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Journal articles on the topic 'Comparative genomics'

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Published: 4 June 2021
Last updated: 30 July 2024

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1

Furlong, Rebecca F., and Ziheng Yang. "Comparative genomics: Comparative genomics coming of age." Heredity 91, no. 6 (October 22, 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 (November 1, 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 (November 17, 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 (December 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 (January 1, 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 (September 22, 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 (August 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 (May 31, 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 (May 10, 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 (January 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 (September 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 (October 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 (September 22, 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 and other pathways, and the local sequence identity between the genes of these twoCryptosporidiumspecies. Our observations show that the phenotypic differences betweenC. hominisandC. parvumare not due to gross genome rearrangements, structural alterations, gene deletions or insertions, metabolic capabilities, or other obvious genomic alterations. Rather, the results indicate that these genomes exhibit a remarkable structural and compositional conservation and suggest that the phenotypic differences observed are due to subtle variations in the sequences of proteins that act at the interface between the parasite and its host.
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16

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

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17

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

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18

Bofkin, L., and S. Whelan. "Comparative genomics: Functional needles in a genomic haystack." Heredity 92, no. 5 (April 26, 2004): 363–64. http://dx.doi.org/10.1038/sj.hdy.6800429.

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19

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 (May 31, 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 Database through comparative genomic analysis using 86 publicly available fungal genomic data against fungal pathogenicity-related databases, such as Pathogenic-Host Interaction Database (PHI-base), Carbohydrate-Active enZymes Database (CAZy), and Database of Fungal Virulence Factory (DFVF).
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20

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

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21

Louis, Alexandra, Matthieu Muffato, and Hugues Roest Crollius. "Genomicus: five genome browsers for comparative genomics in eukaryota." Nucleic Acids Research 41, no. D1 (November 26, 2012): D700—D705. http://dx.doi.org/10.1093/nar/gks1156.

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22

Craig, Rory J., Ahmed R. Hasan, Rob W. Ness, and Peter D. Keightley. "Comparative genomics of Chlamydomonas." Plant Cell 33, no. 4 (February 2, 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. reinhardtii genome. We identify the major centromeric repeat in C. reinhardtii as a LINE transposable element homologous to Zepp (the centromeric repeat in Coccomyxa subellipsoidea) and infer that centromere locations and structure are likely conserved in C. incerta and C. schloesseri. We report extensive rearrangements, but limited gene turnover, between the minus mating type loci of these Chlamydomonas species. We produce an eight-species core-Reinhardtinia whole-genome alignment, which we use to identify several hundred false positive and missing genes in the C. reinhardtii annotation and >260,000 evolutionarily conserved elements in the C. reinhardtii genome. In summary, these resources will enable comparative genomics analyses for C. reinhardtii, significantly extending the analytical toolkit for this emerging model system.
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23

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

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24

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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25

Sivashankari, Selvarajan, and Piramanayagam Shanmughavel. "Comparative genomics - A perspective." Bioinformation 1, no. 9 (January 2, 2007): 376–78. http://dx.doi.org/10.6026/97320630001376.

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26

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

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27

Brüggemann, Holger, and Gerhard Gottschalk. "Comparative Genomics of Clostridia." Annals of the New York Academy of Sciences 1125, no. 1 (March 26, 2008): 73–81. http://dx.doi.org/10.1196/annals.1419.021.

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28

Kant, Ravi, Jochen Blom, Airi Palva, Roland J. Siezen, and Willem M. de Vos. "Comparative genomics of Lactobacillus." Microbial Biotechnology 4, no. 3 (October 21, 2010): 323–32. http://dx.doi.org/10.1111/j.1751-7915.2010.00215.x.

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29

Herrero, Javier, Matthieu Muffato, Kathryn Beal, Stephen Fitzgerald, Leo Gordon, Miguel Pignatelli, Albert J. Vilella, et al. "Ensembl comparative genomics resources." Database 2016 (2016): bav096. http://dx.doi.org/10.1093/database/bav096.

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30

Herrero, Javier, Matthieu Muffato, Kathryn Beal, Stephen Fitzgerald, Leo Gordon, Miguel Pignatelli, Albert J. Vilella, et al. "Ensembl comparative genomics resources." Database 2016 (2016): baw053. http://dx.doi.org/10.1093/database/baw053.

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31

Margulies, E. H. "Confidence in comparative genomics." Genome Research 18, no. 2 (February 1, 2008): 199–200. http://dx.doi.org/10.1101/gr.7228008.

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32

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

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33

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 (May 1, 2005): 8–14. http://dx.doi.org/10.14411/fp.2005.002.

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34

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

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35

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

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36

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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37

Vu, T. H. "Comparative Genomics Sheds Light on Mechanisms of Genomic Imprinting." Genome Research 10, no. 11 (November 1, 2000): 1660–63. http://dx.doi.org/10.1101/gr.166200.

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38

Wang, Jiacheng, Yaojia Chen, and Quan Zou. "Comparative Genomics and Functional Genomics Analysis in Plants." International Journal of Molecular Sciences 24, no. 7 (March 31, 2023): 6539. http://dx.doi.org/10.3390/ijms24076539.

