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ORCIDLennart Martens
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- affiliation: Ghent University, Department of Biomolecular Medicine, Ghent, Belgium
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Books and Theses
- 2013
[b1]Ingvar Eidhammer, Harald Barsnes, Geir Egil Eide, Lennart Martens:
Computational and Statistical Methods for Protein Quantification by Mass Spectrometry. Wiley 2013, ISBN 978-1-119-96400-1, pp. I-XX, 1-334
Journal Articles
- 2024
- [j35]Mikaela Koutrouli
, Katerina C. Nastou, Pau Piera Líndez, Robbin Bouwmeester, Simon Rasmussen, Lennart Martens, Lars Juhl Jensen:
FAVA: high-quality functional association networks inferred from scRNA-seq and proteomics data. Bioinform. 40(2) (2024) - 2023
- [j34]Tanja Holstein, Franziska Kistner, Lennart Martens, Thilo Muth:
PepGM: a probabilistic graphical model for taxonomic inference of viral proteome samples with associated confidence scores. Bioinform. 39(5) (2023) - [j33]David Teschner, David Gomez-Zepeda, Arthur Declercq, Mateusz K. Lacki, Seymen Avci, Konstantin Bob, Ute Distler, Thomas Michna, Lennart Martens, Stefan Tenzer, Andreas Hildebrandt:
Ionmob: a Python package for prediction of peptide collisional cross-section values. Bioinform. 39(9) (2023) - [j32]Arthur Declercq, Robbin Bouwmeester, Cristina Chiva, Eduard Sabidó, Aurélie Hirschler, Christine Carapito, Lennart Martens, Sven Degroeve, Ralf Gabriels:
Updated MS²PIP web server supports cutting-edge proteomics applications. Nucleic Acids Res. 51(W1): 338-342 (2023) - 2022
- [j31]Pieter Verschaffelt, James H. Collier, Alexander Botzki, Lennart Martens, Peter Dawyndt, Bart Mesuere:
Unipept Visualizations: an interactive visualization library for biological data. Bioinform. 38(2): 562-563 (2022) - [j30]Mihaly Varadi, Stephen Anyango, David R. Armstrong, John M. Berrisford, Preeti Choudhary, Mandar S. Deshpande, Nurul Nadzirin, Sreenath Nair, Lukás Pravda, Ahsan Tanweer, Bissan Al-Lazikani, Claudia Andreini, Geoffrey J. Barton, David Bednar, Karel Berka, Tom L. Blundell, Kelly Brock, José María Carazo, Jirí Damborský, Alessia David, Sucharita Dey, Roland L. Dunbrack Jr., Juan Fernández-Recio, Franca Fraternali, Toby J. Gibson, Manuela Helmer-Citterich, David Hoksza, Thomas A. Hopf, David Jakubec, Natarajan Kannan, Radoslav Krivák, Manjeet Kumar, Emmanuel D. Levy, Nir London, José Ramón Macías, Mallur Srivatsan Madhusudhan, Debora S. Marks, Lennart Martens, Stuart A McGowan, Jake E. McGreig, Vivek Modi, R. Gonzalo Parra, Gerardo Pepe, Damiano Piovesan, Jaime Prilusky, Valeria Putignano, Leandro G. Radusky, Pathmanaban Ramasamy, Atilio O. Rausch, Nathalie Reuter, Luis A. Rodriguez, Nathan J. Rollins, Antonio Rosato, Pawel Rubach, Luis Serrano, Gulzar Singh, Petr Skoda, Carlos Oscar Sánchez Sorzano, Jan Stourac, Joanna I. Sulkowska, Radka Svobodová Vareková, Natalia Tichshenko, Silvio C. E. Tosatto, Wim F. Vranken, Mark N. Wass, Dandan Xue, Daniel Zaidman, Janet M. Thornton, Michael J. E. Sternberg, Christine A. Orengo, Sameer Velankar:
PDBe-KB: collaboratively defining the biological context of structural data. Nucleic Acids Res. 50(D1): 534-542 (2022) - 2020
- [j29]Pieter Verschaffelt, Philippe Van Thienen, Tim Van Den Bossche, Felix Van der Jeugt, Caroline De Tender, Lennart Martens, Peter Dawyndt, Bart Mesuere:
Unipept CLI 2.0: adding support for visualizations and functional annotations. Bioinform. 36(14): 4220-4221 (2020) - 2019
- [j28]Gwendolien Sergeant, Lennart Martens, Marleen Van Troys, Paola Masuzzo:
DoRes within CellMissy: dose-response analysis on cell migration and related data. Bioinform. 35(4): 696-697 (2019) - [j27]Ana S. C. Silva, Robbin Bouwmeester, Lennart Martens, Sven Degroeve:
Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functions. Bioinform. 35(24): 5243-5248 (2019) - [j26]Pieter-Jan Volders, Jasper Anckaert, Kenneth Verheggen, Justine Nuytens, Lennart Martens, Pieter Mestdagh, Jo Vandesompele:
LNCipedia 5: towards a reference set of human long non-coding RNAs. Nucleic Acids Res. 47(Database-Issue): D135-D139 (2019) - [j25]Ralf Gabriels, Lennart Martens, Sven Degroeve:
Updated MS²PIP web server delivers fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques. Nucleic Acids Res. 47(Webserver-Issue): W295-W299 (2019) - 2018
- [j24]Surya Gupta, Demet Turan, Jan Tavernier, Lennart Martens:
The online Tabloid Proteome: an annotated database of protein associations. Nucleic Acids Res. 46(Database-Issue): D581-D585 (2018) - 2017
- [j23]Surya Gupta, Veronic De Puysseleyr, José Van der Heyden, Davy Maddelein, Irma Lemmens, Sam Lievens, Sven Degroeve, Jan Tavernier, Lennart Martens:
MAPPI-DAT: data management and analysis for protein-protein interaction data from the high-throughput MAPPIT cell microarray platform. Bioinform. 33(9): 1424-1425 (2017) - [j22]Kevin Titeca, Pieter Meysman, Kris Laukens, Lennart Martens, Jan Tavernier, Sven Eyckerman:
sfinx: an R package for the elimination of false positives from affinity purification-mass spectrometry datasets. Bioinform. 33(12): 1902-1904 (2017) - 2016
- [j21]Volodimir Olexiouk, Jeroen Crappé, Steven Verbruggen, Kenneth Verheggen, Lennart Martens, Gerben Menschaert:
sORFs.org: a repository of small ORFs identified by ribosome profiling. Nucleic Acids Res. 44(Database-Issue): 324-329 (2016) - 2015
- [j20]Pieter-Jan Volders, Kenneth Verheggen, Gerben Menschaert, Klaas Vandepoele, Lennart Martens, Jo Vandesompele, Pieter Mestdagh:
An update on LNCipedia: a database for annotated human lncRNA sequences. Nucleic Acids Res. 43(Database-Issue): 174-180 (2015) - [j19]Sven Degroeve, Davy Maddelein, Lennart Martens:
MS2PIP prediction server: compute and visualize MS2 peak intensity predictions for CID and HCD fragmentation. Nucleic Acids Res. 43(Webserver-Issue): W326-W330 (2015) - [j18]Davy Maddelein, Niklaas Colaert, Iain Buchanan, Niels Hulstaert, Kris Gevaert, Lennart Martens:
The iceLogo web server and SOAP service for determining protein consensus sequences. Nucleic Acids Res. 43(Webserver-Issue): W543-W546 (2015) - 2013
- [j17]Elizabeth Stewart, Todd Smith, Andrea De Souza, Jack Faris, Lennart Martens, Sophie Mohin, Vural Özdemir, Courtney MacNealy-Koch, Eugene Kolker:
Delsa Workshop IV: Launching the Quantified Human Initiative. Big Data 1(3): 187-190 (2013) - [j16]Eugene Kolker, Vural Özdemir, Lennart Martens, William Hancock, Gordon A. Anderson, Nathaniel Anderson, Sukru Aynacioglu, Ancha V. Baranova, Shawn R. Campagna, Rui Chen, John Choiniere, Stephen P. Dearth, Wu-Chun Feng, Lynnette Ferguson, Geoffrey C. Fox, Dmitrij Frishman, Robert Grossman, Allison P. Heath, Roger Higdon, Mara H. Hutz, Imre Janko, Lihua Jiang, Sanjay Joshi, Alexander E. Kel, Joseph W. Kemnitz, Isaac S. Kohane, Natali Kolker, Doron Lancet, Elaine Lee, Weizhong Li, Andrey Lisitsa, Adrian Llerena, Courtney MacNealy-Koch, Jean-Claude Marshall, Paola Masuzzo, Amanda May, George Mias, Matthew E. Monroe, Elizabeth Montague, Sean D. Mooney, Alexey I. Nesvizhskii, Santosh Noronha, Gilbert S. Omenn, Harsha Rajasimha, Preveen Ramamoorthy, Jerry Sheehan, Larry Smarr, Charles V. Smith, Todd Smith, Michael Snyder, Srikanth Rapole, Sanjeeva Srivastava, Larissa Stanberry, Elizabeth Stewart, Stefano Toppo, Peter Uetz, Kenneth Verheggen, Brynn H. Voy, Louise Warnich, Steven W. Wilhelm, Gregory Yandl:
Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications. Big Data 1(4): 196-201 (2013) - [j15]Paola Masuzzo, Niels Hulstaert, Lynn Huyck, Christophe Ampe, Marleen Van Troys, Lennart Martens:
CellMissy: a tool for management, storage and analysis of cell migration data produced in wound healing-like assays. Bioinform. 29(20): 2661-2663 (2013) - [j14]Sven Degroeve, Lennart Martens:
MS2PIP: a tool for MS/MS peak intensity prediction. Bioinform. 29(24): 3199-3203 (2013) - [j13]Pieter-Jan Volders, Kenny Helsens, Xiaowei Wang, Björn Menten, Lennart Martens, Kris Gevaert, Jo Vandesompele, Pieter Mestdagh:
LNCipedia: a database for annotated human lncRNA transcript sequences and structures. Nucleic Acids Res. 41(Database-Issue): 246-251 (2013) - [j12]Niklaas Colaert, Davy Maddelein, Francis Impens, Petra Van Damme, Kim Plasman, Kenny Helsens, Niels Hulstaert, Joël Vandekerckhove, Kris Gevaert, Lennart Martens:
The Online Protein Processing Resource (TOPPR): a database and analysis platform for protein processing events. Nucleic Acids Res. 41(Database-Issue): 333-337 (2013) - [j11]Lennart Martens:
About Dice, Bouldering, and Team Empowerment: Running the CompOmics Group at VIB and Ghent University, Belgium. PLoS Comput. Biol. 9(11) (2013) - 2011
- [j10]Harald Barsnes, Marc Vaudel, Niklaas Colaert, Kenny Helsens, Albert Sickmann, Frode S. Berven, Lennart Martens:
compomics-utilities: an open-source Java library for computational proteomics. BMC Bioinform. 12: 70 (2011) - 2010
- [j9]Harald Barsnes, Richard G. Côté, Ingvar Eidhammer, Lennart Martens:
OLS Dialog: An open-source front end to the Ontology Lookup Service. BMC Bioinform. 11: 34 (2010) - [j8]Juan Antonio Vizcaíno, Richard G. Côté, Florian Reisinger, Harald Barsnes, Joseph M. Foster, Jonathan Rameseder, Henning Hermjakob, Lennart Martens:
The Proteomics Identifications database: 2010 update. Nucleic Acids Res. 38(Database-Issue): 736-742 (2010) - [j7]Richard G. Côté, Florian Reisinger, Lennart Martens, Harald Barsnes, Juan Antonio Vizcaíno, Henning Hermjakob:
The Ontology Lookup Service: bigger and better. Nucleic Acids Res. 38(Web-Server-Issue): 155-160 (2010) - 2008
- [j6]Philip Jones, Richard G. Côté, Sang Yun Cho, Sebastian Klie, Lennart Martens, Antony F. Quinn, David Thorneycroft, Henning Hermjakob:
PRIDE: new developments and new datasets. Nucleic Acids Res. 36(Database-Issue): 878-883 (2008) - [j5]Richard G. Côté, Philip Jones, Lennart Martens, Rolf Apweiler, Henning Hermjakob:
The Ontology Lookup Service: more data and better tools for controlled vocabulary queries. Nucleic Acids Res. 36(Web-Server-Issue): 372-376 (2008) - 2007
- [j4]Richard G. Côté, Philip Jones, Lennart Martens, Samuel Kerrien, Florian Reisinger, Quan Lin, Rasko Leinonen, Rolf Apweiler, Henning Hermjakob:
The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases. BMC Bioinform. 8 (2007) - 2006
- [j3]Lennart Martens, Geert Monsieur, Christophe Ampe, Kris Gevaert, Joël Vandekerckhove:
Cell_motility: a cross-platform, open source application for the study of cell motion paths. BMC Bioinform. 7: 289 (2006) - [j2]Philip Jones, Richard G. Côté, Lennart Martens, Antony F. Quinn, Chris F. Taylor, William Derache, Henning Hermjakob, Rolf Apweiler:
PRIDE: a public repository of protein and peptide identifications for the proteomics community. Nucleic Acids Res. 34(Database-Issue): 659-663 (2006) - 2005
- [j1]Lennart Martens, Joël Vandekerckhove, Kris Gevaert:
DBToolkit: processing protein databases for peptide-centric proteomics. Bioinform. 21(17): 3584-3585 (2005)
Conference and Workshop Papers
- 2007
- [c2]Sebastian Klie, Lennart Martens, Juan Antonio Vizcaíno, Richard G. Côté, Philip Jones, Rolf Apweiler, Alexander Hinneburg, Henning Hermjakob:
An Application of Latent Topic Document Analysis to Large-Scale Proteomics Databases. German Conference on Bioinformatics 2007: 174-184 - [c1]Sebastian Klie, Alexander Hinneburg, Lennart Martens, Juan Antonio Vizcaíno, Richard G. Côté, Philip Jones, Rolf Apweiler, Henning Hermjakob:
Analysing latent topics in large-scale proteomics. LWA 2007: 73-80
Parts in Books or Collections
- 2012
- [p2]Marc Vaudel, Julia Maria Burkhart, René Peiman Zahedi, Lennart Martens, Albert Sickmann:
iTRAQ Data Interpretation. Quantitative Methods in Proteomics 2012: 501-509 - 2010
- [p1]Philip Jones, Lennart Martens:
Using the PRIDE Proteomics Identifications Database for Knowledge Discovery and Data Analysis. Proteome Bioinformatics 2010: 297-307
Informal and Other Publications
- 2023
- [i4]Rebekah L. Gundry, Lennart Martens, Magnus Palmblad:
Computational Proteomics (Dagstuhl Seminar 23301). Dagstuhl Reports 13(7): 152-165 (2023) - 2021
- [i3]Sebastian Böcker, Rebekah L. Gundry, Lennart Martens, Magnus Palmblad:
Computational Proteomics (Dagstuhl Seminar 21271). Dagstuhl Reports 11(6): 1-13 (2021) - 2019
- [i2]Nuno Bandeira, Lennart Martens:
Computational Proteomics (Dagstuhl Seminar 19351). Dagstuhl Reports 9(8): 70-83 (2019) - 2017
- [i1]Bernhard Küster, Kathryn S. Lilley, Lennart Martens:
Computational Proteomics (Dagstuhl Seminar 17421). Dagstuhl Reports 7(10): 69-83 (2017)
Coauthor Index
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