Publications
| Authors and Title | Details |
|---|---|
87: Multimodal Mass Spectrometry Identifies a Conserved Protective Epitope in S. pyogenes Streptolysin O Tang, Di; Gueto-Tettay, Carlos; Hjortswang, Elisabeth; Ströbaek, Joel; Ekström, Simon; Happonen, Lotta; Malmström, Lars; Malmström, Johan |
Anal Chem (2024) 0(0):0 |
Izadi, Arman; Karami, Yasaman; Bratanis, Eleni; Wrighton, Sebastian; Khakzad, Hamed; Nyblom, Maria; Olofsson, Berit; Happonen, Lotta; Tang, Di; Sundwall,Martin; Godzwon, Magdalena; Chao, Yashuan; Gomez Toledo, Alejandro; Schmidt, Tobias; Ohlin, Mats; Nilges, Michael; Malmström, Johan; Bahnan, Wael; Shannon, Oonagh; Malmström, Lars; Nordenfelt, Pontus |
Nat Commun (2024) 15(1):3600 |
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 |
Hartman, Erik; Scott, Aaron; Karlsson, Christofer; Mohanty, Tirthankar; Vaara, Suvi; Linder, Adam; Malmström, Lars; Malmström, Johan |
Nature communications (2023) 14(1):5359 |
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 |
Scott, Aaron M; Karlsson, Christofer; Mohanty, Tirthankar; Hartman, Erik; Vaara, Suvi T; Linder, Adam; Malmström, Johan; Malmström, Lars |
Communications biology (2023) 6(1):628' |
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 |
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: |
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: |
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: |
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: |
Khakzad, Hamed; Vermeul, Swen; Malmström, Lars |
J Vis Exp (2021) -1: |
Chowdhury, Sounak; Khakzad, Hamed; Bergdahl, Gizem; Lood, Rolf; Ekstrom, Simon; Linke, Dirk; Malmström, Lars; Happonen, Lotta; Malmström, Johan |
mSystems (2021) -1:e0027121 |
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 |
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 |
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 |
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 |
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 |
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: |
Duguet, Thomas; Soichot, Julien; Kuzyakiv, Rostyslav; Malmström, Lars; Tritten, Lucienne |
Front Cell Infect Microbiol (2020) 10:217 |
67: Computational Proteomics with Jupyter and Python Malmstrom, L |
Methods Mol Biol (2019) 1977:4-15 |
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 |
65: Greedy de novo motif discovery to construct motif repositories for bacterial proteomes. Khakzad, Hamed; Malmström, Johan; Malmström, Lars |
BMC Bioinformatics (2019) 20:141 |
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 |
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 |
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 |
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 |
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 |
Sjöholm, Kristoffer; Kilsgård, Ola; Teleman, Johan; Happonen, Lotta; Malmström, Lars; Malmström, Johan |
Mol Cell Proteomics (2017) 16(4 suppl 1):S29-S41 |
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 |
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 |
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 |
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 |
Malmström, Erik; Kilsgård, Ola; Hauri, Simon; Smeds, Emanuel; Herwald, Heiko; Malmström, Lars; Malmström, Johan |
Nat Commun (2016) 7:10261 |
53: Reproducible quantitative proteotype data matrices for systems biology. Röst, Hannes; Malmström, Lars; Aebersold, Ruedi |
Mol Biol Cell (2015) 26:3926-31 |
Walzthoeni, Thomas; Joachimiak, Lukasz; Rosenberger, George; Röst, Hannes; Malmström, Lars; Leitner, Alexander; Frydman, Judith; Aebersold, Ruedi |
Nat Methods (2015) 12(12):1185-90 |
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 |
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 |
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 |
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 |
47: Efficient visualization of high-throughput targeted proteomics experiments: TAPIR. Röst, Hannes; Rosenberger, George; Aebersold, Ruedi; Malmström, Lars |
Bioinformatics (2015) 31(14):2415-7 |
46: The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. |
Nucleic Acids Res (2015) 44(D1):D27-37 |
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 |
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 |
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 |
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 |
Rosenberger, George; Ludwig, Christina; Röst, Hannes; Aebersold, Ruedi; Malmström, Lars |
Bioinformatics (2014) 30(17):2511-3 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
24: Xwalk: Computing and Visualizing Distances in Cross-linking Experiments. Kahraman, Abdullah; Malmström, Lars; Aebersold, Ruedi |
Bioinformatics (2011) 27:2163-4 |
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 |
Nunn, Brook; Ting, Ying; Malmström, Lars; Tsai, Yihsuan; Squier, Angela; Goodlett, David; Harvey, H |
Limnol. Oceanogr. (2010) 55:1790-1804 |
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 |
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 |
Malmström, Lars; Hou, Liming; Atkins, William; Goodlett, David |
Rapid Commun Mass Spectrom (2009) 23:459-461 |
Goo, Young; Liu, Alvin; Ryu, Soyoung; Shaffer, Scott; Malmström, Lars; Page, Laura; Nguyen, Liem; Doneanu, Catalin; Goodlett, David |
Prostate (2009) 69:49-61 |
Pacheco, Benny; Maccarana, Marco; Goodlett, David; Malmström, Anders; Malmström, Lars |
J Biol Chem (2009) 284:1741-7 |
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 |
Malmström, Lars; Riffle, Michael; Strauss, Charlie; Chivian, Dylan; Davis, Trisha; Bonneau, Richard; Baker, David |
PLoS Biol (2007) 5:e76 |
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 |
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 |
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 |
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 |
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 |
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 |
8: The yeast resource center public data repository. Riffle, Michael; Malmström, Lars; Davis, Trisha |
Nucleic Acids Res (2005) 33:D378-82 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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