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Items: 1 to 50 of 774

1.

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.

2.

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.

3.

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 Sep 5. pii: 201811874. doi: 10.1073/pnas.1811874115. [Epub ahead of print]

PMID:
30185561
4.

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.

5.

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.

6.

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.

7.

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.

8.

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.

PMID:
29945935
9.

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.

10.

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.

PMID:
29899147
11.

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.

12.

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.

PMID:
29698646
13.

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.

PMID:
29599191
14.

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.

15.

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 20. doi: 10.1099/mgen.0.000163. [Epub ahead of print]

16.

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
17.

Advancing translational research and precision medicine with targeted proteomics.

Uzozie AC, Aebersold R.

J Proteomics. 2018 Feb 22. pii: S1874-3919(18)30076-9. doi: 10.1016/j.jprot.2018.02.021. [Epub ahead of print]

PMID:
29476807
18.

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.

PMID:
29443976
19.

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
20.

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.

21.

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;:.

PMID:
29358758
22.

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.

23.

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.

24.

Systems Pharmacology Dissection of Cholesterol Regulation Reveals Determinants of Large Pharmacodynamic Variability between Cell Lines.

Blattmann P, Henriques D, Zimmermann M, Frommelt F, Sauer U, Saez-Rodriguez J, Aebersold R.

Cell Syst. 2017 Dec 27;5(6):604-619.e7. doi: 10.1016/j.cels.2017.11.002. Epub 2017 Dec 6.

25.

Molecular basis of AKAP79 regulation by calmodulin.

Patel N, Stengel F, Aebersold R, Gold MG.

Nat Commun. 2017 Nov 22;8(1):1681. doi: 10.1038/s41467-017-01715-w.

26.

Systematic proteome and proteostasis profiling in human Trisomy 21 fibroblast cells.

Liu Y, Borel C, Li L, Müller T, Williams EG, Germain PL, Buljan M, Sajic T, Boersema PJ, Shao W, Faini M, Testa G, Beyer A, Antonarakis SE, Aebersold R.

Nat Commun. 2017 Oct 31;8(1):1212. doi: 10.1038/s41467-017-01422-6.

27.

Systems proteomics approaches to study bacterial pathogens: application to Mycobacterium tuberculosis.

Banaei-Esfahani A, Nicod C, Aebersold R, Collins BC.

Curr Opin Microbiol. 2017 Oct;39:64-72. doi: 10.1016/j.mib.2017.09.013. Epub 2017 Oct 13. Review.

28.

The SysteMHC Atlas project.

Shao W, Pedrioli PGA, Wolski W, Scurtescu C, Schmid E, Vizcaíno JA, Courcelles M, Schuster H, Kowalewski D, Marino F, Arlehamn CSL, Vaughan K, Peters B, Sette A, Ottenhoff THM, Meijgaarden KE, Nieuwenhuizen N, Kaufmann SHE, Schlapbach R, Castle JC, Nesvizhskii AI, Nielsen M, Deutsch EW, Campbell DS, Moritz RL, Zubarev RA, Ytterberg AJ, Purcell AW, Marcilla M, Paradela A, Wang Q, Costello CE, Ternette N, van Veelen PA, van Els CACM, Heck AJR, de Souza GA, Sollid LM, Admon A, Stevanovic S, Rammensee HG, Thibault P, Perreault C, Bassani-Sternberg M, Aebersold R, Caron E.

Nucleic Acids Res. 2018 Jan 4;46(D1):D1237-D1247. doi: 10.1093/nar/gkx664.

29.

The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays.

Schwenk JM, Omenn GS, Sun Z, Campbell DS, Baker MS, Overall CM, Aebersold R, Moritz RL, Deutsch EW.

J Proteome Res. 2017 Dec 1;16(12):4299-4310. doi: 10.1021/acs.jproteome.7b00467. Epub 2017 Oct 10.

30.

Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry.

Collins BC, Hunter CL, Liu Y, Schilling B, Rosenberger G, Bader SL, Chan DW, Gibson BW, Gingras AC, Held JM, Hirayama-Kurogi M, Hou G, Krisp C, Larsen B, Lin L, Liu S, Molloy MP, Moritz RL, Ohtsuki S, Schlapbach R, Selevsek N, Thomas SN, Tzeng SC, Zhang H, Aebersold R.

