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Items: 1 to 50 of 801

1.

Histone epiproteomic profiling distinguishes oligodendroglioma, IDH-mutant and 1p/19q co-deleted from IDH-mutant astrocytoma and reveals less tri-methylation of H3K27 in oligodendrogliomas.

Feller C, Felix M, Weiss T, Herold-Mende C, Zhang F, Kockmann T, Sahm F, Aebersold R, von Deimling A, Reuss DE.

Acta Neuropathol. 2019 Nov 26. doi: 10.1007/s00401-019-02096-8. [Epub ahead of print] No abstract available.

PMID:
31773240
2.

Arabidopsis proteome and the mass spectral assay library.

Zhang H, Liu P, Guo T, Zhao H, Bensaddek D, Aebersold R, Xiong L.

Sci Data. 2019 Nov 22;6(1):278. doi: 10.1038/s41597-019-0294-0.

3.

Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines.

Guo T, Luna A, Rajapakse VN, Koh CC, Wu Z, Liu W, Sun Y, Gao H, Menden MP, Xu C, Calzone L, Martignetti L, Auwerx C, Buljan M, Banaei-Esfahani A, Ori A, Iskar M, Gillet L, Bi R, Zhang J, Zhang H, Yu C, Zhong Q, Varma S, Schmitt U, Qiu P, Zhang Q, Zhu Y, Wild PJ, Garnett MJ, Bork P, Beck M, Liu K, Saez-Rodriguez J, Elloumi F, Reinhold WC, Sander C, Pommier Y, Aebersold R.

iScience. 2019 Nov 22;21:664-680. doi: 10.1016/j.isci.2019.10.059. Epub 2019 Oct 31.

4.

Review of Batch Effects Prevention, Diagnostics, and Correction Approaches.

Čuklina J, Pedrioli PGA, Aebersold R.

Methods Mol Biol. 2020;2051:373-387. doi: 10.1007/978-1-4939-9744-2_16.

PMID:
31552638
5.

High-throughput proteomic analysis of FFPE tissue samples facilitates tumor stratification.

Zhu Y, Weiss T, Zhang Q, Sun R, Wang B, Yi X, Wu Z, Gao H, Cai X, Ruan G, Zhu T, Xu C, Lou S, Yu X, Gillet L, Blattmann P, Saba K, Fankhauser CD, Schmid MB, Rutishauser D, Ljubicic J, Christiansen A, Fritz C, Rupp NJ, Poyet C, Rushing E, Weller M, Roth P, Haralambieva E, Hofer S, Chen C, Jochum W, Gao X, Teng X, Chen L, Zhong Q, Wild PJ, Aebersold R, Guo T.

Mol Oncol. 2019 Nov;13(11):2305-2328. doi: 10.1002/1878-0261.12570. Epub 2019 Sep 18.

6.

CryoEM structures of Arabidopsis DDR complexes involved in RNA-directed DNA methylation.

Wongpalee SP, Liu S, Gallego-Bartolomé J, Leitner A, Aebersold R, Liu W, Yen L, Nohales MA, Kuo PH, Vashisht AA, Wohlschlegel JA, Feng S, Kay SA, Zhou ZH, Jacobsen SE.

Nat Commun. 2019 Sep 2;10(1):3916. doi: 10.1038/s41467-019-11759-9.

7.

Elucidating essential kinases of endothelin signalling by logic modelling of phosphoproteomics data.

Schäfer A, Gjerga E, Welford RW, Renz I, Lehembre F, Groenen PM, Saez-Rodriguez J, Aebersold R, Gstaiger M.

Mol Syst Biol. 2019 Aug;15(8):e8828. doi: 10.15252/msb.20198828.

8.

Mass Spectrometric Exploration of the Biochemical Basis of Living Systems.

Aebersold R, Blattmann P.

Chimia (Aarau). 2019 Aug 21;73(7):540-548. doi: 10.2533/chimia.2019.540.

PMID:
31431214
9.

The interactome of KRAB zinc finger proteins reveals the evolutionary history of their functional diversification.

Helleboid PY, Heusel M, Duc J, Piot C, Thorball CW, Coluccio A, Pontis J, Imbeault M, Turelli P, Aebersold R, Trono D.

EMBO J. 2019 Sep 16;38(18):e101220. doi: 10.15252/embj.2018101220. Epub 2019 Aug 12.

10.

The MLL1 trimeric catalytic complex is a dynamic conformational ensemble stabilized by multiple weak interactions.

