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Resource: Subtelomeric CTCF and cohesin binding site organization using improved subtelomere assemblies and a novel annotation pipeline
- Nicholas Stong,
- Zhong Deng,
- Ravi Gupta,
- Sufen Hu,
- Shiela Paul,
- Amber K. Weiner,
- Evan E. Eichler,
- Tina Graves,
- Catrina C. Fronick,
- Laura Courtney,
- Richard K. Wilson,
- Paul M. Lieberman,
- Ramana V. Davuluri,
- and Harold Riethman
Genome Res. June 2014 24: 1039-1050; Published in Advance March 27, 2014, doi:10.1101/gr.166983.113
...detectable visually (e.g., Figure 1. Sequence organization of updated subtelomere sequence assemblies. The assemblies are oriented with the telomere on the left and aligned to maximize paralogous blocks of SREs following the methods described in Linardopoulou et al. (2005). Regions of the assemblies...
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LETTER: Gene-breaking: A new paradigm for human retrotransposon-mediated gene evolution
- Sarah J. Wheelan,
- Yasunori Aizawa,
- Jeffrey S. Han,
- and Jef D. Boeke
Genome Res. August 2005 15: 1073-1078; Published in Advance July 15, 2005, doi:10.1101/gr.3688905
...for mRNA-to-genomic alignments. Genome Res. 11 : 1952 –1957. Gene-breaking: A new paradigm for human retrotransposon-mediated gene evolution Sarah J. Wheelan 1 , 2 , Yasunori Aizawa 1 , 2 , Jeffrey S. Han 1 , and Jef D. Boeke 1 , 3 1 Department of Molecular Biology and Genetics, The Johns Hopkins...
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Methods: Computational Discovery of Internal Micro-Exons
- Natalia Volfovsky,
- Brian J. Haas,
- and Steven L. Salzberg
Genome Res. June 2003 13: 1216-1221; doi:10.1101/gr.677503
....D., Myers, E.W., Li, P.W., Mural, R.J., Sutton, G.G., Smith, H.O., Yandell, M., Evans, C.A., Holt, R.A., et al. 2001 . The sequence of the human . Science 291 : 1304 –1351. ↵ Wheelan, S.J., Church, D.M., and Ostell, J.M. 2001 . Spidey: A tool for mRNA-to-genomic alignments. Genome Res. 11 : 1952 –1957. ↵ Xu...
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Research: Protein variation in blood-dwelling schistosome worms generated by differential splicing of micro-exon gene transcripts
- Ricardo DeMarco,
- William Mathieson,
- Sophia J. Manuel,
- Gary P. Dillon,
- Rachel S. Curwen,
- Peter D. Ashton,
- Alasdair C. Ivens,
- Matthew Berriman,
- Sergio Verjovski-Almeida,
- and R. Alan Wilson
Genome Res. August 2010 20: 1112-1121; Published in Advance July 6, 2010, doi:10.1101/gr.100099.109
...and immunolocalization showed that MEG transcripts and proteins were restricted to glands or epithelia exposed to the external environment. The ability of schistosomes to produce a complex pool of variant proteins aligns them with the other major groups of blood parasites, but using a completely different mechanism. We...
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Methods: Gene and alternative splicing annotation with AIR
- Liliana Florea,
- Valentina Di Francesco,
- Jason Miller,
- Russell Turner,
- Alison Yao,
- Michael Harris,
- Brian Walenz,
- Clark Mobarry,
- Gennady V. Merkulov,
- Rosane Charlab,
- Ian Dew,
- Zuoming Deng,
- Sorin Istrail,
- Peter Li,
- and Granger Sutton
Genome Res. January 2005 15: 54-66; doi:10.1101/gr.2889405
...on alignments of protein and cDNA (EST, mRNA) sequences with genomic sequences (Procrustes, Gelfand et al. 1996 ; EstGenome, Mott 1997 ; sim4, Florea et al. 1998 ; GeneWise, Birney and Durbin 2000 ; Spidey, Wheelan et al. 2001 ) depend critically on the completeness and quality of sequences used. More recently...
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LETTER: Analysis of Human mRNAs With the Reference Genome Sequence Reveals Potential Errors, Polymorphisms, and RNA Editing
- Terrence S. Furey,
- Mark Diekhans,
- Yontao Lu,
- Tina A. Graves,
- Lachlan Oddy,
- Jennifer Randall-Maher,
- LaDeana W. Hillier,
- Richard K. Wilson,
- and David Haussler
Genome Res. October 15, 2004 14: 2034-2040; doi:10.1101/gr.2467904
....L., Feingold, E.A., and Collins, F.S. 1999 . The mammalian gene collection. Science 286 : 455 -457. ↵ Wheelan, S.J., Church, D.M., and Ostell, J.M. 2001 . Spidey: A tool for mRNA-to-genomic alignments. Genome Res. 11 : 1952 -1957. ↵ Yu, W., Andersson, B., Worley, K., Muzny, D., Ding, Y., Liu, W., Ricafrente, J...
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LETTER: Mapping and Initial Analysis of Human Subtelomeric Sequence Assemblies
- Harold Riethman,
- Anthony Ambrosini,
- Carlos Castaneda,
- Jeffrey Finklestein,
- Xue-Lan Hu,
- Uma Mudunuri,
- Sheila Paul,
- and Jun Wei
Genome Res. January 2004 14: 18-28; doi:10.1101/gr.1245004
...., Sandkuijl, L., Padberg, G.W., Frants, R.R., and van Der Maarel, S.M. 2000 . Interchromosomal repeat array interactions between chromosomes 4 and 10: A model for subtelomeric plasticity. Hum. Mol. Genet. 9 : 2879 -2884. ↵ Wheelan, S.J., Church, D.M., and Ostell, J.M. 2001 . Spidey: A tool for mRNA-to-genomic...
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LETTER: Shannon Information Theoretic Computation of Synonymous Codon Usage Biases in Coding Regions of Human and Mouse Genomes
- Barry Zeeberg
Genome Res. June 1, 2002 12: 944-955; doi:10.1101/gr.213402
..., 2001) spanning each RefSeq was determined from Spidey (Wheelan, Church, and Ostell 2001) alignments. Each contig containing a Spidey hit was partitioned into adjacent 20 kb segments, and the GC content was computed for each segment. Finally, the average GC content for the adjacent genomic segments...
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PERSPECTIVE: Genome annotation past, present, and future: How to define an ORF at each locus
- Michael R. Brent
Genome Res. December 2005 15: 1777-1786; doi:10.1101/gr.3866105
...reading frame (ORF) for every gene—the first plateau on the long climb toward a comprehensive catalog. These strategies—sequencing randomly selected cDNA clones, aligning protein sequences identified in other organisms, sequencing more genomes, and manual curation—will have to be supplemented by large...
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LETTER: Abundant novel transcriptional units and unconventional gene pairs on human chromosome 22
- Leonard Lipovich and
- Mary-Claire King
Genome Res. January 2006 16: 45-54; Published in Advance December 12, 2005, doi:10.1101/gr.3883606
...conservation and localized to gaps in the human–mouse BLASTZ alignment. Novel TUs were richer in exonic primate-specific interspersed repetitive elements ( P = 0.001) and were more likely to rely on splice junctions provided by them, than were known genes: 19% of spliced TUs, versus 5% of spliced genes, had...

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