Comparative genomics (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "Comparative genomics" in English language version.

refsWebsite

Global rank English rank

115nih.gov

4^th place

72doi.org

2^nd place

19harvard.edu

18^th place

17^th place

9semanticscholar.org

11^th place

8^th place

3worldcat.org

5^th place

2nature.com

234^th place

397^th place

1psu.edu

207^th place

136^th place

1computational-genomics.net

low place

1unt.edu

1,336^th place

769^th place

1ucsc.edu

3,619^th place

2,621^st place

1archive.today

14^th place

1ensembl.org

1,626^th place

1,007^th place

1lbl.gov

2,509^th place

2,329^th place

1handle.net

102^nd place

76^th place

1genomeweb.com

low place

archive.today

"Ensembl Genome Browser". Archived from the original on 2013-10-21.

computational-genomics.net

Cristianini N, Hahn M (2006). Introduction to Computational Genomics. Cambridge University Press. ISBN 978-0-521-67191-0.

doi.org

Darling AE, Miklós I, Ragan MA (July 2008). "Dynamics of genome rearrangement in bacterial populations". PLOS Genetics. 4 (7): e1000128. doi:10.1371/journal.pgen.1000128. PMC 2483231. PMID 18650965.
Xia X (2013). Comparative Genomics. SpringerBriefs in Genetics. Heidelberg: Springer. doi:10.1007/978-3-642-37146-2. ISBN 978-3-642-37145-5. S2CID 5491782.
Wei L, Liu Y, Dubchak I, Shon J, Park J (April 2002). "Comparative genomics approaches to study organism similarities and differences". Journal of Biomedical Informatics. 35 (2): 142–150. doi:10.1016/s1532-0464(02)00506-3. PMID 12474427.
Bennett MD, Leitch IJ, Price HJ, Johnston JS (April 2003). "Comparisons with Caenorhabditis (approximately 100 Mb) and Drosophila (approximately 175 Mb) using flow cytometry show genome size in Arabidopsis to be approximately 157 Mb and thus approximately 25% larger than the Arabidopsis genome initiative estimate of approximately 125 Mb". Annals of Botany. 91 (5): 547–557. doi:10.1093/aob/mcg057. PMC 4242247. PMID 12646499.
Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, Puiu D, et al. (2009). "A whole-genome assembly of the domestic cow, Bos taurus". Genome Biology. 10 (4): R42. doi:10.1186/gb-2009-10-4-r42. ISSN 1465-6906. PMC 2688933. PMID 19393038.
Holečková B, Schwarzbacherová V, Galdíková M, Koleničová S, Halušková J, Staničová J, et al. (2021-08-27). "Chromosomal Aberrations in Cattle". Genes. 12 (9): 1330. doi:10.3390/genes12091330. ISSN 2073-4425. PMC 8468509. PMID 34573313.
Elsik CG, Tellam RL, Worley KC (2009-04-24). "The Genome Sequence of Taurine Cattle: A window to ruminant biology and evolution". Science. 324 (5926): 522–528. Bibcode:2009Sci...324..522A. doi:10.1126/science.1169588. ISSN 0036-8075. PMC 2943200. PMID 19390049.
Liu D, Hunt M, Tsai IJ (January 2018). "Inferring synteny between genome assemblies: a systematic evaluation". BMC Bioinformatics. 19 (1): 26. doi:10.1186/s12859-018-2026-4. PMC 5791376. PMID 29382321.
Vergara IA, Chen N (September 2010). "Large synteny blocks revealed between Caenorhabditis elegans and Caenorhabditis briggsae genomes using OrthoCluster". BMC Genomics. 11: 516. doi:10.1186/1471-2164-11-516. PMC 2997010. PMID 20868500.
Tang H, Lyons E, Pedersen B, Schnable JC, Paterson AH, Freeling M (April 2011). "Screening synteny blocks in pairwise genome comparisons through integer programming". BMC Bioinformatics. 12: 102. doi:10.1186/1471-2105-12-102. PMC 3088904. PMID 21501495.
Ehrlich J, Sankoff D, Nadeau JH (September 1997). "Synteny conservation and chromosome rearrangements during mammalian evolution". Genetics. 147 (1): 289–296. doi:10.1093/genetics/147.1.289. PMC 1208112. PMID 9286688.
Zhang G, Li B, Li C, Gilbert MT, Jarvis ED, Wang J (2014-12-11). "Comparative genomic data of the Avian Phylogenomics Project". GigaScience. 3 (1): 26. doi:10.1186/2047-217X-3-26. PMC 4322804. PMID 25671091.
Howe KL, Bolt BJ, Cain S, Chan J, Chen WJ, Davis P, et al. (January 2016). "WormBase 2016: expanding to enable helminth genomic research". Nucleic Acids Research. 44 (D1): D774–D780. doi:10.1093/nar/gkv1217. PMC 4702863. PMID 26578572.
The C. elegans Sequencing Consortium (December 1998). "Genome sequence of the nematode C. elegans: a platform for investigating biology". Science. 282 (5396): 2012–2018. doi:10.1126/science.282.5396.2012. PMID 9851916.
Wong S, Wolfe KH (July 2005). "Birth of a metabolic gene cluster in yeast by adaptive gene relocation". Nature Genetics. 37 (7): 777–782. doi:10.1038/ng1584. PMID 15951822.
Luebeck EG (October 2010). "Cancer: Genomic evolution of metastasis". Nature. 467 (7319): 1053–1055. Bibcode:2010Natur.467.1053L. doi:10.1038/4671053a. PMID 20981088.
Ruelens P, de Maagd RA, Proost S, Theißen G, Geuten K, Kaufmann K (2013). "FLOWERING LOCUS C in monocots and the tandem origin of angiosperm-specific MADS-box genes". Nature Communications. 4: 2280. Bibcode:2013NatCo...4.2280R. doi:10.1038/ncomms3280. PMID 23955420.
Kemkemer C, Kohn M, Cooper DN, Froenicke L, Högel J, Hameister H, et al. (April 2009). "Gene synteny comparisons between different vertebrates provide new insights into breakage and fusion events during mammalian karyotype evolution". BMC Evolutionary Biology. 9 (1): 84. Bibcode:2009BMCEE...9...84K. doi:10.1186/1471-2148-9-84. PMC 2681463. PMID 19393055.
Hu B, Xie G, Lo CC, Starkenburg SR, Chain PS (November 2011). "Pathogen comparative genomics in the next-generation sequencing era: genome alignments, pangenomics and metagenomics". Briefings in Functional Genomics. 10 (6): 322–333. doi:10.1093/bfgp/elr042. PMID 22199376.
Argos P, Kamer G, Nicklin MJ, Wimmer E (September 1984). "Similarity in gene organization and homology between proteins of animal picornaviruses and a plant comovirus suggest common ancestry of these virus families". Nucleic Acids Research. 12 (18): 7251–7267. doi:10.1093/nar/12.18.7251. PMC 320155. PMID 6384934.
McGeoch DJ, Davison AJ (May 1986). "DNA sequence of the herpes simplex virus type 1 gene encoding glycoprotein gH, and identification of homologues in the genomes of varicella-zoster virus and Epstein-Barr virus". Nucleic Acids Research. 14 (10): 4281–4292. doi:10.1093/nar/14.10.4281. PMC 339861. PMID 3012465.
Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, et al. (July 1995). "Whole-genome random sequencing and assembly of Haemophilus influenzae Rd". Science. 269 (5223): 496–512. Bibcode:1995Sci...269..496F. doi:10.1126/science.7542800. PMID 7542800.
Fraser CM, Gocayne JD, White O, Adams MD, Clayton RA, Fleischmann RD, et al. (October 1995). "The minimal gene complement of Mycoplasma genitalium". Science. 270 (5235): 397–403. Bibcode:1995Sci...270..397F. doi:10.1126/science.270.5235.397. PMID 7569993. S2CID 29825758.
Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, et al. (October 1996). "Life with 6000 genes". Science. 274 (5287): 546, 563–546, 567. Bibcode:1996Sci...274..546G. doi:10.1126/science.274.5287.546. PMID 8849441. S2CID 16763139.
Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, et al. (March 2000). "The genome sequence of Drosophila melanogaster". Science. 287 (5461): 2185–2195. Bibcode:2000Sci...287.2185.. CiteSeerX 10.1.1.549.8639. doi:10.1126/science.287.5461.2185. PMID 10731132.
Rubin GM, Yandell MD, Wortman JR, Gabor Miklos GL, Nelson CR, Hariharan IK, et al. (March 2000). "Comparative genomics of the eukaryotes". Science. 287 (5461): 2204–2215. Bibcode:2000Sci...287.2204.. doi:10.1126/science.287.5461.2204. PMC 2754258. PMID 10731134.
Batzoglou S, Pachter L, Mesirov JP, Berger B, Lander ES (July 2000). "Human and mouse gene structure: comparative analysis and application to exon prediction". Genome Research. 10 (7): 950–958. doi:10.1101/gr.10.7.950. PMC 310911. PMID 10899144.
Ureta-Vidal A, Ettwiller L, Birney E (April 2003). "Comparative genomics: genome-wide analysis in metazoan eukaryotes". Nature Reviews. Genetics. 4 (4): 251–262. doi:10.1038/nrg1043. PMID 12671656. S2CID 2037634.
Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, Chen N, et al. (November 2003). "The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics". PLOS Biology. 1 (2): E45. doi:10.1371/journal.pbio.0000045. PMC 261899. PMID 14624247.
"Newly Sequenced Worm a Boon for Worm Biologists". PLOS Biology. 1 (2): e4. 2003. doi:10.1371/journal.pbio.0000044. PMC 261884.
Liu GE, Hou Y, Zhu B, Cardone MF, Jiang L, Cellamare A, et al. (May 2010). "Analysis of copy number variations among diverse cattle breeds". Genome Research. 20 (5): 693–703. doi:10.1101/gr.105403.110. PMC 2860171. PMID 20212021.
Liu Y, Mu Y, Wang W, Ahmed Z, Wei X, Lei C, et al. (2023). "Analysis of genomic copy number variations through whole-genome scan in Chinese Qaidam cattle". Frontiers in Veterinary Science. 10: 1148070. doi:10.3389/fvets.2023.1148070. PMC 10103646. PMID 37065216.
Bornstein K, Gryan G, Chang ES, Marchler-Bauer A, Schneider VA (September 2023). "The NIH Comparative Genomics Resource: addressing the promises and challenges of comparative genomics on human health". BMC Genomics. 24 (1): 575. doi:10.1186/s12864-023-09643-4. PMC 10523801. PMID 37759191.
Zoonomia C, Serres A, Armstrong J, Johnson J, Marinescu VD, Murén E, et al. (November 2020). "A comparative genomics multitool for scientific discovery and conservation". Nature. 587 (7833): 240–245. Bibcode:2020Natur.587..240Z. doi:10.1038/s41586-020-2876-6. PMC 7759459. PMID 33177664.
Lappalainen T, Scott AJ, Brandt M, Hall IM (March 2019). "Genomic Analysis in the Age of Human Genome Sequencing". Cell. 177 (1): 70–84. doi:10.1016/j.cell.2019.02.032. PMC 6532068. PMID 30901550.
Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J (March 2014). "A general framework for estimating the relative pathogenicity of human genetic variants". Nature Genetics. 46 (3): 310–315. doi:10.1038/ng.2892. PMC 3992975. PMID 24487276.
de la Fuente R, Díaz-Villanueva W, Arnau V, Moya A (February 2023). "Genomic Signature in Evolutionary Biology: A Review". Biology. 12 (2): 322. doi:10.3390/biology12020322. PMC 9953303. PMID 36829597.
Verma S, Thakur A, Katoch S, Shekhar C, Wani AH, Kumar S, et al. (October 2017). "Differences in innate and adaptive immune response traits of Pahari (Indian non-descript indigenous breed) and Jersey crossbred cattle". Veterinary Immunology and Immunopathology. 192: 20–27. doi:10.1016/j.vetimm.2017.09.003. PMID 29042011.
Pratas D, Silva RM, Pinho AJ, Ferreira PJ (May 2015). "An alignment-free method to find and visualise rearrangements between pairs of DNA sequences". Scientific Reports. 5: 10203. Bibcode:2015NatSR...510203P. doi:10.1038/srep10203. PMC 4434998. PMID 25984837.
Via A, De Las Rivas J, Attwood TK, Landsman D, Brazas MD, Leunissen JA, et al. (October 2011). "Ten simple rules for developing a short bioinformatics training course". PLOS Computational Biology. 7 (10): e1002245. Bibcode:2011PLSCB...7E2245V. doi:10.1371/journal.pcbi.1002245. PMC 3203054. PMID 22046119.
Damas J, Corbo M, Kim J, Turner-Maier J, Farré M, Larkin DM, et al. (October 2022). "Evolution of the ancestral mammalian karyotype and syntenic regions". Proceedings of the National Academy of Sciences of the United States of America. 119 (40): e2209139119. Bibcode:2022PNAS..11909139D. doi:10.1073/pnas.2209139119. PMC 9550189. PMID 36161960.
Prjibelski AD, Korobeynikov AI, Lapidus AL (2019-01-01). "Sequence Analysis". In Ranganathan S, Gribskov M, Nakai K, Schönbach C (eds.). Encyclopedia of Bioinformatics and Computational Biology. Oxford: Academic Press. pp. 292–322. doi:10.1016/b978-0-12-809633-8.20106-4. ISBN 978-0-12-811432-2. S2CID 226247797.
Haubold B, Wiehe T (September 2004). "Comparative genomics: methods and applications". Die Naturwissenschaften. 91 (9): 405–421. Bibcode:2004NW.....91..405H. doi:10.1007/s00114-004-0542-8. PMID 15278216.
Dunn CW, Zapata F, Munro C, Siebert S, Hejnol A (January 2018). "Pairwise comparisons across species are problematic when analyzing functional genomic data". Proceedings of the National Academy of Sciences of the United States of America. 115 (3): E409–E417. Bibcode:2018PNAS..115E.409D. doi:10.1073/pnas.1707515115. PMC 5776959. PMID 29301966.
Hardison RC, Oeltjen J, Miller W (October 1997). "Long human-mouse sequence alignments reveal novel regulatory elements: a reason to sequence the mouse genome". Genome Research. 7 (10): 959–966. doi:10.1101/gr.7.10.959. PMID 9331366.
Elgar G, Sandford R, Aparicio S, Macrae A, Venkatesh B, Brenner S (April 1996). "Small is beautiful: comparative genomics with the pufferfish (Fugu rubripes)". Trends in Genetics. 12 (4): 145–150. doi:10.1016/0168-9525(96)10018-4. PMID 8901419.
