Lennart Martens
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Biology
Lennart Martens's Degrees
- PhD Bioinformatics Ghent University
- Masters Bioinformatics Ghent University
- Bachelors Biochemistry Ghent University
Why Is Lennart Martens Influential?
(Suggest an Edit or Addition)Lennart Martens's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- ProteomeXchange provides globally co-ordinated proteomics data submission and dissemination (2014) (2398)
- The minimum information about a proteomics experiment (MIAPE) (2007) (704)
- The first comprehensive and quantitative analysis of human platelet protein composition allows the comparative analysis of structural and functional pathways. (2012) (629)
- Improved visualization of protein consensus sequences by iceLogo (2009) (603)
- mzML—a Community Standard for Mass Spectrometry Data* (2010) (565)
- Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides (2003) (549)
- PRIDE: The proteomics identifications database (2005) (547)
- LNCipedia: a database for annotated human lncRNA transcript sequences and structures (2012) (472)
- PeptideShaker enables reanalysis of MS-derived proteomics data sets (2015) (445)
- SearchGUI: An open‐source graphical user interface for simultaneous OMSSA and X!Tandem searches (2011) (336)
- LNCipedia 5: towards a reference set of human long non-coding RNAs (2018) (314)
- PRIDE: a public repository of protein and peptide identifications for the proteomics community (2005) (279)
- The Proteomics Identifications database: 2010 update (2009) (255)
- A guide to the Proteomics Identifications Database proteomics data repository (2009) (237)
- SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification (2017) (220)
- Chromatographic Isolation of Methionine-containing Peptides for Gel-free Proteome Analysis (2002) (219)
- Caspase-specific and nonspecific in vivo protein processing during Fas-induced apoptosis (2005) (217)
- An update on LNCipedia: a database for annotated human lncRNA sequences (2015) (207)
- An update on LNCipedia: a database for annotated human lncRNA sequences (2014) (178)
- PRIDE Converter: making proteomics data-sharing easy (2009) (176)
- Getting intimate with trypsin, the leading protease in proteomics. (2013) (167)
- Human Proteinpedia enables sharing of human protein data (2008) (164)
- The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases (2007) (146)
- Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1. (2016) (144)
- DBToolkit: processing protein databases for peptide-centric proteomics (2005) (140)
- PRIDE: new developments and new datasets (2007) (139)
- An improved toolbox to unravel the plant cellular machinery by tandem affinity purification of Arabidopsis protein complexes (2014) (135)
- The MetaProteomeAnalyzer: a powerful open-source software suite for metaproteomics data analysis and interpretation. (2015) (134)
- The Ontology Lookup Service: bigger and better (2010) (125)
- The human platelet proteome mapped by peptide‐centric proteomics: A functional protein profile (2005) (124)
- Large-scale identification of N-terminal peptides in the halophilic archaea Halobacterium salinarum and Natronomonas pharaonis. (2007) (121)
- PRIDE Inspector: a tool to visualize and validate MS proteomics data (2011) (120)
- The PRoteomics IDEntification (PRIDE) Converter 2 Framework: An Improved Suite of Tools to Facilitate Data Submission to the PRIDE Database and the ProteomeXchange Consortium* (2012) (116)
- Global differential non-gel proteomics by quantitative and stable labeling of tryptic peptides with oxygen-18. (2004) (115)
- Peptide and protein quantification: A map of the minefield (2010) (107)
- Navigating through metaproteomics data: A logbook of database searching (2015) (99)
- MS2PIP: a tool for MS/MS peak intensity prediction (2013) (98)
- Unipept 4.0: Functional Analysis of Metaproteome Data. (2018) (97)
- sORFs.org: a repository of small ORFs identified by ribosome profiling (2015) (95)
- TraML—A Standard Format for Exchange of Selected Reaction Monitoring Transition Lists* (2011) (92)
- compomics-utilities: an open-source Java library for computational proteomics (2011) (91)
- Time-resolved characterization of cAMP/PKA-dependent signaling reveals that platelet inhibition is a concerted process involving multiple signaling pathways. (2014) (90)
- The Ontology Lookup Service: more data and better tools for controlled vocabulary queries (2008) (90)
- A la carte proteomics with an emphasis on gel‐free techniques (2007) (88)
- Improving the reliability and throughput of mass spectrometry‐based proteomics by spectrum quality filtering (2006) (86)
- Anatomy and evolution of database search engines-a central component of mass spectrometry based proteomic workflows. (2020) (84)
