Browsing by Author "Ishii, Y"

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Open Access
Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.
(Nature, 2002-12-05) Okazaki, Y; Furuno, M; Kasukawa, T; Adachi, J; Bono, H; Kondo, S; Nikaido, I; Osato, N; Osato, N; Saito, R; Suzuki, H; Yamanaka, I; Kiyosawa, H; Yagi, K; Tomaru, Y; Hasegawa, Y; Nogami, A; Schönbach, C; Gojobori, T; Baldarelli, R; Hill, DP; Bult, C; Hume, DA; Hume, DA; Quackenbush, J; Schriml, LM; Kanapin, A; Matsuda, H; Batalov, S; Beisel, KW; Blake, JA; Bradt, D; Brusic, V; Chothia, C; Corbani, LE; Cousins, S; Dalla, E; Dragani, TA; Fletcher, CF; Forrest, A; Frazer, KS; Gaasterland, T; Gariboldi, M; Gissi, C; Godzik, A; Gough, J; Grimmond, S; Gustincich, S; Hirokawa, N; Jackson, IJ; Jarvis, ED; Kanai, A; Kawaji, H; Kawasawa, Y; Kedzierski, RM; King, BL; Konagaya, A; Kurochkin, IV; Lee, Y; Lenhard, B; Lyons, PA; Maglott, DR; Maltais, L; Marchionni, L; McKenzie, L; Miki, H; Nagashima, T; Numata, K; Okido, T; Pavan, WJ; Pertea, G; Pesole, G; Petrovsky, N; Pillai, R; Pontius, JU; Qi, D; Ramachandran, S; Ravasi, T; Reed, JC; Reed, DJ; Reid, J; Ring, BZ; Ringwald, M; Sandelin, A; Schneider, C; Semple, CAM; Setou, M; Shimada, K; Sultana, R; Takenaka, Y; Taylor, MS; Teasdale, RD; Tomita, M; Verardo, R; Wagner, L; Wahlestedt, C; Wang, Y; Watanabe, Y; Wells, C; Wilming, LG; Wynshaw-Boris, A; Yanagisawa, M; Yang, I; Yang, L; Yuan, Z; Zavolan, M; Zhu, Y; Zimmer, A; Carninci, P; Hayatsu, N; Hirozane-Kishikawa, T; Konno, H; Nakamura, M; Sakazume, N; Sato, K; Shiraki, T; Waki, K; Kawai, J; Aizawa, K; Arakawa, T; Fukuda, S; Hara, A; Hashizume, W; Imotani, K; Ishii, Y; Itoh, M; Kagawa, I; Miyazaki, A; Sakai, K; Sasaki, D; Shibata, K; Shinagawa, A; Yasunishi, A; Yoshino, M; Waterston, R; Lander, ES; Rogers, J; Birney, E; Hayashizaki, Y; FANTOM Consortium; RIKEN Genome Exploration Research Group Phase I & II Team
Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 'transcriptional units', contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.
Open Access
Gradual Bidding in Ebay-Like Auctions
(Economic Research Initiatives at Duke (ERID), 2013-09-05) Ambrus, A; Ishii, Y; Burns, J
This paper shows that in online auctions like eBay, if bidders can only place bids at random times, then many di fferent equilibria arise besides truthful bidding, despite the option to leave proxy bids. These equilibria can involve gradual bidding, periods of inactivity, and waiting to start bidding towards the end of the auction - bidding behaviors common on eBay. Bidders in such equilibria implicitly collude to keep the increase of the winning price slow over the duration of the auction. In a common value environment, we characterize a class of equilibria that include the one in which bidding at any price is maximally delayed, and all bids minimally increment the price. The seller's revenue can be a small fraction of what could be obtained at a sealed-bid second-price auction, and in the worst equilibrium it is decreasing in the value of the object. With many bidders, we show that this equilibrium has the feature that bidders are passive until near the end of the auction, and then they start bidding incrementally.
Open Access
On Asynchronicity of Moves and Coordination
(Economic Research Initiatives at Duke (ERID), 2015-03-23) Ambrus, A; Ishii, Y
This paper shows that asynchronicity of moves can lead to a unique prediction in coordination games, in an infinite-horizon setting, under certain conditions on off-equilibrium payoffs. In two-player games we derive necessary and sufficient conditions for play ultimately being absorbed in the Pareto dominant Nash equilibrium of the stage game, for every Markov perfect equilibrium. For players patient enough, the condition is that the Pareto dominant Nash equilibrium is also risk dominant, but for lower levels of patience the condition departs from simple risk-dominance. For general n-player symmetric games with patient players, we show that a necessary and sufficient condition for the Pareto dominant Nash equilibrium to be the unique limit outcome in all symmetric Markov perfect equilibrium is a particular generalization of risk-dominance for more than two players. We provide extensions to the unique selection results to all subgame perfect Nash equilibria, and to coordination games in which different players prefer different Nash equilibria of the stage game.