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List of works by Klaas Vandepoele

A Collection of Conserved Noncoding Sequences to Study Gene Regulation in Flowering Plants

scientific article published on 03 June 2016

A DNA-binding-site landscape and regulatory network analysis for NAC transcription factors in Arabidopsis thaliana

scientific article published on 9 June 2014

A Guide to the PLAZA 3.0 Plant Comparative Genomic Database

scientific article published on January 2017

A Repressor Protein Complex Regulates Leaf Growth in Arabidopsis.

scientific article

A functional and evolutionary perspective on transcription factor binding in Arabidopsis thaliana.

scientific article published on 31 October 2014

A generic tool for transcription factor target gene discovery in Arabidopsis cell suspension cultures based on tandem chromatin affinity purification.

scientific article published on 22 January 2014

A greedy, graph-based algorithm for the alignment of multiple homologous gene lists

scientific article

A high quality draft consensus sequence of the genome of a heterozygous grapevine variety

scientific article

A new evolutionary model for the vertebrate actin family including two novel groups

scientific article published on 24 September 2019

A small CDC25 dual-specificity tyrosine-phosphatase isoform in Arabidopsis thaliana

scientific article

A widespread alternative squalene epoxidase participates in eukaryote steroid biosynthesis

scientific article published on 26 November 2018

ANGUSTIFOLIA3 binds to SWI/SNF chromatin remodeling complexes to regulate transcription during Arabidopsis leaf development

scientific article

An improved toolbox to unravel the plant cellular machinery by tandem affinity purification of Arabidopsis protein complexes

scientific article published on 18 December 2014

An update on LNCipedia: a database for annotated human lncRNA sequences

scientific article published on 31 March 2015

An update on LNCipedia: a database for annotated human lncRNA sequences.

scientific article

Ancient duplication of cereal genomes

scientific article

Are We There Yet? Reliably Estimating the Completeness of Plant Genome Sequences

scientific article published on 10 August 2016

Associated Bacteria Affect Sexual Reproduction by Altering Gene Expression and Metabolic Processes in a Biofilm Inhabiting Diatom

scientific article published on 02 August 2019

Author Correction: The Seminavis robusta genome provides insights into the evolutionary adaptations of benthic diatoms

scientific article published on 16 October 2020

BLSSpeller: exhaustive comparative discovery of conserved cis-regulatory elements

scientific article published on 08 August 2015

Building genomic profiles for uncovering segmental homology in the twilight zone

scientific article

Capturing the phosphorylation and protein interaction landscape of the plant TOR kinase

scientific article published on 04 March 2019

Charting plant gene functions in the multi-omics and single-cell era

scientific article published in 2023

Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors

scientific article published in 2021

CoExpNetViz: Comparative Co-Expression Networks Construction and Visualization Tool

scientific article published in January 2015

Cold nights impair leaf growth and cell cycle progression in maize through transcriptional changes of cell cycle genes

scientific article

Comparative co-expression analysis in plant biology

scientific article published on 10 May 2012

Comparative network analysis reveals that tissue specificity and gene function are important factors influencing the mode of expression evolution in Arabidopsis and rice

scientific article

Comparative transcriptomics enables the identification of functional orthologous genes involved in early leaf growth

scientific article published on 12 August 2019

Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants

scientific article published on 4 February 2013

Curse: building expression atlases and co-expression networks from public RNA-Seq data

scientific article published on 01 August 2019

Detecting the undetectable: uncovering duplicated segments in Arabidopsis by comparison with rice

scientific article published in December 2002

Dissecting plant genomes with the PLAZA comparative genomics platform

scientific article published on 23 December 2011

Drought tolerance conferred to sugarcane by association with Gluconacetobacter diazotrophicus: a transcriptomic view of hormone pathways.

scientific article published on 9 December 2014

Dynamic Changes in ANGUSTIFOLIA3 Complex Composition Reveal a Growth Regulatory Mechanism in the Maize Leaf.

scientific article

ERF115 controls root quiescent center cell division and stem cell replenishment

scientific article published on 24 October 2013

Enhanced Maps of Transcription Factor Binding Sites Improve Regulatory Networks Learned from Accessible Chromatin Data

scientific article published on 25 July 2019

Ensemble gene function prediction database reveals genes important for complex I formation in Arabidopsis thaliana

scientific article published on 4 December 2017

Evidence that rice and other cereals are ancient aneuploids

scientific article published in September 2003

Evolution of vascular plants through redeployment of ancient developmental regulators

scientific article published on 24 December 2019

Evolutionary relationships and expression analysis of EUL domain proteins in rice (Oryza sativa).

