Publications

Authors and Title	Details
85: Quantification of adaptive immune responses against protein binding interfaces in the streptococcal M1 protein Torres-Sangiao, E; Happonen, L; Heusel, M; Palm, F; Gueto-Tettay, C; Malmström, Lars; Shannon, O; Malmström, Johan	Mol Cell Proteomics (2024) 2024 Mar 23:100753 - Impact: 7.0 - Citations: 0 - DOI: 10.1016/j.mcpro.2024.100753
84: Interpreting biologically informed neural networks for enhanced proteomic biomarker discovery and pathway analysis Hartman, Erik; Scott, Aaron; Karlsson, Christofer; Mohanty, Tirthankar; Vaara, Suvi; Linder, Adam; Malmström, Lars; Malmström, Johan	Nature communications (2023) 14(1):5359 - Impact: 17.694 - Citations: 8 - DOI: 10.1038/s41467-023-41146-4
83: A pharmacoproteomic landscape of organotypic intervention responses in Gram-negative sepsis Mohanty, Tirthankar; Karlsson, Christofer A Q; Chao, Yashuan; Malmström, Erik; Bratanis, Eleni; Grentzmann, Andrietta; Mørch, Martina; Nizet, Victor; Malmström, Lars; Linder, Adam; Shannon, Oonagh; Malmström, Johan	Nature communications (2023) 14(1):3603 - Impact: 17.694 - Citations: 6 - DOI: 10.1038/s41467-023-39269-9
82: Generalized precursor prediction boosts identification rates and accuracy in mass spectrometry based proteomics. Scott, Aaron M; Karlsson, Christofer; Mohanty, Tirthankar; Hartman, Erik; Vaara, Suvi T; Linder, Adam; Malmström, Johan; Malmström, Lars	Communications biology (2023) 6(1):628' - Impact: 6.548 - Citations: 3 - DOI: 10.1038/s42003-023-04977-x
81: Shigella IpaA mediates actin bundling through diffusible vinculin oligomers with activation imprint Cesar Valencia-Gallardo, Daniel-Isui Aguilar-Salvador, Hamed Khakzad, Benjamin Cocom-Chan, Charles Bou-Nader, Christophe Velours, Yosra Zarrouk, Christophe Le Clainche, Christian Malosse, Diogo Borges Lima, Nicole Quenech'Du, Bilal Mazhar, Sami Essid, Marc Fontecave, Atef Asnacios, Julia Chamot-Rooke, Lars Malmström, Guy Tran Van Nhieu	Cell Rep. (2023) 42(4):112405 - Impact: 9.995 - Citations: 3 - DOI: 10.1016/j.celrep.2023.112405
80: Proteogenomics decodes the evolution of human ipsilateral breast cancer Tommaso De Marchi, Paul Theodor Pyl, Martin Sjostrom, Susanne Erika Reinsbach, Sebastian DiLorenzo, Bjorn Nystedt, Lena Tran, Gyula Pekar, Fredrik Warnberg, Irma Fredriksson, Per Malmström, Marten Ferno, Lars Malmström, Johan Malmstöm, Emma Nimeus	Commun Biol. (2023) 6(1):139: - Impact: 6.548 - Citations: 2 - DOI: 10.1038/s42003-023-04526-6
79: Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics. Carlos Gueto-Tettay, Di Tang, Lotta Happonen, Moritz Heusel, Hamed Khakzad, Johan Malmström, Lars Malmström	PLoS Comput Biol (2023) e1010457: - Impact: 4.53 - Citations: 5 - DOI: 10.1371/journal.pcbi.1010457
78: A human monoclonal antibody bivalently binding two different epitopes in streptococcal M protein mediates immune function Wael Bahnan, Lotta Happonen, Hamed Khakzad, Vibha Kumra Ahnlide, Therese de Neergaard, Sebastian Wrighton, Oscar Andre, Eleni Bratanis, Di Tang, Thomas Hellmark, Lars Björck, Oonagh Shannon, Lars Malmström, Johan Malmström & Pontus Nordenfelt	EMBO Mol Med (2022) e16208: - Impact: 12.137 - Citations: 7 - DOI: 10.15252/emmm.202216208
77: Spike-Dependent Opsonization Indicates Both Dose-Dependent Inhibition of Phagocytosis and That Non-Neutralizing Antibodies Can Confer Protection to SARS-CoV-2 Bahnan, Wael; Wrighton, Sebastian; Sundwall, Martin; Bläckberg, Anna; Larsson, Olivia; Höglund, Urban; Khakzad, Hamed; Godzwon, Magdalena; Walle, Maria; Elder, Elisabeth; Söderlund-Strand, Anna; Happonen, Lotta; André, Oscar; Kumra-Ahnlide, Johannes; Hellmark, Thomas; Wendel-Hansen, Vidar; Pa-Wallin, Robert; Malmstöm, Johan; Malmström, Lars; Ohlin, Mats; Rasmussen, Magnus; Nordenfelt, Pontus	Frontiers in Immunology (2022) 12: - Impact: 7.561 - Citations: 44 - DOI: 10.3389/fimmu.2021.808932
76: Quaternary Structure Modeling Through Chemical Cross-Linking Mass Spectrometry: Extending TX-MS Jupyter Reports. Khakzad, Hamed; Vermeul, Swen; Malmström, Lars	J Vis Exp (2021) -1: - Impact: 1.4 - Citations: 0 - DOI: 10.3791/60311
76: Streptococcus pyogenes Forms Serotype- and Local Environment-Dependent Interspecies Protein Complexes. Chowdhury, Sounak; Khakzad, Hamed; Bergdahl, Gizem; Lood, Rolf; Ekstrom, Simon; Linke, Dirk; Malmström, Lars; Happonen, Lotta; Malmström, Johan	mSystems (2021) -1:e0027121 - Impact: 5.85 - Citations: 9 - DOI: 10.1128/mSystems.00271-21
74: Proteogenomic Workflow Reveals Molecular Phenotypes Related to Breast Cancer Mammographic Appearance De Marchi, Tommaso ; Pyl, Paul; Sjöström, Martin; Klasson, Stina; Sartor, Hanna; Tran, Lena; Pekar, Gyula; Malmström, Johan; Malmström, Lars; Niméus, Emma	J Proteome Res (2021) 0:0 - Impact: 4.07 - Citations: 15 - DOI: 10.1021/acs.jproteome.1c00243
73: Cerebrospinal fluid proteome maps detect pathogen-specific host response patterns in meningitis Bakochi, Anahita; Mohanty, Tirthankar; Pyl, Paul; Gueto-Tettay, Carlos; Malmström, Lars; Linder, Adam; Malmström, Johan	Elife (2021) 0:Online ahead of print - Impact: 7.08 - Citations: 14 - DOI: 10.7554/eLife.64159
72: The structure of human dermatan sulfate epimerase 1 emphasizes the importance of C5-epimerization of glucuronic acid in higher organisms. Hasan, Mahmudul; Khakzad, Hamed; Happonen, Lotta; Sundin, Anders; Unge, Johan; Mueller, Uwe; Malmström, Johan; Westergren-Thorsson, Gunilla; Malmström, Lars; Ellervik, Ulf; Malmström, Anders; Tykesson, Emil	Chem Sci (2021) 12:1869-1885 - Impact: 9.35 - Citations: 5 - DOI: 10.1039/d0sc05971d
71: Structural determination of Streptococcus pyogenes M1 protein interactions with human immunoglobulin G using integrative structural biology. Khakzad, Hamed; Happonen, Lotta; Karami, Yasaman; Chowdhury, Sounak; Bergdahl, Gizem; Nilges, Michael; Tran Van Nhieu, Guy; Malmström, Johan; Malmström, Lars	PLoS Comput Biol (2021) 17:e1008169 - Impact: 4.43 - Citations: 16 - DOI: 10.1371/journal.pcbi.1008169
70: In vivo Cross-Linking MS of the Complement System MAC Assembled on Live Gram-Positive Bacteria. Khakzad, Hamed; Happonen, Lotta; Tran Van Nhieu, Guy; Malmström, Johan; Malmström, Lars	Front Genet (2020) 11:612475 - Impact: 3.79 - Citations: 8 - DOI: 10.3389/fgene.2020.612475
69: Macromolecular modeling and design in Rosetta: recent methods and frameworks. Leman, Julia; Weitzner, Brian; Lewis, Steven; Adolf-Bryfogle, Jared; Alam, Nawsad; Alford, Rebecca; Aprahamian, Melanie; Baker, David; Barlow, Kyle; Barth, Patrick; Basanta, Benjamin; Bender, Brian; Blacklock, Kristin; Bonet, Jaume; Boyken, Scott; Bradley, Phil; Bystroff, Chris; Conway, Patrick; Cooper, Seth; Correia, Bruno; Coventry, Brian; Das, Rhiju; De Jong, René; DiMaio, Frank; Dsilva, Lorna; Dunbrack, Roland; Ford, Alexander; Frenz, Brandon; Fu, Darwin; Geniesse, Caleb; Goldschmidt, Lukasz; Gowthaman, Ragul; Gray, Jeffrey; Gront, Dominik; Guffy, Sharon; Horowitz, Scott; Huang, Po-Ssu; Huber, Thomas; Jacobs, Tim; Jeliazkov, Jeliazko; Johnson, David; Kappel, Kalli; Karanicolas, John; Khakzad, Hamed; Khar, Karen; Khare, Sagar; Khatib, Firas; Khramushin, Alisa; King, Indigo; Kleffner, Robert; Koepnick, Brian; Kortemme, Tanja; Kuenze, Georg; Kuhlman, Brian; Kuroda, Daisuke; Labonte, Jason; Lai, Jason; Lapidoth, Gideon; Leaver-Fay, Andrew; Lindert, Steffen; Linsky, Thomas; London, Nir; Lubin, Joseph; Lyskov, Sergey; Maguire, Jack; Malmström, Lars; Marcos, Enrique; Marcu, Orly; Marze, Nicholas; Meiler, Jens; Moretti, Rocco; Mulligan, Vikram; Nerli, Santrupti; Norn, Christoffer; ÓConchúir, Shane; Ollikainen, Noah; Ovchinnikov, Sergey; Pacella, Michael; Pan, Xingjie; Park, Hahnbeom; Pavlovicz, Ryan; Pethe, Manasi; Pierce, Brian; Pilla, Kala; Raveh, Barak; Renfrew, P; Burman, Shourya; Rubenstein, Aliza; Sauer, Marion; Scheck, Andreas; Schief, William; Schueler-Furman, Ora; Sedan, Yuval; Sevy, Alexander; Sgourakis, Nikolaos; Shi, Lei; Siegel, Justin; Silva, Daniel-Adriano; Smith, Shannon; Song, Yifan; Stein, Amelie; Szegedy, Maria; Teets, Frank; Thyme, Summer; Wang, Ray; Watkins, Andrew; Zimmerman, Lior; Bonneau, Richard	Nat Methods (2020) -1: - Impact: 28.47 - Citations: 563 - DOI: 10.1038/s41592-020-0848-2
68: Extracellular Vesicle-Contained microRNA of C. elegans as a Tool to Decipher the Molecular Basis of Nematode Parasitism. Duguet, Thomas; Soichot, Julien; Kuzyakiv, Rostyslav; Malmström, Lars; Tritten, Lucienne	Front Cell Infect Microbiol (2020) 10:217 - Impact: 3.52 - Citations: 19 - DOI: 10.3389/fcimb.2020.00217
67: Computational Proteomics with Jupyter and Python Malmstrom, L	Methods Mol Biol (2019) 1977:4-15 - Impact: 0 - Citations: 6 - DOI: 10.1007/978-1-4939-9232-4_15
66: A quantitative Streptococcus pyogenes-human protein-protein interaction map reveals localization of opsonizing antibodies. Happonen, Lotta; Hauri, Simon; Svensson Birkedal, Gabriel; Karlsson, Christofer; de Neergaard, Therese; Khakzad, Hamed; Nordenfelt, Pontus; Wikström, Mats; Wisniewska, Magdalena; Björck, Lars; Malmström, Lars; Malmström, Johan	Nat Commun (2019) 10:2727 - Impact: 13.69 - Citations: 47 - DOI: 10.1038/s41467-019-10583-5
65: Greedy de novo motif discovery to construct motif repositories for bacterial proteomes. Khakzad, Hamed; Malmström, Johan; Malmström, Lars	BMC Bioinformatics (2019) 20:141 - Impact: 2.21 - Citations: 3 - DOI: 10.1186/s12859-019-2686-8
64: Rapid determination of quaternary protein structures in complex biological samples. Hauri, Simon; Khakzad, Hamed; Happonen, Lotta; Teleman, Johan; Malmström, Johan; Malmström, Lars	Nat Commun (2019) 10:192 - Impact: 12.12 - Citations: 53 - DOI: 10.1038/s41467-018-07986-1
63: Comprehensive ADP-ribosylome analysis identifies tyrosine as an ADP-ribose acceptor site. Leslie Pedrioli, Deena; Leutert, Mario; Bilan, Vera; Nowak, Kathrin; Gunasekera, Kapila; Ferrari, Elena; Imhof, Ralph; Malmström, Lars; Hottiger, Michael	EMBO Rep (2018) 19(8):e45310 - Impact: 3.22 - Citations: 90 - DOI: 10.15252/embr.201745310
62: Quantitative proteomic characterization of the lung extracellular matrix in chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis. Åhrman, Emma; Hallgren, Oskar; Malmström, Lars; Hedström, Ulf; Malmström, Anders; Bjermer, Leif; Zhou, Xiao-Hong; Westergren-Thorsson, Gunilla; Malmström, Johan	J Proteomics (2018) 189:23-33 - Impact: 4.27 - Citations: 68 - DOI: 10.1016/j.jprot.2018.02.027
61: An objective comparison of cell-tracking algorithms. Ulman, Vladimír; Maška, Martin; Magnusson, Klas; Ronneberger, Olaf; Haubold, Carsten; Harder, Nathalie; Matula, Pavel; Matula, Petr; Svoboda, David; Radojevic, Miroslav; Smal, Ihor; Rohr, Karl; Jaldén, Joakim; Blau, Helen; Dzyubachyk, Oleh; Lelieveldt, Boudewijn; Xiao, Pengdong; Li, Yuexiang; Cho, Siu-Yeung; Dufour, Alexandre; Olivo-Marin, Jean-Christophe; Reyes-Aldasoro, Constantino; Solis-Lemus, Jose; Bensch, Robert; Brox, Thomas; Stegmaier, Johannes; Mikut, Ralf; Wolf, Steffen; Hamprecht, Fred; Esteves, Tiago; Quelhas, Pedro; Demirel, Ömer; Malmström, Lars; Jug, Florian; Tomancak, Pavel; Meijering, Erik; Muñoz-Barrutia, Arrate; Kozubek, Michal; Ortiz-de-Solorzano, Carlos	Nat Methods (2017) 14(12):1141-1152 - Impact: 25.06 - Citations: 552 - DOI: 10.1038/nmeth.4473
60: Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS. Rosenberger, George; Liu, Yansheng; Röst, Hannes; Ludwig, Christina; Buil, Alfonso; Bensimon, Ariel; Soste, Martin; Spector, Tim; Dermitzakis, Emmanouil; Collins, Ben; Malmström, Lars; Aebersold, Ruedi	Nat Biotechnol (2017) 35(8):781-788 - Impact: 41.67 - Citations: 130 - DOI: 10.1038/nbt.3908
