| Year |
Citation |
Score |
| 2024 |
Van Den Bossche T, Verschaffelt P, Vande Moortele T, Dawyndt P, Martens L, Mesuere B. Biodiversity Analysis of Metaproteomics Samples with Unipept: A Comprehensive Tutorial. Methods in Molecular Biology (Clifton, N.J.). 2836: 183-215. PMID 38995542 DOI: 10.1007/978-1-0716-4007-4_11 |
0.748 |
|
| 2024 |
Declercq A, Demeulemeester N, Gabriels R, Bouwmeester R, Degroeve S, Martens L. Bioinformatics Pipeline for Processing Single-Cell Data. Methods in Molecular Biology (Clifton, N.J.). 2817: 221-239. PMID 38907156 DOI: 10.1007/978-1-0716-3934-4_15 |
0.827 |
|
| 2024 |
Staes A, Mendes Maia T, Dufour S, Bouwmeester R, Gabriels R, Martens L, Gevaert K, Impens F, Devos S. Benefit of In Silico Predicted Spectral Libraries in Data-Independent Acquisition Data Analysis Workflows. Journal of Proteome Research. PMID 38666436 DOI: 10.1021/acs.jproteome.4c00048 |
0.739 |
|
| 2024 |
Siraj A, Bouwmeester R, Declercq A, Welp L, Chernev A, Wulf A, Urlaub H, Martens L, Degroeve S, Kohlbacher O, Sachsenberg T. Intensity and retention time prediction improves the rescoring of protein-nucleic acid cross-links. Proteomics. 24: e2300144. PMID 38629965 DOI: 10.1002/pmic.202300144 |
0.807 |
|
| 2024 |
Bouwmeester R, Richardson K, Denny R, Wilson ID, Degroeve S, Martens L, Vissers JPC. Predicting ion mobility collision cross sections and assessing prediction variation by combining conventional and data driven modeling. Talanta. 274: 125970. PMID 38621320 DOI: 10.1016/j.talanta.2024.125970 |
0.784 |
|
| 2024 |
Buur LM, Declercq A, Strobl M, Bouwmeester R, Degroeve S, Martens L, Dorfer V, Gabriels R. MSRescore 3.0 Is a Modular, Flexible, and User-Friendly Platform to Boost Peptide Identifications, as Showcased with MS Amanda 3.0. Journal of Proteome Research. PMID 38491990 DOI: 10.1021/acs.jproteome.3c00785 |
0.834 |
|
| 2024 |
Koutrouli M, Nastou K, Líndez PP, Bouwmeester R, Rasmussen S, Martens L, Jensen LJ. FAVA: High-quality functional association networks inferred from scRNA-seq and proteomics data. Bioinformatics (Oxford, England). PMID 38192003 DOI: 10.1093/bioinformatics/btae010 |
0.733 |
|
| 2023 |
Sakarika M, Kerckhof FM, Van Peteghem L, Pereira A, Van Den Bossche T, Bouwmeester R, Gabriels R, Van Haver D, Ulčar B, Martens L, Impens F, Boon N, Ganigué R, Rabaey K. The nutritional composition and cell size of microbial biomass for food applications are defined by the growth conditions. Microbial Cell Factories. 22: 254. PMID 38072930 DOI: 10.1186/s12934-023-02265-1 |
0.771 |
|
| 2023 |
Claeys T, Van Den Bossche T, Perez-Riverol Y, Gevaert K, Vizcaíno JA, Martens L. lesSDRF is more: maximizing the value of proteomics data through streamlined metadata annotation. Nature Communications. 14: 6743. PMID 37875519 DOI: 10.1038/s41467-023-42543-5 |
0.747 |
|
| 2023 |
Verschaffelt P, Tanca A, Abbondio M, Van Den Bossche T, Moortele TV, Dawyndt P, Martens L, Mesuere B. Unipept Desktop 2.0: Construction of Targeted Reference Protein Databases for Metaproteogenomics Analyses. Journal of Proteome Research. PMID 37459443 DOI: 10.1021/acs.jproteome.3c00091 |
0.771 |
|
| 2023 |
Declercq A, Bouwmeester R, Chiva C, Sabidó E, Hirschler A, Carapito C, Martens L, Degroeve S, Gabriels R. Updated MS²PIP web server supports cutting-edge proteomics applications. Nucleic Acids Research. PMID 37140039 DOI: 10.1093/nar/gkad335 |
0.831 |
|
| 2023 |
Holstein T, Kistner F, Martens L, Muth T. PepGM: a probabilistic graphical model for taxonomic inference of viral proteome samples with associated confidence scores. Bioinformatics (Oxford, England). 39. PMID 37129543 DOI: 10.1093/bioinformatics/btad289 |
0.7 |
|
| 2023 |
Claeys T, Menu M, Bouwmeester R, Gevaert K, Martens L. Machine Learning on Large-Scale Proteomics Data Identifies Tissue and Cell-Type Specific Proteins. Journal of Proteome Research. PMID 36963412 DOI: 10.1021/acs.jproteome.2c00644 |
0.716 |
|
| 2023 |
Boone M, Ramasamy P, Zuallaert J, Bouwmeester R, Van Moer B, Maddelein D, Turan D, Hulstaert N, Eeckhaut H, Vandermarliere E, Martens L, Degroeve S, De Neve W, Vranken W, Callewaert N. Author Correction: Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit. Nature Communications. 14: 1072. PMID 36828852 DOI: 10.1038/s41467-023-36844-y |
0.775 |
|
| 2023 |
Neely BA, Dorfer V, Martens L, Bludau I, Bouwmeester R, Degroeve S, Deutsch EW, Gessulat S, Käll L, Palczynski P, Payne SH, Rehfeldt TG, Schmidt T, Schwämmle V, Uszkoreit J, et al. Toward an Integrated Machine Learning Model of a Proteomics Experiment. Journal of Proteome Research. PMID 36744821 DOI: 10.1021/acs.jproteome.2c00711 |
0.8 |
|
| 2023 |
Debrie E, Malfait M, Gabriels R, Declerq A, Sticker A, Martens L, Clement L. Quality Control for the Target Decoy Approach for Peptide Identification. Journal of Proteome Research. PMID 36648107 DOI: 10.1021/acs.jproteome.2c00423 |
0.774 |
|
| 2022 |
Gabriels R, Declercq A, Bouwmeester R, Degroeve S, Martens L. psm_utils: A High-Level Python API for Parsing and Handling Peptide-Spectrum Matches and Proteomics Search Results. Journal of Proteome Research. PMID 36508242 DOI: 10.1021/acs.jproteome.2c00609 |
0.821 |
|
| 2022 |
Provez L, Van Puyvelde B, Corveleyn L, Demeulemeester N, Verhelst S, Lintermans B, Daled S, Roels J, Clement L, Martens L, Deforce D, Van Vlierberghe P, Dhaenens M. An interactive mass spectrometry atlas of histone posttranslational modifications in T-cell acute leukemia. Scientific Data. 9: 626. PMID 36243775 DOI: 10.1038/s41597-022-01736-1 |
0.326 |
|
| 2022 |
Declercq A, Bouwmeester R, Hirschler A, Carapito C, Degroeve S, Martens L, Gabriels R. MSRescore: Data-driven rescoring dramatically boosts immunopeptide identification rates. Molecular & Cellular Proteomics : McP. 100266. PMID 35803561 DOI: 10.1016/j.mcpro.2022.100266 |
0.812 |
|
| 2022 |
Ramasamy P, Vandermarliere E, Vranken WF, Martens L. Panoramic Perspective on Human Phosphosites. Journal of Proteome Research. 21: 1894-1915. PMID 35793420 DOI: 10.1021/acs.jproteome.2c00164 |
0.791 |
|
| 2022 |
Shiferaw GA, Gabriels R, Bouwmeester R, Van Den Bossche T, Vandermarliere E, Martens L, Volders PJ. Sensitive and Specific Spectral Library Searching with CompOmics Spectral Library Searching Tool and Percolator. Journal of Proteome Research. 21: 1365-1370. PMID 35446579 DOI: 10.1021/acs.jproteome.2c00075 |
0.815 |
|
| 2022 |
Van Puyvelde B, Daled S, Willems S, Gabriels R, Gonzalez de Peredo A, Chaoui K, Mouton-Barbosa E, Bouyssié D, Boonen K, Hughes CJ, Gethings LA, Perez-Riverol Y, Bloomfield N, Tate S, Schiltz O, ... Martens L, et al. A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics. Scientific Data. 9: 126. PMID 35354825 DOI: 10.1038/s41597-022-01216-6 |
0.328 |
|
| 2022 |
Schallert K, Verschaffelt P, Mesuere B, Benndorf D, Martens L, Van Den Bossche T. : An Efficient Tool to Create Protein (Sub)groups from Percolator Output Files. Journal of Proteome Research. 21: 1175-1180. PMID 35143215 DOI: 10.1021/acs.jproteome.1c00685 |
0.753 |
|
| 2022 |
Delhaye L, De Bruycker E, Volders PJ, Fijalkowska D, De Sutter D, Degroeve S, Martens L, Mestdagh P, Eyckerman S. Orthogonal proteomics methods to unravel the HOTAIR interactome. Scientific Reports. 12: 1513. PMID 35087108 DOI: 10.1038/s41598-022-05405-6 |
0.797 |
|
| 2021 |
Van Den Bossche T, Kunath BJ, Schallert K, Schäpe SS, Abraham PE, Armengaud J, Arntzen MØ, Bassignani A, Benndorf D, Fuchs S, Giannone RJ, Griffin TJ, Hagen LH, Halder R, Henry C, ... ... Martens L, et al. Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows. Nature Communications. 12: 7305. PMID 34911965 DOI: 10.1038/s41467-021-27542-8 |
0.812 |
|
| 2021 |
Boone M, Ramasamy P, Zuallaert J, Bouwmeester R, Van Moer B, Maddelein D, Turan D, Hulstaert N, Eeckhaut H, Vandermarliere E, Martens L, Degroeve S, De Neve W, Vranken W, Callewaert N. Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit. Nature Communications. 12: 6414. PMID 34741024 DOI: 10.1038/s41467-021-26720-y |
0.803 |
|
| 2021 |
Bouwmeester R, Gabriels R, Hulstaert N, Martens L, Degroeve S. DeepLC can predict retention times for peptides that carry as-yet unseen modifications. Nature Methods. 18: 1363-1369. PMID 34711972 DOI: 10.1038/s41592-021-01301-5 |
0.801 |
|
| 2021 |
Van Puyvelde B, Van Uytfanghe K, Tytgat O, Van Oudenhove L, Gabriels R, Bouwmeester R, Daled S, Van Den Bossche T, Ramasamy P, Verhelst S, De Clerck L, Corveleyn L, Willems S, Debunne N, Wynendaele E, ... ... Martens L, et al. Cov-MS: A Community-Based Template Assay for Mass-Spectrometry-Based Protein Detection in SARS-CoV-2 Patients. Jacs Au. 1: 750-765. PMID 34254058 DOI: 10.1021/jacsau.1c00048 |
0.803 |
|
| 2021 |
Salz R, Bouwmeester R, Gabriels R, Degroeve S, Martens L, Volders PJ, 't Hoen PAC. Personalized Proteome: Comparing Proteogenomics and Open Variant Search Approaches for Single Amino Acid Variant Detection. Journal of Proteome Research. 20: 3353-3364. PMID 33998808 DOI: 10.1021/acs.jproteome.1c00264 |
0.82 |
|
| 2021 |
Gong S, Gaccioli F, Dopierala J, Sovio U, Cook E, Volders PJ, Martens L, Kirk PDW, Richardson S, Smith GCS, Charnock-Jones DS. The RNA landscape of the human placenta in health and disease. Nature Communications. 12: 2639. PMID 33976128 DOI: 10.1038/s41467-021-22695-y |