Nat Commun. 2017 Aug 21;8(1):291. doi: 10.1038/s41467-017-00249-5.

31.

Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses.

Rosenberger G, Bludau I, Schmitt U, Heusel M, Hunter CL, Liu Y, MacCoss MJ, MacLean BX, Nesvizhskii AI, Pedrioli PGA, Reiter L, Röst HL, Tate S, Ting YS, Collins BC, Aebersold R.

Nat Methods. 2017 Sep;14(9):921-927. doi: 10.1038/nmeth.4398. Epub 2017 Aug 21.

32.

A Case for a Human Immuno-Peptidome Project Consortium.

Caron E, Aebersold R, Banaei-Esfahani A, Chong C, Bassani-Sternberg M.

Immunity. 2017 Aug 15;47(2):203-208. doi: 10.1016/j.immuni.2017.07.010.

33.

Delayed effects of transcriptional responses in Mycobacterium tuberculosis exposed to nitric oxide suggest other mechanisms involved in survival.

Cortes T, Schubert OT, Banaei-Esfahani A, Collins BC, Aebersold R, Young DB.

Sci Rep. 2017 Aug 15;7(1):8208. doi: 10.1038/s41598-017-08306-1.

34.

Impact of Alternative Splicing on the Human Proteome.

Liu Y, Gonzàlez-Porta M, Santos S, Brazma A, Marioni JC, Aebersold R, Venkitaraman AR, Wickramasinghe VO.

Cell Rep. 2017 Aug 1;20(5):1229-1241. doi: 10.1016/j.celrep.2017.07.025.

35.

Integrating highly quantitative proteomics and genome-scale metabolic modeling to study pH adaptation in the human pathogen Enterococcus faecalis.

Großeholz R, Koh CC, Veith N, Fiedler T, Strauss M, Olivier B, Collins BC, Schubert OT, Bergmann F, Kreikemeyer B, Aebersold R, Kummer U.

NPJ Syst Biol Appl. 2016 Sep 8;2:16017. doi: 10.1038/npjsba.2016.17. eCollection 2016.

36.

Protein kinase D at the Golgi controls NLRP3 inflammasome activation.

Zhang Z, Meszaros G, He WT, Xu Y, de Fatima Magliarelli H, Mailly L, Mihlan M, Liu Y, Puig Gámez M, Goginashvili A, Pasquier A, Bielska O, Neven B, Quartier P, Aebersold R, Baumert TF, Georgel P, Han J, Ricci R.

J Exp Med. 2017 Sep 4;214(9):2671-2693. doi: 10.1084/jem.20162040. Epub 2017 Jul 17.

37.

Application of SWATH Proteomics to Mouse Biology.

Wu Y, Williams EG, Aebersold R.

Curr Protoc Mouse Biol. 2017 Jun 19;7(2):130-143. doi: 10.1002/cpmo.28.

38.

Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS.

Rosenberger G, Liu Y, Röst HL, Ludwig C, Buil A, Bensimon A, Soste M, Spector TD, Dermitzakis ET, Collins BC, Malmström L, Aebersold R.

Nat Biotechnol. 2017 Aug;35(8):781-788. doi: 10.1038/nbt.3908. Epub 2017 Jun 12.

39.

A Class of Environmental and Endogenous Toxins Induces BRCA2 Haploinsufficiency and Genome Instability.

Tan SLW, Chadha S, Liu Y, Gabasova E, Perera D, Ahmed K, Constantinou S, Renaudin X, Lee M, Aebersold R, Venkitaraman AR.

Cell. 2017 Jun 1;169(6):1105-1118.e15. doi: 10.1016/j.cell.2017.05.010.

40.

Quantitative proteomics: challenges and opportunities in basic and applied research.

Schubert OT, Röst HL, Collins BC, Rosenberger G, Aebersold R.

Nat Protoc. 2017 Jul;12(7):1289-1294. doi: 10.1038/nprot.2017.040. Epub 2017 Jun 1.

PMID:
28569762
41.

Updated Reference Genome Sequence and Annotation of Mycobacterium bovis AF2122/97.

Malone KM, Farrell D, Stuber TP, Schubert OT, Aebersold R, Robbe-Austerman S, Gordon SV.