- The impact of sequence database choice on metaproteomic results in gut microbiota studies (2016) (84)
- Taking Aim at Moving Targets in Computational Cell Migration. (2016) (84)
- ms_lims, a simple yet powerful open source laboratory information management system for MS‐driven proteomics (2010) (84)
- Reversible labeling of cysteine‐containing peptides allows their specific chromatographic isolation for non‐gel proteome studies (2004) (84)
- ThermoRawFileParser: modular, scalable and cross-platform RAW file conversion (2019) (80)
- A Golden Age for Working with Public Proteomics Data (2017) (76)
- DeNovoGUI: An Open Source Graphical User Interface for de Novo Sequencing of Tandem Mass Spectra (2013) (70)
- Diagonal reverse-phase chromatography applications in peptide-centric proteomics: ahead of catalogue-omics? (2005) (69)
- Searching for a needle in a stack of needles: challenges in metaproteomics data analysis. (2013) (66)
- Exploring the potential of public proteomics data (2015) (66)
- Quality control in mass spectrometry-based proteomics. (2018) (66)
- Updated MS²PIP web server delivers fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques (2019) (65)
- DeepLC can predict retention times for peptides that carry as-yet unseen modifications (2020) (64)
- Proteome-wide characterization of N-glycosylation events by diagonal chromatography. (2006) (62)
- Global phosphoproteome analysis on human HepG2 hepatocytes using reversed‐phase diagonal LC (2005) (61)
- Colonic metaproteomic signatures of active bacteria and the host in obesity (2015) (60)
- Protein identification based on matrix assisted laser desorption/ionization‐post source decay‐mass spectrometry (2001) (60)
- Proteomics data repositories: Providing a safe haven for your data and acting as a springboard for further research (2010) (60)
- MS2PIP prediction server: compute and visualize MS2 peak intensity predictions for CID and HCD fragmentation (2015) (59)
- Analysis of the resolution limitations of peptide identification algorithms. (2011) (58)
- Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project (2005) (57)
- The PSI semantic validator: A framework to check MIAPE compliance of proteomics data (2009) (56)
- Peptizer, a Tool for Assessing False Positive Peptide Identifications and Manually Validating Selected Results*S (2008) (56)
- XTandem Parser: An open‐source library to parse and analyse X!Tandem MS/MS search results (2010) (56)
- iTRAQ protein quantification: A quality‐controlled workflow (2011) (55)
- jmzML, an open‐source Java API for mzML, the PSI standard for MS data (2010) (55)
- Bioinformatics analysis of a Saccharomyces cerevisiae N-terminal proteome provides evidence of alternative translation initiation and post-translational N-terminal acetylation. (2011) (55)
- Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phase (2006) (54)
- Machine learning applications in proteomics research: How the past can boost the future (2014) (54)
- Metaproteomic data analysis at a glance: advances in computational microbial community proteomics (2016) (53)
- moFF: a robust and automated approach to extract peptide ion intensities (2016) (53)
- MascotDatfile: An open‐source library to fully parse and analyse MASCOT MS/MS search results (2007) (52)
- Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories (2005) (52)
- D‐score: A search engine independent MD‐score (2013) (51)
- HUPO Brain Proteome Project: Summary of the pilot phase and introduction of a comprehensive data reprocessing strategy (2006) (50)
- Comprehensive and Empirical Evaluation of Machine Learning Algorithms for Small Molecule LC Retention Time Prediction. (2019) (49)
- The RNA landscape of the human placenta in health and disease (2021) (49)
- Chromatographic retention time prediction for posttranslationally modified peptides (2012) (48)
- Current methods for global proteome identification (2012) (48)
- A complex standard for protein identification, designed by evolution. (2012) (48)
- Challenges and promise at the interface of metaproteomics and genomics: an overview of recent progress in metaproteogenomic data analysis (2019) (47)
- The PSI formal document process and its implementation on the PSI website (2007) (47)
- Annotating the human proteome: beyond establishing a parts list. (2007) (46)
- Computational Methods for Mass Spectrometry Proteomics (2008) (46)
- qcML: An Exchange Format for Quality Control Metrics from Mass Spectrometry Experiments* (2014) (45)
- Predicting tryptic cleavage from proteomics data using decision tree ensembles. (2013) (44)
- Peptide identification quality control (2011) (44)
- Proteomics data validation: why all must provide data. (2007) (44)
- Thermo-msf-parser: an open source Java library to parse and visualize Thermo Proteome Discoverer msf files. (2011) (42)
