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Page 1
Global and Site-Specific Effect of Phosphorylation on Protein Turnover.
Wu C, Ba Q, Lu D, Li W, Salovska B, Hou P, Mueller T, Rosenberger G, Gao E, Di Y, Zhou H, Fornasiero EF, Liu Y. Wu C, et al. Among authors: liu y. Dev Cell. 2021 Jan 11;56(1):111-124.e6. doi: 10.1016/j.devcel.2020.10.025. Epub 2020 Nov 24. Dev Cell. 2021. PMID: 33238149 Free PMC article.
Network-based elucidation of colon cancer drug resistance by phosphoproteomic time-series analysis.
Rosenberger G, Li W, Turunen M, He J, Subramaniam PS, Pampou S, Griffin AT, Karan C, Kerwin P, Murray D, Honig B, Liu Y, Califano A. Rosenberger G, et al. Among authors: liu y. bioRxiv [Preprint]. 2023 Feb 16:2023.02.15.528736. doi: 10.1101/2023.02.15.528736. bioRxiv. 2023. Update in: Nat Commun. 2024 May 9;15(1):3909. doi: 10.1038/s41467-024-47957-3. PMID: 36824919 Free PMC article. Updated. Preprint.
7SK methylation by METTL3 promotes transcriptional activity.
Perez-Pepe M, Desotell AW, Li H, Li W, Han B, Lin Q, Klein DE, Liu Y, Goodarzi H, Alarcón CR. Perez-Pepe M, et al. Among authors: liu y. Sci Adv. 2023 May 10;9(19):eade7500. doi: 10.1126/sciadv.ade7500. Epub 2023 May 10. Sci Adv. 2023. PMID: 37163588 Free PMC article.
Reciprocal inhibition of PIN1 and APC/CCDH1 controls timely G1/S transition and creates therapeutic vulnerability.
Ke S, Dang F, Wang L, Chen JY, Naik MT, Thavamani A, Liu Y, Li W, Kim N, Naik NM, Sui H, Tang W, Qiu C, Koikawa K, Batalini F, Wang X, Clohessy JG, Heng YJ, Lahav G, Gray NS, Zho XZ, Wei W, Wulf GM, Lu KP. Ke S, et al. Among authors: liu y. Res Sq [Preprint]. 2023 Jan 19:rs.3.rs-2447544. doi: 10.21203/rs.3.rs-2447544/v1. Res Sq. 2023. PMID: 36711754 Free PMC article. Preprint.
Oncogene-like addiction to aneuploidy in human cancers.
Girish V, Lakhani AA, Thompson SL, Scaduto CM, Brown LM, Hagenson RA, Sausville EL, Mendelson BE, Kandikuppa PK, Lukow DA, Yuan ML, Stevens EC, Lee SN, Schukken KM, Akalu SM, Vasudevan A, Zou C, Salovska B, Li W, Smith JC, Taylor AM, Martienssen RA, Liu Y, Sun R, Sheltzer JM. Girish V, et al. Among authors: liu y. Science. 2023 Aug 25;381(6660):eadg4521. doi: 10.1126/science.adg4521. Epub 2023 Aug 25. Science. 2023. PMID: 37410869 Free PMC article.
Reciprocal antagonism of PIN1-APC/CCDH1 governs mitotic protein stability and cell cycle entry.
Ke S, Dang F, Wang L, Chen JY, Naik MT, Li W, Thavamani A, Kim N, Naik NM, Sui H, Tang W, Qiu C, Koikawa K, Batalini F, Stern Gatof E, Isaza DA, Patel JM, Wang X, Clohessy JG, Heng YJ, Lahav G, Liu Y, Gray NS, Zhou XZ, Wei W, Wulf GM, Lu KP. Ke S, et al. Among authors: liu y. Nat Commun. 2024 Apr 15;15(1):3220. doi: 10.1038/s41467-024-47427-w. Nat Commun. 2024. PMID: 38622115 Free PMC article.