59: Targeted proteomics and absolute protein quantification for the construction of a stoichiometric host-pathogen surface density model. Sjöholm, Kristoffer; Kilsgård, Ola; Teleman, Johan; Happonen, Lotta; Malmström, Lars; Malmström, Johan	Mol Cell Proteomics (2017) 16(4 suppl 1):S29-S41 - Impact: 5.91 - Citations: 27 - DOI: 10.1074/mcp.M116.063966
58: FAIRDOMHub: a repository and collaboration environment for sharing systems biology research. 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; Malmström, Lars; Rinn, Bernd; Müller, Wolfgang; Goble, Carole	Nucleic Acids Res (2016) 4;45(D1):D404-D407 - Impact: 8.81 - Citations: 119 - DOI: 10.1093/nar/gkw1032
57: TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics. Röst, Hannes; Liu, Yansheng; DAgostino, Giuseppe; Zanella, Matteo; Navarro, Pedro; Rosenberger, George; Collins, Ben; Gillet, Ludovic; Testa, Giuseppe; Malmström, Lars; Aebersold, Ruedi	Nat Methods (2016) 13(9):777-83 - Impact: 25.06 - Citations: 186 - DOI: 10.1038/nmeth.3954
56: OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Röst, 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; Malmström, Lars; Aebersold, Ruedi; Reinert, Knut; Kohlbacher, Oliver	Nat Methods (2016) 13:741-8 - Impact: 25.06 - Citations: 613 - DOI: 10.1038/nmeth.3959
55: Deciphering the Mode of Action of the Processive Polysaccharide Modifying Enzyme Dermatan Sulfate Epimerase 1 by Hydrogen-Deuterium Exchange Mass Spectrometry. Tykesson, Emil; Mao, Yang; Maccarana, Marco; Pu, Yi; Gao, Jinshan; Lin, Cheng; Zaia, Joseph; Westergren-Thorsson, Gunilla; Ellervik, Ulf; Malmström, Lars; Malmström, Anders	Chem Sci (2016) 7:1447-1456 - Impact: 9.21 - Citations: 18 - DOI: 10.1039/C5SC03798K
54: Large-scale inference of protein tissue origin in gram-positive sepsis plasma using quantitative targeted proteomics. Malmström, Erik; Kilsgård, Ola; Hauri, Simon; Smeds, Emanuel; Herwald, Heiko; Malmström, Lars; Malmström, Johan	Nat Commun (2016) 7:10261 - Impact: 11.47 - Citations: 106 - DOI: 10.1038/ncomms10261
53: Reproducible quantitative proteotype data matrices for systems biology. Röst, Hannes; Malmström, Lars; Aebersold, Ruedi	Mol Biol Cell (2015) 26:3926-31 - Impact: 4.55 - Citations: 58 - DOI: 10.1091/mbc.E15-07-0507
52: xTract: software for characterizing conformational changes of protein complexes by quantitative cross-linking mass spectrometry. Walzthoeni, Thomas; Joachimiak, Lukasz; Rosenberger, George; Röst, Hannes; Malmström, Lars; Leitner, Alexander; Frydman, Judith; Aebersold, Ruedi	Nat Methods (2015) 12(12):1185-90 - Impact: 25.95 - Citations: 101 - DOI: 10.1038/nmeth.3631
51: Quantitative proteogenomics of human pathogens using DIA-MS. Malmström, Lars; Bakochi, Anahita; Svensson, Gabriel; Kilsgård, Ola; Lantz, Henrik; Petersson, Ann; Hauri, Simon; Karlsson, Christofer; Malmström, Johan	J Proteomics (2015) 129:98-107 - Impact: 3.93 - Citations: 30 - DOI: 10.1016/j.jprot.2015.09.012
50: Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-Independent Acquisition Mass Spectrometry. Parker, Sarah; Roest, Hannes; Rosenberger, George; Collins, Ben; Malmström, Lars; Amodei, Dario; Venkatraman, Vidya; Raedschelders, Koen; Van Eyk, Jennifer; Aebersold, Ruedi	Mol Cell Proteomics (2015) 14(10):2800-13 - Impact: 7.25 - Citations: 85 - DOI: 10.1074/mcp.O114.042267
49: A Combined Shotgun and Targeted Mass Spectrometry Strategy for Breast Cancer Biomarker Discovery. Sjöström, Martin; Ossola, Reto; Breslin, Thomas; Rinner, Oliver; Malmström, Lars; Schmidt, Alexander; Aebersold, Ruedi; Malmström, Johan; Niméus, Emma	J Proteome Res (2015) 14(7):2807-18 - Impact: 5.0 - Citations: 42 - DOI: 10.1021/acs.jproteome.5b00315
