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Items: 1 to 50 of 193

1.

A folded conformation of MukBEF and cohesin.

Bürmann F, Lee BG, Than T, Sinn L, O'Reilly FJ, Yatskevich S, Rappsilber J, Hu B, Nasmyth K, Löwe J.

Nat Struct Mol Biol. 2019 Mar;26(3):227-236. doi: 10.1038/s41594-019-0196-z. Epub 2019 Mar 4.

PMID:
30833788
2.

Sequential Digestion with Trypsin and Elastase in Cross-Linking Mass Spectrometry.

Dau T, Gupta K, Berger I, Rappsilber J.

Anal Chem. 2019 Mar 13. doi: 10.1021/acs.analchem.8b05222. [Epub ahead of print]

PMID:
30817130
3.

Fission Yeast NDR/LATS Kinase Orb6 Regulates Exocytosis via Phosphorylation of the Exocyst Complex.

Tay YD, Leda M, Spanos C, Rappsilber J, Goryachev AB, Sawin KE.

Cell Rep. 2019 Feb 5;26(6):1654-1667.e7. doi: 10.1016/j.celrep.2019.01.027.

4.

Molecular interactions between Hel2 and RNA supporting ribosome-associated quality control.

Winz ML, Peil L, Turowski TW, Rappsilber J, Tollervey D.

Nat Commun. 2019 Feb 4;10(1):563. doi: 10.1038/s41467-019-08382-z.

5.

Posttranscriptional Regulation of 14q32 MicroRNAs by the CIRBP and HADHB during Vascular Regeneration after Ischemia.

Downie Ruiz Velasco A, Welten SMJ, Goossens EAC, Quax PHA, Rappsilber J, Michlewski G, Nossent AY.

Mol Ther Nucleic Acids. 2019 Mar 1;14:329-338. doi: 10.1016/j.omtn.2018.11.017. Epub 2018 Dec 6.

6.

Data-independent acquisition improves quantitative cross-linking mass spectrometry.

Müller F, Kolbowski L, Bernhardt OM, Reiter L, Rappsilber J.

Mol Cell Proteomics. 2019 Jan 16. pii: mcp.TIR118.001276. doi: 10.1074/mcp.TIR118.001276. [Epub ahead of print]

7.

Noncovalently Associated Peptides Observed during Liquid Chromatography-Mass Spectrometry and Their Effect on Cross-Link Analyses.

Giese SH, Belsom A, Sinn L, Fischer L, Rappsilber J.

Anal Chem. 2019 Feb 19;91(4):2678-2685. doi: 10.1021/acs.analchem.8b04037. Epub 2019 Feb 1.

8.

Proteome analysis of human neutrophil granulocytes from patients with monogenic disease using data-independent acquisition.

Grabowski P, Hesse S, Hollizeck S, Rohlfs M, Behrends U, Sherkat R, Tamary H, Ünal E, Somech R, Patıroğlu T, Canzar S, van der Werff Ten Bosch J, Klein C, Rappsilber J.

Mol Cell Proteomics. 2019 Jan 10. pii: mcp.RA118.001141. doi: 10.1074/mcp.RA118.001141. [Epub ahead of print]

9.

A programmed wave of uridylation-primed mRNA degradation is essential for meiotic progression and mammalian spermatogenesis.

Morgan M, Kabayama Y, Much C, Ivanova I, Di Giacomo M, Auchynnikava T, Monahan JM, Vitsios DM, Vasiliauskaitė L, Comazzetto S, Rappsilber J, Allshire RC, Porse BT, Enright AJ, O'Carroll D.

Cell Res. 2019 Mar;29(3):221-232. doi: 10.1038/s41422-018-0128-1. Epub 2019 Jan 7.

PMID:
30617251
10.

The depolymerase activity of MCAK shows a graded response to Aurora B kinase phosphorylation through allosteric regulation.

