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Journal articles on the topic 'Comparative genomics'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 July 2025

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1

Furlong, Rebecca F., and Ziheng Yang. "Comparative genomics: Comparative genomics coming of age." Heredity 91, no. 6 (2003): 533–34. http://dx.doi.org/10.1038/sj.hdy.6800372.

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2

HURST, L. D. "Comparative Genomics." Journal of Medical Genetics 38, no. 11 (2001): 807. http://dx.doi.org/10.1136/jmg.38.11.807.

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3

Hardison, Ross C. "Comparative Genomics." PLoS Biology 1, no. 2 (2003): e58. http://dx.doi.org/10.1371/journal.pbio.0000058.

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4

Hochachka✠, P., T. P. Mommsen, and P. Walsh. "Comparative Genomics." Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology 133, no. 4 (2002): 461–62. http://dx.doi.org/10.1016/s1096-4959(02)00170-7.

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5

Elgar, G. "Comparative Genomics." Briefings in Bioinformatics 2, no. 2 (2001): 200–202. http://dx.doi.org/10.1093/bib/2.2.200.

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6

Miller, Webb, Kateryna D. Makova, Anton Nekrutenko, and Ross C. Hardison. "COMPARATIVE GENOMICS." Annual Review of Genomics and Human Genetics 5, no. 1 (2004): 15–56. http://dx.doi.org/10.1146/annurev.genom.5.061903.180057.

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7

Bachhawat, Anand K. "Comparative genomics." Resonance 11, no. 8 (2006): 22–40. http://dx.doi.org/10.1007/bf02855776.

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8

Copeland, N. G. "GENOMICS: Enhanced: Mmu 16--Comparative Genomic Highlights." Science 296, no. 5573 (2002): 1617–18. http://dx.doi.org/10.1126/science.1073127.

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9

Pain, Arnab, Lisa Crossman, and Julian Parkhill. "Comparative Apicomplexan genomics." Nature Reviews Microbiology 3, no. 6 (2005): 454–55. http://dx.doi.org/10.1038/nrmicro1174.

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10

Holding, Cathy. "Caenorhabditis comparative genomics." Genome Biology 4 (2003): spotlight—20031118–08. http://dx.doi.org/10.1186/gb-spotlight-20031118-02.

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11

Little, P. "Editorial: Comparative genomics." Briefings in Functional Genomics and Proteomics 3, no. 1 (2004): 5–6. http://dx.doi.org/10.1093/bfgp/3.1.5.

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12

Ranford-Cartwright, Lisa, and Elena Gómez-Díaz. "Plasmodium comparative genomics." Briefings in Functional Genomics 18, no. 5 (2019): 267–69. http://dx.doi.org/10.1093/bfgp/elz020.

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13

Cole, Stewart T. "Comparative mycobacterial genomics." Current Opinion in Microbiology 1, no. 5 (1998): 567–71. http://dx.doi.org/10.1016/s1369-5274(98)80090-8.

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14

Enard, Wolfgang, and Svante Pääbo. "COMPARATIVE PRIMATE GENOMICS." Annual Review of Genomics and Human Genetics 5, no. 1 (2004): 351–78. http://dx.doi.org/10.1146/annurev.genom.5.061903.180040.

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15

Mazurie, Aurélien J., João M. Alves, Luiz S. Ozaki, Shiguo Zhou, David C. Schwartz, and Gregory A. Buck. "Comparative Genomics ofCryptosporidium." International Journal of Genomics 2013 (2013): 1–8. http://dx.doi.org/10.1155/2013/832756.

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Until recently, the apicomplexan parasites,Cryptosporidium hominisandC. parvum, were considered the same species. However, the two parasites, now considered distinct species, exhibit significant differences in host range, infectivity, and pathogenicity, and their sequenced genomes exhibit only 95–97% identity. The availability of the complete genome sequences of these organisms provides the potential to identify the genetic variations that are responsible for the phenotypic differences between the two parasites. We compared the genome organization and structure, gene composition, the metabolic

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16

Jun, Se-Ran, Michael R. Leuze, Intawat Nookaew, et al. "Ebolavirus comparative genomics." FEMS Microbiology Reviews 39, no. 5 (2015): 764–78. https://doi.org/10.5281/zenodo.13536319.

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(Uploaded by Plazi for the Bat Literature Project) The 2014 Ebola outbreak in West Africa is the largest documented for this virus. To examine the dynamics of this genome, we compare more than 100 currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms a distinct group from all other sequenced viral genomes. All filovirus genomes sequenced to date encode proteins with similar functions and gene order, although there is considerable divergence in sequences between the three genera Ebolavirus, Cuevavirus

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17

Jun, Se-Ran, Michael R. Leuze, Intawat Nookaew, et al. "Ebolavirus comparative genomics." FEMS Microbiology Reviews 39, no. 5 (2015): 764–78. https://doi.org/10.5281/zenodo.13536319.

