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MINI‐AC : inference of plant gene regulatory networks using bulk or single‐cell accessible chromatin profiles
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- Journal Article
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Transcription factors KANADI 1, MYB DOMAIN PROTEIN 44, and PHYTOCHROME INTERACTING FACTOR 4 regulate long intergenic noncoding RNAs expressed in Arabidopsis roots
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- Journal Article
- A1
- open access
Dicer-like 3a mediates intergenerational resistance against root-knot nematodes in rice via hormone responses
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- Journal Article
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Predicting transcriptional responses to heat and drought stress from genomic features using a machine learning approach in rice
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- Journal Article
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Diatom adhesive trail proteins acquired by horizontal gene transfer from bacteria serve as primers for marine biofilm formation
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- Journal Article
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Plant lineage-specific PIKMIN1 drives APC/CCCS52A2 E3-ligase activity-dependent cell division
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- Journal Article
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Rhizogenic agrobacterium protein RolB interacts with the TOPLESS repressor proteins to reprogram plant immunity and development
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- Journal Article
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A redundant transcription factor network steers spatiotemporal Arabidopsis triterpene synthesis
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- Journal Article
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Distinctive and complementary roles of E2F transcription factors during plant replication stress responses
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- Book Chapter
- open access
Characterization of gene regulatory networks in plants using new methods and data types
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- Book Chapter
- open access
Prediction of transcription factor regulators and gene regulatory networks in tomato using binding site information
(2023) Plant gene regulatory networks : methods and protocols. In Methods in Molecular Biology 2698. p.323-349 -
- Journal Article
- A1
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Charting plant gene functions in the multi-omics and single-cell era
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- Journal Article
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PLAZA 5.0 : extending the scope and power of comparative and functional genomics in plants
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- Journal Article
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Spatiotemporal expression profile of novel and known small RNAs throughout rice plant development focussing on seed tissues
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- Journal Article
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- open access
The gene regulation knowledge commons : the action area of GREEKC
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- Journal Article
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MINI-EX : integrative inference of single-cell gene regulatory networks in plants
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- Journal Article
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Identification of growth regulators using cross-species network analysis in plants
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- Journal Article
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- open access
The ÓMICAS alliance, an international research program on multi-omics for crop breeding optimization
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- Journal Article
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JASPAR 2022 : the 9th release of the open-access database of transcription factor binding profiles
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- Journal Article
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Chromosome-scale assembly and annotation of the perennial ryegrass genome
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Integrative inference of transcriptional networks in Arabidopsis yields novel ROS signalling regulators
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- Journal Article
- A1
- open access
The quest for orthologs Orthology Benchmark Service in 2022
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- Journal Article
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Comparative genomics reveals new functional insights in uncultured MAST species
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- Journal Article
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Comment on ‘Hayai-annotation plants : an ultrafast and comprehensive functional gene annotation system in plants’ : the importance of taking the GO graph structure into account
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- Journal Article
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A network-based comparative framework to study conservation and divergence of proteomes in plant phylogenies
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- Journal Article
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Gene expression during bacterivorous growth of a widespread marine heterotrophic flagellate
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- Journal Article
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Evolutionary genomics of sex-related chromosomes at the base of the green lineage
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Integrative inference of transcriptional networks in Arabidopsis yields novel ROS signalling regulators
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- Journal Article
- A1
- open access
TRAPID 2.0 : a web application for taxonomic and functional analysis of de novo transcriptomes
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- Journal Article
- A1
- open access
Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors
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- Journal Article
- A1
- open access
Multi‐omics network‐based functional annotation of unknown Arabidopsis genes
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- Journal Article
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- open access
Mitotic recombination between homologous chromosomes drives genomic diversity in diatoms
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- Journal Article
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Subfunctionalization of paralog transcription factors contributes to regulation of alkaloid pathway branch choice in Catharanthus roseus
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- Journal Article
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- open access
Light intensity and spectral composition drive reproductive success in the marine benthic diatom Seminavis robusta
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- Journal Article
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- open access
Mating type specific transcriptomic response to sex inducing pheromone in the pennate diatom Seminavis robusta
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Diurnal transcript profiling of the diatom Seminavis robusta reveals adaptations to a benthic lifestyle
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- Journal Article
- A1
- open access
Canonical correlations reveal adaptive loci and phenotypic responses to climate in perennial ryegrass
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- Journal Article
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Comprehensive and functional analysis of horizontal gene transfer events in diatoms
