List of works - Berend Snel

A Domain-Centric Analysis of Oomycete Plant Pathogen Genomes Reveals Unique Protein Organization ⬇️

scientific article published on November 30, 2010

A TPR domain–containing N-terminal module of MPS1 is required for its kinetochore localization by Aurora B

scientific article

A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation

scientific article

A high-resolution gene expression atlas of epistasis between gene-specific transcription factors exposes potential mechanisms for genetic interactions.

scientific article published on 23 December 2015

A predicted functional gene network for the plant pathogen Phytophthora infestans as a framework for genomic biology

scientific article

A subfamily of putative cytokinin receptors is revealed by an analysis of the evolution of the two-component signaling system of plants

scientific article published on 11 February 2014

ABI4: versatile activator and repressor

scientific article published on 20 November 2012

Arabidopsis PLETHORA transcription factors control phyllotaxis.

scientific article

Arrayed BUB recruitment modules in the kinetochore scaffold KNL1 promote accurate chromosome segregation

scientific article published on December 2013

Assessment of phylogenomic and orthology approaches for phylogenetic inference

scientific article published on 19 January 2007

Bioinformatic inference of specific and general transcription factor binding sites in the plant pathogen Phytophthora infestans

scientific article

Coevolution of gene families in prokaryotes

scientific article published on 29 January 2008

Cohesive versus flexible evolution of functional modules in eukaryotes

scientific article

Combining data from genomes, Y2H and 3D structure indicates that BolA is a reductase interacting with a glutaredoxin

scientific article

Comparative Genome Analysis of the Mollicutes

Comparative Genome Analysis: Exploiting the Context of Genes to Infer Evolution and Predict Function

article

Comparative genomics for reliable protein-function prediction from genomic data

scientific article

Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes

scientific article published on October 2008

Complex fate of paralogs

scientific article

Conflicting phylogenetic position of Schizosaccharomyces pombe

scientific article published in October 2006

Conservation of gene order: a fingerprint of proteins that physically interact

scientific article (publication date: September 1998)

Contribution of the epigenetic mark H3K27me3 to functional divergence after whole genome duplication in Arabidopsis ⬇️

scientific article published on October 3, 2012

Correlation between sequence conservation and the genomic context after gene duplication

scientific article

Correlation between sequence conservation and the genomic context after gene duplication.

scientific article

DOWNY MILDEW RESISTANT 6 and DMR6-LIKE OXYGENASE 1 are partially redundant but distinct suppressors of immunity in Arabidopsis.

scientific article published on 9 December 2014

Database independent proteomics analysis of the ostrich and human proteome.

scientific article published on 22 December 2011

Deciphering the evolution and metabolism of an anammox bacterium from a community genome

scientific article

Distinctive expansion of potential virulence genes in the genome of the oomycete fish pathogen Saprolegnia parasitica

scientific article

Domains in plexins: links to integrins and transcription factors

scientific article published in July 1999

Domestication of self-splicing introns during eukaryogenesis: the rise of the complex spliceosomal machinery

scientific article published in December 2017

Effector identification in the lettuce downy mildew Bremia lactucae by massively parallel transcriptome sequencing.

scientific article published in February 2012

Enrichment of homologs in insignificant BLAST hits by co-complex network alignment

scientific article

Evaluating experimental bias and completeness in comparative phosphoproteomics analysis.

scientific article

Evolution and function of the mitotic checkpoint

scientific article published on August 2012

Evolution of the Ras-like small GTPases and their regulators

scientific article (publication date: 2011)

Evolution of the TOR pathway

scientific article

Evolutionary acquisition of cysteines determines FOXO paralog-specific redox signaling

scientific article

Evolutionary dynamics of the kinetochore network in eukaryotes as revealed by comparative genomics.

scientific article published on 22 June 2017

Exploitation of gene context

scientific article published in June 2000

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

scientific article

Extensive translational regulation during seed germination revealed by polysomal profiling.

scientific article

Function prediction and protein networks

scientific article

Functional overlap and regulatory links shape genetic interactions between signaling pathways.

