List of works - Lukas Käll

A Protein Standard That Emulates Homology for the Characterization of Protein Inference Algorithms

scientific article published on 16 April 2018

A combined transmembrane topology and signal peptide prediction method

scientific article (publication date: 14 May 2004)

A cross-validation scheme for machine learning algorithms in shotgun proteomics

scientific article

A general model of G protein-coupled receptor sequences and its application to detect remote homologs

scientific article published in February 2006

A guideline to proteome-wide α-helical membrane protein topology predictions

scientific article

A novel transmembrane topology of presenilin based on reconciling experimental and computational evidence

article

A protein standard that emulates homology for the characterization of protein inference algorithms

scholarly article published 19 December 2017

A simple null model for inferences from network enrichment analysis

scientific article published in PLoS ONE

Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server

scientific article

An HMM posterior decoder for sequence feature prediction that includes homology information

scientific article published in June 2005

Assigning significance to peptides identified by tandem mass spectrometry using decoy databases

scientific article published on 08 December 2007

Chromatographic retention time prediction for posttranslationally modified peptides

scientific article published in April 2012

CoExpresso: assess the quantitative behavior of protein complexes in human cells

article by Morteza H Chalabi et al published 9 January 2019 in BMC Bioinformatics

Computational mass spectrometry-based proteomics

scientific article published on December 2011

Covariation of Peptide Abundances Accurately Reflects Protein Concentration Differences

scientific article

Crux: rapid open source protein tandem mass spectrometry analysis

scientific article published on 9 September 2014

DeMix-Q: Quantification-Centered Data Processing Workflow

scientific article

Determining the calibration of confidence estimation procedures for unique peptides in shotgun proteomics

scientific article published on 23 December 2012

Enhanced peptide identification by electron transfer dissociation using an improved Mascot Percolator

scientific article

Expanding the use of spectral libraries in proteomics

Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0.

scientific article

Fast and accurate database searches with MS-GF+Percolator

scientific article published on 23 December 2013

Focus on the spectra that matter by clustering of quantification data in shotgun proteomics

scientific article published on 26 June 2020

From sequence to structure to networks

scientific article published on 4 November 2008

Gene-specific correlation of RNA and protein levels in human cells and tissues

scientific article published on 20 October 2016

GradientOptimizer: an open-source graphical environment for calculating optimized gradients in reversed-phase liquid chromatography

scientific article published on 15 May 2014

HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics.

scientific article published on 17 November 2013

IPeak: An open source tool to combine results from multiple MS/MS search engines

scientific article published on 6 May 2015

Improvements to the percolator algorithm for Peptide identification from shotgun proteomics data sets

scientific article

Integrated Identification and Quantification Error Probabilities for Shotgun Proteomics

scholarly article by Matthew The & Lukas Käll published March 2019 in Molecular & Cellular Proteomics

Integrated identification and quantification error probabilities for shotgun proteomics

MaRaCluster: A Fragment Rarity Metric for Clustering Fragment Spectra in Shotgun Proteomics

scientific article published on 14 December 2015

Mass fingerprinting of complex mixtures: protein inference from high-resolution peptide masses and predicted retention times

scientific article published on 11 October 2013

Membrane protein shaving with thermolysin can be used to evaluate topology predictors

scientific article published in May 2013

Membrane topology of the Drosophila OR83b odorant receptor

scientific article published on 20 November 2007

Multi-omic data analysis using Galaxy.

scientific article

Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry

scientific article published on August 2008

Nonparametric Bayesian evaluation of differential protein quantification

scientific article published on 11 September 2013

On using samples of known protein content to assess the statistical calibration of scores assigned to peptide-spectrum matches in shotgun proteomics

scientific article published on 24 March 2011

Optimized nonlinear gradients for reversed-phase liquid chromatography in shotgun proteomics

scientific article published on 24 July 2013

Peptide retention time prediction

scientific article

Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data

scientific article published on 27 July 2015

Posterior error probabilities and false discovery rates: two sides of the same coin

scientific article published on 04 December 2007

Prediction of Transmembrane Topology and Signal Peptide Given a Protein’s Amino Acid Sequence ⬇️

scientific article published on January 1, 2010

QVALITY: non-parametric estimation of q-values and posterior error probabilities

scientific article published on 4 February 2009

Quality assessments of peptide-spectrum matches in shotgun proteomics

Quantitative behavior of protein complexes in human cells

article published in 2018

Rapid and accurate peptide identification from tandem mass spectra

scientific article published on 28 May 2008

Recognizing uncertainty increases robustness and reproducibility of mass spectrometry-based protein inferences

scientific article published on 19 November 2012

Reliability of transmembrane predictions in whole-genome data

scientific article

Response to “Comparison and Evaluation of Clustering Algorithms for Tandem Mass Spectra”

scholarly article by Johannes Griss et al published 23 April 2018 in Journal of Proteome Research