An in vivo screen identifies NAT10 as a master regulator of brain metastasis.
Chen JF, Xu P, Cai WL, Chen H, Wingrove E, Shi X, Li W, Biancon G, Zhang M, Balabaki A, Krop ED, Asare E, Zhang Y, Yin M, Tebaldi T, Meier JL, Westbrook TF, Halene S, Liu Y, Shen H, Nguyen DX, Yan Q. Chen JF, et al. Among authors: liu y. Sci Adv. 2025 Mar 28;11(13):eads6021. doi: 10.1126/sciadv.ads6021. Epub 2025 Mar 26. Sci Adv. 2025. PMID: 40138393 Free PMC article.
Post-translational modification and phenotype.
Salovska B, Liu Y. Salovska B, et al. Among authors: liu y. Proteomics. 2023 Feb;23(3-4):e2200535. doi: 10.1002/pmic.202200535. Proteomics. 2023. PMID: 36799530 No abstract available.
A proteome-wide quantitative platform for nanoscale spatially resolved extraction of membrane proteins into native nanodiscs.
Brown C, Ghosh S, McAllister R, Kumar M, Walker G, Sun E, Aman T, Panda A, Kumar S, Li W, Coleman J, Liu Y, Rothman JE, Bhattacharyya M, Gupta K. Brown C, et al. Among authors: liu y. bioRxiv [Preprint]. 2024 Aug 4:2024.02.10.579775. doi: 10.1101/2024.02.10.579775. bioRxiv. 2024. Update in: Nat Methods. 2025 Feb;22(2):412-421. doi: 10.1038/s41592-024-02517-x. PMID: 38405833 Free PMC article. Updated. Preprint.
Strategies to enable large-scale proteomics for reproducible research.
Poulos RC, Hains PG, Shah R, Lucas N, Xavier D, Manda SS, Anees A, Koh JMS, Mahboob S, Wittman M, Williams SG, Sykes EK, Hecker M, Dausmann M, Wouters MA, Ashman K, Yang J, Wild PJ, deFazio A, Balleine RL, Tully B, Aebersold R, Speed TP, Liu Y, Reddel RR, Robinson PJ, Zhong Q. Poulos RC, et al. Among authors: liu y. Nat Commun. 2020 Jul 30;11(1):3793. doi: 10.1038/s41467-020-17641-3. Nat Commun. 2020. PMID: 32732981 Free PMC article.
Role of AMPK in Atrial Metabolic Homeostasis and Substrate Preference.
Toksoy Z, Ma Y, Goedeke L, Li W, Hu X, Wu X, Cacheux M, Liu Y, Akar FG, Shulman GI, Young LH. Toksoy Z, et al. Among authors: liu y. bioRxiv [Preprint]. 2024 Aug 30:2024.08.29.608789. doi: 10.1101/2024.08.29.608789. bioRxiv. 2024. PMID: 39257756 Free PMC article. Preprint.
An Extensive Atlas of Proteome and Phosphoproteome Turnover Across Mouse Tissues and Brain Regions.
Li W, Dasgupta A, Yang K, Wang S, Hemandhar-Kumar N, Yarbro JM, Hu Z, Salovska B, Fornasiero EF, Peng J, Liu Y. Li W, et al. Among authors: liu y. bioRxiv [Preprint]. 2024 Oct 17:2024.10.15.618303. doi: 10.1101/2024.10.15.618303. bioRxiv. 2024. Update in: Cell. 2025 Apr 17;188(8):2267-2287.e21. doi: 10.1016/j.cell.2025.02.021. PMID: 39464138 Free PMC article. Updated. Preprint.
Author Correction: π-HuB: the proteomic navigator of the human body.