McHugh T, Zou J, Volkov VA, Bertin A, Talapatra SK, Rappsilber J, Dogterom M, Welburn JPI.

J Cell Sci. 2019 Jan 14;132(4). pii: jcs228353. doi: 10.1242/jcs.228353.

11.

Quantitative cross-linking/mass spectrometry to elucidate structural changes in proteins and their complexes.

Chen ZA, Rappsilber J.

Nat Protoc. 2019 Jan;14(1):171-201. doi: 10.1038/s41596-018-0089-3.

PMID:
30559374
12.

A Primer on Data Analytics in Functional Genomics: How to Move from Data to Insight?

Grabowski P, Rappsilber J.

Trends Biochem Sci. 2019 Jan;44(1):21-32. doi: 10.1016/j.tibs.2018.10.010. Epub 2018 Dec 3. Review.

13.

Gain-of-function DNMT3A mutations cause microcephalic dwarfism and hypermethylation of Polycomb-regulated regions.

Heyn P, Logan CV, Fluteau A, Challis RC, Auchynnikava T, Martin CA, Marsh JA, Taglini F, Kilanowski F, Parry DA, Cormier-Daire V, Fong CT, Gibson K, Hwa V, Ibáñez L, Robertson SP, Sebastiani G, Rappsilber J, Allshire RC, Reijns MAM, Dauber A, Sproul D, Jackson AP.

Nat Genet. 2019 Jan;51(1):96-105. doi: 10.1038/s41588-018-0274-x. Epub 2018 Nov 26.

PMID:
30478443
14.

The kinetochore module Okp1CENP-Q/Ame1CENP-U is a reader for N-terminal modifications on the centromeric histone Cse4CENP-A.

Anedchenko EA, Samel-Pommerencke A, Tran Nguyen TM, Shahnejat-Bushehri S, Pöpsel J, Lauster D, Herrmann A, Rappsilber J, Cuomo A, Bonaldi T, Ehrenhofer-Murray AE.

EMBO J. 2019 Jan 3;38(1). pii: e98991. doi: 10.15252/embj.201898991. Epub 2018 Nov 2.

PMID:
30389668
15.

Cross-linking mass spectrometry: methods and applications in structural, molecular and systems biology.

O'Reilly FJ, Rappsilber J.

Nat Struct Mol Biol. 2018 Nov;25(11):1000-1008. doi: 10.1038/s41594-018-0147-0. Epub 2018 Oct 29. Review.

PMID:
30374081
16.

Protein Dynamics in Solution by Quantitative Crosslinking/Mass Spectrometry.

Chen ZA, Rappsilber J.

Trends Biochem Sci. 2018 Nov;43(11):908-920. doi: 10.1016/j.tibs.2018.09.003. Epub 2018 Oct 11. Review.

17.

In-Search Assignment of Monoisotopic Peaks Improves the Identification of Cross-Linked Peptides.

Lenz S, Giese SH, Fischer L, Rappsilber J.

J Proteome Res. 2018 Nov 2;17(11):3923-3931. doi: 10.1021/acs.jproteome.8b00600. Epub 2018 Oct 24.

18.

Quantitative Proteomics of the Mitotic Chromosome Scaffold Reveals the Association of BAZ1B with Chromosomal Axes.

Ohta S, Taniguchi T, Sato N, Hamada M, Taniguchi H, Rappsilber J.

Mol Cell Proteomics. 2019 Feb;18(2):169-181. doi: 10.1074/mcp.RA118.000923. Epub 2018 Sep 28.

PMID:
30266865
19.

Heterologous Biosynthesis, Modifications and Structural Characterization of Ruminococcin-A, a Lanthipeptide From the Gut Bacterium Ruminococcus gnavus E1, in Escherichia coli.

Ongey EL, Giessmann RT, Fons M, Rappsilber J, Adrian L, Neubauer P.

