Aldrin Kay‐Yuen Yim
A5033750303- Single-cell and spatial transcriptomics
- Genomics and Phylogenetic Studies
- Neurogenesis and neuroplasticity mechanisms
- Immune cells in cancer
- Neuroinflammation and Neurodegeneration Mechanisms
- RNA modifications and cancer
- Mycobacterium research and diagnosis
- Cancer-related molecular mechanisms research
- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- Glioma Diagnosis and Treatment
- Bacteriophages and microbial interactions
- Allergic Rhinitis and Sensitization
- Ear and Head Tumors
- Gene expression and cancer classification
- Advanced biosensing and bioanalysis techniques
- Cancer Genomics and Diagnostics
- Autophagy in Disease and Therapy
- Immune Cell Function and Interaction
- Vascular Malformations Diagnosis and Treatment
- Antibiotic Resistance in Bacteria
- Plant Molecular Biology Research
- Endoplasmic Reticulum Stress and Disease
- Cell Image Analysis Techniques
- Plant nutrient uptake and metabolism
Washington University in St. Louis
2018-2024
James S. McDonnell Foundation
2024
Chinese University of Hong Kong
2007-2018
Using a whole-genome-sequencing approach to explore germplasm resources can serve as an important strategy for crop improvement, especially in investigating wild accessions that may contain useful genetic have been lost during the domestication process. Here we sequence and assemble draft genome of soybean construct recombinant inbred population genotyping-by-sequencing phenotypic analyses identify multiple QTLs relevant traits interest agriculture. We use combination de novo sequencing data...
Abstract Neutrophils are implicated in multiple homeostatic and pathological processes, but whether functional diversity requires discrete neutrophil subsets is not known. Here, we apply single-cell RNA sequencing to neutrophils from normal inflamed mouse tissues. Whereas conventional clustering yields alternative organizational structures, diffusion mapping plus velocity discloses a single developmental spectrum, ordered chronologically. Termed here neutrotime, this spectrum extends...
Abstract Comprehensive whole-genome structural variation detection is challenging with current approaches. With diploid cells as DNA source and the presence of numerous repetitive elements, short-read sequencing cannot be used to detect efficiently. In this report, we show that genome mapping long, fluorescently labeled molecules imaged on nanochannel arrays can for without sequencing. While haplotyping not achieved, local phasing (across >150-kb regions) routine, from parental...
Molecular and behavioral responses to opioids are thought be primarily mediated by neurons, although there is accumulating evidence that other cell types play a prominent role in drug addiction. To investigate cell-type-specific opioid responses, we performed single-cell RNA sequencing (scRNA-seq) of the nucleus accumbens mice following acute morphine treatment. Differential expression analysis uncovered unique morphine-dependent transcriptional oligodendrocytes astrocytes. We examined...
To obtain a comprehensive understanding of transcriptomic reprogramming under salt stress, we performed whole-transcriptome sequencing on the leaf and root soybean seedlings subjected to treatment in time-course experiment (0, 1, 2, 4, 24, 48 hr). This time series dataset enabled us identify important hubs connections gene expressions. We highlighted analysis phytohormone signaling pathways their possible crosstalks. Differential expressions were also found among those genes involved carbon...
Abstract Whereas microglia are recognized as fundamental players in central nervous system (CNS) development and function, much less is known about macrophages of the peripheral (PNS). Here, by comparing gene expression across neural conventional tissue-resident macrophages, we identified transcripts that were shared among resident well selectively enriched PNS macrophages. Remarkably, constitutively expressed genes previously to be upregulated activated during aging, neurodegeneration, or...
Abstract Vestibular schwannomas (VS) are benign tumors that lead to significant neurologic and otologic morbidity. How VS heterogeneity the tumor microenvironment (TME) contribute pathogenesis remains poorly understood. In this study, we perform scRNA-seq on 15 VS, with paired scATAC-seq ( n = 6) exome sequencing 12). We identify diverse Schwann cell (SC), stromal, immune populations in TME find repair-like MHC-II antigen-presenting SCs associated myeloid infiltrate, implicating a nerve...
