Publications by authors named "Yasushi Ishihama"

100Publications

GlycoPOST realizes FAIR principles for glycomics mass spectrometry data.

Nucleic Acids Res 2020 Nov 11. Epub 2020 Nov 11.

Division of Bioinformatics, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan.

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http://dx.doi.org/10.1093/nar/gkaa1012DOI Listing
November 2020

Isolation of acetylated and unmodified protein N-terminal peptides by strong cation exchange chromatographic separation of TrypN-digested peptides.

Mol Cell Proteomics 2020 Nov 2. Epub 2020 Nov 2.

Grad School of Pharmaceutical Sciences, Kyoto University, Japan

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http://dx.doi.org/10.1074/mcp.TIR120.002148DOI Listing
November 2020

Quantitative nascent proteome profiling by dual pulse labeling with O-propargyl-puromycin and stable isotope labeled amino acids.

J Biochem 2020 Sep 14. Epub 2020 Sep 14.

Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan.

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http://dx.doi.org/10.1093/jb/mvaa104DOI Listing
September 2020

Extending the Separation Space with Trapped Ion Mobility Spectrometry Improves the Accuracy of Isobaric Tag-Based Quantitation in Proteomic LC/MS/MS.

Anal Chem 2020 06 28;92(12):8037-8040. Epub 2020 May 28.

Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.

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http://dx.doi.org/10.1021/acs.analchem.0c01695DOI Listing
June 2020

Mitochondrial lipoylation integrates age-associated decline in brown fat thermogenesis.

Nat Metab 2019 Sep 16;1(9):886-898. Epub 2019 Sep 16.

University of California, San Francisco Diabetes Center, San Francisco, CA, USA.

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http://dx.doi.org/10.1038/s42255-019-0106-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169975PMC
September 2019

Blood concentrations of small extracellular vesicles are determined by a balance between abundant secretion and rapid clearance.

J Extracell Vesicles 2020 26;9(1):1696517. Epub 2019 Nov 26.

Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan.

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http://dx.doi.org/10.1080/20013078.2019.1696517DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6882433PMC
November 2019

Mass Spectrometry-Compatible Subcellular Fractionation for Proteomics.

J Proteome Res 2020 01 17;19(1):75-84. Epub 2019 Oct 17.

Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences , Kyoto University , Sakyo-ku, Kyoto 606-8501 , Japan.

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http://dx.doi.org/10.1021/acs.jproteome.9b00347DOI Listing
January 2020

Large-scale Discovery of Substrates of the Human Kinome.

Sci Rep 2019 07 19;9(1):10503. Epub 2019 Jul 19.

Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan.

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http://dx.doi.org/10.1038/s41598-019-46385-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6642169PMC
July 2019

Removal of Interference MS/MS Spectra for Accurate Quantification in Isobaric Tag-Based Proteomics.

J Proteome Res 2019 06 6;18(6):2535-2544. Epub 2019 May 6.

Center for iPS Cell Research and Application , Kyoto University , Kyoto 606-8507 , Japan.

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http://dx.doi.org/10.1021/acs.jproteome.9b00078DOI Listing
June 2019

Comparative proteomics of Helicobacter pylori strains reveals geographical features rather than genomic variations.

Genes Cells 2019 Feb 20;24(2):139-150. Epub 2019 Jan 20.

Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan.

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http://dx.doi.org/10.1111/gtc.12662DOI Listing
February 2019

Phosphorylation of the Ribosomal Protein RPL12/uL11 Affects Translation during Mitosis.

Mol Cell 2018 10 13;72(1):84-98.e9. Epub 2018 Sep 13.

Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany; Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2018.08.019DOI Listing
October 2018

"Biomolecular Mass Spectrometry".

Anal Sci 2018 ;34(9):989

Faculty of Pharmaceutical Sciences, Tokyo University of Science.

