A5040973022- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- Epigenetics and DNA Methylation
- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Vitamin D Research Studies
- Genetic diversity and population structure
- Bone health and osteoporosis research
- Tryptophan and brain disorders
- Schizophrenia research and treatment
- Bat Biology and Ecology Studies
- Pharmacological Effects and Toxicity Studies
- Animal Genetics and Reproduction
- Cancer-related molecular mechanisms research
- Acute Ischemic Stroke Management
- Neuroinflammation and Neurodegeneration Mechanisms
- Cerebrovascular and Carotid Artery Diseases
- Neuroscience and Music Perception
- Bioinformatics and Genomic Networks
- Diet and metabolism studies
- Marine animal studies overview
- Stroke Rehabilitation and Recovery
- Evolution and Paleontology Studies
Harbin Institute of Technology
2025
University of Massachusetts Chan Medical School
2019-2024
Bozhou People's Hospital
2024
Children's Hospital
2024
Wenzhou City People's Hospital
2023-2024
Weifang People's Hospital
2023
Zoological Society of San Diego
2023
University of California, Santa Cruz
2023
Harvard University
2023
UMass Memorial Medical Center
2022
Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes 240 species, we identify bases that, when mutated, are likely affect fitness and alter disease risk. At least 332 million (~10.7%) in human genome unusually conserved across species (evolutionarily constrained) relative neutrally evolving repeats, 4552 ultraconserved elements nearly perfectly conserved. Of 101 significantly constrained single bases, 80% outside protein-coding exons half...
Annotating coding genes and inferring orthologs are two classical challenges in genomics evolutionary biology that have traditionally been approached separately, limiting scalability. We present TOGA (Tool to infer Orthologs from Genome Alignments), a method integrates structural gene annotation orthology inference. implements different paradigm orthologous loci, improves ortholog detection of conserved compared with state-of-the-art methods, handles even highly fragmented assemblies. scales...
The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis genetic variation across an alignment 241 mammal genome assemblies, addressing prior concerns regarding limited genomic sampling species. compared neutral genome-wide phylogenomic signals using concatenation coalescent-based approaches, interrogated chromosomes, analyzed extensive catalogs structural variants. Interordinal...
Thousands of genomic regions have been associated with heritable human diseases, but attempts to elucidate biological mechanisms are impeded by an inability discern which positions functionally important. Evolutionary constraint is a powerful predictor function, agnostic cell type or disease mechanism. Single-base phyloP scores from 240 mammals identified 3.3% the genome as significantly constrained and likely functional. We compared annotation, association studies, copy-number variation,...
We examined transposable element (TE) content of 248 placental mammal genome assemblies, the largest de novo TE curation effort in eukaryotes to date. found that although mammals resemble one another total and diversity, they show substantial differences with regard recent accumulation. This includes multiple expansion quiescence events across mammalian tree. Young TEs, particularly long interspersed elements, drive increases size, whereas DNA transposons are associated smaller genomes....
Human accelerated regions (HARs) are conserved genomic loci that evolved at an rate in the human lineage and may underlie human-specific traits. We generated HARs chimpanzee with automated pipeline alignment of 241 mammalian genomes. Combining deep learning chromatin capture experiments neural progenitor cells, we discovered a significant enrichment topologically associating domains containing variants change three-dimensional (3D) genome organization. Differential gene expression between...
Understanding the regulatory landscape of human genome is a long-standing objective modern biology. Using reference-free alignment across 241 mammalian genomes produced by Zoonomia Consortium, we charted evolutionary trajectories for 0.92 million candidate cis-regulatory elements (cCREs) and 15.6 transcription factor binding sites (TFBSs). We identified 439,461 cCREs 2,024,062 TFBSs under constraint. Genes near constrained perform fundamental cellular processes, whereas genes...
Species persistence can be influenced by the amount, type, and distribution of diversity across genome, suggesting a potential relationship between historical demography resilience. In this study, we surveyed genetic variation single genomes 240 mammals that compose Zoonomia alignment to evaluate how effective population size (
Protein-coding differences between species often fail to explain phenotypic diversity, suggesting the involvement of genomic elements that regulate gene expression such as enhancers. Identifying associations enhancers and phenotypes is challenging because enhancer activity can be tissue-dependent functionally conserved despite low sequence conservation. We developed Tissue-Aware Conservation Inference Toolkit (TACIT) associate candidate with species' using predictions from machine learning...
Conserved genomic sequences disrupted in humans may underlie uniquely human phenotypic traits. We identified and characterized 10,032 human-specific conserved deletions (hCONDELs). These short (average 2.56 base pairs) are enriched for brain functions across genetic, epigenomic, transcriptomic datasets. Using massively parallel reporter assays six cell types, we discovered 800 hCONDELs conferring significant differences regulatory activity, half of which enhance rather than disrupt function....
Abstract Identifying transcriptional enhancers and their target genes is essential for understanding gene regulation the impact of human genetic variation on disease 1–6 . Here we create evaluate a resource >13 million enhancer-gene regulatory interactions across 352 cell types tissues, by integrating predictive models, measurements chromatin state 3D contacts, large-scale perturbations generated ENCODE Consortium 7 We first systematic benchmarking pipeline to compare assembling dataset...
Inflammatory cytokines are fundamental mediators of the organismal response to injury, infection, or other harmful stimuli. To elucidate early and mostly direct transcriptional signatures inflammatory cytokines, we profiled all immunologic cell types by RNAseq after systemic exposure IL1β, IL6, TNFα. Our results revealed a significant overlap in responses, with broad divergence between myeloid lymphoid cells, but very few cell-type-specific responses. Pathway motif analysis identified...
Abstract The morphologically and functionally distinct cell types of a multicellular organism are maintained by their unique epigenomes gene expression programs. Phase III the ENCODE Project profiled 66 mouse across twelve tissues at daily intervals from embryonic day 11.5 to birth. Applying ChromHMM algorithm these epigenomes, we annotated eighteen chromatin states with characteristics promoters, enhancers, transcribed regions, repressed quiescent regions. Our integrative analyses delineate...
Decrypting the rearrangements that drive mammalian chromosome evolution is critical to understanding molecular bases of speciation, adaptation, and disease susceptibility. Using 8 scaffolded 26 chromosome-scale genome assemblies representing 23/26 mammal orders, we computationally reconstructed ancestral karyotypes syntenic relationships at 16 nodes along phylogeny. Three different reference genomes (human, sloth, cattle) phylogenetically distinct superorders were used assess bias in expand...
Vocal production learning ("vocal learning") is a convergently evolved trait in vertebrates. To identify brain genomic elements associated with mammalian vocal learning, we integrated genomic, anatomical, and neurophysiological data from the Egyptian fruit bat (
Graphene oxide (GO) is an attractive alternative for large-scale production of graphene, but its general structure still under debate due to complicated nonstoichiometric nature. Here we perform a set femtosecond pump–probe experiments on as-synthesized GO extrapolate structural information in situ. Remarkably, it observed that, these highly oxidized samples, the ultrafast graphene-like dynamics intrinsic pristine graphene completely dominant over wide energy region and can be modified by...
Inflammation plays an important role in stroke. Many inflammatory markers peripheral blood are proved to be associated with stroke severity or prognosis. But few comprehensive models scales evaluate the post-stroke depression (PSD) have been reported. In this study, we aimed compare level of systemic inflammation between PSD and non-PSD patients explore association these PSD.Totally, 432 ischemic were consecutively enrolled study received 1 month follow-up. We used 17-Hamilton Rating Scale...
Transcriptomic analyses have revealed an unexpected complexity in the eukaryote transcriptome, which includes not only protein-coding transcripts but also expanding catalog of noncoding RNAs (ncRNAs). Diverse coding and (ncRNAs) perform functions through interaction with each other various cellular processes. In this project, we developed RAID (http://www.rna-society.org/raid), RNA-associated (RNA–RNA/RNA–protein) database. intends to provide scientific community all-in-one resources for...
Sulfate-reducing bacteria (SRB) are anaerobic microorganisms that use sulfate as a terminal electron acceptor for the oxidation of organic compounds or H2. These organisms can cause serious problem in, example, offshore oil industry, due to production sulfide. Thus, it is fundamental and practical importance identify potent selective inhibitors SRB. In this study, neutral red was identified previously unrecognized inhibitor SRB, with several orders magnitude higher potency than most commonly...
Over 20 months, we prospectively assessed the yield of cultures for Salmonella, Shigella, and Campylobacter spp. from adults children. In first 10 53% (567 1,097) specimens were patients who had been in hospital > 3 days. Overall, only 2.6% (29 contained pathogens, all < or = second days not cultured unless special reasons existed. Thirty percent (368 1,229) rejected. Concurrently, 7.5% (51 677) stool children positive. Only one positive specimen came a child Neither consistency nor...
Enhancers are distal cis-regulatory elements that modulate gene expression. They depleted of nucleosomes and enriched in specific histone modifications; thus, calling DNase-seq mark ChIP-seq peaks can predict enhancers. We evaluated nine peak-calling algorithms for predicting enhancers validated by transgenic mouse assays. DNase H3K27ac were consistently more predictive than H3K4me1/2/3 H3K9ac peaks. DFilter Hotspot2 the best peak callers, while HOMER, MUSIC, MACS2, F-seq callers. observed...
Major depressive disorder is an ordinary mental disorder, and suicide considered to be a major concern among patients with MDD. Previous studies focused on the relationship between attempts metabolism in elderly MDD, while ignore young people. The aim of this study find potential MDD way prevent ultimately reduce MDD.Cross-sectional design was employed study.740 aged 18 45 years old had been consecutively recruited 2011 2017, 128 whom attempts. Their serum samples used monitor fasting blood...