0.674 |
|
| 2021 |
Verbruggen S, Gessulat S, Gabriels R, Matsaroki A, Van de Voorde H, Kuster B, Degroeve S, Martens L, Van Criekinge W, Wilhelm M, Menschaert G. Spectral prediction features as a solution for the search space size problem in proteogenomics. Molecular & Cellular Proteomics : McP. 100076. PMID 33823297 DOI: 10.1016/j.mcpro.2021.100076 |
0.705 |
|
| 2021 |
Verschaffelt P, Van Den Bossche T, Gabriel W, Burdukiewicz M, Soggiu A, Martens L, Renard BY, Schiebenhoefer H, Mesuere B. MegaGO: A Fast Yet Powerful Approach to Assess Functional Gene Ontology Similarity across Meta-Omics Data Sets. Journal of Proteome Research. PMID 33661648 DOI: 10.1021/acs.jproteome.0c00926 |
0.737 |
|
| 2021 |
Verschaffelt P, Van Den Bossche T, Martens L, Dawyndt P, Mesuere B. Unipept Desktop: A Faster, More Powerful Metaproteomics Results Analysis Tool. Journal of Proteome Research. PMID 33401902 DOI: 10.1021/acs.jproteome.0c00855 |
0.751 |
|
| 2020 |
Smith S, Zhu S, Joos L, Roberts I, Nikonorova N, Vu LD, Stes E, Cho H, Larrieu A, Xuan W, Goodall B, van de Cotte B, Waite JM, Rigal A, Ramans Harborough S, ... ... Martens L, et al. The CEP5 Peptide Promotes Abiotic Stress Tolerance, As Revealed by Quantitative Proteomics, and Attenuates the AUX/IAA Equilibrium in Arabidopsis. Molecular & Cellular Proteomics : McP. 19: 1248-1262. PMID 33451502 DOI: 10.1074/mcp.RA119.001826 |
0.653 |
|
| 2020 |
Sticker A, Goeminne L, Martens L, Clement L. Robust Summarization and Inference in Proteome-wide Label-free Quantification. Molecular & Cellular Proteomics : McP. 19: 1209-1219. PMID 33451409 DOI: 10.1074/mcp.RA119.001624 |
0.788 |
|
| 2020 |
Mehta S, Easterly CW, Sajulga R, Millikin RJ, Argentini A, Eguinoa I, Martens L, Shortreed MR, Smith LM, McGowan T, Kumar P, Johnson JE, Griffin TJ, Jagtap PD. Precursor Intensity-Based Label-Free Quantification Software Tools for Proteomic and Multi-Omic Analysis within the Galaxy Platform. Proteomes. 8. PMID 32650610 DOI: 10.3390/Proteomes8030015 |
0.828 |
|
| 2020 |
Ramasamy P, Turan D, Tichshenko N, Hulstaert N, Vandermarliere E, Vranken W, Martens L. Scop3P: A Comprehensive Resource of Human Phosphosites within Their Full Context. Journal of Proteome Research. PMID 32508104 DOI: 10.1021/Acs.Jproteome.0C00306 |
0.808 |
|
| 2020 |
Verschaffelt P, Van Thienen P, Van Den Bossche T, Van der Jeugt F, De Tender C, Martens L, Dawyndt P, Mesuere B. Unipept CLI 2.0: adding support for visualisations and functional annotations. Bioinformatics (Oxford, England). PMID 32492134 DOI: 10.1093/Bioinformatics/Btaa553 |
0.769 |
|
| 2020 |
Van Den Bossche T, Verschaffelt P, Schallert K, Barsnes H, Dawyndt P, Benndorf D, Renard BY, Mesuere B, Martens L, Muth T. Connecting MetaProteomeAnalyzer and PeptideShaker to Unipept for seamless end-to-end metaproteomics data analysis. Journal of Proteome Research. PMID 32431147 DOI: 10.1021/Acs.Jproteome.0C00136 |
0.807 |
|
| 2020 |
Smith S, Zhu S, Joos L, Roberts I, Nikonorova N, Vu LD, Stes E, Cho H, Larrieu A, Xuan W, Goodall B, van de Cotte B, Waite JM, Rigal A, R Harborough SR, ... ... Martens L, et al. The CEP5 peptide promotes abiotic stress tolerance, as revealed by quantitative proteomics, and attenuates the AUX/IAA equilibrium in Arabidopsis. Molecular & Cellular Proteomics : McP. PMID 32404488 DOI: 10.1074/Mcp.Ra119.001826 |
0.678 |
|
| 2020 |
Gonzalez-Beltran AN, Masuzzo P, Ampe C, Bakker GJ, Besson S, Eibl RH, Friedl P, Gunzer M, Kittisopikul M, Dévédec SEL, Leo S, Moore J, Paran Y, Prilusky J, Rocca-Serra P, ... ... Martens L, et al. Community standards for open cell migration data. Gigascience. 9. PMID 32396199 DOI: 10.1093/Gigascience/Giaa041 |
0.806 |
|
| 2020 |
Shiferaw GA, Vandermarliere E, Hulstaert N, Gabriels R, Martens L, Volders PJ. COSS: A Fast and User-Friendly Tool for Spectral Library Searching. Journal of Proteome Research. PMID 32384242 DOI: 10.1021/Acs.Jproteome.9B00743 |
0.817 |
|
| 2020 |
Sticker A, Goeminne L, Martens L, Clement L. Robust summarization and inference in proteome-wide label-free quantification. Molecular & Cellular Proteomics : McP. PMID 32321741 DOI: 10.1074/Mcp.Ra119.001624 |
0.787 |
|
| 2020 |
Bouwmeester R, Martens L, Degroeve S. Generalized Calibration Across Liquid Chromatography Setups for Generic Prediction of Small-Molecule Retention Times. Analytical Chemistry. PMID 32281370 DOI: 10.1021/Acs.Analchem.0C00233 |
0.786 |
|
| 2020 |
Bouwmeester R, Gabriels R, Bossche TVD, Martens L, Degroeve S. The Age of Data-Driven Proteomics: How Machine Learning Enables Novel Workflows. Proteomics. e1900351. PMID 32267083 DOI: 10.1002/Pmic.201900351 |
0.804 |
|
| 2020 |
Maia TM, Staes A, Plasman K, Pauwels J, Boucher K, Argentini A, Martens L, Montoye T, Gevaert K, Impens F. Simple Peptide Quantification Approach for MS-Based Proteomics Quality Control. Acs Omega. 5: 6754-6762. PMID 32258910 DOI: 10.1021/acsomega.0c00080 |
0.811 |
|
| 2020 |
Goeminne LJE, Sticker A, Martens L, Gevaert K, Clement L. MSqRob takes the missing hurdle: uniting intensity- and count-based proteomics. Analytical Chemistry. PMID 32227882 DOI: 10.1021/Acs.Analchem.9B04375 |
0.771 |
|
| 2020 |
Gouma S, Vermeire T, Van Gucht S, Martens L, Hutse V, Cremer J, Rota PA, Leroux-Roels G, Koopmans M, van Binnendijk R, Vandermarliere E. Publisher Correction: Differences in antigenic sites and other functional regions between genotype A and G mumps virus surface proteins. Scientific Reports. 10: 5456. PMID 32198462 DOI: 10.1038/S41598-020-62301-7 |
0.774 |
|
| 2020 |
Van Puyvelde B, Willems S, Gabriels R, Daled S, De Clerck L, Vande Casteele S, Staes A, Impens F, Deforce D, Martens L, Degroeve S, Dhaenens M. Removing the Hidden Data Dependency of DIA with Predicted Spectral Libraries. Proteomics. 20: e1900306. PMID 31981311 DOI: 10.1002/Pmic.201900306 |
0.728 |
|
| 2020 |
Van Puyvelde B, Willems S, Gabriels R, Daled S, De Clerck L, Vande Casteele S, Staes A, Impens F, Deforce D, Martens L, Degroeve S, Dhaenens M. Front Cover: Removing the Hidden Data Dependency of DIA with Predicted Spectral Libraries Proteomics. 20: 2070021. DOI: 10.1002/Pmic.202070021 |
0.678 |
|
| 2019 |
Hulstaert N, Shofstahl J, Sachsenberg T, Walzer M, Barsnes H, Martens L, Perez-Riverol Y. ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion. Journal of Proteome Research. PMID 31755270 DOI: 10.1021/Acs.Jproteome.9B00328 |
0.817 |
|
| 2019 |
Nye LC, Williams JP, Munjoma NC, Letertre MPM, Coen M, Bouwmeester R, Martens L, Swann JR, Nicholson JK, Plumb RS, McCullagh M, Gethings LA, Lai S, Langridge JI, Vissers JPC, et al. A comparison of collision cross section values obtained via travelling wave ion mobility-mass spectrometry and ultra high performance liquid chromatography-ion mobility-mass spectrometry: Application to the characterisation of metabolites in rat urine. Journal of Chromatography. A. PMID 31285057 DOI: 10.1016/J.Chroma.2019.06.056 |
0.72 |
|
| 2019 |
Silva ASC, Bouwmeester R, Martens L, Degroeve S. Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functions. Bioinformatics (Oxford, England). PMID 31077310 DOI: 10.1093/Bioinformatics/Btz383 |
0.804 |
|
| 2019 |
Gabriels R, Martens L, Degroeve S. Updated MS²PIP web server delivers fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques. Nucleic Acids Research. PMID 31028400 DOI: 10.1093/Nar/Gkz299 |
0.706 |
|
| 2019 |
Schiebenhoefer H, Van Den Bossche T, Fuchs S, Renard BY, Muth T, Martens L. Challenges and promise at the interface of metaproteomics and genomics: an overview of recent progress in metaproteogenomic data analysis. Expert Review of Proteomics. PMID 31002542 DOI: 10.1080/14789450.2019.1609944 |
0.842 |
|
| 2019 |
Ivanova H, Wagner LE, Tanimura A, Vandermarliere E, Luyten T, Welkenhuyzen K, Alzayady KJ, Wang L, Hamada K, Mikoshiba K, De Smedt H, Martens L, Yule DI, Parys JB, Bultynck G. Bcl-2 and IP compete for the ligand-binding domain of IPRs modulating Ca signaling output. Cellular and Molecular Life Sciences : Cmls. PMID 30989245 DOI: 10.1007/S00018-019-03091-8 |
0.65 |
|
| 2019 |
Bouwmeester R, Martens L, Degroeve S. Comprehensive and empirical evaluation of machine learning algorithms for small molecule LC retention time prediction. Analytical Chemistry. PMID 30702864 DOI: 10.1021/Acs.Analchem.8B05820 |
0.785 |
|
| 2018 |
Buthelezi SG, Dirr HW, Chakauya E, Chikwamba R, Martens L, Tsekoa TL, Vandermarliere E, Stoychev SH. The study of degradation mechanisms of glyco-engineered plant produced anti-rabies monoclonal antibodies E559 and 62-71-3. Plos One. 13: e0209373. PMID 30571707 DOI: 10.1371/Journal.Pone.0209373 |
0.668 |
|
| 2018 |
Kreft L, Turan D, Hulstaert N, Botzki A, Martens L, Vandermarliere E. Scop3D: online visualization of mutation rates on protein structure. Journal of Proteome Research. PMID 30540477 DOI: 10.1021/Acs.Jproteome.8B00681 |
0.807 |
|
| 2018 |
Argentini A, Staes A, Grüning BA, Mehta S, Easterly C, Griffin TJ, Jagtap P, Impens F, Martens L. An update on the moFF Algorithm for label-free quantitative proteomics. Journal of Proteome Research. PMID 30511867 DOI: 10.1021/Acs.Jproteome.8B00708 |
0.822 |
|
| 2018 |
Vermeire T, Barbezange C, Francart A, Hamouda A, Litzroth A, Hutse V, Martens L, Vandermarliere E, Van Gucht S. Sera from different age cohorts in Belgium show limited cross-neutralization between the mumps vaccine and outbreak strains. Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases. 25: 907.e1-907.e6. PMID 30502489 DOI: 10.1016/J.Cmi.2018.11.016 |
0.753 |
|
| 2018 |
Volders PJ, Anckaert J, Verheggen K, Nuytens J, Martens L, Mestdagh P, Vandesompele J. LNCipedia 5: towards a reference set of human long non-coding RNAs. Nucleic Acids Research. PMID 30371849 DOI: 10.1093/Nar/Gky1031 |
0.782 |
|
| 2018 |
Gouma S, Vermeire T, Van Gucht S, Martens L, Hutse V, Cremer J, Rota PA, Leroux-Roels G, Koopmans M, Binnendijk RV, Vandermarliere E. Differences in antigenic sites and other functional regions between genotype A and G mumps virus surface proteins. Scientific Reports. 8: 13337. PMID 30190529 DOI: 10.1038/S41598-018-31630-Z |
0.772 |
|
| 2018 |
C Silva AS, Palmer A, Kovalev V, Tarasov A, Alexandrov T, Martens L, Degroeve S. Data-driven rescoring of metabolite annotations significantly improves sensitivity. Analytical Chemistry. PMID 30188119 DOI: 10.1021/Acs.Analchem.8B03224 |
0.691 |
|
| 2018 |
Sergeant G, Martens L, Van Troys M, Masuzzo P. DoRes within CellMissy: dose-response analysis on cell migration and related data. Bioinformatics (Oxford, England). PMID 30052834 DOI: 10.1093/Bioinformatics/Bty634 |
0.793 |
|
| 2018 |
Tardaguila M, de la Fuente L, Marti C, Pereira C, Pardo-Palacios FJ, Del Risco H, Ferrell M, Mellado M, Macchietto M, Verheggen K, Edelmann M, Ezkurdia I, Vazquez J, Tress M, Mortazavi A, ... Martens L, et al. Corrigendum: SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification. Genome Research. 28: 1096. PMID 29967126 DOI: 10.1101/Gr.239137.118 |
0.741 |
|
| 2018 |
Yılmaz Ş, Shiferaw GA, Rayo J, Economou A, Martens L, Vandermarliere E. Cross-linked peptide identification: A computational forest of algorithms. Mass Spectrometry Reviews. PMID 29529716 DOI: 10.1002/Mas.21559 |
0.816 |
|
| 2018 |
Van Troys M, Masuzzo P, Huyck L, Bakkali K, Waterschoot D, Martens L, Ampe C. Analysis of Invasion Dynamics of Matrix-Embedded Cells in a Multisample Format. Methods in Molecular Biology (Clifton, N.J.). 1749: 79-117. PMID 29525993 DOI: 10.1007/978-1-4939-7701-7_9 |
0.758 |
|
| 2018 |
De Wilde B, Beckers A, Lindner S, Kristina A, De Preter K, Depuydt P, Mestdagh P, Sante T, Lefever S, Hertwig F, Peng Z, Shi LM, Lee S, Vandermarliere E, Martens L, et al. The mutational landscape of,anddriven murine neuroblastoma mimics human disease. Oncotarget. 9: 8334-8349. PMID 29492199 DOI: 10.18632/Oncotarget.23614 |
0.664 |
|
| 2018 |
Tardaguila M, de la Fuente L, Marti C, Pereira C, Pardo-Palacios FJ, Del Risco H, Ferrell M, Mellado M, Macchietto M, Verheggen K, Edelmann M, Ezkurdia I, Vazquez J, Tress M, Mortazavi A, ... Martens L, et al. SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification. Genome Research. PMID 29440222 DOI: 10.1101/Gr.222976.117 |
0.765 |
|
| 2018 |
Muth T, Kohrs F, Heyer R, Benndorf D, Rapp E, Reichl U, Martens L, Renard BY. MPA Portable: A Stand-Alone Software Package for Analyzing Metaproteome Samples on the Go. Analytical Chemistry. 90: 685-689. PMID 29215871 DOI: 10.1021/Acs.Analchem.7B03544 |
0.756 |
|
| 2018 |
Mehta S, Easterly C, Johnson JE, Gruening B, Argentini A, Millikin RJ, Shortreed MR, McGowan T, Kumar P, Martens L, Smith LM, Griffin TJ, Jagtap P. Evaluation of moFF and FlashLFQ for label free peptide quantification in proteomic workflows within Galaxy-P framework. F1000research. 7. DOI: 10.7490/F1000Research.1115792.1 |
0.793 |
|
| 2017 |
Chambers MC, Jagtap PD, Johnson JE, McGowan T, Kumar P, Onsongo G, Guerrero CR, Barsnes H, Vaudel M, Martens L, Grüning B, Cooke IR, Heydarian M, Reddy KL, Griffin TJ. An Accessible Proteogenomics Informatics Resource for Cancer Researchers. Cancer Research. 77: e43-e46. PMID 29092937 DOI: 10.1158/0008-5472.Can-17-0331 |
0.789 |
|
| 2017 |
Gupta S, Turan D, Tavernier J, Martens L. The online Tabloid Proteome: an annotated database of protein associations. Nucleic Acids Research. PMID 29040688 DOI: 10.1093/Nar/Gkx930 |
0.823 |
|
| 2017 |
Verheggen K, Raeder H, Berven FS, Martens L, Barsnes H, Vaudel M. Anatomy and evolution of database search engines-a central component of mass spectrometry based proteomic workflows. Mass Spectrometry Reviews. PMID 28902424 DOI: 10.1002/Mas.21543 |
0.819 |
|
| 2017 |
Bittremieux W, Tabb DL, Impens F, Staes A, Timmerman E, Martens L, Laukens K. Quality control in mass spectrometry-based proteomics. Mass Spectrometry Reviews. PMID 28802010 DOI: 10.1002/Mas.21544 |
0.358 |
|
| 2017 |
Vizcaíno JA, Walzer M, Jiménez RC, Bittremieux W, Bouyssié D, Carapito C, Corrales F, Ferro M, Heck AJR, Horvatovich P, Hubalek M, Lane L, Laukens K, Levander F, Lisacek F, ... ... Martens L, et al. A community proposal to integrate proteomics activities in ELIXIR. F1000research. 6. PMID 28713550 DOI: 10.12688/F1000Research.11751.1 |
0.338 |
|
| 2017 |
Sticker A, Martens L, Clement L. Mass spectrometrists should search for all peptides, but assess only the ones they care about. Nature Methods. 14: 643-644. PMID 28661493 DOI: 10.1038/Nmeth.4338 |
0.737 |
|
| 2017 |
Mesuere B, Van der Jeugt F, Willems T, Naessens T, Devreese B, Martens L, Dawyndt P. High-throughput metaproteomics data analysis with Unipept: A tutorial. Journal of Proteomics. PMID 28552653 DOI: 10.1016/J.Jprot.2017.05.022 |
0.454 |
|
| 2017 |
Verheggen K, Volders PJ, Mestdagh P, Menschaert G, Van Damme P, Gevaert K, Martens L, Vandesompele J. Noncoding after All: Biases in Proteomics Data Do Not Explain Observed Absence of lncRNA Translation Products. Journal of Proteome Research. 16: 2508-2515. PMID 28534634 DOI: 10.1021/Acs.Jproteome.7B00085 |
0.798 |
|
| 2017 |
Gupta S, Verheggen K, Tavernier J, Martens L. An unbiased protein association study on the public human proteome reveals biological connections between co-occurring protein pairs. Journal of Proteome Research. PMID 28480704 DOI: 10.1021/Acs.Jproteome.6B01066 |
0.824 |
|
| 2017 |
Gupta S, De Puysseleyr V, Van der Heyden J, Maddelein D, Lemmens I, Lievens S, Degroeve S, Tavernier J, Martens L. MAPPI-DAT: data management and analysis for protein-protein interaction data from the high-throughput MAPPIT cell microarray platform. Bioinformatics (Oxford, England). 33: 1424-1425. PMID 28453684 DOI: 10.1093/Bioinformatics/Btx014 |
0.816 |
|
| 2017 |
Willems P, Ndah E, Jonckheere V, Stael S, Sticker A, Martens L, Van Breusegem F, Gevaert K, Van Damme P. N-terminal Proteomics Assisted Profiling of the Unexplored Translation Initiation Landscape in Arabidopsis thaliana. Molecular & Cellular Proteomics : McP. 16: 1064-1080. PMID 28432195 DOI: 10.1074/Mcp.M116.066662 |
0.81 |
|
| 2017 |
Masuzzo P, Huyck L, Simiczyjew A, Ampe C, Martens L, Van Troys M. An end-to-end software solution for the analysis of high-throughput single-cell migration data. Scientific Reports. 7: 42383. PMID 28205527 DOI: 10.1038/Srep42383 |
0.79 |
|
| 2017 |
Titeca K, Meysman P, Laukens K, Martens L, Tavernier J, Eyckerman S. sfinx: an R package for the elimination of false positives from affinity purification - mass spectrometry datasets. Bioinformatics (Oxford, England). PMID 28186257 DOI: 10.1093/Bioinformatics/Btx076 |
0.302 |
|
| 2017 |
Martens L, Vizcaíno JA. A Golden Age for Working with Public Proteomics Data. Trends in Biochemical Sciences. 42: 333-341. PMID 28118949 DOI: 10.1016/J.Tibs.2017.01.001 |
0.431 |
|
| 2017 |
Gupta S, De Puysseleyr V, Van der Heyden J, Maddelein D, Lemmens I, Lievens S, Degroeve S, Tavernier J, Martens L. MAPPI-DAT: data management and analysis for protein-protein interaction data from the high-throughput MAPPIT cell microarray platform. Bioinformatics (Oxford, England). PMID 28104627 DOI: 10.1093/bioinformatics/btx014 |
0.816 |
|
| 2017 |
Yilmaz Ş, Vandermarliere E, Martens L. Methods to Calculate Spectrum Similarity. Methods in Molecular Biology (Clifton, N.J.). 1549: 75-100. PMID 27975285 DOI: 10.1007/978-1-4939-6740-7_7 |
0.804 |
|
| 2016 |
Martens L. Public proteomics data: How the field has evolved from sceptical inquiry to the promise of proteomics. Eupa Open Proteomics. 11: 42-44. PMID 29900110 DOI: 10.1016/J.Euprot.2016.02.005 |
0.349 |
|
| 2016 |
Verheggen K, Martens L, Berven FS, Barsnes H, Vaudel M. Database Search Engines: Paradigms, Challenges and Solutions. Advances in Experimental Medicine and Biology. 919: 147-156. PMID 27975215 DOI: 10.1007/978-3-319-41448-5_6 |
0.819 |
|
| 2016 |
Argentini A, Goeminne LJ, Verheggen K, Hulstaert N, Staes A, Clement L, Martens L. moFF: a robust and automated approach to extract peptide ion intensities. Nature Methods. 13: 964-966. PMID 27898063 DOI: 10.1038/Nmeth.4075 |
0.78 |
|
| 2016 |
Lievens S, Van der Heyden J, Masschaele D, De Ceuninck L, Petta I, Gupta S, De Puysseleir V, Vauthier V, Lemmens I, De Clercq D, Defever D, Vanderroost N, De Smet AS, Eyckerman S, Van Calenbergh S, ... Martens L, et al. Proteome-scale binary interactomics in human cells. Molecular & Cellular Proteomics : McP. PMID 27803151 DOI: 10.1074/Mcp.M116.061994 |
0.733 |
|
