R. Alan Harris
A5089677011- Epigenetics and DNA Methylation
- Chromosomal and Genetic Variations
- Genomics and Phylogenetic Studies
- Genomic variations and chromosomal abnormalities
- Primate Behavior and Ecology
- Genomics and Chromatin Dynamics
- RNA modifications and cancer
- Genomics and Rare Diseases
- Birth, Development, and Health
- Cancer-related molecular mechanisms research
- Evolution and Genetic Dynamics
- Cancer Genomics and Diagnostics
- Inflammatory Bowel Disease
- Diet and metabolism studies
- Genetic Syndromes and Imprinting
- MicroRNA in disease regulation
- Single-cell and spatial transcriptomics
- Gut microbiota and health
- Infant Nutrition and Health
- Neonatal Respiratory Health Research
- T-cell and B-cell Immunology
- Immune Cell Function and Interaction
- CRISPR and Genetic Engineering
- Adipose Tissue and Metabolism
- Reproductive System and Pregnancy
Baylor Genetics
2016-2025
Baylor College of Medicine
2016-2025
NSF’s NOIRLab
2020-2024
Texas Children's Hospital
2011-2016
Livingstone College
2016
The University of Texas Health Science Center at Houston
2015
University at Albany, State University of New York
2013-2015
Albany State University
2013-2015
University of Houston
2010-2014
Magellan Aerospace (Canada)
2014
The reference human genome sequence set the stage for studies of genetic variation and its association with disease, but epigenomic lack a similar reference. To address this need, NIH Roadmap Epigenomics Consortium generated largest collection so far epigenomes primary cells tissues. Here we describe integrative analysis 111 as part programme, profiled histone modification patterns, DNA accessibility, methylation RNA expression. We establish global maps regulatory elements, define modules...
The rhesus macaque (Macaca mulatta) is an abundant primate species that diverged from the ancestors of Homo sapiens about 25 million years ago. Because they are genetically and physiologically similar to humans, monkeys most widely used nonhuman in basic applied biomedical research. We determined genome sequence Indian-origin Macaca mulatta female compared data with chimpanzees humans reveal structure ancestral genomes identify evidence for positive selection lineage-specific expansions...
Abstract Background Dynamic changes to the epigenome play a critical role in establishing and maintaining cellular phenotype during differentiation, but little is known about normal methylomic differences that occur between functionally distinct areas of brain. We characterized intra- inter-individual variation across whole blood multiple regions brain from donors. Results Distinct tissue-specific patterns DNA methylation were identified, with highly significant over-representation...
Throughout most of the mammalian genome, genetically regulated developmental programming establishes diverse yet predictable epigenetic states across differentiated cells and tissues. At metastable epialleles (MEs), conversely, epigenotype is established stochastically in early embryo then maintained lineages, resulting dramatic systemic interindividual variation regulation. In mouse, maternal nutrition affects this process, with permanent phenotypic consequences for offspring. MEs have not...
Gibbons are small arboreal apes that display an accelerated rate of evolutionary chromosomal rearrangement and occupy a key node in the primate phylogeny between Old World monkeys great apes. Here we present assembly analysis northern white-cheeked gibbon (Nomascus leucogenys) genome. We describe propensity for gibbon-specific retrotransposon (LAVA) to insert into chromosome segregation genes alter transcription by providing premature termination site, suggesting possible molecular mechanism...
We report the whole-genome sequence of common marmoset (Callithrix jacchus). The 2.26-Gb genome a female was assembled using Sanger read data (6×) and shotgun strategy. A first analysis has permitted comparison with genomes apes Old World monkeys identification specific features that might contribute to unique biology this diminutive primate, including genetic changes may influence body size, frequent twinning chimerism. observed positive selection in growth hormone/insulin-like factor genes...
A high-quality rhesus macaque genome Genome technology has improved substantially since the first full organismal genomes were generated. Applying new technology, Warren et al. refined of macaque, a model nonhuman primate. Long-read and other recent advances in sequencing applied to generate with far fewer gaps helped refine locations numbers repetitive elements. Furthermore, authors performed resequencing among populations identify genetic variability macaque. Thus, previously incomplete...
The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact genomic on fundamental biological processes. Analysis that insight into long-standing questions evolutionary conservation biology is urgent given severe threats these are facing. Here, we present high-coverage whole-genome data from 233 representing 86% genera all 16 families. This dataset was used, together with fossil calibration, create a nuclear DNA...
Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding their clinical relevance remains largely incomplete. To systematically decipher the effects human variants, we obtained whole-genome data for 809 individuals from 233 primate species and identified 4.3 million common protein-altering variants with orthologs in humans. We show that these can be inferred to have nondeleterious humans based on presence at high allele...
