Käll L

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Family name Käll
Given name Lukas
Initials L
ORCID

ORCID 0000-0001-5689-9797
Affiliations

46 publications

PubMed DOI Crossref
Pairwise Attention: Leveraging Mass Differences to Enhance De Novo Sequencing of Mass Spectra.
Lapin J, Nilsson A, Wilhelm M, Käll L
J. Proteome Res. 24 (7) 3722-3730 [2025-07-04; online 2025-06-02]
PubMed DOI Crossref
Open-Source and FAIR Research Software for Proteomics.
Perez-Riverol Y, Bittremieux W, Noble WS, ..., Käll L, Fondrie WE
J. Proteome Res. 24 (5) 2222-2234 [2025-05-02; online 2025-04-23]
PubMed DOI Crossref
How to Train a Postprocessor for Tandem Mass Spectrometry Proteomics Database Search While Maintaining Control of the False Discovery Rate.
Freestone J, Käll L, Noble WS, Keich U
J. Proteome Res. 24 (5) 2266-2279 [2025-05-02; online 2025-03-31]
DOI Crossref
Pairwise Attention: Leveraging Mass Differences to Enhance De Novo Sequencing of Mass Spectra
Lapin J, Nilsson A, Wilhelm M, Käll L
- - (-) - [2025-04-03; online 2025-04-03]
DOI Crossref
Author response: Simultaneous polyclonal antibody sequencing and epitope mapping by cryo electron microscopy and mass spectrometry – a perspective
Schulte D, Šiborová M, Käll L, Snijder J
- - (-) - [2025-03-18; online 2025-03-18]
DOI Crossref
Simultaneous polyclonal antibody sequencing and epitope mapping by cryo electron microscopy and mass spectrometry – a perspective
Schulte D, Šiborová M, Käll L, Snijder J
- - (-) - [2025-03-18; online 2025-03-18]
PubMed DOI Crossref
ProHap enables human proteomic database generation accounting for population diversity.
Vašíček J, Kuznetsova KG, Skiadopoulou D, ..., Käll L, Vaudel M
Nat. Methods 22 (2) 273-277 [2025-02-00; online 2024-12-09]
DOI Crossref
Met-ID: An Open-Source Software for Comprehensive Annotation of Multiple On-Tissue Chemical Modifications in MALDI-MSI
Bjärterot P, Nilsson A, Shariatgorji R, ..., Käll L, Andrén PE
- - (-) - [2025-01-27; online 2025-01-27]
DOI Crossref
Simultaneous polyclonal antibody sequencing and epitope mapping by cryo electron microscopy and mass spectrometry – a perspective
Schulte D, Šiborová M, Käll L, Snijder J
- - (-) - [2025-01-16; online 2025-01-16]
PubMed DOI Crossref
quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data.
Dai C, Pfeuffer J, Wang H, ..., Kohlbacher O, Perez-Riverol Y
Nat. Methods 21 (9) 1603-1607 [2024-09-00; online 2024-07-04]
PubMed DOI Crossref
Spatial landmark detection and tissue registration with deep learning.
Ekvall M, Bergenstråhle L, Andersson A, ..., Käll L, Lundeberg J
Nat. Methods 21 (4) 673-679 [2024-04-00; online 2024-03-04]
PubMed DOI Crossref
Automated model building and protein identification in cryo-EM maps.
Jamali K, Käll L, Zhang R, ..., Kimanius D, Scheres SHW
Nature 628 (8007) 450-457 [2024-04-00; online 2024-02-26]
PubMed DOI Crossref
Pathway analysis through mutual information.