- Analyzing large-scale proteomics projects with latent semantic indexing. (2008) (41)
- Up-to-Date Workflow for Plant (Phospho)proteomics Identifies Differential Drought-Responsive Phosphorylation Events in Maize Leaves. (2016) (40)
- ProteoCloud: a full-featured open source proteomics cloud computing pipeline. (2013) (39)
- Toward more transparent and reproducible omics studies through a common metadata checklist and data publications. (2014) (39)
- Proteome-derived Peptide Libraries to Study the Substrate Specificity Profiles of Carboxypeptidases* (2013) (38)
- Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functions (2018) (37)
- Introduction to opportunities and pitfalls in functional mass spectrometry based proteomics. (2014) (35)
- High-throughput metaproteomics data analysis with Unipept: A tutorial. (2018) (35)
- Summarization vs Peptide-Based Models in Label-Free Quantitative Proteomics: Performance, Pitfalls, and Data Analysis Guidelines. (2015) (35)
- Structural investigation of B-Raf paradox breaker and inducer inhibitors. (2015) (34)
- Computational quality control tools for mass spectrometry proteomics (2017) (34)
- Implementation and application of a versatile clustering tool for tandem mass spectrometry data (2007) (33)
- Identification of Quantitative Proteomic Differences between Mycobacterium tuberculosis Lineages with Altered Virulence (2016) (33)
- Ryanodine receptors are targeted by anti-apoptotic Bcl-XL involving its BH4 domain and Lys87 from its BH3 domain (2015) (33)
- The iceLogo web server and SOAP service for determining protein consensus sequences (2015) (33)
- A new functional, chemical proteomics technology to identify purine nucleotide binding sites in complex proteomes. (2006) (33)
- Mass spectrometrists should search for all peptides, but assess only the ones they care about (2017) (33)
- MPA Portable: A Stand-Alone Software Package for Analyzing Metaproteome Samples on the Go (2017) (32)
- N-terminal Proteomics Assisted Profiling of the Unexplored Translation Initiation Landscape in Arabidopsis thaliana * (2017) (32)
- OMSSA Parser: An open‐source library to parse and extract data from OMSSA MS/MS search results (2009) (32)
- Removing the hidden data dependency of DIA with predicted spectral libraries (2019) (32)
- A posteriori quality control for the curation and reuse of public proteomics data (2011) (31)
- Protein structure as a means to triage proposed PTM sites (2013) (31)
- Viewing the proteome: How to visualize proteomics data? (2015) (30)
- A decoy-free approach to the identification of peptides. (2015) (30)
- Noncoding after All: Biases in Proteomics Data Do Not Explain Observed Absence of lncRNA Translation Products. (2017) (30)
- Database on Demand – An online tool for the custom generation of FASTA‐formatted sequence databases (2009) (28)
- Crowdsourcing in proteomics: public resources lead to better experiments (2013) (28)
- Four stage liquid chromatographic selection of methionyl peptides for peptide-centric proteome analysis: the proteome of human multipotent adult progenitor cells. (2006) (28)
- The Age of Data‐Driven Proteomics: How Machine Learning Enables Novel Workflows (2020) (27)
- Bcl-2 and IP3 compete for the ligand-binding domain of IP3Rs modulating Ca2+ signaling output (2019) (27)
- Protein complex analysis: From raw protein lists to protein interaction networks. (2017) (26)
- The power of cooperative investigation: Summary and comparison of the HUPO Brain Proteome Project pilot study results (2006) (26)
- A comparison of the HUPO Brain Proteome Project pilot with other proteomics studies (2006) (26)
- Community standards for open cell migration data (2019) (26)
- 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. (2019) (25)
- Cell_motility: a cross-platform, open source application for the study of cell motion paths (2006) (25)
- Do you speak open science? Resources and tips to learn the language (2017) (25)
- Combining quantitative proteomics data processing workflows for greater sensitivity (2011) (25)
- jTraqX: A free, platform independent tool for isobaric tag quantitation at the protein level (2010) (25)
- An end-to-end software solution for the analysis of high-throughput single-cell migration data (2017) (25)
- Xilmass: A New Approach toward the Identification of Cross-Linked Peptides. (2016) (24)
- Corrigendum: SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification. (2018) (24)
- RIBAR and xRIBAR: Methods for reproducible relative MS/MS-based label-free protein quantification. (2011) (24)
- Integral quantification accuracy estimation for reporter ion-based quantitative proteomics (iQuARI). (2012) (23)
- Functional annotation of proteins identified in human brain during the HUPO Brain Proteome Project pilot study (2006) (23)
