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INSIGHT/OUTLOOK: Interrelating Different Types of Genomic Data, from Proteome to Secretome: 'Oming in on Function
- Dov Greenbaum,
- Nicholas M. Luscombe,
- Ronald Jansen,
- Jiang Qian,
- and Mark Gerstein
Genome Res. September 1, 2001 11: 1463-1468; doi:10.1101/gr.207401
...of how and why a protein is secreted is valuable as the bacterium's ability to export numerous enzymes enables it to degrade extracellular substrates and survive in a continuously changing environment. Moreover, it will eventually allow these bacteria to be employed as “cellular factories” for secreting...
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Research: Meta-analysis of human and mouse ALS astrocytes reveals multi-omic signatures of inflammatory reactive states
- Oliver J. Ziff,
- Benjamin E. Clarke,
- Doaa M. Taha,
- Hamish Crerar,
- Nicholas M. Luscombe,
- and Rickie Patani
Genome Res. January 2022 32: 71-84; Published in Advance December 28, 2021, doi:10.1101/gr.275939.121
..., transmembrane protein 259 (Tmem259, also known as membralin), was shown to maintain expression of Slc1a2, and astrocyte-specific membralin deletion led to the accumulation of extracellular glutamate, resulting in motor neuron death (Jiang et al. 2019).In response to a wide variety of stimuli, astrocytes can...
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Research: Venus flytrap carnivorous lifestyle builds on herbivore defense strategies
- Felix Bemm,
- Dirk Becker,
- Christina Larisch,
- Ines Kreuzer,
- Maria Escalante-Perez,
- Waltraud X. Schulze,
- Markus Ankenbrand,
- Anna-Lena Van de Weyer,
- Elzbieta Krol,
- Khaled A. Al-Rasheid,
- Axel Mithöfer,
- Andreas P. Weber,
- Jörg Schultz,
- and Rainer Hedrich
Genome Res. June 2016 26: 812-825; Published in Advance May 4, 2016, doi:10.1101/gr.202200.115
.... 2014). Both processes are related to oxidative stress management and are essential for controlling protein translation and maturation (Howell 2013). These signals likely originate in active glands characterized by persisting translation, folding, and targeting of extracellular hydrolases (see above...
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LETTER: Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis
- Timothy P. Stinear,
- Torsten Seemann,
- Paul F. Harrison,
- Grant A. Jenkin,
- John K. Davies,
- Paul D.R. Johnson,
- Zahra Abdellah,
- Claire Arrowsmith,
- Tracey Chillingworth,
- Carol Churcher,
- Kay Clarke,
- Ann Cronin,
- Paul Davis,
- Ian Goodhead,
- Nancy Holroyd,
- Kay Jagels,
- Angela Lord,
- Sharon Moule,
- Karen Mungall,
- Halina Norbertczak,
- Michael A. Quail,
- Ester Rabbinowitsch,
- Danielle Walker,
- Brian White,
- Sally Whitehead,
- Pamela L.C. Small,
- Roland Brosch,
- Lalita Ramakrishnan,
- Michael A. Fischbach,
- Julian Parkhill,
- and Stewart T. Cole
Genome Res. May 2008 18: 729-741; Published in Advance April 10, 2008, doi:10.1101/gr.075069.107
...and vertebrate hosts, as well as of a generalist, equipped to survive under changing and sometimes extracellular environmental conditions ( Stamm and Brown 2004 ). A dichotomous lifestyle was first proposed by the seminal transmission studies of Clark and Shepard (1963) when they observed that fish, parenterally...
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COMMENTARY: A Guide to the Mammalian Genome
- Yasushi Okazaki and
- David A. Hume
Genome Res. June 2003 13: 1267-1272; doi:10.1101/gr.1445603
...DNA sequence. Genome Res. (this issue). ↵ Grimmond, S.M., Miranda, K.C., Yuan, Z., Davis, M.J., Hume, D.A., Yagi, K., Tominaga, N., Bono, H., Hayashizaki, Y., Okazaki, Y., et al. 2003 . The Mouse secretome: Functional classification of the proteins secreted into the extracellular environment. Genome Res. (this...
