Lennart Martens - Publications

217 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
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  1
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  1
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  1
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  0.68
2018 Schuster M, Moeller M, Bornemann L, Bessen C, Sobczak C, Schmitz S, Witjes L, Kruithoff K, Kohn C, Just O, Kündgen A, Pundt N, Pelzer B, Ampe C, Van Troys M, ... ... Martens L, et al. Surveillance of Myelodysplastic Syndrome via Migration Analyses of Blood Neutrophils: A Potential Prognostic Tool. Journal of Immunology (Baltimore, Md. : 1950). PMID 30446567 DOI: 10.4049/jimmunol.1801071  0.64
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  1
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  1
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  1
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  0.64
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  1
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  1
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  0.64
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  1
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  1
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  0.68
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  1
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  0.76
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  1
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  0.64
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  0.64
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  0.68
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  1
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  1
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  1
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  0.64
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  0.64
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  0.76
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  0.64
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  1
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  1
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  1
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  1
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  0.76
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  0.68
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  0.92
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  1
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  1
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  0.6
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  0.56
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  1
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  0.68
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  1
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  1
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  1
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  1
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  0.6
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  0.76
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  0.44
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  1
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  0.64
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  1
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  0.76
2015 Blackburn JM, Martens L. The challenge of metaproteomic analysis in human samples. Expert Review of Proteomics. PMID 26687021 DOI: 10.1586/14789450.2016.1135058  1
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  1
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  1
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  1
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  1
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  0.92
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  1
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  0.68
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  0.6
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  0.64
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  1
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  1
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  1
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  1
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  1
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  0.6
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  1
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  1
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  1
2014 Vizcaíno JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Ríos D, Dianes JA, Sun Z, Farrah T, Bandeira N, Binz PA, Xenarios I, Eisenacher M, Mayer G, Gatto L, ... ... Martens L, et al. ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nature Biotechnology. 32: 223-6. PMID 24727771 DOI: 10.1038/nbt.2839  1
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  1
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  1
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  1
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  1
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  1
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  1
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  0.72
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  1
2013 Martens L. About Dice, Bouldering, and Team Empowerment: Running the CompOmics Group at VIB and Ghent University, Belgium Plos Computational Biology. 9. PMID 24244140 DOI: 10.1371/journal.pcbi.1003332  1
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  1
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  1
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  0.92
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  1
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  1
