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Items: 1 to 50 of 79

1.

Deep learning adds an extra dimension to peptide fragmentation.

Röst HL.

Nat Methods. 2019 Jun;16(6):469-470. doi: 10.1038/s41592-019-0428-5. No abstract available.

PMID:
31147636
2.

Longitudinal multi-omics of host-microbe dynamics in prediabetes.

Zhou W, Sailani MR, Contrepois K, Zhou Y, Ahadi S, Leopold SR, Zhang MJ, Rao V, Avina M, Mishra T, Johnson J, Lee-McMullen B, Chen S, Metwally AA, Tran TDB, Nguyen H, Zhou X, Albright B, Hong BY, Petersen L, Bautista E, Hanson B, Chen L, Spakowicz D, Bahmani A, Salins D, Leopold B, Ashland M, Dagan-Rosenfeld O, Rego S, Limcaoco P, Colbert E, Allister C, Perelman D, Craig C, Wei E, Chaib H, Hornburg D, Dunn J, Liang L, Rose SMS, Kukurba K, Piening B, Rost H, Tse D, McLaughlin T, Sodergren E, Weinstock GM, Snyder M.

Nature. 2019 May;569(7758):663-671. doi: 10.1038/s41586-019-1236-x. Epub 2019 May 29.

PMID:
31142858
3.

DIAlignR Provides Precise Retention Time Alignment Across Distant Runs in DIA and Targeted Proteomics.

Gupta S, Ahadi S, Zhou W, Röst H.

Mol Cell Proteomics. 2019 Apr;18(4):806-817. doi: 10.1074/mcp.TIR118.001132. Epub 2019 Jan 31.

PMID:
30705124
4.

Initial Guidelines for Manuscripts Employing Data-independent Acquisition Mass Spectrometry for Proteomic Analysis.

Chalkley RJ, MacCoss MJ, Jaffe JD, Röst HL.

Mol Cell Proteomics. 2019 Jan;18(1):1-2. doi: 10.1074/mcp.E118.001286. No abstract available.

6.

High-frequency actionable pathogenic exome variants in an average-risk cohort.

Rego S, Dagan-Rosenfeld O, Zhou W, Sailani MR, Limcaoco P, Colbert E, Avina M, Wheeler J, Craig C, Salins D, Röst HL, Dunn J, McLaughlin T, Steinmetz LM, Bernstein JA, Snyder MP.

Cold Spring Harb Mol Case Stud. 2018 Dec 17;4(6). pii: a003178. doi: 10.1101/mcs.a003178. Print 2018 Dec.

7.

Expanding the Use of Spectral Libraries in Proteomics.

Deutsch EW, Perez-Riverol Y, Chalkley RJ, Wilhelm M, Tate S, Sachsenberg T, Walzer M, Käll L, Delanghe B, Böcker S, Schymanski EL, Wilmes P, Dorfer V, Kuster B, Volders PJ, Jehmlich N, Vissers JPC, Wolan DW, Wang AY, Mendoza L, Shofstahl J, Dowsey AW, Griss J, Salek RM, Neumann S, Binz PA, Lam H, Vizcaíno JA, Bandeira N, Röst H.

J Proteome Res. 2018 Dec 7;17(12):4051-4060. doi: 10.1021/acs.jproteome.8b00485. Epub 2018 Oct 11.

8.

From hype to reality: data science enabling personalized medicine.

Fröhlich H, Balling R, Beerenwinkel N, Kohlbacher O, Kumar S, Lengauer T, Maathuis MH, Moreau Y, Murphy SA, Przytycka TM, Rebhan M, Röst H, Schuppert A, Schwab M, Spang R, Stekhoven D, Sun J, Weber A, Ziemek D, Zupan B.

BMC Med. 2018 Aug 27;16(1):150. doi: 10.1186/s12916-018-1122-7.

9.

Integrative Personal Omics Profiles during Periods of Weight Gain and Loss.