scientific article published on 30 May 2017

Evolutionary trails of plant steroid genes.

scientific article published on 08 April 2015

Exploring the plant transcriptome through phylogenetic profiling

scientific article published in January 2005

Functional Analysis of the Arabidopsis TETRASPANIN Gene Family in Plant Growth and Development

scientific article

Functional characterization of the Arabidopsis transcription factor bZIP29 reveals its role in leaf and root development

scientific article

GSyellow, a Multifaceted Tag for Functional Protein Analysis in Monocot and Dicot Plants

scientific article published on 20 April 2018

Gearing up to handle the mosaic nature of life in the quest for orthologs

scientific article published on 30 August 2017

Gene duplication and biased functional retention of paralogs in bacterial genomes

scientific article published in April 2004

Gene expression during bacterivorous growth of a widespread marine heterotrophic flagellate

scientific article published on 12 September 2020

Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage

scientific article

Gene space completeness in complex plant genomes

scientific article published on 21 February 2019

Genome Analyses of the Microalga Picochlorum Provide Insights into the Evolution of Thermotolerance in the Green Lineage

scientific article published on 01 September 2018

Genome-wide analysis of core cell cycle genes in Arabidopsis

scientific article

Genome-wide analysis of the diatom cell cycle unveils a novel type of cyclins involved in environmental signaling

scientific article

Genome-wide characterization of differential transcript usage in Arabidopsis thaliana

scientific article published on 14 October 2017

Genome-wide identification of potential plant E2F target genes

scientific article

How many genes are there in plants (... and why are they there)?

scientific article

Hydrogen peroxide-induced gene expression across kingdoms: a comparative analysis

scientific article published on 10 January 2008

Identification and evolution of gene regulatory networks: insights from comparative studies in plants

scientific article published on 12 February 2020

Identification of cis-regulatory elements specific for different types of reactive oxygen species in Arabidopsis thaliana.

scientific article published on 28 February 2012

Identification of novel regulatory modules in dicotyledonous plants using expression data and comparative genomics

scientific article (publication date: 2006)

Identification of putative cancer genes through data integration and comparative genomics between plants and humans.

scientific article

Inference of plant gene regulatory networks using data-driven methods: A practical overview

scientific article published on 31 October 2019

Inference of transcriptional networks in Arabidopsis through conserved noncoding sequence analysis.

scientific article published on 2 July 2014

Insights into the Evolution of Multicellularity from the Sea Lettuce Genome

scientific article published on 13 September 2018

Investigating ancient duplication events in the Arabidopsis genome

scientific article

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

scholarly article by Aziz Khan et al published 4 January 2018 in Nucleic Acids Research

JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles

scientific article published in 2021

KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis

scientific article published on 28 May 2018

MAGIC: access portal to a cross-platform gene expression compendium for maize.

scientific article published on 8 January 2014

Major events in the genome evolution of vertebrates: paranome age and size differ considerably between ray-finned fishes and land vertebrates

scientific article (publication date: 10 February 2004)

Mating type specific transcriptomic response to sex inducing pheromone in the pennate diatom Seminavis robusta

scientific article published on 07 October 2020

Metagenomes of the picoalga Bathycoccus from the Chile coastal upwelling

scientific article

Molecular and physiological analysis of growth-limiting drought stress in Brachypodium distachyon leaves

scientific article published on 25 September 2012

Neofunctionalization of Mitochondrial Proteins and Incorporation into Signaling Networks in Plants

article

Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds

scientific article published on 07 January 2020

Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds

scientific article published on 12 June 2019

Novel plant-specific cyclin-dependent kinase inhibitors induced by biotic and abiotic stresses.

scientific article published on 28 June 2007

On the origin and evolution of vertebrate and viral profilins

scientific article

Overcoming challenges in variant calling: exploring sequence diversity in candidate genes for plant development in perennial ryegrass (Lolium perenne)

scientific article published on 01 February 2019

PLAZA 3.0: an access point for plant comparative genomics

scientific article

PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics

scientific article published on 23 October 2017

PLAZA: a comparative genomics resource to study gene and genome evolution in plants

scientific article published on 29 December 2009

PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization.

scientific article

Phylogenomic analysis of gene co-expression networks reveals the evolution of functional modules.

scientific article

Plant lineage-specific PIKMIN1 drives APC/CCCS52A2 E3-ligase activity-dependent cell division

scientific article published in 2022

Plastid gene expression and plant development require a plastidic protein of the mitochondrial transcription termination factor family

scientific article

Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression

scientific article

Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes.

