A5046811254- Bioinformatics and Genomic Networks
- Genetic Mapping and Diversity in Plants and Animals
- Legume Nitrogen Fixing Symbiosis
- Gene expression and cancer classification
- Genomics and Phylogenetic Studies
- Plant nutrient uptake and metabolism
- Asthma and respiratory diseases
- Mycorrhizal Fungi and Plant Interactions
- Plant Parasitism and Resistance
- Receptor Mechanisms and Signaling
- Steroid Chemistry and Biochemistry
- Eosinophilic Esophagitis
- Estrogen and related hormone effects
- Agronomic Practices and Intercropping Systems
- Plant Molecular Biology Research
- Acute Myeloid Leukemia Research
- Cancer Genomics and Diagnostics
- Plant and animal studies
- Epigenetics and DNA Methylation
- Nematode management and characterization studies
- Plant Pathogenic Bacteria Studies
- Plant-Microbe Interactions and Immunity
- Genomics and Chromatin Dynamics
- Genetic Associations and Epidemiology
- Pharmacological Receptor Mechanisms and Effects
Max Planck Institute for Plant Breeding Research
2023-2025
University of Cambridge
2019-2024
Sainsbury Laboratory
2019-2024
Cornell University
2017-2023
Weill Cornell Medicine
2017-2023
Yonsei University
2013-2020
ENT and Allergy
2000-2007
Guy's Hospital
1988-2003
Abstract The reconstruction of transcriptional regulatory networks (TRNs) is a long-standing challenge in human genetics. Numerous computational methods have been developed to infer interactions between factors (TFs) and target genes from high-throughput data their performance evaluation requires gold-standard interactions. Here we present database literature-curated TF-target interactions, TRRUST ( t ranscriptional r egulatory elationships u nravelled by s entence-based ext-mining,...
Plants associate with beneficial arbuscular mycorrhizal fungi facilitating nutrient acquisition. Arbuscular produce chitooligosaccharides (COs) and lipo-chitooligosaccharides (LCOs), that promote symbiosis signalling resultant oscillations in nuclear-associated calcium. The activation of must be balanced immunity signalling, which fungal interactions is promoted by COs resulting from the chitinaceous cell wall. Here we demonstrate ranging CO4-CO8 can induce Medicago truncatula. CO perception...
1. Lipoxin A4 (LXA4) and lipoxin B4 (LXB4) have been evaluated for their capacities to modulate neutrophil (PMN) migration endothelial cell adherence using compounds prepared by total chemical synthesis. 2. Increased PMN was seen with concentrations of LXA4 from 10−9 mol/l 10−7 mol/l. 100-fold less potent than leukotriene (LTB4) it elicited only one-half the maximal response LTB4. 3. The (5S,6S,15S)-isomer induced a weak migratory LXB4 inactive, suggesting that activity stereospecific. 4....
Arabidopsis thaliana is a reference plant that has been studied intensively for several decades. Recent advances in high-throughput experimental technology have enabled the generation of an unprecedented amount data from A. thaliana, which facilitated data-driven approaches to unravel genetic organization phenotypes. We previously published description genome-scale functional gene network AraNet, was constructed by integrating multiple co-functional networks inferred diverse types, and we...
Abstract Most plants associate with beneficial arbuscular mycorrhizal (AM) fungi that facilitate soil nutrient acquisition. Prior to contact, partner recognition triggers reciprocal genetic remodelling enable colonisation. The plant Dwarf14-Like (D14L) receptor conditions pre-symbiotic perception of AM fungi, and also detects the smoke constituent karrikin. D14L-dependent signalling mechanisms, underpinning symbiosis are unknown. Here, we present identification a negative regulator from...
Many important crops are members of the Poaceae family, which develop root systems characterized by a high degree initiation from belowground basal nodes shoot, termed crown. Although this postembryonic shoot-borne system represents major conduit for water uptake, little is known about effect availability on its development. Here we demonstrate that in model C4 grass Setaria viridis, crown locally senses and suppresses postemergence growth under deficit. This response was observed field room...
