Genomic phylostratigraphy (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "Genomic phylostratigraphy" in English language version.

refsWebsite

Global rank English rank

25nih.gov

4^th place

17doi.org

2^nd place

3harvard.edu

18^th place

17^th place

3semanticscholar.org

11^th place

8^th place

doi.org

Domazet-Loso T, Brajković J, Tautz D (November 2007). "A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages". Trends in Genetics. 23 (11): 533–539. doi:10.1016/j.tig.2007.08.014. PMID 18029048.
Barrera-Redondo, Josué; Lotharukpong, Jaruwatana Sodai; Drost, Hajk-Georg; Coelho, Susana M. (24 March 2023). "Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra". Genome Biology. 24 (1): 1552–1554. doi:10.1186/s13059-023-02895-z. PMC 10037820. PMID 10037820.
Arendsee Z, Li J, Singh U, Seetharam A, Dorman K, Wurtele ES (October 2019). "phylostratr: a framework for phylostratigraphy". Bioinformatics. 35 (19): 3617–3627. bioRxiv 10.1101/360164. doi:10.1093/bioinformatics/btz171. PMID 30873536.
Buchfink, Benjamin; Reuter, Klaus; Drost, Hajk-Georg (April 2021). "Sensitive protein alignments at tree-of-life scale using DIAMOND". Nature Methods. 18 (4): 366–368. doi:10.1038/s41592-021-01101-x. PMC 8026399. PMID 33828273.
Domazet-Loso T, Tautz D (May 2010). "Phylostratigraphic tracking of cancer genes suggests a link to the emergence of multicellularity in metazoa". BMC Biology. 8 (1): 66. doi:10.1186/1741-7007-8-66. PMC 2880965. PMID 20492640.
Zhang L, Tan Y, Fan S, Zhang X, Zhang Z (February 2019). "Phylostratigraphic analysis of gene co-expression network reveals the evolution of functional modules for ovarian cancer". Scientific Reports. 9 (1): 2623. Bibcode:2019NatSR...9.2623Z. doi:10.1038/s41598-019-40023-9. PMC 6384884. PMID 30796309.
Domazet-Lošo T, Tautz D (December 2010). "A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns". Nature. 468 (7325): 815–818. Bibcode:2010Natur.468..815D. doi:10.1038/nature09632. PMID 21150997. S2CID 1417664.
Quint M, Drost HG, Gabel A, Ullrich KK, Bönn M, Grosse I (October 2012). "A transcriptomic hourglass in plant embryogenesis". Nature. 490 (7418): 98–101. Bibcode:2012Natur.490...98Q. doi:10.1038/nature11394. PMID 22951968. S2CID 4404460.
Cheng X, Hui JH, Lee YY, Wan Law PT, Kwan HS (June 2015). "A "developmental hourglass" in fungi". Molecular Biology and Evolution. 32 (6): 1556–1566. doi:10.1093/molbev/msv047. PMID 25725429.
Xie Y, Kwan HS, Chan PL, Wu W, Chiou J, Chang J (2022-07-16). "The Phylotranscriptomic Hourglass Pattern in Fungi: An Updated Model". bioRxiv: 2022.07.14.500038. doi:10.1101/2022.07.14.500038. S2CID 250646039.
Futo M, Opašić L, Koska S, Čorak N, Široki T, Ravikumar V, et al. (January 2021). "Embryo-Like Features in Developing Bacillus subtilis Biofilms". Molecular Biology and Evolution. 38 (1): 31–47. doi:10.1093/molbev/msaa217. PMC 7783165. PMID 32871001.
Moyers BA, Zhang J (January 2015). "Phylostratigraphic bias creates spurious patterns of genome evolution". Molecular Biology and Evolution. 32 (1): 258–267. doi:10.1093/molbev/msu286. PMC 4271527. PMID 25312911.
Casola C (November 2018). "From De Novo to "De Nono": The Majority of Novel Protein-Coding Genes Identified with Phylostratigraphy Are Old Genes or Recent Duplicates". Genome Biology and Evolution. 10 (11): 2906–2918. doi:10.1093/gbe/evy231. PMC 6239577. PMID 30346517.
Moyers BA, Zhang J (August 2018). Martin B (ed.). "Toward Reducing Phylostratigraphic Errors and Biases". Genome Biology and Evolution. 10 (8): 2037–2048. doi:10.1093/gbe/evy161. PMC 6105108. PMID 30060201.
Domazet-Lošo T, Carvunis AR, Albà MM, Šestak MS, Bakaric R, Neme R, Tautz D (April 2017). "No Evidence for Phylostratigraphic Bias Impacting Inferences on Patterns of Gene Emergence and Evolution". Molecular Biology and Evolution. 34 (4): 843–856. doi:10.1093/molbev/msw284. PMC 5400388. PMID 28087778.
Tautz, Diethard; Domazet-Lošo, Tomislav (October 2011). "The evolutionary origin of orphan genes". Nature Reviews Genetics. 12 (10): 692–702. doi:10.1038/nrg3053.
Weisman, Caroline M.; Murray, Andrew W.; Eddy, Sean R. (2 November 2020). "Many, but not all, lineage-specific genes can be explained by homology detection failure". PLOS Biology. 18 (11): e3000862. doi:10.1371/journal.pbio.3000862. PMC 7660931. PMID 33137085.

