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Publications
Top cited & the latest publications available from here
＜Papers＞
（2012）
- Short-chain fatty acid receptor GPR41-mediated activation of sympathetic neurons involves synapsin 2b phosphorylation
Daisuke Inoue, Ikuo Kimura, Masaki Wakabayashi, Hiroki Tsumoto, Kentaro Ozawa, Takafumi Hara, Yoshinori Takei, Akira Hirasawa, Yasushi Ishihama, Gozoh Tsujimoto.
FEBS lett., in press.
- Ectopic Expression of Hmgn2 Antagonizes Mouse Erythroid Differentiation in Vitro.
K. Kulkeaw, T. Inoue, C. Mizuochi, Y. Horio, Y. Ishihama, D. Sugiyama.
Cell Biol Int., in press.
- Human Proteome Analysis by Using Reversed Phase Monolithic Silica Capillary Columns with Enhanced Sensitivity.
M. Iwasaki, N. Sugiyama, N. Tanaka, Y. Ishihama.
J Chromatogr A., in press.
- Shotguns in the Front Line: Phosphoproteomics in Plants.
H. Nakagami, N. Sugiyama, Y. Ishihama, K. Shirasu.
Plant Cell Physiol., in press.
（2011）
- OryzaPG-DB: Rice Proteome Database based on Shotgun Proteogenomics.
M. Helmy, M. Tomita, Y. Ishihama
BMC Plant Biology 11, 63 (2011).
- Integrative Features of the Yeast Phosphoproteome and Protein–Protein Interaction Map.
N. Yachie, R. Saito, N. Sugiyama, M. Tomita, Y. Ishihama
PLoS Computational Biology 7, e1001064 (2011).
- Use of Stable Isotope Labeling by Amino Acids in Cell Culture as a Spike-in Standard in Quantitative Proteomics.
T. Geiger, J. R. Wisniewski, J. Cox, S. Zanivan, M. Kruger, Y. Ishihama, M. Mann
Nature Protocols 6, 147–157 (2011).
（2010）
- Detection of Rap1A as a Yessotoxin Binding Protein from Blood Cell Membranes.
S. Ujihara, T. Oishi, R. Mouri, R. Tamate, K. Konoki, N. Matsumori, M. Murata, Y. Oshima, N. Sugiyama, M. Tomita, Y. Ishihama
Bioorg. Med. Chem. Lett. 20, 6443-6446 (2010).
- A Systematic Survey of in vivo Obligate Chaperonin-Dependent Substrates.
K. Fujiwara, Y. Ishihama, K. Nakahigashi, T. Soga, H. Taguchi
EMBO J. 29, 1552-1564 (2010).
- One-Dimensional Capillary Liquid Chromatographic Separation
Coupled with Tandem Mass Spectrometry Unveils the Escherichia coli
Proteome on a Microarray Scale.
M. Iwasaki, S. Miwa, T. Ikegami, M. Tomita, N. Tanaka, Y. Ishihama
Anal. Chem. 82, 2616-2620 (2010).
- Quantitative
Proteome and Phosphoproteome Analyses of Cultured Cells Based on SILAC
Labeling without Requirement of Serum Dialysis.
K. Imami, N. Sugiyama, M. Tomita, Y. Ishihama
Mol. Biosyst. 6, 594-602 (2010).
- Large-Scale Comparative Phosphoproteomics Identifies Conserved Phosphorylation Sites in Plants.
H. Nakagami, N. Sugiyama, K. Mochida, A. Daudi, Y. Yoshida, T. Toyoda, M. Tomita, Y. Ishihama, K. Shirasu
Plant. Physiol. 153, 1161-1174 (2010).
- emPAI
Calc--for the Estimation of Protein Abundance from Large-Scale
Identification Data by Liquid Chromatography-Tandem Mass Spectrometry.
K. Shinoda, M. Tomita, Y. Ishihama
Bioinformatics 26, 576-577 (2010).
- Development of Titania Particles Used for Phosphopeptide Enrichment in Mass Spectrometry-based Phosphoproteomics.
Y. Kyono, N. Sugiyama, K. Imami, K. Miyazaki, M. Ohira, M. Tomita, Y. Ishihama
J. Mass Spectrom. Soc. Jpn. 58, 129-138 (2010).
- Chemical Dephosphorylation for Identification of Multiply Phosphorylated Peptides and Phosphorylation Site Determination.
Y. Kyono, N. Sugiyama, M. Tomita, Y. Ishihama
Rapid Commun. Mass Spectrom. 24, 2277-2282 (2010).
- Towards the Systematic Discovery of Signal Transduction Networks Using Phosphorylation Dynamics Data.
H. Imamura, N. Yachie, R. Saito, Y. Ishihama, M. Tomita
BMC Bioinformatics 11, 232 (2010).
＜Reviews＞
- Peptide Identification by Searching Large-Scale Tandem
Mass Spectra against Large Databases: Bioinformatics Methods in
Proteogenomics
M. Helmy, M. Tomita, Y. Ishihama
Genes, Genomes and Genomics 6 (Special Issue 1), 76-85 (2012).
- Development of Dual Stable Isotope Labeling by Amino Acids in Cell Culture and Application to Quantitative Proteomics.
K. Imami, M. Tomita, Y. Ishihama.
J. Mass Spectrom. Soc. Jpn. 58, 81-87 (2010).
＜Books＞
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