scientific article published in December 2010

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

scientific article

Gene context conservation of a higher order than operons.

scientific article

Gene duplications contribute to the overrepresentation of interactions between proteins of a similar age.

scientific article

Genesis of chromatin and transcription dynamics in the origin of species

scientific article published on May 2015

Genome evolution

scientific article published on 01 January 2000

Genome phylogeny based on gene content

scientific article (publication date: 1999)

Genome trees and the nature of genome evolution

scientific article

Genomes in Flux: The Evolution of Archaeal and Proteobacterial Gene Content

article

Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties

scientific article

In-depth qualitative and quantitative profiling of tyrosine phosphorylation using a combination of phosphopeptide immunoaffinity purification and stable isotope dimethyl labeling

scientific article

Increased sucrose levels mediate selective mRNA translation in Arabidopsis

scientific article

Inferring the Evolutionary History of Your Favorite Protein: A Guide for Molecular Biologists

scientific article published on 01 May 2019

Integrating Phylogenetics With Intron Positions Illuminates the Origin of the Complex Spliceosome

scientific article published in 2023

Large-scale genetic perturbations reveal regulatory networks and an abundance of gene-specific repressors.

scientific article

Measuring the impact of gene prediction on gene loss estimates in Eukaryotes by quantifying falsely inferred absences

scientific article published on 28 August 2019

Mosaic origin of the eukaryotic kinetochore

scientific article published on 24 May 2019

Novel pipeline identifies new upstream ORFs and non-AUG initiating main ORFs with conserved amino acid sequences in the 5' leader of mRNAs in

scientific article published on 19 December 2018

Origin and evolution of the peroxisomal proteome

scientific article

Orthology prediction at scalable resolution by phylogenetic tree analysis

scientific article

Pathway alignment: application to the comparative analysis of glycolytic enzymes

scientific article

Pathway alignment: application to the comparative analysis of glycolytic enzymes

scientific article published in 1999

Phylogenomics reveal a robust fungal tree of life

scientific article published on December 2006

Phylogenomics-guided discovery of a novel conserved cassette of short linear motifs in BubR1 essential for the spindle checkpoint.

scientific article published on December 2016

Phylogeny of the CDC25 homology domain reveals rapid differentiation of Ras pathways between early animals and fungi.

scientific article published on 28 June 2009

Predicting disease genes using protein-protein interactions.

scientific article published on 12 April 2006

Predicting gene function by conserved co-expression

scientific article

Predicting protein function by genomic context: quantitative evaluation and qualitative inferences

scientific article published on August 2000

Protein complex evolution does not involve extensive network rewiring.

scientific article

Quantifying modularity in the evolution of biomolecular systems

scientific article published on March 2004

Quantitative label-free phosphoproteomics of six different life stages of the late blight pathogen Phytophthora infestans reveals abundant phosphorylation of members of the CRN effector family.

scientific article published on 17 March 2014

Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames.

scientific article published on September 2000

Reconstruction of Oomycete Genome Evolution Identifies Differences in Evolutionary Trajectories Leading to Present-Day Large Gene Families ⬇️

scientific article published on January 9, 2012

SHOT: a web server for the construction of genome phylogenies

scientific article published on 01 March 2002

SOMBRERO, BEARSKIN1, and BEARSKIN2 regulate root cap maturation in Arabidopsis

scientific article

STRING 7--recent developments in the integration and prediction of protein interactions

scientific article

STRING: a database of predicted functional associations between proteins

scientific article

STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene

scientific article

STRING: known and predicted protein-protein associations, integrated and transferred across organisms

scientific article

Shared protein complex subunits contribute to explaining disrupted co-occurrence

scientific article

Signature genes as a phylogenomic tool

scientific article (publication date: August 2008)

Small homologous blocks in phytophthora genomes do not point to an ancient whole-genome duplication.

scientific article published on May 2014

Spatial Organization in Protein Kinase A Signaling Emerged at the Base of Animal Evolution.