- An open data ecosystem for cell migration research. (2015) (23)
- Human Proteome Organization Proteomics Standards Initiative: data standardization, a view on developments and policy. (2007) (22)
- Spectral Prediction Features as a Solution for the Search Space Size Problem in Proteogenomics (2021) (22)
- Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications (2013) (22)
- Resolution of protein structure by mass spectrometry. (2016) (22)
- iMonDB: Mass Spectrometry Quality Control through Instrument Monitoring. (2015) (22)
- Cross-linked peptide identification: A computational forest of algorithms. (2018) (22)
- PDBe-KB: collaboratively defining the biological context of structural data (2021) (22)
- A global analysis of peptide fragmentation variability (2011) (22)
- Shedding light on black boxes in protein identification (2014) (21)
- Cov-MS: A Community-Based Template Assay for Mass-Spectrometry-Based Protein Detection in SARS-CoV-2 Patients (2021) (21)
- Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 workshop report. (2013) (21)
- A comparison of MS2‐based label‐free quantitative proteomic techniques with regards to accuracy and precision (2011) (20)
- MS2Rescore: Data-Driven Rescoring Dramatically Boosts Immunopeptide Identification Rates (2021) (20)
- Analysis of the experimental detection of central nervous system‐related genes in human brain and cerebrospinal fluid datasets (2008) (20)
- Distributed computing and data storage in proteomics: Many hands make light work, and a stronger memory (2014) (20)
- The Online Protein Processing Resource (TOPPR): a database and analysis platform for protein processing events (2012) (19)
- Differences in antigenic sites and other functional regions between genotype A and G mumps virus surface proteins (2018) (19)
- jTraML: An Open Source Java API for TraML, the PSI Standard for Sharing SRM Transitions (2011) (19)
- The challenge of metaproteomic analysis in human samples (2016) (19)
- Simple Peptide Quantification Approach for MS-Based Proteomics Quality Control (2020) (18)
- Bringing proteomics into the clinic: The need for the field to finally take itself seriously (2013) (18)
- An Accessible Proteogenomics Informatics Resource for Cancer Researchers. (2017) (18)
- Protein Identification and Characterization by MS (2007) (18)
- PRIDE: Data Submission and Analysis (2010) (17)
- Data Management of Sensitive Human Proteomics Data: Current Practices, Recommendations, and Perspectives for the Future (2021) (17)
- Database Search Engines: Paradigms, Challenges and Solutions. (2016) (17)
- OLS Dialog: An open-source front end to the Ontology Lookup Service (2010) (17)
- Getting a grip on proteomics data – Proteomics Data Collection (ProDaC) (2009) (17)
- SFINX: Straightforward Filtering Index for Affinity Purification-Mass Spectrometry Data Analysis. (2016) (17)
- Computational and Statistical Methods for Protein Quantification by Mass Spectrometry (2013) (17)
- Bioinformatics challenges in mass spectrometry-driven proteomics. (2011) (17)
- FragmentationAnalyzer: An open‐source tool to analyze MS/MS fragmentation data (2010) (16)
- Pride-asap: Automatic fragment ion annotation of identified PRIDE spectra☆ (2013) (16)
- An extra dimension in protein tagging by quantifying universal proteotypic peptides using targeted proteomics (2016) (16)
- A case study on the comparison of different software tools for automated quantification of peptides. (2011) (15)
- Phospho-iTRAQ: assessing isobaric labels for the large-scale study of phosphopeptide stoichiometry. (2015) (15)
- Proteome-scale Binary Interactomics in Human Cells* (2016) (15)
- Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows (2021) (14)
- Methods to Calculate Spectrum Similarity. (2017) (14)
- MSqRob takes the missing hurdle: uniting intensity- and count-based proteomics. (2020) (14)
- The CEP5 Peptide Promotes Abiotic Stress Tolerance, As Revealed by Quantitative Proteomics, and Attenuates the AUX/IAA Equilibrium in Arabidopsis (2020) (14)
- Towards a human proteomics atlas (2012) (14)
- CellMissy: a tool for management, storage and analysis of cell migration data produced in wound healing-like assays (2013) (14)
- Proteomics databases and repositories. (2011) (14)
- Generalized Calibration Across LC-setups for Generic Prediction of Small Molecule Retention Times. (2020) (14)
- OMSSAGUI: An open‐source user interface component to configure and run the OMSSA search engine (2008) (13)
- PRIDE and "Database on Demand" as valuable tools for computational proteomics. (2011) (13)
- Unsupervised Quality Assessment of Mass Spectrometry Proteomics Experiments by Multivariate Quality Control Metrics. (2016) (13)
- Charting online OMICS resources: A navigational chart for clinical researchers (2009) (13)
- Quality Control in Proteomics (2011) (13)
