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Peer-reviewed articles

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64. Rosenberger, George; Liu, Yansheng; Rost, Hannes; Ludwig, Christina; Buil, Alfonso; Bensimon, Ariel; Soste, Martin; Spector, Tim; Dermitzakis, Emmanouil; Collins, Ben; Malmstrom, Lars; Aebersold, Ruedi; Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS. Nat Biotechnol (2017), Epub ahead of print: 0.
63. Sjoholm, Kristoffer; Kilsgård, Ola; Teleman, Johan; Happonen, Lotta; Malmstrom, Lars; Malmstrom, Johan; Targeted proteomics and absolute protein quantification for the construction of a stoichiometric host-pathogen surface density model. Mol Cell Proteomics (2017), Epub ahead of print]: 0.
62. Wolstencroft, Katherine; Krebs, Olga; Snoep, Jacky; Stanford, Natalie; Bacall, Finn; Golebiewski, Martin; Kuzyakiv, Rostyk; Nguyen, Quyen; Owen, Stuart; Soiland-Reyes, Stian; Straszewski, Jakub; van Niekerk, David; Williams, Alan; Malmstrom, Lars; Rinn, Bernd; Müller, Wolfgang; Goble, Carole; FAIRDOMHub: a repository and collaboration environment for sharing systems biology research. Nucleic Acids Res (2016), 0: 0-0.
61. Rost, Hannes; Sachsenberg, Timo; Aiche, Stephan; Bielow, Chris; Weisser, Hendrik; Aicheler, Fabian; Andreotti, Sandro; Ehrlich, Hans-Christian; Gutenbrunner, Petra; Kenar, Erhan; Liang, Xiao; Nahnsen, Sven; Nilse, Lars; Pfeuffer, Julianus; Rosenberger, George; Rurik, Marc; Schmitt, Uwe; Veit, Johannes; Walzer, Mathias; Wojnar, David; Wolski, Witold; Schilling, Oliver; Choudhary, Jyoti; Malmstrom, Lars; Aebersold, Ruedi; Reinert, Knut; Kohlbacher, Oliver; OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Methods (2016), 13: 741-8.
60. Rost, Hannes; Liu, Yansheng; DAgostino, Giuseppe; Zanella, Matteo; Navarro, Pedro; Rosenberger, George; Collins, Ben; Gillet, Ludovic; Testa, Giuseppe; Malmstrom, Lars; Aebersold, Ruedi; TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics. Nat Methods (2016), Epub ahead of print: 0.
59. Tykesson, Emil; Mao, Yang; Maccarana, Marco; Pu, Yi; Gao, Jinshan; Lin, Cheng; Zaia, Joseph; Westergren-Thorsson, Gunilla; Ellervik, Ulf; Malmstrom, Lars; Malmstrom, Anders; Deciphering the Mode of Action of the Processive Polysaccharide Modifying Enzyme Dermatan Sulfate Epimerase 1 by Hydrogen-Deuterium Exchange Mass Spectrometry. Chem Sci (2016), 7: 1447-1456.
58. Malmstrom, Erik; Kilsgård, Ola; Hauri, Simon; Smeds, Emanuel; Herwald, Heiko; Malmstrom, Lars; Malmstrom, Johan; Large-scale inference of protein tissue origin in gram-positive sepsis plasma using quantitative targeted proteomics. Nat Commun (2016), 7: 10261.
57. The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. Nucleic Acids Res (2015), -1: HASH(0x25ef490).
56. Rost, Hannes; Malmstrom, Lars; Aebersold, Ruedi; Reproducible quantitative proteotype data matrices for systems biology. Mol Biol Cell (2015), 26: 3926-31.
55. Walzthoeni, Thomas; Joachimiak, Lukasz; Rosenberger, George; Rost, Hannes; Malmstrom, Lars; Leitner, Alexander; Frydman, Judith; Aebersold, Ruedi; xTract: software for characterizing conformational changes of protein complexes by quantitative cross-linking mass spectrometry. Nat Methods (2015), 0: Epub ahead of print.
54. Malmstrom, Lars; Bakochi, Anahita; Svensson, Gabriel; Kilsgård, Ola; Lantz, Henrik; Petersson, Ann; Hauri, Simon; Karlsson, Christofer; Malmstrom, Johan; Quantitative proteogenomics of human pathogens using DIA-MS. J Proteomics (2015), 0: Epub ahead of print.
