A5088190941- Advanced biosensing and bioanalysis techniques
- Single-cell and spatial transcriptomics
- CRISPR and Genetic Engineering
- Cell Image Analysis Techniques
- Advanced Fluorescence Microscopy Techniques
- Molecular Biology Techniques and Applications
- Genomics and Chromatin Dynamics
- RNA Interference and Gene Delivery
- Chromosomal and Genetic Variations
- Gene expression and cancer classification
- Health, Environment, Cognitive Aging
- Advanced Biosensing Techniques and Applications
- DNA and Nucleic Acid Chemistry
- DNA and Biological Computing
- Biosensors and Analytical Detection
- MicroRNA in disease regulation
- Cancer-related molecular mechanisms research
- Modular Robots and Swarm Intelligence
- Bioinformatics and Genomic Networks
- RNA and protein synthesis mechanisms
- Biomedical and Engineering Education
- SARS-CoV-2 detection and testing
- Cytomegalovirus and herpesvirus research
- Genomics and Phylogenetic Studies
Harvard University
2017-2024
Center for Systems Biology
2017-2022
Boston VA Research Institute
2022
Howard Hughes Medical Institute
2022
Inspire
2018
Transformative technologies are enabling the construction of three dimensional (3D) maps tissues with unprecedented spatial and molecular resolution. Over next seven years, NIH Common Fund Human Biomolecular Atlas Program (HuBMAP) intends to develop a widely accessible framework for comprehensively mapping human body at single-cell resolution by supporting technology development, data acquisition, detailed mapping. HuBMAP will integrate its efforts other funding agencies, programs,...
Chromosome organization is crucial for genome function. Here, we present a method visualizing chromosomal DNA at super-resolution and then integrating Hi-C data to produce three-dimensional models of chromosome organization. Using the microscopy methods OligoSTORM OligoDNA-PAINT, trace 8 megabases human 19, structures ranging in size from few kilobases over megabase. Focusing on regions that contribute compartments, discover distinct that, spite considerable variability, can predict whether...
Significance FISH enables researchers to visualize the subcellular distribution of RNA and DNA molecules in individual cells. The recent development methods employing probes composed synthetic oligonucleotides (oligos) allows tightly control aspects probe design such as binding energy genomic specificity. Although oligo are central many recently developed massively multiplexed superresolution imaging methods, no dedicated computational utility exists facilitate on genome-wide scale. Here, we...
Abstract We present Light-Seq, an approach for multiplexed spatial indexing of intact biological samples using light-directed DNA barcoding in fixed cells and tissues followed by ex situ sequencing. Light-Seq combines spatially targeted, rapid photocrosslinking barcodes onto complementary DNAs with a one-step stitching reaction to create pooled, indexed sequencing libraries. This enables selection multiple cell populations tissue full-transcriptome based on location, morphology or protein...
The SABER Technology Signal Amplification By Exchange Reaction (SABER) method is used for amplifying signal from multiplexed in situ fluorescence staining experiments. Developed by the Yin and Cepko labs at Harvard University Wyss Institute, technique uses Primer Reactions (PERs) to generate three-letter (A, T, C) concatemeric sequences bulk vitro reactions. These concatemers can then be hybridized fixed cells tissues act as scaffolds that localize fluorescent 'imager' strands. further...
There is increasing demand for single-stranded DNA (ssDNA) of lengths >200 nucleotides (nt) in synthetic biology, biological imaging and bionanotechnology. Existing methods to produce high-purity long ssDNA face limitations scalability, complexity protocol steps and/or yield. We present a rapid, high-yielding user-friendly method vitro production with up at least seven kilobases. Polymerase chain reaction (PCR) forward primer bearing methanol-responsive polymer generates tagged amplicon that...
Abstract We report the single-strand Recombinase Polymerase Amplification (ssRPA) method, which merges fast, isothermal amplification of RPA with subsequent rapid conversion double-strand DNA amplicon to single strands, and hence enables facile hybridization-based, high-specificity readout. demonstrate utility ssRPA for sensitive (4 copies per 50 µL reaction within 10 min, or 8 min) visual detection SARS-CoV-2 RNA spiked samples, as well clinical saliva nasopharyngeal swabs in VTM water, on...