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http://dx.doi.org/10.2116/analsci.GE1809DOI Listing
October 2018

Retention Order Reversal of Phosphorylated and Unphosphorylated Peptides in Reversed-Phase LC/MS.

Anal Sci 2018 Sep 27;34(9):1037-1041. Epub 2018 Jul 27.

Graduate School of Pharmaceutical Sciences, Kyoto University.

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http://dx.doi.org/10.2116/analsci.18SCP11DOI Listing
September 2018

Necrostatin-7 suppresses RANK-NFATc1 signaling and attenuates macrophage to osteoclast differentiation.

Biochem Biophys Res Commun 2018 09 7;503(2):544-549. Epub 2018 Jul 7.

Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan; Department of Pathobiology, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.bbrc.2018.05.153DOI Listing
September 2018

Phosphoproteomic profiling reveals ABA-responsive phosphosignaling pathways in Physcomitrella patens.

Plant J 2018 05 23;94(4):699-708. Epub 2018 Apr 23.

Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei, Tokyo, 184-8588, Japan.

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http://dx.doi.org/10.1111/tpj.13891DOI Listing
May 2018

Peptide Retention in Hydrophilic Strong Anion Exchange Chromatography Is Driven by Charged and Aromatic Residues.

Anal Chem 2018 04 21;90(7):4635-4640. Epub 2018 Mar 21.

Bioanalytics, Institute of Biotechnology , Technische Universität Berlin , 13355 Berlin , Germany.

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http://pubs.acs.org/doi/10.1021/acs.analchem.7b05157
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http://dx.doi.org/10.1021/acs.analchem.7b05157DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5937359PMC
April 2018

Phospholipid flippase ATP11C is endocytosed and downregulated following Ca-mediated protein kinase C activation.

Nat Commun 2017 11 10;8(1):1423. Epub 2017 Nov 10.

Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan.

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http://dx.doi.org/10.1038/s41467-017-01338-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5680300PMC
November 2017

Progress in a selective method for the determination of the acetaldehyde-derived DNA adducts by using HILIC-ESI-MS/MS.

Talanta 2018 Jan 25;177:12-17. Epub 2017 Sep 25.

Gifu Pharmaceutical University, Daigaku-nishi, Gifu 501-1196, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.talanta.2017.09.055DOI Listing
January 2018

Absolute Phosphorylation Stoichiometry Analysis by Motif-Targeting Quantitative Mass Spectrometry.

Methods Mol Biol 2017 ;1636:313-325

Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan.

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http://dx.doi.org/10.1007/978-1-4939-7154-1_20DOI Listing
April 2018

Identifications of Putative PKA Substrates with Quantitative Phosphoproteomics and Primary-Sequence-Based Scoring.

J Proteome Res 2017 04 15;16(4):1825-1830. Epub 2017 Mar 15.

Graduate School of Pharmaceutical Sciences, Kyoto University , Sakyo-ku, Kyoto 606-8501, Japan.

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http://dx.doi.org/10.1021/acs.jproteome.7b00087DOI Listing
April 2017

Secretome analysis to elucidate metalloprotease-dependent ectodomain shedding of glycoproteins during neuronal differentiation.

Genes Cells 2017 Feb 13;22(2):237-244. Epub 2017 Jan 13.

Department of Growth Regulation, Institute for Frontier Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan.

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http://dx.doi.org/10.1111/gtc.12466DOI Listing
February 2017

A conditional proteomics approach to identify proteins involved in zinc homeostasis.

Nat Methods 2016 Nov 12;13(11):931-937. Epub 2016 Sep 12.

Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan.

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http://dx.doi.org/10.1038/nmeth.3998DOI Listing
November 2016

Flagellin FliC Phosphorylation Affects Type 2 Protease Secretion and Biofilm Dispersal in Pseudomonas aeruginosa PAO1.

PLoS One 2016 4;11(10):e0164155. Epub 2016 Oct 4.