| 2016 |
Tanca A, Palomba A, Fraumene C, Pagnozzi D, Manghina V, Deligios M, Muth T, Rapp E, Martens L, Addis MF, Uzzau S. The impact of sequence database choice on metaproteomic results in gut microbiota studies. Microbiome. 4: 51. PMID 27671352 DOI: 10.1186/S40168-016-0196-8 |
0.717 |
|
| 2016 |
Vu LD, Stes E, Van Bel M, Nelissen H, Maddelein D, Inzé D, Coppens F, Martens L, Gevaert K, De Smet I. An up-to-date workflow for plant (phospho)proteomics identifies differential drought-responsive phosphorylation events in maize leaves. Journal of Proteome Research. PMID 27643528 DOI: 10.1021/Acs.Jproteome.6B00348 |
0.803 |
|
| 2016 |
Yılmaz Ş, Drepper F, Hulstaert N, Cernic M, Gevaert K, Economou A, Warscheid B, Martens L, Vandermarliere E. Xilmass: a new approach towards the identification of cross-linked peptides. Analytical Chemistry. PMID 27642655 DOI: 10.1021/Acs.Analchem.6B01585 |
0.811 |
|
| 2016 |
Buthelezi SG, Dirr HW, Chakauya E, Chikwamba R, Martens L, Tsekoa TL, Stoychev SH, Vandermarliere E. The Lyssavirus glycoprotein: A key to cross-immunity. Virology. 498: 250-256. PMID 27614701 DOI: 10.1016/J.Virol.2016.08.034 |
0.658 |
|
| 2016 |
Bittremieux W, Valkenborg D, Martens L, Laukens K. Computational quality control tools for mass spectrometry proteomics. Proteomics. PMID 27549080 DOI: 10.1002/Pmic.201600159 |
0.349 |
|
| 2016 |
Deutsch EW, Overall CM, Van Eyk JE, Baker MS, Paik YK, Weintraub ST, Lane L, Martens L, Vandenbrouck Y, Kusebauch U, Hancock WS, Hermjakob H, Aebersold R, Moritz RL, Omenn GS. Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1. Journal of Proteome Research. 15: 3961-3970. PMID 27490519 DOI: 10.1021/Acs.Jproteome.6B00392 |
0.426 |
|
| 2016 |
Arora R, Di Michele M, Stes E, Vandermarliere E, Martens L, Gevaert K, Van Heerde E, Linders JT, Brehmer D, Jacoby E, Bonnet P. Correction to Structural Investigation of B-Raf Paradox Breaker and Inducer Inhibitors. Journal of Medicinal Chemistry. PMID 27385554 DOI: 10.1021/Acs.Jmedchem.6B00941 |
0.637 |
|
| 2016 |
Muth T, Renard BY, Martens L. Metaproteomic data analysis at a glance: advances in computational microbial community proteomics. Expert Review of Proteomics. PMID 27376173 DOI: 10.1080/14789450.2016.1209418 |
0.688 |
|
| 2016 |
Peters JS, Calder B, Gonnelli G, Degroeve S, Rajaonarifara E, Mulder N, Soares NC, Martens L, Blackburn JM. Identification of Quantitative Proteomic Differences between Mycobacterium tuberculosis Lineages with Altered Virulence. Frontiers in Microbiology. 7: 813. PMID 27303394 DOI: 10.3389/Fmicb.2016.00813 |
0.807 |
|
| 2016 |
Vandemoortele G, Staes A, Gonnelli G, Samyn N, De Sutter D, Vandermarliere E, Timmerman E, Gevaert K, Martens L, Eyckerman S. An extra dimension in protein tagging by quantifying universal proteotypic peptides using targeted proteomics. Scientific Reports. 6: 27220. PMID 27264994 DOI: 10.1038/Srep27220 |
0.822 |
|
| 2016 |
Yılmaz Ş, Victor B, Hulstaert N, Vandermarliere E, Barsnes H, Degroeve S, Gupta S, Sticker A, Gabriël S, Dorny P, Palmblad M, Martens L. A pipeline for differential proteomics in unsequenced species. Journal of Proteome Research. PMID 27089233 DOI: 10.1021/Acs.Jproteome.6B00140 |
0.794 |
|
| 2016 |
Maes E, Kelchtermans P, Bittremieux W, De Grave K, Degroeve S, Hooyberghs J, Mertens I, Baggerman G, Ramon J, Laukens K, Martens L, Valkenborg D. Designing biomedical proteomics experiments: state-of-the-art and future perspectives. Expert Review of Proteomics. 13: 495-511. PMID 27031651 DOI: 10.1586/14789450.2016.1172967 |
0.788 |
|
| 2016 |
Bittremieux W, Meysman P, Martens L, Valkenborg D, Laukens K. Unsupervised Quality Assessment of Mass Spectrometry Proteomics Experiments by Multivariate Quality Control Metrics. Journal of Proteome Research. 15: 1300-7. PMID 26974716 DOI: 10.1021/Acs.Jproteome.6B00028 |
0.311 |
|
| 2016 |
Titeca K, Meysman P, Gevaert K, Tavernier J, Laukens K, Martens L, Eyckerman S. SFINX: Straightforward Filtering Index for Affinity Purification-Mass Spectrometry Data Analysis. Journal of Proteome Research. 15: 332-8. PMID 26616242 DOI: 10.1021/Acs.Jproteome.5B00666 |
0.41 |
|
| 2016 |
Olexiouk V, Crappé J, Verbruggen S, Verhegen K, Martens L, Menschaert G. sORFs.org: a repository of small ORFs identified by ribosome profiling. Nucleic Acids Research. 44: D324-9. PMID 26527729 DOI: 10.1093/Nar/Gkv1175 |
0.432 |
|
| 2016 |
Verheggen K, Maddelein D, Hulstaert N, Martens L, Barsnes H, Vaudel M. Pladipus Enables Universal Distributed Computing in Proteomics Bioinformatics. Journal of Proteome Research. 15: 707-12. PMID 26510693 DOI: 10.1021/Acs.Jproteome.5B00850 |
0.79 |
|
| 2016 |
Masuzzo P, Van Troys M, Ampe C, Martens L. Taking Aim at Moving Targets in Computational Cell Migration. Trends in Cell Biology. 26: 88-110. PMID 26481052 DOI: 10.1016/J.Tcb.2015.09.003 |
0.76 |
|
| 2016 |
Vaudel M, Verheggen K, Csordas A, Raeder H, Berven FS, Martens L, Vizcaíno JA, Barsnes H. Exploring the potential of public proteomics data. Proteomics. 16: 214-25. PMID 26449181 DOI: 10.1002/Pmic.201500295 |
0.821 |
|
| 2016 |
Argentini A, Goeminne LJE, Verheggen K, Hulstaert N, Staes A, Clement L, Martens L. Using moFF to Extract Peptide Ion Intensities from LC-MS experiments Protocol Exchange. DOI: 10.1038/Protex.2016.085 |
0.79 |
|
| 2016 |
Vermeire T, Gouma S, Van Gucht S, Martens L, Hutse V, Cremer J, Rota P, Leroux-Roels G, Koopmans M, Van Binnendijk R, Vandermarliere E. Differences among mumps virus surface proteins between genotype G and other genotypes and their potential effect on mumps virus immunity and pathogenesis Journal of Clinical Virology. 82: S20. DOI: 10.1016/J.Jcv.2016.08.037 |
0.76 |
|
| 2015 |
Meysman P, Titeca K, Eyckerman S, Tavernier J, Goethals B, Martens L, Valkenborg D, Laukens K. Protein complex analysis: From raw protein lists to protein interaction networks. Mass Spectrometry Reviews. PMID 26709718 DOI: 10.1002/Mas.21485 |
0.388 |
|
| 2015 |
Kelchtermans P, Silva AS, Argentini A, Staes A, Vandenbussche J, Laukens K, Valkenborg D, Martens L. Open-Source, Platform-Independent Library and Online Scripting Environment for Accessing Thermo Scientific RAW Files. Journal of Proteome Research. 14: 4940-3. PMID 26477298 DOI: 10.1021/Acs.Jproteome.5B00778 |
0.813 |
|
| 2015 |
Di Michele M, Stes E, Vandermarliere E, Arora R, Astorga-Wells J, Vandenbussche J, van Heerde E, Zubarev R, Bonnet P, Linders JT, Jacoby E, Brehmer D, Martens L, Gevaert K. Limited Proteolysis Combined with Stable Isotope Labeling Reveals Conformational Changes in Protein (Pseudo)kinases upon Binding Small Molecules. Journal of Proteome Research. 14: 4179-93. PMID 26293246 DOI: 10.1021/Acs.Jproteome.5B00282 |
0.649 |
|
| 2015 |
Kolmeder CA, Ritari J, Verdam FJ, Muth T, Keskitalo S, Varjosalo M, Fuentes S, Greve JW, Buurman WA, Reichl U, Rapp E, Martens L, Palva A, Salonen A, Rensen SS, et al. Colonic metaproteomic signatures of active bacteria and the host in obesity. Proteomics. PMID 26255997 DOI: 10.1002/Pmic.201500049 |
0.698 |
|
| 2015 |
Glibert P, Meert P, Van Steendam K, Martens L, Deforce D, Dhaenens M. Phospho-iTRAQ data article: Assessing isobaric labels for the large-scale study of phosphopeptide stoichiometry. Data in Brief. 4: 60-5. PMID 26217764 DOI: 10.1016/J.Dib.2015.04.012 |
0.407 |
|
| 2015 |
Nasso S, Goetze S, Martens L. Ariadne's Thread: A Robust Software Solution Leading to Automated Absolute and Relative Quantification of SRM Data. Journal of Proteome Research. 14: 3779-92. PMID 26123309 DOI: 10.1021/Pr500996S |
0.403 |
|
| 2015 |
Degroeve S, Maddelein D, Martens L. MS2PIP prediction server: compute and visualize MS2 peak intensity predictions for CID and HCD fragmentation. Nucleic Acids Research. 43: W326-30. PMID 25990723 DOI: 10.1093/Nar/Gkv542 |
0.802 |
|
| 2015 |
Maddelein D, Colaert N, Buchanan I, Hulstaert N, Gevaert K, Martens L. The iceLogo web server and SOAP service for determining protein consensus sequences. Nucleic Acids Research. 43: W543-6. PMID 25897125 DOI: 10.1093/Nar/Gkv385 |
0.797 |
|
| 2015 |
Vervliet T, Lemmens I, Vandermarliere E, Decrock E, Ivanova H, Monaco G, Sorrentino V, Nadif Kasri N, Missiaen L, Martens L, De Smedt H, Leybaert L, Parys JB, Tavernier J, Bultynck G. Ryanodine receptors are targeted by anti-apoptotic Bcl-XL involving its BH4 domain and Lys87 from its BH3 domain. Scientific Reports. 5: 9641. PMID 25872771 DOI: 10.1038/Srep09641 |
0.652 |
|
| 2015 |
Volders PJ, Verheggen K, Menschaert G, Vandepoele K, Martens L, Vandesompele J, Mestdagh P. An update on LNCipedia: a database for annotated human lncRNA sequences. Nucleic Acids Research. 43: 4363-4. PMID 25829178 DOI: 10.1093/nar/gkv295 |
0.737 |
|
| 2015 |
Goeminne LJ, Argentini A, Martens L, Clement L. Summarization vs Peptide-Based Models in Label-Free Quantitative Proteomics: Performance, Pitfalls, and Data Analysis Guidelines. Journal of Proteome Research. 14: 2457-65. PMID 25827922 DOI: 10.1021/Pr501223T |
0.829 |
|
| 2015 |
Bittremieux W, Willems H, Kelchtermans P, Martens L, Laukens K, Valkenborg D. iMonDB: Mass Spectrometry Quality Control through Instrument Monitoring. Journal of Proteome Research. 14: 2360-6. PMID 25798920 DOI: 10.1021/Acs.Jproteome.5B00127 |