Front Microbiol. 2018 Jul 26;9:1688. doi: 10.3389/fmicb.2018.01688. eCollection 2018.

20.

Epigenetic Variability Confounds Transcriptome but Not Proteome Profiling for Coexpression-based Gene Function Prediction.

Grabowski P, Kustatscher G, Rappsilber J.

Mol Cell Proteomics. 2018 Nov;17(11):2082-2090. doi: 10.1074/mcp.RA118.000935. Epub 2018 Jul 24.

21.

Exportin Crm1 is repurposed as a docking protein to generate microtubule organizing centers at the nuclear pore.

Bao XX, Spanos C, Kojidani T, Lynch EM, Rappsilber J, Hiraoka Y, Haraguchi T, Sawin KE.

Elife. 2018 May 29;7. pii: e33465. doi: 10.7554/eLife.33465.

22.

False discovery rate estimation and heterobifunctional cross-linkers.

Fischer L, Rappsilber J.

PLoS One. 2018 May 10;13(5):e0196672. doi: 10.1371/journal.pone.0196672. eCollection 2018.

23.

xiSPEC: web-based visualization, analysis and sharing of proteomics data.

Kolbowski L, Combe C, Rappsilber J.

Nucleic Acids Res. 2018 Jul 2;46(W1):W473-W478. doi: 10.1093/nar/gky353.

24.

JAMI: a Java library for molecular interactions and data interoperability.

Sivade Dumousseau M, Koch M, Shrivastava A, Alonso-López D, De Las Rivas J, Del-Toro N, Combe CW, Meldal BHM, Heimbach J, Rappsilber J, Sullivan J, Yehudi Y, Orchard S.

BMC Bioinformatics. 2018 Apr 11;19(1):133. doi: 10.1186/s12859-018-2119-0.

25.

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.

26.

Protein Tertiary Structure by Crosslinking/Mass Spectrometry.

Schneider M, Belsom A, Rappsilber J.

Trends Biochem Sci. 2018 Mar;43(3):157-169. doi: 10.1016/j.tibs.2017.12.006. Epub 2018 Jan 31. Review.

27.

Small angle X-ray scattering and cross-linking for data assisted protein structure prediction in CASP 12 with prospects for improved accuracy.

Ogorzalek TL, Hura GL, Belsom A, Burnett KH, Kryshtafovych A, Tainer JA, Rappsilber J, Tsutakawa SE, Fidelis K.

Proteins. 2018 Mar;86 Suppl 1:202-214. doi: 10.1002/prot.25452. Epub 2018 Feb 7.

28.

Genes Important for Schizosaccharomyces pombe Meiosis Identified Through a Functional Genomics Screen.

Blyth J, Makrantoni V, Barton RE, Spanos C, Rappsilber J, Marston AL.

Genetics. 2018 Feb;208(2):589-603. doi: 10.1534/genetics.117.300527. Epub 2017 Dec 19.

29.

On the Reproducibility of Label-Free Quantitative Cross-Linking/Mass Spectrometry.

Müller F, Fischer L, Chen ZA, Auchynnikava T, Rappsilber J.

J Am Soc Mass Spectrom. 2018 Feb;29(2):405-412. doi: 10.1007/s13361-017-1837-2. Epub 2017 Dec 18.

30.

Comprehensive identification of proteins binding to RNA G-quadruplex motifs in the 5' UTR of tumor-associated mRNAs.

Serikawa T, Spanos C, von Hacht A, Budisa N, Rappsilber J, Kurreck J.

Biochimie. 2018 Jan;144:169-184. doi: 10.1016/j.biochi.2017.11.003. Epub 2017 Nov 10.

PMID:
29129743
31.

RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination.

Choudhury NR, Heikel G, Trubitsyna M, Kubik P, Nowak JS, Webb S, Granneman S, Spanos C, Rappsilber J, Castello A, Michlewski G.

BMC Biol. 2017 Nov 8;15(1):105. doi: 10.1186/s12915-017-0444-9.

