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Method: Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq
- Alejandro Paniagua,
- Cristina Agustín-García,
- Francisco J. Pardo-Palacios,
- Thomas Brown,
- Maite De Maria,
- Nancy D. Denslow,
- Camila J. Mazzoni,
- and Ana Conesa
Genome Res. April 2025 35: 1053-1064; Published in Advance December 23, 2024, doi:10.1101/gr.279864.124
...identified 4906 novel loci exclusively present in the LRB annotation and 2225 loci unique to the NCBI annotation. To better characterize these loci, we evaluated the support for the isoforms found in these loci using known sequences from other mammalian species. Of the 5707 isoforms of the LRB annotation...
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Research: The evolution of duplicate gene expression in mammalian organs
- Katerina Guschanski,
- Maria Warnefors,
- and Henrik Kaessmann
Genome Res. September 2017 27: 1461-1474; Published in Advance July 25, 2017, doi:10.1101/gr.215566.116
.... Here, we report a large-scale study of the expression evolution of DNA-based functional gene duplicates in three major mammalian lineages (placental mammals, marsupials, egg-laying monotremes) and birds, on the basis of RNA sequencing (RNA-seq) data from nine species and eight organs. We observe...
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LETTER: Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences
- David C. King,
- James Taylor,
- Laura Elnitski,
- Francesca Chiaromonte,
- Webb Miller,
- and Ross C. Hardison
Genome Res. August 2005 15: 1051-1060; Published in Advance July 15, 2005, doi:10.1101/gr.3642605
...Evaluation of regulatory potential and conservation scores for detecting cis -regulatory modules in aligned mammalian genome sequences David C. King 1 , 2 , James Taylor 1 , 3 , Laura Elnitski 1 , 2 , 6 , Francesca Chiaromonte 1 , 4...
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Methods: Detection of nonneutral substitution rates on mammalian phylogenies
- Katherine S. Pollard,
- Melissa J. Hubisz,
- Kate R. Rosenbloom,
- and Adam Siepel
Genome Res. January 2010 20: 110-121; Published in Advance October 26, 2009, doi:10.1101/gr.097857.109
...distributions of numbers of substitutions, and the genomic evolutionary rate profiling (GERP) test. All four tests have been implemented in a freely available program called phyloP. Based on extensive simulation experiments, these tests are remarkably similar in statistical power. With 36 mammalian species...
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Methods: Genome-wide nucleotide-level mammalian ancestor reconstruction
- Benedict Paten,
- Javier Herrero,
- Stephen Fitzgerald,
- Kathryn Beal,
- Paul Flicek,
- Ian Holmes,
- and Ewan Birney
Genome Res. November 2008 18: 1829-1843; Published in Advance October 10, 2008, doi:10.1101/gr.076521.108
...Genome-wide nucleotide-level mammalian ancestor reconstruction Benedict Paten 1 , 4 , Javier Herrero 2 , Stephen Fitzgerald 2 , Kathryn Beal 2 , Paul Flicek 2 , Ian Holmes 3 , and Ewan Birney 2 , 4 1...
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RESOURCE: eShadow: A Tool for Comparing Closely Related Sequences
- Ivan Ovcharenko,
- Dario Boffelli,
- and Gabriela G. Loots
Genome Res. June 2004 14: 1191-1198; doi:10.1101/gr.1773104
...in mammalian s. Nucleic Acids Res. 28 : 4364 –4375. ↵ Chenna, R., Sugawara, H., Koike, T., Lopez, R., Gibson, T.J., Higgins, D.G., and Thompson, J.D. 2003 . Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 31 : 3497 –3500. ↵ Cline, M., Hughey, R., and Karplus, K. 2002...
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ARTICLE: Identification and Characterization of Multi-Species Conserved Sequences
- Elliott H. Margulies,
- Mathieu Blanchette,
- NISC Comparative Sequencing Program,
- David Haussler,
- and Eric D. Green
Genome Res. December 2003 13: 2507-2518; doi:10.1101/gr.1602203
...of all functional elements in the human . Recent comparative analyses of the human and mouse sequences suggest that ∼5% of the mammalian is under active selection and thus likely serves a functional role ( International Mouse Genome Sequencing Consortium 2002 ; Roskin et al. 2003 ). Within...
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LETTER: Mosaic Organization of Orthologous Sequences in Grass Genomes
- Rentao Song,
- Victor Llaca,
- and Joachim Messing
Genome Res. October 1, 2002 12: 1549-1555; Published in Advance September 13, 2002, doi:10.1101/gr.268302
...hotspots along chromosomes is then manifested during speciation, and a mosaic of conserved segments interspersed with nonconserved segments becomes apparent in the comparison of orthologous regions of different species. Do Grass Genomes Have a Faster Evolutionary Clock? Mammalian s, which diverged much...
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METHODS: An Assessment of Gene Prediction Accuracy in Large DNA Sequences
- Roderic Guigó,
- Pankaj Agarwal,
- Josep F. Abril,
- Moisés Burset,
- and James W. Fickett
Genome Res. October 1, 2000 10: 1631-1642; doi:10.1101/gr.122800
...of mammalian genomic DNA using exon amplification. Nat. Genet. 6 : 98 – 105 . ↵ Claverie J.-M. ( 1997 ) Computational methods for the identification of genes in vertebrate genomic sequences. Hum. Mol. Genet. 6 : 1735 – 1744 . ↵ Couch F.J. , Rommens J.M. , Neuhausen S.L. , Couch E.J. , Rommens J.M. , Neuhausen...
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LETTER: Comparison of Human Chromosome 21 Conserved Nongenic Sequences (CNGs) With the Mouse and Dog Genomes Shows That Their Selective Constraint Is Independent of Their Genic Environment
- Emmanouil T. Dermitzakis,
- Ewen Kirkness,
- Scott Schwarz,
- Ewan Birney,
- Alexandre Reymond,
- and Stylianos E. Antonarakis
Genome Res. May 2004 14: 852-859; Published in Advance April 12, 2004, doi:10.1101/gr.1934904
...of a large number of conserved nongenic sequences (CNGs). The functional significance of this nongenic conservation remains unknown, however. The availability of the sequence of a third mammalian genome, the dog, allows for a large-scale analysis of evolutionary attributes of CNGs in mammals. We have aligned...

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