prof. dr. ir. Gerben Menschaert
- ORCID iD
- 0000-0002-7575-2085
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- Conference Paper
- open access
Multimodal Deregulation of Imprinted Gene HM13 leads to Pan-Cancer Upregulation of Putative Oncogene MCTS2
(2023) -
- Miscellaneous
- open access
Editorial : sORF encoded peptides in health and disease
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Standardized annotation of translated open reading frames
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- Journal Article
- A1
- open access
CpG transformer for imputation of single-cell methylomes
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- Conference Paper
- C3
- open access
Role of coelomocytes and immunity in axenic dietary restriction
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Downregulation of the FTO m(6)A RNA demethylase promotes EMT-mediated progression of epithelial tumors and sensitivity to Wnt inhibitors
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- Journal Article
- A1
- open access
Identification of non-canonical translation products in C. elegans using tandem mass spectrometry
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- Journal Article
- A1
- open access
Ion mobility coupled to a time-of-flight mass analyzer combined with fragment intensity predictions improves identification of classical bioactive peptides and small open reading frame-encoded peptides
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- Journal Article
- A1
- open access
Explainability in transformer models for functional genomics
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- Journal Article
- A1
- open access
Spectral prediction features as a solution for the search space size problem in proteogenomics
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- Journal Article
- A1
- open access
Functional role of Tet-mediated RNA hydroxymethylcytosine in mouse ES cells and during differentiation
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The hunt for sORFs : a multidisciplinary strategy
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- Journal Article
- A1
- open access
Mitochondrial peptide BRAWNIN is essential for vertebrate respiratory complex III assembly
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A methodology for discovering novel brain-relevant peptides : combination of ribosome profiling and peptidomics
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- Journal Article
- A1
- open access
A combined strategy of neuropeptide prediction and tandem mass spectrometry identifies evolutionarily conserved ancient neuropeptides in the sea anemone Nematostella vectensis
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Multiple solvent elution, a method to counter the effects of coelution and ion suppression in LC-MS analysis in bottom up proteomics
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- Journal Article
- A1
- open access
Beyond genes : re-identifiability of proteomic data and its implications for personalized medicine
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- Journal Article
- A1
- open access
PROTEOFORMER 2.0 : further developments in the ribosome profiling-assisted proteogenomic hunt for new proteoforms
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- Journal Article
- A1
- open access
DeepRibo : a neural network for precise gene annotation of prokaryotes by combining ribosome profiling signal and binding site patterns
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Proteomics Standards Initiative extended FASTA format
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DeepRibo : precise gene annotation of prokaryotes using deep learning and ribosome profiling data, validated with mass spectrometry data
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- Conference Paper
- C3
- open access
DeepRibo : precise gene annotation of prokaryotes using deep learning and ribosome profiling data
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- Journal Article
- A1
- open access
mQC : a post-mapping data exploration tool for ribosome profiling
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Deletion 6q drives T-cell leukemia progression by ribosome modulation
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- Journal Article
- A1
- open access
Mass spectrometric evidence for neuropeptide-amidating enzymes in Caenorhabditis elegans
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Short open reading frames and their encoded peptides
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Comprehensive peptide analysis of mouse brain striatum identifies novel sORF-encoded polypeptides
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- Journal Article
- A1
- open access
The proBAM and proBed standard formats : enabling a seamless integration of genomics and proteomics data
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- Journal Article
- A1
- open access
Discovery of noncanonical translation initiation sites through mass spectrometric analysis of protein N termini
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A gene family coding for salivary proteins (SHOT) of the polyphagous spider mite Tetranychus urticae exhibits fast host-dependent transcriptional plasticity
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- Journal Article
- A1
- open access
An update on sORFs.org : a repository of small ORFs identified by ribosome profiling
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Proteogenomics from a bioinformatics angle : a growing field
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- Journal Article
- A1
- open access
REPARATION : ribosome profiling assisted (re-)annotation of bacterial genomes
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- Journal Article
- A1
- open access
eIF1 modulates the recognition of suboptimal translation initiation sites and steers gene expression via uORFs
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In search of lost small peptides
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Proteomics Standards Initiative : fifteen years of progress and future work
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proBAMconvert : a conversion tool for proBAM/proBed
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- Journal Article
- A1
- open access
Noncoding after all : biases in proteomics data do not explain observed absence of lncRNA translation products
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The salivary protein repertoire of the polyphagous spider mite Tetranychus urticae: a quest for effectors
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- Journal Article
- A1
- open access
A role for human N-alpha acetyltransferase 30 (Naa30) in maintaining mitochondrial integrity
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Fast and reliable quantitative peptidomics with labelpepmatch
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Identification of small novel coding sequences, a proteogenomic endeavor
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- Journal Article
- A1
- open access
sORFs.org : a repository of small ORFs identified by ribosome profiling
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- Journal Article
- A1
- open access
An update on LNCipedia : a database for annotated human lncRNA sequences
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- Journal Article
- A1
- open access
PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration
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A proteogenomics approach integrating proteomics and ribosome profiling increases the efficiency of protein identification and enables the discovery of alternative translation start sites
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- Journal Article
- A2
- open access
Little things make big things happen : a summary of micropeptide encoding genes
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N-terminal proteomics and ribosome profiling provide a comprehensive view of the alternative translation initiation landscape in mice and men
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Colorado potato beetle (Coleoptera) gut transcriptome analysis: expression of RNA interference-related genes
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- Conference Paper
- C3
- open access
Mass spectrometry and ribosome profiling, a perfect combination towards a more comprehensive identification strategy of true in vivo protein forms