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List of works by Johan Malmström

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

scientific article

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

scientific article published on 05 June 2015

A comprehensive analysis of the Streptococcus pyogenes and human plasma protein interaction network

scientific article published on 14 February 2014

A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas

scientific article

A high-quality catalog of the Drosophila melanogaster proteome

scientific article

A novel role for pro-coagulant microvesicles in the early host defense against streptococcus pyogenes.

scientific article

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

scientific article published on 21 June 2019

Absolute quantification of microbial proteomes at different states by directed mass spectrometry

scientific article

Activation of platelet-derived growth factor pathway in human asthmatic pulmonary-derived mesenchymal cells

scientific article

Advances in proteomic workflows for systems biology

scientific article

Analysis of Bacterial Surface Interactions with Mass Spectrometry-Based Proteomics

scientific article

Antibody orientation at bacterial surfaces is related to invasive infection.

scientific article

Antiproliferative Heparan Sulfate Inhibiting Hyaluronan and Transforming Growth Factor-β Expression in Human Lung Fibroblast Cells: A Possible Antifibrotic Therapy?

Automated quality control system for LC-SRM setups

scientific article

Automated selected reaction monitoring software for accurate label-free protein quantification

scientific article

Automated workflow for large-scale selected reaction monitoring experiments

scientific article published on 10 February 2012

Biglycan isoforms with differences in polysaccharide substitution and core protein in human lung fibroblasts

scientific article

Biosynthesis of dermatan sulfate: chondroitin-glucuronate C5-epimerase is identical to SART2

scientific article

Cancer associated proteins in blood plasma: Determining normal variation

scientific article published on 28 April 2016

Characterization of Released Polypeptides During an Interferon-γ-Dependent Antibacterial Response in Airway Epithelial Cells ⬇️

scientific article published on August 21, 2012

Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes

scientific article

Complement Activation Occurs at the Surface of Platelets Activated by Streptococcal M1 Protein and This Results in Phagocytosis of Platelets

scientific article published on 12 December 2018

Complete Removal of Extracellular IgG Antibodies in a Randomized Dose-Escalation Phase I Study with the Bacterial Enzyme IdeS--A Novel Therapeutic Opportunity

scientific article published on 15 July 2015

Comprehensive Mass Spectrometric Survey of Streptococcus pyogenes Subcellular Proteomes

scientific article published on 21 November 2017

Comprehensive Proteomic Characterization of Ontogenic Changes in Hematopoietic Stem and Progenitor Cells.

scientific article

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

scientific article

Data processing has major impact on the outcome of quantitative label-free LC-MS analysis

scientific article

Data processing methods and quality control strategies for label-free LC-MS protein quantification

scientific article

Development of Phage-Based Antibody Fragment Reagents for Affinity Enrichment of Bacterial Immunoglobulin G Binding Proteins

scientific article published on 9 October 2015

Different fractions of human serum glycoproteins bind galectin-1 or galectin-8, and their ratio may provide a refined biomarker for pathophysiological conditions in cancer and inflammatory disease

scientific article published on 17 January 2012

Differential compartmentalization of Streptococcus pyogenes virulence factors and host protein binding properties as a mechanism for host adaptation.

scientific article

Dinosaur: A Refined Open-Source Peptide MS Feature Detector

scientific article published on 25 May 2016

Exploring the context of the lung proteome within the airway mucosa following allergen challenge

scientific article published in March 2004

Functional and phenotypical comparison of myofibroblasts derived from biopsies and bronchoalveolar lavage in mild asthma and scleroderma

scientific article

Functional and structural properties of a novel protein and virulence factor (Protein sHIP) in Streptococcus pyogenes

scientific article

Galectin-8 in IgA nephritis: decreased binding of IgA by galectin-8 affinity chromatography and associated increased binding in non-IgA serum glycoproteins.

scientific article published on 16 December 2011

Glycoproteomic identification of galectin-3 and -8 ligands in bronchoalveolar lavage of mild asthmatics and healthy subjects

scientific article published on 04 January 2012

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

scholarly article by Hamed Khakzad et al published 18 April 2019 in BMC Bioinformatics

Heparan sulfate upregulates platelet-derived growth factor receptors on human lung fibroblasts

scientific article published on 01 December 1998

Improvements in Mass Spectrometry Assay Library Generation for Targeted Proteomics

scientific article

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

scientific article

Leucocyte recruitment and molecular fortification of keratinocytes triggered by streptococcal M1 protein.