Semi-supervised learning for peptide identification from shotgun proteomics datasets.

scientific article

Solution to Statistical Challenges in Proteomics Is More Statistics, Not Less

scientific article published on 10 August 2015

Spatial multimodal analysis of transcriptomes and metabolomes in tissues

scientific article published on 4 September 2023

Speeding Up Percolator

scientific article published on 23 August 2019

Survival analysis of pathway activity as a prognostic determinant in breast cancer

scientific article published on 28 March 2022

The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides

scientific article published on 12 May 2015

Training, selection, and robust calibration of retention time models for targeted proteomics

scientific article

Transmembrane topology and signal peptide prediction using dynamic bayesian networks

scientific article

Triqler for MaxQuant: Enhancing Results from MaxQuant by Bayesian Error Propagation and Integration

publication published on 04 March 2021

Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations

scientific article published on 24 July 2008

List of works by Lukas Käll

A Protein Standard That Emulates Homology for the Characterization of Protein Inference Algorithms

A combined transmembrane topology and signal peptide prediction method

A cross-validation scheme for machine learning algorithms in shotgun proteomics

A general model of G protein-coupled receptor sequences and its application to detect remote homologs

A guideline to proteome-wide α-helical membrane protein topology predictions

A novel transmembrane topology of presenilin based on reconciling experimental and computational evidence

A protein standard that emulates homology for the characterization of protein inference algorithms

A simple null model for inferences from network enrichment analysis

Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server

An HMM posterior decoder for sequence feature prediction that includes homology information

Assigning significance to peptides identified by tandem mass spectrometry using decoy databases

Chromatographic retention time prediction for posttranslationally modified peptides

CoExpresso: assess the quantitative behavior of protein complexes in human cells

Computational mass spectrometry-based proteomics

Covariation of Peptide Abundances Accurately Reflects Protein Concentration Differences

Crux: rapid open source protein tandem mass spectrometry analysis

DeMix-Q: Quantification-Centered Data Processing Workflow

Determining the calibration of confidence estimation procedures for unique peptides in shotgun proteomics

Enhanced peptide identification by electron transfer dissociation using an improved Mascot Percolator

Expanding the use of spectral libraries in proteomics

Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0.

Fast and accurate database searches with MS-GF+Percolator

Focus on the spectra that matter by clustering of quantification data in shotgun proteomics

Focus on the spectra that matter by clustering of quantification data in shotgun proteomics

From sequence to structure to networks

Gene-specific correlation of RNA and protein levels in human cells and tissues

GradientOptimizer: an open-source graphical environment for calculating optimized gradients in reversed-phase liquid chromatography

HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics.

IPeak: An open source tool to combine results from multiple MS/MS search engines

Improvements to the percolator algorithm for Peptide identification from shotgun proteomics data sets

Integrated Identification and Quantification Error Probabilities for Shotgun Proteomics

Integrated identification and quantification error probabilities for shotgun proteomics

MaRaCluster: A Fragment Rarity Metric for Clustering Fragment Spectra in Shotgun Proteomics

Mass fingerprinting of complex mixtures: protein inference from high-resolution peptide masses and predicted retention times

Membrane protein shaving with thermolysin can be used to evaluate topology predictors

Membrane topology of the Drosophila OR83b odorant receptor

Multi-omic data analysis using Galaxy.

Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry

Nonparametric Bayesian evaluation of differential protein quantification

On using samples of known protein content to assess the statistical calibration of scores assigned to peptide-spectrum matches in shotgun proteomics

Optimized nonlinear gradients for reversed-phase liquid chromatography in shotgun proteomics

Peptide retention time prediction

Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data

Posterior error probabilities and false discovery rates: two sides of the same coin

Prediction of Transmembrane Topology and Signal Peptide Given a Protein’s Amino Acid Sequence ⬇️

QVALITY: non-parametric estimation of q-values and posterior error probabilities

Quality assessments of peptide-spectrum matches in shotgun proteomics

Quantitative behavior of protein complexes in human cells

Rapid and accurate peptide identification from tandem mass spectra

Recognizing uncertainty increases robustness and reproducibility of mass spectrometry-based protein inferences

Reliability of transmembrane predictions in whole-genome data

Response to “Comparison and Evaluation of Clustering Algorithms for Tandem Mass Spectra”

Semi-supervised learning for peptide identification from shotgun proteomics datasets.

Solution to Statistical Challenges in Proteomics Is More Statistics, Not Less

Spatial multimodal analysis of transcriptomes and metabolomes in tissues

Speeding Up Percolator

Survival analysis of pathway activity as a prognostic determinant in breast cancer

The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides

Training, selection, and robust calibration of retention time models for targeted proteomics

Transmembrane topology and signal peptide prediction using dynamic bayesian networks

Triqler for MaxQuant: Enhancing Results from MaxQuant by Bayesian Error Propagation and Integration

Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations