Publications

You can find a list of our scientific publications here. Please see also Pubmed, Google Scholar and ORCiD.

  1. Gupta S, Ahadi S, Zhou W, Rost H. DIAlignR provides precise retention time alignment across distant runs in DIA and targeted proteomics. Mol Cell Proteomics. 2019 Jan 31. Article Full Text Github
  2. Chalkley RJ, MacCoss MJ, Jaffe JD, Röst HL. Initial Guidelines for Manuscripts Employing Data-independent Acquisition Mass Spectrometry for Proteomic Analysis. Mol Cell Proteomics. 2019 Jan;18(1):1-2. Full Text
  3. 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. High-frequency actionable pathogenic exome variants in an average-risk cohort. Cold Spring Harb Mol Case Stud. 2018 Dec 17;4(6). Full Text
  4. Deutsch E, Perez-Riverol Y, Chalkley R, Wilhelm M, Tate S, Sachsenberg T, Walzer M, Käll L, Delanghe B, Böcker S, Schymanski E, Wilmes P, Dorfer V, Kuster B, Volders P, Jehmlich N, Vissers J, Wolan D, Wang A, Mendoza L, Shofstahl J, Dowsey A, Griss J, Salek R, Neumann S, Binz P, Lam H, Vizcaíno J, Bandeira N, Röst H. Expanding the use of spectral libraries in proteomics Journal of Proteome Research. October 1, 2018 Article Text
  5. Gruening B, Sallou O, Moreno P, Leprevost FD, Ménager H, Søndergaard D, Röst H, Sachsenberg T, O'Connor B, Madeira F, Angel VD, Crusoe MR, Varma S, Blankenberg D, Jimenez RC, Perez-Riverol Y. Recommendations for the packaging and containerizing of bioinformatics software. F1000Research. 2018/6/14 Full Text
  6. 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. (alphabetical order) From Hype to Reality: Data Science enabling Personalized Medicine. BMC Medicine.
    Full Text
  7. 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. Integrative Personal Omics Profiles during Periods of Weight Gain and Loss. Cell Syst. 2018 Jan 16. Full Text
  8. Rosenberger G*, Bludau I,*, Schmitt U, Heusel M, Liu Y, MacCoss MJ, MacLean BX, Nesvizhskii AI, Pedrioli PGA, Reiter L, Röst HL, Tate S, Ting YS, Collins BC, Aebersold R. Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses. Nat Methods. 2017 Sep. 14(9):921-927.
    Article Full Text
  9. Shi Z, Fujii K, Kovary KM, Genuth NR, Röst HL, Teruel MN, Barna M. Heterogeneous Ribosomes Preferentially Translate Distinct Subpools of mRNAs Genome-wide. Mol Cell. 2017 Jul 6;67(1):71-83.e7. Article
  10. Rosenberger G, Liu Y, Röst HL, Ludwig C, Buil A, Bensimon A, Soste M, Spector TD, Dermitzakis ET, Collins BC, Malmström L, Aebersold R. Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS. Nat Biotechnol. 2017 Aug;35(8):781-788. Article Full Text
  11. Schubert OT, Röst HL, Collins BC, Rosenberger G, Aebersold R. Quantitative proteomics: challenges and opportunities in basic and applied research. Nat Protoc. 2017 Jul;12(7):1289-1294. Article
  12. 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
  13. 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)
  14. 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 Full Text
  15. 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 Github
  16. 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 Article Github
  17. 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
  18. 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 Full Text
  19. Röst HL, Malmström L, Aebersold R. Reproducible quantitative proteotype data matrices for systems biology. Mol Biol Cell. 2015 Nov Article Full Text
  20. 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
  21. 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. Article
  22. 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. Article
  23. 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. Article Github Website
  24. 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 Full Text
  25. 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.
    Article
  26. 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. Article
  27. 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. Article
  28. 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. Article Preprint (accepted version) Website
  29. 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
  30. 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. Article Preprint (submitted version)
  31. 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 Full Text
  32. 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 Full Text
  33. 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 Full Text
  34. 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. Full Text Article
  35. 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 Website
  36. 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