Boffelli D, McAuliffe J, Ovcharenko D, Lewis KD, Ovcharenko I, Pachter L, et al. (February 2003). "Phylogenetic shadowing of primate sequences to find functional regions of the human genome". Science. 299 (5611): 1391–1394. doi:10.1126/science.1081331. PMID 12610304.
Dewey CN (2012). "Whole-Genome Alignment". In Anisimova M (ed.). Evolutionary Genomics. Methods in Molecular Biology. Vol. 855. Totowa, NJ: Humana Press. pp. 237–257. doi:10.1007/978-1-61779-582-4_8. ISBN 978-1-61779-581-7. PMID 22407711.
Goel M, Sun H, Jiao W, Schneeberger K (2019). "SyRI: Finding genomic rearrangements and local sequence differences from whole-genome assemblies". Genome Biology. 20 (1): 277. doi:10.1186/s13059-019-1911-0. PMC 6913012. PMID 31842948.
Haubold B, Wiehe T (September 2004). "Comparative genomics: methods and applications". Die Naturwissenschaften. 91 (9): 405–421. Bibcode:2004NW.....91..405H. doi:10.1007/s00114-004-0542-8. PMID 15278216. S2CID 2041895.
Liu D, Hunt M, Tsai IJ (January 2018). "Inferring synteny between genome assemblies: a systematic evaluation". BMC Bioinformatics. 19 (1): 26. doi:10.1186/s12859-018-2026-4. PMC 5791376. PMID 29382321.
Duran C, Edwards D, Batley J (2009). "Genetic Maps and the Use of Synteny". Plant Genomics. Methods in Molecular Biology. Vol. 513. pp. 41–55. doi:10.1007/978-1-59745-427-8_3. ISBN 978-1-58829-997-0. PMID 19347649.
Soh J, Gordon PM, Sensen CW (March 2012). "The Bluejay genome browser". Current Protocols in Bioinformatics. 37. John Wiley & Sons, Inc. Chapter 10, Unit 10.9. doi:10.1002/0471250953.bi1009s37. ISBN 9780471250951. PMID 22389011. S2CID 34553139.
Goel M, Sun H, Jiao WB, Schneeberger K (December 2019). "SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies". Genome Biology. 20 (1): 277. doi:10.1186/s13059-019-1911-0. PMC 6913012. PMID 31842948.
Haug-Baltzell A, Stephens SA, Davey S, Scheidegger CE, Lyons E (July 2017). "SynMap2 and SynMap3D: web-based whole-genome synteny browsers". Bioinformatics. 33 (14): 2197–2198. doi:10.1093/bioinformatics/btx144. PMID 28334338.
Lin HN, Hsu WL (February 2020). "GSAlign: an efficient sequence alignment tool for intra-species genomes". BMC Genomics. 21 (1): 182. doi:10.1186/s12864-020-6569-1. PMC 7041101. PMID 32093618.
Thorvaldsdóttir H, Robinson JT, Mesirov JP (March 2013). "Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration". Briefings in Bioinformatics. 14 (2): 178–192. doi:10.1093/bib/bbs017. PMC 3603213. PMID 22517427.
Chen X, Schulz-Trieglaff O, Shaw R, Barnes B, Schlesinger F, Källberg M, et al. (April 2016). "Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications". Bioinformatics. 32 (8): 1220–1222. doi:10.1093/bioinformatics/btv710. PMID 26647377.
Abyzov A, Urban AE, Snyder M, Gerstein M (June 2011). "CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing". Genome Research. 21 (6): 974–984. doi:10.1101/gr.114876.110. PMC 3106330. PMID 21324876.
Elnitski L, Riemer C, Schwartz S, Hardison R, Miller W (February 2003). "PipMaker: a World Wide Web server for genomic sequence alignments". Current Protocols in Bioinformatics. Chapter 10. Chapter 10, Unit 10.2. doi:10.1002/0471250953.bi1002s00. PMID 18428692.
Pal K, Bystry V, Reigl T, Demko M, Krejci A, Touloumenidou T, et al. (December 2017). "GLASS: assisted and standardized assessment of gene variations from Sanger sequence trace data". Bioinformatics. 33 (23): 3802–3804. doi:10.1093/bioinformatics/btx423. PMID 29036643.
Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A (January 2018). "MUMmer4: A fast and versatile genome alignment system". PLOS Computational Biology. 14 (1): e1005944. Bibcode:2018PLSCB..14E5944M. doi:10.1371/journal.pcbi.1005944. PMC 5802927. PMID 29373581.
Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, et al. (November 2010). "Genome-wide association studies of 14 agronomic traits in rice landraces". Nature Genetics. 42 (11): 961–967. doi:10.1038/ng.695. PMID 20972439. S2CID 439442.
Morrell PL, Buckler ES, Ross-Ibarra J (December 2011). "Crop genomics: advances and applications". Nature Reviews. Genetics. 13 (2): 85–96. doi:10.1038/nrg3097. PMID 22207165. S2CID 13358998.
Seib KL, Zhao X, Rappuoli R (October 2012). "Developing vaccines in the era of genomics: a decade of reverse vaccinology". Clinical Microbiology and Infection. 18 (Suppl 5): 109–116. doi:10.1111/j.1469-0691.2012.03939.x. hdl:10072/50260. PMID 22882709.
Maione D, Margarit I, Rinaudo CD, Masignani V, Mora M, Scarselli M, et al. (July 2005). "Identification of a universal Group B streptococcus vaccine by multiple genome screen". Science. 309 (5731): 148–150. Bibcode:2005Sci...309..148M. doi:10.1126/science.1109869. PMC 1351092. PMID 15994562.
Rasko DA, Rosovitz MJ, Myers GS, Mongodin EF, Fricke WF, Gajer P, et al. (October 2008). "The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates". Journal of Bacteriology. 190 (20): 6881–6893. doi:10.1128/JB.00619-08. PMC 2566221. PMID 18676672.
Sadee W (August 2011). "Genomics and personalized medicine". International Journal of Pharmaceutics. 415 (1–2): 2–4. doi:10.1016/j.ijpharm.2011.04.048. PMID 21539903.
Glusman G, Rowen L, Lee I, Boysen C, Roach JC, Smit AF, et al. (September 2001). "Comparative genomics of the human and mouse T cell receptor loci". Immunity. 15 (3): 337–349. doi:10.1016/s1074-7613(01)00200-x. PMID 11567625.
Rogers J, Gibbs RA (May 2014). "Comparative primate genomics: emerging patterns of genome content and dynamics". Nature Reviews. Genetics. 15 (5): 347–359. doi:10.1038/nrg3707. PMC 4113315. PMID 24709753.
Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL, Lorente-Galdos B, et al. (July 2013). "Great ape genetic diversity and population history". Nature. 499 (7459): 471–475. Bibcode:2013Natur.499..471P. doi:10.1038/nature12228. PMC 3822165. PMID 23823723.
Zeng J, Konopka G, Hunt BG, Preuss TM, Geschwind D, Yi SV (September 2012). "Divergent whole-genome methylation maps of human and chimpanzee brains reveal epigenetic basis of human regulatory evolution". American Journal of Human Genetics. 91 (3): 455–465. doi:10.1016/j.ajhg.2012.07.024. PMC 3511995. PMID 22922032.