48: Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry. Röst, Hannes; Schmitt, Uwe; Aebersold, Ruedi; Malmström, Lars	PLoS One (2015) 10(4):e0125108 - Impact: 3.53 - Citations: 22 - DOI: 10.1371/journal.pone.0125108
47: Efficient visualization of high-throughput targeted proteomics experiments: TAPIR. Röst, Hannes; Rosenberger, George; Aebersold, Ruedi; Malmström, Lars	Bioinformatics (2015) 31(14):2415-7 - Impact: 4.62 - Citations: 12 - DOI: 10.1093/bioinformatics/btv152
46: The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases.	Nucleic Acids Res (2015) 44(D1):D27-37 - Impact: 8.81 - Citations: 51 - DOI: 10.1093/nar/gkv1310
45: Using synthetic peptides to benchmark peptide identification software and search parameters for MS/MS data analysis Quandt, Andreas; Espona Pernas, Lucia; Balasko, Akos; Weisser, Hendrik; Brusniak, Mi-Youn; Kunszt, Peter; Aebersold, Ruedi; Malmström, Lars	EuPA Open Proteomics (2014) 5:21-31 - Impact: 0.0 - Citations: 15 - DOI: 10.1016/j.euprot.2014.10.001
44: DIANA - algorithmic improvements for analysis of data-independent acquisition MS data. Teleman, Johan; Röst, Hannes; Rosenberger, George; Schmitt, Uwe; Malmström, Lars; Malmström, Johan; Levander, Fredrik	Bioinformatics (2014) 31(4):555-62 - Impact: 4.62 - Citations: 117 - DOI: 10.1093/bioinformatics/btu686
43: Functional and Structural Properties of a Novel Protein and Virulence Factor (sHIP) in Streptococcus pyogenes. Wisniewska, Magdalena; Happonen, Lotta; Kahn, Fredrik; Varjosalo, Markku; Malmström, Lars; Rosenberger, George; Karlsson, Christofer; Cazzamali, Giuseppe; Pozdnyakova, Irina; Frick, Inga-Maria; Björck, Lars; Streicher, Werner; Malmström, Johan; Wikström, Mats	J Biol Chem (2014) 289(26):18175-88 - Impact: 4.6 - Citations: 9 - DOI: 10.1074/jbc.M114.565978
42: iPortal: the swiss grid proteomics portal: Requirements and new features based on experience and usability considerations Kunszt, Peter; Blum, Lorenz; Hullar, Bela; Schmid, Emanuel; Srebniak, Adam; Wolski, Witold; Rinn, Bernd; Elmer, Franz-Josef; Ramakrishnan, Chandrasekhar; Quandt, Andreas; Malmström, Lars	Concurrency and Computation: Practice and Experience (2014) 27(2):433-445 - Impact: 0.78 - Citations: 46 - DOI: 10.1002/cpe.3294
41: aLFQ: An R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data. Rosenberger, George; Ludwig, Christina; Röst, Hannes; Aebersold, Ruedi; Malmström, Lars	Bioinformatics (2014) 30(17):2511-3 - Impact: 4.62 - Citations: 65 - DOI: 10.1093/bioinformatics/btu200
40: OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. Röst, Hannes; Rosenberger, George; Navarro, Pedro; Gillet, Ludovic; Miladinović, Saša; Schubert, Olga; Wolski, Witold; Collins, Ben; Malmström, Johan; Malmström, Lars; Aebersold, Ruedi	Nat Biotechnol (2014) 32:219-23 - Impact: 39.08 - Citations: 797 - DOI: 10.1038/nbt.2841
39: Numerical compression schemes for proteomics mass spectrometry data. Teleman, Johan; Dowsey, Andrew; Gonzalez-Galarza, Faviel; Perkins, Simon; Pratt, Brian; Rost, Hannes; Malmström, Lars; Malmström, Johan; Jones, Andrew; Deutsch, Eric; Levander, Fredrik	Mol Cell Proteomics (2014) 13(6):1537-42 - Impact: 7.25 - Citations: 52 - DOI: 10.1074/mcp.O114.037879
38: pyOpenMS: A Python-based interface to the OpenMS mass-spectrometry algorithm library. Röst, Hannes; Schmitt, Uwe; Aebersold, Ruedi; Malmström, Lars	Proteomics (2014) 14:74-7 - Impact: 3.97 - Citations: 121 - DOI: 10.1002/pmic.201300246
37: A divergent Pseudomonas aeruginosa palmitoyltransferase essential for cystic fibrosis-specific lipid A. Thaipisuttikul, Iyarit; Hittle, Lauren; Chandra, Ramesh; Zangari, Daniel; Dixon, Charneal; Garrett, Teresa; Rasko, David; Dasgupta, Nandini; Moskowitz, Samuel; Malmström, Lars; Goodlett, David; Miller, Samuel; Bishop, Russell; Ernst, Robert	Mol Microbiol (2013) 91(1):158-74 - Impact: 5.03 - Citations: 59 - DOI: 10.1111/mmi.12451