scientific article published on 3 October 2017

Nanocapillary liquid chromatography interfaced to tandem matrix-assisted laser desorption/ionization and electrospray ionization-mass spectrometry: mapping the nuclear proteome of human fibroblasts

scientific article published in November 2003

Neutrophil extracellular traps in the central nervous system hinder bacterial clearance during pneumococcal meningitis

scientific article published on 10 April 2019

Numerical compression schemes for proteomics mass spectrometry data

scientific article

On-chip microextraction for proteomic sample preparation of in-gel digests

scientific article

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

scientific article published in March 2014

Optimized peptide separation and identification for mass spectrometry based proteomics via free-flow electrophoresis

scientific article published in September 2006

Perspectives of targeted mass spectrometry for protein biomarker verification

scientific article published on 07 October 2009

PhosphoPep--a phosphoproteome resource for systems biology research in Drosophila Kc167 cells

scientific article

Protein expression changes in ovarian cancer during the transition from benign to malignant

scientific article

Proteins of novel lactic acid bacteria from Apis mellifera mellifera: an insight into the production of known extra-cellular proteins during microbial stress.

scientific article

Proteoglycan and proteome profiling of central human pulmonary fibrotic tissue utilizing miniaturized sample preparation: a feasibility study

scientific article

Proteome annotations and identifications of the human pulmonary fibroblast

scientific article

Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans

scientific article published on 15 July 2009

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

scientific article published on January 1, 2012

Proteomic 2DE database for spot selection, automated annotation, and data analysis

scientific article

Proteomic analysis identifies candidate proteins associated with distant recurrences in breast cancer after adjuvant chemotherapy

scientific article

Proteomics -- the protein expression technology to study connective tissue biology.

scientific article

Quantifying extracellular matrix turnover in human lung scaffold cultures

scientific article published on 3 April 2018

Quantitative Mass Spectrometry To Study Inflammatory Cartilage Degradation and Resulting Interactions with the Complement System

scientific article published on 14 September 2016

Quantitative proteogenomics of human pathogens using DIA-MS.

scientific article published on 14 September 2015

Quantitative proteomic analysis of fibroblast nuclear proteins after stimulation with mitogen activated protein kinase inhibiting heparan sulfate

scientific article

Quantitative proteomic characterization of lung-MSC and bone marrow-MSC using DIA-mass spectrometry

scientific article published on 24 August 2017

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

scientific article published in March 2018

Quantitative proteomics of microbes: Principles and applications to virulence ⬇️

scientific article published on 04 July 2011

Rapid determination of quaternary protein structures in complex biological samples

scientific article published in Nature Communications

Rtt101 and Mms1 in budding yeast form a CUL4(DDB1)-like ubiquitin ligase that promotes replication through damaged DNA

scientific article

Saliva-Induced Clotting Captures Streptococci: Novel Roles for Coagulation and Fibrinolysis in Host Defense and Immune Evasion

scientific article published on 25 July 2016

Sepsis 2016 Agra, India. Agra, India. 5-6 February 2016

article by Surinder Kumar Sharma et al published 2 March 2016 in Critical Care

Simian Virus 40 depends on ER protein folding and quality control factors for entry into host cells

scientific article

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

scientific article published on 28 April 2012

Stimulation of blood mononuclear cells with bacterial virulence factors leads to the release of pro-coagulant and pro-inflammatory microparticles

scientific article published on 10 November 2011

Streptococcus pyogenes evades adaptive immunity through specific IgG glycan hydrolysis

scientific article published on 15 May 2019

Streptococcus pyogenes in human plasma: adaptive mechanisms analyzed by mass spectrometry-based proteomics

scientific article published on 23 November 2011

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

scientific article published on 07 January 2021

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

scientific article published on 19 February 2020

Structure and Interactions of a Dimeric Variant of sHIP, a Novel Virulence Determinant of Streptococcus pyogenes

scientific article

Surface proteins of group G Streptococcus in different phases of growth: patterns of production and implications for the host-bacteria relationship

scientific article published on 12 November 2013

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

scientific article published on 9 February 2017

Targeted mass spectrometry analysis of neutrophil-derived proteins released during sepsis progression

scientific article published on 7 August 2014

Targeting hepatocytes from liver tissue by laser capture microdissection and proteomics expression profiling

scientific article published in November 2003

The TLR2 Antagonist Staphylococcal Superantigen-Like Protein 3 Acts as a Virulence Factor to Promote Bacterial Pathogenicity in vivo

scientific article published on September 2017

The quantitative proteome of a human cell line.

scientific article

Transforming growth factor-beta 1 specifically induce proteins involved in the myofibroblast contractile apparatus

scientific article published on 6 February 2004

Two-dimensional separation of human plasma proteins using iterative free-flow electrophoresis

scientific article published in December 2007

Visual proteomics of the human pathogen Leptospira interrogans

scientific article

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