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The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics.

Deutsch EW, Bandeira N, Sharma V, Perez-Riverol Y, Carver JJ, Kundu DJ, García-Seisdedos D, Jarnuczak AF, Hewapathirana S, Pullman BS, Wertz J, Sun Z, Kawano S, Okuda S, Watanabe Y, Hermjakob H, MacLean B, MacCoss MJ, Zhu Y, Ishihama Y, Vizcaíno JA.

Nucleic Acids Res. 2019 Nov 5. pii: gkz984. doi: 10.1093/nar/gkz984. [Epub ahead of print]


Surgical Treatment of Lumbar Herniated Nucleus Pulposus Combined with Residual Bony Fragment of Apophyseal Ring Fracture in High-Level Athletes : A Report of Two Cases.

Sugimine Y, Sakaeda K, Yamashita K, Manabe H, Sugiura K, Hayashi F, Ishihama Y, Takata Y, Sakai T, Maeda T, Tateishi T, Sairyo K.

J Med Invest. 2019;66(3.4):358-361. doi: 10.2152/jmi.66.358.


Minimally invasive cervical micro-endoscopic foraminotomy for C6 radiculopathy with overlooked scapular winging - A case report.

Ishihama Y, Tezuka F, Manabe H, Yamashita K, Takata Y, Sakai T, Chikawa T, Sairyo K.

J Med Invest. 2019;66(3.4):340-343. doi: 10.2152/jmi.66.340.


Accurate diagnosis of low back pain in adult elite athletes.

Yamashita K, Sugiura K, Manabe H, Ishihama Y, Tezuka F, Takata Y, Sakai T, Maeda T, Sairyo K.

J Med Invest. 2019;66(3.4):252-257. doi: 10.2152/jmi.66.252.


A novel surgical concept of transforaminal full-endoscopic lumbar undercutting laminectomy (TE-LUL) for central canal stenosis of the lumbar spine with local anesthesia : A case report and literature review.

Sairyo K, Yamashita K, Manabe H, Ishihama Y, Sugiura K, Tezuka F, Takata Y, Sakai T, Omichi Y, Takamatsu N, Hashimoto A, Maeda T.

J Med Invest. 2019;66(3.4):224-229. doi: 10.2152/jmi.66.224.


Operating Costs of Full-endoscopic Lumbar Spine Surgery in Japan.

Manabe H, Tezuka F, Yamashita K, Sugiura K, Ishihama Y, Takata Y, Sakai T, Maeda T, Sairyo K.

Neurol Med Chir (Tokyo). 2019 Oct 17. doi: 10.2176/nmc.oa.2019-0139. [Epub ahead of print]


Mass Spectrometry-Compatible Subcellular Fractionation for Proteomics.

Masuda T, Sugiyama N, Tomita M, Ohtsuki S, Ishihama Y.

J Proteome Res. 2019 Oct 17. doi: 10.1021/acs.jproteome.9b00347. [Epub ahead of print]


Large-scale Discovery of Substrates of the Human Kinome.

Sugiyama N, Imamura H, Ishihama Y.

Sci Rep. 2019 Jul 19;9(1):10503. doi: 10.1038/s41598-019-46385-4.


Transforaminal full-endoscopic lumbar discectomy under local anesthesia in awake and aware conditions: the inside-out and outside-in techniques.

Yoshinari H, Tezuka F, Yamashita K, Manabe H, Hayashi F, Ishihama Y, Sugiura K, Takata Y, Sakai T, Maeda T, Sairyo K.

Curr Rev Musculoskelet Med. 2019 Jun 24:311-317. doi: 10.1007/s12178-019-09565-3. [Epub ahead of print] Review.


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

Iwasaki M, Tabata T, Kawahara Y, Ishihama Y, Nakagawa M.

J Proteome Res. 2019 Jun 7;18(6):2535-2544. doi: 10.1021/acs.jproteome.9b00078. Epub 2019 May 6.


Algal Protein Kinase, Triacylglycerol Accumulation Regulator 1, Modulates Cell Viability and Gametogenesis in Carbon/Nitrogen-Imbalanced Conditions.

Shinkawa H, Kajikawa M, Nomura Y, Ogura M, Sawaragi Y, Yamano T, Nakagami H, Sugiyama N, Ishihama Y, Kanesaki Y, Yoshikawa H, Fukuzawa H.

Plant Cell Physiol. 2019 Apr 1;60(4):916-930. doi: 10.1093/pcp/pcz010.


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

Sugiyama N, Miyake S, Lin MH, Wakabayashi M, Marusawa H, Nishiumi S, Yoshida M, Ishihama Y.

