Publications
Research articles
  1. Leprevost FD, 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. BioContainers: An open-source and community-driven framework for software standardization. Bioinformatics. 2017 Mar 30. Article
  2. Röst HL, Aebersold R, Schubert OT. Automated SWATH Data Analysis Using Targeted Extraction of Ion Chromatograms. Methods Mol Biol. 2017;1550:289-307. Article Full Text (BioRxiv)
  3. 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. A multicenter study benchmarks software tools for label-free proteome quantification. Nat Biotechnol. 2016 Oct 3. Article
  4. 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. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Methods. 2016 Aug 30;13(9):741-8. Article
  5. Röst HL, Liu Y, D'Agostino G, Zanella M, Navarro P, Rosenberger G, Collins BC, Gillet L, Testa G, Malmström L, Aebersold R. TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics. Nat Methods. 2016 Sep;13(9):777-83. Article
  6. Müller DB, Schubert OT, Röst H, Aebersold R, Vorholt JA. Systems-level proteomics of two ubiquitous leaf commensals reveals complementary adaptive traits for phyllosphere colonization. Mol Cell Proteomics. 2016 Jul 25. Article Full Text
  7. Walzthoeni T, Joachimiak LA, Rosenberger G, Röst HL, Malmström L, Leitner A, Frydman J, Aebersold R. xTract: software for characterizing conformational changes of protein complexes by quantitative cross-linking mass spectrometry. Nat Methods. 2015 Dec;12(12):1185-90. Article
  8. Röst HL, Malmström L, Aebersold R. Reproducible quantitative proteotype data matrices for systems biology. Mol Biol Cell. 2015 Nov Article
  9. Parker SJ, Roest HL, Rosenberger G, Collins BC, Malstroem L, Amodei D, Venkatraman V, Raedschelders K, Van Eyk JE, Aebersold R. Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-Independent Acquisition Mass Spectrometry. Mol Cell Proteomics. 2015 Jul Article Full Text
  10. Schubert OT, Ludwig C, Kogadeeva M, Zimmermann M, Rosenberger G, Gengenbacher M, Gillet LC, Collins BC, Röst HL Kaufmann SH, Sauer U, Aebersold R. Absolute Proteome Composition and Dynamics during Dormancy and Resuscitation of Mycobacterium tuberculosis. Cell Host Microbe. 2015 Jul 8;18(1):96-108. Full Text
  11. Röst H, Schmitt U, Aebersold R, Malmström L. Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry PLoS One. 2015 Apr 30;10(4):e0125108. Full Text
  12. Röst H, Rosenberger G, Aebersold R, Malmström L. Efficient visualization of high-throughput targeted proteomics experiments: TAPIR Bioinformatics. 2015 Jul 15;31(14):2415-7. Preprint (submitted version) Website Full Text
  13. Guo T, Kouvonen T, Koh CC, Gillet LC, Wolski WE, Röst HL, Rosenberger G, Collins BC, Blum LC, Gillessen S, Joerger M, Jochum W, Aebersold R. Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps. Nature Medicine. 2015 Apr;21(4):407-13. Article (PMC) Full Text
  14. Teleman J, Röst H, Rosenberger G, Schmitt U, Malmström L, Malmström J, Levander F. DIANA-algorithmic improvements for analysis of data-independent acquisition MS data. Bioinformatics. 2015 Feb 15;31(4):555-62. Full Text
  15. 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. A repository of assays to quantify 10,000 human proteins by SWATH-MS. Scientific Data. 2014. Sept 16. Full Text
  16. Rosenberger G, Ludwig C, Röst HL, Aebersold R, Malmström L. aLFQ: An R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data. Bioinformatics. 2014 Apr 20. Full Text
  17. Röst HL*, Rosenberger G*, Navarro P, Gillet L, Miladinović SM, Schubert OT, Wolski W, Collins BC, Malmström J, Malmström L, Aebersold R. OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. Nat Biotechnol. 2014 Mar 10;32(3):219-23. Preprint (accepted version) Website Full Text
  18. Teleman J, Dowsey AW, Gonzalez-Galarza FF, Perkins S, Pratt B, Rost H, Malmstrom L, Malmstrom J, Jones AR, Deutsch EW, Levander F. Numerical compression schemes for proteomics mass spectrometry data. Mol Cell Proteomics. 2014 Mar 27. Article Full Text
