Relevant bibliographies by topics / Genomic phylostratigraphy

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Conference papers

Academic literature on the topic 'Genomic phylostratigraphy'

Author: Grafiati
Published: 2 June 2025
Last updated: 31 July 2025

Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles

Select a source type:

Consult the lists of relevant articles, books, theses, conference reports, and other scholarly sources on the topic 'Genomic phylostratigraphy.'

Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.

You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.

Journal articles on the topic "Genomic phylostratigraphy"

1

Moyers, Bryan A., and Jianzhi Zhang. "Phylostratigraphic Bias Creates Spurious Patterns of Genome Evolution." Molecular Biology and Evolution 32, no. 1 (2014): 258–67. http://dx.doi.org/10.1093/molbev/msu286.

Full text
Abstract:
Phylostratigraphy is a method for dating the evolutionary emergence of a gene or gene family by identifying its homologs across the tree of life, typically by using BLAST searches. Applying this method to all genes in a species, or genomic phylostratigraphy, allows investigation of genome-wide patterns in new gene origination at different evolutionary times and thus has been extensively used. However, gene age estimation depends on the challenging task of detecting distant homologs via sequence similarity, which is expected to have differential accuracies for different genes. Here, we evaluate
APA, Harvard, Vancouver, ISO, and other styles
2

Domazet-Lošo, Tomislav, Josip Brajković, and Diethard Tautz. "A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages." Trends in Genetics 23, no. 11 (2007): 533–39. http://dx.doi.org/10.1016/j.tig.2007.08.014.

Full text
APA, Harvard, Vancouver, ISO, and other styles
3

Shi, Lei, Abderahmane Derouiche, Santosh Pandit, et al. "Evolutionary Analysis of the Bacillus subtilis Genome Reveals New Genes Involved in Sporulation." Molecular Biology and Evolution 37, no. 6 (2020): 1667–78. http://dx.doi.org/10.1093/molbev/msaa035.

Full text
Abstract:
Abstract Bacilli can form dormant, highly resistant, and metabolically inactive spores to cope with extreme environmental challenges. In this study, we examined the evolutionary age of Bacillus subtilis sporulation genes using the approach known as genomic phylostratigraphy. We found that B. subtilis sporulation genes cluster in several groups that emerged at distant evolutionary time-points, suggesting that the sporulation process underwent several stages of expansion. Next, we asked whether such evolutionary stratification of the genome could be used to predict involvement in sporulation of
APA, Harvard, Vancouver, ISO, and other styles
4

Nesterenko, Maksim, and Aleksei Miroliubov. "From head to rootlet: comparative transcriptomic analysis of a rhizocephalan barnacle Peltogaster reticulata (Crustacea: Rhizocephala)." F1000Research 11 (May 27, 2022): 583. http://dx.doi.org/10.12688/f1000research.110492.1.

Full text
Abstract:
Background: Rhizocephalan barnacles stand out in the diverse world of metazoan parasites. The body of a rhizocephalan female is modified beyond revealing any recognizable morphological features, consisting of the interna, the system of rootlets, and the externa, a sac-like reproductive body. Moreover, rhizocephalans have an outstanding ability to control their hosts, literally turning them into “zombies”. Despite all these amazing traits, there is no genomic and transcriptomic data about any Rhizocephala. Methods: We collected transcriptomes from four body parts of an adult female rhizocephala
APA, Harvard, Vancouver, ISO, and other styles
5

Nesterenko, Maksim, and Aleksei Miroliubov. "From head to rootlet: comparative transcriptomic analysis of a rhizocephalan barnacle Peltogaster reticulata (Crustacea: Rhizocephala)." F1000Research 11 (January 9, 2023): 583. http://dx.doi.org/10.12688/f1000research.110492.2.

Full text
Abstract:
Background: Rhizocephalan barnacles stand out in the diverse world of metazoan parasites. The body of a rhizocephalan female is modified beyond revealing any recognizable morphological features, consisting of the interna, a system of rootlets, and the externa, a sac-like reproductive body. Moreover, rhizocephalans have an outstanding ability to control their hosts, literally turning them into “zombies”. Despite all these amazing traits, there are no genomic or transcriptomic data about any Rhizocephala. Methods: We collected transcriptomes from four body parts of an adult female rhizocephalan
APA, Harvard, Vancouver, ISO, and other styles
6

Ivanov, R. A., A. M. Mukhin, F. V. Kazantsev, et al. "Orthoweb: a software package for evolutionary analysis of gene networks." Vavilov Journal of Genetics and Breeding 28, no. 8 (2025): 874–81. https://doi.org/10.18699/vjgb-24-95.

Full text
Abstract:
This article introduces Orthoweb (https://orthoweb.sysbio.cytogen.ru/), a software package developed for the calculation of evolutionary indices, including phylostratigraphic indices and divergence indices (Ka/Ks) for individual genes as well as for gene networks. The phylostratigraphic age index (PAI) allows the evolutionary stage of a gene’s emergence (and thus indirectly the approximate time of its origin, known as “evolutionary age”) to be assessed based on the analysis of orthologous genes across closely and distantly related taxa. Additionally, Orthoweb supports the calculation of the tr
APA, Harvard, Vancouver, ISO, and other styles
7

Glover, Natasha, Christophe Dessimoz, Ingo Ebersberger, et al. "Advances and Applications in the Quest for Orthologs." Molecular Biology and Evolution 36, no. 10 (2019): 2157–64. http://dx.doi.org/10.1093/molbev/msz150.