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39

Alam, Intikhab, Mike Cornell, Darren M. Soanes, Cornelia Hedeler, Han Min Wong, Magnus Rattray, Simon J. Hubbard, Nicholas J. Talbot, Stephen G. Oliver, and Norman W. Paton. "A Methodology for Comparative Functional Genomics." Journal of Integrative Bioinformatics 4, no. 3 (December 1, 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 which comparative analyses are constructed over a foundation based on sequence clusters and evolutionary relationships. This methodology has been applied in a systematic study of the fungi, and we describe how comparative analyses have been implemented as an analysis library over the e-Fungi data warehouse.
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40

Gupta, N., J. Benhamida, V. Bhargava, D. Goodman, E. Kain, I. Kerman, N. Nguyen, et al. "Comparative proteogenomics: Combining mass spectrometry and comparative genomics to analyze multiple genomes." Genome Research 18, no. 7 (July 1, 2008): 1133–42. http://dx.doi.org/10.1101/gr.074344.107.

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41

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 (November 18, 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 reconstructions from all eukaryotes kingdoms available in Ensembl and Ensembl Genomes databases complemented with four additional instances specific to taxonomic groups of interest. New visualization and query tools are described in this manuscript. Genomicus is freely available at http://www.genomicus.bio.ens.psl.eu/genomicus.
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42

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 (January 16, 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 current analyses emphasize gene families for which some functional data is already available, resulting in a growing gap between functionally well-characterized genes/organisms and the universe of unknowns. This leaves unknown genes on the ‘dark side’ of genomes, a problem that will not be mitigated by sequencing more and more genomes, unless we develop tools to infer functional hypotheses for unknown genes in a systematic manner. We provide an inventory of recently developed methods capable of predicting gene-gene and gene-trait associations based on comparative data, then argue that realizing the full potential of whole genome datasets requires the integration of phylogenetic comparative methods into genomics, a rich but underutilized toolbox for looking into the past.
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43

Riley, Robert, Sajeet Haridas, Kenneth H. Wolfe, Mariana R. Lopes, Chris Todd Hittinger, Markus Göker, Asaf A. Salamov, et al. "Comparative genomics of biotechnologically important yeasts." Proceedings of the National Academy of Sciences 113, no. 35 (August 17, 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 distribution, encode many pathways of interest. Genomics can predict some biochemical traits precisely, but the genomic basis of others, such as xylose utilization, remains unresolved. Our data also provide insight into early evolution of ascomycetes. We document the loss of H3K9me2/3 heterochromatin, the origin of ascomycete mating-type switching, and panascomycete synteny at the MAT locus. These data and analyses will facilitate the engineering of efficient biosynthetic and degradative pathways and gateways for genomic manipulation.
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44

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 (May 24, 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-active birth and death process mediated by intron-encoded homing endonucleases that began before the Faustovirus radiation. Genome-wide alignments indicated that despite genomes retaining high levels of gene collinearity, the central region containing the MCP gene together with the extremities of the chromosomes evolved at a faster rate due to increased indel accumulation and local rearrangements. The fluctuation of the nucleotide composition along the Faustovirus (FV) genomes is mostly imprinted by the consistent nucleotide bias of coding sequences and provided no evidence for a single DNA replication origin like in circular bacterial genomes.
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45

Van Bel, Michiel, Sebastian Proost, Elisabeth Wischnitzki, Sara Movahedi, Christopher Scheerlinck, Yves Van de Peer, and Klaas Vandepoele. "Dissecting Plant Genomes with the PLAZA Comparative Genomics Platform." Plant Physiology 158, no. 2 (December 23, 2011): 590–600. http://dx.doi.org/10.1104/pp.111.189514.

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46

BARNSTEAD, MARY, and DARRELL J. DOYLE. "Microbial Genomes III: Sequencing, Functional Characterization, and Comparative Genomics." Microbial & Comparative Genomics 4, no. 1 (January 1999): 1–4. http://dx.doi.org/10.1089/omi.1.1999.4.1.

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47

Jones, N. C., and P. A. Pevzner. "Comparative genomics reveals unusually long motifs in mammalian genomes." Bioinformatics 22, no. 14 (July 15, 2006): e236-e242. http://dx.doi.org/10.1093/bioinformatics/btl265.

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48

Riipinen, Katja-Anneli, Päivi Forsman, and Tapani Alatossava. "The genomes and comparative genomics of Lactobacillus delbrueckii phages." Archives of Virology 156, no. 7 (April 5, 2011): 1217–33. http://dx.doi.org/10.1007/s00705-011-0980-5.

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49

DeLuca, T. F., J. Cui, J. Y. Jung, K. C. St. Gabriel, and D. P. Wall. "Roundup 2.0: enabling comparative genomics for over 1800 genomes." Bioinformatics 28, no. 5 (January 13, 2012): 715–16. http://dx.doi.org/10.1093/bioinformatics/bts006.

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50

Sarropoulou, E., D. Nousdili, A. Magoulas, and G. Kotoulas. "Linking the Genomes of Nonmodel Teleosts Through Comparative Genomics." Marine Biotechnology 10, no. 3 (February 23, 2008): 227–33. http://dx.doi.org/10.1007/s10126-007-9066-5.

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