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Resource: Global networks of functional coupling in eukaryotes from comprehensive data integration
- Andrey Alexeyenko and
- Erik L.L. Sonnhammer
Genome Res. June 2009 19: 1107-1116; Published in Advance February 25, 2009, doi:10.1101/gr.087528.108
...generated a network in C. intestinalis , for which no large proteomics or genomics data set is yet available. As a positive TS, we used pathway members inferred via orthology. The input data came from the seven eukaryotes listed above, and the resulting Ciona network contained 38,445 links with a confidence...
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RESOURCE: Generation, Annotation, Evolutionary Analysis, and Database Integration of 20,000 Unique Sea Urchin EST Clusters
- Albert J. Poustka,
- Detlef Groth,
- Steffen Hennig,
- Sabine Thamm,
- Andrew Cameron,
- Alfred Beck,
- Richard Reinhardt,
- Ralf Herwig,
- Georgia Panopoulou,
- and Hans Lehrach
Genome Res. December 2003 13: 2736-2746; doi:10.1101/gr.1674103
...of the identified genes to the genome of the urochordate Ciona intestinalis indicate that at least one quarter of the genes thought to be chordate specific were already present at the base of deuterostome evolution. Comparison of the number of gene copies in sea urchins to those in chordates and vertebrates...
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LETTER: The amphioxus genome illuminates vertebrate origins and cephalochordate biology
- Linda Z. Holland,
- Ricard Albalat,
- Kaoru Azumi,
- Èlia Benito-Gutiérrez,
- Matthew J. Blow,
- Marianne Bronner-Fraser,
- Frederic Brunet,
- Thomas Butts,
- Simona Candiani,
- Larry J. Dishaw,
- David E.K. Ferrier,
- Jordi Garcia-Fernàndez,
- Jeremy J. Gibson-Brown,
- Carmela Gissi,
- Adam Godzik,
- Finn Hallböök,
- Dan Hirose,
- Kazuyoshi Hosomichi,
- Tetsuro Ikuta,
- Hidetoshi Inoko,
- Masanori Kasahara,
- Jun Kasamatsu,
- Takeshi Kawashima,
- Ayuko Kimura,
- Masaaki Kobayashi,
- Zbynek Kozmik,
- Kaoru Kubokawa,
- Vincent Laudet,
- Gary W. Litman,
- Alice C. McHardy,
- Daniel Meulemans,
- Masaru Nonaka,
- Robert P. Olinski,
- Zeev Pancer,
- Len A. Pennacchio,
- Mario Pestarino,
- Jonathan P. Rast,
- Isidore Rigoutsos,
- Marc Robinson-Rechavi,
- Graeme Roch,
- Hidetoshi Saiga,
- Yasunori Sasakura,
- Masanobu Satake,
- Yutaka Satou,
- Michael Schubert,
- Nancy Sherwood,
- Takashi Shiina,
- Naohito Takatori,
- Javier Tello,
- Pavel Vopalensky,
- Shuichi Wada,
- Anlong Xu,
- Yuzhen Ye,
- Keita Yoshida,
- Fumiko Yoshizaki,
- Jr-Kai Yu,
- Qing Zhang,
- Christian M. Zmasek,
- Pieter J. de Jong,
- Kazutoyo Osoegawa,
- Nicholas H. Putnam,
- Daniel S. Rokhsar,
- Noriyuki Satoh,
- and Peter W.H. Holland
Genome Res. July 2008 18: 1100-1111; Published in Advance June 18, 2008, doi:10.1101/gr.073676.107
..., including those of protostomes, such as nematodes ( C. elegans Sequencing Consortium 1998 ; Stein et al. 2003 ) and insects ( Adams et al. 2000 ; Mongin et al. 2004 ; The Honeybee Genome Sequencing Consortium 2006 ), and deuterostomes, such as the urochordate Ciona intestinalis ( Dehal et al. 2002...
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REVIEW: Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques
- Laura Elnitski,
- Victor X. Jin,
- Peggy J. Farnham,
- and Steven J.M. Jones
Genome Res. December 2006 16: 1455-1464; Published in Advance October 19, 2006, doi:10.1101/gr.4140006
...enhancer elements. Intraspecies comparative approaches in Ciona intestinalis highlight the versatility of this model organism. Boffelli et al. (2004) identified candidate regulatory regions undergoing the slowest mutation rates relative to the surrounding rates and tested them for functional activity...
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