He F, Aebersold R, Baker MS, Bian X, Bo X, Chan DW, Chang C, Chen L, Chen X, Chen YJ, Cheng H, Collins BC, Corrales F, Cox J, E W, Van Eyk JE, Fan J, Faridi P, Figeys D, Gao GF, Gao W, Gao ZH, Goda K, Goh WWB, Gu D, Guo C, Guo T, He Y, Heck AJR, Hermjakob H, Hunter T, Iyer NG, Jiang Y, Jimenez CR, Joshi L, Kelleher NL, Li M, Li Y, Lin Q, Liu CH, Liu F, Liu GH, Liu Y, Liu Z, Low TY, Lu B, Mann M, Meng A, Moritz RL, Nice E, Ning G, Omenn GS, Overall CM, Palmisano G, Peng Y, Pineau C, Poon TCW, Purcell AW, Qiao J, Reddel RR, Robinson PJ, Roncada P, Sander C, Sha J, Song E, Srivastava S, Sun A, Sze SK, Tang C, Tang L, Tian R, Vizcaíno JA, Wang C, Wang C, Wang X, Wang X, Wang Y, Weiss T, Wilhelm M, Winkler R, Wollscheid B, Wong L, Xie L, Xie W, Xu T, Xu T, Yan L, Yang J, Yang X, Yates J, Yun T, Zhai Q, Zhang B, Zhang H, Zhang L, Zhang L, Zhang P, Zhang Y, Zheng YZ, Zhong Q, Zhu Y; π-HuB Consortium. He F, et al. Among authors: liu gh, liu z, liu y, liu ch, liu f. Nature. 2025 Jan;637(8046):E22. doi: 10.1038/s41586-024-08555-x. Nature. 2025. PMID: 39715925 No abstract available.
A PKD-MFF signaling axis couples mitochondrial fission to mitotic progression.
Pangou E, Bielska O, Guerber L, Schmucker S, Agote-Arán A, Ye T, Liao Y, Puig-Gamez M, Grandgirard E, Kleiss C, Liu Y, Compe E, Zhang Z, Aebersold R, Ricci R, Sumara I. Pangou E, et al. Among authors: liu y. Cell Rep. 2021 May 18;35(7):109129. doi: 10.1016/j.celrep.2021.109129. Cell Rep. 2021. PMID: 34010649 Free article.
Multi-omic measurements of heterogeneity in HeLa cells across laboratories.
Liu Y, Mi Y, Mueller T, Kreibich S, Williams EG, Van Drogen A, Borel C, Frank M, Germain PL, Bludau I, Mehnert M, Seifert M, Emmenlauer M, Sorg I, Bezrukov F, Bena FS, Zhou H, Dehio C, Testa G, Saez-Rodriguez J, Antonarakis SE, Hardt WD, Aebersold R. Liu Y, et al. Nat Biotechnol. 2019 Mar;37(3):314-322. doi: 10.1038/s41587-019-0037-y. Epub 2019 Feb 18. Nat Biotechnol. 2019. PMID: 30778230 Free article.
Comparative analysis of mRNA and protein degradation in prostate tissues indicates high stability of proteins.
Shao W, Guo T, Toussaint NC, Xue P, Wagner U, Li L, Charmpi K, Zhu Y, Wu J, Buljan M, Sun R, Rutishauser D, Hermanns T, Fankhauser CD, Poyet C, Ljubicic J, Rupp N, Rüschoff JH, Zhong Q, Beyer A, Ji J, Collins BC, Liu Y, Rätsch G, Wild PJ, Aebersold R. Shao W, et al. Among authors: liu y. Nat Commun. 2019 Jun 7;10(1):2524. doi: 10.1038/s41467-019-10513-5. Nat Commun. 2019. PMID: 31175306 Free PMC article.
A Global Screen for Assembly State Changes of the Mitotic Proteome by SEC-SWATH-MS.
Heusel M, Frank M, Köhler M, Amon S, Frommelt F, Rosenberger G, Bludau I, Aulakh S, Linder MI, Liu Y, Collins BC, Gstaiger M, Kutay U, Aebersold R. Heusel M, et al. Among authors: liu y. Cell Syst. 2020 Feb 26;10(2):133-155.e6. doi: 10.1016/j.cels.2020.01.001. Epub 2020 Feb 5. Cell Syst. 2020. PMID: 32027860 Free PMC article.
