A5028798751- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- Cancer-related molecular mechanisms research
- Neurogenesis and neuroplasticity mechanisms
- Single-cell and spatial transcriptomics
- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- MicroRNA in disease regulation
- Congenital heart defects research
- Plant Molecular Biology Research
- Data Management and Algorithms
- Gene expression and cancer classification
- Developmental Biology and Gene Regulation
- Transgenic Plants and Applications
- Click Chemistry and Applications
- Neuroinflammation and Neurodegeneration Mechanisms
- Autism Spectrum Disorder Research
- Plant-Microbe Interactions and Immunity
- Plant Virus Research Studies
- Cancer-related gene regulation
- Genetics, Bioinformatics, and Biomedical Research
- Machine Learning in Materials Science
- Network Security and Intrusion Detection
- Genetics and Neurodevelopmental Disorders
- Data Mining Algorithms and Applications
University of California, Davis
2025
Stanford University
2013-2020
Circuit Therapeutics (United States)
2018
University of Notre Dame
2009
In the developing brain, neurons expressing VEGF-A and blood vessels grow in close apposition, but many of molecular pathways regulating neuronal neurovascular system development remain to be deciphered. Here, we show that miR-9 links neurogenesis angiogenesis through formation VEGF-A. We found directly targets transcription factors TLX ONECUTs regulate expression. inhibition leads increased ONECUT expression, resulting overexpression. This untimely increase signal thickening at expense...
The neocortex is a mammalian-specific structure that responsible for higher functions such as cognition, emotion and perception. To gain insight into its evolution the gene regulatory codes pattern it, we studied overlap of active developmental enhancers with transposable element (TE) families compared this to uniformly shuffled enhancers. Here show striking enrichment MER130 repeat family among in mouse dorsal cerebral wall, which gives rise neocortex, at embryonic day 14.5. We instances...
Many important model organisms for biomedical and evolutionary research have sequenced genomes, but occupy a phylogenetically isolated position, evolutionarily distant from other genomes. This phylogenetic isolation is exemplified zebrafish, vertebrate cis-regulation, development human disease, whose distance to all currently fish exceeds the between chicken. Such large distances make it difficult align genomes use them comparative analysis beyond gene-focused questions. In particular,...
Exome sequencing studies have identified multiple genes harboring de novo loss-of-function (LoF) variants in individuals with autism spectrum disorders (ASD), including TBR1 , a master regulator of cortical development. We performed ChIP-seq for during mouse neurogenesis and show that TBR1-bound regions are enriched adjacent to ASD genes. were also among differentially expressed Tbr1 knockouts, which together the data, suggests direct transcriptional regulation. Of nine examined, seven...
Recent advances in single-cell technologies are paving the way to a comprehensive understanding of cellular complexity brain. Protocols for transcriptomics combine variety sophisticated methods purpose isolating heavily interconnected and heterogeneous neuronal cell types relatively intact healthy state. The emphasis transcriptome studies has thus far been on comparing library generation sequencing techniques that enable measurement minute amounts starting material from single cell. However,...
Genetic studies have identified a core set of transcription factors and target genes that control the development neocortex, region human brain responsible for higher cognition. The specific regulatory interactions between these factors, many key upstream downstream genes, enhancers mediate all remain mostly uncharacterized. We perform p300 ChIP-seq to identify over 6,600 candidate active in dorsal cerebral wall embryonic day 14.5 (E14.5) mice. Over 95% peaks we measure are conserved human....
Thousands of human disease-associated single nucleotide polymorphisms (SNPs) lie in the non-coding genome, but only a handful have been demonstrated to affect gene expression and biology. We computationally identified risk-associated SNPs deeply conserved non-exonic elements (CNEs) potentially contributing 45 diseases. further that CNE1/rs17421627 associated with retinal vasculature defects showed transcriptional activity zebrafish retina, while introducing allele completely abolished CNE1...
Abstract Linking sequence variation to phenotypic effects is critical for efficient exploitation of large genomic datasets. Here we present a novel approach combining directed evolution with protein language modeling characterize naturally-evolved variants rice immune receptor. Using high-throughput evolution, engineered the receptor Pik-1 bind and recognize fungal proteins Avr-PikC Avr-PikF, which evade detection by currently characterized alleles. A model was fine-tuned on this data...
Significance Neurons of the cerebral cortex arise from a common progenitor pool that progressively generates different cell subtypes with distinct features, including deep layer (DL) and upper (UL) projection neurons. Several transcription factors (TFs) are known to specify whether will become UL or DL; however, it is still unknown which upstream downstream contribute this fate decision. Here, we deeply characterize differential gene expression chromatin accessibility DL We identify TFs...
Abstract Rapid development of immune receptors that protect crops from emerging pathogens is a critical challenge 1,2 . While novel recognize previously undetected pathogen effectors could provide protection against wider range pathogens, engineering such has been constrained by the low throughput and speed in planta testing. We established yeast surface display as high platform to recapitulate plant receptor-ligand interactions evolve new binding capabilities. Using this directed evolution...
While investigating methods to predict small molecule potencies, we found random forests or support vector machines paired with extended-connectivity fingerprints (ECFP) consistently outperformed recently developed methods. A detailed investigation into regression algorithms and molecular revealed gradient-boosted decision trees, particularly CatBoost, in conjunction a combination of ECFP, Avalon, ErG fingerprints, as well 200 properties, be most effective. Incorporating graph neural network...
Distributed PRocessing in Mobile Environments (DPRiME) is a framework for processing large data sets across an ad-hoc network. Developed to address the shortcomings of Google's MapReduce outside fully-connected network, DPRiME separates nodes on network into master and workers; distributes sections available one-hop workers process parallel. Upon returning results its master, worker assigned unfinished task. Five mining classifiers were implemented data: decision trees, k-means, k-nearest...
Abstract We are only just beginning to catalog the vast diversity of cell types in cerebral cortex. Such categorization is a first step toward understanding how diversification relates function. All cortical projection neurons arise from uniform pool progenitor cells that lines ventricles forebrain. It still unclear these generate more than fifty unique mature defined by their distinct gene expression profiles. Here we compare and chromatin accessibility two subclasses with divergent...