scientific article

Systematic discovery of analogous enzymes in thiamin biosynthesis

scientific article

Targeted quantitative phosphoproteomics approach for the detection of phospho-tyrosine signaling in plants

scientific article published on December 2011

The Arabidopsis bZIP transcription factor family-an update

scientific article published on 01 June 2018

The PLETHORA Gene Regulatory Network Guides Growth and Cell Differentiation in Arabidopsis Roots

scientific article

The R-spondin protein family

scientific article

The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise

scientific article published in May 2004

The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract

scientific article

The histone modification H3K27me3 is retained after gene duplication and correlates with conserved noncoding sequences in Arabidopsis.

scientific article published on March 2014

The identification of functional modules from the genomic association of genes

scientific article

The molecular basis of monopolin recruitment to the kinetochore

scientific article published on 30 April 2019

The phylogenetic distribution of frataxin indicates a role in iron-sulfur cluster protein assembly

scientific article published on 01 October 2001

The phylogeny of C/S1 bZIP transcription factors reveals a shared algal ancestry and the pre-angiosperm translational regulation of S1 transcripts

scientific article

The plant Polycomb repressive complex 1 (PRC1) existed in the ancestor of seed plants and has a complex duplication history

scientific article published on 13 March 2015

The spread of the first introns in proto-eukaryotic paralogs

scientific article published on 19 May 2022

The vertebrate mitotic checkpoint protein BUBR1 is an unusual pseudokinase.

scientific article published in June 2012

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

scientific article

Timing the origin of eukaryotic cellular complexity with ancient duplications

scientific article published on 26 October 2020

Toward Automatic Reconstruction of a Highly Resolved Tree of Life

scientific article

Tyrosine phosphorylation profiling in FGF-2 stimulated human embryonic stem cells.

scientific article

Unique Phylogenetic Distributions of the Ska and Dam1 Complexes Support Functional Analogy and Suggest Multiple Parallel Displacements of Ska by Dam1.

scientific article published on 4 May 2017

Variation and evolution of biomolecular systems: searching for functional relevance

scientific article

Widespread Recurrent Patterns of Rapid Repeat Evolution in the Kinetochore Scaffold KNL1.

scientific article published on 8 August 2015

List of works by Berend Snel

A Domain-Centric Analysis of Oomycete Plant Pathogen Genomes Reveals Unique Protein Organization ⬇️

A TPR domain–containing N-terminal module of MPS1 is required for its kinetochore localization by Aurora B

A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation

A high-resolution gene expression atlas of epistasis between gene-specific transcription factors exposes potential mechanisms for genetic interactions.

A predicted functional gene network for the plant pathogen Phytophthora infestans as a framework for genomic biology

A subfamily of putative cytokinin receptors is revealed by an analysis of the evolution of the two-component signaling system of plants

ABI4: versatile activator and repressor

Arabidopsis PLETHORA transcription factors control phyllotaxis.

Arrayed BUB recruitment modules in the kinetochore scaffold KNL1 promote accurate chromosome segregation

Assessment of phylogenomic and orthology approaches for phylogenetic inference

Bioinformatic inference of specific and general transcription factor binding sites in the plant pathogen Phytophthora infestans

Coevolution of gene families in prokaryotes

Cohesive versus flexible evolution of functional modules in eukaryotes

Combining data from genomes, Y2H and 3D structure indicates that BolA is a reductase interacting with a glutaredoxin

Comparative Genome Analysis of the Mollicutes

Comparative Genome Analysis: Exploiting the Context of Genes to Infer Evolution and Predict Function

Comparative genomics for reliable protein-function prediction from genomic data

Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes

Complex fate of paralogs

Conflicting phylogenetic position of Schizosaccharomyces pombe

Conservation of gene order: a fingerprint of proteins that physically interact

Contribution of the epigenetic mark H3K27me3 to functional divergence after whole genome duplication in Arabidopsis ⬇️

Correlation between sequence conservation and the genomic context after gene duplication

Correlation between sequence conservation and the genomic context after gene duplication.

