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List of works by Kris Laukens

(1)H NMR based metabolomics of CSF and blood serum: a metabolic profile for a transgenic rat model of Huntington disease.

scientific article

1H-NMR study of the metabolome of an exceptionally anoxia tolerant vertebrate, the crucian carp (Carassius carassius)

article published in 2012

2-D DIGE reveals changes in wheat xylanase inhibitor protein families due to Fusarium graminearum DeltaTri5 infection and grain development

scientific article published on June 2010

A bioanalytical method for the proteome wide display and analysis of protein complexes from whole plant cell lysates

article

A community proposal to integrate proteomics activities in ELIXIR

scientific article

A generic approach for "shotgun" analysis of the soluble proteome of plant cell suspension cultures

scientific article

A hormone and proteome approach to picturing the initial metabolic events during Plasmodiophora brassicae infection on Arabidopsis.

scientific article

A manually curated network of the PML nuclear body interactome reveals an important role for PML-NBs in SUMOylation dynamics

scientific article

A novel cell division factor from tobacco 2B-13 cells that induced cell division in auxin-starved tobacco BY-2 cells.

scientific article

A primer to frequent itemset mining for bioinformatics

scientific article

A quantitative portrait of three xylanase inhibiting protein families in different wheat cultivars using 2D-DIGE and multivariate statistical tools

scientific article published on 24 February 2009

A tandem affinity purification-based technology platform to study the cell cycle interactome in Arabidopsis thaliana

scientific article

A tutorial in small molecule identification via electrospray ionization-mass spectrometry: The practical art of structural elucidation

scientific article

AcoSeeD: An Ant Colony Optimization for Finding Optimal Spaced Seeds in Biological Sequence Search

Alternative experimental design with an applied normalization scheme can improve statistical power in 2D-DIGE experiments.

scientific article published in October 2010

An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data

scientific article

Apolipoprotein L1 Variant Associated with Increased Susceptibility to Trypanosome Infection

scientific article published on 12 April 2016

Auranofin reveals therapeutic anticancer potential by triggering distinct molecular cell death mechanisms and innate immunity in mutant p53 non-small cell lung cancer

scientific article published on 19 March 2021

Banana (Musa spp.) as a model to study the meristem proteome: acclimation to osmotic stress

scientific article

Best practices for hybridization design in two-colour microarray analysis

scientific article published on 28 May 2009

Bioinformatics approaches for the functional interpretation of protein lists: from ontology term enrichment to network analysis

scientific article published on 20 February 2015

COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia

scientific article

COLOMBOS v3.0: leveraging gene expression compendia for cross-species analyses

scientific article published on 19 November 2015

ClusTCR: a python interface for rapid clustering of large sets of CDR3 sequences with unknown antigen specificity

scientific article published in 2021

Comparative analysis of gene expression: uncovering expression conservation and divergence between Salmonella enterica serovar Typhimurium strains LT2 and 14028S.

scientific article published in January 2015

Compound Characterization and Metabolic Profile Elucidation after In Vitro Gastrointestinal and Hepatic Biotransformation of an Herniaria hirsuta Extract Using Unbiased Dynamic Metabolomic Data Analysis

scientific article published on 16 March 2020

Computational quality control tools for mass spectrometry proteomics

scientific article

Construction of a two-dimensional gel electrophoresis protein database for the Nicotiana tabacum cv. Bright Yellow-2 cell suspension culture

scientific article published on March 2004

Current and future deep learning algorithms for tandem mass spectrometry (MS/MS)‐based small molecule structure elucidation

scientific article published in 2021

Cyclic AMP affinity purification and ESI-QTOF MS-MS identification of cytosolic glyceraldehyde 3-phosphate dehydrogenase and two nucleoside diphosphate kinase isoforms from tobacco BY-2 cells.

scientific article

Cytokinin affinity purification and identification of a tobacco BY-2 adenosine kinase

scientific article

Designing biomedical proteomics experiments: state-of-the-art and future perspectives

scientific article published on 31 March 2016

Diagnosing enterovirus meningitis via blood transcriptomics: an alternative for lumbar puncture?

scientific article published on 23 August 2019

Dietary flavanols modulate the transcription of genes associated with cardiovascular pathology without changes in their DNA methylation state.

scientific article

Discovery of Spatially Cohesive Itemsets in Three-Dimensional Protein Structures

scientific article published on September 2014

Ectopic microRNA-150-5p transcription sensitizes glucocorticoid therapy response in MM1S multiple myeloma cells but fails to overcome hormone therapy resistance in MM1R cells

scientific article

Efficient reduction of candidate matches in peptide spectrum library searching using the top k most intense peaks

scientific article published on 24 July 2014

Erratum to: Immunological evasion of immediate-early varicella zoster virus proteins

scientific article published on 23 April 2016

Experimental and hybridisation design in microarray analysis: Best practices

scientific article published in 2008

Exposure of HepaRG Cells to Sodium Saccharin Underpins the Importance of Including Non-Hepatotoxic Compounds When Investigating Toxicological Modes of Action Using Metabolomics

scientific article published on 04 November 2019

Extremely Fast and Accurate Open Modification Spectral Library Searching of High-Resolution Mass Spectra Using Feature Hashing and Graphics Processing Units

scientific article published on 30 August 2019

Fast Open Modification Spectral Library Searching through Approximate Nearest Neighbor Indexing

scientific article published on 13 September 2018

Fast liquid chromatography coupled to electrospray tandem mass spectrometry peptide sequencing for cross-species protein identification

scientific article published on January 2003

Flexible network reconstruction from relational databases with Cytoscape and CytoSQL.

scientific article

Fragment ion intensity prediction improves the identification rate of non-tryptic peptides in timsTOF

scientific article published in 2024

Functional genomics in a non-model crop: transcriptomics or proteomics?

scientific article

Genome-Wide SNP Analysis Reveals Distinct Origins of Trypanosoma evansi and Trypanosoma equiperdum

scientific article published on 25 May 2017

Getting your peaks in line: a review of alignment methods for NMR spectral data

scientific article

Gradual soil water depletion results in reversible changes of gene expression, protein profiles, ecophysiology, and growth performance in Populus euphratica, a poplar growing in arid regions

scientific article

Grasping frequent subgraph mining for bioinformatics applications

article

Highlights from the 11th ISCB Student Council Symposium 2015 : Dublin, Ireland. 10 July 2015

scientific article

In vitro assessment of hepatotoxicity by metabolomics: a review

scientific article published on 25 August 2018

InSourcerer: a high-throughput method to search for unknown metabolite modifications by mass spectrometry.

scientific article published in June 2017

Increased herpes zoster risk associated with poor HLA-A immediate early 62 protein (IE62) affinity.

scientific article published in December 2017

Integrated genomic and metabolomic profiling of ISC1, an emerging Leishmania donovani population in the Indian subcontinent

scientific article published on 19 April 2018

Integration of gel-based proteome data with pProRep.

scientific article

Large‐scale tandem mass spectrum clustering using fast nearest neighbor searching

scientific article published in 2021

Lipopolysaccharide-responsive phosphoproteins in Nicotiana tabacum cells

scientific article

MESSAR: Automated recommendation of metabolite substructures from tandem mass spectra

scientific article published on 16 January 2020

MIND: A Double-Linear Model To Accurately Determine Monoisotopic Precursor Mass in High-Resolution Top-Down Proteomics

scientific article published on 23 July 2019

Machine learning applications in proteomics research: how the past can boost the future

scientific article published on 21 January 2014

Mechanistic toxicity study of perfluorooctanoic acid in zebrafish suggests mitochondrial dysfunction to play a key role in PFOA toxicity

scientific article published on 18 February 2013

Memory CD4 T cell receptor repertoire data mining as a tool for identifying cytomegalovirus serostatus

scientific article published on 15 June 2018

Metabolomics analysis of the toxicity pathways of triphenyl phosphate in HepaRG cells and comparison to oxidative stress mechanisms caused by acetaminophen

scientific article

Mining the Enriched Subgraphs for Specific Vertices in a Biological Graph.

scientific article published on 7 June 2016

Mining the entire Protein DataBank for frequent spatially cohesive amino acid patterns.

scientific article

Mining the human proteome for conserved mechanisms.

scientific article published on 13 February 2015

Multidisciplinary study of the secondary immune response in grandparents re-exposed to chickenpox

scientific article

Multiplexed Spliced-Leader Sequencing: A high-throughput, selective method for RNA-seq in Trypanosomatids

scientific article

Nanopore Sequencing for Mycobacterium tuberculosis: a Critical Review of the Literature, New Developments, and Future Opportunities

publication published on 16 June 2021

Next generation functional proteomics in non-model plants: A survey on techniques and applications for the analysis of protein complexes and post-translational modifications

scientific article published on 21 February 2011

On the feasibility of mining CD8+ T cell receptor patterns underlying immunogenic peptide recognition

scientific article published on 04 August 2017

On the viability of unsupervised T-cell receptor sequence clustering for epitope preference

scientific article published on 01 May 2019

Open-Source, Platform-Independent Library and Online Scripting Environment for Accessing Thermo Scientific RAW Files

scientific article published on 19 October 2015

Organization of proteomics data with YassDB.