Full text
Abstract:
Abstract Gene families evolve by the processes of speciation (creating orthologs), gene duplication (paralogs), and horizontal gene transfer (xenologs), in addition to sequence divergence and gene loss. Orthologs in particular play an essential role in comparative genomics and phylogenomic analyses. With the continued sequencing of organisms across the tree of life, the data are available to reconstruct the unique evolutionary histories of tens of thousands of gene families. Accurate reconstruction of these histories, however, is a challenging computational problem, and the focus of the Quest
APA, Harvard, Vancouver, ISO, and other styles
8

Jers, Carsten, Hrvoje Mišetić, Vaishnavi Ravikumar, et al. "Gene age and genome organization in Escherichia coli and Bacillus subtilis." Frontiers in Microbiology 16 (June 18, 2025). https://doi.org/10.3389/fmicb.2025.1512923.

Full text
Abstract:
Using genomic phylostratigraphy, we examined the organization of Escherichia coli and Bacillus subtilis genomes from the perspective of evolutionary age of their genes. Phylostratigraphy analysis classifies individual genes into age-related bins, called phylostrata. Based on this analysis, several common features emerged in the genomes of the two model bacteria. More recent genes tend to be shorter and are expressed less frequently, or only in specific conditions. In terms of genomic location, new genes are enriched in areas containing prophages, suggesting a link with horizontal gene transfer
APA, Harvard, Vancouver, ISO, and other styles
9

Sestak, Martin Sebastijan, Vedran Bozicevic, Robert Bakaric, Vedran Dunjko, and Tomislav Domazet-Loso. "Phylostratigraphic profiles reveal a deep evolutionary history of the vertebrate head sensory systems." April 12, 2013. https://doi.org/10.1186/1742-9994-10-18.

Full text
Abstract:
Background The vertebrate head is a highly derived trait with a heavy concentration of sophisticated sensory organs that allow complex behaviour in this lineage. The head sensory structures arise during vertebrate development from cranial placodes and the neural crest. It is generally thought that derivatives of these ectodermal embryonic tissues played a central role in the evolutionary transition at the onset of vertebrates. Despite the obvious importance of head sensory organs for vertebrate biology, their evolutionary history is still uncertain. Results To give a fresh perspective on the a
APA, Harvard, Vancouver, ISO, and other styles
10

Barrera-Redondo, Josué, Jaruwatana Sodai Lotharukpong, Hajk-Georg Drost, and Susana M. Coelho. "Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra." Genome Biology 24, no. 1 (2023). http://dx.doi.org/10.1186/s13059-023-02895-z.

Full text
Abstract:
AbstractWe present GenEra (https://github.com/josuebarrera/GenEra), a DIAMOND-fueled gene-family founder inference framework that addresses previously raised limitations and biases in genomic phylostratigraphy, such as homology detection failure. GenEra also reduces computational time from several months to a few days for any genome of interest. We analyze the emergence of taxonomically restricted gene families during major evolutionary transitions in plants, animals, and fungi. Our results indicate that the impact of homology detection failure on inferred patterns of gene emergence is lineage
APA, Harvard, Vancouver, ISO, and other styles
More sources

Dissertations / Theses on the topic "Genomic phylostratigraphy"

1

Chen, Cho-Yi, and 陳卓逸. "Dissecting Human Protein Interactome and MicroRNARegulome via Genomic Phylostratigraphy Analysis." Thesis, 2015. http://ndltd.ncl.edu.tw/handle/12491501907290456531.

Full text
Abstract:
博士<br>國立臺灣大學<br>基因體與系統生物學學位學程<br>103<br>Genomic phylostratigraphy has been demonstrated as a powerful strategy to systematically study various biology questions. Here we made an attempt to utilize this technique in biological network contexts to study several issues that still remained unexplored in the fields of protein interactome and miRNA reg-ulome. In network biology, the protein-protein interaction (PPI) network offers a conceptual framework for better understanding the functional organization of the proteome. However, typical network analyses focused only on the topo-logical space, thu
APA, Harvard, Vancouver, ISO, and other styles

Conference papers on the topic "Genomic phylostratigraphy"

1

"Phylostratigraphic approach in evolutionary analysis: comparison of methods." In Bioinformatics of Genome Regulation and Structure/ Systems Biology. institute of cytology and genetics siberian branch of the russian academy of science, Novosibirsk State University, 2020. http://dx.doi.org/10.18699/bgrs/sb-2020-141.

Full text
APA, Harvard, Vancouver, ISO, and other styles
2

"792 BGRS/SB-2022 Phylostratigraphic analysis of human cancers transcriptomic data." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-457.

Full text
APA, Harvard, Vancouver, ISO, and other styles
You might also be interested in the extended bibliographies on the topic 'Genomic phylostratigraphy' for particular source types:
Journal articles
We offer discounts on all premium plans for authors whose works are included in thematic literature selections. Contact us to get a unique promo code!

To the bibliography