harvard.edu

ui.adsabs.harvard.edu

Zhang L, Tan Y, Fan S, Zhang X, Zhang Z (February 2019). "Phylostratigraphic analysis of gene co-expression network reveals the evolution of functional modules for ovarian cancer". Scientific Reports. 9 (1): 2623. Bibcode:2019NatSR...9.2623Z. doi:10.1038/s41598-019-40023-9. PMC 6384884. PMID 30796309.
Domazet-Lošo T, Tautz D (December 2010). "A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns". Nature. 468 (7325): 815–818. Bibcode:2010Natur.468..815D. doi:10.1038/nature09632. PMID 21150997. S2CID 1417664.
Quint M, Drost HG, Gabel A, Ullrich KK, Bönn M, Grosse I (October 2012). "A transcriptomic hourglass in plant embryogenesis". Nature. 490 (7418): 98–101. Bibcode:2012Natur.490...98Q. doi:10.1038/nature11394. PMID 22951968. S2CID 4404460.

nih.gov

pubmed.ncbi.nlm.nih.gov

Domazet-Loso T, Brajković J, Tautz D (November 2007). "A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages". Trends in Genetics. 23 (11): 533–539. doi:10.1016/j.tig.2007.08.014. PMID 18029048.
Barrera-Redondo, Josué; Lotharukpong, Jaruwatana Sodai; Drost, Hajk-Georg; Coelho, Susana M. (24 March 2023). "Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra". Genome Biology. 24 (1): 1552–1554. doi:10.1186/s13059-023-02895-z. PMC 10037820. PMID 10037820.
Arendsee Z, Li J, Singh U, Seetharam A, Dorman K, Wurtele ES (October 2019). "phylostratr: a framework for phylostratigraphy". Bioinformatics. 35 (19): 3617–3627. bioRxiv 10.1101/360164. doi:10.1093/bioinformatics/btz171. PMID 30873536.
Buchfink, Benjamin; Reuter, Klaus; Drost, Hajk-Georg (April 2021). "Sensitive protein alignments at tree-of-life scale using DIAMOND". Nature Methods. 18 (4): 366–368. doi:10.1038/s41592-021-01101-x. PMC 8026399. PMID 33828273.
Domazet-Loso T, Tautz D (May 2010). "Phylostratigraphic tracking of cancer genes suggests a link to the emergence of multicellularity in metazoa". BMC Biology. 8 (1): 66. doi:10.1186/1741-7007-8-66. PMC 2880965. PMID 20492640.
Zhang L, Tan Y, Fan S, Zhang X, Zhang Z (February 2019). "Phylostratigraphic analysis of gene co-expression network reveals the evolution of functional modules for ovarian cancer". Scientific Reports. 9 (1): 2623. Bibcode:2019NatSR...9.2623Z. doi:10.1038/s41598-019-40023-9. PMC 6384884. PMID 30796309.
Domazet-Lošo T, Tautz D (December 2010). "A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns". Nature. 468 (7325): 815–818. Bibcode:2010Natur.468..815D. doi:10.1038/nature09632. PMID 21150997. S2CID 1417664.
Quint M, Drost HG, Gabel A, Ullrich KK, Bönn M, Grosse I (October 2012). "A transcriptomic hourglass in plant embryogenesis". Nature. 490 (7418): 98–101. Bibcode:2012Natur.490...98Q. doi:10.1038/nature11394. PMID 22951968. S2CID 4404460.
Cheng X, Hui JH, Lee YY, Wan Law PT, Kwan HS (June 2015). "A "developmental hourglass" in fungi". Molecular Biology and Evolution. 32 (6): 1556–1566. doi:10.1093/molbev/msv047. PMID 25725429.
Futo M, Opašić L, Koska S, Čorak N, Široki T, Ravikumar V, et al. (January 2021). "Embryo-Like Features in Developing Bacillus subtilis Biofilms". Molecular Biology and Evolution. 38 (1): 31–47. doi:10.1093/molbev/msaa217. PMC 7783165. PMID 32871001.
Moyers BA, Zhang J (January 2015). "Phylostratigraphic bias creates spurious patterns of genome evolution". Molecular Biology and Evolution. 32 (1): 258–267. doi:10.1093/molbev/msu286. PMC 4271527. PMID 25312911.
Casola C (November 2018). "From De Novo to "De Nono": The Majority of Novel Protein-Coding Genes Identified with Phylostratigraphy Are Old Genes or Recent Duplicates". Genome Biology and Evolution. 10 (11): 2906–2918. doi:10.1093/gbe/evy231. PMC 6239577. PMID 30346517.
Moyers BA, Zhang J (August 2018). Martin B (ed.). "Toward Reducing Phylostratigraphic Errors and Biases". Genome Biology and Evolution. 10 (8): 2037–2048. doi:10.1093/gbe/evy161. PMC 6105108. PMID 30060201.
Domazet-Lošo T, Carvunis AR, Albà MM, Šestak MS, Bakaric R, Neme R, Tautz D (April 2017). "No Evidence for Phylostratigraphic Bias Impacting Inferences on Patterns of Gene Emergence and Evolution". Molecular Biology and Evolution. 34 (4): 843–856. doi:10.1093/molbev/msw284. PMC 5400388. PMID 28087778.
Weisman, Caroline M.; Murray, Andrew W.; Eddy, Sean R. (2 November 2020). "Many, but not all, lineage-specific genes can be explained by homology detection failure". PLOS Biology. 18 (11): e3000862. doi:10.1371/journal.pbio.3000862. PMC 7660931. PMID 33137085.

