AI
for Brain Health
We are recruiting neuroscience and bioinformatics students to develop genomics, AI methods, and animal and brain organoid models for delaying brain aging. Both graduate and undergraduate students are welcome to apply.
Sheng Zhong completed his training at Peking University and Stanford University, earning his Ph.D. from Harvard University. He is currently a Professor at the University of California, San Diego, where he directs the Center for Liquid Biopsy Research, serves as the organizational hub leader for the NIH-funded 4D Nucleome (4DN) Program, and leads a Transformative Technology Development team within the Human BioMolecular Atlas Program (HuBMAP). Sheng's work has been recognized with the NIH Director's Pioneer Award and the NIDDK Catalyst Award. He is a fellow of both the American Institute for Medical and Biological Engineering (AIMBE) and the Asia-Pacific Artificial Intelligence Association (AAIA). Nine of his former trainees are contributing to science and engineering as tenure-track faculty.
Our lab has uncovered a critical causal pathway underlying sporadic Alzheimer's disease and identified a promising therapeutic compound (Cell, 2025).
We invented MUSIC (Multi-Nucleic Acid Interaction Mapping in Single Cell), a technique enabling simultaneous profiling of multiplex chromatin interactions, gene expression, and RNA-chromatin associations within a single nucleus (Nature, 2024). Applying MUSIC to human brain tissues, we discovered distinct chromatin conformation signatures associated with aging and Alzheimer’s disease.
Our team developed PROPER-seq (Protein-Protein Interaction by Sequencing), a method to massively map protein-protein interactions (Molecular Cell, 2021), and PRIM-seq for comprehensive mapping of protein-RNA interactions (Nature Biotechnology, in press).
We pioneered MARIO (Mapping RNA Interactome in vivo) technology, facilitating large-scale identification of RNA-RNA interactions directly from human tissues (Nature Communications, 2016). Additionally, we invented MARGI (Mapping RNA-Genome Interactions), a technique revealing thousands of chromatin-associated RNAs (caRNAs) and their genomic attachment sites (Current Biology, 2017; Nature Protocols, 2019; eLife, 2024). Using MARGI, we and our collaborators elucidated caRNA roles in modulating 3-dimensional genome architecture (Nature Communications, 2023; Molecular Cell, 2023), regulating gene expression (Nature Communications, 2020, 2025), mediating mitochondrial-to-nuclear signaling (eLife, 2024), and driving fusion RNA biogenesis (PNAS, 2019a). Collectively, this work introduced the concept of caRNAs as key epigenomic regulators (Trends in Genetics, 2018).
We developed SILVER-seq, a method for extracellular RNA (exRNA) sequencing from ultra-small volumes of liquid biopsies. This method creates a foundation for future diagnostic trials using finger-prick blood tests for early cancer recurrence monitoring (PNAS, 2019b). Our team identified and validated exRNA of PHGDH as a reliable biomarker for early Alzheimer's detection (Current Biology, 2020; Cell Metabolism, 2022) and demonstrated exRNA’s predictive capacity for embryo quality in human IVF culture media (Cell Genomics, 2024).
We independently discovered cell-surface RNAs—nuclear-encoded RNAs stably attached to the cell surface—and provided the earliest evidence for their role in mediating cell-cell interactions (Genome Biology, 2020).
Our research revealed that the earliest cell-fate decisions in mouse embryos occur earlier than the widely accepted 8-cell stage (Genome Research, 2014). Furthermore, we introduced Rainbow-seq, combining cell lineage tracing and single-cell RNA sequencing into a single streamlined experiment (iScience, 2018b).
Our findings highlighted the essential regulatory roles of transposons in mammalian genomes, revealing their necessity in preimplantation embryonic development across species, including humans (Genome Research, 2010). This transformative discovery was featured in Nature's "Hidden Differences," emphasizing how transposons alter gene regulation by "jumping" in front of genes (Nature, 2010). We further established the feasibility of annotating cis-regulatory sequences through cross-species epigenomic comparisons (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
