We are recruiting bioinformatics, biotechnology, molecular biology, and neuroscience students to co-develop pioneering single-cell and spatial multiomics technologies, brain organoid models, animal models, analyze human brains. Both graduate and undergraduate students are welcome to apply.
Sheng Zhong is a Professor of Bioengineering at UC San Diego. He received an NIH Director's Pioneer Award and an NIDDK Catalyst Award. He serves as the director for UCSD Center for Liquid Biopsy Research and the director for the organizational hub of the NIH funded 4D Nucleome (4DN) Program. He leads a Transformative Technology Development team for the Human BioMolecular Atlas Program (HuBMAP). He is a fellow of American Institute for Medical and Biological Engineering (AIMBE) and a fellow of Asia-Pacific Artificial Intelligence Association (AAIA). Nine of his previous trainees are contributing to science on tenure-track faculty positions.
Our lab invented the MUSIC (Multi-Nucleic Acid Interaction Mapping in Single Cell) technique for concurrent profiling of multiplex chromatin interactions, gene expression, and RNA-chromatin associations within a single nucleus (Nature, 2024). Applying MUSIC to human brain specimens, we reported chromatin conformation signatures of ageing and Alzheimer's disease.
We invented the MARIO (Mapping RNA interactome in vivo) technology to massively reveal RNA-RNA interactions from human tissue (Nature Comm, 2016) and the MARGI (Mapping RNA-Genome Interactions) technology for revealing thousands of chromatin-associated RNAs (caRNA) and their respective genomic interaction sites (Current Biology, 2017; Nature Protocols, 2019; eLife, 2024). Leveraging MARGI, our collaborators and we characterized caRNA’s roles in modulating the 3-dimensional genome organization (Nature Comm, 2023; Molecular Cell, 2023), regulating gene expression during the progression of diabetes (Nature Comm, 2020), mediating mitochondrial-to-nuclear signaling (eLife, 2024), and the biogenesis of fusion RNAs (PNAS 2019a). These results inspired the idea that caRNA is a layer of the epigenome (Trends Genetics, 2018).
We developed SILVER-seq for extracellular RNA (exRNA) sequencing from ultra-small volumes of liquid biopsy, solidifying a basis for future in vitro diagnostic trials using finger-prick blood for monitoring cancer recurrence (PNAS, 2019b). We identified and validated the exRNA of PHGDH as a biomarker for early detection of Alzheimer's disease (Current Biology, 2020; Cell Metabolism, 2022). We demonstrated exRNA in human IVF culture media predicts embryo quality (Cell Genomics, 2024).
We contributed to discovering the nuclear-encoded RNAs that are stably attached to the cell surface and exposed to the extracellular space, called membrane-associated extracellular RNAs (maxRNAs). maxRNAs are functional components of the cell surface and mediate cell-cell interactions (Genome Biology, 2020).
We contributed to discovering that the earliest cell fate decision in mouse is made sooner than the commonly thought 8-cell stage (Genome Res, 2014). Our Rainbow-seq technology combined tracing of cell division history and single-cell RNA sequencing into one experiment (iScience 2018b).
We contributed to revealing that transposons are indispensable regulatory sequences in the mammalian genomes. Species-specific transposons are required for preimplantation embryonic development in humans and other mammals (Genome Res, 2010). Nature highlighted this discovery as "Hidden Differences," reporting that "transposons or 'jumping genes' had hopped in front of the genes, changing their regulation" (Nature, 2010). We contributed to establishing the proof-of-principle that cis-regulatory sequences can be annotated by cross-species epigenomic comparison (Cell, 2012).
Complete list of publications on Google Scholar, NCBI
Build your own genome browser website.
Internet search for genomic big data.
Analyze RNA interaction data.
Comparative Epigenome Browser.
Sequence mapping on personal genome.
Genome annotation using temporal epigenomic data.
Entry to NIH 4D Nucleome network.
Fracklin Antonio Hall 4301, University of California San Diego, 9500 Gilman Dr. #0433, La Jolla, CA 92093 - 0433