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- Miscellaneous
- open access
The Seminavis robusta genome provides insights into the evolutionary adaptations of benthic diatoms (vol 11, 3320, 2020)
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- Journal Article
- A1
- open access
Comparative transcriptomics enables the identification of functional orthologous genes involved in early leaf growth
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- Journal Article
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Virus-host coexistence in phytoplankton through the genomic lens
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- Journal Article
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Light regulation of LHCX genes in the benthic diatom Seminavis robusta
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- Journal Article
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- open access
Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds
(2020) PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 117(5). p.2551-2559 -
- Journal Article
- A1
- open access
Evolution of vascular plants through redeployment of ancient developmental regulators
(2020) PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 117(1). p.733-740 -
Identification and evolution of gene regulatory networks : insights from comparative studies in plants
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- Journal Article
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- open access
Inference of plant gene regulatory networks using data-driven methods : a practical overview
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- Journal Article
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- open access
Distinctive growth and transcriptional changes of the diatom Seminavis robusta in response to quorum sensing related compounds
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- Journal Article
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- open access
The Seminavis robusta genome provides insights into the evolutionary adaptations of benthic diatoms
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- Journal Article
- A2
- open access
The medium-size noncoding RNA transcriptome of Ostreococcus tauri, the smallest living eukaryote, reveals a large family of small nucleolar RNAs displaying multiple genomic expression strategies
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A new evolutionary model for the vertebrate actin family including two novel groups
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- Journal Article
- A1
- open access
Enhanced maps of transcription factor binding sites improve regulatory networks learned from accessible chromatin data
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- Journal Article
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Gene space completeness in complex plant genomes
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Capturing the phosphorylation and protein interaction landscape of the plant TOR kinase
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- Journal Article
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Neofunctionalization of mitochondrial proteins and incorporation into signaling networks in plants
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Curse : building expression atlases and co-expression networks from public RNA-Seq data
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- Journal Article
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- open access
A widespread alternative squalene epoxidase participates in eukaryote steroid biosynthesis
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- Journal Article
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Overcoming challenges in variant calling : exploring sequence diversity in candidate genes for plant development in perennial ryegrass (Lolium perenne)
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Understanding genetic control of root system architecture in soybean : insights into the genetic basis of lateral root number
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- Journal Article
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- open access
Associated bacteria affect sexual reproduction by altering gene expression and metabolic processes in a biofilm inhabiting diatom
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- Journal Article
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Gearing up to handle the mosaic nature of life in the quest for orthologs
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- Journal Article
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- open access
JASPAR 2018 : update of the open-access database of transcription factor binding profiles and its web framework
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The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution
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- Journal Article
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- open access
PLAZA 4.0 : an integrative resource for functional, evolutionary and comparative plant genomics
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- Journal Article
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- open access
Genome analyses of the microalga Picochlorum provide insights into the evolution of thermotolerance in the green lineage
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Insights into the evolution of multicellularity from the sea lettuce genome
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- Journal Article
- A1
- open access
GSyellow, a multifaceted tag for functional protein analysis in monocot and dicot plants
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- Journal Article
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- open access
KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis
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- Journal Article
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- open access
TF2Network : predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information
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Ensemble gene function prediction database reveals genes important for complex I formation in Arabidopsis thaliana
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Identifying drivers of sympatric speciation in the marine benthic diatom Seminavis robusta using metabolic analysis and whole-genome resequencing
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Genome-wide characterization of differential transcript usage in Arabidopsis thaliana
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The transcription factor MYB29 is a regulator of ALTERNATIVE OXIDASE1a
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- Journal Article
- A1
- open access
The transcriptional repressor complex FRS7-FRS12 regulates flowering time and growth in Arabidopsis
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Phylogenomic analysis of gene co-expression networks reveals the evolution of functional modules
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- Journal Article
- A1
- open access
Evolutionary relationships and expression analysis of EUL domain proteins in rice (Oryza sativa)
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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
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PhyD3 : a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization
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The plastid genome in Cladophorales green algae is encoded by hairpin chromosomes
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A guide to the PLAZA 3.0 plant comparative genomic database
(2017) Plant genomics databases : methods and protocols. In Methods in Molecular Biology 1533. p.183-200 -
- Journal Article
- A1
- open access
A collection of conserved noncoding sequences to study gene regulation in flowering plants