scientific article

Osmotic stress inhibits leaf growth of Arabidopsis thaliana by enhancing ARF-mediated auxin responses

scientific article published on 19 February 2020

PRiSM: a prototype for exhaustive, restriction-free database searching for mass spectrometry-based identification

scientific article published on 02 October 2020

Plasma donor-derived cell-free DNA kinetics after kidney transplantation using a single tube multiplex PCR assay

scientific article published in PLoS ONE

Practical Approaches for Mining Frequent Patterns in Molecular Datasets

scientific article

Prediction of kinase-specific phosphorylation sites using conditional random fields

scientific article published on 20 October 2008

Preparation of protein extracts from recalcitrant plant tissues: an evaluation of different methods for two-dimensional gel electrophoresis analysis

scientific article

Proceedings of the EuBIC developer's meeting 2018

article

Protein complex analysis: From raw protein lists to protein interaction networks

scientific article published on 28 December 2015

Proteome analysis of non-model plants: a challenging but powerful approach

scientific article published on July 2008

Proteomic analysis of posterior capsular plaques in congenital unilateral cataract

scientific article published on 03 October 2018

Proteomic profiling of cellular targets of lipopolysaccharide-induced signalling in Nicotiana tabacum BY-2 cells

scientific article

QCQuan: A Web Tool for the Automated Assessment of Protein Expression and Data Quality of Labeled Mass Spectrometry Experiments

scientific article published on 11 April 2019

Quality control in mass spectrometry-based proteomics

scientific article published on 12 August 2017

Revelation of the metabolic pathway of hederacoside C using an innovative data analysis strategy for dynamic multiclass biotransformation experiments

scientific article published on 25 February 2019

SFINX: Straightforward Filtering Index for Affinity Purification-Mass Spectrometry Data Analysis

scientific article

Structural properties of prokaryotic promoter regions correlate with functional features

scientific article

Tailored liquid chromatography-mass spectrometry analysis improves the coverage of the intracellular metabolome of HepaRG cells.

scientific article published on 23 January 2017

Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana

scientific article

The Absence of C-5 DNA Methylation in Leishmania donovani Allows DNA Enrichment from Complex Samples

scientific article published on 18 August 2020

The radiosensitising effect of gemcitabine and its main metabolite dFdU under low oxygen conditions is in vitro not dependent on functional HIF-1 protein

scientific article

The role of monocytes in the development of Tuberculosis-associated Immune Reconstitution Inflammatory Syndrome

scientific article published on 25 July 2013

The use of plasma donor-derived, cell-free DNA to monitor acute rejection after kidney transplantation

scientific article published on 01 April 2020

The use of the isotopic distribution as a complementary quality metric to assess tandem mass spectra results

scientific article published on 31 December 2013

Towards automated discrimination of lipids versus peptides from full scan mass spectra

scientific article

Toxicogenomics of the flame retardant tris (2-butoxyethyl) phosphate in HepG2 cells using RNA-seq

scientific article published on 9 October 2017

Transcriptome profiling in blood before and after hepatitis B vaccination shows significant differences in gene expression between responders and non-responders

article

Transcriptome profiling of HepG2 cells exposed to the flame retardant 9,10-dihydro-9-oxa-10-phosphaphenanthrene 10-oxide (DOPO)

scientific article published on 12 March 2018

Unraveling tobacco BY-2 protein complexes with BN PAGE/LC-MS/MS and clustering methods

scientific article published on 02 April 2011

Unravelling associations between unassigned mass spectrometry peaks with frequent itemset mining techniques

scientific article

Unsupervised Quality Assessment of Mass Spectrometry Proteomics Experiments by Multivariate Quality Control Metrics

scientific article

Untargeted liquid chromatography-mass spectrometry metabolomics to assess drug-induced cholestatic features in HepaRG® cells

scientific article published on 16 July 2019

Use of structural DNA properties for the prediction of transcription-factor binding sites in Escherichia coli

scientific article published on 4 November 2010

Using Expert Driven Machine Learning to Enhance Dynamic Metabolomics Data Analysis

scientific article published on 20 March 2019

Varicella-zoster virus-derived major histocompatibility complex class I-restricted peptide affinity is a determining factor in the HLA risk profile for the development of postherpetic neuralgia

scientific article published on 29 October 2014

Visualizing the agreement of peptide assignments between different search engines

scientific article published on 12 November 2019

Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues

scientific article published on 01 September 2019

Withaferin A induces heme oxygenase (HO-1) expression in endothelial cells via activation of the Keap1/Nrf2 pathway

scientific article

iMonDB: Mass Spectrometry Quality Control through Instrument Monitoring

scientific article published on 2 April 2015

jqcML: an open-source java API for mass spectrometry quality control data in the qcML format

scientific article

pBRIT: Gene Prioritization by Correlating Functional and Phenotypic Annotations Through Integrative Data Fusion

scientific article published on 14 February 2018

qcML: an exchange format for quality control metrics from mass spectrometry experiments

scientific article published on 23 April 2014

sfinx: an R package for the elimination of false positives from affinity purification-mass spectrometry datasets

scientific article

speaq 2.0: A complete workflow for high-throughput 1D NMR spectra processing and quantification.

scientific article

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