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LETTER: Analysis of the Mouse Transcriptome for Genes Involved in the Function of the Nervous System
- Stefano Gustincich,
- Serge Batalov,
- Kirk W. Beisel,
- Hidemasa Bono,
- Piero Carninci,
- Colin F. Fletcher,
- Sean Grimmond,
- Nobutaka Hirokawa,
- Erich D. Jarvis,
- Tim Jegla,
- Yuka Kawasawa,
- Julianna LeMieux,
- Harukata Miki,
- Elio Raviola,
- Rohan D. Teasdale,
- Naoko Tominaga,
- Ken Yagi,
- Andreas Zimmer,
- RIKEN GER Group,
- GSL Members,
- Yoshihide Hayashizaki,
- and Yasushi Okazaki
Genome Res. June 2003 13: 1395-1401; doi:10.1101/gr.1135303
...., Hayashizaki, Y., and Okazaki, Y., 2003 . The mouse secretome: Functional classification of the proteins secreted into the extracellular environment. Genome Res. (this issue). ↵ Gusella, J.F., Persichetti, F., and MacDonald, M.E. 1997 . The genetic defect causing Huntington's disease: Repeated in other...
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LETTER: Systematic Expression Profiling of the Mouse Transcriptome Using RIKEN cDNA Microarrays
- Hidemasa Bono,
- Ken Yagi,
- Takeya Kasukawa,
- Itoshi Nikaido,
- Naoko Tominaga,
- Rika Miki,
- Yosuke Mizuno,
- Yasuhiro Tomaru,
- Hitoshi Goto,
- Hiroyuki Nitanda,
- Daisuke Shimizu,
- Hirochika Makino,
- Tomoyuki Morita,
- Junshin Fujiyama,
- Takehito Sakai,
- Takashi Shimoji,
- David A. Hume,
- RIKEN GER Group,
- GSL Members,
- Yoshihide Hayashizaki,
- and Yasushi Okazaki
Genome Res. June 2003 13: 1318-1323; doi:10.1101/gr.1075103
...: 1425 -1433. ↵ Grimmond, S.M., Miranda, K.C., Yuan, Z., Davis, M.J., Hume, D.A., Yagi, K., Tominaga, N., Bono, H., Hayashizaki, Y., Okazaki, Y., et al. 2003 . The Mouse Secretome: Functional classification of the proteins secreted into the extracellular environment. Genome Res. (this issue). ↵ Ichikawa...
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ARTICLE: Identification of Putative Noncoding RNAs Among the RIKEN Mouse Full-Length cDNA Collection
- Koji Numata,
- Akio Kanai,
- Rintaro Saito,
- Shinji Kondo,
- Jun Adachi,
- Laurens G. Wilming,
- David A. Hume,
- RIKEN GER Group,
- GSL Members,
- Yoshihide Hayashizaki,
- and Masaru Tomita
Genome Res. June 2003 13: 1301-1306; doi:10.1101/gr.1011603
...., Hayashizaki, Y., Okazaki, Y., et al. 2003 . The mouse secretome: Functional classification of the proteins secreted into the extracellular environment. Genome Res. (this issue). ↵ Grosshans, H. and Slack, F.J. 2002 . Micro-RNAs: Small is plentiful. J. Cell. Biol. 156 : 17 -21. ↵ Hatada, I., Morita, S., Obata...
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LETTER: CDS Annotation in Full-Length cDNA Sequence
- Masaaki Furuno,
- Takeya Kasukawa,
- Rintaro Saito,
- Jun Adachi,
- Harukazu Suzuki,
- Richard Baldarelli,
- Yoshihide Hayashizaki,
- and Yasushi Okazaki
Genome Res. June 2003 13: 1478-1487; doi:10.1101/gr.1060303
.... 5 : 81 -87. ↵ Grimmond, S.M., Miranda, K.C., Yuan, Z., Davis, M.J., Hume, D.A., Yagi, K., Tominaga, N., Bono, H., Hayashizaki, Y., Okazaki, Y., et al. 2003 . The mouse secretome. Functional classification of the proteins secreted into the extracellular environment. Genome Res. (this issue). ↵ Hentze...
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ARTICLE: Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome
- Timothy Ravasi,
- Harukazu Suzuki,
- Ken C. Pang,
- Shintaro Katayama,
- Masaaki Furuno,
- Rie Okunishi,
- Shiro Fukuda,
- Kelin Ru,
- Martin C. Frith,
- M. Milena Gongora,
- Sean M. Grimmond,
- David A. Hume,
- Yoshihide Hayashizaki,
- and John S. Mattick
Genome Res. January 2006 16: 11-19; Published in Advance December 12, 2005, doi:10.1101/gr.4200206
...by common environmental signals. In addition, -wide transcriptome analysis has identified large numbers of developmentally coordinated non-coding transcripts in Drosophila that are more conserved than non-expressed non-coding sequences ( Stolc et al. 2004 ). In well-characterized loci, such as the bithorax...

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