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  1
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  1
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  1
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: 10.1021/pr4001114  1
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  1
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  1
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  1
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  1
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  1
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  1
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  0.92
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  0.72
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  0.72
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  1
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  1
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  1
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  1
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  1
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  1
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  0.92
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  1
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  1
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  1
2012 Wang R, Fabregat A, Ríos D, Ovelleiro D, Foster JM, Côté RG, Griss J, Csordas A, Perez-Riverol Y, Reisinger F, Hermjakob H, Martens L, Vizcaíno JA. PRIDE Inspector: a tool to visualize and validate MS proteomics data. Nature Biotechnology. 30: 135-7. PMID 22318026 DOI: 10.1038/nbt.2112  1
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  1
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  1
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  1
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  0.72
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  1
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  1
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  0.72
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  0.72
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  1
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  0.72
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  1
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  1
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  1
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  1
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  1
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  1
2011 Martens L, Vizcaíno JA, Banks R. Quality control in proteomics. Proteomics. 11: 1015-6. PMID 21374817 DOI: 10.1002/pmic.201190020  0.64
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  0.72
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  1
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  1
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  1
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  1
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  1
2011 Martens L. Proteomics databases and repositories Methods in Molecular Biology (Clifton, N.J.). 694: 213-227. PMID 21082437  1
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  0.64
2011 Abrahams JP, Apweiler R, Balling R, Bertero MG, Bujnicki JM, Chayen NE, Chène P, Corthals GL, Dyl?g T, Förster F, Heck AJ, Henderson PJ, Herwig R, Jehenson P, Kokalj SJ, ... ... Martens L, et al. "4D Biology for health and disease" workshop report. New Biotechnology. 28: 291-3. PMID 20951846 DOI: 10.1016/j.nbt.2010.10.003  1
2011 Martens L, Chambers M, Sturm M, Kessner D, Levander F, Shofstahl J, Tang WH, Römpp A, Neumann S, Pizarro AD, Montecchi-Palazzi L, Tasman N, Coleman M, Reisinger F, Souda P, et al. mzML--a community standard for mass spectrometry data. Molecular & Cellular Proteomics : McP. 10: R110.000133. PMID 20716697 DOI: 10.1074/mcp.R110.000133  1
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  1
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  1
2010 Martens L. A report on the ESF workshop on quality control in proteomics Molecular Biosystems. 6: 935-938. PMID 20436974 DOI: 10.1039/c003912h  1
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  0.64
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  1
2010 Côté RG, Reisinger F, Martens L. jmzML, an open-source Java API for mzML, the PSI standard for MS data. Proteomics. 10: 1332-5. PMID 20127693 DOI: 10.1002/pmic.200900719  0.56
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  1
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  0.68
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  1
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  1
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  1
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  0.72
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  1
2009 Vizcaíno JA, Mueller M, Hermjakob H, Martens L. Charting online OMICS resources: A navigational chart for clinical researchers. Proteomics. Clinical Applications. 3: 18-29. PMID 21136933 DOI: 10.1002/prca.200800082  0.64
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  0.72
2009 Montecchi-Palazzi L, Kerrien S, Reisinger F, Aranda B, Jones AR, Martens L, Hermjakob H. The PSI semantic validator: A framework to check MIAPE compliance of proteomics data Proteomics. 9: 5112-5119. PMID 19834897 DOI: 10.1002/pmic.200900189  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2008 Eisenacher M, Hardt T, Martens L, Häkkinen J, Apweiler R, Hamacher M, Meyer HE, Stephan C. Proteomics Data Collection - 3rd ProDaC workshop April 22nd 2008, Toledo, Spain. Proteomics. 8: 4163-7. PMID 18814333 DOI: 10.1002/pmic.200800515  1
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  0.72
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  1
2008 Côté RG, Jones P, Martens L, Apweiler R, Hermjakob H. The Ontology Lookup Service: more data and better tools for controlled vocabulary queries. Nucleic Acids Research. 36: W372-6. PMID 18467421 DOI: 10.1093/nar/gkn252  1
