Lista de obras - Lukas Käll - Dominio Público Uruguay

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

artículo científico publicado en 2004

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

artículo científico publicado en 2012

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

artículo científico publicado en 2006

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

artículo científico publicado en 2012

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

artículo científico publicado en 2018

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

artículo científico publicado en 2007

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

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 2011

Covariation of Peptide Abundances Accurately Reflects Protein Concentration Differences

artículo científico publicado en 2017

Crux: rapid open source protein tandem mass spectrometry analysis

artículo científico publicado en 2014

DeMix-Q: Quantification-Centered Data Processing Workflow

artículo científico publicado en 2016

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

artículo científico publicado en 2012

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

artículo científico publicado en 2012

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.

artículo científico publicado en 2016

Fast and accurate database searches with MS-GF+Percolator

artículo científico publicado en 2013

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

artículo científico publicado en 2020

From sequence to structure to networks

artículo científico publicado en 2008

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

artículo científico publicado en 2016

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

artículo científico publicado en 2014

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

artículo científico publicado en 2013

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

artículo científico publicado en 2015

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

artículo científico publicado en 2009

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

artículo científico publicado en 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.

artículo científico publicado en 2013

Membrane topology of the Drosophila OR83b odorant receptor

artículo científico publicado en 2007

Multi-omic data analysis using Galaxy.

artículo científico publicado en 2015

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

artículo científico publicado en 2008

Nonparametric Bayesian evaluation of differential protein quantification

artículo científico publicado en 2013

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

artículo científico publicado en 2011

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

artículo científico publicado en 2013

Peptide retention time prediction

artículo científico publicado en 2016

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

artículo científico publicado en 2015

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

artículo científico publicado en 2007

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

artículo científico publicado el 1 de enero de 2010

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

artículo científico publicado en 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

artículo científico publicado en 2008

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

artículo científico publicado en 2012

Reliability of transmembrane predictions in whole-genome data

artículo científico publicado en 2002

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.

artículo científico publicado en 2007

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

artículo científico publicado en 2015

Spatial multimodal analysis of transcriptomes and metabolomes in tissues

artículo científico publicado en 2023

Speeding Up Percolator

scientific article published on 23 August 2019

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

artículo científico publicado en 2022

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

artículo científico

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

artículo científico publicado en 2010

Transmembrane topology and signal peptide prediction using dynamic bayesian networks

artículo científico publicado en 2008

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

artículo científico publicado en 2008

Lista de obras de 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