  19. Röst HL*, Schmitt U*, Aebersold R, Malmström L. pyOpenMS: a Python-based interface to the OpenMS mass-spectrometry algorithm library. Proteomics. 2014 Jan;14(1):74-7. Preprint (submitted version) Full Text
  20. Collins BC, Gillet LC, Rosenberger G, Röst HL, Vichalkovski A, Gstaiger M, Aebersold R. Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system. Nat Methods. 2013 Dec;10(12):1246-53. Article (PMC) Full Text
  21. 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 SH, Moritz RL, Aebersold R. The Mtb proteome library: a resource of assays to quantify the complete proteome of Mycobacterium tuberculosis. Cell Host Microbe. 2013 May 15;13(5):602-12. Article (PMC) Full Text
  22. 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. A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis. Nature. 2013 Feb 14;494(7436):266-70. Article (PMC) Full Text
  23. 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. Reproducible quantification of cancer-associated proteins in body fluids using targeted proteomics. Sci Transl Med. 2012 Jul 11;4(142):142ra94. Article (PMC) Full Text
  24. Röst H, Malmström L, Aebersold R. A computational tool to detect and avoid redundancy in selected reaction monitoring. Mol Cell Proteomics. 2012 Aug;11(8):540-9. Article Full Text Website
  25. Gillet LC, Navarro P, Tate S, Röst H, Selevsek N, Reiter L, Bonner R, Aebersold R. Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol Cell Proteomics. 2012 Jun;11(6):O111.016717. Article Full Text (free)
Conference contributions
  1. Röst HL, Liu Y, D'Agostino G, Zanella M, Navarro P, Rosenberger G, Collins BC, Gillet L, Testa G, Malmström L, Aebersold R. TRIC: An automated alignment strategy for reproducible protein quantification in targeted proteomics. HUPO 2016
  2. Rosenberger G, Liu Y, Röst HL, Ludwig C, Buil A, Soste M, Spector T, Dermitzakis E, Malmström Lars, Aebersold R. Targeting peptidoforms via SWATH-MS: Quantification of PTM Variability in Human Blood Plasma. HUPO 2016.
  3. Sara Ahadi, Hannes Rost, Christie Hunter, Liang Liang, Shannon Rego, Orit Dagan-Rosenfeld, Denis Salins, Mike Snyder. Profiling Biochemical Individuality: Human Personal Omics Profiling (hPOP). HUPO 2016.
  4. Leprevost F, Aflitos SA, Gruning B, Roest H, Barsnes H, Jimenez R, Hermjakob H, Nesvizhskii A, Perez-Riverol Y. BioDocker: An Open Source and Community-Driven Framework for Software Standardization in Proteomics. ASMS 2016
  5. Röst HL, Liu Y, D'Agostino G, Zanella M, Navarro P, Rosenberger G, Collins BC, Gillet L, Testa G, Malmström L, Aebersold R. A Novel alignment strategy for SWATH-MS to generate comprehensive proteomics data matrices. ASMS 2016
  6. Röst HL, Liu Y, D'Agostino G, Zanella M, Navarro P, Rosenberger G, Collins BC, Gillet L, Testa G, Malmström L, Aebersold R. An automated alignment strategy for reproducible protein quantification in targeted proteomics. HUPO 2015
  7. Pratik J., Parker S., Gruening B., Cooke I., Roest H., Rosenberger G., Johnson J., Parker L., Van Eyk J., Aebersold R., Griffin T. Democratizing and expanding the reach of DIA Mass Spectrometry: Developing OpenSWATH tools and workflows within user-friendly Galaxy-P platform. ASMS 2015
  8. Cheng L., Chang C., Liu Y., Röst H., Meena Choi M., Aebersold R., Vitek O. Statistical elimination of spectral features with large between-run variation enhances quantitative protein-level conclusions in experiments with data-independent spectral acquisition. US HUPO 2015
  9. Röst H., Karlsson C, Musser J, Malmström J, Aebersold R, Malmström L. High-throughput targeted SWATH-MS proteomics of a human pathogen implicates novel protein quantitative trait loci (pQTL) in the regulation of key virulence factors. HUPO 2014
  10. Parker S., Rosenberger G., Roest H., Collins B., Malstroem L., Van Eyk J., Aebersold R. Generation of a set of Common Internal Retention Time Standards for iRT alignment in SWATH-MS . US HUPO 2014.