2008 Hamacher M, Eisenacher M, Tribl F, Stephan C, Marcus K, Hardt T, Wiltfang J, Martens L, Desiderio D, Gutstein H, Young MP, Meyer HE. The HUPO brain proteome project wish list - Summary of the 9th HUPO BPP workshop: 9-10 January 2008, Barbados Proteomics. 8: 2160-2164. PMID 18452233 DOI: 10.1002/pmic.200800090  1
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  1
2008 Eisenacher M, Hardt T, Hamacher M, Martens L, Häkkinen J, Levander F, Apweiler R, Meyer HE, Stephan C. Proteomics Data Collection - 2nd ProDaC Workshop 5 October 2007, Seoul, Korea. Proteomics. 8: 1326-30. PMID 18318011 DOI: 10.1002/pmic.200701098  1
2008 Orchard S, Martens L, Tasman J, Binz PA, Albar JP, Hermjakob H. 6th HUPO annual world congress - Proteomics standards initiative workshop: 6-10 October 2007, Seoul, Korea Proteomics. 8: 1331-1333. PMID 18318010 DOI: 10.1002/pmic.200701086  1
2008 Mueller M, Vizcaíno JA, Jones P, Côté R, Thorneycroft D, Apweiler R, Hermjakob H, Martens L. Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets. Proteomics. 8: 1138-48. PMID 18283668 DOI: 10.1002/pmic.200700761  1
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  1
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  1
2007 Côté RG, Jones P, Martens L, Kerrien S, Reisinger F, Lin Q, Leinonen R, Apweiler R, Hermjakob H. The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases. Bmc Bioinformatics. 8: 401. PMID 17945017 DOI: 10.1186/1471-2105-8-401  1
2007 Martens L, Orchard S, Apweiler R, Hermjakob H. Human Proteome Organization Proteomics Standards Initiative: data standardization, a view on developments and policy. Molecular & Cellular Proteomics : McP. 6: 1666-7. PMID 17766694  1
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  0.84
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  1
2007 Eisenacher M, Hardt T, Hamacher M, Martens L, Häkkinen J, Levander F, Apweiler R, Meyer HE, Stephan C. Proteomics Data Collection - the 1st ProDaC workshop 26 April 2007 Ecole Normale Supérieur, Lyon, France. Proteomics. 7: 3034-7. PMID 17683037 DOI: 10.1002/pmic.200700554  1
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  0.72
2007 Martens L, Hermjakob H. Proteomics data validation: Why all must provide data Molecular Biosystems. 3: 518-522. PMID 17639125 DOI: 10.1039/b705178f  1
2007 Hamacher M, Stephan C, Eisenacher M, Lewczuk P, Wiltfang J, Martens L, Vizcaíno JA, Kwon KH, Yoo JS, Park YM, Beckers J, Horsch M, de Angelis MH, Cho ZH, Apweiler R, et al. High Performance Proteomics: 7th HUPO Brain Proteome Project Workshop March 7-9, 2007 Wellcome Trust Conference Centre, Hinxton, UK. Proteomics. 7: 2490-6. PMID 17610211 DOI: 10.1002/pmic.200700449  1
2007 Vizcaíno JA, Martens L, Hermjakob H, Julian RK, Paton NW. The PSI formal document process and its implementation on the PSI website. Proteomics. 7: 2355-7. PMID 17570517 DOI: 10.1002/pmic.200700064  1
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  1
2007 Mueller M, Martens L, Apweiler R. Annotating the human proteome: beyond establishing a parts list. Biochimica Et Biophysica Acta. 1774: 175-91. PMID 17223395 DOI: 10.1016/j.bbapap.2006.11.011  1
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  0.72
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  0.64
2006 Ghesquière B, Van Damme J, Martens L, Vandekerckhove J, Gevaert K. Proteome-wide characterization of N-glycosylation events by diagonal chromatography. Journal of Proteome Research. 5: 2438-47. PMID 16944957 DOI: 10.1021/pr060186m  0.64
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  1
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  1
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  1
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  1
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  1
2006 Martens L, Monsieur G, Ampe C, Gevaert K, Vandekerckhove J. Cell_motility: a cross-platform, open source application for the study of cell motion paths. Bmc Bioinformatics. 7: 289. PMID 16762054 DOI: 10.1186/1471-2105-7-289  0.64
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  0.64
2006 Hamacher M, Stephan C, Blüggel M, Chamrad D, Körting G, Martens L, Müller M, Hermjakob H, Parkinson D, Dowsey A, Reidegeld KA, Marcus K, Dunn MJ, Meyer HE, Apweiler R. The HUPO Brain Proteome Project jamboree: centralised summary of the pilot studies. Proteomics. 6: 1719-21. PMID 16525999 DOI: 10.1002/pmic.200600069  1
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  0.84
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  1
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  0.64
2005 Van Damme P, Martens L, Van Damme J, Hugelier K, Staes A, Vandekerckhove J, Gevaert K. Caspase-specific and nonspecific in vivo protein processing during Fas-induced apoptosis. Nature Methods. 2: 771-7. PMID 16179924 DOI: 10.1038/nmeth792  0.64
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  1
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  1
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  0.64
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  1
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  0.64
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  0.64
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  0.64
2004 Staes A, Demol H, Van Damme J, Martens L, Vandekerckhove J, Gevaert K. Global differential non-gel proteomics by quantitative and stable labeling of tryptic peptides with oxygen-18. Journal of Proteome Research. 3: 786-91. PMID 15359732  0.64
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  0.64
2003 Gevaert K, Goethals M, Martens L, Van Damme J, Staes A, Thomas GR, Vandekerckhove J. Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides. Nature Biotechnology. 21: 566-9. PMID 12665801 DOI: 10.1038/nbt810  0.64
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  0.64
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