scientific article

Quantitative cDNA-AFLP analysis for genome-wide expression studies

scientific article published on 18 March 2003

ROS signaling: the new wave?

scientific article published on 07 April 2011

Recent developments in computational approaches for uncovering genomic homology

scientific article published in November 2004

SHUGOSHINs and PATRONUS protect meiotic centromere cohesion in Arabidopsis thaliana.

scientific article published on 12 February 2014

Selection for Improved Energy Use Efficiency and Drought Tolerance in Canola Results in Distinct Transcriptome and Epigenome Changes

scientific article published on 16 June 2015

Small-scale gene duplications played a major role in the recent evolution of wheat chromosome 3B

scientific article

Spatiotemporal expression profile of novel and known small RNAs throughout rice plant development focussing on seed tissues

scientific article published on 11 January 2022

Structural and functional partitioning of bread wheat chromosome 3B.

scientific article

Systematic identification of functional plant modules through the integration of complementary data sources

scientific article (publication date: July 2012)

TF2Network: predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information.

scientific article published on 20 December 2017

TRAPID 2.0: a web application for taxonomic and functional analysis of de novo transcriptomes

scientific article published on 01 September 2021

TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes.

scientific article

Tetraspanin genes in plants

scientific article published on 23 March 2012

The MCM-binding protein ETG1 aids sister chromatid cohesion required for postreplicative homologous recombination repair

scientific article

The P. patens chromosome-scale assembly reveals moss genome structure and evolution. ⬇️

scientific article

The PRA1 gene family in Arabidopsis

article

The Phaeodactylum genome reveals the evolutionary history of diatom genomes

scientific article

The Plastid Genome In Cladophorales Green Algae Is Encoded By Hairpin Plasmids

The Plastid Genome in Cladophorales Green Algae Is Encoded by Hairpin Chromosomes.

scientific article

The Seminavis robusta genome provides insights into the evolutionary adaptations of benthic diatoms

scientific article published on 03 July 2020

The Transcription Factor MYB29 Is a Regulator of ALTERNATIVE OXIDASE1a.

scientific article published on 6 February 2017

The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice

scientific article published on November 2002

The flowering world: a tale of duplications

scientific article published on 07 October 2009

The gain and loss of genes during 600 million years of vertebrate evolution

scientific article published on 24 May 2006

The hidden duplication past of Arabidopsis thaliana

scientific article

The medium-size noncoding RNA transcriptome of <i>Ostreococcus tauri</i>, the smallest living eukaryote, reveals a large family of small nucleolar RNAs displaying multiple genomic expression strategies

scientific article published on 09 October 2020

The membrane-bound NAC transcription factor ANAC013 functions in mitochondrial retrograde regulation of the oxidative stress response in Arabidopsis

scientific article

The mouse thymosin beta15 gene family displays unique complexity and encodes a functional thymosin repeat

scientific journal article

The mutation nrpb1-A325V in the largest subunit of RNA polymerase II suppresses compromised growth of Arabidopsis plants deficient in a function of the general transcription factor IIF.

scientific article

The transcriptional repressor complex FRS7-FRS12 regulates flowering time and growth in Arabidopsis.

scientific article

Transcription factors KANADI 1, MYB DOMAIN PROTEIN 44, and PHYTOCHROME INTERACTING FACTOR 4 regulate long intergenic noncoding RNAs expressed in Arabidopsis roots

scientific article published in 2023

Transcriptome analysis during cell division in plants

scientific article

Type II metacaspases Atmc4 and Atmc9 of Arabidopsis thaliana cleave substrates after arginine and lysine

scientific article

Understanding genetic control of root system architecture in soybean: Insights into the genetic basis of lateral root number

scientific article published on 15 June 2018

Unraveling transcriptional control in Arabidopsis using cis-regulatory elements and coexpression networks

scientific article published on 08 April 2009

Unravelling cis-regulatory elements in the genome of the smallest photosynthetic eukaryote: phylogenetic footprinting in Ostreococcus

scientific article published on 20 August 2009

Virus-host coexistence in phytoplankton through the genomic lens

scientific article published on 01 April 2020

Virus-host coexistence in phytoplankton through the genomic lens: Supplementary Material

scholarly article published 7 January 2019

Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species

scholarly article

i-ADHoRe 3.0--fast and sensitive detection of genomic homology in extremely large data sets

scientific article

pico-PLAZA, a genome database of microbial photosynthetic eukaryotes

scientific article

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