Kaustov L, Lemak A, Wu H, Faini M, Fan L, Fang X, Zeng H, Duan S, Allali-Hassani A, Li F, Wei Y, Vedadi M, Aebersold R, Wang Y, Houliston S, Arrowsmith CH.

Nucleic Acids Res. 2019 Sep 26;47(17):9433-9447. doi: 10.1093/nar/gkz697.

11.

Author Correction: Epigenetic stress responses induce muscle stem-cell ageing by Hoxa9 developmental signals.

Schwörer S, Becker F, Feller C, Baig AH, Köber U, Henze H, Kraus JM, Xin B, Lechel A, Lipka DB, Varghese CS, Schmidt M, Rohs R, Aebersold R, Medina KL, Kestler HA, Neri F, von Maltzahn J, Tümpel S, Rudolph KL.

Nature. 2019 Aug;572(7769):E11-E15. doi: 10.1038/s41586-019-1455-1.

PMID:
31363230
12.

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.

Cell Rep. 2019 Jul 16;28(3):832-843.e7. doi: 10.1016/j.celrep.2019.06.046.

13.

A Targeted Mass Spectrometry Strategy for Developing Proteomic Biomarkers: A Case Study of Epithelial Ovarian Cancer.

Hüttenhain R, Choi M, Martin de la Fuente L, Oehl K, Chang CV, Zimmermann AK, Malander S, Olsson H, Surinova S, Clough T, Heinzelmann-Schwarz V, Wild PJ, Dinulescu DM, Niméus E, Vitek O, Aebersold R.

Mol Cell Proteomics. 2019 Sep;18(9):1836-1850. doi: 10.1074/mcp.RA118.001221. Epub 2019 Jul 9.

PMID:
31289117
14.

Proteomic identification of a marker signature for MAPKi resistance in melanoma.

Paulitschke V, Eichhoff O, Gerner C, Paulitschke P, Bileck A, Mohr T, Cheng PF, Leitner A, Guenova E, Saulite I, Freiberger SN, Irmisch A, Knapp B, Zila N, Chatziisaak TP, Stephan J, Mangana J, Kunstfeld R, Pehamberger H, Aebersold R, Dummer R, Levesque MP.

EMBO J. 2019 Aug 1;38(15):e95874. doi: 10.15252/embj.201695874. Epub 2019 Jun 26.

PMID:
31267558
15.

Quantitative Interactomics in Primary T Cells Provides a Rationale for Concomitant PD-1 and BTLA Coinhibitor Blockade in Cancer Immunotherapy.

Celis-Gutierrez J, Blattmann P, Zhai Y, Jarmuzynski N, Ruminski K, Grégoire C, Ounoughene Y, Fiore F, Aebersold R, Roncagalli R, Gstaiger M, Malissen B.

Cell Rep. 2019 Jun 11;27(11):3315-3330.e7. doi: 10.1016/j.celrep.2019.05.041.

16.

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.

Nat Commun. 2019 Jun 7;10(1):2524. doi: 10.1038/s41467-019-10513-5.

17.

A new class of protein biomarkers based on subcellular distribution: application to a mouse liver cancer model.

Sajic T, Ciuffa R, Lemos V, Xu P, Leone V, Li C, Williams EG, Makris G, Banaei-Esfahani A, Heikenwalder M, Schoonjans K, Aebersold R.

Sci Rep. 2019 May 6;9(1):6913. doi: 10.1038/s41598-019-43091-z.

18.

First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study.

Iacobucci C, Piotrowski C, Aebersold R, Amaral BC, Andrews P, Bernfur K, Borchers C, Brodie NI, Bruce JE, Cao Y, Chaignepain S, Chavez JD, Claverol S, Cox J, Davis T, Degliesposti G, Dong MQ, Edinger N, Emanuelsson C, Gay M, Götze M, Gomes-Neto F, Gozzo FC, Gutierrez C, Haupt C, Heck AJR, Herzog F, Huang L, Hoopmann MR, Kalisman N, Klykov O, Kukačka Z, Liu F, MacCoss MJ, Mechtler K, Mesika R, Moritz RL, Nagaraj N, Nesati V, Neves-Ferreira AGC, Ninnis R, Novák P, O'Reilly FJ, Pelzing M, Petrotchenko E, Piersimoni L, Plasencia M, Pukala T, Rand KD, Rappsilber J, Reichmann D, Sailer C, Sarnowski CP, Scheltema RA, Schmidt C, Schriemer DC, Shi Y, Skehel JM, Slavin M, Sobott F, Solis-Mezarino V, Stephanowitz H, Stengel F, Stieger CE, Trabjerg E, Trnka M, Vilaseca M, Viner R, Xiang Y, Yilmaz S, Zelter A, Ziemianowicz D, Leitner A, Sinz A.

