List of works - Vera van Noort

A Genome-Based Species Taxonomy of the Lactobacillus Genus Complex

scientific article published on 03 September 2019

A VersaTile-driven platform for rapid hit-to-lead development of engineered lysins

scientific article published on 03 June 2020

A quantitative liposome microarray to systematically characterize protein-lipid interactions

scientific article published on 24 November 2013

A suppressor of axillary meristem maturation promotes longevity in flowering plants

scientific article published on 13 April 2020

ARA-PEPs: a repository of putative sORF-encoded peptides in Arabidopsis thaliana.

scientific article

Adaptation to High Ethanol Reveals Complex Evolutionary Pathways

scientific article published on 6 November 2015

An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum

scientific article published on 14 November 2014

Annotation of the M. tuberculosis hypothetical orfeome: adding functional information to more than half of the uncharacterized proteins

scientific article

Assessment of phylogenomic and orthology approaches for phylogenetic inference

scientific article published on 19 January 2007

Bioinformatic analysis of functional differences between the immunoproteasome and the constitutive proteasome

scientific article published on 30 August 2003

CART-a chemical annotation retrieval toolkit

scientific article

Canonical germinant receptor is dispensable for spore germination in Clostridium botulinum group II strain NCTC 11219.

scientific article published on 13 November 2017

Catabolic task division between two near-isogenic subpopulations co-existing in a herbicide-degrading bacterial consortium: consequences for the interspecies consortium metabolic model.

scientific article

Catabolism of the groundwater micropollutant 2,6-dichlorobenzamide beyond 2,6-dichlorobenzoate is plasmid encoded in Aminobacter sp. MSH1

scientific article published on 08 July 2018

Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding

scientific article published on January 2013

Combinatorial gene regulation in Plasmodium falciparum

scientific article

Combining sequencing approaches to fully resolve a carbapenemase-encoding megaplasmid in a Pseudomonas shirazica clinical strain

scientific article published on 01 January 2019

Comments on "Human dominant disease genes are enriched in paralogs originating from whole genome duplication".

scientific article

Community-led comparative genomic and phenotypic analysis of the aquaculture pathogen Pseudomonas baetica a390T sequenced by Ion semiconductor and Nanopore technologies.

scientific article published in May 2018

Comparative genomics for reliable protein-function prediction from genomic data

scientific article

Comparative genomics of the Rab protein family in Apicomplexan parasites

scientific article published on 08 February 2008

Consistent mutational paths predict eukaryotic thermostability

scientific article

Correlated duplications and losses in the evolution of palmitoylation writer and eraser families

scientific article

Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium.

scientific article published on 28 February 2012

Deciphering a global network of functionally associated post-translational modifications

scientific article

Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium

scientific article

Dietary intervention and health in patients with systemic lupus erythematosus: A systematic review of the evidence

scientific article published on 17 May 2018

Digital phagograms: predicting phage infectivity through a multilayer machine learning approach

scientific article published in February 2022

Discovery and validation of the antimetastatic activity of citalopram in colorectal cancer

scientific article published on 11 February 2015

Drug discovery in the age of systems biology: the rise of computational approaches for data integration.

scientific article

Drug-induced regulation of target expression

scientific article

Effects of acetylation and phosphorylation on subunit interactions in three large eukaryotic complexes

scientific article published on 04 September 2018

Evolution and functional cross-talk of protein post-translational modifications

scientific article

Evolutionary conservation of Ebola virus proteins predicts important functions at residue level.

scientific article

Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactions

scientific article

FLAMS: Find Lysine Acylations and other Modification Sites

scientific article published in 2024

Gene co-regulation is highly conserved in the evolution of eukaryotes and prokaryotes

scientific article

Genome-driven elucidation of phage-host interplay and impact of phage resistance evolution on bacterial fitness

scientific article published in February 2022

Genomics of an endemic cystic fibrosis Burkholderia multivorans strain reveals low within-patient evolution but high between-patient diversity

scientific article published in 2021

Human monogenic disease genes have frequently functionally redundant paralogs

scientific article

Impact of genome reduction on bacterial metabolism and its regulation.