  11. Collins B., Gillet L., Ludwig C., Rosenberger G., Röst H.L., Vichalkovski A., Gstaiger M., Aebersold R. Developments in SWATH mass spectrometry and applications in quantitative interaction proteomics . US HUPO 2014.
  12. Cheng L., Liu Y., Chang C., Roest H., Aebersold R., Vitek O. Statistical elimination of spectral features with large between-run variation enhances quantitative protein-level conclusions in experiments with data-independent spectral acquisition. ASMS2014.
  13. Amodei D., Marsh D., Röst H., Espona Pernas L., Rosenberger G., Aebersold R., Mallick P., Maccoss M.J., Maclean B. Multi-Instrument, Skyline-Based Comparison of DIA Peptide Identification and Statistical Confidence Tools Enables Improved, Novel Peak Scoring Strategy. ASMS2014
  14. Röst H., Rosenberger G., Navarro P., Gillet G., Miladinovic S., Schubert O., Wolski W., Malmstroem J., Malmstroem L., Aebersold R. OpenSWATH: Automated, targeted analysis of mass spectrometric data generated by data-independent acquisition. ASMS2013
  15. Chang C., Selevsek N., Gillet L., Roest H., Aebersold R., Vitek O. Statistical selection of informative features for protein quantification in data-independent spectral acquisition. ASMS2013.
  16. Collins B. C., Gillet L., Rosenberger G., Röst H. L., Gstaiger M., Aebersold R. Towards a deep and temporal representation of protein interaction networks via AP-SWATH. ASMS2013
  17. Maclean B., Marsh D., Röst H., Espona Pernas L., Rosenberger G., Aebersold R., MacCoss M. Integration of mProphet chromatogram peak identification probability model into Skyline. ASMS2013
  18. Schubert O., Ludwig C., Mouritsen J., Roest H., Rosenberger G., Arthur P., Claassen M., Campbell D., Sun Z., Farrah T., Gengenbacher M., Kaufmann S. H. E., Moritz R., Aebersold R. Development and application of assays for targeted MS analysis of the complete proteome of Mycobacterium tuberculosis by SRM and SWATH-MS. ASMS2013
  19. Röst H., Rosenberger G., Navarro P., Gillet G., Miladinovic S., Schubert O., Wolski W., Malmstroem J., Malmstroem L., Aebersold R. A software for targeted analysis of DIA (data-independent acquisition) mass spectrometric data. Proteomic Forum 2013
  20. Röst H., Rosenberger G., Malmstroem L., Aebersold R. Novel computational methods in DIA (data-independent acquisition) data analysis. Swiss Proteomics Society PhD Symposium, Basel. Poster prize.
  21. Hüttenhain R., Soste M., Selevsek N., Röst H., Sethi A., Carapito C., Deutsch E., Farrah T., Kusebauch U., Moritz R., Niméus-Malmström E. E. Rinner O., Aebersold R. A mass spectrometric map for reproducible quantification of cancer-associated proteins in body fluids. HUPO2012-384
  22. Ludwig C., Röst H., Claassen M., Aebersold R. Estimating Absolute Protein Abundances using Targeted Mass Spectrometric Techniques (SRM and SWATH-MS). ASMS2012.
  23. Hüttenhain R., Soste M., Selevsek N., Liu Y., Röst H., Sethi A., Carapito C., Farrah T., Deutsch E., Kusebauch U., Moritz R., Niméus-Malmström E., Rinner O., Aebersold R. A mass spectrometric map for cancer-associated proteins. ASMS2012.
  24. Röst H. L., Malmström L., Aebersold R. Detecting and Avoiding redundancy in selected reaction monitoring (SRM) - a computational approach to design selective SRM assays. HUPO11-1705.
  25. Gillet L., Navarro P., Tate S., Röst H., Bonner R., Aebersold R. Swath MS: a novel data independent acquisition method with sequential precursor isolation windows allowing unlimited SRM-like data analysis and quantification. ASMS2011.
  26. Röst H., Dessimoz C., Gonnet G. Phylogenetic detection of lateral gene transfer. PhyloSIB 2009. June 2, 2009.