Searching journal content for articles similar to Johnson et al. 14 (12): 2448.

Displaying results 1-10 of 15

For checked items

view abstracts
download to citation manager

Select this article
Resource: Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis
- Rui Yokomori,
- Kotaro Shimai,
- Koki Nishitsuji,
- Yutaka Suzuki,
- Takehiro G. Kusakabe,
- and Kenta Nakai
Genome Res. January 2016 26: 140-150; Published in Advance December 14, 2015, doi:10.1101/gr.184648.114
.....org (Yoshihama et al. 2002; Perry 2005; Yamashita et al. 2008; Parry et al. 2010). The tunicate Ciona intestinalis, which is an invertebrate chordate, has recently emerged as a powerful model organism for biological research (Sasakura et al. 2012; Stolfi and Christiaen 2012). The draft sequence of C...
Select this article
PERSPECTIVE: Unraveling genomic regulatory networks in the simple chordate, Ciona intestinalis
- Weiyang Shi,
- Michael Levine,
- and Brad Davidson
Genome Res. December 2005 15: 1668-1674; doi:10.1101/gr.3768905
...-posterior cell polarity of notochord cells. Curr. Biol. 15 : 79 -85. ↵ Johnson, D.S., Davidson, B., Brown, C.D., Smith, W.C., and Sidow, A. 2004 . Noncoding regulatory sequences of Ciona exhibit strong correspondence between evolutionary constraint and functional importance. Genome Res. 14 : 2448 -2456...
Select this article
RESOURCE: Chromosomal mapping of 170 BAC clones in the ascidian Ciona intestinalis
- Eiichi Shoguchi,
- Takeshi Kawashima,
- Yutaka Satou,
- Makoto Hamaguchi,
- Tadasu Sin-I,
- Yuji Kohara,
- Nik Putnam,
- Daniel S. Rokhsar,
- and Nori Satoh
Genome Res. February 2006 16: 297-303; Published in Advance December 14, 2005, doi:10.1101/gr.4156606
...sequences of Ciona exhibit strong correspondence between evolutionary constraint and functional importance. Genome Res. 14 : 2448 -2456. ↵ Kobayashi, M., Matsuda, M., Asakawa, S., Shimizu, N., Nagahama, Y., Satou, Y., and Satoh, N. 2002 . Construction of BAC libraries derived from the ascidian Ciona...
Select this article
Methods: Diploid genome reconstruction of Ciona intestinalis and comparative analysis with Ciona savignyi
- Jong Hyun Kim,
- Michael S. Waterman,
- and Lei M. Li
Genome Res. July 2007 17: 1101-1110; Published in Advance June 13, 2007, doi:10.1101/gr.5894107
...Siepel et al. (2005) when the assembled sizes of the two Ciona species are considered (116.7 Mb and 157 Mb) ( Dehal et al. 2002 ; Vinson et al. 2005 ). One possible explanation is that in the Ciona intestinalis , relatively short noncoding regions, possibly regulatory elements, are under strong...
OPEN ACCESS ARTICLE
Select this article
Methods: Assembly of polymorphic genomes: Algorithms and application to Ciona savignyi
- Jade P. Vinson,
- David B. Jaffe,
- Keith O'Neill,
- Elinor K. Karlsson,
- Nicole Stange-Thomann,
- Scott Anderson,
- Jill P. Mesirov,
- Nori Satoh,
- Yutaka Satou,
- Chad Nusbaum,
- Bruce Birren,
- James E. Galagan,
- and Eric S. Lander
Genome Res. August 2005 15: 1127-1135; doi:10.1101/gr.3722605
...haplotypes separately and then merging them to obtain a reference sequence. Our method was developed to assemble the genome of the sea squirt Ciona savignyi , which was sequenced to a depth of 12.7× from a single wild individual. By comparing finished clones of the two haplotypes we determined...
Select this article
ARTICLE: Ancient duplicated conserved noncoding elements in vertebrates: A genomic and functional analysis
- Gayle K. McEwen,
- Adam Woolfe,
- Debbie Goode,
- Tanya Vavouri,
- Heather Callaway,
- and Greg Elgar
Genome Res. April 2006 16: 451-465; Published in Advance March 13, 2006, doi:10.1101/gr.4143406
...conserved sequences with an interesting evolutionary history. They have remained practically unchanged in the 450 million years (Myr) since the divergence of fish and mammals (sequence identity of &gt;74% over at least 100 bases) but do not appear to be conserved in urochordates, such as Ciona intestinalis...
Select this article
LETTER: Experimental validation of predicted mammalian erythroid cis-regulatory modules
- Hao Wang,
- Ying Zhang,
- Yong Cheng,
- Yuepin Zhou,
- David C. King,
- James Taylor,
- Francesca Chiaromonte,
- Jyotsna Kasturi,
- Hanna Petrykowska,
- Brian Gibb,
- Christine Dorman,
- Webb Miller,
- Louis C. Dore,
- John Welch,
- Mitchell J. Weiss,
- and Ross C. Hardison
Genome Res. December 2006 16: 1480-1492; Published in Advance October 12, 2006, doi:10.1101/gr.5353806
...is strongly associated with evolutionary conservation in noncoding regulatory regions of Ciona ( Johnson et al. 2004 ). Another approach using aligned genomic sequences to predict CRMs is the computation of regulatory potential (RP), which captures context and pattern information in addition to conservation...
OPEN ACCESS ARTICLE
Select this article
ARTICLE: De novo discovery of a tissue-specific gene regulatory module in a chordate
- David S. Johnson,
- Qing Zhou,
- Kasumi Yagi,
- Nori Satoh,
- Wing Wong,
- and Arend Sidow
Genome Res. October 2005 15: 1315-1324; Published in Advance September 16, 2005, doi:10.1101/gr.4062605
...of Ciona exhibit strong correspondence between evolutionary constraint and functional importance. Genome Res. 14 : 2448 -2456. ↵ Kellis, M., Patterson, N., Endrizzi, M., Birren, B., and Lander, E.S. 2003 . Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423...
Select this article
LETTER: Close sequence comparisons are sufficient to identify human cis-regulatory elements
- Shyam Prabhakar,
- Francis Poulin,
- Malak Shoukry,
- Veena Afzal,
- Edward M. Rubin,
- Olivier Couronne,
- and Len A. Pennacchio
Genome Res. July 2006 16: 855-863; Published in Advance June 12, 2006, doi:10.1101/gr.4717506
...Close sequence comparisons are sufficient to identify human cis -regulatory elements Shyam Prabhakar 1 , 2 , 4 , Francis Poulin 1 , 3 , Malak Shoukry 1 , Veena Afzal 1 , Edward M. Rubin 1 , 2 , Olivier Couronne 1 , 2...
Select this article
Research: Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logic
- Annelien Verfaillie,
- Dmitry Svetlichnyy,
- Hana Imrichova,
- Kristofer Davie,
- Mark Fiers,
- Zeynep Kalender Atak,
- Gert Hulselmans,
- Valerie Christiaens,
- and Stein Aerts
Genome Res. July 2016 26: 882-895; Published in Advance May 18, 2016, doi:10.1101/gr.204149.116
...Figs. S29, S30). Taken together, these results suggest that functionality is predictable by the sequence and decreases gradually by the strength of the TP53 binding site. Discussion The functional annotation of all regulatory elements in the noncoding part of the human is a key challenge in biology...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Johnson et al. 14 (12): 2448.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: