L. Malmström

发表

xTract: software for characterizing conformational changes of protein complexes by quantitative cross-linking mass spectrometry

Lars Malmström, Ruedi Aebersold, Hannes L Röst, 2015, Nature Methods.

Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics

Hamed Khakzad, J. Malmström, L. Happonen, 2022, bioRxiv.

A pharmacoproteomic landscape of organotypic intervention responses in Gram-negative sepsis

V. Nizet, J. Malmström, C. Karlsson, 2022, bioRxiv.

A human monoclonal antibody bivalently binding two different epitopes in streptococcal M protein protects against infection

L. Björck, Hamed Khakzad, J. Malmström, 2022, bioRxiv.

Protection induced by a human monoclonal antibody recognizing two different epitopes in a conserved region of streptococcal M proteins

L. Björck, Hamed Khakzad, J. Malmström, 2021 .

Bacterial clearance caused by a single anti-M protein antibody simultaneously binding two separate epitopes

L. Björck, Hamed Khakzad, J. Malmström, 2021 .

The importance of fibroblasts in remodelling of the human uterine cervix during pregnancy and parturition.

E. Eklund, A. Malmström, A. Holmberg, 2007, Molecular human reproduction.

A divergent Pseudomonas aeruginosa palmitoyltransferase essential for cystic fibrosis‐specific lipid A

Samuel I. Miller, D. Goodlett, D. Rasko, 2014, Molecular microbiology.

Structural determination of Streptococcus pyogenes M1 protein interactions with human immunoglobulin G using integrative structural biology

M. Nilges, Yasaman Karami, Hamed Khakzad, 2020, bioRxiv.

Streptococcus pyogenes in Human Plasma

Andreas Quandt, Lars Malmström, Ruedi Aebersold, 2011, The Journal of Biological Chemistry.

The path to preservation: Using proteomics to decipher the fate of diatom proteins during microbial degradation

Ying S. Ting, B. Nunn, D. Goodlett, 2010 .

Genome-wide structural and functional protein characterization by ab initio protein structure prediction

Lars Malmström, L. Malmström, 2005 .

Assigning function to yeast proteins by integration of technologies.

Brian E Snydsman, D. Baker, S. Fields, 2003, Molecular cell.

Deciphering diatom biochemical pathways via whole-cell proteomics.

B. Nunn, D. Goodlett, Lars Malmström, 2009, Aquatic microbial ecology : international journal.

Automated prediction of CASP‐5 structures using the Robetta server

Lars Malmström, David Baker, Timothy Robertson, 2003, Proteins.

Deciphering the mode of action of the processive polysaccharide modifying enzyme dermatan sulfate epimerase 1 by hydrogen–deuterium exchange mass spectrometry

J. Zaia, Lars Malmström, A. Malmström, 2015, Chemical science.

De novo prediction of three-dimensional structures for major protein families.

Richard Bonneau, D. Baker, C. Strauss, 2002, Journal of molecular biology.

OpenMS: a flexible open-source software platform for mass spectrometry data analysis

K. Reinert, R. Aebersold, O. Kohlbacher, 2016, Nature Methods.

Extracellular Vesicle-Contained microRNA of C. elegans as a Tool to Decipher the Molecular Basis of Nematode Parasitism

Lars Malmström, T. Duguet, R. Kuzyakiv, 2020, Frontiers in Cellular and Infection Microbiology.

Improving the Swiss Grid Proteomics Portal: Requirements and new Features based on Experience and Usability Considerations

Lorenz Blum, Béla Hullár, Emanuel Schmid, 2013, IWSG.

Streptococcus pyogenes Forms Serotype- and Local Environment-Dependent Interspecies Protein Complexes

Hamed Khakzad, D. Linke, J. Malmström, 2021, mSystems.

Streptococcus pyogenes forms serotype and local environment-dependent inter-species protein complexes

Hamed Khakzad, D. Linke, J. Malmström, 2021, bioRxiv.

Targeted Proteomics and Absolute Protein Quantification for the Construction of a Stoichiometric Host-Pathogen Surface Density Model*

Lars Malmström, Johan Teleman, Johan Malmström, 2017, Molecular & Cellular Proteomics.

“A Proteogenomic workflow reveals distinct molecular phenotypes related to breast cancer appearance”

Paul Theodor Pyl, S. Klasson, Lars Malmström, 2020, bioRxiv.

Identification of secreted glycoproteins of human prostate and bladder stromal cells by comparative quantitative proteomics

D. Goodlett, Lars Malmström, S. Shaffer, 2009, The Prostate.

Cerebrospinal fluid proteome maps detect pathogen-specific host response patterns in meningitis

Paul Theodor Pyl, Lars Malmström, J. Malmström, 2020, bioRxiv.

Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes

Lars Malmström, Ruedi Aebersold, Johan Malmström, 2012, Nature Communications.

Quantitative proteomics of microbes: Principles and applications to virulence

Lars Malmström, Ruedi Aebersold, Johan Malmström, 2011, Proteomics.

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Brian D. Weitzner, Lars Malmström, Karen R. Khar, 2020, Nature Methods.

Structural Probing of a Protein Phosphatase 2A Network by Chemical Cross-Linking and Mass Spectrometry

R. Aebersold, Raymond H. Mak, F. Hartl, 2012, Science.

Greedy de novo motif discovery to construct motif repositories for bacterial proteomes

Lars Malmström, Johan Malmström, Hamed Khakzad, 2019, BMC Bioinformatics.

aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data

Lars Malmström, Ruedi Aebersold, George Rosenberger, 2014, Bioinform..

Automated workflow for large-scale selected reaction monitoring experiments.

Lars Malmström, Ruedi Aebersold, Nathalie Selevsek, 2012, Journal of proteome research.

Spike-Dependent Opsonization Indicates Both Dose-Dependent Inhibition of Phagocytosis and That Non-Neutralizing Antibodies Can Confer Protection to SARS-CoV-2

Hamed Khakzad, L. Happonen, W. Bahnan, 2022, Frontiers in Immunology.

The Yeast Resource Center Public Data Repository

Lars Malmström, Michael Riffle, Trisha N. Davis, 2004, Nucleic Acids Res..

Splicosomal and serine and arginine-rich splicing factors as targets for TGF-β

J. Malmström, G. Marko‐Varga, P. Juhasz, 2012, Fibrogenesis & tissue repair.

The Proteome Folding Project: proteome-scale prediction of structure and function.

Lars Malmström, Richard Bonneau, Trisha N Davis, 2011, Genome research.

Superfamily Assignments for the Yeast Proteome through Integration of Structure Prediction with the Gene Ontology

Richard Bonneau, D. Baker, C. Strauss, 2007, PLoS biology.

Functional and Structural Properties of a Novel Protein and Virulence Factor (Protein sHIP) in Streptococcus pyogenes *

L. Björck, M. Varjosalo, George A. Rosenberger, 2014, The Journal of Biological Chemistry.

, Streptococcus pyogenes ( Protein sHIP ) in Novel Protein and Virulence Factor Functional and Structural Properties of a Microbiology

Lars Malmström, L. Björck, M. Varjosalo, 2014 .

A tool for the automated, targeted analysis of data-independent acquisition MS-data: OpenSWATH

Ben C. Collins, Olga T. Schubert, Saša M. Miladinović, 2014 .

An automated pipeline for high-throughput label-free quantitative proteomics.

Andreas Quandt, Lars Malmström, Ruedi Aebersold, 2013, Journal of proteome research.

FAIRDOMHub: a repository and collaboration environment for sharing systems biology research

Bernd Rinn, Lars Malmström, Carole A. Goble, 2016, Nucleic Acids Res..

Cross-Link Guided Molecular Modeling with ROSETTA

Lars Malmström, Ruedi Aebersold, Alexander Leitner, 2013, PloS one.

Xwalk: computing and visualizing distances in cross-linking experiments

Lars Malmström, Ruedi Aebersold, Abdullah Kahraman, 2011, Bioinform..

TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics

Lars Malmström, Giuseppe Testa, Ruedi Aebersold, 2016, Nature Methods.

Quantitative proteogenomics of human pathogens using DIA-MS.

Lars Malmström, Johan Malmström, Henrik Lantz, 2015, Journal of proteomics.

openBIS: a flexible framework for managing and analyzing complex data in biology research

Bernd Rinn, Franz-Josef Elmer, Chandrasekhar Ramakrishnan, 2011, BMC Bioinformatics.

Proteogenomic Workflow Reveals Molecular Phenotypes Related to Breast Cancer Mammographic Appearance

Paul Theodor Pyl, S. Klasson, J. Malmström, 2021, Journal of proteome research.

Comprehensive ADP‐ribosylome analysis identifies tyrosine as an ADP‐ribose acceptor site

Lars Malmström, M. Hottiger, Kapila Gunasekera, 2018, EMBO reports.

Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS

Lars Malmström, Ruedi Aebersold, Hannes L Röst, 2017, Nature Biotechnology.

Large-scale inference of protein tissue origin in gram-positive sepsis plasma using quantitative targeted proteomics

Lars Malmström, Johan Malmström, Erik Malmström, 2016, Nature Communications.

DIANA - algorithmic improvements for analysis of data-independent acquisition MS data

Lars Malmström, Fredrik Levander, Johan Teleman, 2015, Bioinform..

Numerical Compression Schemes for Proteomics Mass Spectrometry Data*

Lars Malmström, Fredrik Levander, Johan Teleman, 2014, Molecular & Cellular Proteomics.

The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases

Oliver Horlacher, Damian Szklarczyk, Christian von Mering, 2015, Nucleic Acids Res..

Generalized peakgroup scoring boosts identification rates and accuracy in mass spectrometry based discovery proteomics

J. Malmström, S. Vaara, C. Karlsson, 2022, bioRxiv.

Quantitative proteomic characterization of the lung extracellular matrix in chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis.

J. Malmström, A. Malmström, E. Åhrman, 2018, Journal of proteomics.

Structure prediction for CASP7 targets using extensive all‐atom refinement with Rosetta@home

Lars Malmström, David Baker, Dylan Chivian, 2007, Proteins.

Free modeling with Rosetta in CASP6

David E. Kim, P. Bradley, K. Misura, 2005, Proteins.

Proteomics: A new research area for the biomedical field

Lars Malmström, J. Malmström, G. Marko‐Varga, 2005 .

Identification of the Active Site of DS-epimerase 1 and Requirement of N-Glycosylation for Enzyme Function*

D. Goodlett, A. Malmström, M. Maccarana, 2009, Journal of Biological Chemistry.

Supplementary material to “TRIC: An automated alignment strategy to obtain comprehensive data matrices in targeted proteomics data”

Ben C. Collins, R. Aebersold, H. Röst, 2016 .

Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry

Lars Malmström, Ruedi Aebersold, Uwe Schmitt, 2015, PloS one.

Business intelligence strategies enables rapid analysis of quantitative proteomics data

Lars Malmström, Johan Malmström, Pontus Nordenfelt, 2012 .

Bioinformatic challenges in targeted proteomics.

Lars Malmström, Daniel Reker, D. Reker, 2012, Journal of proteome research.

A Computational Tool to Detect and Avoid Redundancy in Selected Reaction Monitoring

Lars Malmström, Ruedi Aebersold, Hannes Röst, 2012, Molecular & Cellular Proteomics.

PROTEINS: Structure, Function, and Bioinformatics Suppl 7:193–200 (2005) Automated Prediction of Domain Boundaries in CASP6 Targets Using Ginzu and RosettaDOM

Lars Malmström, David Baker, Dylan Chivian, 2022 .

Proteomics analysis of liver pathological calcification suggests a role for the IQ motif containing GTPase activating protein 1 in myofibroblast function

H. Vali, P. Bioulac-Sage, D. Boismenu, 2009, Proteomics. Clinical applications.

pyOpenMS: A Python‐based interface to the OpenMS mass‐spectrometry algorithm library

Lars Malmström, Ruedi Aebersold, Hannes L Röst, 2014, Proteomics.

A quantitative Streptococcus pyogenes–human protein–protein interaction map reveals localization of opsonizing antibodies

Lars Malmström, L. Björck, Hamed Khakzad, 2019, Nature Communications.