- Mass spectrometry-driven proteomics: an introduction. (2011) (12)
- Asn3, a reliable, robust, and universal lock mass for improved accuracy in LC-MS and LC-MS/MS. (2013) (12)
- Using the PRIDE Proteomics Identifications Database for Knowledge Discovery and Data Analysis (2010) (11)
- Data standards and controlled vocabularies for proteomics. (2008) (11)
- Critical Assessment of Metaproteome Investigation (CAMPI): A Multi-Lab Comparison of Established Workflows (2021) (11)
- Surveillance of Myelodysplastic Syndrome via Migration Analyses of Blood Neutrophils: A Potential Prognostic Tool (2018) (11)
- A Pipeline for Differential Proteomics in Unsequenced Species. (2016) (11)
- Designing biomedical proteomics experiments: state-of-the-art and future perspectives (2016) (11)
- Scop3P: a comprehensive resource of human phosphosites within their full context (2019) (11)
- A community proposal to integrate proteomics activities in ELIXIR (2017) (11)
- Sigpep: Calculating unique peptide signature transition sets in a complete proteome background (2012) (10)
- Proteomics for everyday use: Activities of the HUPO Brain Proteome Project during the 5th HUPO World Congress (2007) (10)
- 5th HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK – Setting the Analysis Frame (2005) (10)
- jqcML: an open-source java API for mass spectrometry quality control data in the qcML format. (2014) (10)
- Scop3D: Three‐dimensional visualization of sequence conservation (2015) (10)
- Robust summarization and inference in proteome-wide label-free quantification (2019) (10)
- COSS: A fast and user-friendly tool for spectral library searching. (2020) (9)
- Using the Proteomics Identifications Database (PRIDE) (2008) (9)
- iPRG 2011: A Study on the Identification of Electron Transfer Dissociation (ETD) Mass Spectra (2011) (9)
- The HUPO initiative on Model Organism Proteomes, iMOP (2012) (9)
- MSqRob takes the missing hurdle: uniting intensity- and count-based proteomics (2019) (9)
- Pladipus Enables Universal Distributed Computing in Proteomics Bioinformatics. (2016) (9)
- Update on the moFF Algorithm for Label-Free Quantitative Proteomics. (2018) (9)
- A reproducibility‐based evaluation procedure for quantifying the differences between MS/MS peak intensity normalization methods (2011) (8)
- A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics (2021) (8)
- Precursor Intensity-Based Label-Free Quantification Software Tools for Proteomic and Multi-Omic Analysis within the Galaxy Platform (2020) (8)
- The Lyssavirus glycoprotein: A key to cross-immunity. (2016) (8)
- Unipept Desktop: A Faster, More Powerful Metaproteomics Results Analysis Tool. (2021) (8)
- MegaGO: A Fast Yet Powerful Approach to Assess Functional Gene Ontology Similarity across Meta-Omics Data Sets. (2021) (8)
- Connecting MetaProteomeAnalyzer and PeptideShaker to Unipept for seamless end-to-end metaproteomics data analysis. (2020) (8)
- Data-Driven Rescoring of Metabolite Annotations Significantly Improves Sensitivity. (2018) (7)
- Proteomics Data Collection – The 1st ProDaC workshop 26 April 2007 Ecole Normale Supérieur, Lyon, France (2007) (7)
- Unraveling the specificities of the different human methionine sulfoxide reductases (2014) (7)
- JSparklines: Making tabular proteomics data come alive (2015) (7)
- A report on the ESF workshop on quality control in proteomics. (2010) (7)
- Scop3P: a comprehensive resource of human phosphosites within their full context. (2020) (7)
- Limited Proteolysis Combined with Stable Isotope Labeling Reveals Conformational Changes in Protein (Pseudo)kinases upon Binding Small Molecules. (2015) (7)
- Resilience in the proteomics data ecosystem: How the field cares for its data (2013) (7)
- Unipept CLI 2.0: adding support for visualizations and functional annotations (2020) (7)
- The mutational landscape of MYCN, Lin28b and ALKF1174L driven murine neuroblastoma mimics human disease (2017) (6)
- 6th HUPO Annual World Congress – Proteomics Standards Initiative Workshop 6–10 October 2007, Seoul, Korea (2008) (6)
- Unbiased dynamic characterization of RNA-protein interactions by OOPS (2018) (6)
- Proteomics Data Collection – 2nd ProDaC Workshop 5 October 2007, Seoul, Korea (2008) (6)
- The HUPO Brain Proteome Project Jamboree: Centralised summary of the pilot studies (2006) (6)
- COSS: A fast and user-friendly tool for spectral library searching (2019) (6)
- Immunopeptidomics-based design of mRNA vaccine formulations against Listeria monocytogenes (2022) (6)
- ionbot: a novel, innovative and sensitive machine learning approach to LC-MS/MS peptide identification (2021) (5)
- Pout2Prot: an efficient tool to create protein (sub)groups from Percolator output files (2021) (5)
- MegaGO: a fast yet powerful approach to assess functional similarity across meta-omics data sets (2020) (5)