scientific article published in November 2009

Insight into structure and assembly of the nuclear pore complex by utilizing the genome of a eukaryotic thermophile

scientific article

Integrated Multi-Omics Analysis of Mechanisms Underlying Yeast Ethanol Tolerance

scientific article published on 08 July 2021

Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances

scientific article published on 14 January 2016

Integrative omics analysis of Pseudomonas aeruginosa virus PA5oct highlights the molecular complexity of jumbo phages

scientific article published on 10 March 2020

Integrative omics analysis of Pseudomonas aeruginosa virus PA5oct highlights the molecular complexity of jumbo phages

scientific article published on 22 June 2019

Large-scale docking predicts that sORF-encoded peptides may function through protein-peptide interactions in Arabidopsis thaliana

scientific article published in PLoS ONE

Large-scale docking predicts that sORF-encoded peptides may function through protein-peptide interactions in Arabidopsis thaliana

Lipid Cooperativity as a General Membrane-Recruitment Principle for PH Domains

scientific article published on 19 August 2015

Molecular dynamics shows complex interplay and long-range effects of post-translational modifications in yeast protein interactions

scientific article published on 12 May 2021

Network neighbors of drug targets contribute to drug side-effect similarity

scientific article

New Bacteriophages against Emerging Lineages ST23 and ST258 of Klebsiella pneumoniae and Efficacy Assessment in Galleria mellonella Larvae

scientific article published on 03 May 2019

Novel drug candidates for the treatment of metastatic colorectal cancer through global inverse gene-expression profiling

scientific article published on 18 July 2014

Orthology prediction at scalable resolution by phylogenetic tree analysis

scientific article

Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution ⬇️

scientific article published on February 2008

Predicting gene function by conserved co-expression

scientific article

Prediction of drug combinations by integrating molecular and pharmacological data

scientific article

Proteome organization in a genome-reduced bacterium

scientific journal article

Proteomic profiling of Plasmodium sporozoite maturation identifies new proteins essential for parasite development and infectivity

scientific article

Quality control and statistical evaluation of combinatorial DNA libraries using nanopore sequencing

scientific article published on 01 October 2020

Repeatability of published microarray gene expression analyses

scientific article

Resurrected Protein Interaction Networks Reveal the Innovation Potential of Ancient Whole Genome Duplication

article

Spike-in SILAC proteomic approach reveals the vitronectin as an early molecular signature of liver fibrosis in hepatitis C infections with hepatic iron overload

scientific article published on May 2014

Strand misalignments lead to quasipalindrome correction

article

The complete genome of 2,6-dichlorobenzamide (BAM) degrader Aminobacter sp. MSH1 suggests a polyploid chromosome, phylogenetic reassignment, and functions of plasmids

scientific article published on 23 September 2021

The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model

scientific article

Transcriptome Complexity in a Genome-Reduced Bacterium

scientific article

UV crosslinked mRNA-binding proteins captured from leaf mesophyll protoplasts

scientific article

yMap: an automated method to map yeast variants to protein modifications and functional regions

scientific article

List of works by Vera van Noort

A Genome-Based Species Taxonomy of the Lactobacillus Genus Complex

A VersaTile-driven platform for rapid hit-to-lead development of engineered lysins

A quantitative liposome microarray to systematically characterize protein-lipid interactions

A suppressor of axillary meristem maturation promotes longevity in flowering plants

ARA-PEPs: a repository of putative sORF-encoded peptides in Arabidopsis thaliana.

Adaptation to High Ethanol Reveals Complex Evolutionary Pathways

An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum

Annotation of the M. tuberculosis hypothetical orfeome: adding functional information to more than half of the uncharacterized proteins

Assessment of phylogenomic and orthology approaches for phylogenetic inference

Bioinformatic analysis of functional differences between the immunoproteasome and the constitutive proteasome

CART-a chemical annotation retrieval toolkit

Canonical germinant receptor is dispensable for spore germination in Clostridium botulinum group II strain NCTC 11219.

Catabolic task division between two near-isogenic subpopulations co-existing in a herbicide-degrading bacterial consortium: consequences for the interspecies consortium metabolic model.