While CD4+ T cell depletion is key to disease progression in people living with HIV and SIV-infected macaques, the mechanisms underlying this remain incompletely understood, most death involving uninfected cells. In contrast, SIV infection of "natural" hosts such as sooty mangabeys does not cause AIDS despite high-level viremia. Here, we report that CARD8 inflammasome activated immediately after entry by viral protease encapsulated incoming virions. Sensing activity leads rapid pyroptosis...
MicroRNAs (miRNAs) are short, non-coding RNAs that target and silence protein coding genes through 3′-UTR elements. Evidence increasingly assigns an immunosuppressive role for miRNAs in immunity, but relatively few have been studied, overall understanding of the importance these regulatory transcripts complex <i>in vivo</i> systems is lacking. Here we applied multiple technologies to globally analyze miRNA expression function allergic lung disease, experimental model asthma. Deep sequencing...
Fifteen patients with a variety of myoclonic syndromes were studied clinically, pharmacologically, and physiologically. CSF tryptophan, 5HIAA, HVA also measured. Of these patients, 8 improved to varying degrees by therapy 5HTP, tryptophan in combination MAOI (but not alone), clonazepam. This group included 6 cases post-anoxic myoclonus, one case post-traumatic myoclonus undiagnosed non-progressive focal epilepsy. In this low levels 5HIAA found compared non-responsive controls. Two dysynergia...
While breast milk has unique health advantages for infants, the mechanisms by which it regulates physiology of newborns are incompletely understood. miRNAs have been described as functioning transcellularly, and previously isolated in cell-free exosomal form from bodily liquids (serum, saliva, urine) tissues, including mammary tissue. We hypothesized that general, fat globules particular, contain significant numbers known limited novel miRNA species detectable with massively parallel...
In nonhuman primates, we previously demonstrated that a maternal high-fat diet (MHFD) induces fetal nonalcoholic fatty liver disease (NAFLD) and alters the metabolome. These changes are accompanied by altered acetylation of histone H3 (H3K14ac). However, mechanism behind this alteration in remains unknown. As SIRT1 is both lysine deacetylase crucial sensor cellular metabolism, hypothesized may be involved epigenomic alterations. Here show utero exposure to MHFD, but not obesity per se,...
Nuage are amorphous ultrastructural granules in the cytoplasm of male germ cells as divergent Drosophila, Xenopus, and Homo sapiens. Most nuage cytoplasmic ribonucleoprotein structures implicated diverse RNA metabolism including regulation PIWI-interacting (piRNA) synthesis by PIWI family (i.e., MILI, MIWI2, MIWI). MILI is prominent embryonic early post-natal also called germinal that often associated with mitochondria intermitochondrial cement. We find GASZ (Germ cell protein Ankyrin...
Developmental epigenetic changes, such as DNA methylation, have been recognized potential pathogenic factors in inflammatory bowel diseases, the hallmark of which is an exaggerated immune response against luminal microbes. A methyl-donor (MD) diet can modify methylation at select murine genomic loci during early development. The components MDs are routinely incorporated into prenatal human supplements. Therefore, we studied effects maternal MD supplementation on offspring colitis...
Small non-coding RNAs, such as microRNAs (miRNAs), are involved in diverse biological processes including organ development and tissue differentiation. Global disruption of miRNA biogenesis Dicer knockout mice disrupts early embryogenesis primordial germ cell formation. However, the role miRNAs folliculogenesis is poorly understood. In order to identify a full transcriptome set small RNAs expressed newborn (NB) ovary, we extracted RNA fraction from mouse NB ovary tissues subjected it massive...
We analyzed genome sequences from 6 baboon species and found evidence of ancient recent hybridization among divergent species.
The connection between intestinal micro-biota and host physiology is increasingly becoming recognized. details of this dynamic interaction, however, remain to be explored. Toll-like receptor 2 (Tlr2) important for its role in bacterial recognition, inflammation, obesity-related metabolic changes. Therefore, we sought determine the epigenomic metagenomic consequences Tlr2 deficiency colonic mucosa mice gain insights into biological pathways that shape interface gut mammalian host. Colonic...
Inflammatory bowel diseases (IBDs) are heterogeneous disorders with complex aetiology. Quantitative genetic studies suggest that only a small proportion of the disease variance observed in IBD is accounted for by variation, indicating potential role differential epigenetic regulation The aim this study was to assess genome-wide DNA methylation changes specifically associated ulcerative colitis (UC), Crohn's (CD) and activity.DNA quantified peripheral blood mononuclear cells (PBMCs) from 149...
Abstract Zika virus (ZIKV) is an emerging mosquito-borne ( Aedes genus) arbovirus of the Flaviviridae family. Although ZIKV has been predominately associated with a mild or asymptomatic dengue-like disease, its appearance in Americas accompanied by multi-fold increase reported incidence fetal microcephaly and brain malformations. The source mode vertical transmission from mother to fetus presumptively transplacental, although causal link explaining interval delay between maternal symptoms...