Lars Malmström Institute for Computational Science University of Zurich Biography Publications Institution JoVE Articles Lars Malmström has not added a biography. If you are Lars Malmström and would like to personalize this page please email our Author Liaison for assistance. Publications Proteogenomic Workflow Reveals Molecular Phenotypes Related to Breast Cancer Mammographic Appearance Journal of Proteome Research. 05, 2021 | Pubmed ID: 33855848 Extracellular Vesicle-Contained MicroRNA of As a Tool to Decipher the Molecular Basis of Nematode Parasitism Frontiers in Cellular and Infection Microbiology. 2020 | Pubmed ID: 32523895 Macromolecular Modeling and Design in Rosetta: Recent Methods and Frameworks Nature Methods. 07, 2020 | Pubmed ID: 32483333 Publisher Correction: OpenSWATH Enables Automated, Targeted Analysis of Data-independent Acquisition MS Data Nature Biotechnology. 03, 2020 | Pubmed ID: 32094660 Structural Proteomics, Electron Cryo-microscopy and Structural Modeling Approaches in Bacteria-human Protein Interactions Medical Microbiology and Immunology. Jun, 2020 | Pubmed ID: 32072248 A Quantitative Streptococcus Pyogenes-human Protein-protein Interaction Map Reveals Localization of Opsonizing Antibodies Nature Communications. 06, 2019 | Pubmed ID: 31227708 Greedy De Novo Motif Discovery to Construct Motif Repositories for Bacterial Proteomes BMC Bioinformatics. Apr, 2019 | Pubmed ID: 30999854 Computational Proteomics with Jupyter and Python Methods in Molecular Biology (Clifton, N.J.). 2019 | Pubmed ID: 30980332 Rapid Determination of Quaternary Protein Structures in Complex Biological Samples Nature Communications. 01, 2019 | Pubmed ID: 30643114 Comprehensive ADP-ribosylome Analysis Identifies Tyrosine As an ADP-ribose Acceptor Site EMBO Reports. 08, 2018 | Pubmed ID: 29954836 Quantitative Proteomic Characterization of the Lung Extracellular Matrix in Chronic Obstructive Pulmonary Disease and Idiopathic Pulmonary Fibrosis Journal of Proteomics. 10, 2018 | Pubmed ID: 29501846 An Objective Comparison of Cell-tracking Algorithms Nature Methods. Dec, 2017 | Pubmed ID: 29083403 Inference and Quantification of Peptidoforms in Large Sample Cohorts by SWATH-MS Nature Biotechnology. Aug, 2017 | Pubmed ID: 28604659 Targeted Proteomics and Absolute Protein Quantification for the Construction of a Stoichiometric Host-Pathogen Surface Density Model Molecular & Cellular Proteomics : MCP. 04, 2017 | Pubmed ID: 28183813 FAIRDOMHub: a Repository and Collaboration Environment for Sharing Systems Biology Research Nucleic Acids Research. 01, 2017 | Pubmed ID: 27899646 OpenMS: a Flexible Open-source Software Platform for Mass Spectrometry Data Analysis Nature Methods. Aug, 2016 | Pubmed ID: 27575624 TRIC: an Automated Alignment Strategy for Reproducible Protein Quantification in Targeted Proteomics Nature Methods. 09, 2016 | Pubmed ID: 27479329 Deciphering the Mode of Action of the Processive Polysaccharide Modifying Enzyme Dermatan Sulfate Epimerase 1 by Hydrogen-Deuterium Exchange Mass Spectrometry Chemical Science. Feb, 2016 | Pubmed ID: 26900446 Large-scale Inference of Protein Tissue Origin in Gram-positive Sepsis Plasma Using Quantitative Targeted Proteomics Nature Communications. Jan, 2016 | Pubmed ID: 26732734 Reproducible Quantitative Proteotype Data Matrices for Systems Biology Molecular Biology of the Cell. Nov, 2015 | Pubmed ID: 26543201 XTract: Software for Characterizing Conformational Changes of Protein Complexes by Quantitative Cross-linking Mass Spectrometry Nature Methods. Dec, 2015 | Pubmed ID: 26501516 Quantitative Proteogenomics of Human Pathogens Using DIA-MS Journal of Proteomics. Nov, 2015 | Pubmed ID: 26381203 Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-independent Acquisition Mass Spectrometry Molecular & Cellular Proteomics : MCP. Oct, 2015 | Pubmed ID: 26199342 Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry PloS One. 2015 | Pubmed ID: 25927999 Efficient Visualization of High-throughput Targeted Proteomics Experiments: TAPIR Bioinformatics (Oxford, England). Jul, 2015 | Pubmed ID: 25788625 DIANA--algorithmic Improvements for Analysis of Data-independent Acquisition MS Data Bioinformatics (Oxford, England). Feb, 2015 | Pubmed ID: 25348213 ALFQ: an R-package for Estimating Absolute Protein Quantities from Label-free LC-MS/MS Proteomics Data Bioinformatics (Oxford, England). Sep, 2014 | Pubmed ID: 24753486 OpenSWATH Enables Automated, Targeted Analysis of Data-independent Acquisition MS Data Nature Biotechnology. Mar, 2014 | Pubmed ID: 24727770 PyOpenMS: a Python-based Interface to the OpenMS Mass-spectrometry Algorithm Library Proteomics. Jan, 2014 | Pubmed ID: 24420968 Cross-link Guided Molecular Modeling with ROSETTA PloS One. 2013 | Pubmed ID: 24069194 Proteome-wide Selected Reaction Monitoring Assays for the Human Pathogen Streptococcus Pyogenes Nature Communications. 2012 | Pubmed ID: 23250431 A Computational Tool to Detect and Avoid Redundancy in Selected Reaction Monitoring Molecular & Cellular Proteomics : MCP. Aug, 2012 | Pubmed ID: 22535207 Streptococcus Pyogenes in Human Plasma: Adaptive Mechanisms Analyzed by Mass Spectrometry-based Proteomics The Journal of Biological Chemistry. Jan, 2012 | Pubmed ID: 22117078 OpenBIS: a Flexible Framework for Managing and Analyzing Complex Data in Biology Research BMC Bioinformatics. Dec, 2011 | Pubmed ID: 22151573 Quaternary Structure Modeling Through Chemical Cross-Linking Mass Spectrometry: Extending TX-MS Jupyter Reports Hamed Khakzad1,2, Swen Vermeul3, Lars Malmström4,5,6 1Equipe Signalisation Calcique et Infections Microbiennes, Ecole Normale Supérieure Paris-Saclay, 2Institut National de la Santé et de la Recherche Médicale, 3Scientific IT Services, ETH Zurich, 4Institute for Computational Science, University of Zurich, 5S3IT, University of Zurich, 6Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University JoVE 60311 Biochemistry
Quaternary Structure Modeling Through Chemical Cross-Linking Mass Spectrometry: Extending TX-MS Jupyter Reports Hamed Khakzad1,2, Swen Vermeul3, Lars Malmström4,5,6 1Equipe Signalisation Calcique et Infections Microbiennes, Ecole Normale Supérieure Paris-Saclay, 2Institut National de la Santé et de la Recherche Médicale, 3Scientific IT Services, ETH Zurich, 4Institute for Computational Science, University of Zurich, 5S3IT, University of Zurich, 6Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University JoVE 60311 Biochemistry