π-HuB: the proteomic navigator of the human body.
He F, Aebersold R, Baker MS, Bian X, Bo X, Chan DW, Chang C, Chen L, Chen X, Chen YJ, Cheng H, Collins BC, Corrales F, Cox J, E W, Van Eyk JE, Fan J, Faridi P, Figeys D, Gao GF, Gao W, Gao ZH, Goda K, Goh WWB, Gu D, Guo C, Guo T, He Y, Heck AJR, Hermjakob H, Hunter T, Iyer NG, Jiang Y, Jimenez CR, Joshi L, Kelleher NL, Li M, Li Y, Lin Q, Liu CH, Liu F, Liu GH, Liu Y, Liu Z, Low TY, Lu B, Mann M, Meng A, Moritz RL, Nice E, Ning G, Omenn GS, Overall CM, Palmisano G, Peng Y, Pineau C, Poon TCW, Purcell AW, Qiao J, Reddel RR, Robinson PJ, Roncada P, Sander C, Sha J, Song E, Srivastava S, Sun A, Sze SK, Tang C, Tang L, Tian R, Vizcaíno JA, Wang C, Wang C, Wang X, Wang X, Wang Y, Weiss T, Wilhelm M, Winkler R, Wollscheid B, Wong L, Xie L, Xie W, Xu T, Xu T, Yan L, Yang J, Yang X, Yates J, Yun T, Zhai Q, Zhang B, Zhang H, Zhang L, Zhang L, Zhang P, Zhang Y, Zheng YZ, Zhong Q, Zhu Y; π-HuB Consortium. He F, et al. Among authors: liu gh, liu z, liu y, liu ch, liu f. Nature. 2024 Dec;636(8042):322-331. doi: 10.1038/s41586-024-08280-5. Epub 2024 Dec 11. Nature. 2024. PMID: 39663494 Review.
Breast Cancer Classification Based on Proteotypes Obtained by SWATH Mass Spectrometry.
Bouchal P, Schubert OT, Faktor J, Capkova L, Imrichova H, Zoufalova K, Paralova V, Hrstka R, Liu Y, Ebhardt HA, Budinska E, Nenutil R, Aebersold R. Bouchal P, et al. Among authors: liu y. Cell Rep. 2019 Jul 16;28(3):832-843.e7. doi: 10.1016/j.celrep.2019.06.046. Cell Rep. 2019. PMID: 31315058 Free PMC article.
Human and mouse proteomics reveals the shared pathways in Alzheimer's disease and delayed protein turnover in the amyloidome.
Yarbro JM, Han X, Dasgupta A, Yang K, Liu D, Shrestha HK, Zaman M, Wang Z, Yu K, Lee DG, Vanderwall D, Niu M, Sun H, Xie B, Chen PC, Jiao Y, Zhang X, Wu Z, Chepyala SR, Fu Y, Li Y, Yuan ZF, Wang X, Poudel S, Vagnerova B, He Q, Tang A, Ronaldson PT, Chang R, Yu G, Liu Y, Peng J. Yarbro JM, et al. Among authors: liu y, liu d. Nat Commun. 2025 Feb 11;16(1):1533. doi: 10.1038/s41467-025-56853-3. Nat Commun. 2025. PMID: 39934151 Free PMC article.
Similarities and Differences of Blood N-Glycoproteins in Five Solid Carcinomas at Localized Clinical Stage Analyzed by SWATH-MS.
Sajic T, Liu Y, Arvaniti E, Surinova S, Williams EG, Schiess R, Hüttenhain R, Sethi A, Pan S, Brentnall TA, Chen R, Blattmann P, Friedrich B, Niméus E, Malander S, Omlin A, Gillessen S, Claassen M, Aebersold R. Sajic T, et al. Among authors: liu y. Cell Rep. 2018 May 29;23(9):2819-2831.e5. doi: 10.1016/j.celrep.2018.04.114. Cell Rep. 2018. PMID: 29847809 Free article.
