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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: 0
- 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: 2
- 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: 2
- 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: 4
- 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: 41
- 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: 15
- 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: 546
- 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: 46
- 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: 52
- 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: 89
- 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: 66
- 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: 541
- 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: 26
- 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: 118
- 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: 184
- 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: 602
- 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: 105
- 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: 83
- 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: 50
- 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: 14
- 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: 8
- 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: 792
- 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: 51
- 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: 114
- 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: 180
- 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: 15
- 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: 112
- 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: 50
- 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: 160
- 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: 24
- 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: 32
- 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: 272
- 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: 73
- 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: 196
- 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: 199
- 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: 41
- 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: 367
- 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