0.806 |
|
| 2015 |
Muth T, Kolmeder CA, Salojärvi J, Keskitalo S, Varjosalo M, Verdam FJ, Rensen SS, Reichl U, de Vos WM, Rapp E, Martens L. Navigating through metaproteomics data: A logbook of database searching. Proteomics. PMID 25778831 DOI: 10.1002/Pmic.201400560 |
0.74 |
|
| 2015 |
Martens L, Kohlbacher O, Weintraub ST. Managing expectations when publishing tools and methods for computational proteomics. Journal of Proteome Research. 14: 2002-4. PMID 25764342 DOI: 10.1021/Pr501318D |
0.39 |
|
| 2015 |
Vandermarliere E, Maddelein D, Hulstaert N, Stes E, Di Michele M, Gevaert K, Jacoby E, Brehmer D, Martens L. PepShell: visualization of conformational proteomics data. Journal of Proteome Research. 14: 1987-90. PMID 25728987 DOI: 10.1021/Pr5012125 |
0.818 |
|
| 2015 |
Gonnelli G, Stock M, Verwaeren J, Maddelein D, De Baets B, Martens L, Degroeve S. A decoy-free approach to the identification of peptides. Journal of Proteome Research. 14: 1792-8. PMID 25714903 DOI: 10.1021/Pr501164R |
0.811 |
|
| 2015 |
Muth T, Behne A, Heyer R, Kohrs F, Benndorf D, Hoffmann M, Lehtevä M, Reichl U, Martens L, Rapp E. The MetaProteomeAnalyzer: a powerful open-source software suite for metaproteomics data analysis and interpretation. Journal of Proteome Research. 14: 1557-65. PMID 25660940 DOI: 10.1021/Pr501246W |
0.753 |
|
| 2015 |
Vermeire T, Vermaere S, Schepens B, Saelens X, Van Gucht S, Martens L, Vandermarliere E. Scop3D: three-dimensional visualization of sequence conservation. Proteomics. 15: 1448-52. PMID 25641949 DOI: 10.1002/Pmic.201400354 |
0.803 |
|
| 2015 |
Arora R, Di Michele M, Stes E, Vandermarliere E, Martens L, Gevaert K, Van Heerde E, Linders JT, Brehmer D, Jacoby E, Bonnet P. Structural investigation of B-Raf paradox breaker and inducer inhibitors. Journal of Medicinal Chemistry. 58: 1818-31. PMID 25611072 DOI: 10.1021/Jm501667N |
0.643 |
|
| 2015 |
Vaudel M, Burkhart JM, Zahedi RP, Oveland E, Berven FS, Sickmann A, Martens L, Barsnes H. PeptideShaker enables reanalysis of MS-derived proteomics data sets. Nature Biotechnology. 33: 22-4. PMID 25574629 DOI: 10.1038/Nbt.3109 |
0.763 |
|
| 2015 |
Van Leene J, Eeckhout D, Cannoot B, De Winne N, Persiau G, Van De Slijke E, Vercruysse L, Dedecker M, Verkest A, Vandepoele K, Martens L, Witters E, Gevaert K, De Jaeger G. An improved toolbox to unravel the plant cellular machinery by tandem affinity purification of Arabidopsis protein complexes. Nature Protocols. 10: 169-87. PMID 25521792 DOI: 10.1038/Nprot.2014.199 |
0.411 |
|
| 2015 |
Glibert P, Meert P, Van Steendam K, Van Nieuwerburgh F, De Coninck D, Martens L, Dhaenens M, Deforce D. Phospho-iTRAQ: assessing isobaric labels for the large-scale study of phosphopeptide stoichiometry. Journal of Proteome Research. 14: 839-49. PMID 25510630 DOI: 10.1021/Pr500889V |
0.435 |
|
| 2015 |
Oveland E, Muth T, Rapp E, Martens L, Berven FS, Barsnes H. Viewing the proteome: how to visualize proteomics data? Proteomics. 15: 1341-55. PMID 25504833 DOI: 10.1002/Pmic.201400412 |
0.792 |
|
| 2015 |
Masuzzo P, Martens L, Ampe C, Anderson KI, Barry J, De Wever O, Debeir O, Decaestecker C, Dolznig H, Friedl P, Gaggioli C, Geiger B, Goldberg IG, Horn E, et al. An open data ecosystem for cell migration research. Trends in Cell Biology. 25: 55-8. PMID 25484346 DOI: 10.1016/J.Tcb.2014.11.005 |
0.764 |
|
| 2015 |
Barsnes H, Vaudel M, Martens L. JSparklines: making tabular proteomics data come alive. Proteomics. 15: 1428-31. PMID 25422159 DOI: 10.1002/Pmic.201400356 |
0.77 |
|
| 2015 |
Volders PJ, Verheggen K, Menschaert G, Vandepoele K, Martens L, Vandesompele J, Mestdagh P. An update on LNCipedia: a database for annotated human lncRNA sequences. Nucleic Acids Research. 43: D174-80. PMID 25378313 DOI: 10.1093/Nar/Gku1060 |
0.791 |
|
| 2015 |
Vermeire T, Vermaere S, Van Gucht S, Hutse V, Martens L, Vandermarliere E. Computational analysis of mumps surface proteins reveals their interaction mechanism Journal of Clinical Virology. 70: S34. DOI: 10.1016/J.Jcv.2015.07.084 |
0.779 |
|
| 2015 |
Verheggen K, Martens L. Ten years of public proteomics data: How things have evolved, and where the next ten years should lead us Eupa Open Proteomics. 8: 28-35. DOI: 10.1016/J.Euprot.2015.07.014 |
0.754 |
|
| 2014 |
Vandermarliere E, Stes E, Gevaert K, Martens L. Resolution of protein structure by mass spectrometry. Mass Spectrometry Reviews. PMID 25536908 DOI: 10.1002/Mas.21450 |
0.738 |
|
| 2014 |
Bittremieux W, Kelchtermans P, Valkenborg D, Martens L, Laukens K. jqcML: an open-source java API for mass spectrometry quality control data in the qcML format. Journal of Proteome Research. 13: 3484-7. PMID 24906114 DOI: 10.1021/Pr401274Z |
0.81 |
|
| 2014 |
Vaudel M, Barsnes H, Martens L, Berven FS. Bioinformatics for proteomics: opportunities at the interface between the scientists, their experiments, and the community. Methods in Molecular Biology (Clifton, N.J.). 1156: 239-48. PMID 24791993 DOI: 10.1007/978-1-4939-0685-7_16 |
0.758 |
|
| 2014 |
Walzer M, Pernas LE, Nasso S, Bittremieux W, Nahnsen S, Kelchtermans P, Pichler P, van den Toorn HW, Staes A, Vandenbussche J, Mazanek M, Taus T, Scheltema RA, Kelstrup CD, Gatto L, ... ... Martens L, et al. qcML: an exchange format for quality control metrics from mass spectrometry experiments. Molecular & Cellular Proteomics : McP. 13: 1905-13. PMID 24760958 DOI: 10.1074/Mcp.M113.035907 |
0.807 |
|
| 2014 |
Vandermarliere E, Ghesquière B, Jonckheere V, Gevaert K, Martens L. Unraveling the specificities of the different human methionine sulfoxide reductases. Proteomics. 14: 1990-8. PMID 24737740 DOI: 10.1002/Pmic.201300357 |
0.64 |
|
| 2014 |
Vaudel M, Venne AS, Berven FS, Zahedi RP, Martens L, Barsnes H. Shedding light on black boxes in protein identification. Proteomics. 14: 1001-5. PMID 24678044 DOI: 10.1002/Pmic.201300488 |
0.795 |
|
| 2014 |
Kolker E, Özdemir V, Martens L, Hancock W, Anderson G, Anderson N, Aynacioglu S, Baranova A, Campagna SR, Chen R, Choiniere J, Dearth SP, Feng WC, Ferguson L, Fox G, et al. Toward more transparent and reproducible omics studies through a common metadata checklist and data publications. Omics : a Journal of Integrative Biology. 18: 10-4. PMID 24456465 DOI: 10.1089/Omi.2013.0149 |
0.802 |
|
| 2014 |
Beck F, Geiger J, Gambaryan S, Veit J, Vaudel M, Nollau P, Kohlbacher O, Martens L, Walter U, Sickmann A, Zahedi RP. Time-resolved characterization of cAMP/PKA-dependent signaling reveals that platelet inhibition is a concerted process involving multiple signaling pathways. Blood. 123: e1-e10. PMID 24324209 DOI: 10.1182/Blood-2013-07-512384 |
0.602 |
|
| 2014 |
Kelchtermans P, Bittremieux W, De Grave K, Degroeve S, Ramon J, Laukens K, Valkenborg D, Barsnes H, Martens L. Machine learning applications in proteomics research: how the past can boost the future. Proteomics. 14: 353-66. PMID 24323524 DOI: 10.1002/Pmic.201300289 |
0.787 |
|
| 2014 |
Muth T, Weilnböck L, Rapp E, Huber CG, Martens L, Vaudel M, Barsnes H. DeNovoGUI: an open source graphical user interface for de novo sequencing of tandem mass spectra. Journal of Proteome Research. 13: 1143-6. PMID 24295440 DOI: 10.1021/Pr4008078 |
0.818 |
|
| 2014 |
Verheggen K, Barsnes H, Martens L. Distributed computing and data storage in proteomics: many hands make light work, and a stronger memory. Proteomics. 14: 367-77. PMID 24285552 DOI: 10.1002/Pmic.201300288 |
0.788 |
|
| 2014 |
Vaudel M, Sickmann A, Martens L. Introduction to opportunities and pitfalls in functional mass spectrometry based proteomics. Biochimica Et Biophysica Acta. 1844: 12-20. PMID 23845992 DOI: 10.1016/J.Bbapap.2013.06.019 |
0.707 |
|
| 2014 |
Yılmaz Ş, Victor B, Hulstaert N, Gonnelli G, Dorny P, Palmblad M, Martens L. Comparing fragmentation spectra from two parasitic worm species to discover unique peptides F1000research. 5. DOI: 10.7490/F1000Research.1094933.1 |
0.808 |
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| 2013 |
Kolker E, Özdemir V, Martens L, Hancock W, Anderson G, Anderson N, Aynacioglu S, Baranova A, Campagna SR, Chen R, Choiniere J, Dearth SP, Feng WC, Ferguson L, Fox G, et al. Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications. Big Data. 1: 196-201. PMID 27447251 DOI: 10.1089/big.2013.0039 |
0.802 |
|
| 2013 |
Staes A, Vandenbussche J, Demol H, Goethals M, Yilmaz S, Hulstaert N, Degroeve S, Kelchtermans P, Martens L, Gevaert K. Asn3, a reliable, robust, and universal lock mass for improved accuracy in LC-MS and LC-MS/MS Analytical Chemistry. 85: 11054-11060. PMID 24134513 DOI: 10.1021/Ac4027093 |
0.795 |
|
| 2013 |
Degroeve S, Martens L, Jurisica I. MS2PIP: A tool for MS/MS peak intensity prediction Bioinformatics. 29: 3199-3203. PMID 24078703 DOI: 10.1093/Bioinformatics/Btt544 |
0.729 |
|
| 2013 |
Masuzzo P, Hulstaert N, Huyck L, Ampe C, Van Troys M, Martens L. CellMissy: a tool for management, storage and analysis of cell migration data produced in wound healing-like assays. Bioinformatics (Oxford, England). 29: 2661-3. PMID 23918247 DOI: 10.1093/Bioinformatics/Btt437 |
0.799 |
|
| 2013 |
Vandermarliere E, Mueller M, Martens L. Getting intimate with trypsin, the leading protease in proteomics. Mass Spectrometry Reviews. 32: 453-65. PMID 23775586 DOI: 10.1002/Mas.21376 |
