A5061566377- Single-cell and spatial transcriptomics
- Cancer Genomics and Diagnostics
- Cell Image Analysis Techniques
- SARS-CoV-2 and COVID-19 Research
- Genetics and Neurodevelopmental Disorders
- COVID-19 Clinical Research Studies
- Bioinformatics and Genomic Networks
- CRISPR and Genetic Engineering
- Fungal Plant Pathogen Control
- Congenital heart defects research
- Pluripotent Stem Cells Research
- Neonatal Respiratory Health Research
- Gene Regulatory Network Analysis
- Sulfur-Based Synthesis Techniques
- Energy Load and Power Forecasting
- COVID-19 diagnosis using AI
- AI in cancer detection
- Plant Virus Research Studies
- Epigenetics and DNA Methylation
- Radical Photochemical Reactions
- Catalytic C–H Functionalization Methods
- Smart Grid and Power Systems
- Hippo pathway signaling and YAP/TAZ
- Mitochondrial Function and Pathology
- Immune cells in cancer
Cincinnati Children's Hospital Medical Center
2020-2025
Semiconductor Manufacturing International (China)
2024
Massachusetts General Hospital
2023-2024
Harvard University
2023-2024
University of Cincinnati
2020-2023
Zhejiang University
2018-2023
Tianjin Normal University
2020-2021
Hospital Research Foundation
2020
Sabin Vaccine Institute
2020
The human lung plays vital roles in respiration, host defense, and basic physiology. Recent technological advancements such as single-cell RNA sequencing genetic lineage tracing have revealed novel cell types enriched functional properties of existing lung. time has come to take a new census. Initiated by members the NHLBI-funded LungMAP Consortium aided experts biology community, we synthesized current data into comprehensive practical cellular census Identities normal are captured...
Abstract Accurate cell type identification is a key and rate-limiting step in single-cell data analysis. Single-cell references with comprehensive types, reproducible functionally validated identities, common nomenclatures are much needed by the research community for automated annotation, integration, sharing. Here, we develop computational pipeline utilizing LungMAP CellCards as dictionary to consolidate transcriptomic datasets of 104 human lungs 17 mouse lung samples construct reference...
Abstract Analysis of the human hematopoietic progenitor compartment is being transformed by single-cell multimodal approaches. Cellular indexing transcriptomes and epitopes sequencing (CITE-seq) enables coupled surface protein transcriptome profiling, thereby revealing genomic programs underlying states. To perform CITE-seq systematically on primary bone marrow cells, we used titrations with 266 antibodies (antibody-derived tags) machine learning to optimize a panel 132 antibodies....
Heterozygous NRXN1 deletions constitute the most prevalent currently known single-gene mutation associated with schizophrenia, and additionally predispose to multiple other neurodevelopmental disorders. Engineered heterozygous impaired neurotransmitter release in human neurons, suggesting a synaptic pathophysiological mechanism. Utilizing this observation for drug discovery, however, requires confidence its robustness validity. Here, we describe multicenter effort test generality of pivotal...
Abstract De novo mutations and copy number deletions in NRXN1 (2p16.3) pose a significant risk for schizophrenia (SCZ). It is unclear how impact cortical development cell type-specific manner disease background modulates these phenotypes. Here, we leveraged human pluripotent stem cell-derived forebrain organoid models carrying heterozygous isogenic SCZ patient genetic backgrounds conducted single-cell transcriptomic analysis over the course of brain from 3 weeks to 3.5 months. Intriguingly,...
An efficient protocol to direct sulfonamidation or sulfonation of electron-deficient alkenes for furnishing alkylsulfonamides sulfonates has been achieved.
An improved understanding of the human lung necessitates advanced systems models informed by an ever-increasing repertoire molecular omics, cellular imaging, and pathological datasets. To centralize standardize information across broad research efforts, we expanded LungMAP.net website into a new gateway portal. This portal connects spectrum networks, bulk single-cell multiomics data, diverse collection image data that span mammalian development disease. The are standardized species...
Plant diseases are seriously endangering agricultural production. The emergence of drug resistance has brought great challenges to the prevention and control plant diseases. There is an urgent need for new candidates. In this work, we achieved efficient synthesis pulmonarins A B in 64% 59% overall yield, respectively. Pulmonarins were found have good antiviral activities against tobacco mosaic virus (TMV) first time. series pulmonarin derivatives designed, synthesized, evaluated their...
Hepatoblastoma (HB) is the most common primary liver malignancy of childhood, and molecular investigations are limited effective treatment options for chemoresistant disease lacking. There a knowledge gap in investigation key driver cells HB tumor. Here we show single cell ribonucleic acid sequencing (scRNAseq) analysis human tumor, background liver, patient derived xenograft (PDX) to demonstrate gene expression patterns within tumor identify intratumor subtype heterogeneity define differing...