Background Cell free RNA (cfRNA) contains transcript fragments from multiple cell types, making it useful for cancer detection in clinical settings. However, the pathophysiological origins of cfRNAs plasma colorectal (CRC) patients remain unclear. Methods To identify tissue-specific contributions transcriptomic profile, we used a published single-cell transcriptomics profile to deconvolute type abundance among paired samples CRC who underwent tumor-ablative surgery. We further validated...
Multidrug-resistant Acinetobacter baumannii, a major hospital-acquired pathogen, is serious health threat and poses great challenge to healthcare providers. Although there have been many genomic studies on the evolution antibiotic resistance of this species, very limited transcriptome its responses antibiotics. We conducted comparative transcriptomic study 12 strains with different growth rates profiles, including 3 fast-growing pan-drug-resistant strains, under separate treatment...
Axon loss contributes to many common neurodegenerative disorders. In healthy axons, the axon survival factor NMNAT2 inhibits SARM1, central executioner of programmed degeneration. We identified 2 rare missense variants in brothers afflicted with a progressive neuropathy syndrome. The polymorphisms resulted amino acid substitutions V98M and R232Q, which reduced NAD+-synthetase activity. generated mouse model mirror human syndrome found that Nmnat2V98M/R232Q compound-heterozygous CRISPR mice...
The 20 canonical amino acids of the genetic code have been invariant over 3 billion years biological evolution. Although various aminoacyl-tRNA synthetases can charge their cognate tRNAs with acid analogs, there has no known displacement any from code. Experimental departure this universal protein alphabet comprising was first achieved in mutants Bacillus subtilis QB928 strain, which after serial selection and mutagenesis led to HR23 strain that could use 4-fluorotryptophan (4FTrp) but not...
RNA-sequencing is a powerful tool in studying RNomics. However, the highly abundance of ribosomal RNAs (rRNA) and transfer RNA (tRNA) have predominated sequencing reads, thereby hindering study lowly expressed genes. Therefore, rRNA depletion prior to often performed order preserve subtle alteration gene expression especially those at relatively low levels. One commercially available methods use DNA or probes hybridize target RNAs. there always concern with non-specific binding unintended...
Small RNAs, including microRNAs (miRNAs) and phased small interfering RNAs (phasiRNAs; from PHAS loci), play key roles in plant development. Cultivated soybean, Glycine max, contributes a great deal to food production, but, compared its wild kin, soja, it may lose some genetic information during domestication. In this work, we analyzed the sRNA profiles of different tissues both cultivated (C08) soybeans (W05) at three stages A total 443 known miRNAs 15 novel showed varying abundances...
ABSTRACT Axon loss contributes to many common neurodegenerative disorders. In healthy axons, the axon survival factor NMNAT2 inhibits SARM1, central executioner of programmed degeneration. We identified two rare missense variants in brothers afflicted with a progressive neuropathy syndrome. The polymorphisms result amino acid substitutions, V98M and R232Q, which reduce NAD + -synthetase activity. generated mouse model human syndrome found that Nmnat2 / R232Q compound-heterozygous CRISPR mice...
Genetic testing for neurodegenerative diseases (NDs) is highly challenging because of genetic heterogeneity and overlapping manifestations. Targeted-gene panels (TGPs), coupled with next-generation sequencing (NGS), can facilitate the profiling a large repertoire ND-related genes. Due to technical limitations inherent in NGS TGPs, short tandem repeat (STR) variations are often ignored. However, STR expansions known cause such NDs as Huntington's disease spinocerebellar ataxias type 3 (SCA3)....
RNA sequencing (RNA-seq) measures gene expression levels and permits splicing analysis. Many existing aligners are capable of mapping millions reads onto a reference genome. For that can be mapped to multiple positions along the genome (multireads), these may either randomly assign them location, or discard altogether. Either way could bias downstream analyses. Meanwhile, challenges remain in alignment spanning across splice junctions. Existing splicing-aware rely on read-count method...
Introduction: Sporadic vestibular schwannomas (VS) are benign tumors but can lead to significant neurologic and otologic morbidity. The treatment for growing or symptomatic VS consists of radiosurgery open surgical resection, both which associated with At present, the underlying tumor pathophysiology, particularly regarding microenvironment (TME) its role in pathogenesis, remains poorly understood, making it challenging devise alternative strategies VS.