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List of works by Lars 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 computational tool to detect and avoid redundancy in selected reaction monitoring

scientific article

A divergent Pseudomonas aeruginosa palmitoyltransferase essential for cystic fibrosis-specific lipid A.

scientific article

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

scientific article published on 21 June 2019

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

scientific article

An objective comparison of cell-tracking algorithms.

scientific article published on 30 October 2017

Assigning function to yeast proteins by integration of technologies.

scientific article

Automated prediction of CASP-5 structures using the Robetta server.

scientific article

Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM.

scientific article

Automated workflow for large-scale selected reaction monitoring experiments

scientific article published on 10 February 2012

Bioinformatic challenges in targeted proteomics

scientific article published on 23 August 2012

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

scientific article published on 28 June 2018

Computational Proteomics with Jupyter and Python

scientific article published on 01 January 2019

Cross-link guided molecular modeling with ROSETTA

scientific article

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

scientific article

De Novo Prediction of Three-dimensional Structures for Major Protein Families

scientific article published on 01 September 2002

Deciphering diatom biochemical pathways via whole-cell proteomics.

scientific article published on June 2009

Efficient visualization of high-throughput targeted proteomics experiments: TAPIR.

scientific article published on 18 March 2015

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

scientific article

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

scientific article

Free modeling with Rosetta in CASP6

scientific article

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

scientific article

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

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

scientific article

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

scientific article

Identification of the active site of DS-epimerase 1 and requirement of N-glycosylation for enzyme function

scientific article

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

scientific article

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

scientific article

Macromolecular modeling and design in Rosetta: recent methods and frameworks

scientific article published on 01 June 2020

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

Numerical compression schemes for proteomics mass spectrometry data

scientific article

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

scientific article

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

scientific article published in March 2014

Prediction of CASP6 structures using automated Robetta protocols

scientific article

Protein structure modeling

scientific article

Proteome annotations and identifications of the human pulmonary fibroblast

scientific article

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

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

scientific article published on 01 March 2009

Quantification of Adaptive Immune Responses Against Protein-Binding Interfaces in the Streptococcal M1 Protein

scientific article published in 2024

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

Reproducible quantitative proteotype data matrices for systems biology

scientific article

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

scientific article published on 14 January 2022

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

scientific article published on 28 April 2012

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

scientific article published on 23 November 2011

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

scientific article

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

scientific article published on 07 January 2021

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

scientific article

Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology

scientific article

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

scientific article published on August 2016

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

scientific article published on 9 February 2017

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

scientific article

The Yeast Resource Center Public Data Repository

scientific article

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

scientific article

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

scientific article published in 2014

Xwalk: computing and visualizing distances in cross-linking experiments

scientific article

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

scientific article

pyOpenMS: a Python-based interface to the OpenMS mass-spectrometry algorithm library

scientific article published on January 2014

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

scientific article

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