36: Cross-Link Guided Molecular Modeling with ROSETTA. Kahraman, Abdullah; Herzog, Franz; Leitner, Alexander; Rosenberger, George; Aebersold, Ruedi; Malmström, Lars	PLoS One (2013) 8:e73411 - Impact: 3.53 - Citations: 174 - DOI: 10.1371/journal.pone.0073411
35: An automated pipeline for high-throughput label-free quantitative proteomics. Weisser, Hendrik; Nahnsen, Sven; Grossmann, Jonas; Nilse, Lars; Quandt, Andreas; Brauer, Hendrik; Sturm, Marc; Kenar, Erhan; Kohlbacher, Oliver; Aebersold, Ruedi; Malmström, Lars	J Proteome Res (2013) 12(4):1628-44 - Impact: 5.0 - Citations: 181 - DOI: 10.1021/pr300992u
34: Business intelligence strategies enables rapid analysis of quantitative proteomics data Malmström, Lars; Nordenfelt, Pontus; Malmström, Johan	Journal of Proteome Science and Computational Biology (2012) 1:5 - Impact: 0.0 - Citations: 6 - DOI: 10.7243/2050-2273-1-5
33: Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes. Karlsson, Christofer; Malmström, Lars; Aebersold, Ruedi; Malmström, Johan	Nat Commun (2012) 3:1301 - Impact: 10.02 - Citations: 76 - DOI: 10.1038/ncomms2297
32: Structural probing of a protein phosphatase 2A network by chemical cross-linking and mass spectrometry. Herzog, Franz; Kahraman, Abdullah; Boehringer, Daniel; Mak, Raymond; Bracher, Andreas; Walzthoeni, Thomas; Leitner, Alexander; Beck, Martin; Hartl, Franz-Ulrich; Ban, Nenad; Malmström, Lars; Aebersold, Ruedi	Science (2012) 337:1348-52 - Impact: 31.03 - Citations: 441 - DOI: 10.1126/science.1221483
31: Splicosomal and serine and arginine-rich splicing factors as targets for TGF-beta. Hallgren, Oskar; Malmström, Johan; Malmström, Lars; Andersson-Sjöland, Annika; Wildt, Marie; Tufvesson, Ellen; Juhasz, Peer; Marko-Varga, Gyorgy; Westergren-Thorsson, Gunilla	Fibrogenesis Tissue Repair (2012) 5:6 - Impact: 2.97 - Citations: 16 - DOI: 10.1186/1755-1536-5-6
30: A computational tool to detect and avoid redundancy in selected reaction monitoring. Rost, Hannes; Malmström, Lars; Aebersold, Ruedi	Mol Cell Proteomics (2012) 11:540-9 - Impact: 7.25 - Citations: 114 - DOI: 10.1074/mcp.M111.013045
29: Automated workflow for large-scale Selected Reaction Monitoring experiments. Malmström, Lars; Malmström, Johan; Selevsek, Nathalie; Rosenberger, George; Aebersold, Ruedi	J Proteome Res (2012) 11:1644-53 - Impact: 5.06 - Citations: 27 - DOI: 10.1021/pr200844d
28: openBIS: a flexible framework for managing and analyzing complex data in biology research. Bauch, Angela; Adamczyk, Izabela; Buczek, Piotr; Elmer, Franz-Josef; Enimanev, Kaloyan; Glyzewski, Pawel; Kohler, Manuel; Pylak, Tomasz; Quandt, Andreas; Ramakrishnan, Chandrasekhar; Beisel, Christian; Malmström, Lars; Aebersold, Ruedi; Rinn, Bernd	BMC Bioinformatics (2011) 12:468 - Impact: 2.75 - Citations: 155 - DOI: 10.1186/1471-2105-12-468
27: Streptococcus pyogenes in human plasma: adaptive mechanisms analyzed by mass spectrometry based proteomics. Malmström, Johan; Karlsson, Christofer; Nordenfelt, Pontus; Ossola, Reto; Weisser, Hendrik; Quandt, Andreas; Hansson, Karin; Aebersold, Ruedi; Malmström, Lars; Bjorck, Lars	J Biol Chem (2011) 287:1415-25 - Impact: 4.77 - Citations: 51 - DOI: 10.1074/jbc.M111.267674
26: Accelerating 3D Protein Modeling Using Cloud Computing Kunszt, Peter; Malmström, Lars; Fantini, Nicola; Subholt, Wibke; Lautenschlager, Marcel; Reifler, Roland; Ruckstuhl, Stefan	Seventh IEEE International Conference on e-Science Workshops (2011) 2011:166-169 - Impact: 0.0 - Citations: 5 - DOI: 10.1109/eScienceW.2011.12
25: The proteome folding project: Proteome-scale prediction of structure and function. Drew, Kevin; Winters, Patrick; Butterfoss, Glenn; Berstis, Viktors; Uplinger, Keith; Armstrong, Jonathan; Riffle, Michael; Schweighofer, Erik; Bovermann, Bill; Goodlett, David; Davis, Trisha; Shasha, Dennis; Malmström, Lars; Bonneau, Richard	Genome Res (2011) 21:1981-94 - Impact: 13.61 - Citations: 52 - DOI: 10.1101/gr.121475.111