DOWNY MILDEW RESISTANT 6 and DMR6-LIKE OXYGENASE 1 are partially redundant but distinct suppressors of immunity in Arabidopsis.

Database independent proteomics analysis of the ostrich and human proteome.

Deciphering the evolution and metabolism of an anammox bacterium from a community genome

Distinctive expansion of potential virulence genes in the genome of the oomycete fish pathogen Saprolegnia parasitica

Domains in plexins: links to integrins and transcription factors

Domestication of self-splicing introns during eukaryogenesis: the rise of the complex spliceosomal machinery

Effector identification in the lettuce downy mildew Bremia lactucae by massively parallel transcriptome sequencing.

Enrichment of homologs in insignificant BLAST hits by co-complex network alignment

Evaluating experimental bias and completeness in comparative phosphoproteomics analysis.

Evolution and function of the mitotic checkpoint

Evolution of the Ras-like small GTPases and their regulators

Evolution of the TOR pathway

Evolutionary acquisition of cysteines determines FOXO paralog-specific redox signaling

Evolutionary dynamics of the kinetochore network in eukaryotes as revealed by comparative genomics.

Exploitation of gene context

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

Extensive translational regulation during seed germination revealed by polysomal profiling.

Function prediction and protein networks

Functional overlap and regulatory links shape genetic interactions between signaling pathways.

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

Gene context conservation of a higher order than operons.

Gene duplications contribute to the overrepresentation of interactions between proteins of a similar age.

Genesis of chromatin and transcription dynamics in the origin of species

Genome evolution

Genome phylogeny based on gene content

Genome trees and the nature of genome evolution

Genomes in Flux: The Evolution of Archaeal and Proteobacterial Gene Content

Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties

In-depth qualitative and quantitative profiling of tyrosine phosphorylation using a combination of phosphopeptide immunoaffinity purification and stable isotope dimethyl labeling

Increased sucrose levels mediate selective mRNA translation in Arabidopsis

Inferring the Evolutionary History of Your Favorite Protein: A Guide for Molecular Biologists

Integrating Phylogenetics With Intron Positions Illuminates the Origin of the Complex Spliceosome

Large-scale genetic perturbations reveal regulatory networks and an abundance of gene-specific repressors.

Measuring the impact of gene prediction on gene loss estimates in Eukaryotes by quantifying falsely inferred absences

Mosaic origin of the eukaryotic kinetochore

Mosaic origin of the eukaryotic kinetochore

Novel pipeline identifies new upstream ORFs and non-AUG initiating main ORFs with conserved amino acid sequences in the 5' leader of mRNAs in

Origin and evolution of the peroxisomal proteome

Orthology prediction at scalable resolution by phylogenetic tree analysis

Pathway alignment: application to the comparative analysis of glycolytic enzymes

Pathway alignment: application to the comparative analysis of glycolytic enzymes

Phylogenomics reveal a robust fungal tree of life

Phylogenomics-guided discovery of a novel conserved cassette of short linear motifs in BubR1 essential for the spindle checkpoint.

Phylogeny of the CDC25 homology domain reveals rapid differentiation of Ras pathways between early animals and fungi.

Predicting disease genes using protein-protein interactions.

Predicting gene function by conserved co-expression

Predicting protein function by genomic context: quantitative evaluation and qualitative inferences

Protein complex evolution does not involve extensive network rewiring.

Quantifying modularity in the evolution of biomolecular systems

Quantitative label-free phosphoproteomics of six different life stages of the late blight pathogen Phytophthora infestans reveals abundant phosphorylation of members of the CRN effector family.

Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames.

Reconstruction of Oomycete Genome Evolution Identifies Differences in Evolutionary Trajectories Leading to Present-Day Large Gene Families ⬇️

SHOT: a web server for the construction of genome phylogenies

SOMBRERO, BEARSKIN1, and BEARSKIN2 regulate root cap maturation in Arabidopsis

STRING 7--recent developments in the integration and prediction of protein interactions