A5028363830- Genetics, Aging, and Longevity in Model Organisms
- CRISPR and Genetic Engineering
- RNA Research and Splicing
- Bioinformatics and Genomic Networks
- SARS-CoV-2 and COVID-19 Research
- Reproductive Biology and Fertility
- Photosynthetic Processes and Mechanisms
- Animal Genetics and Reproduction
- Microbial Metabolic Engineering and Bioproduction
- Evolution and Genetic Dynamics
- Microtubule and mitosis dynamics
- Chromosomal and Genetic Variations
- Advanced biosensing and bioanalysis techniques
- Pluripotent Stem Cells Research
- Genomics and Phylogenetic Studies
- MicroRNA in disease regulation
- Genetics, Bioinformatics, and Biomedical Research
- RNA modifications and cancer
- Mitochondrial Function and Pathology
- Genomics and Chromatin Dynamics
- DNA Repair Mechanisms
- Viral gastroenteritis research and epidemiology
- Fungal and yeast genetics research
- Algal biology and biofuel production
- RNA and protein synthesis mechanisms
New York University
2016-2025
New York University Abu Dhabi
2016-2025
Dana-Farber Cancer Institute
2004
Harvard University
2004
Institut de Génétique Moléculaire de Montpellier
2004
University of Namur
2004
Baylor College of Medicine
2004
Cornell University
1998-2002
Zero to Three
2001
NEC (Japan)
1998
To initiate studies on how protein-protein interaction (or "interactome") networks relate to multicellular functions, we have mapped a large fraction of the Caenorhabditis elegans interactome network. Starting with subset metazoan-specific proteins, more than 4000 interactions were identified from high-throughput, yeast two-hybrid (HT=Y2H) screens. Independent coaffinity purification assays experimentally validated overall quality this Y2H data set. Together already described and interologs...
Despite the successes of genomics, little is known about how genetic information produces complex organisms. A look at crucial functional elements fly and worm genomes could change that. The National Human Genome Research Institute's modENCODE project (the model organism ENCyclopedia Of DNA Elements) was set up in 2007 with goal identifying all sequence-based two important experimental organisms, Caenorhabditis elegans Drosophila melanogaster. Armed data, geneticists will be able to...
Despite the prominence of Caenorhabditis elegans as a major developmental and genetic model system, its phylogenetic relationship to closest relatives has not been resolved. Resolution these relationships is necessary for studying steps that underlie life history, genomic, morphological evolution this important system. By using data from five different nuclear genes 10 species currently in culture, we find well resolved phylogeny reveals three striking patterns animal group: (i)...
Three-prime untranslated regions (3'UTRs) of metazoan messenger RNAs (mRNAs) contain numerous regulatory elements, yet remain largely uncharacterized. Using polyA capture, 3' rapid amplification complementary DNA (cDNA) ends, full-length cDNAs, and RNA-seq, we defined approximately 26,000 distinct 3'UTRs in Caenorhabditis elegans for 85% the 18,328 experimentally supported protein-coding genes revised 40% gene models. Alternative 3'UTR isoforms are frequent, often differentially expressed...
A major challenge in controlling the COVID-19 pandemic is high false-negative rate of commonly used RT-PCR methods for SARS-CoV-2 detection clinical samples. Accurate particularly challenging samples with low viral loads that are below limit (LoD) standard one- or two-step methods. In this study, we implemented a three-step approach and quantification employs reverse transcription, targeted cDNA preamplification, nano-scale qPCR based on commercially available microfluidic chip. Using...
ABSTRACT Asymmetric cell divisions, critically important to specify types in the development of multicellular organisms, require polarized distribution cytoplasmic components and proper alignment mitotic apparatus. In Caenorhabditis elegans, maternally expressed protein, PAR-3, is localized one pole asymmetrically dividing blastomeres required for these asymmetric divisions. this paper, we report that an atypical protein kinase C (PKC-3) essential divisions co-localizes with PAR-3. Embryos...
We describe a trainable system for analyzing videos of developing C. elegans embryos. The automatically detects, segments, and locates cells nuclei in microscopic images. was designed as the central component fully automated phenotyping system. contains three modules 1) convolutional network trained to classify each pixel into five categories: cell wall, cytoplasm, nucleus membrane, nucleus, outside medium; 2) an energy-based model, which cleans up output by learning local consistency...
As a step towards comprehensive functional analysis of genomes, systematic gene knockout projects have been initiated in several organisms [1]. In metazoans like C. elegans, however, maternal contribution can mask the effects knockouts on embryogenesis. RNA interference (RNAi) provides an alternative rapid approach to obtain loss-of-function information that also reveal embryonic roles for genes targeted [2,3]. We used RNAi analyze random set ovarian transcripts and identified 81 with...
Accurate gene model annotation of reference genomes is critical for making them useful. The modENCODE project has improved the D. melanogaster genome by using deep and diverse high-throughput data. Since transcriptional activity that been evolutionarily conserved likely to have an advantageous function, we performed large-scale interspecific comparisons increase confidence in predicted annotations. To support comparative genomics, filled divergence gaps Drosophila phylogeny generating draft...
High transmissibility is a hallmark of the Omicron variant SARS-CoV-2. Understanding molecular determinants Omicron’s will impact development intervention strategies. Here we map electrostatic potential surface Spike protein to show that major SARS-CoV-2 variants have accumulated positive charges in solvent-exposed regions protein, especially its ACE2-binding interface. Significantly, Spike-ACE2 complex has complementary surfaces. In contrast, interfaces between and neutralizing antibodies...
Embryogenesis is an essential and stereotypic process that nevertheless evolves among species. Its essentiality may favor the accumulation of cryptic genetic variation (CGV) has no effect in wild-type but enhances or suppresses effects rare disruptions to gene function. Here, we adapted a classical modifier screen interrogate alleles segregating natural populations Caenorhabditis elegans: induced knockdowns used quantitative methodology examine how variants modify penetrance embryonic...
Background: The endemic Hawaiian drosophilids, a unique group that are remarkable for their diversity and rapid proliferation, provide model analysis of the process insular speciation. Founder events accompanying random drift, together with shifts in sexual selection, appear to explain dramatic divergence male morphology mating behaviour among these flies, but forces do not account spectacular ecological diversification into wide array breeding niches. Although recognized as contributing...