Anal Chem. 2019 Jun 4;91(11):6953-6961. doi: 10.1021/acs.analchem.9b00658. Epub 2019 May 22.

19.

Disentangling Genetic and Environmental Effects on the Proteotypes of Individuals.

Romanov N, Kuhn M, Aebersold R, Ori A, Beck M, Bork P.

Cell. 2019 May 16;177(5):1308-1318.e10. doi: 10.1016/j.cell.2019.03.015. Epub 2019 Apr 25.

20.

Sensitive Quantitative Proteomics of Human Hematopoietic Stem and Progenitor Cells by Data-independent Acquisition Mass Spectrometry.

Amon S, Meier-Abt F, Gillet LC, Dimitrieva S, Theocharides APA, Manz MG, Aebersold R.

Mol Cell Proteomics. 2019 Jul;18(7):1454-1467. doi: 10.1074/mcp.TIR119.001431. Epub 2019 Apr 11.

21.

The Chaperonin TRiC/CCT Associates with Prefoldin through a Conserved Electrostatic Interface Essential for Cellular Proteostasis.

Gestaut D, Roh SH, Ma B, Pintilie G, Joachimiak LA, Leitner A, Walzthoeni T, Aebersold R, Chiu W, Frydman J.

Cell. 2019 Apr 18;177(3):751-765.e15. doi: 10.1016/j.cell.2019.03.012. Epub 2019 Apr 4.

PMID:
30955883
22.

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.

Nat Biotechnol. 2019 Mar;37(3):314-322. doi: 10.1038/s41587-019-0037-y. Epub 2019 Feb 18.

PMID:
30778230
23.

Generation of a zebrafish SWATH-MS spectral library to quantify 10,000 proteins.

Blattmann P, Stutz V, Lizzo G, Richard J, Gut P, Aebersold R.

Sci Data. 2019 Feb 12;6:190011. doi: 10.1038/sdata.2019.11.

24.

MINA-1 and WAGO-4 are part of regulatory network coordinating germ cell death and RNAi in C. elegans.

Sendoel A, Subasic D, Ducoli L, Keller M, Michel E, Kohler I, Singh KD, Zheng X, Brümmer A, Imig J, Kishore S, Wu Y, Kanitz A, Kaech A, Mittal N, Matia-González AM, Gerber AP, Zavolan M, Aebersold R, Hall J, Allain FH, Hengartner MO.

Cell Death Differ. 2019 Oct;26(10):2157-2178. doi: 10.1038/s41418-019-0291-z. Epub 2019 Feb 6.

PMID:
30728462
25.

Complex-centric proteome profiling by SEC-SWATH-MS.

Heusel M, Bludau I, Rosenberger G, Hafen R, Frank M, Banaei-Esfahani A, van Drogen A, Collins BC, Gstaiger M, Aebersold R.

Mol Syst Biol. 2019 Jan 14;15(1):e8438. doi: 10.15252/msb.20188438.

26.

Proteomics goes parallel.

Collins BC, Aebersold R.

Nat Biotechnol. 2018 Nov 9;36(11):1051-1053. doi: 10.1038/nbt.4288. No abstract available.

PMID:
30412198
27.

Identification of Protein Abundance Changes in Hepatocellular Carcinoma Tissues Using PCT-SWATH.

Zhu Y, Zhu J, Lu C, Zhang Q, Xie W, Sun P, Dong X, Yue L, Sun Y, Yi X, Zhu T, Ruan G, Aebersold R, Huang S, Guo T.

Proteomics Clin Appl. 2019 Jan;13(1):e1700179. doi: 10.1002/prca.201700179. Epub 2018 Nov 19.

PMID:
30365225
28.

Separation of blood microsamples by exploiting sedimentation at the microscale.

Forchelet D, Béguin S, Sajic T, Bararpour N, Pataky Z, Frias M, Grabherr S, Augsburger M, Liu Y, Charnley M, Déglon J, Aebersold R, Thomas A, Renaud P.