Jeuken GS, Käll L
Bioinformatics 40 (1) - [2024-01-02; online 2024-01-10]
DOI Crossref
Semi-supervised Learning While Controlling the FDR with an Application to Tandem Mass Spectrometry Analysis
Freestone J, Käll L, Noble WS, Keich U
- - (-) 448-453 [2024-00-00; online 2024-05-17]
DOI Crossref
ProHap enables proteomic database generation accounting for population diversity
Vašíček J, Kuznetsova KG, Skiadopoulou D, ..., Käll L, Vaudel M
- - (-) - [2023-12-24; online 2023-12-24]
DOI Crossref
How to train a post-processor for tandem mass spectrometry proteomics database search while maintaining control of the false discovery rate
Freestone J, Käll L, Noble WS, Keich U
- - (-) - [2023-10-31; online 2023-10-31]
PubMed DOI Crossref
Retention Time and Fragmentation Predictors Increase Confidence in Identification of Common Variant Peptides.
Skiadopoulou D, Vašíček J, Kuznetsova K, ..., Käll L, Vaudel M
J. Proteome Res. 22 (10) 3190-3199 [2023-10-06; online 2023-09-01]
PubMed DOI Crossref
Triqler for Protein Summarization of Data from Data-Independent Acquisition Mass Spectrometry.
Truong P, The M, Käll L
J. Proteome Res. 22 (4) 1359-1366 [2023-04-07; online 2023-03-29]
DOI Crossref
Retention time and fragmentation predictors increase confidence in variant peptide identification
Skiadopoulou D, Vašíček J, Kuznetsova K, Käll L, Vaudel M
- - (-) - [2023-04-01; online 2023-04-01]
PubMed DOI Crossref
Toward an Integrated Machine Learning Model of a Proteomics Experiment.
Neely BA, Dorfer V, Martens L, ..., Wilhelm M, Palmblad M
J. Proteome Res. 22 (3) 681-696 [2023-03-03; online 2023-02-06]
PubMed DOI Crossref
Finding haplotypic signatures in proteins.
Vašíček J, Skiadopoulou D, Kuznetsova KG, ..., Käll L, Vaudel M
Gigascience 12 (-) - [2022-12-28; online 2023-10-31]
DOI Crossref
Finding Haplotypic Signatures in Proteins
Vašíček J, Skiadopoulou D, Kuznetsova KG, ..., Käll L, Vaudel M
- - (-) - [2022-11-24; online 2022-11-24]
DOI Crossref
Pathway Analysis Through Mutual Information
Jeuken GS, Käll L
- - (-) - [2022-07-02; online 2022-07-02]
PubMed DOI Crossref
Prosit Transformer: A transformer for Prediction of MS2 Spectrum Intensities.
Ekvall M, Truong P, Gabriel W, Wilhelm M, Käll L
J. Proteome Res. 21 (5) 1359-1364 [2022-05-06; online 2022-04-12]
PubMed DOI Crossref
Putting Humpty Dumpty Back Together Again: What Does Protein Quantification Mean in Bottom-Up Proteomics?
Plubell DL, Käll L, Webb-Robertson BJ, ..., Wu CC, MacCoss MJ
J. Proteome Res. 21 (4) 891-898 [2022-04-01; online 2022-02-27]
PubMed DOI Crossref
Interpretation of the DOME Recommendations for Machine Learning in Proteomics and Metabolomics.
Palmblad M, Böcker S, Degroeve S, ..., Noble WS, Wilhelm M
J. Proteome Res. 21 (4) 1204-1207 [2022-04-01; online 2022-02-04]
PubMed DOI Crossref
Survival analysis of pathway activity as a prognostic determinant in breast cancer.
Jeuken GS, Tobin NP, Käll L
PLoS Comput Biol 18 (3) e1010020 [2022-03-00; online 2022-03-28]
DOI Crossref
A comprehensive evaluation of consensus spectrum generation methods in proteomics
Luo X, Bittremieux W, Griss J, ..., Kall L, Perez-Riverol Y
- - (-) - [2022-01-27; online 2022-01-27]
DOI Crossref
Survival analysis of pathway activity as a prognostic determinant in breast cancer
Jeuken GS, Tobin NP, Käll L
- - (-) - [2021-05-20; online 2021-05-20]
PubMed DOI Crossref
Triqler for MaxQuant: Enhancing Results from MaxQuant by Bayesian Error Propagation and Integration.