53. Parker, Sarah; Roest, Hannes; Rosenberger, George; Collins, Ben; Malmstrom, Lars; Amodei, Dario; Venkatraman, Vidya; Raedschelders, Koen; Van Eyk, Jennifer; Aebersold, Ruedi; Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-Independent Acquisition Mass Spectrometry. Mol Cell Proteomics (2015), -1: Epub ahead of print.
52. Sjostrom, Martin; Ossola, Reto; Breslin, Thomas; Rinner, Oliver; Malmstrom, Lars; Schmidt, Alexander; Aebersold, Ruedi; Malmstrom, Johan; Niméus, Emma; A Combined Shotgun and Targeted Mass Spectrometry Strategy for Breast Cancer Biomarker Discovery. J Proteome Res (2015), : Epub ahead of print.
51. Rost, Hannes; Schmitt, Uwe; Aebersold, Ruedi; Malmstrom, Lars; Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry. PLoS One (2015), 10(4): e0125108.
50. Rost, Hannes; Rosenberger, George; Aebersold, Ruedi; Malmstrom, Lars; Efficient visualization of high-throughput targeted proteomics experiments: TAPIR. Bioinformatics (2015), 0: -.
49. Quandt, Andreas; Espona Pernas, Lucia; Balasko, Akos; Weisser, Hendrik; Brusniak, Mi-Youn; Kunszt, Peter; Aebersold, Ruedi; Malmstrom, Lars; Using synthetic peptides to benchmark peptide identification software and search parameters for MS/MS data analysis. EuPA Open Proteomics (2014), 5: 21-31.
48. Teleman, Johan; Rost, Hannes; Rosenberger, George; Schmitt, Uwe; Malmstrom, Lars; Malmstrom, Johan; Levander, Fredrik; DIANA - algorithmic improvements for analysis of data-independent acquisition MS data. Bioinformatics (2014), : .
47. Wisniewska, Magdalena; Happonen, Lotta; Kahn, Fredrik; Varjosalo, Markku; Malmstrom, Lars; Rosenberger, George; Karlsson, Christofer; Cazzamali, Giuseppe; Pozdnyakova, Irina; Frick, Inga-Maria; Bjorck, Lars; Streicher, Werner; Malmstrom, Johan; Wikstrom, Mats; Functional and Structural Properties of a Novel Protein and Virulence Factor (sHIP) in Streptococcus pyogenes. J Biol Chem (2014), 289(26): 18175-88.
46. Kunszt, Peter; Blum, Lorenz; Hullar, Bela; Schmid, Emanuel; Srebniak, Adam; Wolski, Witold; Rinn, Bernd; Elmer, Franz-Josef; Ramakrishnan, Chandrasekhar; Quandt, Andreas; Malmstrom, Lars; iPortal: the swiss grid proteomics portal: Requirements and new features based on experience and usability considerations. Concurrency and Computation: Practice and Experience (2014), 0: -.
45. Rosenberger, George; Ludwig, Christina; Rost, Hannes; Aebersold, Ruedi; Malmstrom, Lars; aLFQ: An R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data. Bioinformatics (2014), Epub ahead of print: .
44. Rost, Hannes; Rosenberger, George; Navarro, Pedro; Gillet, Ludovic; Miladinović, Saša; Schubert, Olga; Wolski, Witold; Collins, Ben; Malmstrom, Johan; Malmstrom, Lars; Aebersold, Ruedi; OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. Nat Biotechnol (2014), 32: 219-23.
43. Teleman, Johan; Dowsey, Andrew; Gonzalez-Galarza, Faviel; Perkins, Simon; Pratt, Brian; Rost, Hannes; Malmstrom, Lars; Malmstrom, Johan; Jones, Andrew; Deutsch, Eric; Levander, Fredrik; Numerical compression schemes for proteomics mass spectrometry data. Mol Cell Proteomics (2014), -: .
42. Rost, Hannes; Schmitt, Uwe; Aebersold, Ruedi; Malmstrom, Lars; pyOpenMS: A Python-based interface to the OpenMS mass-spectrometry algorithm library. Proteomics (2014), 14: 74-7.
41. Thaipisuttikul, Iyarit; Hittle, Lauren; Chandra, Ramesh; Zangari, Daniel; Dixon, Charneal; Garrett, Teresa; Rasko, David; Dasgupta, Nandini; Moskowitz, Samuel; Malmstrom, Lars; Goodlett, David; Miller, Samuel; Bishop, Russell; Ernst, Robert; A divergent Pseudomonas aeruginosa palmitoyltransferase essential for cystic fibrosis-specific lipid A. Mol Microbiol (2013), 0: Epub ahead of print.
40. Kahraman, Abdullah; Herzog, Franz; Leitner, Alexander; Rosenberger, George; Aebersold, Ruedi; Malmstrom, Lars; Cross-Link Guided Molecular Modeling with ROSETTA. PLoS One (2013), 8: e73411.
39. Kunszt, Peter; Blum, Lorenz; Hullar, Bela; Schmid, Emanuel; Srebniak, Adam; Wolski, Witold; Rinn, Bernd; Elmer, Franz-Josef; Ramakrishnan, Chandrasekhar; Quandt, Andreas; Malmstrom, Lars; Improving the Swiss Grid Proteomics Portal: Requirements and new Features based on Experience and Usability Considerations. conf proc. of the 5th International Workshop on Science Gateways (IWSG 2013), Zurich, 3-5 June 2013, in CEUR Workshop Proceedings Vol 993 (2013), 993: -.
38. Weisser, Hendrik; Nahnsen, Sven; Grossmann, Jonas; Nilse, Lars; Quandt, Andreas; Brauer, Hendrik; Sturm, Marc; Kenar, Erhan; Kohlbacher, Oliver; Aebersold, Ruedi; Malmstrom, Lars; An automated pipeline for high-throughput label-free quantitative proteomics. J Proteome Res (2013), -: Epub ahead of print.
37. Malmstrom, Lars; Nordenfelt, Pontus; Malmstrom, Johan; Business intelligence strategies enables rapid analysis of quantitative proteomics data. Journal of Proteome Science and Computational Biology (2012), 1 (1): -.
36. Karlsson, Christofer; Malmstrom, Lars; Aebersold, Ruedi; Malmstrom, Johan; Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes. Nat Commun (2012), 3: 1301.
35. Herzog, Franz; Kahraman, Abdullah; Boehringer, Daniel; Mak, Raymond; Bracher, Andreas; Walzthoeni, Thomas; Leitner, Alexander; Beck, Martin; Hartl, Franz-Ulrich; Ban, Nenad; Malmstrom, Lars; Aebersold, Ruedi; Structural probing of a protein phosphatase 2A network by chemical cross-linking and mass spectrometry. Science (2012), 337: 1348-52.
34. Reker, Daniel; Malmstrom, Lars; Bioinformatic challenges in targeted proteomics. J Proteome Res (2012), 11: 4393-402.
33. Hallgren, Oskar; Malmstrom, Johan; Malmstrom, Lars; Andersson-Sjoland, Annika; Wildt, Marie; Tufvesson, Ellen; Juhasz, Peer; Marko-Varga, Gyorgy; Westergren-Thorsson, Gunilla; Splicosomal and serine and arginine-rich splicing factors as targets for TGF-beta. Fibrogenesis Tissue Repair (2012), 5: 6.
32. Rost, Hannes; Malmstrom, Lars; Aebersold, Ruedi; A computational tool to detect and avoid redundancy in selected reaction monitoring. Mol Cell Proteomics (2012), 11: 540-9.
31. Malmstrom, Lars; Malmstrom, Johan; Selevsek, Nathalie; Rosenberger, George; Aebersold, Ruedi; Automated workflow for large-scale Selected Reaction Monitoring experiments. J Proteome Res (2012), 11: 1644-53.
30. Bauch, Angela; Adamczyk, Izabela; Buczek, Piotr; Elmer, Franz-Josef; Enimanev, Kaloyan; Glyzewski, Pawel; Kohler, Manuel; Pylak, Tomasz; Quandt, Andreas; Ramakrishnan, Chandrasekhar; Beisel, Christian; Malmstrom, Lars; Aebersold, Ruedi; Rinn, Bernd; openBIS: a flexible framework for managing and analyzing complex data in biology research. BMC Bioinformatics (2011), 12: 468.
29. Malmstrom, Johan; Karlsson, Christofer; Nordenfelt, Pontus; Ossola, Reto; Weisser, Hendrik; Quandt, Andreas; Hansson, Karin; Aebersold, Ruedi; Malmstrom, Lars; Bjorck, Lars; Streptococcus pyogenes in human plasma: adaptive mechanisms analyzed by mass spectrometry based proteomics. J Biol Chem (2011), 287: 1415-25.