Metabolites Biology Lab, Department of Biological Sciences, National University of Singapore, Singapore, Singapore.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0164155PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5049796PMC
June 2017

MEKK1-dependent phosphorylation of calponin-3 tunes cell contractility.

J Cell Sci 2016 10 15;129(19):3574-3582. Epub 2016 Aug 15.

Mechanobiology Institute, National University of Singapore, 117411 Singapore Mechanobiology Laboratory, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan

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http://jcs.biologists.org/content/joces/early/2016/08/15/jcs
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http://jcs.biologists.org/lookup/doi/10.1242/jcs.189415
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http://dx.doi.org/10.1242/jcs.189415DOI Listing
October 2016

Identification of Mitosis-Specific Phosphorylation in Mitotic Chromosome-Associated Proteins.

J Proteome Res 2016 09 17;15(9):3331-41. Epub 2016 Aug 17.

Graduate School of Pharmaceutical Sciences, Kyoto University 46-29 Yoshidashimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan.

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http://dx.doi.org/10.1021/acs.jproteome.6b00512DOI Listing
September 2016

Improved Proteome and Phosphoproteome Analysis on a Cation Exchanger by a Combined Acid and Salt Gradient.

Anal Chem 2016 08 2;88(16):7899-903. Epub 2016 Aug 2.

Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition , Ibaraki, Osaka 567-0085, Japan.

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http://dx.doi.org/10.1021/acs.analchem.6b01232DOI Listing
August 2016

Membrane-Spanning Sequences in Endoplasmic Reticulum Proteins Promote Phospholipid Flip-Flop.

Biophys J 2016 Jun;110(12):2689-2697

Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2016.05.023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4919424PMC
June 2016

Large-scale profiling of protein kinases for cellular signaling studies by mass spectrometry and other techniques.

J Pharm Biomed Anal 2016 Oct 27;130:264-272. Epub 2016 May 27.

Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.jpba.2016.05.046DOI Listing
October 2016

Comprehensive identification of translation start sites by tetracycline-inhibited ribosome profiling.

DNA Res 2016 Jun 23;23(3):193-201. Epub 2016 Mar 23.

Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan

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http://dx.doi.org/10.1093/dnares/dsw008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4909307PMC
June 2016

Uncovering Phosphorylation-Based Specificities through Functional Interaction Networks.

Mol Cell Proteomics 2016 Jan 16;15(1):236-45. Epub 2015 Nov 16.

From the ‡European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD;

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http://dx.doi.org/10.1074/mcp.M115.052357DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4762521PMC
January 2016

Phosphoproteomics Identifies CK2 as a Negative Regulator of Beige Adipocyte Thermogenesis and Energy Expenditure.

Cell Metab 2015 Dec 8;22(6):997-1008. Epub 2015 Nov 8.

UCSF Diabetes Center and Department of Cell and Tissue Biology, University of California, San Francisco, 35 Medical Center Way, San Francisco, CA 94143-0669, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cmet.2015.09.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4670581PMC
December 2015

Temporal Phosphoproteome Dynamics Induced by an ATP Synthase Inhibitor Citreoviridin.

Mol Cell Proteomics 2015 Dec 26;14(12):3284-98. Epub 2015 Oct 26.

From the ‡Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 106, Taiwan; §Department of Life Science, National Taiwan University, Taipei 106, Taiwan; ‡‡Genome and Systems Biology Degree Program, National Taiwan University, Taipei 106, Taiwan; §§Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 106, Taiwan

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http://www.mcponline.org/lookup/doi/10.1074/mcp.M115.051383
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http://dx.doi.org/10.1074/mcp.M115.051383DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4762618PMC
December 2015

Extended Coverage of Singly and Multiply Phosphorylated Peptides from a Single Titanium Dioxide Microcolumn.

Anal Chem 2015 Oct 6;87(20):10213-21. Epub 2015 Oct 6.

Graduate School of Pharmaceutical Sciences, Kyoto University , 46-29, Yoshida-Shimo-Adachi-Cho, Sakyo-ku, Kyoto, 606-8501, Japan.

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http://dx.doi.org/10.1021/acs.analchem.5b01216DOI Listing
October 2015

Systematic profiling of the bacterial phosphoproteome reveals bacterium-specific features of phosphorylation.

Sci Signal 2015 Sep 15;8(394):rs10. Epub 2015 Sep 15.

Department of Molecular and Cellular Bioanalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan.

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http://dx.doi.org/10.1126/scisignal.aaa3117DOI Listing
September 2015

Feasibility of label-free phosphoproteomics and application to base-line signaling of colorectal cancer cell lines.

J Proteomics 2015 Sep 1;127(Pt B):247-58. Epub 2015 Apr 1.

OncoProteomics Laboratory, VU University Medical Center, Amsterdam, The Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.jprot.2015.03.019DOI Listing
September 2015

PCTK1 regulates integrin-dependent spindle orientation via protein kinase A regulatory subunit KAP0 and myosin X.

Mol Cell Biol 2015 Apr 20;35(7):1197-208. Epub 2015 Jan 20.

Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto, Japan Department of Cell Biology, Institute for Virus Research, Kyoto University, Sakyo-ku, Kyoto, Japan

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http://dx.doi.org/10.1128/MCB.01017-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4355539PMC
April 2015

Pregnenolone functions in centriole cohesion during mitosis.

Chem Biol 2014 Dec;21(12):1707-21

Department of Cell Biology, Institute for Virus Research, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan; Department of Cell and Developmental Biology, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.chembiol.2014.11.005DOI Listing
December 2014

Phosphorylation of mitochondrial polyubiquitin by PINK1 promotes Parkin mitochondrial tethering.

PLoS Genet 2014 Dec 4;10(12):e1004861. Epub 2014 Dec 4.

Department of Research for Parkinson's Disease, Juntendo University Graduate School of Medicine, Tokyo, Japan.

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http://dx.doi.org/10.1371/journal.pgen.1004861DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4256268PMC
December 2014

Application of partially fluorinated carboxylic acids as ion-pairing reagents in LC/ESI-MS.

Talanta 2014 Sep 19;127:219-24. Epub 2014 Apr 19.

Pharmaceutical Science and Technology Core Function Unit, Eisai Product Creation Systems, Eisai Co. Ltd., 5-1-3 Tokodai, Tsukuba, Ibaraki 300-2635, Japan.

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http://dx.doi.org/10.1016/j.talanta.2014.03.060DOI Listing
September 2014

Large-scale identification of phosphorylation sites for profiling protein kinase selectivity.

J Proteome Res 2014 Jul 4;13(7):3410-9. Epub 2014 Jun 4.

Graduate School of Pharmaceutical Sciences, Kyoto University , 46-29 Yoshidashimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan.

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http://dx.doi.org/10.1021/pr500319yDOI Listing
July 2014

[Quantitation of cellular phosphorylation dynamics by phosphoproteomics approaches].

Yakugaku Zasshi 2014 ;134(4):521-7

Graduate School of Pharmaceutical Sciences, Kyoto University.

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http://dx.doi.org/10.1248/yakushi.13-00251-4DOI Listing
August 2014

Hydrophilic interaction chromatography using a meter-scale monolithic silica capillary column for proteomics LC-MS.

Anal Chem 2014 Apr 3;86(8):3817-24. Epub 2014 Apr 3.

Eisai Co., Ltd , Pharmaceutical Science and Technology Core Function Unit, Global Formulation Research, Kawashima, Kakamigahara, Gifu 501-6195, Japan.

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http://pubs.acs.org/doi/10.1021/ac4038625
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http://dx.doi.org/10.1021/ac4038625DOI Listing
April 2014

Phosphoproteome analysis of formalin-fixed and paraffin-embedded tissue sections mounted on microscope slides.

J Proteome Res 2014 Feb 23;13(2):915-24. Epub 2013 Dec 23.

Graduate School of Pharmaceutical Sciences, Kyoto University , Sakyo-ku, Kyoto 606-8501, Japan.

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http://dx.doi.org/10.1021/pr400960rDOI Listing
February 2014

p38-Mediated phosphorylation of Eps15 endocytic adaptor protein.

FEBS Lett 2014 Jan 21;588(1):131-7. Epub 2013 Nov 21.

Department of Cancer Cell Biology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.febslet.2013.11.020DOI Listing
January 2014

Inhibition of endocytic vesicle fusion by Plk1-mediated phosphorylation of vimentin during mitosis.

Cell Cycle 2014 25;13(1):126-37. Epub 2013 Oct 25.

Department of Cell Biology; Institute for Virus Research; Kyoto University; Sakyo-ku, Kyoto, Japan; Department of Mammalian Regulatory Network; Graduate School of Biostudies; Kyoto University; Sakyo-ku, Kyoto, Japan.

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http://dx.doi.org/10.4161/cc.26866DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3925722PMC
September 2014

Estrogen response element-GFP (ERE-GFP) introduced MCF-7 cells demonstrated the coexistence of multiple estrogen-deprivation resistant mechanisms.

J Steroid Biochem Mol Biol 2014 Jan 13;139:61-72. Epub 2013 Oct 13.

Department of Molecular and Functional Dynamics, Tohoku University Graduate School of Medicine, Aoba-ku, Sendai 980-8575, Japan.

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http://dx.doi.org/10.1016/j.jsbmb.2013.08.012DOI Listing
January 2014

Genetics and phosphoproteomics reveal a protein phosphorylation network in the abscisic acid signaling pathway in Arabidopsis thaliana.

Sci Signal 2013 Apr 9;6(270):rs8. Epub 2013 Apr 9.

Faculty of Agriculture and Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.

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http://dx.doi.org/10.1126/scisignal.2003509DOI Listing
April 2013

Metabolomic profiling of lung and prostate tumor tissues by capillary electrophoresis time-of-flight mass spectrometry.

Metabolomics 2013 Apr 2;9(2):444-453. Epub 2012 Nov 2.

Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata Japan ; Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa Japan.

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http://link.springer.com/10.1007/s11306-012-0452-2
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http://dx.doi.org/10.1007/s11306-012-0452-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608864PMC
April 2013

Effect of phospholipid composition on discoidal HDL formation.

Biochim Biophys Acta 2013 May 25;1828(5):1340-6. Epub 2013 Jan 25.

Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan.

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https://linkinghub.elsevier.com/retrieve/pii/S00052736130002
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http://dx.doi.org/10.1016/j.bbamem.2013.01.012DOI Listing
May 2013

Effects of lipid membrane curvature on lipid packing state evaluated by isothermal titration calorimetry.

Langmuir 2013 Jan 7;29(3):857-60. Epub 2013 Jan 7.

Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan.

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http://dx.doi.org/10.1021/la304532kDOI Listing
January 2013

Integrated view of the human chromosome X-centric proteome project.

J Proteome Res 2013 Jan 21;12(1):58-61. Epub 2012 Dec 21.

Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata, Japan.

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http://dx.doi.org/10.1021/pr300844pDOI Listing
January 2013

Rapid and deep profiling of human induced pluripotent stem cell proteome by one-shot NanoLC-MS/MS analysis with meter-scale monolithic silica columns.

J Proteome Res 2013 Jan 4;12(1):214-21. Epub 2012 Dec 4.

Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.

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http://dx.doi.org/10.1021/pr300837uDOI Listing
January 2013

In-depth membrane proteomic study of breast cancer tissues for the generation of a chromosome-based protein list.