ensembl.org

asia.ensembl.org

"Ensembl Genome Browser". Archived from the original on 2013-10-21.

genomeweb.com

"Group a Streptococcus Vaccine Target Candidates Identified from Global Genome Set". 28 May 2019.

handle.net

hdl.handle.net

Seib KL, Zhao X, Rappuoli R (October 2012). "Developing vaccines in the era of genomics: a decade of reverse vaccinology". Clinical Microbiology and Infection. 18 (Suppl 5): 109–116. doi:10.1111/j.1469-0691.2012.03939.x. hdl:10072/50260. PMID 22882709.

harvard.edu

ui.adsabs.harvard.edu

Elsik CG, Tellam RL, Worley KC (2009-04-24). "The Genome Sequence of Taurine Cattle: A window to ruminant biology and evolution". Science. 324 (5926): 522–528. Bibcode:2009Sci...324..522A. doi:10.1126/science.1169588. ISSN 0036-8075. PMC 2943200. PMID 19390049.
Luebeck EG (October 2010). "Cancer: Genomic evolution of metastasis". Nature. 467 (7319): 1053–1055. Bibcode:2010Natur.467.1053L. doi:10.1038/4671053a. PMID 20981088.
Ruelens P, de Maagd RA, Proost S, Theißen G, Geuten K, Kaufmann K (2013). "FLOWERING LOCUS C in monocots and the tandem origin of angiosperm-specific MADS-box genes". Nature Communications. 4: 2280. Bibcode:2013NatCo...4.2280R. doi:10.1038/ncomms3280. PMID 23955420.
Kemkemer C, Kohn M, Cooper DN, Froenicke L, Högel J, Hameister H, et al. (April 2009). "Gene synteny comparisons between different vertebrates provide new insights into breakage and fusion events during mammalian karyotype evolution". BMC Evolutionary Biology. 9 (1): 84. Bibcode:2009BMCEE...9...84K. doi:10.1186/1471-2148-9-84. PMC 2681463. PMID 19393055.
Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, et al. (July 1995). "Whole-genome random sequencing and assembly of Haemophilus influenzae Rd". Science. 269 (5223): 496–512. Bibcode:1995Sci...269..496F. doi:10.1126/science.7542800. PMID 7542800.
Fraser CM, Gocayne JD, White O, Adams MD, Clayton RA, Fleischmann RD, et al. (October 1995). "The minimal gene complement of Mycoplasma genitalium". Science. 270 (5235): 397–403. Bibcode:1995Sci...270..397F. doi:10.1126/science.270.5235.397. PMID 7569993. S2CID 29825758.
Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, et al. (October 1996). "Life with 6000 genes". Science. 274 (5287): 546, 563–546, 567. Bibcode:1996Sci...274..546G. doi:10.1126/science.274.5287.546. PMID 8849441. S2CID 16763139.
Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, et al. (March 2000). "The genome sequence of Drosophila melanogaster". Science. 287 (5461): 2185–2195. Bibcode:2000Sci...287.2185.. CiteSeerX 10.1.1.549.8639. doi:10.1126/science.287.5461.2185. PMID 10731132.
Rubin GM, Yandell MD, Wortman JR, Gabor Miklos GL, Nelson CR, Hariharan IK, et al. (March 2000). "Comparative genomics of the eukaryotes". Science. 287 (5461): 2204–2215. Bibcode:2000Sci...287.2204.. doi:10.1126/science.287.5461.2204. PMC 2754258. PMID 10731134.
Zoonomia C, Serres A, Armstrong J, Johnson J, Marinescu VD, Murén E, et al. (November 2020). "A comparative genomics multitool for scientific discovery and conservation". Nature. 587 (7833): 240–245. Bibcode:2020Natur.587..240Z. doi:10.1038/s41586-020-2876-6. PMC 7759459. PMID 33177664.
Pratas D, Silva RM, Pinho AJ, Ferreira PJ (May 2015). "An alignment-free method to find and visualise rearrangements between pairs of DNA sequences". Scientific Reports. 5: 10203. Bibcode:2015NatSR...510203P. doi:10.1038/srep10203. PMC 4434998. PMID 25984837.
Via A, De Las Rivas J, Attwood TK, Landsman D, Brazas MD, Leunissen JA, et al. (October 2011). "Ten simple rules for developing a short bioinformatics training course". PLOS Computational Biology. 7 (10): e1002245. Bibcode:2011PLSCB...7E2245V. doi:10.1371/journal.pcbi.1002245. PMC 3203054. PMID 22046119.
Damas J, Corbo M, Kim J, Turner-Maier J, Farré M, Larkin DM, et al. (October 2022). "Evolution of the ancestral mammalian karyotype and syntenic regions". Proceedings of the National Academy of Sciences of the United States of America. 119 (40): e2209139119. Bibcode:2022PNAS..11909139D. doi:10.1073/pnas.2209139119. PMC 9550189. PMID 36161960.
Haubold B, Wiehe T (September 2004). "Comparative genomics: methods and applications". Die Naturwissenschaften. 91 (9): 405–421. Bibcode:2004NW.....91..405H. doi:10.1007/s00114-004-0542-8. PMID 15278216.
Dunn CW, Zapata F, Munro C, Siebert S, Hejnol A (January 2018). "Pairwise comparisons across species are problematic when analyzing functional genomic data". Proceedings of the National Academy of Sciences of the United States of America. 115 (3): E409–E417. Bibcode:2018PNAS..115E.409D. doi:10.1073/pnas.1707515115. PMC 5776959. PMID 29301966.
Haubold B, Wiehe T (September 2004). "Comparative genomics: methods and applications". Die Naturwissenschaften. 91 (9): 405–421. Bibcode:2004NW.....91..405H. doi:10.1007/s00114-004-0542-8. PMID 15278216. S2CID 2041895.
Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A (January 2018). "MUMmer4: A fast and versatile genome alignment system". PLOS Computational Biology. 14 (1): e1005944. Bibcode:2018PLSCB..14E5944M. doi:10.1371/journal.pcbi.1005944. PMC 5802927. PMID 29373581.
Maione D, Margarit I, Rinaudo CD, Masignani V, Mora M, Scarselli M, et al. (July 2005). "Identification of a universal Group B streptococcus vaccine by multiple genome screen". Science. 309 (5731): 148–150. Bibcode:2005Sci...309..148M. doi:10.1126/science.1109869. PMC 1351092. PMID 15994562.
Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL, Lorente-Galdos B, et al. (July 2013). "Great ape genetic diversity and population history". Nature. 499 (7459): 471–475. Bibcode:2013Natur.499..471P. doi:10.1038/nature12228. PMC 3822165. PMID 23823723.

lbl.gov

genome.lbl.gov

"VISTA tools".

nature.com

Touchman J (2010). "Comparative Genomics". Nature Education Knowledge. 3 (10): 13.
"Copy Number Variation | Learn Science at Scitable". www.nature.com. Retrieved 2024-05-03.