Sci Rep. 2018 Sep 20;8(1):14101. doi: 10.1038/s41598-018-32314-4.

29.

Molecular basis for disassembly of an importin:ribosomal protein complex by the escortin Tsr2.

Schütz S, Michel E, Damberger FF, Oplová M, Peña C, Leitner A, Aebersold R, Allain FH, Panse VG.

Nat Commun. 2018 Sep 10;9(1):3669. doi: 10.1038/s41467-018-06160-x.

30.

Insights into autophagosome biogenesis from structural and biochemical analyses of the ATG2A-WIPI4 complex.

Chowdhury S, Otomo C, Leitner A, Ohashi K, Aebersold R, Lander GC, Otomo T.

Proc Natl Acad Sci U S A. 2018 Oct 16;115(42):E9792-E9801. doi: 10.1073/pnas.1811874115. Epub 2018 Sep 5.

31.

Data-independent acquisition-based SWATH-MS for quantitative proteomics: a tutorial.

Ludwig C, Gillet L, Rosenberger G, Amon S, Collins BC, Aebersold R.

Mol Syst Biol. 2018 Aug 13;14(8):e8126. doi: 10.15252/msb.20178126. Review.

32.

Multi-region proteome analysis quantifies spatial heterogeneity of prostate tissue biomarkers.

Guo T, Li L, Zhong Q, Rupp NJ, Charmpi K, Wong CE, Wagner U, Rueschoff JH, Jochum W, Fankhauser CD, Saba K, Poyet C, Wild PJ, Aebersold R, Beyer A.

Life Sci Alliance. 2018 May 29;1(2). pii: e201800042. doi: 10.26508/lsa.201800042.

33.

A tissue-based draft map of the murine MHC class I immunopeptidome.

Schuster H, Shao W, Weiss T, Pedrioli PGA, Roth P, Weller M, Campbell DS, Deutsch EW, Moritz RL, Planz O, Rammensee HG, Aebersold R, Caron E.

Sci Data. 2018 Aug 7;5:180157. doi: 10.1038/sdata.2018.157.

34.

Systems pharmacology using mass spectrometry identifies critical response nodes in prostate cancer.

Ebhardt HA, Root A, Liu Y, Gauthier NP, Sander C, Aebersold R.

NPJ Syst Biol Appl. 2018 Jul 2;4:26. doi: 10.1038/s41540-018-0064-1. eCollection 2018.

35.

Quantifying and Localizing the Mitochondrial Proteome Across Five Tissues in A Mouse Population.

Williams EG, Wu Y, Wolski W, Kim JY, Lan J, Hasan M, Halter C, Jha P, Ryu D, Auwerx J, Aebersold R.

Mol Cell Proteomics. 2018 Sep;17(9):1766-1777. doi: 10.1074/mcp.RA118.000554. Epub 2018 Jun 26.

36.

Lipidated apolipoprotein E4 structure and its receptor binding mechanism determined by a combined cross-linking coupled to mass spectrometry and molecular dynamics approach.

Henry N, Krammer EM, Stengel F, Adams Q, Van Liefferinge F, Hubin E, Chaves R, Efremov R, Aebersold R, Vandenbussche G, Prévost M, Raussens V, Deroo S.

PLoS Comput Biol. 2018 Jun 22;14(6):e1006165. doi: 10.1371/journal.pcbi.1006165. eCollection 2018 Jun.

37.

Conformational control and DNA-binding mechanism of the metazoan origin recognition complex.

Bleichert F, Leitner A, Aebersold R, Botchan MR, Berger JM.

Proc Natl Acad Sci U S A. 2018 Jun 26;115(26):E5906-E5915. doi: 10.1073/pnas.1806315115. Epub 2018 Jun 13.

38.

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.

Cell Rep. 2018 May 29;23(9):2819-2831.e5. doi: 10.1016/j.celrep.2018.04.114.

39.

A Proteomic Connectivity Map.

Feller C, Aebersold R.

Cell Syst. 2018 Apr 25;6(4):403-405. doi: 10.1016/j.cels.2018.04.007.

40.

AP-SWATH Reveals Direct Involvement of VCP/p97 in Integrated Stress Response Signaling Through Facilitating CReP/PPP1R15B Degradation.

Hülsmann J, Kravic B, Weith M, Gstaiger M, Aebersold R, Collins BC, Meyer H.

Mol Cell Proteomics. 2018 Jul;17(7):1295-1307. doi: 10.1074/mcp.RA117.000471. Epub 2018 Mar 29.

