A5036010236- Epigenetics and DNA Methylation
- Genomics and Chromatin Dynamics
- RNA modifications and cancer
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Genetic Mapping and Diversity in Plants and Animals
- SARS-CoV-2 and COVID-19 Research
- Circadian rhythm and melatonin
- Psychological and Temporal Perspectives Research
- Gene Regulatory Network Analysis
- Genetics and Neurodevelopmental Disorders
- Genetic Associations and Epidemiology
- Molecular Biology Techniques and Applications
- Health, Environment, Cognitive Aging
- vaccines and immunoinformatics approaches
- Developmental Biology and Gene Regulation
- Pancreatic function and diabetes
- Myasthenia Gravis and Thymoma
- Diabetes Management and Research
- Diabetes Treatment and Management
- RNA Research and Splicing
- Peripheral Neuropathies and Disorders
- Viral gastroenteritis research and epidemiology
- Pituitary Gland Disorders and Treatments
- Diabetes and associated disorders
University of California, Los Angeles
2017-2024
Colgate University
2016-2018
University of Iowa
2017
Infinium methylation arrays are not available for the vast majority of non-human mammals. Moreover, even if species-specific were available, probe differences between them would confound cross-species comparisons. To address these challenges, we developed mammalian array, a single custom array that measures up to 36k CpGs per species well conserved across many species. We designed set probes can tolerate specific mutations. annotate in over 200 and report CpG island status chromatin states...
Using DNA methylation profiles (
Generalized anxiety and major depression have become increasingly common in the United States, affecting 18.6 percent of adult population. Mood disorders can be debilitating, are often correlated with poor general health, life dissatisfaction, need for disability benefits due to inability work. Recent evidence suggests that some mood a circadian component, disruptions rhythms may even trigger development these disorders. However, molecular mechanisms this interaction not well understood....
Abstract Infinium methylation arrays are not available for the vast majority of non-human mammals. Moreover, even if species-specific were available, probe differences between them would confound cross-species comparisons. To address these challenges, we developed mammalian array, a single custom array that measures 36k CpGs well conserved across species. We designed set probes on can tolerate specific mutations. annotate in over 200 species and report CpG island status chromatin states...
Abstract Recent reports highlight that human decision-making is influenced by the time of day and whether one a morning or evening person (i.e., chronotype). Here, we test these behavioral effects are associated with endogenous biological rhythms. We asked participants to complete two well-established tasks in evening: matrix task (an ethical decision task) balloon analog risk (BART; risk-taking task), measured their chronotype ways. First, completed self-report measure, Horne-Östberg...
Taming cell-to-cell variability in gene expression is critical for precise pattern formation during embryonic development. To investigate the source and buffering mechanism of variability, we studied a biological clock, vertebrate segmentation controlling spatiotemporal patterning vertebral column. By counting single transcripts clock genes zebrafish, show that have low RNA amplitudes primarily driven by extrinsic sources, which suppressed Notch signaling. We further noise surprisingly...
Identifying genomic regions with functional properties that are conserved between human and mouse is an important challenge in the context of model studies. To address this, we develop a method to learn score evidence conservation at genomics level by integrating information from compendium epigenomic, transcription factor binding, transcriptomic data mouse. The method, Learning Evidence Conservation Integrated Functional annotations (LECIF), trains neural networks generate this for genomes....
The availability of genome-wide epigenomic datasets enables in-depth studies epigenetic modifications and their relationships with chromatin structures gene expression. Various alignment tools have been developed to align nucleotide or protein sequences in order identify structurally similar regions. However, there are currently no methods specifically designed for comparing multi-track signals detecting common patterns that may explain functional evolutionary similarities. We propose a new...
Given the global impact and severity of COVID-19, there is a pressing need for better understanding SARS-CoV-2 genome mutations. Multi-strain sequence alignments coronaviruses (CoV) provide important information interpreting its variation. We apply comparative genomics method, ConsHMM, to multi-strain CoV annotate every base with conservation states based on alignment patterns among CoV. The learned show distinct enrichment genes, protein domains, other regions interest. Certain are strongly...
A recent study in Genome Biology has characterized the evolution of candidate hominoid-specific liver enhancers by using massively parallel reporter assays (MPRAs).
Identifying pairwise associations between genomic loci is an important challenge for which large and diverse collections of epigenomic transcription factor (TF) binding data can potentially be informative. We therefore developed Learning Evidence Pairwise Association from Epigenomic TF (LEPAE). LEPAE uses neural networks to quantify evidence association pairs windows large-scale along with distance information. applied using thousands human datasets. present additional that captures...
ABSTRACT The availability of genome-wide epigenomic datasets enables in-depth studies epigenetic modifications and their relationships with chromatin structures gene expression. Various alignment tools have been developed to align nucleotide or protein sequences in order identify structurally similar regions. However, there are currently no methods specifically designed for comparing multi-track signals detecting common patterns that may explain functional evolutionary similarities. We...
Abstract Given the global impact and severity of COVID-19, there is a pressing need for better understanding SARS-CoV-2 genome mutations. Multi-strain sequence alignments coronaviruses (CoV) provide important information interpreting its variation. We apply comparative genomics method, ConsHMM, to multi-strain CoV annotate every base with conservation states based on alignment patterns among CoV. The learned show distinct enrichment genes, protein domains, other regions interest. Certain are...
Abstract Annotations of evolutionary sequence constraint based on multi-species genome alignments and genome-wide maps epigenomic marks transcription factor binding provide important complementary information for understanding the human genetic variation. Here we developed Constrained Non-Exonic Predictor (CNEP) to quantify evidence each base in being an evolutionarily constrained non-exonic element from input over 60,000 features. We find that CNEP score outperforms baseline related...
Abstract Annotations of evolutionarily constraint provide important information for variant prioritization. Genome-wide maps epigenomic marks and transcription factor binding complementary interpreting a subset such prioritized variants. Here we developed the Constrained Non-Exonic Predictor (CNEP) to quantify evidence each base in human genome being constrained non-exonic element from over 60,000 features. We find that CNEP score outperforms baseline related existing scores at predicting...
Abstract Identifying genomic regions with functional properties that are conserved between human and mouse is an important challenge in the context of model studies. To address this, we take a novel approach learn score evidence conservation at genomics level by integrating large-scale information compendium epigenomic, transcription factor binding, transcriptomic data from mouse. The computational method developed to do Learning Evidence Conservation Integrated Functional annotations...