32.

Architecture of TAF11/TAF13/TBP complex suggests novel regulation properties of general transcription factor TFIID.

Gupta K, Watson AA, Baptista T, Scheer E, Chambers AL, Koehler C, Zou J, Obong-Ebong I, Kandiah E, Temblador A, Round A, Forest E, Man P, Bieniossek C, Laue ED, Lemke EA, Rappsilber J, Robinson CV, Devys D, Tora L, Berger I.

Elife. 2017 Nov 7;6. pii: e30395. doi: 10.7554/eLife.30395.

33.

ComplexViewer: visualization of curated macromolecular complexes.

Combe CW, Sivade MD, Hermjakob H, Heimbach J, Meldal BHM, Micklem G, Orchard S, Rappsilber J.

Bioinformatics. 2017 Nov 15;33(22):3673-3675. doi: 10.1093/bioinformatics/btx497.

34.

RNA polymerase II stalling at pre-mRNA splice sites is enforced by ubiquitination of the catalytic subunit.

Milligan L, Sayou C, Tuck A, Auchynnikava T, Reid JE, Alexander R, Alves FL, Allshire R, Spanos C, Rappsilber J, Beggs JD, Kudla G, Tollervey D.

Elife. 2017 Oct 13;6. pii: e27082. doi: 10.7554/eLife.27082.

35.

14-3-3 regulation of Ncd reveals a new mechanism for targeting proteins to the spindle in oocytes.

Beaven R, Bastos RN, Spanos C, Romé P, Cullen CF, Rappsilber J, Giet R, Goshima G, Ohkura H.

J Cell Biol. 2017 Oct 2;216(10):3029-3039. doi: 10.1083/jcb.201704120. Epub 2017 Aug 31.

36.

Pervasive coexpression of spatially proximal genes is buffered at the protein level.

Kustatscher G, Grabowski P, Rappsilber J.

Mol Syst Biol. 2017 Aug 23;13(8):937. doi: 10.15252/msb.20177548.

37.

Phosphorylation of SOS1 on tyrosine 1196 promotes its RAC GEF activity and contributes to BCR-ABL leukemogenesis.

Gerboth S, Frittoli E, Palamidessi A, Baltanas FC, Salek M, Rappsilber J, Giuliani C, Troglio F, Rolland Y, Pruneri G, Kreutmair S, Pallavicini I, Zobel M, Cinquanta M, Minucci S, Gomez C, Santos E, Illert AL, Scita G.

Leukemia. 2018 Mar;32(3):820-827. doi: 10.1038/leu.2017.267. Epub 2017 Aug 18.

38.

Capturing protein communities by structural proteomics in a thermophilic eukaryote.

Kastritis PL, O'Reilly FJ, Bock T, Li Y, Rogon MZ, Buczak K, Romanov N, Betts MJ, Bui KH, Hagen WJ, Hennrich ML, Mackmull MT, Rappsilber J, Russell RB, Bork P, Beck M, Gavin AC.

Mol Syst Biol. 2017 Jul 25;13(7):936. doi: 10.15252/msb.20167412.

39.

The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics.

Vizcaíno JA, Mayer G, Perkins S, Barsnes H, Vaudel M, Perez-Riverol Y, Ternent T, Uszkoreit J, Eisenacher M, Fischer L, Rappsilber J, Netz E, Walzer M, Kohlbacher O, Leitner A, Chalkley RJ, Ghali F, Martínez-Bartolomé S, Deutsch EW, Jones AR.

Mol Cell Proteomics. 2017 Jul;16(7):1275-1285. doi: 10.1074/mcp.M117.068429. Epub 2017 May 17.

40.

Transposon-driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution.

Davis MP, Carrieri C, Saini HK, van Dongen S, Leonardi T, Bussotti G, Monahan JM, Auchynnikava T, Bitetti A, Rappsilber J, Allshire RC, Shkumatava A, O'Carroll D, Enright AJ.