nih.gov

pubmed.ncbi.nlm.nih.gov

Darling AE, Miklós I, Ragan MA (July 2008). "Dynamics of genome rearrangement in bacterial populations". PLOS Genetics. 4 (7): e1000128. doi:10.1371/journal.pgen.1000128. PMC 2483231. PMID 18650965.
Wei L, Liu Y, Dubchak I, Shon J, Park J (April 2002). "Comparative genomics approaches to study organism similarities and differences". Journal of Biomedical Informatics. 35 (2): 142–150. doi:10.1016/s1532-0464(02)00506-3. PMID 12474427.
Bennett MD, Leitch IJ, Price HJ, Johnston JS (April 2003). "Comparisons with Caenorhabditis (approximately 100 Mb) and Drosophila (approximately 175 Mb) using flow cytometry show genome size in Arabidopsis to be approximately 157 Mb and thus approximately 25% larger than the Arabidopsis genome initiative estimate of approximately 125 Mb". Annals of Botany. 91 (5): 547–557. doi:10.1093/aob/mcg057. PMC 4242247. PMID 12646499.
Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, Puiu D, et al. (2009). "A whole-genome assembly of the domestic cow, Bos taurus". Genome Biology. 10 (4): R42. doi:10.1186/gb-2009-10-4-r42. ISSN 1465-6906. PMC 2688933. PMID 19393038.
Holečková B, Schwarzbacherová V, Galdíková M, Koleničová S, Halušková J, Staničová J, et al. (2021-08-27). "Chromosomal Aberrations in Cattle". Genes. 12 (9): 1330. doi:10.3390/genes12091330. ISSN 2073-4425. PMC 8468509. PMID 34573313.
Elsik CG, Tellam RL, Worley KC (2009-04-24). "The Genome Sequence of Taurine Cattle: A window to ruminant biology and evolution". Science. 324 (5926): 522–528. Bibcode:2009Sci...324..522A. doi:10.1126/science.1169588. ISSN 0036-8075. PMC 2943200. PMID 19390049.
Liu D, Hunt M, Tsai IJ (January 2018). "Inferring synteny between genome assemblies: a systematic evaluation". BMC Bioinformatics. 19 (1): 26. doi:10.1186/s12859-018-2026-4. PMC 5791376. PMID 29382321.
Vergara IA, Chen N (September 2010). "Large synteny blocks revealed between Caenorhabditis elegans and Caenorhabditis briggsae genomes using OrthoCluster". BMC Genomics. 11: 516. doi:10.1186/1471-2164-11-516. PMC 2997010. PMID 20868500.
Tang H, Lyons E, Pedersen B, Schnable JC, Paterson AH, Freeling M (April 2011). "Screening synteny blocks in pairwise genome comparisons through integer programming". BMC Bioinformatics. 12: 102. doi:10.1186/1471-2105-12-102. PMC 3088904. PMID 21501495.
Ehrlich J, Sankoff D, Nadeau JH (September 1997). "Synteny conservation and chromosome rearrangements during mammalian evolution". Genetics. 147 (1): 289–296. doi:10.1093/genetics/147.1.289. PMC 1208112. PMID 9286688.
Zhang G, Li B, Li C, Gilbert MT, Jarvis ED, Wang J (2014-12-11). "Comparative genomic data of the Avian Phylogenomics Project". GigaScience. 3 (1): 26. doi:10.1186/2047-217X-3-26. PMC 4322804. PMID 25671091.
Howe KL, Bolt BJ, Cain S, Chan J, Chen WJ, Davis P, et al. (January 2016). "WormBase 2016: expanding to enable helminth genomic research". Nucleic Acids Research. 44 (D1): D774–D780. doi:10.1093/nar/gkv1217. PMC 4702863. PMID 26578572.
The C. elegans Sequencing Consortium (December 1998). "Genome sequence of the nematode C. elegans: a platform for investigating biology". Science. 282 (5396): 2012–2018. doi:10.1126/science.282.5396.2012. PMID 9851916.
Wong S, Wolfe KH (July 2005). "Birth of a metabolic gene cluster in yeast by adaptive gene relocation". Nature Genetics. 37 (7): 777–782. doi:10.1038/ng1584. PMID 15951822.
Luebeck EG (October 2010). "Cancer: Genomic evolution of metastasis". Nature. 467 (7319): 1053–1055. Bibcode:2010Natur.467.1053L. doi:10.1038/4671053a. PMID 20981088.
Ruelens P, de Maagd RA, Proost S, Theißen G, Geuten K, Kaufmann K (2013). "FLOWERING LOCUS C in monocots and the tandem origin of angiosperm-specific MADS-box genes". Nature Communications. 4: 2280. Bibcode:2013NatCo...4.2280R. doi:10.1038/ncomms3280. PMID 23955420.
Kemkemer C, Kohn M, Cooper DN, Froenicke L, Högel J, Hameister H, et al. (April 2009). "Gene synteny comparisons between different vertebrates provide new insights into breakage and fusion events during mammalian karyotype evolution". BMC Evolutionary Biology. 9 (1): 84. Bibcode:2009BMCEE...9...84K. doi:10.1186/1471-2148-9-84. PMC 2681463. PMID 19393055.
Hu B, Xie G, Lo CC, Starkenburg SR, Chain PS (November 2011). "Pathogen comparative genomics in the next-generation sequencing era: genome alignments, pangenomics and metagenomics". Briefings in Functional Genomics. 10 (6): 322–333. doi:10.1093/bfgp/elr042. PMID 22199376.
Argos P, Kamer G, Nicklin MJ, Wimmer E (September 1984). "Similarity in gene organization and homology between proteins of animal picornaviruses and a plant comovirus suggest common ancestry of these virus families". Nucleic Acids Research. 12 (18): 7251–7267. doi:10.1093/nar/12.18.7251. PMC 320155. PMID 6384934.
McGeoch DJ, Davison AJ (May 1986). "DNA sequence of the herpes simplex virus type 1 gene encoding glycoprotein gH, and identification of homologues in the genomes of varicella-zoster virus and Epstein-Barr virus". Nucleic Acids Research. 14 (10): 4281–4292. doi:10.1093/nar/14.10.4281. PMC 339861. PMID 3012465.
Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, et al. (July 1995). "Whole-genome random sequencing and assembly of Haemophilus influenzae Rd". Science. 269 (5223): 496–512. Bibcode:1995Sci...269..496F. doi:10.1126/science.7542800. PMID 7542800.
Fraser CM, Gocayne JD, White O, Adams MD, Clayton RA, Fleischmann RD, et al. (October 1995). "The minimal gene complement of Mycoplasma genitalium". Science. 270 (5235): 397–403. Bibcode:1995Sci...270..397F. doi:10.1126/science.270.5235.397. PMID 7569993. S2CID 29825758.
Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, et al. (October 1996). "Life with 6000 genes". Science. 274 (5287): 546, 563–546, 567. Bibcode:1996Sci...274..546G. doi:10.1126/science.274.5287.546. PMID 8849441. S2CID 16763139.
Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, et al. (March 2000). "The genome sequence of Drosophila melanogaster". Science. 287 (5461): 2185–2195. Bibcode:2000Sci...287.2185.. CiteSeerX 10.1.1.549.8639. doi:10.1126/science.287.5461.2185. PMID 10731132.
Rubin GM, Yandell MD, Wortman JR, Gabor Miklos GL, Nelson CR, Hariharan IK, et al. (March 2000). "Comparative genomics of the eukaryotes". Science. 287 (5461): 2204–2215. Bibcode:2000Sci...287.2204.. doi:10.1126/science.287.5461.2204. PMC 2754258. PMID 10731134.
Batzoglou S, Pachter L, Mesirov JP, Berger B, Lander ES (July 2000). "Human and mouse gene structure: comparative analysis and application to exon prediction". Genome Research. 10 (7): 950–958. doi:10.1101/gr.10.7.950. PMC 310911. PMID 10899144.
Ureta-Vidal A, Ettwiller L, Birney E (April 2003). "Comparative genomics: genome-wide analysis in metazoan eukaryotes". Nature Reviews. Genetics. 4 (4): 251–262. doi:10.1038/nrg1043. PMID 12671656. S2CID 2037634.
Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, Chen N, et al. (November 2003). "The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics". PLOS Biology. 1 (2): E45. doi:10.1371/journal.pbio.0000045. PMC 261899. PMID 14624247.
Liu GE, Hou Y, Zhu B, Cardone MF, Jiang L, Cellamare A, et al. (May 2010). "Analysis of copy number variations among diverse cattle breeds". Genome Research. 20 (5): 693–703. doi:10.1101/gr.105403.110. PMC 2860171. PMID 20212021.
Liu Y, Mu Y, Wang W, Ahmed Z, Wei X, Lei C, et al. (2023). "Analysis of genomic copy number variations through whole-genome scan in Chinese Qaidam cattle". Frontiers in Veterinary Science. 10: 1148070. doi:10.3389/fvets.2023.1148070. PMC 10103646. PMID 37065216.
Bornstein K, Gryan G, Chang ES, Marchler-Bauer A, Schneider VA (September 2023). "The NIH Comparative Genomics Resource: addressing the promises and challenges of comparative genomics on human health". BMC Genomics. 24 (1): 575. doi:10.1186/s12864-023-09643-4. PMC 10523801. PMID 37759191.
Zoonomia C, Serres A, Armstrong J, Johnson J, Marinescu VD, Murén E, et al. (November 2020). "A comparative genomics multitool for scientific discovery and conservation". Nature. 587 (7833): 240–245. Bibcode:2020Natur.587..240Z. doi:10.1038/s41586-020-2876-6. PMC 7759459. PMID 33177664.
Lappalainen T, Scott AJ, Brandt M, Hall IM (March 2019). "Genomic Analysis in the Age of Human Genome Sequencing". Cell. 177 (1): 70–84. doi:10.1016/j.cell.2019.02.032. PMC 6532068. PMID 30901550.
Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J (March 2014). "A general framework for estimating the relative pathogenicity of human genetic variants". Nature Genetics. 46 (3): 310–315. doi:10.1038/ng.2892. PMC 3992975. PMID 24487276.
de la Fuente R, Díaz-Villanueva W, Arnau V, Moya A (February 2023). "Genomic Signature in Evolutionary Biology: A Review". Biology. 12 (2): 322. doi:10.3390/biology12020322. PMC 9953303. PMID 36829597.