Abstract Multiplexed fluorescence imaging is typically limited to three- five-plex on standard setups. Sequential methods based iterative labeling and enable practical higher multiplexing, but generally require a complex fluidic setup with several rounds of slow buffer exchange (tens minutes an hour for each step). We report the thermal-plex method, which removes steps provides fluidic-free, rapid sequential imaging. Thermal-plex uses simple DNA probes that are engineered fluoresce...
SUMMARY Fluorescent in situ hybridization (FISH) reveals the abun-dance and positioning of nucleic acid sequences fixed sam-ples can be combined with cell segmentation to produce a powerful single gene expression assay. However, it re-mains difficult label more than few targets visu-alize acids environments such as thick tissue using conventional FISH technologies. Recently, meth-ods have been developed for multiplexed amplification signals, yet remains challenging achieve high lev-els...
Abstract Super-resolution chromatin imaging techniques are emerging as powerful tools for spatial genomics. However, it remains challenging to visualize the genome on order of tens nanometers, a scale that can reveal rich structural detail about nuclear organization. Here we introduce Decode-PAINT, multiplexed in situ method, which leverages rapid diffraction-limited pre-decoding and DNA-PAINT (DNA points accumulation nanoscale topography). Decode-PAINT visualizes multiple discrete genomic...
Abstract Chromosome structure is thought to be crucial for proper functioning of the nucleus. Here, we present a method visualizing chromosomal DNA at super-resolution and then integrating Hi-C data produce three-dimensional models chromosome organization. We begin by applying Oligopaint probes single-molecule localization microscopy methods OligoSTORM OligoDNA-PAINT image 8 megabases human 19, discovering that regions contributing compartments can form distinct structures. Intriguingly, our...
Abstract Probing the molecular organization of tissues requires in situ analysis by microscopy. However current limitations multiplexing, sensitivity, and throughput collectively constitute a major barrier for comprehensive single-cell profiling proteins. Here, we report Immunostaining with Signal Amplification By Exchange Reaction (Immuno-SABER), rapid, highly multiplexed signal amplification method that simultaneously tackles these key challenges. Immuno-SABER utilizes DNA-barcoded...
We present a rapid, scalable, user-friendly method for in vitro production of high-purity single-stranded DNA (ssDNA) ranging from 89–3315 nucleotides length. PCR with forward primer bearing methanol-responsive polymer generates tagged amplicon that enables selective precipitation the modified strand under denaturing conditions. demonstrate recovered ssDNA can be used CRISPR/Cas9 homology-directed repair human cells, DNA-origami folding, and fluorescent situ hybridization.
Oligonucleotide (oligo)-based fluorescence in situ hybridization (FISH) has emerged as an important tool for the study of chromosome organization and gene expression been empowered by commercial availability highly complex pools oligos. However, a dedicated bioinformatic design utility yet to be created specifically purpose identifying optimal oligo FISH probe sequences on genome-wide scale. Here, we introduce OligoMiner, rapid robust computational pipeline genome-scale probes that affords...
We present Light-Seq, an approach for multiplexed spatial indexing of intact biological samples using light-directed DNA barcoding infixed cells and tissues followed by ex situ sequencing. Light-Seq combines spatially targeted, rapid photocrosslinking barcodes onto complementary DNAs in with a one-step stitching reaction to create pooled, indexed sequencing libraries. This enables selection multiple cell populations fixed tissue full-transcriptome based on location, morphology or protein...
We present Light-Seq, an approach for multiplexed spatial indexing of intact biological samples using light-directed DNA barcoding infixed cells and tissues followed by ex situ sequencing. Light-Seq combines spatially targeted, rapid photocrosslinking barcodes onto complementary DNAs in with a one-step stitching reaction to create pooled, indexed sequencing libraries. This enables selection multiple cell populations fixed tissue full-transcriptome based on location, morphology or protein...
We present Light-Seq, an approach for multiplexed spatial indexing of intact biological samples using light-directed DNA barcoding infixed cells and tissues followed by ex situ sequencing. Light-Seq combines spatially targeted, rapid photocrosslinking barcodes onto complementary DNAs in with a one-step stitching reaction to create pooled, indexed sequencing libraries. This enables selection multiple cell populations fixed tissue full-transcriptome based on location, morphology or protein...