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(Uploaded by Plazi for the Bat Literature Project) The 2014 Ebola outbreak in West Africa is the largest documented for this virus. To examine the dynamics of this genome, we compare more than 100 currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms a distinct group from all other sequenced viral genomes. All filovirus genomes sequenced to date encode proteins with similar functions and gene order, although there is considerable divergence in sequences between the three genera Ebolavirus, Cuevavirus

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18

Froschauer, A., I. Braasch, and J. Volff. "Fish Genomes, Comparative Genomics and Vertebrate Evolution." Current Genomics 7, no. 1 (2006): 43–57. http://dx.doi.org/10.2174/138920206776389766.

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19

Hughes, Austin L. "Comparative Genomics: Genomes of mice and men." Heredity 90, no. 2 (2003): 115–16. http://dx.doi.org/10.1038/sj.hdy.6800222.

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20

Bofkin, L., and S. Whelan. "Comparative genomics: Functional needles in a genomic haystack." Heredity 92, no. 5 (2004): 363–64. http://dx.doi.org/10.1038/sj.hdy.6800429.

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21

Tan, Kenneth Lee Shean, and Saharuddin Bin Mohamad. "CFPG: Creating a Common Fungal Pathogenic Genes Database through Data Mining." Chiang Mai Journal of Science 51, no. 3 (2024): 1–11. http://dx.doi.org/10.12982/cmjs.2024.038.

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Fu ngal pathogenicity is one of the most vigorously tackled ecological and medicinal issues facing many scientists. Comparative genomics is an extremely important methodology and tool used to understand fungal pathogenicity, and it allows the development of early diagnostic tools for fungal-inflicted diseases across different host organisms. However, comparative genomics depends heavily on readily available fungal pathogenic gene databases to enable downstream genomics study and the development of new diagnosis and detection methods. Here, we have developed the Common Fungal Pathogenic Genes D

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22

Luban, Stanislav, and Daisuke Kihara. "Comparative Genomics of Small RNAs in Bacterial Genomes." OMICS: A Journal of Integrative Biology 11, no. 1 (2007): 58–73. http://dx.doi.org/10.1089/omi.2006.0005.

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23

Louis, Alexandra, Matthieu Muffato, and Hugues Roest Crollius. "Genomicus: five genome browsers for comparative genomics in eukaryota." Nucleic Acids Research 41, no. D1 (2012): D700—D705. http://dx.doi.org/10.1093/nar/gks1156.

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24

Craig, Rory J., Ahmed R. Hasan, Rob W. Ness, and Peter D. Keightley. "Comparative genomics of Chlamydomonas." Plant Cell 33, no. 4 (2021): 1016–41. http://dx.doi.org/10.1093/plcell/koab026.

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Abstract Despite its role as a reference organism in the plant sciences, the green alga Chlamydomonas reinhardtii entirely lacks genomic resources from closely related species. We present highly contiguous and well-annotated genome assemblies for three unicellular C. reinhardtii relatives: Chlamydomonas incerta, Chlamydomonas schloesseri, and the more distantly related Edaphochlamys debaryana. The three Chlamydomonas genomes are highly syntenous with similar gene contents, although the 129.2 Mb C. incerta and 130.2 Mb C. schloesseri assemblies are more repeat-rich than the 111.1 Mb C. reinhard

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25

Oliver, S. G. "Comparative and Functional Genomics." Yeast 1, no. 1 (2000): vii. http://dx.doi.org/10.1155/2000/672640.

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26

Esha Dogra , Prashant Singh, Esha Dogra ,. Prashant Singh. "Comparative Genomics - A Perspective." International Journal of Bio-Technology and Research 9, no. 1 (2019): 5–8. http://dx.doi.org/10.24247/ijbtrjun20192.

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27

Sivashankari, Selvarajan, and Piramanayagam Shanmughavel. "Comparative genomics - A perspective." Bioinformation 1, no. 9 (2007): 376–78. http://dx.doi.org/10.6026/97320630001376.

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28

Hori, Hiroshi, and Nori Satoh. "[Comparative Genomics of Animals]." Zoological Science 22, no. 12 (2005): 1377–79. http://dx.doi.org/10.2108/zsj.22.1377.