Catabolism of the groundwater micropollutant 2,6-dichlorobenzamide beyond 2,6-dichlorobenzoate is plasmid encoded in Aminobacter sp. MSH1

Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding

Combinatorial gene regulation in Plasmodium falciparum

Combining sequencing approaches to fully resolve a carbapenemase-encoding megaplasmid in a Pseudomonas shirazica clinical strain

Comments on "Human dominant disease genes are enriched in paralogs originating from whole genome duplication".

Community-led comparative genomic and phenotypic analysis of the aquaculture pathogen Pseudomonas baetica a390T sequenced by Ion semiconductor and Nanopore technologies.

Comparative genomics for reliable protein-function prediction from genomic data

Comparative genomics of the Rab protein family in Apicomplexan parasites

Consistent mutational paths predict eukaryotic thermostability

Correlated duplications and losses in the evolution of palmitoylation writer and eraser families

Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium.

Deciphering a global network of functionally associated post-translational modifications

Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium

Dietary intervention and health in patients with systemic lupus erythematosus: A systematic review of the evidence

Digital phagograms: predicting phage infectivity through a multilayer machine learning approach

Discovery and validation of the antimetastatic activity of citalopram in colorectal cancer

Drug discovery in the age of systems biology: the rise of computational approaches for data integration.

Drug-induced regulation of target expression

Effects of acetylation and phosphorylation on subunit interactions in three large eukaryotic complexes

Evolution and functional cross-talk of protein post-translational modifications

Evolutionary conservation of Ebola virus proteins predicts important functions at residue level.

Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactions

FLAMS: Find Lysine Acylations and other Modification Sites

Gene co-regulation is highly conserved in the evolution of eukaryotes and prokaryotes

Genome-driven elucidation of phage-host interplay and impact of phage resistance evolution on bacterial fitness

Genomics of an endemic cystic fibrosis Burkholderia multivorans strain reveals low within-patient evolution but high between-patient diversity

Human monogenic disease genes have frequently functionally redundant paralogs

Impact of genome reduction on bacterial metabolism and its regulation.

Insight into structure and assembly of the nuclear pore complex by utilizing the genome of a eukaryotic thermophile

Integrated Multi-Omics Analysis of Mechanisms Underlying Yeast Ethanol Tolerance

Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances

Integrative omics analysis of Pseudomonas aeruginosa virus PA5oct highlights the molecular complexity of jumbo phages

Integrative omics analysis of Pseudomonas aeruginosa virus PA5oct highlights the molecular complexity of jumbo phages

Large-scale docking predicts that sORF-encoded peptides may function through protein-peptide interactions in Arabidopsis thaliana

Large-scale docking predicts that sORF-encoded peptides may function through protein-peptide interactions in Arabidopsis thaliana

Lipid Cooperativity as a General Membrane-Recruitment Principle for PH Domains

Molecular dynamics shows complex interplay and long-range effects of post-translational modifications in yeast protein interactions

Network neighbors of drug targets contribute to drug side-effect similarity

New Bacteriophages against Emerging Lineages ST23 and ST258 of Klebsiella pneumoniae and Efficacy Assessment in Galleria mellonella Larvae

Novel drug candidates for the treatment of metastatic colorectal cancer through global inverse gene-expression profiling

Orthology prediction at scalable resolution by phylogenetic tree analysis

Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution ⬇️

Predicting gene function by conserved co-expression

Prediction of drug combinations by integrating molecular and pharmacological data

Proteome organization in a genome-reduced bacterium

Proteomic profiling of Plasmodium sporozoite maturation identifies new proteins essential for parasite development and infectivity

Quality control and statistical evaluation of combinatorial DNA libraries using nanopore sequencing

Repeatability of published microarray gene expression analyses

Resurrected Protein Interaction Networks Reveal the Innovation Potential of Ancient Whole Genome Duplication

Spike-in SILAC proteomic approach reveals the vitronectin as an early molecular signature of liver fibrosis in hepatitis C infections with hepatic iron overload

Strand misalignments lead to quasipalindrome correction

The complete genome of 2,6-dichlorobenzamide (BAM) degrader Aminobacter sp. MSH1 suggests a polyploid chromosome, phylogenetic reassignment, and functions of plasmids

The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model

Transcriptome Complexity in a Genome-Reduced Bacterium

UV crosslinked mRNA-binding proteins captured from leaf mesophyll protoplasts

yMap: an automated method to map yeast variants to protein modifications and functional regions