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- Journal Article
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- open access
Are we there yet? : reliably estimating the completeness of plant genome sequences
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- Journal Article
- A1
- open access
CoExpNetViz: comparative co-expression networks construction and visualization tool
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- Journal Article
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- open access
Functional characterization of the Arabidopsis transcription factor bZIP29 reveals its role in leaf and root development
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Genomic variation in the FT gene family of perennial ryegrass (Lolium perenne)
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Robust peptide-based models in quantitative proteomics
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- Conference Paper
- C3
- open access
Peptide-level robust ridge regression modeling improves both sensitivity and specificity in quantitative proteomics
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An improved toolbox to unravel the plant cellular machinery by tandem affinity purification of Arabidopsis protein complexes
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- Journal Article
- A1
- open access
PLAZA 3.0 : an access point for plant comparative genomics
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Evolutionary trails of plant steroid genes
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- Journal Article
- A1
- open access
Functional analysis of the Arabidopsis TETRASPANIN gene family in plant growth and development
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- Journal Article
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- open access
Dynamic changes in ANGUSTIFOLIA3 complex composition reveal a growth regulatory mechanism in the maize leaf
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- Journal Article
- A1
- open access
An update on LNCipedia : a database for annotated human lncRNA sequences
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Towards an understanding of the cytological diversity of green seaweeds (Ulvophyceae)
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- Journal Article
- A1
- open access
BLSSpeller : exhaustive comparative discovery of conserved cis-regulatory elements
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- Journal Article
- A1
- open access
A repressor protein complex regulates leaf growth in Arabidopsis
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- Journal Article
- A1
- open access
Selection for improved energy use efficiency and drought tolerance in canola results in distinct transcriptome and epigenome changes
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- Journal Article
- A1
- open access
Small-scale gene duplications played a major role in the recent evolution of wheat chromosome 3B
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- Journal Article
- A1
- open access
A DNA-binding-site landscape and regulatory network analysis for NAC transcription factors in Arabidopsis thaliana
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- Journal Article
- A1
- open access
Drought tolerance conferred to sugarcane by association with Gluconacetobacter diazotrophicus: a transcriptomic view of hormone pathways
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Inference of transcriptional networks in Arabidopsis through conserved noncoding sequence analysis
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A functional and evolutionary perspective on transcription factor binding in Arabidopsis thaliana
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MAGIC: access portal to a cross-platform gene expression compendium for maize
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- Miscellaneous
- open access
Big data and other challenges in the quest for orthologs
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ANGUSTIFOLIA3 binds to SWI/SNF chromatin remodeling complexes to regulate transcription during Arabidopsis leaf development
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A generic tool for transcription factor target gene discovery in Arabidopsis cell suspension cultures based on tandem chromatin affinity purification
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SHUGOSHINs and PATRONUS protect meiotic centromere cohesion in Arabidopsis thaliana
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- Conference Paper
- P1
- open access
A parallel, distributed-memory framework for comparative motif discovery
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Structural and functional partitioning of bread wheat chromosome 3B
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Molecular and physiological analysis of growth-limiting drought stress in Brachypodium distachyon leaves
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Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants
(2013) PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 110(8). p.2898-2903 -
pico-PLAZA, a genome database of microbial photosynthetic eukaryotes
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The membrane-bound NAC transcription factor ANAC013 functions in mitochondrial retrograde regulation of the oxidative stress response in Arabidopsis
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- Conference Paper
- C3
- open access
Comparative motif discovery in the cloud
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ERF115 controls root quiescent center cell division and stem cell replenishment
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- Journal Article
- A1
- open access
TRAPID : an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes
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- Journal Article
- A1
- open access
Toward community standards in the quest for orthologs
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Dissecting plant genomes with the PLAZA comparative genomics platform
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Comparative co-expression analysis in plant biology
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- Journal Article
- A1
- open access
Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage
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Tetraspanin genes in plants
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- Journal Article
- A1
- open access
Systematic identification of functional plant modules through the integration of complementary data sources
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Identification of cis-regulatory elements specific for different types of reactive oxygen species in Arabidopsis thaliana
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Identification of putative cancer genes through data integration and comparative genomics between plants and humans
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- Journal Article
- A1
- open access
Metagenomes of the picoalga Bathycoccus from the Chile coastal upwelling
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- Conference Paper
- C3
- open access
A high performance computing approach to the dicovery of conserved motifs
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- Conference Paper
- C3
- open access
Alignment-free genome-wide comparative motif discovery in 4 Monocot species
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- Journal Article
- A1
- open access
i-ADHoRe 3.0 : fast and sensitive detection of genomic homology in extremely large data sets
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A greedy, graph-based algorithm for the alignment of multiple homologous gene lists
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Plastid gene expression and plant development require a plastidic protein of the mitochondrial transcription termination factor family
(2011) PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 108(16). p.6674-6679 -
ROS signaling: the new wave?
