A5074188388- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- Developmental Biology and Gene Regulation
- Genomics and Phylogenetic Studies
- Cancer-related gene regulation
- Transgenic Plants and Applications
- Phytoplasmas and Hemiptera pathogens
- CRISPR and Genetic Engineering
- Neurobiology and Insect Physiology Research
- Insect Resistance and Genetics
- Insect symbiosis and bacterial influences
- Biochemical and Structural Characterization
- Ubiquitin and proteasome pathways
- Cellular transport and secretion
- Liver physiology and pathology
- Plant Molecular Biology Research
- Bioinformatics and Genomic Networks
- RNA Interference and Gene Delivery
- Signaling Pathways in Disease
- Invertebrate Immune Response Mechanisms
- Chromosomal and Genetic Variations
- ATP Synthase and ATPases Research
- Epigenetics and DNA Methylation
- Animal Genetics and Reproduction
Columbia University
2019-2023
Brain (Germany)
2020
University of Maryland, College Park
2008-2013
Protein-ligand interactions are increasingly profiled at high throughput using affinity selection and massively parallel sequencing. However, these assays do not provide the biophysical parameters that most rigorously quantify molecular interactions. Here we describe a flexible machine learning method, called ProBound, accurately defines sequence recognition in terms of equilibrium binding constants or kinetic rates. This is achieved multi-layered maximum-likelihood framework models both...
Abstract In eukaryotes, members of transcription factor families often exhibit similar DNA binding properties in vitro, yet orchestrate paralog-specific gene regulatory networks vivo. The serially homologous first (T1) and third (T3) thoracic legs Drosophila , which are specified by the Hox proteins Scr Ubx, respectively, offer a unique opportunity to address this paradox Genome-wide analyses using epitope-tagged alleles both loci T1 T3 leg imaginal discs, precursors adult ventral body...
ABSTRACT Fluorescent labeling approaches are crucial for elucidating protein function and dynamics. While enhancer trapping in Drosophila has been useful the characterization of gene transcription, protein-specific visualization vivo more elusive. To overcome these limitations, we developed Endogenous Tagging with a Covalent Hook (FETCH) to label cell surface proteins (CSPs) through stable covalent bond mediated by DogTag-DogCatcher peptide partner system 1 . FETCH leverages spontaneous...
We describe a simple and efficient technique that allows scarless engineering of Drosophila genomic sequences near any landing site containing an inverted attP cassette, such as MiMIC insertion. This two-step method combines phiC31 integrase-mediated site-specific integration homing nuclease-mediated resolution local duplications, efficiently converting the original allele to modified alleles only have desired change(s). Dominant markers incorporated into this allow correct individual flies...
Drosophila polyhomeotic (ph) is one of the important polycomb group genes that linked to human cancer. In mosaic eye imaginal discs, while ph(del), a null allele, causes only non-autonomous overgrowth, ph(505), hypomorphic both autonomous and overgrowth. These allele-specific phenotypes stem from different sensitivities ph mutant cells Upd homologs they secrete.
Chromatin immunoprecipitation (ChIP) is an important technique for characterizing protein–DNA binding in vivo. One drawback of ChIP-based techniques the lack cell type-specificity when profiling complex tissues. To overcome this limitation, we developed SpyChIP to identify type-specific transcription factor (TF) sites native physiological contexts without tissue dissociation or nuclei sorting. takes advantage a specific covalent isopeptide bond that rapidly forms between 15-amino acid SpyTag...
Abstract In eukaryotes, members of large transcription factor families often exhibit similar DNA binding properties in vitro , yet initiate paralog-specific gene regulatory networks vivo . The serially homologous first (T1) and third (T3) thoracic legs Drosophila which result from alternative specified by the Hox proteins Scr Ubx, respectively, offer a unique opportunity to address this paradox Genome-wide analyses using epitope-tagged alleles both loci T1 T3 leg imaginal discs, are...
Abstract Here we describe a Drosophila genome engineering technique that can scarlessly modify genomic sequences near any mapped attP attachment site previously integrated by transposon mobilization or gene targeting. This combines two highly efficient and robust procedures: phiC31 integrase–mediated site‐specific integration homing endonuclease–mediated resolution of local duplications. In this technique, donor fragment containing the desired mutation(s) is first into selected target locus...
ABSTRACT Eukaryotic transcription factors (TFs) form complexes with various partner proteins to recognize their genomic target sites. Yet, how the DNA sequence determines which TF complex forms at any given site is poorly understood. Here we demonstrate that high-throughput in vitro binding assays coupled unbiased computational analysis provides unprecedented insight into of homeodomain adapt stoichiometry and configuration bound DNA. Using inferred knowledge about minor groove width...
Abstract We describe a simple and efficient technique that allows scarless engineering of Drosophila genomic sequences near any landing site containing an inverted attP cassette, such as MiMIC insertion. This 2-step method combines phiC31 integrase mediated site-specific integration homing nuclease-mediated resolution local duplications, efficiently converting the original allele to modified alleles only have desired change(s). Dominant markers incorporated into this allow correct individual...
Abstract Chromatin immunoprecipitation (ChIP) is an important technique for characterizing protein-DNA binding in vivo . One drawback of ChIP based techniques the lack cell type-specificity when profiling complex tissues. To overcome this limitation, we developed SpyChIP to identify type-specific transcription factor (TF) sites native physiological contexts without tissue dissociation or nuclei sorting. takes advantage a specific covalent isopeptide bond that rapidly forms between 15 amino...
ABSTRACT Quantifying sequence-specific protein-ligand interactions is critical for understanding and exploiting numerous cellular processes, including gene regulation signal transduction. Next-generation sequencing (NGS) based assays are increasingly being used to profile these with high-throughput. However, do not provide the biophysical parameters that have long been uncover quantitative rules underlying sequence recognition. We developed a highly flexible machine learning framework,...