- Toward a Successful Clinical Neuroproteomics The 11th HUPO Brain Proteome Project Workshop 3 March, 2009, Kolymbari, Greece (2009) (5)
- Proteomics Data Collection – 3rd ProDaC Workshop April 22nd 2008, Toledo, Spain (2008) (5)
- Managing expectations when publishing tools and methods for computational proteomics. (2015) (5)
- Personalized Proteome: Comparing Proteogenomics and Open Variant Search Approaches for Single Amino Acid Variant Detection (2021) (5)
- Algorithms and databases. (2009) (4)
- Large‐scale Proteomics (2007) (4)
- Data management in mass spectrometry-based proteomics. (2011) (4)
- Submitting proteomics data to PRIDE using PRIDE Converter. (2011) (4)
- Robust Summarization and Inference in Proteome-wide Label-free Quantification (2020) (4)
- Ariadne's Thread: A Robust Software Solution Leading to Automated Absolute and Relative Quantification of SRM Data. (2015) (4)
- A well-ordered nanoflow LC-MS/MS approach for proteome profiling using 200 cm long micro pillar array columns (2018) (4)
- The CEP5 Peptide Promotes Abiotic Stress Tolerance, As Revealed by Quantitative Proteomics, and Attenuates the AUX/IAA Equilibrium in Arabidopsis. (2020) (4)
- Public proteomics data: How the field has evolved from sceptical inquiry to the promise of in silico proteomics☆ (2016) (4)
- The online Tabloid Proteome: an annotated database of protein associations (2017) (4)
- sfinx: an R package for the elimination of false positives from affinity purification‐mass spectrometry datasets (2017) (3)
- Digging deeper into the human proteome: A novel nanoflow LCMS setup using micro pillar array columns (μPAC™) (2018) (3)
- Peptides to Proteins (2007) (3)
- Differences among mumps virus surface proteins between genotype G and other genotypes and their potential effect on mumps virus immunity and pathogenesis (2016) (3)
- Proteomics Data Collection – 5th ProDaC Workshop 4 March 2009, Kolympari, Crete, Greece (2009) (3)
- Targeted Quantification – Selected Reaction Monitoring (2013) (3)
- Unbiased Protein Association Study on the Public Human Proteome Reveals Biological Connections between Co-Occurring Protein Pairs (2017) (3)
- PRIDE: The proteomics identification database (vol 5, pg 3537, 2005) (2005) (3)
- Delsa Workshop IV: Launching the Quantified Human Initiative (2013) (3)
- Proteomics Data Collection – 4th ProDaC Workshop 15 August 2008, Amsterdam, The Netherlands (2009) (3)
- Ten years of public proteomics data: How things have evolved, and where the next ten years should lead us (2015) (3)
- FAVA: High-quality functional association networks inferred from scRNA-seq and proteomics data (2023) (3)
- iTRAQ Data Interpretation (2012) (3)
- "4D Biology for health and disease" workshop report. (2011) (3)
- The Personalized Proteome: Comparing Proteogenomics and Open Variant Search Approaches for Single Amino Acid Variant Detection (2020) (3)
- Analysis of Invasion Dynamics of Matrix-Embedded Cells in a Multisample Format. (2018) (3)
- Sensitive and Specific Spectral Library Searching with CompOmics Spectral Library Searching Tool and Percolator. (2022) (2)
- The HUPO Brain Proteome Project Wish List – Summary of the 9th HUPO BPP Workshop 9–10 January 2008, Barbados (2008) (2)
- Toward an Integrated Machine Learning Model of a Proteomics Experiment (2023) (2)
- Open-Source, Platform-Independent Library and Online Scripting Environment for Accessing Thermo Scientific RAW Files. (2015) (2)
- Computational Proteomics (Dagstuhl Seminar 17421) (2017) (2)
- Using moFF to Extract Peptide Ion Intensities from LC-MS experiments (2016) (2)
- Orthogonal proteomics methods to unravel the HOTAIR interactome (2021) (2)
- The study of degradation mechanisms of glyco-engineered plant produced anti-rabies monoclonal antibodies E559 and 62-71-3 (2018) (2)
- MS 2 Rescore: Data-Driven Rescoring Dramatically Boosts Immunopeptide Identi fi cation Rates (2022) (2)
- Enabling Computational Proteomics by Public and Local Data Management Systems (2012) (2)
- The effect of peptide identification search algorithms on MS2-based label-free protein quantification. (2012) (2)
- HUPO Brain Proteome Project: Summary of the pilot phase and introduction of a comprehensive data reprocessing strategy (2006) (2)
- Protein, Proteome, and Proteomics (2007) (2)
- Bioinformatics for proteomics: opportunities at the interface between the scientists, their experiments, and the community. (2014) (2)
- PepShell: visualization of conformational proteomics data. (2015) (2)
- Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit (2020) (2)
- High Performance Proteomics: 7th HUPO Brain Proteome Project Workshop March 7–9, 2007 Wellcome Trust Conference Centre, Hinxton, UK (2007) (2)
- An Application of Latent Topic Document Analysis to Large-Scale Proteomics Databases (2007) (1)