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29

Brüggemann, Holger, and Gerhard Gottschalk. "Comparative Genomics of Clostridia." Annals of the New York Academy of Sciences 1125, no. 1 (2008): 73–81. http://dx.doi.org/10.1196/annals.1419.021.

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30

Kant, Ravi, Jochen Blom, Airi Palva, Roland J. Siezen, and Willem M. de Vos. "Comparative genomics of Lactobacillus." Microbial Biotechnology 4, no. 3 (2010): 323–32. http://dx.doi.org/10.1111/j.1751-7915.2010.00215.x.

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31

Herrero, Javier, Matthieu Muffato, Kathryn Beal, et al. "Ensembl comparative genomics resources." Database 2016 (2016): bav096. http://dx.doi.org/10.1093/database/bav096.

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32

Herrero, Javier, Matthieu Muffato, Kathryn Beal, et al. "Ensembl comparative genomics resources." Database 2016 (2016): baw053. http://dx.doi.org/10.1093/database/baw053.

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33

Margulies, E. H. "Confidence in comparative genomics." Genome Research 18, no. 2 (2008): 199–200. http://dx.doi.org/10.1101/gr.7228008.

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34

Castresana, Jose. "Comparative genomics and bioenergetics." Biochimica et Biophysica Acta (BBA) - Bioenergetics 1506, no. 3 (2001): 147–62. http://dx.doi.org/10.1016/s0005-2728(01)00227-4.

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35

Keeling, Patrick J., Naomi M. Fast, Joyce S. Law, Bryony A. P. Williams, and Claudio H. Slamovits. "Comparative genomics of microsporidia." Folia Parasitologica 52, no. 1-2 (2005): 8–14. http://dx.doi.org/10.14411/fp.2005.002.

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36

Frederickson, Robert. "Comparative genomics in development." Nature Biotechnology 18, no. 2 (2000): 136. http://dx.doi.org/10.1038/72543.

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37

MITREVA, M., M. BLAXTER, D. BIRD, and J. MCCARTER. "Comparative genomics of nematodes." Trends in Genetics 21, no. 10 (2005): 573–81. http://dx.doi.org/10.1016/j.tig.2005.08.003.

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38

Oliver, S. G. "Comparative and Functional Genomics." Yeast 1, no. 1 (2000): vii. http://dx.doi.org/10.1002/(sici)1097-0061(200004)17:13.0.co;2-b.

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39

Vu, T. H. "Comparative Genomics Sheds Light on Mechanisms of Genomic Imprinting." Genome Research 10, no. 11 (2000): 1660–63. http://dx.doi.org/10.1101/gr.166200.

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40

Wang, Jiacheng, Yaojia Chen, and Quan Zou. "Comparative Genomics and Functional Genomics Analysis in Plants." International Journal of Molecular Sciences 24, no. 7 (2023): 6539. http://dx.doi.org/10.3390/ijms24076539.

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41

Lu, Yueqi, and Quan Zou. "Functional Genomics and Comparative Genomics Analysis in Plants." Current Issues in Molecular Biology 46, no. 12 (2024): 13780–82. https://doi.org/10.3390/cimb46120823.

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42

Alam, Intikhab, Mike Cornell, Darren M. Soanes, et al. "A Methodology for Comparative Functional Genomics." Journal of Integrative Bioinformatics 4, no. 3 (2007): 112–22. http://dx.doi.org/10.1515/jib-2007-69.

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Abstract The continuing and rapid increase in the number of fully sequenced genomes is creating new opportunities for comparative studies. However, although many genomic databases store data from multiple organisms, for the most part they provide limited support for comparative genomics. We argue that refocusing genomic data management to provide more direct support for comparative studies enables systematic identification of important relationships between species, thereby increasing the value that can be obtained from sequenced genomes. The principal result of the paper is a methodology, in

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43

Nagy, László G., Zsolt Merényi, Botond Hegedüs, and Balázs Bálint. "Novel phylogenetic methods are needed for understanding gene function in the era of mega-scale genome sequencing." Nucleic Acids Research 48, no. 5 (2020): 2209–19. http://dx.doi.org/10.1093/nar/gkz1241.

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Abstract Ongoing large-scale genome sequencing projects are forecasting a data deluge that will almost certainly overwhelm current analytical capabilities of evolutionary genomics. In contrast to population genomics, there are no standardized methods in evolutionary genomics for extracting evolutionary and functional (e.g. gene-trait association) signal from genomic data. Here, we examine how current practices of multi-species comparative genomics perform in this aspect and point out that many genomic datasets are under-utilized due to the lack of powerful methodologies. As a result, many curr

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44

Nguyen, Nga Thi Thuy, Pierre Vincens, Jean François Dufayard, Hugues Roest Crollius, and Alexandra Louis. "Genomicus in 2022: comparative tools for thousands of genomes and reconstructed ancestors." Nucleic Acids Research 50, no. D1 (2021): D1025—D1031. http://dx.doi.org/10.1093/nar/gkab1091.