EMBO Rep. 2017 Jul;18(7):1231-1247. doi: 10.15252/embr.201744059. Epub 2017 May 12.

41.

Complementary Benzophenone Cross-Linking/Mass Spectrometry Photochemistry.

Belsom A, Mudd G, Giese S, Auer M, Rappsilber J.

Anal Chem. 2017 May 16;89(10):5319-5324. doi: 10.1021/acs.analchem.6b04938. Epub 2017 May 4.

42.

Optimizing the Parameters Governing the Fragmentation of Cross-Linked Peptides in a Tribrid Mass Spectrometer.

Kolbowski L, Mendes ML, Rappsilber J.

Anal Chem. 2017 May 16;89(10):5311-5318. doi: 10.1021/acs.analchem.6b04935. Epub 2017 Apr 26.

43.

Cross-linking mass spectrometry identifies new interfaces of Augmin required to localise the γ-tubulin ring complex to the mitotic spindle.

Chen JWC, Chen ZA, Rogala KB, Metz J, Deane CM, Rappsilber J, Wakefield JG.

Biol Open. 2017 May 15;6(5):654-663. doi: 10.1242/bio.022905.

44.

Blind testing cross-linking/mass spectrometry under the auspices of the 11th critical assessment of methods of protein structure prediction (CASP11).

Belsom A, Schneider M, Fischer L, Mabrouk M, Stahl K, Brock O, Rappsilber J.

Wellcome Open Res. 2016 Dec 9;1:24. doi: 10.12688/wellcomeopenres.10046.1.

45.

Quirks of Error Estimation in Cross-Linking/Mass Spectrometry.

Fischer L, Rappsilber J.

Anal Chem. 2017 Apr 4;89(7):3829-3833. doi: 10.1021/acs.analchem.6b03745. Epub 2017 Mar 24.

46.

Correction to Optimized Fragmentation Regime for Diazirine Photo-Cross-Linked Peptides.

Giese SH, Belsom A, Rappsilber J.

Anal Chem. 2017 Mar 21;89(6):3802-3803. doi: 10.1021/acs.analchem.7b00046. Epub 2017 Feb 28. No abstract available.

47.

Structural basis of Mcm2-7 replicative helicase loading by ORC-Cdc6 and Cdt1.

Yuan Z, Riera A, Bai L, Sun J, Nandi S, Spanos C, Chen ZA, Barbon M, Rappsilber J, Stillman B, Speck C, Li H.

Nat Struct Mol Biol. 2017 Mar;24(3):316-324. doi: 10.1038/nsmb.3372. Epub 2017 Feb 13.

48.

Cdc14 phosphatase directs centrosome re-duplication at the meiosis I to meiosis II transition in budding yeast.

Fox C, Zou J, Rappsilber J, Marston AL.

Wellcome Open Res. 2017 Jan 5;2:2. doi: 10.12688/wellcomeopenres.10507.2.

49.

Repo-Man/PP1 regulates heterochromatin formation in interphase.

de Castro IJ, Budzak J, Di Giacinto ML, Ligammari L, Gokhan E, Spanos C, Moralli D, Richardson C, de Las Heras JI, Salatino S, Schirmer EC, Ullman KS, Bickmore WA, Green C, Rappsilber J, Lamble S, Goldberg MW, Vinciotti V, Vagnarelli P.

Nat Commun. 2017 Jan 16;8:14048. doi: 10.1038/ncomms14048.

50.

Nano Random Forests to mine protein complexes and their relationships in quantitative proteomics data.

Montaño-Gutierrez LF, Ohta S, Kustatscher G, Earnshaw WC, Rappsilber J.

Mol Biol Cell. 2017 Mar 1;28(5):673-680. doi: 10.1091/mbc.E16-06-0370. Epub 2017 Jan 5.

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