ncbi.nlm.nih.gov

Barrera-Redondo, Josué; Lotharukpong, Jaruwatana Sodai; Drost, Hajk-Georg; Coelho, Susana M. (24 March 2023). "Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra". Genome Biology. 24 (1): 1552–1554. doi:10.1186/s13059-023-02895-z. PMC 10037820. PMID 10037820.
Buchfink, Benjamin; Reuter, Klaus; Drost, Hajk-Georg (April 2021). "Sensitive protein alignments at tree-of-life scale using DIAMOND". Nature Methods. 18 (4): 366–368. doi:10.1038/s41592-021-01101-x. PMC 8026399. PMID 33828273.
Domazet-Loso T, Tautz D (May 2010). "Phylostratigraphic tracking of cancer genes suggests a link to the emergence of multicellularity in metazoa". BMC Biology. 8 (1): 66. doi:10.1186/1741-7007-8-66. PMC 2880965. PMID 20492640.
Zhang L, Tan Y, Fan S, Zhang X, Zhang Z (February 2019). "Phylostratigraphic analysis of gene co-expression network reveals the evolution of functional modules for ovarian cancer". Scientific Reports. 9 (1): 2623. Bibcode:2019NatSR...9.2623Z. doi:10.1038/s41598-019-40023-9. PMC 6384884. PMID 30796309.
Futo M, Opašić L, Koska S, Čorak N, Široki T, Ravikumar V, et al. (January 2021). "Embryo-Like Features in Developing Bacillus subtilis Biofilms". Molecular Biology and Evolution. 38 (1): 31–47. doi:10.1093/molbev/msaa217. PMC 7783165. PMID 32871001.
Moyers BA, Zhang J (January 2015). "Phylostratigraphic bias creates spurious patterns of genome evolution". Molecular Biology and Evolution. 32 (1): 258–267. doi:10.1093/molbev/msu286. PMC 4271527. PMID 25312911.
Casola C (November 2018). "From De Novo to "De Nono": The Majority of Novel Protein-Coding Genes Identified with Phylostratigraphy Are Old Genes or Recent Duplicates". Genome Biology and Evolution. 10 (11): 2906–2918. doi:10.1093/gbe/evy231. PMC 6239577. PMID 30346517.
Moyers BA, Zhang J (August 2018). Martin B (ed.). "Toward Reducing Phylostratigraphic Errors and Biases". Genome Biology and Evolution. 10 (8): 2037–2048. doi:10.1093/gbe/evy161. PMC 6105108. PMID 30060201.
Domazet-Lošo T, Carvunis AR, Albà MM, Šestak MS, Bakaric R, Neme R, Tautz D (April 2017). "No Evidence for Phylostratigraphic Bias Impacting Inferences on Patterns of Gene Emergence and Evolution". Molecular Biology and Evolution. 34 (4): 843–856. doi:10.1093/molbev/msw284. PMC 5400388. PMID 28087778.
Weisman, Caroline M.; Murray, Andrew W.; Eddy, Sean R. (2 November 2020). "Many, but not all, lineage-specific genes can be explained by homology detection failure". PLOS Biology. 18 (11): e3000862. doi:10.1371/journal.pbio.3000862. PMC 7660931. PMID 33137085.

semanticscholar.org

api.semanticscholar.org

Domazet-Lošo T, Tautz D (December 2010). "A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns". Nature. 468 (7325): 815–818. Bibcode:2010Natur.468..815D. doi:10.1038/nature09632. PMID 21150997. S2CID 1417664.
Quint M, Drost HG, Gabel A, Ullrich KK, Bönn M, Grosse I (October 2012). "A transcriptomic hourglass in plant embryogenesis". Nature. 490 (7418): 98–101. Bibcode:2012Natur.490...98Q. doi:10.1038/nature11394. PMID 22951968. S2CID 4404460.
Xie Y, Kwan HS, Chan PL, Wu W, Chiou J, Chang J (2022-07-16). "The Phylotranscriptomic Hourglass Pattern in Fungi: An Updated Model". bioRxiv: 2022.07.14.500038. doi:10.1101/2022.07.14.500038. S2CID 250646039.