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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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One to host them all : genomics of the diverse bacterial endosymbionts of the spider Oedothorax gibbosus
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Genomic insights into adaptation to karst limestone and incipient speciation in East Asian Platycarya spp. (Juglandaceae)
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A panoramic view of the genomic landscape of the genus Streptomyces
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The genome of the king protea, Protea cynaroides
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Govania unica gen. nov., sp. nov., a rare biosphere bacterium that represents a novel family in the class Alphaproteobacteria
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The diversity and zoonotic potential of Staphylococcus pseudintermedius in humans and pet dogs in Trinidad and Tobago
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Paraburkholderia gardini sp. nov. and Paraburkholderia saeva sp. nov. : novel aromatic compound degrading bacteria isolated from garden and forest soil samples
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Comparative genomics and physiology of Akkermansia muciniphila isolates from human intestine reveal specialized mucosal adaptation
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Comparison of Magnoliaceae plastomes : adding Neotropical magnolia to the discussion
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Whole-genome sequences of two Kazachstania barnettii strains isolated from anthropic environments
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BLSSpeller to discover novel regulatory motifs in maize
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Chromosome-scale assembly and annotation of the perennial ryegrass genome
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Evolutionary history and pan-genome dynamics of strawberry (Fragaria spp.)
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Genome and metabolome MS-based mining of a marine strain of Aspergillus affinis
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Functional pangenome analysis reveals high virulence plasticity of Aliarcobacter butzleri and affinity to human mucus
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Genomic aromatic compound degradation potential of novel Paraburkholderia species : Paraburkholderia domus sp. nov., Paraburkholderia haematera sp. nov. and Paraburkholderia nemoris sp. nov.
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Lipopeptide families at the interface between pathogenic and beneficial Pseudomonas-plant interactions
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A critical rebuttal of the proposed division of the genus Arcobacter into six genera using comparative genomic, phylogenetic, and phenotypic criteria
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Evolution of chloroplast retrograde signaling facilitates green plant adaptation to land
(2019) PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 116(11). p.5015-5020 -
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Comparative genomics of Pandoraea, a genus enriched in xenobiotic biodegradation and metabolism
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TF2Network : predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information
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Evidence for a primate origin of zoonotic Helicobacter suis colonizing domesticated pigs
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Identification of small RNAs abundant in Burkholderia cenocepacia biofilms reveal putative regulators with a potential role in carbon and iron metabolism
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Phylogenomic analysis of gene co-expression networks reveals the evolution of functional modules
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Evolution and structural diversification of Nictaba-like lectin genes in food crops with a focus on soybean (Glycine max)
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Modeling the effect of ultraviolet radiation on the photosynthetic potential of Prochlorococcus and Synechococcus cyanobacteria
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Comparative genomics of Burkholderia singularis sp. nov., a low G+C content, free-living bacterium that defies taxonomic dissection of the genus Burkholderia
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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 -
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Phylogenomic analysis reveals an Asian origin for African Burkholderia pseudomallei and further supports melioidosis endemicity in Africa
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A collection of conserved noncoding sequences to study gene regulation in flowering plants
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- Journal Article
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CoExpNetViz: comparative co-expression networks construction and visualization tool
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Divergence between the highly virulent zoonotic pathogen Helicobacter heilmannii and its closest relative, the low-virulence 'Helicobacter ailurogastricus' sp. nov.
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Sequence search and comparative genomic analysis of SUMO-activating enzymes using CoGe
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Evolutionary trails of plant steroid genes
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- Journal Article
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Comparative genome analysis of Pediococcus damnosus LMG 28219, a strain well-adapted to the beer environment
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Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts
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Comparative genome sequencing to assess the genetic diversity and virulence attributes of 15 Vibrio anguillarum isolates
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- Journal Article
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BLSSpeller : exhaustive comparative discovery of conserved cis-regulatory elements
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Reconstruction of phylogenetic trees of prokaryotes using maximal common intervals
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Development of new PCR primers by comparative genomics for the detection of Helicobacter suis in gastric biopsy specimens
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- Journal Article
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The domestication of the probiotic bacterium Lactobacillus acidophilus
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A comparison of Helicobacter pylori and non-Helicobacter pylori Helicobacter spp. binding to canine gastric mucosa with defined gastric glycophenotype
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The Global Invertebrate Genomics Alliance (GIGA): developing community resources to study diverse invertebrate genomes
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- Conference Paper
- P1
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A parallel, distributed-memory framework for comparative motif discovery
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The moss Physcomitrella patens reproductive organ development is highly organized, affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY expression domain
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Transcriptome analyses reveal protein and domain families that delineate stage-related development in the economically important parasitic nematodes, Ostertagia ostertagi and Cooperia oncophora
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TRAPID : an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes
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Orthology Guided Assembly in highly heterozygous crops: creating a reference transcriptome to uncover genetic diversity in Lolium perenne
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- PhD Thesis
- open access
Comparative analysis of plant genomes through data integration
(2012) -
Comparative co-expression analysis in plant biology
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- Journal Article
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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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Journey through the past: 150 million years of plant genome evolution
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Obligate biotrophy features unraveled by the genomic analysis of rust fungi
(2011) PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 108(22). p.9166-9171 -
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
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Chasing the hare: evaluating the phylogenetic utility of a nuclear single copy gene region at and below species level within the species rich group Peperomia (Piperaceae)
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Identification and comparative genomic analysis of signaling and regulatory components in the diatom Thalassiosira pseudonana
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- Journal Article
- A1
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Foxl2 gene and the development of the ovary : a story about goat, mouse, fish and woman
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Towards a prokaryotic genomic taxonomy
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Comparison of the PhoPQ regulon in Escherichia coli and Salmonella typhimurium
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Detection of 91 potential in plant conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes
(2004) PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 101(31). p.11511-11516 -
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Wanda : a database of duplicated fish genes
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Comparative genomics provides evidence for an ancient genome duplication event in fish
(2001) PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES. 356(1414). p.1661-1679 -
The ghost of selection past: rates of evolution and functional divergence of anciently duplicated genes