Piening BD, Zhou W, Contrepois K, Röst H, Gu Urban GJ, Mishra T, Hanson BM, Bautista EJ, Leopold S, Yeh CY, Spakowicz D, Banerjee I, Chen C, Kukurba K, Perelman D, Craig C, Colbert E, Salins D, Rego S, Lee S, Zhang C, Wheeler J, Sailani MR, Liang L, Abbott C, Gerstein M, Mardinoglu A, Smith U, Rubin DL, Pitteri S, Sodergren E, McLaughlin TL, Weinstock GM, Snyder MP.

Cell Syst. 2018 Feb 28;6(2):157-170.e8. doi: 10.1016/j.cels.2017.12.013. Epub 2018 Jan 17.

10.

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.

11.

Heterogeneous Ribosomes Preferentially Translate Distinct Subpools of mRNAs Genome-wide.

Shi Z, Fujii K, Kovary KM, Genuth NR, Röst HL, Teruel MN, Barna M.

Mol Cell. 2017 Jul 6;67(1):71-83.e7. doi: 10.1016/j.molcel.2017.05.021. Epub 2017 Jun 15.

12.

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.

13.

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
14.

BioContainers: an open-source and community-driven framework for software standardization.

da Veiga Leprevost F, Grüning BA, Alves Aflitos S, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Vera Alvarez R, Griss J, Nesvizhskii AI, Perez-Riverol Y.

Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192.

15.

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
16.

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.

17.

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
18.

TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics.

Röst HL, Liu Y, D'Agostino G, Zanella M, Navarro P, Rosenberger G, Collins BC, Gillet L, Testa G, Malmström L, Aebersold R.

Nat Methods. 2016 Sep;13(9):777-83. doi: 10.1038/nmeth.3954. Epub 2016 Aug 1.

19.

Systems-level Proteomics of Two Ubiquitous Leaf Commensals Reveals Complementary Adaptive Traits for Phyllosphere Colonization.

Müller DB, Schubert OT, Röst H, Aebersold R, Vorholt JA.

Mol Cell Proteomics. 2016 Oct;15(10):3256-3269. Epub 2016 Jul 25.

20.

Reproducible quantitative proteotype data matrices for systems biology.

Röst HL, Malmström L, Aebersold R.

Mol Biol Cell. 2015 Nov 5;26(22):3926-31. doi: 10.1091/mbc.E15-07-0507.

21.

xTract: software for characterizing conformational changes of protein complexes by quantitative cross-linking mass spectrometry.

Walzthoeni T, Joachimiak LA, Rosenberger G, Röst HL, Malmström L, Leitner A, Frydman J, Aebersold R.

Nat Methods. 2015 Dec;12(12):1185-90. doi: 10.1038/nmeth.3631. Epub 2015 Oct 26.

22.

Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-independent Acquisition Mass Spectrometry.

Parker SJ, Rost H, Rosenberger G, Collins BC, Malmström L, Amodei D, Venkatraman V, Raedschelders K, Van Eyk JE, Aebersold R.

Mol Cell Proteomics. 2015 Oct;14(10):2800-13. doi: 10.1074/mcp.O114.042267. Epub 2015 Jul 21.

23.

Absolute Proteome Composition and Dynamics during Dormancy and Resuscitation of Mycobacterium tuberculosis.

Schubert OT, Ludwig C, Kogadeeva M, Zimmermann M, Rosenberger G, Gengenbacher M, Gillet LC, Collins BC, Röst HL, Kaufmann SH, Sauer U, Aebersold R.

Cell Host Microbe. 2015 Jul 8;18(1):96-108. doi: 10.1016/j.chom.2015.06.001. Epub 2015 Jun 18.

24.

Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry.

Röst HL, Schmitt U, Aebersold R, Malmström L.

PLoS One. 2015 Apr 30;10(4):e0125108. doi: 10.1371/journal.pone.0125108. eCollection 2015.

25.

Efficient visualization of high-throughput targeted proteomics experiments: TAPIR.

Röst HL, Rosenberger G, Aebersold R, Malmström L.