Genes Cells. 2019 Feb;24(2):139-150. doi: 10.1111/gtc.12662. Epub 2019 Jan 20.


The jPOST environment: an integrated proteomics data repository and database.

Moriya Y, Kawano S, Okuda S, Watanabe Y, Matsumoto M, Takami T, Kobayashi D, Yamanouchi Y, Araki N, Yoshizawa AC, Tabata T, Iwasaki M, Sugiyama N, Tanaka S, Goto S, Ishihama Y.

Nucleic Acids Res. 2019 Jan 8;47(D1):D1218-D1224. doi: 10.1093/nar/gky899.


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

Imami K, Milek M, Bogdanow B, Yasuda T, Kastelic N, Zauber H, Ishihama Y, Landthaler M, Selbach M.

Mol Cell. 2018 Oct 4;72(1):84-98.e9. doi: 10.1016/j.molcel.2018.08.019. Epub 2018 Sep 13.


"Biomolecular Mass Spectrometry".

Ishihama Y, Higashi T.

Anal Sci. 2018;34(9):989. doi: 10.2116/analsci.GE1809. No abstract available.


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

Ogata K, Krokhin OV, Ishihama Y.

Anal Sci. 2018 Sep 10;34(9):1037-1041. doi: 10.2116/analsci.18SCP11. Epub 2018 Jul 27.


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

Fuji H, Ohmae S, Noma N, Takeiri M, Yasutomi H, Izumi K, Ito M, Toyomoto M, Iwaki S, Takemoto K, Seo S, Taura K, Hida S, Aoyama M, Ishihama Y, Hagiwara M, Takeda N, Hatano E, Iwaisako K, Uemoto S, Asagiri M.

Biochem Biophys Res Commun. 2018 Sep 5;503(2):544-549. doi: 10.1016/j.bbrc.2018.05.153. Epub 2018 Jul 7.


Two Ck1δ transcripts regulated by m6A methylation code for two antagonistic kinases in the control of the circadian clock.

Fustin JM, Kojima R, Itoh K, Chang HY, Ye S, Zhuang B, Oji A, Gibo S, Narasimamurthy R, Virshup D, Kurosawa G, Doi M, Manabe I, Ishihama Y, Ikawa M, Okamura H.

Proc Natl Acad Sci U S A. 2018 Jun 5;115(23):5980-5985. doi: 10.1073/pnas.1721371115. Epub 2018 May 21. Erratum in: Proc Natl Acad Sci U S A. 2018 Jul 3;115(27):E6386.


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

Amagai A, Honda Y, Ishikawa S, Hara Y, Kuwamura M, Shinozawa A, Sugiyama N, Ishihama Y, Takezawa D, Sakata Y, Shinozaki K, Umezawa T.

Plant J. 2018 May;94(4):699-708. doi: 10.1111/tpj.13891. Epub 2018 Apr 23.


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

Giese SH, Ishihama Y, Rappsilber J.

Anal Chem. 2018 Apr 3;90(7):4635-4640. doi: 10.1021/acs.analchem.7b05157. Epub 2018 Mar 21.


Phospholipid flippase ATP11C is endocytosed and downregulated following Ca2+-mediated protein kinase C activation.

Takatsu H, Takayama M, Naito T, Takada N, Tsumagari K, Ishihama Y, Nakayama K, Shin HW.

Nat Commun. 2017 Nov 10;8(1):1423. doi: 10.1038/s41467-017-01338-1.


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

Murakami H, Horiba R, Iwata T, Miki Y, Uno B, Sakai T, Kaneko K, Ishihama Y, Teshima N, Esaka Y.

Talanta. 2018 Jan 15;177:12-17. doi: 10.1016/j.talanta.2017.09.055. Epub 2017 Sep 25.


Metabolic shift induced by systemic activation of T cells in PD-1-deficient mice perturbs brain monoamines and emotional behavior.

Miyajima M, Zhang B, Sugiura Y, Sonomura K, Guerrini MM, Tsutsui Y, Maruya M, Vogelzang A, Chamoto K, Honda K, Hikida T, Ito S, Qin H, Sanuki R, Suzuki K, Furukawa T, Ishihama Y, Matsuda F, Suematsu M, Honjo T, Fagarasan S.

Nat Immunol. 2017 Dec;18(12):1342-1352. doi: 10.1038/ni.3867. Epub 2017 Oct 23.


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

Tsai CF, Ku WC, Chen YJ, Ishihama Y.

Methods Mol Biol. 2017;1636:313-325. doi: 10.1007/978-1-4939-7154-1_20.