28. Kunszt, Peter; Malmstrom, Lars; Fantini, Nicola; Subholt, Wibke; Lautenschlager, Marcel; Reifler, Roland; Ruckstuhl, Stefan; Accelerating 3D Protein Modeling Using Cloud Computing. Seventh IEEE International Conference on e-Science Workshops (2011), --: 166-169.
27. Drew, Kevin; Winters, Patrick; Butterfoss, Glenn; Berstis, Viktors; Uplinger, Keith; Armstrong, Jonathan; Riffle, Michael; Schweighofer, Erik; Bovermann, Bill; Goodlett, David; Davis, Trisha; Shasha, Dennis; Malmstrom, Lars; Bonneau, Richard; The proteome folding project: Proteome-scale prediction of structure and function. Genome Res (2011), 21: 1981-94.
26. Malmstrom, Lars; Malmstrom, Johan; Aebersold, Ruedi; Quantitative proteomics of microbes: Principles and applications to virulence. Proteomics (2011), 11: 2947-56.
25. Kahraman, Abdullah; Malmstrom, Lars; Aebersold, Ruedi; Xwalk: Computing and Visualizing Distances in Cross-linking Experiments. Bioinformatics (2011), 27: 2163-4.
24. Kunszt, Peter; Espona Pernas, Lucia; Quandt, Andreas; Schmid, Emanuel; Hunt, Ela; Malmstrom, Lars; The Swiss Grid Proteomics Portal. Proceedings of the Second International Conference on Parallel, Distributed, Grid and Cloud Computing for Engineering (2011), -: 81.
23. Nunn, Brook; Ting, Ying; Malmstrom, Lars; Tsai, Yihsuan; Squier, Angela; Goodlett, David; Harvey, H; The path to preservation: Using proteomics to decipher the fate of diatom proteins during microbial degradation. Limnol. Oceanogr. (2010), 55: 1790-1804.
22. Malmstrom, Lars; Goodlett, David; Protein structure modeling. Methods Mol Biol (2010), 673: 63-72.
21. Kalantari, Fariba; Auguste, Patrick; Ziafazeli, Tahereh; Tzimas, George; Malmstrom, Lars; Bioulac-Sage, Paulette; Boismenu, Daniel; Vali, Hojatollah; Chevet, E; Proteomics analysis of liver pathological calcification suggests a role for the IQ motif containing GTPase activating protein 1 in myofibroblast function. PROTEOMICS - Clinical Applications (2009), 3: 307-321.
20. Nunn, Brook; Aker, Jocelyn; Shaffer, Scott; Tsai, Shannon; Strzepek, Robert; Boyd, Philip; Freeman, Theodore; Brittnacher, Mitchell; Malmstrom, Lars; Goodlett, David; Deciphering diatom biochemical pathways via whole-cell proteomics. Aquat Microb Ecol (2009), 55: 241-253.
19. Malmstrom, Lars; Hou, Liming; Atkins, William; Goodlett, David; On the use of hydrogen/deuterium exchange mass spectrometry data to improve de novo protein structure prediction. Rapid Commun Mass Spectrom (2009), 23: 459-461.
18. Goo, Young; Liu, Alvin; Ryu, Soyoung; Shaffer, Scott; Malmstrom, Lars; Page, Laura; Nguyen, Liem; Doneanu, Catalin; Goodlett, David; Identification of secreted glycoproteins of human prostate and bladder stromal cells by comparative quantitative proteomics. Prostate (2009), 69: 49-61.
17. Pacheco, Benny; Maccarana, Marco; Goodlett, David; Malmstrom, Anders; Malmstrom, Lars; Identification of the active site of DS-epimerase 1 and requirement of N-glycosylation for enzyme function. J Biol Chem (2009), 284: 1741-7.
16. Das, Rhiju; Qian, Bin; Raman, Srivatsan; Vernon, Robert; Thompson, James; Bradley, Philip; Khare, Sagar; Tyka, Michael; Bhat, Divya; Chivian, Dylan; Kim, David; Sheffler, William; Malmstrom, Lars; Wollacott, Andrew; Wang, Chu; Andre, Ingemar; Baker, David; Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. Proteins (2007), 1: 118-128.
15. Malmstrom, Lars; Riffle, Michael; Strauss, Charlie; Chivian, Dylan; Davis, Trisha; Bonneau, Richard; Baker, David; Superfamily Assignments for the Yeast Proteome through Integration of Structure Prediction with the Gene Ontology. PLoS Biol (2007), 5: e76.
