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Authors and Title Details

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: 0
- DOI: 10.3389/fcimb.2020.00217

67: 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: 9
- DOI: 10.1038/s41467-019-10583-5

66: 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: 2
- DOI: 10.1186/s12859-019-2686-8

65: 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: 9
- DOI: 10.1038/s41467-018-07986-1

64: 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: 23
- DOI: 10.15252/embr.201745310

63: 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: 21
- DOI: 10.1016/j.jprot.2018.02.027

62: 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: 169
- DOI: 10.1038/nmeth.4473

61: 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: 58
- DOI: 10.1038/nbt.3908

60: 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: 15
- DOI: 10.1074/mcp.M116.063966

59: 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: 40
- DOI: 10.1093/nar/gkw1032

58: 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: 97
- DOI: 10.1038/nmeth.3954

57: 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: 218
- DOI: 10.1038/nmeth.3959

56: 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: 12
- DOI: 10.1039/C5SC03798K

55: 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: 57
- DOI: 10.1038/ncomms10261

54: 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: 33
- DOI: 10.1091/mbc.E15-07-0507

53: 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: 69
- DOI: 10.1038/nmeth.3631

52: 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: 23
- DOI: 10.1016/j.jprot.2015.09.012

51: 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: 42
- DOI: 10.1074/mcp.O114.042267

50: 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: 31
- DOI: 10.1021/acs.jproteome.5b00315

49: 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: 13
- DOI: 10.1371/journal.pone.0125108

48: 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: 9
- DOI: 10.1093/bioinformatics/btv152

47: The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases.

Nucleic Acids Res (2015) 44(D1):D27-37
- Impact: 8.81
- Citations: 22
- DOI: 10.1093/nar/gkv1310

46: 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: 10
- DOI: 10.1016/j.euprot.2014.10.001

45: 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: 64
- DOI: 10.1093/bioinformatics/btu686

44: 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: 4
- DOI: 10.1074/jbc.M114.565978

43: 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: 32
- DOI: 10.1002/cpe.3294

42: 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: 52
- DOI: 10.1093/bioinformatics/btu200

41: 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: 449
- DOI: 10.1038/nbt.2841

40: 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: 29
- DOI: 10.1074/mcp.O114.037879

39: 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: 56
- DOI: 10.1002/pmic.201300246

38: 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: 28
- DOI: 10.1111/mmi.12451

37: 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: 126
- DOI: 10.1371/journal.pone.0073411

36: Improving 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

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:-
- Impact: 0.0
- Citations: 2
- DOI: 10.1002/cpe.3294

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: 137
- 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: 5
- 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: 67
- 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: 352
- 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: 8
- 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: 88
- 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: 25
- 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: 94
- 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: 36
- 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: 40
- 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: 113
- 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: 21
- 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: 0
- 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: 54
- 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: 2
- 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: 28
- 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: 36
- 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: 246
- 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: 59
- 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: 60
- 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: 25
- 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: 102
- 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: 177
- 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: 177
- 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: 42
- 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: 37
- 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: 310
- 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: 34
- 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: 323
- 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: 19
- 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: 307
- DOI: 10.1016/s0022-2836(02)00698-8