Abstract Quiescence cancer stem-like cells may play key roles in promoting tumor cell heterogeneity and recurrence for many tumors, including glioblastoma (GBM). Here we show that the protein acetyltransferase KAT5 is a regulator of transcriptional, epigenetic, proliferative impacting transitions into G0-like states GBM. activity suppresses emergence quiescent subpopulations with neurodevelopmental progenitor characteristics, while GBM (GSC) self-renewal through coordinately regulating E2F-...
Plant diseases caused by plant viruses and pathogens seriously affect the production storage of food crops. With emergence drug resistance, it is very difficult to control. Natural products are source new discovery. Here, natural product streptindole was found have good antiviral activity against tobacco mosaic virus (TMV) fungicidal activities 14 kinds phytopathogenic fungi. A series derivatives were designed, synthesized, evaluated for their activities. Compounds 4, 5, 11, 12c, 12d, 13d,...
Numerous studies have provided single-cell transcriptome profiles of host responses to SARS-CoV-2 infection. Critically lacking however is a data mine that allows users compare and explore cell gain insights develop new hypotheses. To accomplish this, we harmonized datasets from COVID-19 other control condition blood, bronchoalveolar lavage, tissue samples, derived compendium gene signature modules per type, subtype, clinical condition, compartment. We demonstrate approaches interacting...
Plant viruses and fungi are a serious threat to food security natural ecosystems. The efficient environment-friendly control methods urgently needed help safeguard such resources. Here, we achieved the synthesis of toad alkaloid dehydrobufotenine in eight steps with an overall yield 8% from 5-methoxyindole. A series derivatives were designed, synthesized, evaluated for their antiviral fungicidal activities systematically. It was found first time that these compounds have good anti-plant...
Abstract Single-cell spatial transcriptomics such as in-situ hybridization or sequencing technologies can provide subcellular resolution that enables the identification of individual cell identities, locations, and a deep understanding mechanisms. However, accurate segmentation annotation allows boundaries to be determined remains major challenge limits all above downstream insights. Current machine learning methods heavily rely on nuclei body staining, resulting in significant loss both...
The hydrosulfamoylation of diverse aryl olefins provides facile access to alkylsulfonamides. Here we report a novel protocol utilizing radical-mediated addition and thiol-assisted strategy achieve the styrenes in modest excellent yields under mild economic reaction conditions. methodology was found provide an efficient convenient approach for synthesis anti-migraine drug naratriptan it also can be used late-stage functionalization natural products or medicines.
An advanced functional understanding of omics data is important for elucidating the design logic physiological processes in plants and effectively controlling desired traits plants. We present latest versions Predicted Arabidopsis Interactome Resource (PAIR) gene set linkage analysis (GSLA) tool, which enable interpretation an observed transcriptomic change (differentially expressed genes [DEGs]) (Arabidopsis thaliana) with respect to its impact biological processes. PAIR version 5.0...
Abstract Cells and tissues respond to perturbations in multiple ways that can be sensitively reflected the alterations of gene expression. Current approaches finding quantifying effects on cell-level responses over time disregard temporal consistency identifiable programs. To leverage occurrence these patterns for perturbation analyses, we developed CellDrift (https://github.com/KANG-BIOINFO/CellDrift), a generalized linear model-based functional data analysis method is capable identifying...
Loss-of-function (LOF) mutations in CASK cause severe developmental phenotypes, including microcephaly with pontine and cerebellar hypoplasia, X-linked intellectual disability, autism. Unraveling the pathological mechanisms of CASK-related disorders has been challenging owing to limited human cellular models study dynamic roles this molecule during neuronal maturation synapse development. Here, we investigate cell-autonomous functions cortical excitatory induced neurons (iNs) generated from...
ABSTRACT Accurate cell type identification is a key and rate-limiting step in single data analysis. Single references with comprehensive types, reproducible functional validated identities, common nomenclatures are much needed by the research community to optimize automated annotation facilitate integration, sharing, collaboration. In present study, we developed novel computational pipeline utilize LungMAP CellCards as dictionary consolidate single-cell transcriptomic datasets of 104 human...
Abstract Using a Systems Biology approach, we integrated genomic, transcriptomic, proteomic, and molecular structure information to provide holistic understanding of the COVID-19 pandemic. The expression data analysis Renin Angiotensin System indicates mild nasal, oral or throat infections are likely that gastrointestinal tissues common primary target SARS-CoV-2. Extreme symptoms in lower respiratory system result from secondary-infection possibly by comorbidity-driven upregulation ACE2...
Summary Hypoplastic left heart syndrome (HLHS) is a severe congenital defect with 30% mortality from failure (HF) in the first year of life, but why only some patients suffer early-HF and its cause remain unknown. Modeling using induced pluripotent stem cell-derived cardiomyocytes (iPSC-CM) showed patient iPSC-CM have increased apoptosis, redox stress, failed antioxidant response. This was associated mitochondrial permeability transition pore (mPTP) opening, hyperfusion respiration defects....