- N‐Terminal Combined Fractional Diagonal Chromatographic (COFRADIC) Analysis of the Human Platelet Proteome (2011) (1)
- Mass Spectrometry – MALDI‐TOF (2007) (1)
- psm_utils: A High-Level Python API for Parsing and Handling Peptide-Spectrum Matches and Proteomics Search Results. (2022) (1)
- Unipept Visualizations: an interactive visualization library for biological data (2021) (1)
- Clinical improvement of DM1 patients reflected by reversal of disease-induced gene expression in blood (2022) (1)
- The RNA landscape of the human placenta in health and disease (2021) (1)
- PRIDE: The proteomics identifications database (vol. 5, Issue 13, pp. 3537‐3545) (1)
- Quantification of Post‐Translational Modifications (2013) (1)
- Mass Spectrometry and Protein Identification (2013) (1)
- MAPPI-DAT: data management and analysis for protein–protein interaction data from the high-throughput MAPPIT cell microarray platform (2017) (1)
- Phospho-iTRAQ data article: Assessing isobaric labels for the large-scale study of phosphopeptide stoichiometry (2015) (1)
- Data and text mining MS 2 PIP : a tool for MS / MS peak intensity prediction (2013) (1)
- MAPPI‐DAT: data management and analysis for protein‐protein interaction data from the high‐throughput MAPPIT cell microarray platform (2017) (1)
- An interactive mass spectrometry atlas of histone posttranslational modifications in T-cell acute leukemia (2022) (1)
- About Dice, Bouldering, and Team Empowerment: Running the CompOmics Group at VIB and Ghent University, Belgium (2013) (1)
- Scop3D: Online Visualization of Mutation Rates on Protein Structure. (2018) (1)
- Publisher Correction: Differences in antigenic sites and other functional regions between genotype A and G mumps virus surface proteins (2020) (1)
- Pitfalls in re-analysis of observational omics studies: a post-mortem of the human pathology atlas (2020) (1)
- DoRes within CellMissy: dose-response analysis on cell migration and related data (2018) (1)
- A closer look into the maze of metaproteomics data (2015) (0)
- Protein Level Quantification (2013) (0)
- Protein Separation – 2D Gel Electrophoresis (2007) (0)
- Predicting trypsin cleavage sites based on sequence information (2012) (0)
- acsOmega RGB jca logo.eps (0)
- Erratum: ms_lims, a simple yet powerful open source laboratory information management system for MS‐driven proteomics (0)
- Present and future of proteomics data curation at the PRIDE database (2009) (0)
- Database Searching for de novosequences (2007) (0)
- Study of the kinase switch mechanism in B-RAF upon small molecule binding via mass spectrometry (2013) (0)
- Quality control of proteomics data: performing local as well as global analices (2011) (0)
- MetaProteomeAnalyzer – a software suite for the functional and taxonomic characterization of (meta)proteome data (2014) (0)
- Erratum: XTandem Parser: An open‐source library to parse and analyse X!Tandem MS/MS search results (0)
- Rescoring peptide-to-spectrum-matches based on predicted fragment ion intensities leads to an increased identification rate in metaproteomics (2019) (0)
- Updated MS²PIP web server supports cutting-edge proteomics applications. (2023) (0)
- The open science of the everyday, and why it is our future (0)
- Evaluation of a strategy for parallel protein phosphorylation and expression analysis (2012) (0)
- w2) Spectral and Sequence Database Searching in Proteomics (2011) (0)
- A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics (2022) (0)
- Cov2MS: an automated matrix-independent assay for mass spectrometric detection and measurement of SARS-CoV-2 nucleocapsid protein in infectious patients (2022) (0)
- Author Correction: Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit (2023) (0)
- Computational analysis of mumps surface proteins reveals their interaction mechanism (2015) (0)
- Computational Proteomics (Dagstuhl Seminar 21271) (2021) (0)
- Computational Methods for Fragment Spectrum Interpretation (2010) (0)
- Peptide Separation – HPLC (2007) (0)
- Precursor intensity-based label-free quantification software tools for proteomic and multiomic analysis within the Galaxy Platform (2020) (0)
- Appendix: Statistics (2013) (0)
- Computational Proteomics (Dagstuhl Seminar 19351) (2019) (0)
- Fragment Based MS/MS Quantification (2013) (0)
- Crowdsourcing in proteomics: public resources lead to better experiments (2013) (0)
- Proteomics Enabling Computational Proteomics by Public and Local Data Management Systems (2012) (0)
- Identification and Characterization by MS/MS (2007) (0)
- Analysing latent topics in large-scale proteomics (2007) (0)
- Lncipedia: a novel database for annotated lncRNA sequences and structures (2012) (0)
- Label Free Quantification by MS/MS Spectra (2013) (0)