Integrated Proteogenomic Characterization of HBV-Related Hepatocellular Carcinoma.
Gao Q, Zhu H, Dong L, Shi W, Chen R, Song Z, Huang C, Li J, Dong X, Zhou Y, Liu Q, Ma L, Wang X, Zhou J, Liu Y, Boja E, Robles AI, Ma W, Wang P, Li Y, Ding L, Wen B, Zhang B, Rodriguez H, Gao D, Zhou H, Fan J. Gao Q, et al. Among authors: liu y, liu q. Cell. 2019 Oct 3;179(2):561-577.e22. doi: 10.1016/j.cell.2019.08.052. Cell. 2019. PMID: 31585088 Free article.
A proteogenomic analysis of cervical cancer reveals therapeutic and biological insights.
Yu J, Gui X, Zou Y, Liu Q, Yang Z, An J, Guo X, Wang K, Guo J, Huang M, Zhou S, Zuo J, Chen Y, Deng L, Yuan G, Li N, Song Y, Jia J, Zeng J, Zhao Y, Liu X, Du X, Liu Y, Wang P, Zhang B, Ding L, Robles AI, Rodriguez H, Zhou H, Shao Z, Wu L, Gao D. Yu J, et al. Among authors: liu y, liu x, liu q. Nat Commun. 2024 Nov 22;15(1):10114. doi: 10.1038/s41467-024-53830-0. Nat Commun. 2024. PMID: 39578447 Free PMC article.
Advancing Scientific Communication in Proteomics.
Searle BC, Chazarin B, Collins BC, Kundu DJ, Huang S, Lin Q, Liu Y, Low TY, Saba J, Guo T, Palmisano G, Fert-Bober J. Searle BC, et al. Among authors: liu y. J Proteome Res. 2025 Feb 7;24(2):381-382. doi: 10.1021/acs.jproteome.4c01098. J Proteome Res. 2025. PMID: 39916559 No abstract available.
A Potential Mercury Polymer Mass Tag Probe for Mass Cytometry.
Wong ECN, Yang T, Li X, Liu Y, Majonis D, Abtahi M, Zhang Y, Lee ATY, Closson T, Paluan S, Hawrysh P, Winnik MA. Wong ECN, et al. Among authors: liu y. Anal Chem. 2025 May 22. doi: 10.1021/acs.analchem.5c00580. Online ahead of print. Anal Chem. 2025. PMID: 40404572
Safety and Efficacy of Topical Simvastatin Plus Cholesterol Cream vs Topical Simvastatin Cream Alone for Porokeratosis Ptychotropica: A randomized, single-blind, split-body, placebo-controlled investigator-initiated trial.
Chen Z, Liu Y, Yu H, Li J, Huang X, Xiang R, Mo R, Chen H, Yang Y. Chen Z, et al. Among authors: liu y. J Am Acad Dermatol. 2025 May 20:S0190-9622(25)02180-2. doi: 10.1016/j.jaad.2025.04.082. Online ahead of print. J Am Acad Dermatol. 2025. PMID: 40403974
Brain Characteristics in Patients With Myelin Oligodendrocyte Glycoprotein Antibody-Associated Disorder by 7.0 Tesla MRI.
Su L, Kuchling J, Gao C, Niendorf T, Finke C, Zhang Z, Guo A, Jing J, Tian DC, Li YJ, Zhang M, Shi X, Liu X, Wang H, Liu Y, Chien C, Levy M, Duan Y, Paul F, Shi FD. Su L, et al. Among authors: liu y, liu x. Ann Clin Transl Neurol. 2025 May 22. doi: 10.1002/acn3.70080. Online ahead of print. Ann Clin Transl Neurol. 2025. PMID: 40404603
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