Genome Announc. 2017 Apr 6;5(14). pii: e00157-17. doi: 10.1128/genomeA.00157-17.

42.

Precise Temporal Profiling of Signaling Complexes in Primary Cells Using SWATH Mass Spectrometry.

Caron E, Roncagalli R, Hase T, Wolski WE, Choi M, Menoita MG, Durand S, García-Blesa A, Fierro-Monti I, Sajic T, Heusel M, Weiss T, Malissen M, Schlapbach R, Collins BC, Ghosh S, Kitano H, Aebersold R, Malissen B, Gstaiger M.

Cell Rep. 2017 Mar 28;18(13):3219-3226. doi: 10.1016/j.celrep.2017.03.019.

43.

Structural modeling of protein-RNA complexes using crosslinking of segmentally isotope-labeled RNA and MS/MS.

Dorn G, Leitner A, Boudet J, Campagne S, von Schroetter C, Moursy A, Aebersold R, Allain FH.

Nat Methods. 2017 May;14(5):487-490. doi: 10.1038/nmeth.4235. Epub 2017 Mar 27.

44.

Systematic Analysis of Human Protein Phosphatase Interactions and Dynamics.

Yadav L, Tamene F, Göös H, van Drogen A, Katainen R, Aebersold R, Gstaiger M, Varjosalo M.

Cell Syst. 2017 Apr 26;4(4):430-444.e5. doi: 10.1016/j.cels.2017.02.011. Epub 2017 Mar 18.

45.

Comprehensive proteome analysis of human skeletal muscle in cachexia and sarcopenia: a pilot study.

Ebhardt HA, Degen S, Tadini V, Schilb A, Johns N, Greig CA, Fearon KCH, Aebersold R, Jacobi C.

J Cachexia Sarcopenia Muscle. 2017 Aug;8(4):567-582. doi: 10.1002/jcsm.12188. Epub 2017 Mar 15.

46.

Molecular Details Underlying Dynamic Structures and Regulation of the Human 26S Proteasome.

Wang X, Cimermancic P, Yu C, Schweitzer A, Chopra N, Engel JL, Greenberg C, Huszagh AS, Beck F, Sakata E, Yang Y, Novitsky EJ, Leitner A, Nanni P, Kahraman A, Guo X, Dixon JE, Rychnovsky SD, Aebersold R, Baumeister W, Sali A, Huang L.

Mol Cell Proteomics. 2017 May;16(5):840-854. doi: 10.1074/mcp.M116.065326. Epub 2017 Mar 14.

47.

A curated collection of tissue microarray images and clinical outcome data of prostate cancer patients.

Zhong Q, Guo T, Rechsteiner M, Rüschoff JH, Rupp N, Fankhauser C, Saba K, Mortezavi A, Poyet C, Hermanns T, Zhu Y, Moch H, Aebersold R, Wild PJ.

Sci Data. 2017 Mar 14;4:170014. doi: 10.1038/sdata.2017.14.

48.

In Vivo and in Vitro Proteome Analysis of Human Immunodeficiency Virus (HIV)-1-infected, Human CD4+ T Cells.

Nemeth J, Vongrad V, Metzner KJ, Strouvelle VP, Weber R, Pedrioli P, Aebersold R, Günthard HF, Collins BC.

Mol Cell Proteomics. 2017 Apr;16(4 suppl 1):S108-S123. doi: 10.1074/mcp.M116.065235. Epub 2017 Feb 21.

49.

Automated SWATH Data Analysis Using Targeted Extraction of Ion Chromatograms.

Röst HL, Aebersold R, Schubert OT.

Methods Mol Biol. 2017;1550:289-307. doi: 10.1007/978-1-4939-6747-6_20.

PMID:
28188537
50.

Building ProteomeTools based on a complete synthetic human proteome.

Zolg DP, Wilhelm M, Schnatbaum K, Zerweck J, Knaute T, Delanghe B, Bailey DJ, Gessulat S, Ehrlich HC, Weininger M, Yu P, Schlegl J, Kramer K, Schmidt T, Kusebauch U, Deutsch EW, Aebersold R, Moritz RL, Wenschuh H, Moehring T, Aiche S, Huhmer A, Reimer U, Kuster B.

Nat Methods. 2017 Mar;14(3):259-262. doi: 10.1038/nmeth.4153. Epub 2017 Jan 30.

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