Abstract Many plants associate with arbuscular mycorrhizal fungi for nutrient acquisition, while legumes also nitrogen-fixing rhizobial bacteria. Both associations rely on symbiosis signaling and here we show that cereals can perceive lipochitooligosaccharides (LCOs) activation of signaling, surprisingly including Nod factors produced by However, stringent perception specifically decorated LCOs, is absent in cereals. LCO activated starvation, through transcriptional regulation Nodulation...
Legumes produce specialized root nodules that are distinct from lateral roots in morphology and function, with intracellularly hosting nitrogen-fixing bacteria. We have previously shown a program underpins nodule initiation, but there must be additional developmental regulators confer identity. Here, we show two members of the LIGHT-SENSITIVE SHORT HYPOCOTYL (LSH) transcription factor family, predominantly known to define shoot meristem complexity organ boundaries, function as In parallel...
Rice is the most important staple food crop and a model grass for studies of bioenergy crops. We previously published genome-scale functional network server called RiceNet, constructed by integrating diverse genomics data demonstrated use in genetic dissection rice biotic stress responses its usefulness other species. Since initial construction network, there has been significant increase amount publicly available data. Here, we present an updated prioritization Oryza sativa ssp. japonica,...
Legume nodules create an environment for intracellular bacterial symbionts to fix atmospheric nitrogen. The master regulator NODULE INCEPTION (NIN) controls many aspects of nodule initiation, and we demonstrate that it also regulates the transition nitrogen fixation via proteolytic processing by a signal peptidase complex. Processing NIN results in carboxyl-terminal fragment containing DNA binding motifs, which activates suite genes associated with symbiosome development fixation. Similar is...
Summary Legumes grow specialized root nodules that are distinct from lateral roots in morphology and function, with intracellularly hosting beneficial nitrogen-fixing bacteria provide the plant a nitrogen source. We have previously shown root-like program underpins nodule initiation, but there must be additional developmental programs confer identity. Here, we show two members of LIGHT SENSITIVE SHORT HYPOCOTYL (LSH) transcription factor family, predominantly known to define organ boundaries...
During the last decade, genome-wide association studies (GWAS) have represented a major approach to dissect complex human genetic diseases. Due in part limited statistical power, most identify only small numbers of candidate genes that pass conventional significance thresholds (e.g. P ≤ 5 × 10-8). This limitation can be partly overcome by increasing sample size, but this comes at higher cost. Alternatively, weak signals boosted incorporating independent data. Previously, we demonstrated...
Genome-wide association studies (GWAS) have been applied for the genetic dissection of complex phenotypes in Arabidopsis thaliana. However, significantly associated single-nucleotide polymorphisms (SNPs) could not explain all phenotypic variations. A major reason missing true phenotype-associated loci is strict P-value threshold after adjustment multiple hypothesis tests to reduce false positives. This statistical limitation can be partly overcome by increasing sample size, but at a much...
Maize (Zea mays) has multiple uses in human food, animal fodder, starch and sweetener production as a biofuel, is accordingly the most extensively cultivated cereal worldwide. To enhance maize production, genetic factors underlying important agricultural traits, including stress tolerance flowering, have been explored through forward reverse genetics approaches. Co-functional gene networks are systems biology resources useful identifying trait-associated genes plants by prioritizing...
Cultivated barley (Hordeum vulgare L.) is one of the most produced cereal crops worldwide after maize, bread wheat, and rice. Barley an important crop species not only as a food source, but also in plant genetics because it harbors numerous stress response alleles its genome that can be exploited for engineering. However, functional annotation relatively poor compared with other major crops. Moreover, bioinformatics tools system-wide analyses omics data from are yet available. We have thus...
Receptor-like kinases (RLKs) are key cell signaling components. The rice ARBUSCULAR RECEPTOR-LIKE KINASE 1 (OsARK1) regulates the arbuscular mycorrhizal (AM) association postarbuscule development and belongs to an undefined subfamily of RLKs. Our phylogenetic analysis revealed that ARK1 has ancient paralogue in spermatophytes, ARK2 Single ark2 ark1/ark2 double mutants showed a nonredundant AM symbiotic function for OsARK2 Global transcriptomics identified set genes coregulated by two RLKs,...
Identifying gene neighbourhoods using either distance- or probability-based measures has proven effective in retrieving co-functional links. We report that these two approaches are highly complementary, with differential sensitivity for the core pathway demonstrate integrating improves prediction of both pathways and phenotypes.