A5102944401- Bioinformatics and Genomic Networks
- Cancer-related molecular mechanisms research
- Gene Regulatory Network Analysis
- Gene expression and cancer classification
- RNA Research and Splicing
- Genomics and Chromatin Dynamics
- Autism Spectrum Disorder Research
- CRISPR and Genetic Engineering
- Genetics, Aging, and Longevity in Model Organisms
- Single-cell and spatial transcriptomics
- Genetic Mapping and Diversity in Plants and Animals
- Regulation of Appetite and Obesity
- Biomedical Text Mining and Ontologies
- Virology and Viral Diseases
- Genetics and Neurodevelopmental Disorders
Stanford Medicine
2021-2023
Stanford University
2004-2020
University of Notre Dame
2014-2015
Abstract Background ‘ Long read ’ sequencing methods have been used to identify previously uncharacterized structural variants that cause human genetic diseases. Therefore, we investigated whether long could facilitate analysis of murine models for Results The genomes six inbred strains (BTBR T + Itpr3tf/J, 129Sv1/J, C57BL/6/J, Balb/c/J, A/J, SJL/J) were analyzed using sequencing. Our results revealed (i) Structural are very abundant within the genome (4.8 per gene) and (ii) cannot...
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...
Current “ground truth” knowledge about human aging has been obtained by transferring aging-related from well-studied model species via sequence homology or studying gene expression data. Since proteins function interacting with each other, analyzing protein-protein interaction (PPI) networks in the context of is promising. Unlike existing static network research aging, since cellular functioning dynamic, we recently integrated PPI data to form age-specific networks. Then, predicted as key...
Abstract The genomes of six inbred strains were analyzed using long read (LR) sequencing. results revealed that structural variants (SV) very abundant within the genome mouse (4.8 per gene), which indicates they could impact genetic traits. Analysis relationship between SNP and SV alleles across 53 indicated we have a limited ability to infer whether are present short sequence data, even when nearby known. benefit having more complete map pattern variation was demonstrated by identifying at...
Since human aging is hard to study experimentally due long lifespan and ethical constraints, current "ground truth" knowledge about has mostly been predicted computationally or statistically by transferring the from well-studied model species via sequence homology studying gene expression data. genes, i.e., their protein products, function interacting with each other, analysis of protein-protein interaction (PPI) network data in context promising. Existing studies PPI networks have typically...
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...
Abstract Inbred mouse strains reveal the molecular basis of mammalian traits and diseases, particularly recessive ones. We utilized community curated resources to set up an automated screen discover novel testable gene function hypotheses. Using 11,832 contributed strain-differentiating experiments trait presence/absence scoring, we searched for all where can be split by their phenotypic values (e.g., high vs. low responders). Then, using 48 sequenced strains, found one or more candidate...