0.757 |
|
| 2013 |
Martens L. Bringing proteomics into the clinic: The need for the field to finally take itself seriously Proteomics - Clinical Applications. 7: 388-391. PMID 23637000 DOI: 10.1002/Prca.201300020 |
0.349 |
|
| 2013 |
Tanco S, Lorenzo J, Garcia-Pardo J, Degroeve S, Martens L, Aviles FX, Gevaert K, Van Damme P. Proteome-derived peptide libraries to study the substrate specificity profiles of carboxypeptidases. Molecular & Cellular Proteomics : McP. 12: 2096-110. PMID 23620545 DOI: 10.1074/Mcp.M112.023234 |
0.701 |
|
| 2013 |
Hulstaert N, Reisinger F, Rameseder J, Barsnes H, Vizcaíno JA, Martens L. Pride-asap: automatic fragment ion annotation of identified PRIDE spectra. Journal of Proteomics. 95: 89-92. PMID 23603108 DOI: 10.1016/J.Jprot.2013.04.011 |
0.808 |
|
| 2013 |
Martens L. Resilience in the proteomics data ecosystem: How the field cares for its data Proteomics. 13: 1548-1550. PMID 23596016 DOI: 10.1002/Pmic.201300118 |
0.354 |
|
| 2013 |
Fannes T, Vandermarliere E, Schietgat L, Degroeve S, Martens L, Ramon J. Predicting tryptic cleavage from proteomics data using decision tree ensembles. Journal of Proteome Research. 12: 2253-9. PMID 23517142 DOI: 10.7490/F1000Research.1094824.1 |
0.815 |
|
| 2013 |
Barsnes H, Martens L. Crowdsourcing in proteomics: Public resources lead to better experiments Amino Acids. 44: 1129-1137. PMID 23377569 DOI: 10.1007/S00726-012-1455-Z |
0.63 |
|
| 2013 |
Perez-Riverol Y, Hermjakob H, Kohlbacher O, Martens L, Creasy D, Cox J, Leprevost F, Shan BP, Pérez-Nueno VI, Blazejczyk M, Punta M, Vierlinger K, Valiente PA, Leon K, Chinea G, et al. Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 workshop report. Journal of Proteomics. 87: 134-8. PMID 23376229 DOI: 10.1016/J.Jprot.2013.01.019 |
0.457 |
|
| 2013 |
Vaudel M, Breiter D, Beck F, Rahnenführer J, Martens L, Zahedi RP. D-score: a search engine independent MD-score. Proteomics. 13: 1036-41. PMID 23307401 DOI: 10.1002/Pmic.201200408 |
0.629 |
|
| 2013 |
Muth T, Peters J, Blackburn J, Rapp E, Martens L. Proteocloud: A full-featured open source proteomics cloud computing pipeline Journal of Proteomics. 88: 104-108. PMID 23305951 DOI: 10.1016/J.Jprot.2012.12.026 |
0.724 |
|
| 2013 |
Muth T, Benndorf D, Reichl U, Rapp E, Martens L. Searching for a needle in a stack of needles: Challenges in metaproteomics data analysis Molecular Biosystems. 9: 578-585. PMID 23238088 DOI: 10.1039/C2Mb25415H |
0.713 |
|
| 2013 |
Vandermarliere E, Martens L. Protein structure as a means to triage proposed PTM sites Proteomics. 13: 1028-1035. PMID 23172737 DOI: 10.1002/Pmic.201200232 |
0.703 |
|
| 2013 |
Colaert N, Maddelein D, Impens F, Van Damme P, Plasman K, Helsens K, Hulstaert N, Vandekerckhove J, Gevaert K, Martens L. The Online Protein Processing Resource (TOPPR): a database and analysis platform for protein processing events. Nucleic Acids Research. 41: D333-7. PMID 23093603 DOI: 10.1093/Nar/Gks998 |
0.82 |
|
| 2013 |
Volders PJ, Helsens K, Wang X, Menten B, Martens L, Gevaert K, Vandesompele J, Mestdagh P. LNCipedia: a database for annotated human lncRNA transcript sequences and structures. Nucleic Acids Research. 41: D246-51. PMID 23042674 DOI: 10.1093/Nar/Gks915 |
0.81 |
|
| 2013 |
Masuzzo P, Hulstaert N, Ampe C, Troys MV, Martens L. CellMissy: a tool for management, storage, dissemination and analysis of cell migration data F1000research. 4. DOI: 10.7490/F1000Research.1094821.1 |
0.807 |
|
| 2013 |
Stes E, Vandermarliere E, Linders J, Brehmer D, Martens L, Gevaert K. Study of the kinase switch mechanism in B-RAF upon small molecule binding via mass spectrometry F1000research. 4. DOI: 10.7490/F1000Research.1093063.1 |
0.659 |
|
| 2012 |
Vaudel M, Sickmann A, Martens L. Current methods for global proteome identification. Expert Review of Proteomics. 9: 519-32. PMID 23194269 DOI: 10.1586/Epr.12.51 |
0.716 |
|
| 2012 |
Côté RG, Griss J, Dianes JA, Wang R, Wright JC, van den Toorn HW, van Breukelen B, Heck AJ, Hulstaert N, Martens L, Reisinger F, Csordas A, Ovelleiro D, Perez-Rivevol Y, Barsnes H, et al. The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium. Molecular & Cellular Proteomics : McP. 11: 1682-9. PMID 22949509 DOI: 10.1074/Mcp.O112.021543 |
0.819 |
|
| 2012 |
Vaudel M, Burkhart JM, Radau S, Zahedi RP, Martens L, Sickmann A. Integral quantification accuracy estimation for reporter ion-based quantitative proteomics (iQuARI). Journal of Proteome Research. 11: 5072-80. PMID 22874012 DOI: 10.1021/Pr300247U |
0.624 |
|
| 2012 |
Burkhart JM, Vaudel M, Gambaryan S, Radau S, Walter U, Martens L, Geiger J, Sickmann A, Zahedi RP. The first comprehensive and quantitative analysis of human platelet protein composition allows the comparative analysis of structural and functional pathways. Blood. 120: e73-82. PMID 22869793 DOI: 10.1182/Blood-2012-04-416594 |
0.58 |
|
| 2012 |
Degroeve S, Staes A, De Bock PJ, Martens L. The effect of peptide identification search algorithms on MS2-based label-free protein quantification. Omics : a Journal of Integrative Biology. 16: 443-8. PMID 22804230 DOI: 10.1089/Omi.2011.0137 |
0.744 |
|
| 2012 |
Vaudel M, Burkhart JM, Zahedi RP, Martens L, Sickmann A. ITRAQ data interpretation Methods in Molecular Biology. 893: 501-509. PMID 22665319 DOI: 10.1007/978-1-61779-885-6_30 |
0.64 |
|
| 2012 |
Moruz L, Staes A, Foster JM, Hatzou M, Timmerman E, Martens L, Käll L. Chromatographic retention time prediction for posttranslationally modified peptides. Proteomics. 12: 1151-9. PMID 22577017 DOI: 10.1002/Pmic.201100386 |
0.387 |
|
| 2012 |
Helsens K, Mueller M, Hulstaert N, Martens L. Sigpep: calculating unique peptide signature transition sets in a complete proteome background. Proteomics. 12: 1142-6. PMID 22577015 DOI: 10.1002/Pmic.201100566 |
0.809 |
|
| 2012 |
Helsens K, Martens L. Enabling computational proteomics by public and local data management systems Circulation. Cardiovascular Genetics. 5: 266. PMID 22511708 DOI: 10.1161/Circgenetics.110.957837 |
0.777 |
|
| 2012 |
Vaudel M, Burkhart JM, Breiter D, Zahedi RP, Sickmann A, Martens L. A complex standard for protein identification, designed by evolution. Journal of Proteome Research. 11: 5065-71. PMID 22489649 DOI: 10.1021/Pr300055Q |
0.692 |
|
| 2012 |
Gonnelli G, Hulstaert N, Degroeve S, Martens L. Towards a human proteomics atlas. Analytical and Bioanalytical Chemistry. 404: 1069-77. PMID 22447219 DOI: 10.1007/S00216-012-5940-8 |
0.819 |
|
| 2012 |
Jones AM, Aebersold R, Ahrens CH, Apweiler R, Baerenfaller K, Baker M, Bendixen E, Briggs S, Brownridge P, Brunner E, Daube M, Deutsch EW, Grossniklaus U, Heazlewood J, Hengartner MO, ... ... Martens L, et al. The HUPO initiative on Model Organism Proteomes, iMOP. Proteomics. 12: 340-5. PMID 22290800 DOI: 10.1002/Pmic.201290014 |
0.315 |
|
| 2012 |
Deutsch EW, Chambers M, Neumann S, Levander F, Binz PA, Shofstahl J, Campbell DS, Mendoza L, Ovelleiro D, Helsens K, Martens L, Aebersold R, Moritz RL, Brusniak MY. TraML--a standard format for exchange of selected reaction monitoring transition lists. Molecular & Cellular Proteomics : McP. 11: R111.015040. PMID 22159873 DOI: 10.1074/Mcp.R111.015040 |
0.736 |
|
| 2011 |
Colaert N, Degroeve S, Helsens K, Martens L. Analysis of the resolution limitations of peptide identification algorithms. Journal of Proteome Research. 10: 5555-61. PMID 21995378 DOI: 10.1021/Pr200913A |
0.823 |
|
| 2011 |
Helsens K, Brusniak MY, Deutsch E, Moritz RL, Martens L. jTraML: an open source Java API for TraML, the PSI standard for sharing SRM transitions. Journal of Proteome Research. 10: 5260-3. PMID 21967198 DOI: 10.1021/Pr200664H |
0.737 |
|
| 2011 |
Colaert N, Barsnes H, Vaudel M, Helsens K, Timmerman E, Sickmann A, Gevaert K, Martens L. Thermo-msf-parser: an open source Java library to parse and visualize Thermo Proteome Discoverer msf files. Journal of Proteome Research. 10: 3840-3. PMID 21714566 DOI: 10.1021/Pr2005154 |
0.817 |
|
| 2011 |
Helsens K, Van Damme P, Degroeve S, Martens L, Arnesen T, Vandekerckhove J, Gevaert K. Bioinformatics analysis of a Saccharomyces cerevisiae N-terminal proteome provides evidence of alternative translation initiation and post-translational N-terminal acetylation. Journal of Proteome Research. 10: 3578-89. PMID 21619078 DOI: 10.1021/Pr2002325 |
0.817 |
|
| 2011 |
Colaert N, Gevaert K, Martens L. RIBAR and xRIBAR: Methods for reproducible relative MS/MS-based label-free protein quantification. Journal of Proteome Research. 10: 3183-9. PMID 21604685 DOI: 10.1021/Pr200219X |
0.774 |
|
| 2011 |
Colaert N, Vandekerckhove J, Martens L, Gevaert K. A case study on the comparison of different software tools for automated quantification of peptides. Methods in Molecular Biology (Clifton, N.J.). 753: 373-98. PMID 21604136 DOI: 10.1007/978-1-61779-148-2_25 |
0.789 |
|
| 2011 |
Martens L. Bioinformatics challenges in mass spectrometry-driven proteomics Methods in Molecular Biology. 753: 359-371. PMID 21604135 DOI: 10.1007/978-1-61779-148-2_24 |
0.315 |
|
| 2011 |
Helsens K, Martens L, Vandekerckhove J, Gevaert K. Mass spectrometry-driven proteomics: an introduction. Methods in Molecular Biology (Clifton, N.J.). 753: 1-27. PMID 21604112 DOI: 10.1007/978-1-61779-148-2_1 |