Bioinformatics. 2015 Jul 15;31(14):2415-7. doi: 10.1093/bioinformatics/btv152. Epub 2015 Mar 18.

26.

Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps.

Guo T, Kouvonen P, Koh CC, Gillet LC, Wolski WE, Röst HL, Rosenberger G, Collins BC, Blum LC, Gillessen S, Joerger M, Jochum W, Aebersold R.

Nat Med. 2015 Apr;21(4):407-13. doi: 10.1038/nm.3807. Epub 2015 Mar 2.

27.

Rationally engineered variants of S-adenosylmethionine (SAM) synthase: reduced product inhibition and synthesis of artificial cofactor homologues.

Dippe M, Brandt W, Rost H, Porzel A, Schmidt J, Wessjohann LA.

Chem Commun (Camb). 2015 Feb 28;51(17):3637-40. doi: 10.1039/c4cc08478k.

PMID:
25642798
28.

DIANA--algorithmic improvements for analysis of data-independent acquisition MS data.

Teleman J, Röst HL, Rosenberger G, Schmitt U, Malmström L, Malmström J, Levander F.

Bioinformatics. 2015 Feb 15;31(4):555-62. doi: 10.1093/bioinformatics/btu686. Epub 2014 Oct 27.

29.

aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data.

Rosenberger G, Ludwig C, Röst HL, Aebersold R, Malmström L.

Bioinformatics. 2014 Sep 1;30(17):2511-3. doi: 10.1093/bioinformatics/btu200. Epub 2014 Apr 20.

30.

OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data.

Röst HL, Rosenberger G, Navarro P, Gillet L, Miladinović SM, Schubert OT, Wolski W, Collins BC, Malmström J, Malmström L, Aebersold R.

Nat Biotechnol. 2014 Mar;32(3):219-23. doi: 10.1038/nbt.2841. No abstract available.

PMID:
24727770
31.

Numerical compression schemes for proteomics mass spectrometry data.

Teleman J, Dowsey AW, Gonzalez-Galarza FF, Perkins S, Pratt B, Röst HL, Malmström L, Malmström J, Jones AR, Deutsch EW, Levander F.

Mol Cell Proteomics. 2014 Jun;13(6):1537-42. doi: 10.1074/mcp.O114.037879. Epub 2014 Mar 27.

32.

pyOpenMS: a Python-based interface to the OpenMS mass-spectrometry algorithm library.

Röst HL, Schmitt U, Aebersold R, Malmström L.

Proteomics. 2014 Jan;14(1):74-7. doi: 10.1002/pmic.201300246.

PMID:
24420968
33.

A repository of assays to quantify 10,000 human proteins by SWATH-MS.

Rosenberger G, Koh CC, Guo T, Röst HL, Kouvonen P, Collins BC, Heusel M, Liu Y, Caron E, Vichalkovski A, Faini M, Schubert OT, Faridi P, Ebhardt HA, Matondo M, Lam H, Bader SL, Campbell DS, Deutsch EW, Moritz RL, Tate S, Aebersold R.

Sci Data. 2014 Sep 16;1:140031. doi: 10.1038/sdata.2014.31. eCollection 2014.

34.

Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system.

Collins BC, Gillet LC, Rosenberger G, Röst HL, Vichalkovski A, Gstaiger M, Aebersold R.

Nat Methods. 2013 Dec;10(12):1246-53. doi: 10.1038/nmeth.2703. Epub 2013 Oct 27.

PMID:
24162925
35.

The Mtb proteome library: a resource of assays to quantify the complete proteome of Mycobacterium tuberculosis.

Schubert OT, Mouritsen J, Ludwig C, Röst HL, Rosenberger G, Arthur PK, Claassen M, Campbell DS, Sun Z, Farrah T, Gengenbacher M, Maiolica A, Kaufmann SHE, Moritz RL, Aebersold R.

Cell Host Microbe. 2013 May 15;13(5):602-612. doi: 10.1016/j.chom.2013.04.008.

36.

A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis.