Verma S, Thakur A, Katoch S, Shekhar C, Wani AH, Kumar S, et al. (October 2017). "Differences in innate and adaptive immune response traits of Pahari (Indian non-descript indigenous breed) and Jersey crossbred cattle". Veterinary Immunology and Immunopathology. 192: 20–27. doi:10.1016/j.vetimm.2017.09.003. PMID 29042011.
Pratas D, Silva RM, Pinho AJ, Ferreira PJ (May 2015). "An alignment-free method to find and visualise rearrangements between pairs of DNA sequences". Scientific Reports. 5: 10203. Bibcode:2015NatSR...510203P. doi:10.1038/srep10203. PMC 4434998. PMID 25984837.
Via A, De Las Rivas J, Attwood TK, Landsman D, Brazas MD, Leunissen JA, et al. (October 2011). "Ten simple rules for developing a short bioinformatics training course". PLOS Computational Biology. 7 (10): e1002245. Bibcode:2011PLSCB...7E2245V. doi:10.1371/journal.pcbi.1002245. PMC 3203054. PMID 22046119.
Damas J, Corbo M, Kim J, Turner-Maier J, Farré M, Larkin DM, et al. (October 2022). "Evolution of the ancestral mammalian karyotype and syntenic regions". Proceedings of the National Academy of Sciences of the United States of America. 119 (40): e2209139119. Bibcode:2022PNAS..11909139D. doi:10.1073/pnas.2209139119. PMC 9550189. PMID 36161960.
Altschul SF, Pop M (2017). "Sequence Alignment". In Rosen KH, Shier DR, Goddard W (eds.). Handbook of Discrete and Combinatorial Mathematics (2nd ed.). Boca Raton (FL): CRC Press/Taylor & Francis. ISBN 978-1-58488-780-5. PMID 29206392. Retrieved 2022-12-18.
Haubold B, Wiehe T (September 2004). "Comparative genomics: methods and applications". Die Naturwissenschaften. 91 (9): 405–421. Bibcode:2004NW.....91..405H. doi:10.1007/s00114-004-0542-8. PMID 15278216.
Dunn CW, Zapata F, Munro C, Siebert S, Hejnol A (January 2018). "Pairwise comparisons across species are problematic when analyzing functional genomic data". Proceedings of the National Academy of Sciences of the United States of America. 115 (3): E409–E417. Bibcode:2018PNAS..115E.409D. doi:10.1073/pnas.1707515115. PMC 5776959. PMID 29301966.
Hardison RC, Oeltjen J, Miller W (October 1997). "Long human-mouse sequence alignments reveal novel regulatory elements: a reason to sequence the mouse genome". Genome Research. 7 (10): 959–966. doi:10.1101/gr.7.10.959. PMID 9331366.
Elgar G, Sandford R, Aparicio S, Macrae A, Venkatesh B, Brenner S (April 1996). "Small is beautiful: comparative genomics with the pufferfish (Fugu rubripes)". Trends in Genetics. 12 (4): 145–150. doi:10.1016/0168-9525(96)10018-4. PMID 8901419.
Boffelli D, McAuliffe J, Ovcharenko D, Lewis KD, Ovcharenko I, Pachter L, et al. (February 2003). "Phylogenetic shadowing of primate sequences to find functional regions of the human genome". Science. 299 (5611): 1391–1394. doi:10.1126/science.1081331. PMID 12610304.
Dewey CN (2012). "Whole-Genome Alignment". In Anisimova M (ed.). Evolutionary Genomics. Methods in Molecular Biology. Vol. 855. Totowa, NJ: Humana Press. pp. 237–257. doi:10.1007/978-1-61779-582-4_8. ISBN 978-1-61779-581-7. PMID 22407711.
Goel M, Sun H, Jiao W, Schneeberger K (2019). "SyRI: Finding genomic rearrangements and local sequence differences from whole-genome assemblies". Genome Biology. 20 (1): 277. doi:10.1186/s13059-019-1911-0. PMC 6913012. PMID 31842948.
Haubold B, Wiehe T (September 2004). "Comparative genomics: methods and applications". Die Naturwissenschaften. 91 (9): 405–421. Bibcode:2004NW.....91..405H. doi:10.1007/s00114-004-0542-8. PMID 15278216. S2CID 2041895.
Liu D, Hunt M, Tsai IJ (January 2018). "Inferring synteny between genome assemblies: a systematic evaluation". BMC Bioinformatics. 19 (1): 26. doi:10.1186/s12859-018-2026-4. PMC 5791376. PMID 29382321.
Duran C, Edwards D, Batley J (2009). "Genetic Maps and the Use of Synteny". Plant Genomics. Methods in Molecular Biology. Vol. 513. pp. 41–55. doi:10.1007/978-1-59745-427-8_3. ISBN 978-1-58829-997-0. PMID 19347649.
Bergman NH (2007). Bergman NH (ed.). Comparative Genomics: Volumes 1 and 2. Totowa, New Jersey: Humana Press. ISBN 978-193411-537-4. PMID 21250292.
Soh J, Gordon PM, Sensen CW (March 2012). "The Bluejay genome browser". Current Protocols in Bioinformatics. 37. John Wiley & Sons, Inc. Chapter 10, Unit 10.9. doi:10.1002/0471250953.bi1009s37. ISBN 9780471250951. PMID 22389011. S2CID 34553139.
Goel M, Sun H, Jiao WB, Schneeberger K (December 2019). "SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies". Genome Biology. 20 (1): 277. doi:10.1186/s13059-019-1911-0. PMC 6913012. PMID 31842948.
Haug-Baltzell A, Stephens SA, Davey S, Scheidegger CE, Lyons E (July 2017). "SynMap2 and SynMap3D: web-based whole-genome synteny browsers". Bioinformatics. 33 (14): 2197–2198. doi:10.1093/bioinformatics/btx144. PMID 28334338.
Lin HN, Hsu WL (February 2020). "GSAlign: an efficient sequence alignment tool for intra-species genomes". BMC Genomics. 21 (1): 182. doi:10.1186/s12864-020-6569-1. PMC 7041101. PMID 32093618.
Thorvaldsdóttir H, Robinson JT, Mesirov JP (March 2013). "Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration". Briefings in Bioinformatics. 14 (2): 178–192. doi:10.1093/bib/bbs017. PMC 3603213. PMID 22517427.
Chen X, Schulz-Trieglaff O, Shaw R, Barnes B, Schlesinger F, Källberg M, et al. (April 2016). "Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications". Bioinformatics. 32 (8): 1220–1222. doi:10.1093/bioinformatics/btv710. PMID 26647377.
Abyzov A, Urban AE, Snyder M, Gerstein M (June 2011). "CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing". Genome Research. 21 (6): 974–984. doi:10.1101/gr.114876.110. PMC 3106330. PMID 21324876.
Elnitski L, Riemer C, Schwartz S, Hardison R, Miller W (February 2003). "PipMaker: a World Wide Web server for genomic sequence alignments". Current Protocols in Bioinformatics. Chapter 10. Chapter 10, Unit 10.2. doi:10.1002/0471250953.bi1002s00. PMID 18428692.
Pal K, Bystry V, Reigl T, Demko M, Krejci A, Touloumenidou T, et al. (December 2017). "GLASS: assisted and standardized assessment of gene variations from Sanger sequence trace data". Bioinformatics. 33 (23): 3802–3804. doi:10.1093/bioinformatics/btx423. PMID 29036643.
Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A (January 2018). "MUMmer4: A fast and versatile genome alignment system". PLOS Computational Biology. 14 (1): e1005944. Bibcode:2018PLSCB..14E5944M. doi:10.1371/journal.pcbi.1005944. PMC 5802927. PMID 29373581.
Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, et al. (November 2010). "Genome-wide association studies of 14 agronomic traits in rice landraces". Nature Genetics. 42 (11): 961–967. doi:10.1038/ng.695. PMID 20972439. S2CID 439442.
Morrell PL, Buckler ES, Ross-Ibarra J (December 2011). "Crop genomics: advances and applications". Nature Reviews. Genetics. 13 (2): 85–96. doi:10.1038/nrg3097. PMID 22207165. S2CID 13358998.
Seib KL, Zhao X, Rappuoli R (October 2012). "Developing vaccines in the era of genomics: a decade of reverse vaccinology". Clinical Microbiology and Infection. 18 (Suppl 5): 109–116. doi:10.1111/j.1469-0691.2012.03939.x. hdl:10072/50260. PMID 22882709.
Maione D, Margarit I, Rinaudo CD, Masignani V, Mora M, Scarselli M, et al. (July 2005). "Identification of a universal Group B streptococcus vaccine by multiple genome screen". Science. 309 (5731): 148–150. Bibcode:2005Sci...309..148M. doi:10.1126/science.1109869. PMC 1351092. PMID 15994562.
Rasko DA, Rosovitz MJ, Myers GS, Mongodin EF, Fricke WF, Gajer P, et al. (October 2008). "The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates". Journal of Bacteriology. 190 (20): 6881–6893. doi:10.1128/JB.00619-08. PMC 2566221. PMID 18676672.
Sadee W (August 2011). "Genomics and personalized medicine". International Journal of Pharmaceutics. 415 (1–2): 2–4. doi:10.1016/j.ijpharm.2011.04.048. PMID 21539903.
Glusman G, Rowen L, Lee I, Boysen C, Roach JC, Smit AF, et al. (September 2001). "Comparative genomics of the human and mouse T cell receptor loci". Immunity. 15 (3): 337–349. doi:10.1016/s1074-7613(01)00200-x. PMID 11567625.
Rogers J, Gibbs RA (May 2014). "Comparative primate genomics: emerging patterns of genome content and dynamics". Nature Reviews. Genetics. 15 (5): 347–359. doi:10.1038/nrg3707. PMC 4113315. PMID 24709753.
Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL, Lorente-Galdos B, et al. (July 2013). "Great ape genetic diversity and population history". Nature. 499 (7459): 471–475. Bibcode:2013Natur.499..471P. doi:10.1038/nature12228. PMC 3822165. PMID 23823723.
Zeng J, Konopka G, Hunt BG, Preuss TM, Geschwind D, Yi SV (September 2012). "Divergent whole-genome methylation maps of human and chimpanzee brains reveal epigenetic basis of human regulatory evolution". American Journal of Human Genetics. 91 (3): 455–465. doi:10.1016/j.ajhg.2012.07.024. PMC 3511995. PMID 22922032.

