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LETTER: Quantitative Estimates of Sequence Divergence for Comparative Analyses of Mammalian Genomes
- Gregory M. Cooper,
- Michael Brudno,
- NISC Comparative Sequencing Program,
- Eric D. Green,
- Serafim Batzoglou,
- and Arend Sidow
Genome Res. May 1, 2003 13: 813-820; doi:10.1101/gr.1064503
...) Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294 : 2348 – 2351 . ↵ Nembaware V. , Crum K. , Kelso J. , Seoighe C. ( 2002 ) Impact of the presence of paralogs on sequence divergence in a set of mouse–human orthologs. Genome Res. 12 : 1370 – 1376 . ↵ Ohta T. ( 1995...
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LETTER: Divergence of Spatial Gene Expression Profiles Following Species-Specific Gene Duplications in Human and Mouse
- Lukasz Huminiecki and
- Kenneth H. Wolfe
Genome Res. October 2004 14: 1870-1879; doi:10.1101/gr.2705204
...Abstract To examine the process by which duplicated genes diverge in function, we studied how the gene expression profiles of orthologous gene sets in human and mouse are affected by the presence of additional recent species-specific paralogs. Gene expression profiles were compared across 16 homologous...
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ARTICLE: Comparative Genome Analysis of the Mouse Imprinted Gene Impact and Its Nonimprinted Human Homolog IMPACT: Toward the Structural Basis for Species-Specific Imprinting
- Kohji Okamura,
- Yuriko Hagiwara-Takeuchi,
- Tao Li,
- Thanh H. Vu,
- Momoki Hirai,
- Masahira Hattori,
- Yoshiyuki Sakaki,
- Andrew R. Hoffman,
- and Takashi Ito
Genome Res. December 1, 2000 10: 1878-1889; doi:10.1101/gr.139200
...-iodide. Hybridization signals and banded chromosomes were observed using a fluorescence microscope (Olympus BX, Tokyo) equipped with appropriate filter sets. Tissue Distribution of IMPACT mRNA Tissue distribution of the IMPACT transcript was examined by Northern blot hybridization using filters containing poly...
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Research: The life history of retrocopies illuminates the evolution of new mammalian genes
- Francesco Nicola Carelli,
- Takashi Hayakawa,
- Yasuhiro Go,
- Hiroo Imai,
- Maria Warnefors,
- and Henrik Kaessmann
Genome Res. March 2016 26: 301-314; Published in Advance January 4, 2016, doi:10.1101/gr.198473.115
.... To this end, we clustered the set of retrocopies into 3900 orthologous families, of which 613 represent intact families (11–502 per species),meaning that the parentally inherited coding sequences of the included retrocopies were not disrupted through frameshift or nonsense mutations (Methods; Supplemental...
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Research: The identification and functional annotation of RNA structures conserved in vertebrates
- Stefan E. Seemann,
- Aashiq H. Mirza,
- Claus Hansen,
- Claus H. Bang-Berthelsen,
- Christian Garde,
- Mikkel Christensen-Dalsgaard,
- Elfar Torarinsson,
- Zizhen Yao,
- Christopher T. Workman,
- Flemming Pociot,
- Henrik Nielsen,
- Niels Tommerup,
- Walter L. Ruzzo,
- and Jan Gorodkin
Genome Res. August 2017 27: 1371-1383; Published in Advance May 9, 2017, doi:10.1101/gr.208652.116
...), collectively corresponding to ∼50% of the human (Methods). RNA structure predictions weremade in these putatively orthologous sequence sets by CMfinder, which locally and structurally aligns a set of unaligned sequences, discarding apparently irrelevant ones (Yao et al. 2006). CMfinder is not constrained...
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LETTER: cis-Regulatory and Protein Evolution in Orthologous and Duplicate Genes
- Cristian I. Castillo-Davis,
- Daniel L. Hartl,
- and Guillaume Achaz
Genome Res. August 2004 14: 1530-1536; Published in Advance July 15, 2004, doi:10.1101/gr.2662504
.... J. Mol. Biol. 48 : 443 –453. ↵ Nembaware, V., Crum, K., Kelso, J., and Seoighe, C. 2002 . Impact of the presence of paralogs on sequence divergence in a set of mouse–human orthologs. Genome Res. 12 : 1370 –1376. ↵ Nielsen, R. and Yang, Z. 1998 . Likelihood models for detecting positively selected...
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LETTER: A burst of protein sequence evolution and a prolonged period of asymmetric evolution follow gene duplication in yeast
- Devin R. Scannell and
- Kenneth H. Wolfe
Genome Res. January 2008 18: 137-147; Published in Advance November 19, 2007, doi:10.1101/gr.6341207
...in duplicate ( Davis and Petrov 2004 ). This bias can lead to a scenario where an interspecies comparison of the rates of protein sequence evolution between sets of orthologous genes that either have paralogs or do not have paralogs can fail to detect a true increase in the rate of protein sequence evolution...
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Methods: The difficulty of avoiding false positives in genome scans for natural selection
- Swapan Mallick,
- Sante Gnerre,
- Paul Muller,
- and David Reich
Genome Res. May 2009 19: 922-933; doi:10.1101/gr.086512.108
..., and near insertion/deletion polymorphisms (Methods). Alignments of genes could then be obtained by stripping out introns.We identified divergent sites only at nucleotides that passed a set of aggressive base quality filters. We required the quality score of every nucleotide used in analysis to be at least...
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Research: Massive turnover of functional sequence in human and other mammalian genomes
- Stephen Meader,
- Chris P. Ponting,
- and Gerton Lunter
Genome Res. October 2010 20: 1335-1343; Published in Advance August 6, 2010, doi:10.1101/gr.108795.110
...symmetrically around the mean rate, plus or minus a set percentage (0%–50%), and the rate applied to the entire 5-kb block. Estimation of neutral substitution rates Estimates of dS for the divergence of a species pair were obtained by taking the median dS value for all one-to-one orthologous genes within...
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LETTER: Differential Expansion of Zinc-Finger Transcription Factor Loci in Homologous Human and Mouse Gene Clusters
- Mark Shannon,
- Aaron T. Hamilton,
- Laurie Gordon,
- Elbert Branscomb,
- and Lisa Stubbs
Genome Res. June 2003 13: 1097-1110; Published in Advance May 12, 2003, doi:10.1101/gr.963903
...relationships between genes within this pair of homologous clusters. The results indicate that although the 10 mouse and 21 human genes arose from a common set of ancestral genes, lineage-specific duplications have created new genes in each species. The duplicated copies in each species have diverged...

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