Kenneth Verheggen

Kenneth Verheggen
Vlaams Instituut voor Biotechnologie | VIB · Department of Medical Protein Research, UGent

Doctor of Health Sciences and Bioinformatics

About

33
Publications
5,890
Reads
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1,277
Citations
Introduction
Automatic Distributed Reprocessing and re-annotating public MS2 data-repositories in proteomics
Additional affiliations
October 2012 - present
Ghent University
Position
  • PhD Student
October 2012 - present
Ghent University
Position
  • Research Assistant
Description
  • Teaching practical sessions in : - Biochemistry and molecular biology - Bioinformatics
October 2012 - present
Vlaams Instituut voor Biotechnologie
Position
  • PhD Student
Education
September 2006 - July 2010
University College Howest, Kortrijk, Belgium
Field of study
  • Biochemistry

Publications

Publications (33)
Article
Full-text available
While long non-coding RNA (lncRNA) research in the past has primarily focused on the discovery of novel genes, today it has shifted towards functional annotation of this large class of genes. With thousands of lncRNA studies published every year, the current challenge lies in keeping track of which lncRNAs are functionally described. This is furthe...
Article
The authors would like to correct the omission of a funding source in the Acknowledgments section which was inadvertently excluded from the initial publication of this article. The additional text is as follows and has been updated online: “This project has received funding from the Marie Curie International Research Staff Exchange Scheme within th...
Article
High-throughput sequencing of full-length transcripts using long reads has paved the way for the discovery of thousands of novel transcripts, even in well-annotated mammalian species. The advances in sequencing technology have created a need for studies and tools that can characterize these novel variants. Here, we present SQANTI, an automated pipe...
Article
Full-text available
Sequence database search engines are bioinformatics algorithms that identify peptides from tandem mass spectra using a reference protein sequence database. Two decades of development, notably driven by advances in mass spectrometry, have provided scientists with more than 30 published search engines, each with its own properties. In this review, we...
Preprint
Full-text available
High-throughput sequencing of full-length transcripts using long reads has paved the way for the discovery of thousands of novel transcripts, even in very well annotated organisms as mice and humans. Nonetheless, there is a need for studies and tools that characterize these novel isoforms. Here we present SQANTI, an automated pipeline for the class...
Poster
Full-text available
A novel method, to unravel the biological importance of protein co-occurrence in various mass-spectrometry based proteomics experiments, using computational approach with existing publically available data repositories.
Article
Over the past decade, long non-coding RNAs (lncRNAs) have emerged as novel functional entities of the eukaryotic genome. However, the scientific community remains divided over the amount of true non-coding transcripts among the large number of unannotated transcripts identified by recent large scale and deep RNAsequencing efforts. Here, we systemat...
Article
Full-text available
Mass-spectrometry based, high throughput proteomics experiments produce large amounts of data. While typically acquired to answer specific biological questions, these data can also be re-used in orthogonal ways to reveal new biological knowledge. We here present a novel method for such orthogonal data re-use of public proteomics data. Our method el...
Chapter
The first step in identifying proteins from mass spectrometry based shotgun proteomics data is to infer peptides from tandem mass spectra, a task generally achieved using database search engines. In this chapter, the basic principles of database search engines are introduced with a focus on open source software, and the use of database search engin...
Article
Full-text available
With the advent of ribosome profiling, a next generation sequencing technique providing a “snap-shot’’ of translated mRNA in a cell, many short open reading frames (sORFs) with ribosomal activity were identified. Follow-up studies revealed the existence of functional peptides, so-called micropeptides, translated from these ‘sORFs’, indicating a new...
Article
The use of proteomics bioinformatics substantially contributes to an improved understanding of proteomes, but this novel and in-depth knowledge comes at the cost of increased computational complexity. Parallelization across multiple computers, a strategy termed distributed computing, can be used to handle this increased complexity. However, setting...
Article
Full-text available
In a global effort for scientific transparency, it has become feasible and good practice to share experimental data supporting novel findings. Consequently, the amount of publicly available mass spectrometry-based proteomics data has grown substantially in recent years. With some notable exceptions, this extensive material has however largely been...
Research
Full-text available
We previously proposed 5'-AMP-activated protein kinase (AMPK) dephosphorylation within immune cells as an intracellular mechanism linking exercise and immunosuppression. In this study, AMPK phosphorylation underwent transient (< 1 h) decreases (53.8 ± 7.2% basal) immediately after exercise (45 min of cycling at 70% VO2max) in a cohort of 16 adult m...
Article
Full-text available
Ten years ago, the first public proteomics repositories became available online. This anniversary is therefore an excellent occasion to look back on the past decade and evaluate what has changed in this time period. At the same time however, one should also dare to look forward, and therefore prepare for the next 10 years of proteomics data sharing...
Article
Full-text available
The human genome is pervasively transcribed, producing thousands of non-coding RNA transcripts. The majority of these transcripts are long non-coding RNAs (lncRNAs) and novel lncRNA genes are being identified at rapid pace. To streamline these efforts, we created LNCipedia, an online repository of lncRNA transcripts and annotation. Here, we present...
Article
Modern day proteomics generates ever more complex data, causing the requirements on the storage and processing of such data to outgrow the capacity of most desktop computers. To cope with the increased computational demands, distributed architectures have gained substantial popularity in the recent years. In this review, we provide an overview of t...
Article
Full-text available
Abstract Biological processes are fundamentally driven by complex interactions between biomolecules. Integrated high-throughput omics studies enable multifaceted views of cells, organisms, or their communities. With the advent of new post-genomics technologies, omics studies are becoming increasingly prevalent; yet the full impact of these studies...
Article
Full-text available
Biological processes are fundamentally driven by complex interactions between biomolecules. Integrated high-throughput omics studies enable multifaceted views of cells, organisms, or their communities. With the advent of new post-genomics technologies, omics studies are becoming increasingly prevalent; yet the full impact of these studies can only...
Article
Full-text available
We previously proposed 5'-AMP-activated protein kinase (AMPK) dephosphorylation within immune cells as an intracellular mechanism linking exercise and immunosuppression. In this study, AMPK phosphorylation underwent transient (<1 h) decreases (53.8+/-7.2% basal) immediately after exercise (45 min of cycling at 70% VO2max) in a cohort of 16 adult ma...

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Projects

Projects (2)
Project
Exploring novel strategies to extract new biology, novel sequences and gain insight in the complete proteome.