ncbi.nlm.nih.gov

Darling AE, Miklós I, Ragan MA (July 2008). "Dynamics of genome rearrangement in bacterial populations". PLOS Genetics. 4 (7): e1000128. doi:10.1371/journal.pgen.1000128. PMC 2483231. PMID 18650965.
Bennett MD, Leitch IJ, Price HJ, Johnston JS (April 2003). "Comparisons with Caenorhabditis (approximately 100 Mb) and Drosophila (approximately 175 Mb) using flow cytometry show genome size in Arabidopsis to be approximately 157 Mb and thus approximately 25% larger than the Arabidopsis genome initiative estimate of approximately 125 Mb". Annals of Botany. 91 (5): 547–557. doi:10.1093/aob/mcg057. PMC 4242247. PMID 12646499.
Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, Puiu D, et al. (2009). "A whole-genome assembly of the domestic cow, Bos taurus". Genome Biology. 10 (4): R42. doi:10.1186/gb-2009-10-4-r42. ISSN 1465-6906. PMC 2688933. PMID 19393038.
Holečková B, Schwarzbacherová V, Galdíková M, Koleničová S, Halušková J, Staničová J, et al. (2021-08-27). "Chromosomal Aberrations in Cattle". Genes. 12 (9): 1330. doi:10.3390/genes12091330. ISSN 2073-4425. PMC 8468509. PMID 34573313.
Elsik CG, Tellam RL, Worley KC (2009-04-24). "The Genome Sequence of Taurine Cattle: A window to ruminant biology and evolution". Science. 324 (5926): 522–528. Bibcode:2009Sci...324..522A. doi:10.1126/science.1169588. ISSN 0036-8075. PMC 2943200. PMID 19390049.
Liu D, Hunt M, Tsai IJ (January 2018). "Inferring synteny between genome assemblies: a systematic evaluation". BMC Bioinformatics. 19 (1): 26. doi:10.1186/s12859-018-2026-4. PMC 5791376. PMID 29382321.
Vergara IA, Chen N (September 2010). "Large synteny blocks revealed between Caenorhabditis elegans and Caenorhabditis briggsae genomes using OrthoCluster". BMC Genomics. 11: 516. doi:10.1186/1471-2164-11-516. PMC 2997010. PMID 20868500.
Tang H, Lyons E, Pedersen B, Schnable JC, Paterson AH, Freeling M (April 2011). "Screening synteny blocks in pairwise genome comparisons through integer programming". BMC Bioinformatics. 12: 102. doi:10.1186/1471-2105-12-102. PMC 3088904. PMID 21501495.
Ehrlich J, Sankoff D, Nadeau JH (September 1997). "Synteny conservation and chromosome rearrangements during mammalian evolution". Genetics. 147 (1): 289–296. doi:10.1093/genetics/147.1.289. PMC 1208112. PMID 9286688.
Zhang G, Li B, Li C, Gilbert MT, Jarvis ED, Wang J (2014-12-11). "Comparative genomic data of the Avian Phylogenomics Project". GigaScience. 3 (1): 26. doi:10.1186/2047-217X-3-26. PMC 4322804. PMID 25671091.
Howe KL, Bolt BJ, Cain S, Chan J, Chen WJ, Davis P, et al. (January 2016). "WormBase 2016: expanding to enable helminth genomic research". Nucleic Acids Research. 44 (D1): D774–D780. doi:10.1093/nar/gkv1217. PMC 4702863. PMID 26578572.
Kemkemer C, Kohn M, Cooper DN, Froenicke L, Högel J, Hameister H, et al. (April 2009). "Gene synteny comparisons between different vertebrates provide new insights into breakage and fusion events during mammalian karyotype evolution". BMC Evolutionary Biology. 9 (1): 84. Bibcode:2009BMCEE...9...84K. doi:10.1186/1471-2148-9-84. PMC 2681463. PMID 19393055.
Argos P, Kamer G, Nicklin MJ, Wimmer E (September 1984). "Similarity in gene organization and homology between proteins of animal picornaviruses and a plant comovirus suggest common ancestry of these virus families". Nucleic Acids Research. 12 (18): 7251–7267. doi:10.1093/nar/12.18.7251. PMC 320155. PMID 6384934.
McGeoch DJ, Davison AJ (May 1986). "DNA sequence of the herpes simplex virus type 1 gene encoding glycoprotein gH, and identification of homologues in the genomes of varicella-zoster virus and Epstein-Barr virus". Nucleic Acids Research. 14 (10): 4281–4292. doi:10.1093/nar/14.10.4281. PMC 339861. PMID 3012465.
Rubin GM, Yandell MD, Wortman JR, Gabor Miklos GL, Nelson CR, Hariharan IK, et al. (March 2000). "Comparative genomics of the eukaryotes". Science. 287 (5461): 2204–2215. Bibcode:2000Sci...287.2204.. doi:10.1126/science.287.5461.2204. PMC 2754258. PMID 10731134.
Batzoglou S, Pachter L, Mesirov JP, Berger B, Lander ES (July 2000). "Human and mouse gene structure: comparative analysis and application to exon prediction". Genome Research. 10 (7): 950–958. doi:10.1101/gr.10.7.950. PMC 310911. PMID 10899144.
Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, Chen N, et al. (November 2003). "The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics". PLOS Biology. 1 (2): E45. doi:10.1371/journal.pbio.0000045. PMC 261899. PMID 14624247.
"Newly Sequenced Worm a Boon for Worm Biologists". PLOS Biology. 1 (2): e4. 2003. doi:10.1371/journal.pbio.0000044. PMC 261884.
Liu GE, Hou Y, Zhu B, Cardone MF, Jiang L, Cellamare A, et al. (May 2010). "Analysis of copy number variations among diverse cattle breeds". Genome Research. 20 (5): 693–703. doi:10.1101/gr.105403.110. PMC 2860171. PMID 20212021.
Liu Y, Mu Y, Wang W, Ahmed Z, Wei X, Lei C, et al. (2023). "Analysis of genomic copy number variations through whole-genome scan in Chinese Qaidam cattle". Frontiers in Veterinary Science. 10: 1148070. doi:10.3389/fvets.2023.1148070. PMC 10103646. PMID 37065216.
Bornstein K, Gryan G, Chang ES, Marchler-Bauer A, Schneider VA (September 2023). "The NIH Comparative Genomics Resource: addressing the promises and challenges of comparative genomics on human health". BMC Genomics. 24 (1): 575. doi:10.1186/s12864-023-09643-4. PMC 10523801. PMID 37759191.
Zoonomia C, Serres A, Armstrong J, Johnson J, Marinescu VD, Murén E, et al. (November 2020). "A comparative genomics multitool for scientific discovery and conservation". Nature. 587 (7833): 240–245. Bibcode:2020Natur.587..240Z. doi:10.1038/s41586-020-2876-6. PMC 7759459. PMID 33177664.
Lappalainen T, Scott AJ, Brandt M, Hall IM (March 2019). "Genomic Analysis in the Age of Human Genome Sequencing". Cell. 177 (1): 70–84. doi:10.1016/j.cell.2019.02.032. PMC 6532068. PMID 30901550.
Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J (March 2014). "A general framework for estimating the relative pathogenicity of human genetic variants". Nature Genetics. 46 (3): 310–315. doi:10.1038/ng.2892. PMC 3992975. PMID 24487276.
de la Fuente R, Díaz-Villanueva W, Arnau V, Moya A (February 2023). "Genomic Signature in Evolutionary Biology: A Review". Biology. 12 (2): 322. doi:10.3390/biology12020322. PMC 9953303. PMID 36829597.
Pratas D, Silva RM, Pinho AJ, Ferreira PJ (May 2015). "An alignment-free method to find and visualise rearrangements between pairs of DNA sequences". Scientific Reports. 5: 10203. Bibcode:2015NatSR...510203P. doi:10.1038/srep10203. PMC 4434998. PMID 25984837.
Via A, De Las Rivas J, Attwood TK, Landsman D, Brazas MD, Leunissen JA, et al. (October 2011). "Ten simple rules for developing a short bioinformatics training course". PLOS Computational Biology. 7 (10): e1002245. Bibcode:2011PLSCB...7E2245V. doi:10.1371/journal.pcbi.1002245. PMC 3203054. PMID 22046119.
Damas J, Corbo M, Kim J, Turner-Maier J, Farré M, Larkin DM, et al. (October 2022). "Evolution of the ancestral mammalian karyotype and syntenic regions". Proceedings of the National Academy of Sciences of the United States of America. 119 (40): e2209139119. Bibcode:2022PNAS..11909139D. doi:10.1073/pnas.2209139119. PMC 9550189. PMID 36161960.
Altschul SF, Pop M (2017). "Sequence Alignment". In Rosen KH, Shier DR, Goddard W (eds.). Handbook of Discrete and Combinatorial Mathematics (2nd ed.). Boca Raton (FL): CRC Press/Taylor & Francis. ISBN 978-1-58488-780-5. PMID 29206392. Retrieved 2022-12-18.
Dunn CW, Zapata F, Munro C, Siebert S, Hejnol A (January 2018). "Pairwise comparisons across species are problematic when analyzing functional genomic data". Proceedings of the National Academy of Sciences of the United States of America. 115 (3): E409–E417. Bibcode:2018PNAS..115E.409D. doi:10.1073/pnas.1707515115. PMC 5776959. PMID 29301966.
Goel M, Sun H, Jiao W, Schneeberger K (2019). "SyRI: Finding genomic rearrangements and local sequence differences from whole-genome assemblies". Genome Biology. 20 (1): 277. doi:10.1186/s13059-019-1911-0. PMC 6913012. PMID 31842948.
Liu D, Hunt M, Tsai IJ (January 2018). "Inferring synteny between genome assemblies: a systematic evaluation". BMC Bioinformatics. 19 (1): 26. doi:10.1186/s12859-018-2026-4. PMC 5791376. PMID 29382321.
Bergman NH (2007). Bergman NH (ed.). Comparative Genomics: Volumes 1 and 2. Totowa, New Jersey: Humana Press. ISBN 978-193411-537-4. PMID 21250292.
"Map Viewer".
Goel M, Sun H, Jiao WB, Schneeberger K (December 2019). "SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies". Genome Biology. 20 (1): 277. doi:10.1186/s13059-019-1911-0. PMC 6913012. PMID 31842948.
Lin HN, Hsu WL (February 2020). "GSAlign: an efficient sequence alignment tool for intra-species genomes". BMC Genomics. 21 (1): 182. doi:10.1186/s12864-020-6569-1. PMC 7041101. PMID 32093618.
Thorvaldsdóttir H, Robinson JT, Mesirov JP (March 2013). "Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration". Briefings in Bioinformatics. 14 (2): 178–192. doi:10.1093/bib/bbs017. PMC 3603213. PMID 22517427.
Abyzov A, Urban AE, Snyder M, Gerstein M (June 2011). "CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing". Genome Research. 21 (6): 974–984. doi:10.1101/gr.114876.110. PMC 3106330. PMID 21324876.
Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A (January 2018). "MUMmer4: A fast and versatile genome alignment system". PLOS Computational Biology. 14 (1): e1005944. Bibcode:2018PLSCB..14E5944M. doi:10.1371/journal.pcbi.1005944. PMC 5802927. PMID 29373581.
Maione D, Margarit I, Rinaudo CD, Masignani V, Mora M, Scarselli M, et al. (July 2005). "Identification of a universal Group B streptococcus vaccine by multiple genome screen". Science. 309 (5731): 148–150. Bibcode:2005Sci...309..148M. doi:10.1126/science.1109869. PMC 1351092. PMID 15994562.
Rasko DA, Rosovitz MJ, Myers GS, Mongodin EF, Fricke WF, Gajer P, et al. (October 2008). "The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates". Journal of Bacteriology. 190 (20): 6881–6893. doi:10.1128/JB.00619-08. PMC 2566221. PMID 18676672.
Rogers J, Gibbs RA (May 2014). "Comparative primate genomics: emerging patterns of genome content and dynamics". Nature Reviews. Genetics. 15 (5): 347–359. doi:10.1038/nrg3707. PMC 4113315. PMID 24709753.
Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL, Lorente-Galdos B, et al. (July 2013). "Great ape genetic diversity and population history". Nature. 499 (7459): 471–475. Bibcode:2013Natur.499..471P. doi:10.1038/nature12228. PMC 3822165. PMID 23823723.
Zeng J, Konopka G, Hunt BG, Preuss TM, Geschwind D, Yi SV (September 2012). "Divergent whole-genome methylation maps of human and chimpanzee brains reveal epigenetic basis of human regulatory evolution". American Journal of Human Genetics. 91 (3): 455–465. doi:10.1016/j.ajhg.2012.07.024. PMC 3511995. PMID 22922032.