- MS²PIP : fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques (2019) (0)
- PepGM: A probabilistic graphical model for taxonomic inference of viral proteome samples with associated confidence scores (2022) (0)
- A panoramic perspective on human phosphosites (2022) (0)
- Appendix B: Clustering and Discriminant Analysis (2013) (0)
- A comprehensive approach to mass spectrometry quality control (2014) (0)
- Annotated Spectra for Vu, Stes et al (2016) (0)
- Erratum: FragmentationAnalyzer: An open‐source tool to analyze MS/MS fragmentation data (0)
- Immunopeptidomics-based design of highly effective mRNA vaccine formulations against Listeria monocytogenes (2022) (0)
- Novel bioinformatics tools assisting targeted peptide-centric proteomics and global proteomics data dissemination (2006) (0)
- Bioinformatics challenges in the proteomic analysis of human plasma. (2011) (0)
- Robust summarisation and inference for Label-Free Quantification (2019) (0)
- Differences in antigenic sites and other functional regions between genotype A and G mumps virus surface proteins (2018) (0)
- Comprehensive and empirical evaluation of machine learning algorithms for LC retention time prediction (2018) (0)
- Comparing fragmentation spectra from two parasitic worm species to discover unique peptides (2014) (0)
- Quantitative MS‐based Proteomics (2007) (0)
- The impact of sequence database choice on metaproteomic results in gut microbiota studies (2016) (0)
- Cov2MS: An Automated and Quantitative Matrix-Independent Assay for Mass Spectrometric Measurement of SARS-CoV-2 Nucleocapsid Protein (2022) (0)
- Generalized calibration across LC-setups for generic prediction of small molecule retention times (2020) (0)
- Bcl-2 and IP3 compete for the ligand-binding domain of IP3Rs modulating Ca2+ signaling output (2019) (0)
- Computational Proteomics by Public and Local Data Management Systems (2012) (0)
- TOWARD MORE TRANSPARENT AND REPRODUCIBLE (2013) (0)
- Trans-synaptic dwelling of SARS-CoV-2 particles perturbs neural synapse organization and function (2022) (0)
- IL-29 Is proteomics heading towards medicine? (2003) (0)
- Quality control for the target decoy approach for peptide identification (2022) (0)
- Reporter Based MS/MS Quantification (2013) (0)
- Sensitive and specific spectral library searching with COSS and Percolator (2021) (0)
- Fundamentals of Mass Spectrometry (2007) (0)
- The future of peptide-centric Data-Independent Acquisition is predicted (2019) (0)
- Prediction-based reduction of the search space in metaproteomics (2018) (0)
- Label Based Quantification by MS Spectra (2013) (0)
- MS²DIP: Highly accurate MS2 spectrum prediction for modified peptides & MS²Rescore: Data-driven rescoring dramatically boosts immunopeptide identification rates (2021) (0)
- Evaluation of moFF and FlashLFQ for label free peptide quantification in proteomic workflows within Galaxy-P framework. (2018) (0)
- Biogas plant metaproteome analysis and biomarker search by using the software MetaProteomeAnalyser (2013) (0)
- Machine Learning on Large-Scale Proteomics Data Identifies Tissue and Cell-Type Specific Proteins (2022) (0)
- Protein Quantification by Mass Spectrometry (2013) (0)
- Top‐down Proteomics (2007) (0)
- Fast and accurate MS² peak intensity predictions for multiple fragmentation methods, instruments and labeling techniques (2019) (0)
- Session 19: Plasma Proteomics I (2004) (0)
- Label Based Quantification (2013) (0)
- HUPO Brain Proteome Project pilot phase; Automated reprocessing pipeline for searching heterogenic data (2006) (0)
- Unipept Desktop 2.0: construction of targeted reference protein databases for proteogenomics analyses (2023) (0)
- metrics from mass spectrometry experiments (2014) (0)
- A time of enlightenment : straightforward identification of protein modifications (2019) (0)
- Standards and Databases (2013) (0)
- Correlations of mRNA and Protein Abundances (2013) (0)
- PiTRAQ, a strategy to simultaneously correlate protein expression and phosphorylation stoichiometry between different samples: evaluation on different mass spectrometers (2013) (0)
- Recent developments and new directions for the Galaxy-P project (2016) (0)
- Correction to Structural Investigation of B-Raf Paradox Breaker and Inducer Inhibitors. (2016) (0)
- Tandem MS or MS/MS Analysis (2007) (0)
- CellMissy: a tool for management, storage, dissemination and analysis of cell migration data (2013) (0)
- High‐throughput proteomics and bioinformatics: joined at the hip (2010) (0)
- Sequential Comparison – de novo Sequencing (2007) (0)
- A simple approach for accurate peptide quantification in MS-based proteomics (2019) (0)
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What Schools Are Affiliated With Lennart Martens?
Lennart Martens is affiliated with the following schools:
