Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes

By W. James Kent, Robert Baertsch, A. Hinrichs, Webb Miller, David Haussler. Proceedings of the National Academy of Sciences of the United States of America, 2003

930 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/293c49b834103cb24f9c737441c4a1cd0160feba

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

1. W. James Kent
2. David Haussler
3. Martin C. Frith
4. John S. Mattick
5. W. Fletcher
6. Richard A. Young
7. Paul Flicek
8. Ziheng Yang

In Molecular Biology

1. David Haussler
2. Richard A. Young
3. W. James Kent
4. John S. Mattick
5. Glenn Tesler
6. Mark J. P. Chaisson
7. Adam C. Siepel
8. Robert M. Kuhn

In Plant Science

1. David Haussler
2. W. James Kent
3. Adam C. Siepel
4. Robert M. Kuhn
5. John S. Mattick
6. Martin C. Frith
7. Glenn Tesler
8. Mark J. P. Chaisson

Citations in the corpus

• The UCSC Table Browser data retrieval tool (2004, methodology): “The axtChain program written by Jim Kent produces chained BLASTZ alignments between two species (6).”
• Identification and Classification of Conserved RNA Secondary Structures in the Human Genome (2006, methodology): “The filters were based on the following UCSC Human Genome Browser data: simple and low-complexity repeats from the RepeatMasker track, synteny information from the mouse net track [68], and homology information from the Blastz self track.”
• The UCSC Genome Browser database: 2015 update (2014, methodology): “Harris, unpublished thesis), chain/net (18), multiz (59) and conservation tools from the PHAST package (60).”
• The UCSC genome browser and associated tools (2012, methodology): “Tracks generated at UCSC Most standard browsers are further expanded to include comparative genomic annotations [20] as well as Convert and liftOver capabilities.”
• Genome-Wide Comparative Analysis and Expression Pattern of TCP Gene Families in Arabidopsis thaliana and Oryza sativa (2007, neutral): “Genome duplication events are thought to have occurred during angiosperm evolution (Kent et al. 2003; Cannon et al. 2004; Mehan et al. 2004; Li et al. 2006).”
• INDELible: A Flexible Simulator of Biological Sequence Evolution (2009, background): “This causes a spike in the observed indel-size distribution around 300 bp when the human genome is compared with other genomes (Kent et al. 2003).”
• Pol III binding in six mammalian genomes shows high conservation among amino acid isotypes, despite divergence in tRNA gene usage (2011, positive): “Mouse and human have the best-annotated genomes, with 93.3% and 93.4% of the genomes, respectively, in synteny blocks; more generally, a typical pairwise synteny map aligns each genome with more than 90% of the other genome 39 .”
• The UCSC Genome Browser (2003, neutral): “…and EST tracks found in the mRNA and EST group, the Comparative Genomics group contains a wide variety of pairwise chain and net alignment tracks (Kent et al., 2003; Schwartz et al., 2003) that can be used to look for orthologous regions between organisms, large-scale rearrangements,…”
• Ensembl 2007 (2006, methodology): “WGAs are generated in-house using BLASTz (18) with the resulting set of local alignments processed into a form suitable for the above method using the Axt tools (19).”
• miREvo: an integrative microRNA evolutionary analysis platform for next-generation sequencing experiments (2012, methodology): “comparative genomics alignment pipeline [35-37].”
• Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory (2012, methodology): “The relationship between many existing alignment methods [1,3-5,10-23] is qualitatively illustrated in Figure 1.”