Picotti P, Clément-Ziza M, Lam H, Campbell DS, Schmidt A, Deutsch EW, Röst H, Sun Z, Rinner O, Reiter L, Shen Q, Michaelson JJ, Frei A, Alberti S, Kusebauch U, Wollscheid B, Moritz RL, Beyer A, Aebersold R.

Nature. 2013 Feb 14;494(7436):266-70. doi: 10.1038/nature11835. Epub 2013 Jan 20.

37.

Reproducible quantification of cancer-associated proteins in body fluids using targeted proteomics.

Hüttenhain R, Soste M, Selevsek N, Röst H, Sethi A, Carapito C, Farrah T, Deutsch EW, Kusebauch U, Moritz RL, Niméus-Malmström E, Rinner O, Aebersold R.

Sci Transl Med. 2012 Jul 11;4(142):142ra94. doi: 10.1126/scitranslmed.3003989.

38.

A computational tool to detect and avoid redundancy in selected reaction monitoring.

Röst H, Malmström L, Aebersold R.

Mol Cell Proteomics. 2012 Aug;11(8):540-9. doi: 10.1074/mcp.M111.013045. Epub 2012 Apr 24.

39.

Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis.

Gillet LC, Navarro P, Tate S, Röst H, Selevsek N, Reiter L, Bonner R, Aebersold R.

Mol Cell Proteomics. 2012 Jun;11(6):O111.016717. doi: 10.1074/mcp.O111.016717. Epub 2012 Jan 18.

40.

Freehand three-dimensional assessment of left ventricular volumes and ejection fraction with ultrasound contrast agent LK565.

Geisler T, Rost HC, Wild PS, Zotz R.

Eur J Echocardiogr. 2007 Jan;8(1):19-29. Epub 2006 May 4.

PMID:
16678491
41.
42.

Classification of rheumatoid joint inflammation based on laser imaging.

Schwaighofer A, Tresp V, Mayer P, Krause A, Beuthan J, Rost H, Metzger G, Müller GA, Scheel AK.

IEEE Trans Biomed Eng. 2003 Mar;50(3):375-82.

PMID:
12669994
43.

Behavior of PAHs during cold storage of historically contaminated soil samples.

Rost H, Loibner AP, Hasinger M, Braun R, Szolar OH.

Chemosphere. 2002 Dec;49(10):1239-46.

PMID:
12489720
44.

Assessment of proximal finger joint inflammation in patients with rheumatoid arthritis, using a novel laser-based imaging technique.

Scheel AK, Krause A, Rheinbaben IM, Metzger G, Rost H, Tresp V, Mayer P, Reuss-Borst M, Müller GA.

Arthritis Rheum. 2002 May;46(5):1177-84.

45.
46.

alpha-catenin expression is decreased in human gastric cancers and in the gastric mucosa of first degree relatives.

Yu J, Ebert MP, Miehlke S, Rost H, Lendeckel U, Leodolter A, Stolte M, Bayerdörffer E, Malfertheiner P.

Gut. 2000 May;46(5):639-44.

47.

Intraoperative angiography and embolization in intracranial AVM's and aneurysms.

Molsen HP, Gräwe A, Nisch G, Rost H, Siedschlag WD.

Neurosurg Rev. 1992;15(4):285-8.

PMID:
1480275
48.

Random walk on a chain with dynamic disorder due to correlations.

Bányai L, Würtz D, Rost H.

Phys Rev B Condens Matter. 1987 Apr 1;35(10):5226-5234. No abstract available.

PMID:
9940701
49.

[Blood pressure regulation in neurosurgical interventions in the lumbar area in the seated patient].

Fichtner D, Rost H, Siedschlag WD, Tischer AB, Krischewski J.

Zentralbl Neurochir. 1986;47(4):334-8. German.

PMID:
3564763
50.

[Microorganisms in home-care inhalation devices].

Exner M, Vogel F, Rost HD.

Dtsch Med Wochenschr. 1983 Jan 7;108(1):12-7. German.

PMID:
6848339

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