The M, Käll L
J. Proteome Res. 20 (4) 2062-2068 [2021-04-02; online 2021-03-04]
PubMed DOI Crossref
Performing Selection on a Monotonic Function in Lieu of Sorting Using Layer-Ordered Heaps.
Lucke K, Pennington J, Kreitzberg P, Käll L, Serang O
J. Proteome Res. 20 (4) 1849-1854 [2021-04-02; online 2021-02-02]
DOI Crossref
Can we put Humpty Dumpty back together again? What does protein quantification mean in bottom-up proteomics?
Plubell DL, Käll L, Webb-Robertson BJ, ..., Wu CC, MacCoss MJ
- - (-) - [2021-01-27; online 2021-01-27]
DOI Crossref
Parallelized calculation of permutation tests
Ekvall M, Höhle M, Käll L
- - (-) - [2020-10-02; online 2020-10-02]
DOI Crossref
Integrating identification and quantification uncertainty for differential protein abundance analysis with Triqler
The M, Käll L
- - (-) - [2020-09-25; online 2020-09-25]
PubMed DOI Crossref
Focus on the spectra that matter by clustering of quantification data in shotgun proteomics.
The M, Käll L
Nat Commun 11 (1) 3234 [2020-06-26; online 2020-06-26]
PubMed DOI Crossref
Speeding Up Percolator.
Halloran JT, Zhang H, Kara K, ..., Käll L, Noble WS
J. Proteome Res. 18 (9) 3353-3359 [2019-09-06; online 2019-08-23]
PubMed DOI Crossref
Integrated Identification and Quantification Error Probabilities for Shotgun Proteomics.
The M, Käll L
Mol. Cell Proteomics 18 (3) 561-570 [2019-03-00; online 2018-11-27]
PubMed DOI Crossref
Expanding the Use of Spectral Libraries in Proteomics.
Deutsch EW, Perez-Riverol Y, Chalkley RJ, ..., Bandeira N, Röst H
J. Proteome Res. 17 (12) 4051-4060 [2018-12-07; online 2018-10-11]
DOI Crossref
Focus on the spectra that matter by clustering of quantification data in shotgun proteomics
The M, Käll L
- - (-) - [2018-12-06; online 2018-12-06]
PubMed DOI Crossref
A simple null model for inferences from network enrichment analysis.
Jeuken GS, Käll L
PLoS ONE 13 (11) e0206864 [2018-11-09; online 2018-11-09]
DOI Crossref
Quantitative behavior of protein complexes in human cells
Chalabi MH, Tsiamis V, Käll L, Vandin F, Schwämmle V
- - (-) - [2018-07-11; online 2018-07-11]
DOI Crossref
Integrated identification and quantification error probabilities for shotgun proteomics
The M, Käll L
- - (-) - [2018-06-28; online 2018-06-28]
DOI Crossref
A protein standard that emulates homology for the characterization of protein inference algorithms
The M, Edfors F, Perez-Riverol Y, ..., Forsström B, Käll L
- - (-) - [2017-12-19; online 2017-12-19]
PubMed DOI Crossref
Covariation of Peptide Abundances Accurately Reflects Protein Concentration Differences.
Zhang B, Pirmoradian M, Zubarev R, Käll L
Mol. Cell Proteomics 16 (5) 936-948 [2017-05-00; online 2017-03-16]
PubMed DOI Crossref
DeMix-Q: Quantification-Centered Data Processing Workflow.
Zhang B, Käll L, Zubarev RA
Mol. Cell Proteomics 15 (4) 1467-1478 [2016-04-00; online 2016-01-04]
PubMed DOI Crossref
HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics.
Branca RM, Orre LM, Johansson HJ, ..., Käll L, Lehtiö J
Nat. Methods 11 (1) 59-62 [2014-01-00; online 2013-11-17]
SciLifeLab Data Centre
Publications 9.5.1