24: Xwalk: Computing and Visualizing Distances in Cross-linking Experiments. Kahraman, Abdullah; Malmström, Lars; Aebersold, Ruedi	Bioinformatics (2011) 27:2163-4 - Impact: 5.47 - Citations: 161 - DOI: 10.1093/bioinformatics/btr348
23: The Swiss Grid Proteomics Portal Kunszt, Peter; Espona Pernas, Lucia; Quandt, Andreas; Schmid, Emanuel; Hunt, Ela; Malmström, Lars	Proceedings of the Second International Conference on Parallel, Distributed, Grid and Cloud Computing for Engineering (2011) 95:81 - Impact: 0.0 - Citations: 4 - DOI: 10.4203/ccp.95.81
22: The path to preservation: Using proteomics to decipher the fate of diatom proteins during microbial degradation Nunn, Brook; Ting, Ying; Malmström, Lars; Tsai, Yihsuan; Squier, Angela; Goodlett, David; Harvey, H	Limnol. Oceanogr. (2010) 55:1790-1804 - Impact: 3.38 - Citations: 25 - DOI: 10.4319/lo.2010.55.4.1790
21: Proteomics analysis of liver pathological calcification suggests a role for the IQ motif containing GTPase activating protein 1 in myofibroblast function Kalantari, Fariba; Auguste, Patrick; Ziafazeli, Tahereh; Tzimas, George; Malmström, Lars; Bioulac-Sage, Paulette; Boismenu, Daniel; Vali, Hojatollah; Chevet, E	PROTEOMICS - Clinical Applications (2009) 3:307-321 - Impact: 1.88 - Citations: 3 - DOI: 10.1002/prca.200780133
20: Deciphering diatom biochemical pathways via whole-cell proteomics. Nunn, Brook; Aker, Jocelyn; Shaffer, Scott; Tsai, Shannon; Strzepek, Robert; Boyd, Philip; Freeman, Theodore; Brittnacher, Mitchell; Malmström, Lars; Goodlett, David	Aquat Microb Ecol (2009) 55:241-253 - Impact: 2.19 - Citations: 65 - DOI: 10.3354/ame01284
19: On the use of hydrogen/deuterium exchange mass spectrometry data to improve de novo protein structure prediction. Malmström, Lars; Hou, Liming; Atkins, William; Goodlett, David	Rapid Commun Mass Spectrom (2009) 23:459-461 - Impact: 2.69 - Citations: 3 - DOI: 10.1002/rcm.3882
18: Identification of secreted glycoproteins of human prostate and bladder stromal cells by comparative quantitative proteomics. Goo, Young; Liu, Alvin; Ryu, Soyoung; Shaffer, Scott; Malmström, Lars; Page, Laura; Nguyen, Liem; Doneanu, Catalin; Goodlett, David	Prostate (2009) 69:49-61 - Impact: 3.08 - Citations: 33 - DOI: 10.1002/pros.20853
17: Identification of the active site of DS-epimerase 1 and requirement of N-glycosylation for enzyme function. Pacheco, Benny; Maccarana, Marco; Goodlett, David; Malmström, Anders; Malmström, Lars	J Biol Chem (2009) 284:1741-7 - Impact: 5.33 - Citations: 41 - DOI: 10.1074/jbc.M805479200
16: Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. Das, Rhiju; Qian, Bin; Raman, Srivatsan; Vernon, Robert; Thompson, James; Bradley, Philip; Khare, Sagar; Tyka, Michael; Bhat, Divya; Chivian, Dylan; Kim, David; Sheffler, William; Malmström, Lars; Wollacott, Andrew; Wang, Chu; Andre, Ingemar; Baker, David	Proteins (2007) 1:118-128 - Impact: 3.42 - Citations: 274 - DOI: 10.1002/prot.21636
15: Superfamily Assignments for the Yeast Proteome through Integration of Structure Prediction with the Gene Ontology. Malmström, Lars; Riffle, Michael; Strauss, Charlie; Chivian, Dylan; Davis, Trisha; Bonneau, Richard; Baker, David	PLoS Biol (2007) 5:e76 - Impact: 12.68 - Citations: 70 - DOI: 10.1371/journal.pbio.0050076
14: The importance of fibroblasts in remodelling of the human uterine cervix during pregnancy and parturition. Malmström, Erik; Sennström, Maria; Holmberg, Anna; Frielingsdorf, Helena; Eklund, Erik; Malmström, Lars; Tufvesson, Ellen; Gomez, Maria; Westergren-Thorsson, Gunilla; Ekman-Ordeberg, Gunvor; Malmström, Anders	Mol Hum Reprod (2007) 13:333-41 - Impact: 2.54 - Citations: 74 - DOI: 10.1093/molehr/gal117
13: 2DDB - a bioinformatics solution for analysis of quantitative proteomics data. Malmström, Lars; Marko-Varga, György; Westergren-Thorsson, Gunilla; Laurell, Thomas; Malmström, Johan	BMC Bioinformatics (2006) 7:158 - Impact: 3.78 - Citations: 24 - DOI: 10.1186/1471-2105-7-158
12: Proteomics: A new research area for the biomedical field Malmström, Johan; Malmström, Lars; Marko-Varga, Gyorgy	Journal of Organ Dysfunction (2005) 1:83-94 - Impact: 0.0 - Citations: 8 - DOI: 10.1080/17471060500223910
11: Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM. Kim, David; Chivian, Dylan; Malmström, Lars; Baker, David	Proteins (2005) Suppl 7:193-200 - Impact: 3.42 - Citations: 114 - DOI: 10.1002/prot.20737
10: Prediction of CASP6 structures using automated Robetta protocols. Chivian, Dylan; Kim, David; Malmström, Lars; Schonbrun, Jack; Rohl, Carol; Baker, David	Proteins (2005) Suppl 7:157-66 - Impact: 3.42 - Citations: 197 - DOI: 10.1002/prot.20733
9: Free modeling with Rosetta in CASP6. Bradley, Philip; Malmström, Lars; Qian, Bin; Schonbrun, Jack; Chivian, Dylan; Kim, David; Meiler, Jens; Misura, Kira; Baker, David	Proteins (2005) Suppl 7:128-34 - Impact: 3.42 - Citations: 200 - DOI: 10.1002/prot.20729
8: The yeast resource center public data repository. Riffle, Michael; Malmström, Lars; Davis, Trisha	Nucleic Acids Res (2005) 33:D378-82 - Impact: 6.88 - Citations: 43 - DOI: 10.1093/nar/gki073
7: Quality Assessment of Low Free-Energy Protein Structure Predictions Cazzanti, Luca; Gupta, Maya; Malmström, Lars; Baker, David	Machine Learning for Signal Processing (2005) 2005:375-380 - Impact: 0.0 - Citations: 3 - DOI: 10.1109/MLSP.2005.1532932
6: Proteome annotations and identifications of the human pulmonary fibroblast. Malmström, Johan; Larsen, Kristoffer; Malmström, Lars; Tufvesson, Ellen; Parker, Ken; Marchese, Jason; Williamson, Brian; Hattan, Steve; Patterson, Dale; Martin, Steve; Graber, Armin; Juhasz, H; Westergren-Thorsson, Gunilla; Marko-Varga, György	J Proteome Res (2004) 3:525-37 - Impact: 5.68 - Citations: 42 - DOI: 10.1021/pr034104v
5: Assigning function to yeast proteins by integration of technologies. Hazbun, Tony; Malmström, 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	Mol Cell (2003) 12:1353-65 - Impact: 16.84 - Citations: 335 - DOI: 10.1016/s1097-2765(03)00476-3
4: Nanocapillary liquid chromatography interfaced to tandem matrix-assisted laser desorption/ionization and electrospray ionization-mass spectrometry: Mapping the nuclear proteome of human fibroblasts. Malmström, Johan; Larsen, Kristoffer; Malmström, Lars; Tufvesson, Ellen; Parker, Ken; Marchese, Jason; Williamson, Brian; Patterson, Dale; Martin, Steve; Juhasz, Peter; Westergren-Thorsson, Gunilla; Marko-Varga, György	Electrophoresis (2003) 24:3806-14 - Impact: 3.51 - Citations: 35 - DOI: 10.1002/elps.200305619
3: Automated prediction of CASP-5 structures using the Robetta server. Chivian, Dylan; Kim, David; Malmström, Lars; Bradley, Philip; Robertson, Timothy; Murphy, Paul; Strauss, Charles; Bonneau, Richard; Rohl, Carol; Baker, David	Proteins (2003) 53:524-33 - Impact: 3.42 - Citations: 369 - DOI: 10.1002/prot.10529
2: Proteomic 2DE database for spot selection, automated annotation, and data analysis. Malmström, Lars; Malmström, Johan; Marko-Varga, György; Westergren-Thorsson, Gunilla	J Proteome Res (2002) 1:135-8 - Impact: 5.68 - Citations: 23 - DOI: 10.1021/pr010004i
1: De Novo Prediction of Three-dimensional Structures for Major Protein Families. Bonneau, Richard; Strauss, Charlie; Rohl, Carol; Chivian, Dylan; Bradley, Phillip; Malmström, Lars; Robertson, Tim; Baker, David	J Mol Biol (2002) 322:65 - Impact: 4.15 - Citations: 329 - DOI: 10.1016/s0022-2836(02)00698-8