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Abstract Genomicus is a database and web-server dedicated to comparative genomics in eukaryotes. Its main functionality is to graphically represent the conservation of genomic blocks between multiple genomes, locally around a specific gene of interest or genome-wide through karyotype comparisons. Since 2010 and its first release, Genomicus has synchronized with 60 Ensembl releases and seen the addition of functions that have expanded the type of analyses that users can perform. Today, five public instances of Genomicus are supporting a total number of 1029 extant genomes and 621 ancestral reco

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45

Gupta, N., J. Benhamida, V. Bhargava, et al. "Comparative proteogenomics: Combining mass spectrometry and comparative genomics to analyze multiple genomes." Genome Research 18, no. 7 (2008): 1133–42. http://dx.doi.org/10.1101/gr.074344.107.

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46

Nyshan, U. "THE ROLE OF GENOMICS IN UNDERSTANDING EVOLUTIONARY BIOLOGY." Sciences of Europe, no. 155 (December 27, 2024): 11–14. https://doi.org/10.5281/zenodo.14560977.

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Genomics has transformed our comprehension of evolutionary biology by offering robust tools to examine the genetic framework of life. By conducting a thorough genomic analysis, researchers can elucidate the molecular principles of evolution, track species origin, and ascertain the genetic foundations of adaptability and speciation. Comparative genomics, a fundamental aspect of this discipline, facilitates the identification of conserved and divergent genomic regions among species, providing insights into evolutionary links and functional genomics. Improvements in sequencing technologies and bi

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47

Riley, Robert, Sajeet Haridas, Kenneth H. Wolfe, et al. "Comparative genomics of biotechnologically important yeasts." Proceedings of the National Academy of Sciences 113, no. 35 (2016): 9882–87. http://dx.doi.org/10.1073/pnas.1603941113.

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Ascomycete yeasts are metabolically diverse, with great potential for biotechnology. Here, we report the comparative genome analysis of 29 taxonomically and biotechnologically important yeasts, including 16 newly sequenced. We identify a genetic code change, CUG-Ala, in Pachysolen tannophilus in the clade sister to the known CUG-Ser clade. Our well-resolved yeast phylogeny shows that some traits, such as methylotrophy, are restricted to single clades, whereas others, such as l-rhamnose utilization, have patchy phylogenetic distributions. Gene clusters, with variable organization and distributi

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48

Lamichhaney, Sangeet, Daren C. Card, Phil Grayson, et al. "Integrating natural history collections and comparative genomics to study the genetic architecture of convergent evolution." Philosophical Transactions of the Royal Society B: Biological Sciences 374, no. 1777 (2019): 20180248. http://dx.doi.org/10.1098/rstb.2018.0248.

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Evolutionary convergence has been long considered primary evidence of adaptation driven by natural selection and provides opportunities to explore evolutionary repeatability and predictability. In recent years, there has been increased interest in exploring the genetic mechanisms underlying convergent evolution, in part, owing to the advent of genomic techniques. However, the current ‘genomics gold rush’ in studies of convergence has overshadowed the reality that most trait classifications are quite broadly defined, resulting in incomplete or potentially biased interpretations of results. Geno

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49

Geballa-Koukoulas, Khalil, Hadjer Boudjemaa, Julien Andreani, Bernard La Scola, and Guillaume Blanc. "Comparative Genomics Unveils Regionalized Evolution of the Faustovirus Genomes." Viruses 12, no. 5 (2020): 577. http://dx.doi.org/10.3390/v12050577.

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Faustovirus is a recently discovered genus of large DNA virus infecting the amoeba Vermamoeba vermiformis, which is phylogenetically related to Asfarviridae. To better understand the diversity and evolution of this viral group, we sequenced six novel Faustovirus strains, mined published metagenomic datasets and performed a comparative genomic analysis. Genomic sequences revealed three consistent phylogenetic groups, within which genetic diversity was moderate. The comparison of the major capsid protein (MCP) genes unveiled between 13 and 18 type-I introns that likely evolved through a still-ac

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50

Van Bel, Michiel, Sebastian Proost, Elisabeth Wischnitzki, et al. "Dissecting Plant Genomes with the PLAZA Comparative Genomics Platform." Plant Physiology 158, no. 2 (2011): 590–600. http://dx.doi.org/10.1104/pp.111.189514.

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