41.

Systematic characterization of pan-cancer mutation clusters.

Buljan M, Blattmann P, Aebersold R, Boutros M.

Mol Syst Biol. 2018 Mar 23;14(3):e7974. doi: 10.15252/msb.20177974.

42.

Comparative 'omics analyses differentiate Mycobacterium tuberculosis and Mycobacterium bovis and reveal distinct macrophage responses to infection with the human and bovine tubercle bacilli.

Malone KM, Rue-Albrecht K, Magee DA, Conlon K, Schubert OT, Nalpas NC, Browne JA, Smyth A, Gormley E, Aebersold R, MacHugh DE, Gordon SV.

Microb Genom. 2018 Mar;4(3). doi: 10.1099/mgen.0.000163. Epub 2018 Mar 20.

43.

Author Correction: Structural basis of AAUAAA polyadenylation signal recognition by the human CPSF complex.

Clerici M, Faini M, Muckenfuss LM, Aebersold R, Jinek M.

Nat Struct Mol Biol. 2018 Apr;25(4):355. doi: 10.1038/s41594-018-0044-6.

PMID:
29540792
44.

Advancing translational research and precision medicine with targeted proteomics.

Uzozie AC, Aebersold R.

J Proteomics. 2018 Oct 30;189:1-10. doi: 10.1016/j.jprot.2018.02.021. Epub 2018 Feb 22. Review.

PMID:
29476807
45.

How many human proteoforms are there?

Aebersold R, Agar JN, Amster IJ, Baker MS, Bertozzi CR, Boja ES, Costello CE, Cravatt BF, Fenselau C, Garcia BA, Ge Y, Gunawardena J, Hendrickson RC, Hergenrother PJ, Huber CG, Ivanov AR, Jensen ON, Jewett MC, Kelleher NL, Kiessling LL, Krogan NJ, Larsen MR, Loo JA, Ogorzalek Loo RR, Lundberg E, MacCoss MJ, Mallick P, Mootha VK, Mrksich M, Muir TW, Patrie SM, Pesavento JJ, Pitteri SJ, Rodriguez H, Saghatelian A, Sandoval W, Schlüter H, Sechi S, Slavoff SA, Smith LM, Snyder MP, Thomas PM, Uhlén M, Van Eyk JE, Vidal M, Walt DR, White FM, Williams ER, Wohlschlager T, Wysocki VH, Yates NA, Young NL, Zhang B.

Nat Chem Biol. 2018 Feb 14;14(3):206-214. doi: 10.1038/nchembio.2576.

46.

Integrative Structural Investigation on the Architecture of Human Importin4_Histone H3/H4_Asf1a Complex and Its Histone H3 Tail Binding.

Yoon J, Kim SJ, An S, Cho S, Leitner A, Jung T, Aebersold R, Hebert H, Cho US, Song JJ.

J Mol Biol. 2018 Mar 16;430(6):822-841. doi: 10.1016/j.jmb.2018.01.015. Epub 2018 Jan 31.

PMID:
29408485
47.

Structure of a human cap-dependent 48S translation pre-initiation complex.

Eliseev B, Yeramala L, Leitner A, Karuppasamy M, Raimondeau E, Huard K, Alkalaeva E, Aebersold R, Schaffitzel C.

Nucleic Acids Res. 2018 Mar 16;46(5):2678-2689. doi: 10.1093/nar/gky054.

48.

Structural basis of AAUAAA polyadenylation signal recognition by the human CPSF complex.

Clerici M, Faini M, Muckenfuss LM, Aebersold R, Jinek M.

Nat Struct Mol Biol. 2018 Feb;25(2):135-138. doi: 10.1038/s41594-017-0020-6. Epub 2018 Jan 22. Erratum in: Nat Struct Mol Biol. 2018 Mar 14;:.

49.

Structures of human PRC2 with its cofactors AEBP2 and JARID2.

Kasinath V, Faini M, Poepsel S, Reif D, Feng XA, Stjepanovic G, Aebersold R, Nogales E.

Science. 2018 Feb 23;359(6378):940-944. doi: 10.1126/science.aar5700. Epub 2018 Jan 18.

50.

Structural insights into the assembly and polyA signal recognition mechanism of the human CPSF complex.

Clerici M, Faini M, Aebersold R, Jinek M.

Elife. 2017 Dec 23;6. pii: e33111. doi: 10.7554/eLife.33111.

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