14. Malmstrom, Erik; Sennstrom, Maria; Holmberg, Anna; Frielingsdorf, Helena; Eklund, Erik; Malmstrom, Lars; Tufvesson, Ellen; Gomez, Maria; Westergren-Thorsson, Gunilla; Ekman-Ordeberg, Gunvor; Malmstrom, Anders; The importance of fibroblasts in remodelling of the human uterine cervix during pregnancy and parturition. Mol Hum Reprod (2007), 13: 333-41.
13. Malmstrom, Lars; Marko-Varga, Gyorgy; Westergren-Thorsson, Gunilla; Laurell, Thomas; Malmstrom, Johan; 2DDB - a bioinformatics solution for analysis of quantitative proteomics data. BMC Bioinformatics (2006), 7: 158.
12. Malmstrom, Johan; Malmstrom, Lars; Marko-Varga, Gyorgy; Proteomics: A new research area for the biomedical field. Journal of Organ Dysfunction (2005), 1: 83-94.
11. Kim, David; Chivian, Dylan; Malmstrom, Lars; Baker, David; Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM. Proteins (2005), Suppl 7: 193-200.
10. Chivian, Dylan; Kim, David; Malmstrom, Lars; Schonbrun, Jack; Rohl, Carol; Baker, David; Prediction of CASP6 structures using automated Robetta protocols. Proteins (2005), Suppl 7: 157-66.
9. Bradley, Philip; Malmstrom, Lars; Qian, Bin; Schonbrun, Jack; Chivian, Dylan; Kim, David; Meiler, Jens; Misura, Kira; Baker, David; Free modeling with Rosetta in CASP6. Proteins (2005), Suppl 7: 128-34.
8. Riffle, Michael; Malmstrom, Lars; Davis, Trisha; The yeast resource center public data repository. Nucleic Acids Res (2005), 33: D378-82.
7. Cazzanti, Luca; Gupta, Maya; Malmstrom, Lars; Baker, David; Quality Assessment of Low Free-Energy Protein Structure Predictions. Machine Learning for Signal Processing (2005), -: 375-380.
6. Malmstrom, Johan; Larsen, Kristoffer; Malmstrom, Lars; Tufvesson, Ellen; Parker, Ken; Marchese, Jason; Williamson, Brian; Hattan, Steve; Patterson, Dale; Martin, Steve; Graber, Armin; Juhasz, H; Westergren-Thorsson, Gunilla; Marko-Varga, Gyorgy; Proteome annotations and identifications of the human pulmonary fibroblast. J Proteome Res (2004), 3: 525-37.
5. Hazbun, Tony; Malmstrom, Lars; Anderson, Scott; Graczyk, Beth; Fox, Bethany; Riffle, Michael; Sundin, Bryan; Aranda, J; McDonald, W; Chiu, Chun-Hwei; Snydsman, Brian; Bradley, Phillip; Muller, Eric; Fields, Stanley; Baker, David; Yates, John; Davis, Trisha; Assigning function to yeast proteins by integration of technologies. Mol Cell (2003), 12: 1353-65.
4. Malmstrom, Johan; Larsen, Kristoffer; Malmstrom, Lars; Tufvesson, Ellen; Parker, Ken; Marchese, Jason; Williamson, Brian; Patterson, Dale; Martin, Steve; Juhasz, Peter; Westergren-Thorsson, Gunilla; Marko-Varga, Gyorgy; Nanocapillary liquid chromatography interfaced to tandem matrix-assisted laser desorption/ionization and electrospray ionization-mass spectrometry: Mapping the nuclear proteome of human fibroblasts. Electrophoresis (2003), 24: 3806-14.
3. Chivian, Dylan; Kim, David; Malmstrom, Lars; Bradley, Philip; Robertson, Timothy; Murphy, Paul; Strauss, Charles; Bonneau, Richard; Rohl, Carol; Baker, David; Automated prediction of CASP-5 structures using the Robetta server. Proteins (2003), 53: 524-33.
2. Malmstrom, Lars; Malmstrom, Johan; Marko-Varga, Gyorgy; Westergren-Thorsson, Gunilla; Proteomic 2DE database for spot selection, automated annotation, and data analysis. J Proteome Res (2002), 1: 135-8.
1. Bonneau, Richard; Strauss, Charlie; Rohl, Carol; Chivian, Dylan; Bradley, Phillip; Malmstrom, Lars; Robertson, Tim; Baker, David; De Novo Prediction of Three-dimensional Structures for Major Protein Families. J Mol Biol (2002), 322: 65.