0.737 |
|
| 2011 |
Colaert N, Van Huele C, Degroeve S, Staes A, Vandekerckhove J, Gevaert K, Martens L. Combining quantitative proteomics data processing workflows for greater sensitivity. Nature Methods. 8: 481-3. PMID 21552256 DOI: 10.1038/Nmeth.1604 |
0.823 |
|
| 2011 |
Foster JM, Degroeve S, Gatto L, Visser M, Wang R, Griss J, Apweiler R, Martens L. A posteriori quality control for the curation and reuse of public proteomics data. Proteomics. 11: 2182-94. PMID 21538885 DOI: 10.1002/Pmic.201000602 |
0.729 |
|
| 2011 |
Vaudel M, Burkhart JM, Sickmann A, Martens L, Zahedi RP. Peptide identification quality control Proteomics. 11: 2105-2114. PMID 21500347 DOI: 10.1002/Pmic.201000704 |
0.649 |
|
| 2011 |
Foster JM, Martens L. Bioinformatics challenges in the proteomic analysis of human plasma. Methods in Molecular Biology (Clifton, N.J.). 728: 333-47. PMID 21468959 DOI: 10.1007/978-1-61779-068-3_22 |
0.37 |
|
| 2011 |
Martens L. Data management in mass spectrometry-based proteomics Methods in Molecular Biology. 728: 321-332. PMID 21468958 DOI: 10.1007/978-1-61779-068-3_21 |
0.372 |
|
| 2011 |
Barsnes H, Vaudel M, Colaert N, Helsens K, Sickmann A, Berven FS, Martens L. compomics-utilities: an open-source Java library for computational proteomics. Bmc Bioinformatics. 12: 70. PMID 21385435 DOI: 10.1186/1471-2105-12-70 |
0.833 |
|
| 2011 |
Colaert N, Vandekerckhove J, Gevaert K, Martens L. A comparison of MS2-based label-free quantitative proteomic techniques with regards to accuracy and precision. Proteomics. 11: 1110-3. PMID 21365758 DOI: 10.1002/Pmic.201000521 |
0.782 |
|
| 2011 |
Vaudel M, Barsnes H, Berven FS, Sickmann A, Martens L. SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches. Proteomics. 11: 996-9. PMID 21337703 DOI: 10.1002/Pmic.201000595 |
0.762 |
|
| 2011 |
Burkhart JM, Vaudel M, Zahedi RP, Martens L, Sickmann A. iTRAQ protein quantification: A quality-controlled workflow Proteomics. 11: 1125-1134. PMID 21328540 DOI: 10.1002/Pmic.201000711 |
0.661 |
|
| 2011 |
Barsnes H, Eidhammer I, Martens L. A global analysis of peptide fragmentation variability. Proteomics. 11: 1181-8. PMID 21328539 DOI: 10.1002/Pmic.201000640 |
0.705 |
|
| 2011 |
Degroeve S, Colaert N, Vandekerckhove J, Gevaert K, Martens L. A reproducibility-based evaluation procedure for quantifying the differences between MS/MS peak intensity normalization methods. Proteomics. 11: 1172-80. PMID 21298791 DOI: 10.1002/Pmic.201000605 |
0.812 |
|
| 2011 |
Barsnes H, Vizcaíno JA, Reisinger F, Eidhammer I, Martens L. Submitting proteomics data to PRIDE using PRIDE Converter. Methods in Molecular Biology (Clifton, N.J.). 694: 237-53. PMID 21082439 DOI: 10.1007/978-1-60761-977-2_16 |
0.687 |
|
| 2011 |
Martens L. Proteomics databases and repositories Methods in Molecular Biology (Clifton, N.J.). 694: 213-227. PMID 21082437 |
0.316 |
|
| 2011 |
Vizcaíno JA, Reisinger F, Côté R, Martens L. PRIDE and "Database on Demand" as valuable tools for computational proteomics. Methods in Molecular Biology (Clifton, N.J.). 696: 93-105. PMID 21063943 DOI: 10.1007/978-1-60761-987-1_6 |
0.412 |
|
| 2010 |
Vizcaíno JA, Foster JM, Martens L. Proteomics data repositories: providing a safe haven for your data and acting as a springboard for further research. Journal of Proteomics. 73: 2136-46. PMID 20615486 DOI: 10.1016/J.Jprot.2010.06.008 |
0.449 |
|
| 2010 |
Côté R, Reisinger F, Martens L, Barsnes H, Vizcaino JA, Hermjakob H. The Ontology Lookup Service: bigger and better. Nucleic Acids Research. 38: W155-60. PMID 20460452 DOI: 10.1093/Nar/Gkq331 |
0.63 |
|
| 2010 |
Vizcaíno JA, Reisinger F, Côté R, Martens L. PRIDE: Data submission and analysis. Current Protocols in Protein Science. Unit 25.4. PMID 20393974 DOI: 10.1002/0471140864.ps2504s60 |
0.304 |
|
| 2010 |
Martens L, Hermjakob H. High-throughput proteomics and bioinformatics: Joined at the hip Proteomics. 10: 1103-1104. PMID 20306482 DOI: 10.1002/Pmic.201090016 |
0.304 |
|
| 2010 |
Muth T, Vaudel M, Barsnes H, Martens L, Sickmann A. XTandem Parser: an open-source library to parse and analyse X!Tandem MS/MS search results. Proteomics. 10: 1522-4. PMID 20140905 DOI: 10.1002/Pmic.200900759 |
0.817 |
|
| 2010 |
Barsnes H, Côté RG, Eidhammer I, Martens L. OLS dialog: an open-source front end to the ontology lookup service. Bmc Bioinformatics. 11: 34. PMID 20078892 DOI: 10.1186/1471-2105-11-34 |
0.672 |
|
| 2010 |
Muth T, Keller D, Puetz SM, Martens L, Sickmann A, Boehm AM. jTraqX: a free, platform independent tool for isobaric tag quantitation at the protein level. Proteomics. 10: 1223-5. PMID 20058250 DOI: 10.1002/Pmic.200900374 |
0.721 |
|
| 2010 |
Helsens K, Colaert N, Barsnes H, Muth T, Flikka K, Staes A, Timmerman E, Wortelkamp S, Sickmann A, Vandekerckhove J, Gevaert K, Martens L. ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics. Proteomics. 10: 1261-4. PMID 20058248 DOI: 10.1002/Pmic.200900409 |
0.805 |
|
| 2010 |
Barsnes H, Eidhammer I, Martens L. FragmentationAnalyzer: an open-source tool to analyze MS/MS fragmentation data. Proteomics. 10: 1087-90. PMID 20049869 DOI: 10.1002/Pmic.200900681 |
0.677 |
|
| 2010 |
Jones P, Martens L. Using the PRIDE proteomics identifications database for knowledge discovery and data analysis Methods in Molecular Biology (Clifton, N.J.). 604: 297-307. PMID 20013379 |
0.378 |
|
| 2010 |
Vaudel M, Sickmann A, Martens L. Peptide and protein quantification: a map of the minefield. Proteomics. 10: 650-70. PMID 19953549 DOI: 10.1002/Pmic.200900481 |
0.682 |
|
| 2010 |
Vizcaíno JA, Côté R, Reisinger F, Barsnes H, Foster JM, Rameseder J, Hermjakob H, Martens L. The Proteomics Identifications database: 2010 update. Nucleic Acids Research. 38: D736-42. PMID 19906717 DOI: 10.1093/Nar/Gkp964 |
0.708 |
|
| 2010 |
Muth T, Vaudel M, Barsnes H, Martens L, Sickmann A. Erratum: XTandem Parser: An open-source library to parse and analyse X!Tandem MS/MS search results Proteomics. 10: 2560-2560. DOI: 10.1002/pmic.201090058 |
0.741 |
|
| 2010 |
Barsnes H, Eidhammer I, Martens L. Erratum: FragmentationAnalyzer: An open-source tool to analyze MS/MS fragmentation data Proteomics. 10: 2560-2560. DOI: 10.1002/pmic.201090055 |
0.636 |
|
| 2009 |
Colaert N, Helsens K, Martens L, Vandekerckhove J, Gevaert K. Improved visualization of protein consensus sequences by iceLogo. Nature Methods. 6: 786-7. PMID 19876014 DOI: 10.1038/Nmeth1109-786 |
0.787 |
|
| 2009 |
Reisinger F, Martens L. Database on Demand - An online tool for the custom generation of FASTA-formatted sequence databases Proteomics. 9: 4421-4424. PMID 19725076 DOI: 10.1002/pmic.200900254 |
0.335 |
|
| 2009 |
Vizcaíno JA, Côté R, Reisinger F, Foster JM, Mueller M, Rameseder J, Hermjakob H, Martens L. A guide to the Proteomics Identifications Database proteomics data repository Proteomics. 9: 4276-4283. PMID 19662629 DOI: 10.1002/Pmic.200900402 |
0.347 |
|
| 2009 |
Barsnes H, Huber S, Sickmann A, Eidhammer I, Martens L. OMSSA Parser: an open-source library to parse and extract data from OMSSA MS/MS search results. Proteomics. 9: 3772-4. PMID 19639591 DOI: 10.1002/Pmic.200900037 |
0.667 |
|
| 2009 |
Eisenacher M, Martens L, Barsnes H, Hardt T, Kohl M, Häkkinen J, Apweiler R, Meyer HE, Stephan C. Proteomics Data Collection - 5th ProDaC Workshop: 4 March 2009, Kolympari, Crete, Greece. Proteomics. 9: 3626-9. PMID 19639582 DOI: 10.1002/Pmic.200900205 |
0.649 |
|
| 2009 |
Eisenacher M, Martens L, Hardt T, Kohl M, Barsnes H, Helsens K, Häkkinen J, Levander F, Aebersold R, Vandekerckhove J, Dunn MJ, Lisacek F, Siepen JA, Hubbard SJ, Binz PA, et al. Getting a grip on proteomics data - Proteomics Data Collection (ProDaC). Proteomics. 9: 3928-33. PMID 19637238 DOI: 10.1002/Pmic.200900247 |
0.802 |
|
| 2009 |
Barsnes H, Vizcaíno JA, Eidhammer I, Martens L. PRIDE Converter: making proteomics data-sharing easy. Nature Biotechnology. 27: 598-9. PMID 19587657 DOI: 10.1038/Nbt0709-598 |
0.637 |
|
| 2009 |
Martens L, Apweiler R. Algorithms and databases. Methods in Molecular Biology (Clifton, N.J.). 564: 245-59. PMID 19544027 DOI: 10.1007/978-1-60761-157-8_14 |
0.312 |
|
| 2009 |
Eisenacher M, Kohl M, Martens L, Barsnes H, Hardt T, Levander F, Häkkinen J, Apweiler R, Meyer HE, Stephan C. Proteomics data collection--4th ProDaC workshop 15 August 2008, Amsterdam, The Netherlands. Proteomics. 9: 218-22. PMID 19105180 DOI: 10.1002/Pmic.200800732 |
0.639 |
|
| 2009 |
Vizcaino JA, Hermjakob H, Martens L. Present and future of proteomics data curation at the PRIDE database Nature Precedings. DOI: 10.1038/Npre.2009.3222.1 |
0.409 |
|
| 2008 |
Helsens K, Timmerman E, Vandekerckhove J, Gevaert K, Martens L. Peptizer, a tool for assessing false positive peptide identifications and manually validating selected results. Molecular & Cellular Proteomics : McP. 7: 2364-72. PMID 18667410 DOI: 10.1074/mcp.M800082-MCP200 |
0.754 |
|
| 2008 |
Martens L, Palazzi LM, Hermjakob H. Data standards and controlled vocabularies for proteomics Methods in Molecular Biology. 484: 279-286. PMID 18592186 DOI: 10.1007/978-1-59745-398-1_18 |
0.323 |
|
| 2008 |