Actin-binding protein coronin 1A controls osteoclastic bone resorption by regulating lysosomal secretion of cathepsin K.

Ohmae S, Noma N, Toyomoto M, Shinohara M, Takeiri M, Fuji H, Takemoto K, Iwaisako K, Fujita T, Takeda N, Kawatani M, Aoyama M, Hagiwara M, Ishihama Y, Asagiri M.

Sci Rep. 2017 Mar 16;7:41710. doi: 10.1038/srep41710.


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

Imamura H, Wagih O, Niinae T, Sugiyama N, Beltrao P, Ishihama Y.

J Proteome Res. 2017 Apr 7;16(4):1825-1830. doi: 10.1021/acs.jproteome.7b00087. Epub 2017 Mar 15.


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

Tsumagari K, Shirakabe K, Ogura M, Sato F, Ishihama Y, Sehara-Fujisawa A.

Genes Cells. 2017 Feb;22(2):237-244. doi: 10.1111/gtc.12466. Epub 2017 Jan 13.


An Optimized Chromatographic Strategy for Multiplexing In Parallel Reaction Monitoring Mass Spectrometry: Insights from Quantitation of Activated Kinases.

Urisman A, Levin RS, Gordan JD, Webber JT, Hernandez H, Ishihama Y, Shokat KM, Burlingame AL.

Mol Cell Proteomics. 2017 Feb;16(2):265-277. doi: 10.1074/mcp.M116.058172. Epub 2016 Dec 11.


The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition.

Deutsch EW, Csordas A, Sun Z, Jarnuczak A, Perez-Riverol Y, Ternent T, Campbell DS, Bernal-Llinares M, Okuda S, Kawano S, Moritz RL, Carver JJ, Wang M, Ishihama Y, Bandeira N, Hermjakob H, Vizcaíno JA.

Nucleic Acids Res. 2017 Jan 4;45(D1):D1100-D1106. doi: 10.1093/nar/gkw936. Epub 2016 Oct 18.


jPOSTrepo: an international standard data repository for proteomes.

Okuda S, Watanabe Y, Moriya Y, Kawano S, Yamamoto T, Matsumoto M, Takami T, Kobayashi D, Araki N, Yoshizawa AC, Tabata T, Sugiyama N, Goto S, Ishihama Y.

Nucleic Acids Res. 2017 Jan 4;45(D1):D1107-D1111. doi: 10.1093/nar/gkw1080. Epub 2016 Nov 28.


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

Miki T, Awa M, Nishikawa Y, Kiyonaka S, Wakabayashi M, Ishihama Y, Hamachi I.

Nat Methods. 2016 Nov;13(11):931-937. doi: 10.1038/nmeth.3998. Epub 2016 Sep 12.


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

Suriyanarayanan T, Periasamy S, Lin MH, Ishihama Y, Swarup S.

PLoS One. 2016 Oct 4;11(10):e0164155. doi: 10.1371/journal.pone.0164155. eCollection 2016.


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

Hirata H, Ku WC, Yip AK, Ursekar CP, Kawauchi K, Roy A, Guo AK, Vedula SR, Harada I, Chiam KH, Ishihama Y, Lim CT, Sawada Y, Sokabe M.

J Cell Sci. 2016 Oct 1;129(19):3574-3582. Epub 2016 Aug 15.


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

Ohta S, Kimura M, Takagi S, Toramoto I, Ishihama Y.

J Proteome Res. 2016 Sep 2;15(9):3331-41. doi: 10.1021/acs.jproteome.6b00512. Epub 2016 Aug 17.


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

Adachi J, Hashiguchi K, Nagano M, Sato M, Sato A, Fukamizu K, Ishihama Y, Tomonaga T.

Anal Chem. 2016 Aug 16;88(16):7899-903. doi: 10.1021/acs.analchem.6b01232. Epub 2016 Aug 2.


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

Nakao H, Ikeda K, Ishihama Y, Nakano M.

Biophys J. 2016 Jun 21;110(12):2689-2697. doi: 10.1016/j.bpj.2016.05.023.


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

Sugiyama N, Ishihama Y.

J Pharm Biomed Anal. 2016 Oct 25;130:264-272. doi: 10.1016/j.jpba.2016.05.046. Epub 2016 May 27. Review.


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

Nakahigashi K, Takai Y, Kimura M, Abe N, Nakayashiki T, Shiwa Y, Yoshikawa H, Wanner BL, Ishihama Y, Mori H.

DNA Res. 2016 Jun;23(3):193-201. doi: 10.1093/dnares/dsw008. Epub 2016 Mar 23.


Uncovering Phosphorylation-Based Specificities through Functional Interaction Networks.

Wagih O, Sugiyama N, Ishihama Y, Beltrao P.

Mol Cell Proteomics. 2016 Jan;15(1):236-45. doi: 10.1074/mcp.M115.052357. Epub 2015 Nov 16.


A multi-omic analysis of human naïve CD4+ T cells.

Mitchell CJ, Getnet D, Kim MS, Manda SS, Kumar P, Huang TC, Pinto SM, Nirujogi RS, Iwasaki M, Shaw PG, Wu X, Zhong J, Chaerkady R, Marimuthu A, Muthusamy B, Sahasrabuddhe NA, Raju R, Bowman C, Danilova L, Cutler J, Kelkar DS, Drake CG, Prasad TS, Marchionni L, Murakami PN, Scott AF, Shi L, Thierry-Mieg J, Thierry-Mieg D, Irizarry R, Cope L, Ishihama Y, Wang C, Gowda H, Pandey A.

BMC Syst Biol. 2015 Nov 6;9:75. doi: 10.1186/s12918-015-0225-4.


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

Shinoda K, Ohyama K, Hasegawa Y, Chang HY, Ogura M, Sato A, Hong H, Hosono T, Sharp LZ, Scheel DW, Graham M, Ishihama Y, Kajimura S.

Cell Metab. 2015 Dec 1;22(6):997-1008. doi: 10.1016/j.cmet.2015.09.029. Epub 2015 Nov 8.


Temporal Phosphoproteome Dynamics Induced by an ATP Synthase Inhibitor Citreoviridin.

Hu CW, Hsu CL, Wang YC, Ishihama Y, Ku WC, Huang HC, Juan HF.

Mol Cell Proteomics. 2015 Dec;14(12):3284-98. doi: 10.1074/mcp.M115.051383. Epub 2015 Oct 26.


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

Wakabayashi M, Kyono Y, Sugiyama N, Ishihama Y.

Anal Chem. 2015 Oct 20;87(20):10213-21. doi: 10.1021/acs.analchem.5b01216. Epub 2015 Oct 6.


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

Lin MH, Sugiyama N, Ishihama Y.

Sci Signal. 2015 Sep 15;8(394):rs10. doi: 10.1126/scisignal.aaa3117.


Correction: LATS1 and LATS2 phosphorylate CDC26 to modulate assembly of the tetratricopeptide repeat subcomplex of APC/C.

Masuda K, Chiyoda T, Sugiyama N, Segura-Cabrera A, Kabe Y, Ueki A, Banno K, Suematsu M, Aoki D, Ishihama Y, Saya H, Kuninaka S.

PLoS One. 2015 Apr 10;10(4):e0125308. doi: 10.1371/journal.pone.0125308. eCollection 2015. No abstract available.


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

Piersma SR, Knol JC, de Reus I, Labots M, Sampadi BK, Pham TV, Ishihama Y, Verheul HM, Jimenez CR.

J Proteomics. 2015 Sep 8;127(Pt B):247-58. doi: 10.1016/j.jprot.2015.03.019. Epub 2015 Apr 1.


Large-scale determination of absolute phosphorylation stoichiometries in human cells by motif-targeting quantitative proteomics.

Tsai CF, Wang YT, Yen HY, Tsou CC, Ku WC, Lin PY, Chen HY, Nesvizhskii AI, Ishihama Y, Chen YJ.

Nat Commun. 2015 Mar 27;6:6622. doi: 10.1038/ncomms7622.


LATS1 and LATS2 phosphorylate CDC26 to modulate assembly of the tetratricopeptide repeat subcomplex of APC/C.

Masuda K, Chiyoda T, Sugiyama N, Segura-Cabrera A, Kabe Y, Ueki A, Banno K, Suematsu M, Aoki D, Ishihama Y, Saya H, Kuninaka S.

PLoS One. 2015 Feb 27;10(2):e0118662. doi: 10.1371/journal.pone.0118662. eCollection 2015. Erratum in: PLoS One. 2015;10(4):e0125308. Banno, Koji [corrected to Banno, Kouji].


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

Iwano S, Satou A, Matsumura S, Sugiyama N, Ishihama Y, Toyoshima F.

Mol Cell Biol. 2015 Apr;35(7):1197-208. doi: 10.1128/MCB.01017-14. Epub 2015 Jan 20.


Pregnenolone functions in centriole cohesion during mitosis.

Hamasaki M, Matsumura S, Satou A, Takahashi C, Oda Y, Higashiura C, Ishihama Y, Toyoshima F.

Chem Biol. 2014 Dec 18;21(12):1707-21. doi: 10.1016/j.chembiol.2014.11.005.

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