J Proteome Res 2013 Jan 15;12(1):208-13. Epub 2012 Nov 15.

Laboratory of Proteome Research, National Institute of Biomedical Innovation, Ibaraki, Osaka, Japan.

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http://dx.doi.org/10.1021/pr300824mDOI Listing
January 2013

Nestin protein is phosphorylated in adult neural stem/progenitor cells and not endothelial progenitor cells.

Stem Cells Int 2012 13;2012:430138. Epub 2012 Sep 13.

Department of Emergency and Critical Care Medicine, Keio University School of Medicine, Shinanomachi 35, Shinjuku, Tokyo 160-8582, Japan.

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http://dx.doi.org/10.1155/2012/430138DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3458297PMC
October 2012

Temporal profiling of lapatinib-suppressed phosphorylation signals in EGFR/HER2 pathways.

Mol Cell Proteomics 2012 Dec 10;11(12):1741-57. Epub 2012 Sep 10.

Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.

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http://dx.doi.org/10.1074/mcp.M112.019919DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3518135PMC
December 2012

[Phosphoproteomics-based cancer molecular-targeting therapy and diagnostics].

Gan To Kagaku Ryoho 2012 Jul;39(7):1019-25

Dept. of Molecular & Cellular BioAnalysis, Kyoto University, Japan.

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July 2012

A putative polypeptide N-acetylgalactosaminyltransferase/Williams-Beuren syndrome chromosome region 17 (WBSCR17) regulates lamellipodium formation and macropinocytosis.

J Biol Chem 2012 Sep 11;287(38):32222-35. Epub 2012 Jul 11.

Laboratory of Neuroglycobiology, Department of Molecular Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kyoto 603-8555, Japan.

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http://www.jbc.org/lookup/doi/10.1074/jbc.M112.370932
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http://dx.doi.org/10.1074/jbc.M112.370932DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3442553PMC
September 2012

Mass spectrum sequential subtraction speeds up searching large peptide MS/MS spectra datasets against large nucleotide databases for proteogenomics.

Genes Cells 2012 Aug 12;17(8):633-44. Epub 2012 Jun 12.

Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan.

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http://dx.doi.org/10.1111/j.1365-2443.2012.01615.xDOI Listing
August 2012

Analytical strategies for shotgun phosphoproteomics: status and prospects.

Semin Cell Dev Biol 2012 Oct 5;23(8):836-42. Epub 2012 Jun 5.

Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, 606-8501, Japan.

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http://dx.doi.org/10.1016/j.semcdb.2012.05.007DOI Listing
October 2012

Short-chain fatty acid receptor GPR41-mediated activation of sympathetic neurons involves synapsin 2b phosphorylation.

FEBS Lett 2012 May 21;586(10):1547-54. Epub 2012 Apr 21.

Department of Genomic Drug Discovery Science, Kyoto University Graduate School of Pharmaceutical Sciences, Sakyo-ku, Kyoto, Japan.

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http://dx.doi.org/10.1016/j.febslet.2012.04.021DOI Listing
May 2012

LATS1/WARTS phosphorylates MYPT1 to counteract PLK1 and regulate mammalian mitotic progression.

J Cell Biol 2012 May;197(5):625-41

Division of Gene Regulation, Institute for Advanced Medical Research, Department of Obstetrics and Gynecology, School of Medicine, Keio University, Shinjuku-ku, Tokyo 160-8582, Japan.

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http://dx.doi.org/10.1083/jcb.201110110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3404884PMC
May 2012

The Rice Proteogenomics Database OryzaPG-DB: Development, Expansion, and New Features.

Front Plant Sci 2012 2;3:65. Epub 2012 Apr 2.

Institute for Advanced Biosciences, Keio University Tokyo, Japan.

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http://dx.doi.org/10.3389/fpls.2012.00065DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3355581PMC
August 2012

Estimation and optimization of the peak capacity of one-dimensional gradient high performance liquid chromatography using a long monolithic silica capillary column.

J Chromatogr A 2012 Mar 5;1228:283-91. Epub 2012 Jan 5.

Eisai Co., Ltd., Pharmaceutical Science and Technology Core Function Unit, Global Formulation Japan, Kawashima, Kakamigahara, Gifu 501-6195, Japan.

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http://linkinghub.elsevier.com/retrieve/pii/S002196731200012
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http://dx.doi.org/10.1016/j.chroma.2011.12.088DOI Listing
March 2012

Human proteome analysis by using reversed phase monolithic silica capillary columns with enhanced sensitivity.

J Chromatogr A 2012 Mar 28;1228:292-7. Epub 2011 Oct 28.

Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.

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http://linkinghub.elsevier.com/retrieve/pii/S002196731101601
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http://dx.doi.org/10.1016/j.chroma.2011.10.059DOI Listing
March 2012

Shotguns in the front line: phosphoproteomics in plants.

Plant Cell Physiol 2012 Jan 28;53(1):118-24. Epub 2011 Oct 28.

RIKEN Plant Science Center, Tsurumi-ku, Yokohama, Japan.

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https://academic.oup.com/pcp/article-lookup/doi/10.1093/pcp/
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http://dx.doi.org/10.1093/pcp/pcr148DOI Listing
January 2012

Ectopic expression of Hmgn2 antagonizes mouse erythroid differentiation in vitro.

Cell Biol Int 2012 Feb;36(2):195-202

Advanced Medical Initiatives, Division of Hematopoietic Stem Cells, Department of Advanced Medical Initiatives, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan.

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http://doi.wiley.com/10.1042/CBI20110169
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http://dx.doi.org/10.1042/CBI20110169DOI Listing
February 2012

Microscale phosphoproteome analysis of 10,000 cells from human cancer cell lines.

Anal Chem 2011 Oct 19;83(20):7698-703. Epub 2011 Sep 19.

Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.

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http://dx.doi.org/10.1021/ac201093gDOI Listing
October 2011

Characterization of kinase inhibitors using different phosphorylation states of colony stimulating factor-1 receptor tyrosine kinase.

J Biochem 2012 Jan 31;151(1):47-55. Epub 2011 Aug 31.

Carna Biosciences, Inc, 1-5-5, Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.

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http://dx.doi.org/10.1093/jb/mvr112DOI Listing
January 2012

[New trends in shotgun proteomics].

Authors:
Yasushi Ishihama

Seikagaku 2011 May;83(5):413-8

Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan.

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May 2011

OryzaPG-DB: rice proteome database based on shotgun proteogenomics.

BMC Plant Biol 2011 Apr 12;11:63. Epub 2011 Apr 12.

Institute for Advanced Biosciences, Keio University, 403-1 Daihoji, Tsuruoka, Yamagata 997-0017, Japan.

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http://dx.doi.org/10.1186/1471-2229-11-63DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3094275PMC
April 2011

Functional preconcentration tip of total volume injection for ESI/MS analysis of DNA adducts.

Anal Sci 2011 ;27(2):217-20

Gifu Pharmaceutical University, Daigaku-nishi, Gifu 501-1196, Japan.

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http://dx.doi.org/10.2116/analsci.27.217DOI Listing
July 2011

Integrative features of the yeast phosphoproteome and protein-protein interaction map.

PLoS Comput Biol 2011 Jan 27;7(1):e1001064. Epub 2011 Jan 27.

Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.

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http://dx.doi.org/10.1371/journal.pcbi.1001064DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3029238PMC
January 2011

Use of stable isotope labeling by amino acids in cell culture as a spike-in standard in quantitative proteomics.

Nat Protoc 2011 Feb;6(2):147-57

Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.

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http://www.nature.com/articles/nprot.2010.192
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http://dx.doi.org/10.1038/nprot.2010.192DOI Listing
February 2011