The structure of human dermatan sulfate epimerase 1 emphasizes the importance of C5-epimerization of glucuronic acid in higher organisms† †Electronic supplementary information (ESI) available. See DOI: 10.1039/d0sc05971d

Lars Malmström, Hamed Khakzad, J. Malmström, 2020, Chemical science.

Reproducible quantitative proteotype data matrices for systems biology

R. Aebersold, Lars Malmström, H. Röst, 2015, Molecular biology of the cell.

Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-independent Acquisition Mass Spectrometry*

Lars Malmström, Ruedi Aebersold, Dario Amodei, 2015, Molecular & Cellular Proteomics.

Proteome annotations and identifications of the human pulmonary fibroblast.

Lars Malmström, Kristoffer Larsen, Johan Malmström, 2004, Journal of proteome research.

Prediction of CASP6 structures using automated robetta protocols

Lars Malmström, David Baker, Dylan Chivian, 2005, Proteins.

ipaA triggers vinculin oligomerization to strengthen cell adhesion during Shigella invasion

Hamed Khakzad, M. Fontecave, N. Quenech’du, 2019 .

Vinculin targeting by Shigella IpaA promotes stable cell adhesion independent of mechanotransduction

Lars Malmström, Hamed Khakzad, M. Fontecave, 2019, bioRxiv.

A Combined Shotgun and Targeted Mass Spectrometry Strategy for Breast Cancer Biomarker Discovery.

R. Aebersold, Lars Malmström, O. Rinner, 2015, Journal of proteome research.

Structural proteomics, electron cryo-microscopy and structural modeling approaches in bacteria–human protein interactions

Hamed Khakzad, J. Malmström, Sounak Chowdhury, 2020, Medical Microbiology and Immunology.

Using synthetic peptides to benchmark peptide identification software and search parameters for MS/MS data analysis

Peter Z. Kunszt, Lars Malmström, Ákos Balaskó, 2014 .

Protein structure modeling.

Lars Malmström, David R Goodlett, D. Goodlett, 2010, Methods in molecular biology.

In vivo Cross-Linking MS of the Complement System MAC Assembled on Live Gram-Positive Bacteria

Lars Malmström, Hamed Khakzad, J. Malmström, 2021, Frontiers in Genetics.

Rapid determination of quaternary protein structures in complex biological samples

Hamed Khakzad, J. Malmström, Simon Hauri, 2019, Nature Communications.

2DDB – a bioinformatics solution for analysis of quantitative proteomics data

Lars Malmström, Thomas Laurell, György Marko-Varga, 2006, BMC Bioinformatics.

Publisher Correction: OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data

Ludovic C. Gillet, Ben C. Collins, Olga T. Schubert, 2020, Nature Biotechnology.

Efficient visualization of high-throughput targeted proteomics experiments: TAPIR

Lars Malmström, Ruedi Aebersold, George Rosenberger, 2015, Bioinform..

Computational Proteomics with Jupyter and Python.

Lars Malmström, L. Malmström, 2019, Methods in molecular biology.

Rapid determination of quaternary protein structures in complex biological samples

Lars Malmström, Johan Teleman, Johan Malmström, 2019, Nature Communications.

A Computational Tool to Detect and Avoid Redundancy in Selected Reaction Monitoring

R. Aebersold, H. Röst, L. Malmström, 2012, Molecular & Cellular Proteomics.

Structure prediction for CASP7 targets using extensive all‐atom refinement with Rosetta@home

Andrew M Wollacott, David E. Kim, Chu Wang, 2007, Proteins.

OpenMS: a flexible open-source software platform for mass spectrometry data analysis

K. Reinert, R. Aebersold, O. Kohlbacher, 2016, Nature Methods.

OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data

Ben C. Collins, Olga T. Schubert, Saša M. Miladinović, 2014, Nature Biotechnology.

The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases

Joshua L. Payne, Christian J. A. Sigrist, Brian J. Stevenson, 2015, Nucleic Acids Res..

Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS ROSENBERGER

Ben C. Collins, E. Dermitzakis, H. Röst, 2020 .