Martens L, Jones P, Côté R. Using the Proteomics Identifications Database (PRIDE) Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. PMID 18428683 DOI: 10.1002/0471250953.bi1308s21 |
0.33 |
|
| 2008 |
Mathivanan S, Ahmed M, Ahn NG, Alexandre H, Amanchy R, Andrews PC, Bader JS, Balgley BM, Bantscheff M, Bennett KL, Björling E, Blagoev B, Bose R, Brahmachari SK, Burlingame AS, ... ... Martens L, et al. Human Proteinpedia enables sharing of human protein data. Nature Biotechnology. 26: 164-7. PMID 18259167 DOI: 10.1038/Nbt0208-164 |
0.743 |
|
| 2008 |
Klie S, Martens L, Vizcaíno JA, Côté R, Jones P, Apweiler R, Hinneburg A, Hermjakob H. Analyzing large-scale proteomics projects with latent semantic indexing. Journal of Proteome Research. 7: 182-91. PMID 18047271 DOI: 10.1021/Pr070461K |
0.391 |
|
| 2008 |
Jones P, Côté RG, Cho SY, Klie S, Martens L, Quinn AF, Thorneycroft D, Hermjakob H. PRIDE: New developments and new datasets Nucleic Acids Research. 36: D878-D883. PMID 18033805 DOI: 10.1093/Nar/Gkm1021 |
0.331 |
|
| 2007 |
Flikka K, Meukens J, Helsens K, Vandekerckhove J, Eidhammer I, Gevaert K, Martens L. Implementation and application of a versatile clustering tool for tandem mass spectrometry data. Proteomics. 7: 3245-58. PMID 17708593 DOI: 10.1002/Pmic.200700160 |
0.747 |
|
| 2007 |
Taylor CF, Paton NW, Lilley KS, Binz PA, Julian RK, Jones AR, Zhu W, Apweiler R, Aebersold R, Deutsch EW, Dunn MJ, Heck AJ, Leitner A, Macht M, Mann M, ... Martens L, et al. The minimum information about a proteomics experiment (MIAPE). Nature Biotechnology. 25: 887-93. PMID 17687369 DOI: 10.1038/Nbt1329 |
0.319 |
|
| 2007 |
Gevaert K, Van Damme P, Ghesquière B, Impens F, Martens L, Helsens K, Vandekerckhove J. A la carte proteomics with an emphasis on gel-free techniques. Proteomics. 7: 2698-718. PMID 17640001 DOI: 10.1002/pmic.200700114 |
0.716 |
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| 2007 |
Aivaliotis M, Gevaert K, Falb M, Tebbe A, Konstantinidis K, Bisle B, Klein C, Martens L, Staes A, Timmerman E, Van Damme J, Siedler F, Pfeiffer F, Vandekerckhove J, Oesterhelt D. Large-scale identification of N-terminal peptides in the halophilic archaea Halobacterium salinarum and Natronomonas pharaonis. Journal of Proteome Research. 6: 2195-204. PMID 17444671 DOI: 10.1021/Pr0700347 |
0.393 |
|
| 2007 |
Helsens K, Martens L, Vandekerckhove J, Gevaert K. MascotDatfile: an open-source library to fully parse and analyse MASCOT MS/MS search results. Proteomics. 7: 364-6. PMID 17203510 DOI: 10.1002/pmic.200600682 |
0.75 |
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| 2006 |
Hanoulle X, Van Damme J, Staes A, Martens L, Goethals M, Vandekerckhove J, Gevaert K. A new functional, chemical proteomics technology to identify purine nucleotide binding sites in complex proteomes. Journal of Proteome Research. 5: 3438-45. PMID 17137346 DOI: 10.1021/Pr060313E |
0.307 |
|
| 2006 |
Hamacher M, Apweiler R, Arnold G, Becker A, Blüggel M, Carrette O, Colvis C, Dunn MJ, Fröhlich T, Fountoulakis M, van Hall A, Herberg F, Ji J, Ji J, Kretzschmar H, ... ... Martens L, et al. HUPO Brain Proteome Project: summary of the pilot phase and introduction of a comprehensive data reprocessing strategy. Proteomics. 6: 4890-8. PMID 16927433 DOI: 10.1002/Pmic.200600295 |
0.331 |
|
| 2006 |
Stephan C, Reidegeld KA, Hamacher M, van Hall A, Marcus K, Taylor C, Jones P, Müller M, Apweiler R, Martens L, Körting G, Chamrad DC, Thiele H, Blüggel M, Parkinson D, et al. Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phase. Proteomics. 6: 5015-29. PMID 16927432 DOI: 10.1002/Pmic.200600294 |
0.45 |
|
| 2006 |
Reidegeld KA, Müller M, Stephan C, Blüggel M, Hamacher M, Martens L, Körting G, Chamrad DC, Parkinson D, Apweiler R, Meyer HE, Marcus K. The power of cooperative investigation: summary and comparison of the HUPO Brain Proteome Project pilot study results. Proteomics. 6: 4997-5014. PMID 16912976 DOI: 10.1002/Pmic.200600305 |
0.339 |
|
| 2006 |
Martens L, Müller M, Stephan C, Hamacher M, Reidegeld KA, Meyer HE, Blüggel M, Vandekerckhove J, Gevaert K, Apweiler R. A comparison of the HUPO Brain Proteome Project pilot with other proteomics studies. Proteomics. 6: 5076-86. PMID 16912975 DOI: 10.1002/Pmic.200600291 |
0.329 |
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| 2006 |
Mueller M, Martens L, Reidegeld KA, Hamacher M, Stephan C, Blüggel M, Körting G, Chamrad D, Scheer C, Marcus K, Meyer HE, Apweiler R. Functional annotation of proteins identified in human brain during the HUPO Brain Proteome Project pilot study. Proteomics. 6: 5059-75. PMID 16912974 DOI: 10.1002/Pmic.200600194 |
0.385 |
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| 2006 |
Gevaert K, Pinxteren J, Demol H, Hugelier K, Staes A, Van Damme J, Martens L, Vandekerckhove J. Four stage liquid chromatographic selection of methionyl peptides for peptide-centric proteome analysis: the proteome of human multipotent adult progenitor cells. Journal of Proteome Research. 5: 1415-28. PMID 16739993 DOI: 10.1021/Pr060026A |
0.396 |
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| 2006 |
Flikka K, Martens L, Vandekerckhove J, Gevaert K, Eidhammer I. Improving the reliability and throughput of mass spectrometry-based proteomics by spectrum quality filtering. Proteomics. 6: 2086-94. PMID 16518876 DOI: 10.1002/Pmic.200500309 |
0.438 |
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| 2006 |
Jones P, Côté RG, Martens L, Quinn AF, Taylor CF, Derache W, Hermjakob H, Apweiler R. PRIDE: a public repository of protein and peptide identifications for the proteomics community Nucleic Acids Research.. 34: D659-663. PMID 16381953 DOI: 10.1093/Nar/Gkj138 |
0.371 |
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| 2005 |
Gevaert K, Van Damme P, Martens L, Vandekerckhove J. Diagonal reverse-phase chromatography applications in peptide-centric proteomics: ahead of catalogue-omics? Analytical Biochemistry. 345: 18-29. PMID 16181830 DOI: 10.1016/J.Ab.2005.01.038 |
0.375 |
|
| 2005 |
Stephan C, Hamacher M, Blüggel M, Körting G, Chamrad D, Scheer C, Marcus K, Reidegeld KA, Lohaus C, Schäfer H, Martens L, Jones P, Müller M, Auyeung K, Taylor C, et al. 5th HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK - Setting the analysis frame Proteomics. 5: 3560-3562. PMID 16167371 DOI: 10.1002/Pmic.200500580 |
0.377 |
|
| 2005 |
Adamski M, Blackwell T, Menon R, Martens L, Hermjakob H, Taylor C, Omenn GS, States DJ. Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project. Proteomics. 5: 3246-61. PMID 16104057 DOI: 10.1002/Pmic.200500186 |
0.387 |
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| 2005 |
Gevaert K, Staes A, Van Damme J, De Groot S, Hugelier K, Demol H, Martens L, Goethals M, Vandekerckhove J. Global phosphoproteome analysis on human HepG2 hepatocytes using reversed-phase diagonal LC. Proteomics. 5: 3589-99. PMID 16097034 DOI: 10.1002/Pmic.200401217 |
0.363 |
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| 2005 |
Martens L, Hermjakob H, Jones P, Adamsk M, Taylor C, States D, Gevaert K, Vandekerckhove J, Apweiler R. PRIDE: The proteomics identifications database Proteomics. 5: 3537-3545. PMID 16041671 DOI: 10.1002/Pmic.200401303 |
0.345 |
|
| 2005 |
Martens L, Nesvizhskii AI, Hermjakob H, Adamski M, Omenn GS, Vandekerckhove J, Gevaert K. Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories. Proteomics. 5: 3501-5. PMID 16041670 DOI: 10.1002/Pmic.200401302 |
0.421 |
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| 2005 |
Martens L, Van Damme P, Van Damme J, Staes A, Timmerman E, Ghesquière B, Thomas GR, Vandekerckhove J, Gevaert K. The human platelet proteome mapped by peptide-centric proteomics: a functional protein profile. Proteomics. 5: 3193-204. PMID 16038019 DOI: 10.1002/Pmic.200401142 |
0.44 |
|
| 2005 |
Martens L, Vandekerckhove J, Gevaert K. DBToolkit: processing protein databases for peptide-centric proteomics. Bioinformatics (Oxford, England). 21: 3584-5. PMID 16030071 DOI: 10.1093/bioinformatics/bti588 |
0.33 |
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| 2004 |
Gevaert K, Ghesquière B, Staes A, Martens L, Van Damme J, Thomas GR, Vandekerckhove J. Reversible labeling of cysteine-containing peptides allows their specific chromatographic isolation for non-gel proteome studies. Proteomics. 4: 897-908. PMID 15048972 DOI: 10.1002/Pmic.200300641 |
0.388 |
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| 2002 |
Gevaert K, Van Damme J, Goethals M, Thomas GR, Hoorelbeke B, Demol H, Martens L, Puype M, Staes A, Vandekerckhove J. Chromatographic isolation of methionine-containing peptides for gel-free proteome analysis: identification of more than 800 Escherichia coli proteins. Molecular & Cellular Proteomics : McP. 1: 896-903. PMID 12488465 DOI: 10.1074/mcp.M200061-MCP200 |
0.312 |
|
| 2001 |
Gevaert K, Demol H, Martens L, Hoorelbeke B, Puype M, Goethals M, Van Damme J, De Boeck S, Vandekerckhove J. Protein identification based on matrix assisted laser desorption/ionization-post source decay-mass spectrometry. Electrophoresis. 22: 1645-51. PMID 11425220 DOI: 10.1002/1522-2683(200105)22:9<1645::Aid-Elps1645>3.0.Co;2-Z |
0.463 |
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