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Items: 1 to 50 of 763

1.

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
2.

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 RH, Collins BC, Meyer H.

Mol Cell Proteomics. 2018 Mar 29. pii: mcp.RA117.000471. doi: 10.1074/mcp.RA117.000471. [Epub ahead of print]

3.

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.

4.

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]

5.

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
6.

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
7.

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
8.

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
9.

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.

10.

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
11.

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.

PMID:
29348366
12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

21.

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.

PMID:
28813649
22.

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.

23.

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.

24.

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.

25.

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.

26.

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.

PMID:
28628219
27.

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.

28.

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.

29.

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
30.

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.

31.

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.

32.

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.

33.

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.

34.

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.

35.

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.

36.

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.

37.

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.

38.

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
39.

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.

40.

System-Wide Quantitative Proteomics of the Metabolic Syndrome in Mice: Genotypic and Dietary Effects.

Terfve C, Sabidó E, Wu Y, Gonçalves E, Choi M, Vaga S, Vitek O, Saez-Rodriguez J, Aebersold R.

J Proteome Res. 2017 Feb 3;16(2):831-841. doi: 10.1021/acs.jproteome.6b00815. Epub 2017 Jan 10.

PMID:
27936760
41.

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. 2016 Dec 15;540(7633):428-432. doi: 10.1038/nature20603. Epub 2016 Nov 30.

42.

Highlights of the Biology and Disease-driven Human Proteome Project, 2015-2016.

Van Eyk JE, Corrales FJ, Aebersold R, Cerciello F, Deutsch EW, Roncada P, Sanchez JC, Yamamoto T, Yang P, Zhang H, Omenn GS.

J Proteome Res. 2016 Nov 4;15(11):3979-3987. Epub 2016 Sep 20.

43.

Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1.

Deutsch EW, Overall CM, Van Eyk JE, Baker MS, Paik YK, Weintraub ST, Lane L, Martens L, Vandenbrouck Y, Kusebauch U, Hancock WS, Hermjakob H, Aebersold R, Moritz RL, Omenn GS.

J Proteome Res. 2016 Nov 4;15(11):3961-3970. Epub 2016 Aug 24.

44.

A multicenter study benchmarks software tools for label-free proteome quantification.

Navarro P, Kuharev J, Gillet LC, Bernhardt OM, MacLean B, Röst HL, Tate SA, Tsou CC, Reiter L, Distler U, Rosenberger G, Perez-Riverol Y, Nesvizhskii AI, Aebersold R, Tenzer S.

Nat Biotechnol. 2016 Nov;34(11):1130-1136. doi: 10.1038/nbt.3685. Epub 2016 Oct 3.

45.

Contribution of Mass Spectrometry-Based Proteomics to the Understanding of TNF-α Signaling.

Ciuffa R, Caron E, Leitner A, Uliana F, Gstaiger M, Aebersold R.

J Proteome Res. 2017 Jan 6;16(1):14-33. doi: 10.1021/acs.jproteome.6b00728. Epub 2016 Oct 20. Review.

PMID:
27762135
46.

Liver ubiquitome uncovers nutrient-stress-mediated trafficking and secretion of complement C3.

Magliarelli HF, Matondo M, Mészáros G, Goginashvili A, Erbs E, Zhang Z, Mihlan M, Wolfrum C, Aebersold R, Sumara I, Ricci R.

Cell Death Dis. 2016 Oct 13;7(10):e2411. doi: 10.1038/cddis.2016.312.

47.

A High-Density Map for Navigating the Human Polycomb Complexome.

Hauri S, Comoglio F, Seimiya M, Gerstung M, Glatter T, Hansen K, Aebersold R, Paro R, Gstaiger M, Beisel C.

Cell Rep. 2016 Oct 4;17(2):583-595. doi: 10.1016/j.celrep.2016.08.096.

48.

Mass-spectrometric exploration of proteome structure and function.

Aebersold R, Mann M.

Nature. 2016 Sep 15;537(7620):347-55. doi: 10.1038/nature19949. Review.

PMID:
27629641
49.

Proteome-wide association studies identify biochemical modules associated with a wing-size phenotype in Drosophila melanogaster.

Okada H, Ebhardt HA, Vonesch SC, Aebersold R, Hafen E.

Nat Commun. 2016 Sep 1;7:12649. doi: 10.1038/ncomms12649.

50.

OpenMS: a flexible open-source software platform for mass spectrometry data analysis.

Röst HL, Sachsenberg T, Aiche S, Bielow C, Weisser H, Aicheler F, Andreotti S, Ehrlich HC, Gutenbrunner P, Kenar E, Liang X, Nahnsen S, Nilse L, Pfeuffer J, Rosenberger G, Rurik M, Schmitt U, Veit J, Walzer M, Wojnar D, Wolski WE, Schilling O, Choudhary JS, Malmström L, Aebersold R, Reinert K, Kohlbacher O.

Nat Methods. 2016 Aug 30;13(9):741-8. doi: 10.1038/nmeth.3959.

PMID:
27575624

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