Conference Proceedings

  1. Kaspar-Schoenefeld S, Lubeck M, Koch H, Koch S, Raether O, Speir P, Meier F, Brunner AD, Ha A, Frank M, Collins BC, Aebersold R, Rost H, Mann M. High throughput proteomics: Application of the novel diaPASEF method for 17.5 minute gradients. ASMS 2019
  2. Ha A, Frank M, Meier F, Brunner AD, Kaspar-Schönefeld S, Koch S, Lubeck M, Raether O, Collins BC, Aebersold R, Mann M, Röst H. Mobi-DIK (Ion Mobility DIA Analysis Kit): Targeted analysis software for diaPASEF data improves proteome coverage ASMS 2019
  3. Meier F, Brunner AD, Frank M, Ha A, Voytik E, Kaspar-Schönefeld S, Lubeck M, Koch H, Koch S, Raether O, Collins BC, Aebersold R, Röst H, Mann M. diaPASEF: toward the ideal mass analyzer with data-independent acquisition and parallel accumulation – serial fragmentation ASMS 2019
  4. Bludau I, Frank M, Heusel M, Cai Y, Rosenberger G, Liu Y, Venkitaraman A, Wickramasinghe V, Collins BC, Röst HL, Aebersold R. Data-driven detection of functional proteoforms in SEC-SWATH-MS data ASMS 2019
  5. Alka O, Witting M, Kleigrewe K, Kohlbacher O, Röst HL. OpenSWATH enables automated data processing for data-independent acquisition in metabolomics ASMS 2019
  6. Ahadi S, Röst H, Hornburg D, Mishra T, Zhou W, Contrepois K, Sailani R, Snyder M Longitudinal Multi-omics Profiling in Insulin Resistant and Sensitive Prediabetic Population ASMS 2018
  7. Kuharev J, Distler U, Bernhardt OM, Reiter L, Roest H, Richardson K, Vissers JPC, Tenzer S. Benchmarking data-independent acquisition workflows using hybrid proteome samples and LFQbench. HUPO 2017
  8. Röst HL, Vissers J, Richardson K, Tenzer S, Snyder M. Scanning the precursor range with OpenECHO: Adding precursor specificity back to DIA analysis. HUPO 2017
  9. Röst HL, Vissers J, Richardson K, Snyder M. Scanning the precursor range with OpenECHO: Adding precursor specificity back to DIA analysis. ASMS 2017
  10. Distler U, Kuharev J, Bernhardt OM, Reiter L, Roest H, Kaur-Atwal G, Lennon S, Wildgoose J, Richardson K, Vissers JPC, Tenzer S Scanning Quadrupole Data Independent Acquisition: A Novel Workflow for Targeted and Discovery Proteomics. ASMS 2017
  11. Ahadi S, Roest H, Liang L, Hunter C, Snyder M Profiling Biochemical Individuality: Human Personal Omics Profiling (hPOP). ASMS 2017
  12. Rost HL*, Piening B*, Zhou W*, Contrepois K*, Gu G, Mishra T, Hansen B, Bautista E, Leopold S, Yeh C, Spakowicz D, Kukurba K, Perelman D, Craig C, Colbert E, Salins D, Rego S, Lee S, Zhang C, Wheeler J, Sailani R, Liang L, Abbott C, Gerstein M, Mardinoglu A, Pitteri S, Sodergren E, McLaughlin T, Weinstock G and Snyder M. Personalized Profiling of Diabetes: Longitudinal Multi-omics Profiles Provide Insight into Insulin Resistance. ASMS 2017
  13. 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
  14. 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.
  15. 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.
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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.
  23. 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.
  24. 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.
  25. 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
  26. 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
  27. 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.
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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.
  33. 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
  34. Ludwig C., Röst H., Claassen M., Aebersold R. Estimating Absolute Protein Abundances using Targeted Mass Spectrometric Techniques (SRM and SWATH-MS). ASMS2012.
  35. 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.
  36. 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.
  37. 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.
  38. Röst H., Dessimoz C., Gonnet G. Phylogenetic detection of lateral gene transfer. PhyloSIB 2009. June 2, 2009.
“The imagination of nature is far, far greater than the imagination of man.”
Richard Feynman