Intell. 2, 367368 (2020).

See the article here:
A novel method for identifying key genes in macroevolution based ... - Nature.com