psu.edu

citeseerx.ist.psu.edu

Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, et al. (March 2000). "The genome sequence of Drosophila melanogaster". Science. 287 (5461): 2185–2195. Bibcode:2000Sci...287.2185.. CiteSeerX 10.1.1.549.8639. doi:10.1126/science.287.5461.2185. PMID 10731132.

semanticscholar.org

api.semanticscholar.org

Xia X (2013). Comparative Genomics. SpringerBriefs in Genetics. Heidelberg: Springer. doi:10.1007/978-3-642-37146-2. ISBN 978-3-642-37145-5. S2CID 5491782.
Fraser CM, Gocayne JD, White O, Adams MD, Clayton RA, Fleischmann RD, et al. (October 1995). "The minimal gene complement of Mycoplasma genitalium". Science. 270 (5235): 397–403. Bibcode:1995Sci...270..397F. doi:10.1126/science.270.5235.397. PMID 7569993. S2CID 29825758.
Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, et al. (October 1996). "Life with 6000 genes". Science. 274 (5287): 546, 563–546, 567. Bibcode:1996Sci...274..546G. doi:10.1126/science.274.5287.546. PMID 8849441. S2CID 16763139.
Ureta-Vidal A, Ettwiller L, Birney E (April 2003). "Comparative genomics: genome-wide analysis in metazoan eukaryotes". Nature Reviews. Genetics. 4 (4): 251–262. doi:10.1038/nrg1043. PMID 12671656. S2CID 2037634.
Prjibelski AD, Korobeynikov AI, Lapidus AL (2019-01-01). "Sequence Analysis". In Ranganathan S, Gribskov M, Nakai K, Schönbach C (eds.). Encyclopedia of Bioinformatics and Computational Biology. Oxford: Academic Press. pp. 292–322. doi:10.1016/b978-0-12-809633-8.20106-4. ISBN 978-0-12-811432-2. S2CID 226247797.
Haubold B, Wiehe T (September 2004). "Comparative genomics: methods and applications". Die Naturwissenschaften. 91 (9): 405–421. Bibcode:2004NW.....91..405H. doi:10.1007/s00114-004-0542-8. PMID 15278216. S2CID 2041895.
Soh J, Gordon PM, Sensen CW (March 2012). "The Bluejay genome browser". Current Protocols in Bioinformatics. 37. John Wiley & Sons, Inc. Chapter 10, Unit 10.9. doi:10.1002/0471250953.bi1009s37. ISBN 9780471250951. PMID 22389011. S2CID 34553139.
Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, et al. (November 2010). "Genome-wide association studies of 14 agronomic traits in rice landraces". Nature Genetics. 42 (11): 961–967. doi:10.1038/ng.695. PMID 20972439. S2CID 439442.
Morrell PL, Buckler ES, Ross-Ibarra J (December 2011). "Crop genomics: advances and applications". Nature Reviews. Genetics. 13 (2): 85–96. doi:10.1038/nrg3097. PMID 22207165. S2CID 13358998.

ucsc.edu

genome.ucsc.edu

"UCSC Browser".

unt.edu

digital.library.unt.edu

Boffelli D, McAuliffe J, Ovcharenko D, Lewis KD, Ovcharenko I, Pachter L, et al. (February 2003). "Phylogenetic shadowing of primate sequences to find functional regions of the human genome". Science. 299 (5611): 1391–1394. doi:10.1126/science.1081331. PMID 12610304.

worldcat.org

Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, Puiu D, et al. (2009). "A whole-genome assembly of the domestic cow, Bos taurus". Genome Biology. 10 (4): R42. doi:10.1186/gb-2009-10-4-r42. ISSN 1465-6906. PMC 2688933. PMID 19393038.
Holečková B, Schwarzbacherová V, Galdíková M, Koleničová S, Halušková J, Staničová J, et al. (2021-08-27). "Chromosomal Aberrations in Cattle". Genes. 12 (9): 1330. doi:10.3390/genes12091330. ISSN 2073-4425. PMC 8468509. PMID 34573313.
Elsik CG, Tellam RL, Worley KC (2009-04-24). "The Genome Sequence of Taurine Cattle: A window to ruminant biology and evolution". Science. 324 (5926): 522–528. Bibcode:2009Sci...324..522A. doi:10.1126/science.1169588. ISSN 0036-8075. PMC 2943200. PMID 19390049.