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

  1. Srinivasan A, Sing JC, Gingras AC, Hannes L Röst. Improving Phosphoproteomics Profiling Using Data-Independent Mass Spectrometry. Journal of Proteome Research. 2022 Aug 5;21(8):1789-1799. Article
  2. Badr B, Blutrich R, Chan K, Tong J, Taylor P, Zhang W, Kafri R, Röst HL, Tsao M, Moran MF. Proteomic characterization of a candidate polygenic driver of metabolism in non-small cell lung cancer. Journal of Molecular Biology. 2022 Jul 15;434(13):167636. Article
  3. Fahrner M, Föll MC, Grüning BA, Bernt M, Röst H, Schilling O. Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the Galaxy framework. GigaScience. 2022 Feb 16 Article
  4. Alka O, Shanthamoorthy P, Witting M, Kleigrewe K, Kohlbacher O, Röst HL. DIAMetAlyzer allows automated false-discovery rate-controlled analysis for data-independent acquisition in metabolomics. Nature Communications. 2022/3/15. Article
  5. Charkow J, Röst HL. Trapped Ion Mobility Spectrometry Reduces Spectral Complexity in Mass Spectrometry Based Workflow. Analytical Chemistry. 2021 Dec 9 Article Full Text
  6. Zhang Z, Lai M, Piro AL, Alexeeff SE, Allalou A, Röst HL, Dai FF, Wheeler MB, Gunderson EP. Intensive lactation among women with recent gestational diabetes significantly alters the early postpartum circulating lipid profile: the SWIFT study. BMC Medicine. 2021 Oct 8;19(1):241. Article
  7. Hanau F, Röst H, Ochoa I. mspack: efficient lossless and lossy mass spectrometry data compression. Bioinformatics. 2021 Sep 3;btab636. Article
  8. Shanthamoorthy P, Young A, Röst H. Analyzing Assay Specificity in Metabolomics Using Unique Ion Signature Simulations. Analytical Chemistry. 2021 Aug 24;93(33):11415-11423. Article Full Text
  9. Tan C, Ginzberg MB, Webster R, Iyengar S, Liu S, Papadopoli D, Concannon J, Wang Y, Auld DS, Jenkins JL, Rost H, Topisirovic I, Hilfinger A, Derry WB, Patel N, Kafri R. Cell size homeostasis is maintained by CDK4-dependent activation of p38 MAPK. Developmental Cell. 2021. 56 (12) 1756-1769. e7 Article
  10. Bludau I, Frank M, Dörig C, Cai Y, Heusel M, Rosenberger G, Picotti P, Collins BC, Röst H*, Aebersold R*. Systematic detection of functional proteoform groups from bottom-up proteomic datasets. Nature Communications. 2021. 12 (1) 1-18. Article
  11. Bichmann L, Gupta S, Rosenberger G, Kuchenbecker L, Sachsenberg T, Ewels P, Alka O, Pfeuffer J, Kohlbacher O, Röst H. DIAproteomics: A Multifunctional Data Analysis Pipeline for Data-Independent Acquisition Proteomics and Peptidomics. Journal of Proteome Research. 2021. 20 (7) 3758-3766. Article Full Text
  12. Sachamitr P, Ho J, Campioni F, Ba-Alawi W, Coutinho F, Guilhamon P, Kushida M, Cavalli F, Lee L, Rastegar N, Vu V, Sánchez-Osuna M, Coulombe-Huntington J, Kanshin E, Whetstone H, Durand M, Thibault P, Hart K, Mangos M, Veyhl J, Chen W, Tran N, Duong BC, Aman A, Che X, Lan X, Whitley O, Zaslaver O, Barsyte-Lovejoy D, Richards L, Restall I, Caudy A, Rost H, Bonday ZQ, Bernstein M, Das S, Cusimano M, Spears J, Bader G, Pugh T, Tyers M, Lupien M, Haibe-Kains B, Luchman A, Weiss S, Massirer K, Prinos P, Arrowsmith C, Dirks P. PRMT5 inhibition disrupts splicing and stemness in glioblastoma. Nature Communications. 2021. 12 (1) 1-17. Article
  13. Kutuzova S, Colaianni P, Rost H, Sachsenberg T, Alka O, Kohlbacher O, Burla B, Torta F, Schrubbers L, Kristensen M, Nielsen L, Herrgård MJ, McCloskey D. SmartPeak automates targeted and quantitative metabolomics data processing. Analytical Chemistry. 2020. 92 (24), 15968-15974 Article Full Text
  14. Meier F, Brunner AD, Frank M, Ha A, Bludau I, Voytik E, Kaspar-Schoenefeld S, Lubeck M, Raether O, Bache N, Aebersold R, Collins BC*, Rost HL*, Mann M*. Parallel accumulation–serial fragmentation combined with data-independent acquisition (diaPASEF): Bottom-up proteomics with near optimal ion usage. Nature Methods. 2020. 17 (12), 1229-1236. Article Full Text
  15. Lai M, Al Ril D , Röst HL*, Dai FF*, Gunderson EP*, Wheeler MB*. Underlying dyslipidemia postpartum in women with a recent GDM pregnancy who develop type 2 diabetes. Elife 9, e59153 Article
  16. Liang L, Rasmussen MLH, Piening B, Shen X, Chen S, Röst H, Snyder JK, Tibshirani R, Skotte L, Lee NCY, Contrepois K, Feenstra B, Zackriah H, Snyder M, Melbye M. Metabolic Dynamics and Prediction of Gestational Age and Time to Delivery in Pregnant Women. Cell. 181 (7), 1680-1692. e15 Article
  17. Lai M, Liu Y, Ronnett GV, Wu A, Cox BJ, Dai FF*, Röst HL*, Gunderson EP*, Wheeler MB*. Amino acid and lipid metabolism in post-gestational diabetes and progression to type 2 diabetes: A metabolic profiling study. PLOS Medicine. 2020 May. Article
  18. Gupta S*, Sing J*, Mahmoodi A*, Röst H. DrawAlignR: An interactive tool for across run chromatogram alignment visualization. Proteomics. 2020 May. Article Full Text Github
  19. Xu L, Young A, Zhou A, Röst H. Machine Learning in Mass Spectrometric Analysis of DIA Data. Proteomics. 2020 Feb. Article
  20. Röst HL. Deep learning adds an extra dimension to peptide fragmentation. Nat Methods. 2019 Jun;16(6):469-470. Article
  21. Zhou W*, Sailani R*, 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. Longitudinal multi-omics of host-microbe dynamics in prediabetes. Nature. 2019 May. Article Full Text
  22. 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 (BioRxiv) Github
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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.
  34. 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)
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. Röst HL, Malmström L, Aebersold R. Reproducible quantitative proteotype data matrices for systems biology. Mol Biol Cell. 2015 Nov Article Full Text
  41. 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
  42. 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
  43. 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
  44. 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
  45. 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
  46. 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.
  47. 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
  48. 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
  49. 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
  50. 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
  51. 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)
  52. 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
  53. 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
  54. 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
  55. 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
  56. 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
  57. 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
Lab members are underlined, equal contributions is denoted by asterisk (*).
“The imagination of nature is far, far greater than the imagination of man.”
Richard Feynman