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Comparative network analysis reveals that tissue specificity and gene function are important factors influencing the mode of expression evolution in Arabidopsis and rice
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- Journal Article
- A1
- open access
Genome-wide analysis of the diatom cell cycle unveils a novel type of cyclins involved in environmental signaling
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- Journal Article
- A1
- open access
The MCM-Binding Protein ETG1 Aids Sister Chromatid Cohesion Required for Postreplicative Homologous Recombination Repair
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- Journal Article
- A1
- open access
PLAZA : a comparative genomics resource to study gene and genome evolution in plants
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The Mouse Thymosin Beta15 Gene Family Displays Unique Complexity and Encodes A Functional Thymosin Repeat
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Unraveling Transcriptional Control in Arabidopsis Using cis-Regulatory Elements and Coexpression Networks
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- Journal Article
- A1
- open access
Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression
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Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes
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The flowering world: a tale of duplications
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Unravelling cis-Regulatory Elements in the Genome of the Smallest Photosynthetic Eukaryote: Phylogenetic Footprinting in Ostreococcus
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Hydrogen peroxide-induced gene expression across kingdoms: a comparative analysis
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A constitutional translocation t(1;17)(p36.2;q11.2) in a neuroblastoma patient disrupts the the human NBPF1 and ACCN1 genes
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- Journal Article
- A1
- open access
The PRA1 gene family in Arabidopsis
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Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species
(2008) PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 105(9). p.3427-3432 -
The Phaeodactylum genome reveals the evolutionary history of diatom genomes
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On the origin and evolution of vertebrate and viral profilins
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How many genes are there in plants (... and why are they there)?
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Novel plant-specific cyclin-dependent kinase inhibitors induced by biotic and abiotic stresses
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- Journal Article
- A1
- open access
Cold nights impair leaf growth and cell cycle progression in maize through transcriptional changes of cell cycle genes
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- Journal Article
- A1
- open access
A high quality draft consensus sequence of the genome of a heterozygous grapevine variety
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- Journal Article
- A1
- open access
The gain and loss of genes during 600 million years of vertebrate evolution
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- Journal Article
- A1
- open access
Identification of novel regulatory modules in dicotyledonous plants using expression data and comparative genomics
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- Journal Article
- A1
- open access
Genome-wide identification of potential plant E2F target genes
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- Journal Article
- A1
- open access
Exploring the plant transcriptome through phylogenetic profiling
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Ancient duplication of cereal genomes
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- PhD Thesis
- open access
Mode and tempo of gene and genome evolution in plants
(2005) -
A small CDC25 dual-specificity tyrosine-phosphatase isoform in Arabidopsis thaliana
(2004) PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 101(36). p.13380-13385 -
Type II metacaspases Atmc4 and Atmc9 of Arabidopsis thaliana cleave substrates after arginine and lysine
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Recent developments in computational approaches for uncovering genomic homology
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Gene duplication and biased functional retention of paralogs in bacterial genomes
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Major events in the genome evolution of vertebrates: paranome age and size differ considerably between ray-finned fishes and land vertebrates
(2004) PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 101(6). p.1638-1643 -
Building genomic profiles for uncovering segmental homology in the twilight zone
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The quest for genomic homology
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Building genomic profiles for uncovering segmental homology in the twilight zone
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Quantitative cDNA-AFLP analysis for genome-wide expression studies
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Investigating ancient duplication events in the Arabidopsis genome
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Investigating ancient duplication events in the Arabidopsis genome
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Evidence that rice and other cereals are ancient aneuploids
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- Journal Article
- A1
- open access
Genome-wide analysis of core cell cycle genes in Arabidopsis
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Detecting microcolinearity between Arabidopsis and Rice
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Transcriptome analysis during cell division in plants
(2002) PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 99(23). p.14825-14830 -
The hidden duplication past of Arabidopsis thaliana
(2002) PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 99(21). p.13627-13632 -
The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice
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Detecting the undetectable : uncovering duplicated segments in Arabidopsis by comparison with rice.