Beyond quantification: in situ analysis of transcriptome and pre-mRNA alternative splicing at the nanoscale

Optical Clearing Delivers Ultrasensitive Hyperspectral Dark-Field Imaging for Single-Cell Evaluation

(2016) Yi Cui et al.   ACS Nano

Non-fluorescent quantification of single mRNA with transient absorption microscopy

(2016) Jing Liu et al.   Nanoscale

Super-resolution imaging reveals distinct chromatin folding for different epigenetic states

(2016) Alistair N. Boettiger et al.   NATURE

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

(2016) P. L. Stahl et al.   SCIENCE

Single-Cell Quantification of Cytosine Modifications by Hyperspectral Dark-Field Imaging

(2015) Xiaolei Wang et al.   ACS Nano

Mechanisms and Regulation of Alternative Pre-mRNA Splicing

(2015) Yeon Lee et al.   Annual Review of Biochemistry

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Single-cell screening and quantification of transcripts in cancer tissues by second-harmonic generation microscopy

(2015) Jing Liu et al.   JOURNAL OF BIOMEDICAL OPTICS

The Technology and Biology of Single-Cell RNA Sequencing

(2015) Aleksandra A. Kolodziejczyk et al.   MOLECULAR CELL

Strategies for enhancing the sensitivity of plasmonic nanosensors

(2015) Longhua Guo et al.   Nano Today

Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping

(2015) Jennifer B Treweek et al.   Nature Protocols

Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues

(2015) Je Hyuk Lee et al.   Nature Protocols

Dissecting the behavior and function of MBD3 in DNA methylation homeostasis by single-molecule spectroscopy and microscopy

(2015) Yi Cui et al.   NUCLEIC ACIDS RESEARCH

Quantification and real-time tracking of RNA in live cells using Sticky-flares

(2015) William E. Briley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Vibrational spectroscopic imaging of living systems: An emerging platform for biology and medicine

(2015) J.-X. Cheng et al.   SCIENCE

Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes

(2015) Brian J. Beliveau et al.   Nature Communications

Highly sensitive transient absorption imaging of graphene and graphene oxide in living cells and circulating blood

(2015) Junjie Li et al.   Scientific Reports

Functional roles of alternative splicing factors in human disease

(2015) Benjamin Cieply et al.   Wiley Interdisciplinary Reviews-RNA

Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution

(2015) Moran N Cabili et al.   GENOME BIOLOGY

Fast Vibrational Imaging of Single Cells and Tissues by Stimulated Raman Scattering Microscopy

(2014) Delong Zhang et al.   ACCOUNTS OF CHEMICAL RESEARCH

Second Harmonic Super-resolution Microscopy for Quantification of mRNA at Single Copy Sensitivity

(2014) Jing Liu et al.   ACS Nano

Quantitative real-time kinetics of optogenetic proteins CRY2 and CIB1/N using single-molecule tools

(2014) Yi Cui et al.   ANALYTICAL BIOCHEMISTRY

Single-Cell Phenotyping within Transparent Intact Tissue through Whole-Body Clearing

(2014) Bin Yang et al.   CELL

Genome-wide RNA Tomography in the Zebrafish Embryo

(2014) Jan Philipp Junker et al.   CELL

Detection and quantification of alternative splice sites in Arabidopsis genes AtDCL2 and AtPTB2 with highly sensitive surface enhanced Raman spectroscopy (SERS) and gold nanoprobes

(2014) Ulhas S. Kadam et al.   FEBS LETTERS

RNA sequencing in situ

(2014) Paul Ginart et al.   NATURE BIOTECHNOLOGY

Single-cell in situ RNA profiling by sequential hybridization

(2014) Eric Lubeck et al.   NATURE METHODS

Quantitative imaging of single mRNA splice variants in living cells

(2014) Kyuwan Lee et al.   Nature Nanotechnology

Spatially resolved transcriptomics and beyond

(2014) Nicola Crosetto et al.   NATURE REVIEWS GENETICS

In the right place at the right time: visualizing and understanding mRNA localization

(2014) Adina R. Buxbaum et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Imaging of Endogenous Messenger RNA Splice Variants in Living Cells Reveals Nuclear Retention of Transcripts Inaccessible to Nonsense-Mediated Decay in Arabidopsis

(2014) J. Gohring et al.   PLANT CELL

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

Inside single cells: quantitative analysis with advanced optics and nanomaterials

(2014) Yi Cui et al.   Wiley Interdisciplinary Reviews-Nanomedicine and Nanobiotechnology

Nanoscopy for nanoscience: how super-resolution microscopy extends imaging for nanotechnology

(2014) Sam A. Johnson   Wiley Interdisciplinary Reviews-Nanomedicine and Nanobiotechnology

SERS Nanosensors and Nanoreporters: Golden Opportunities in Biomedical Applications

(2014) Tuan Vo-Dinh et al.   Wiley Interdisciplinary Reviews-Nanomedicine and Nanobiotechnology

Kinetic competition during the transcription cycle results in stochastic RNA processing

(2014) Antoine Coulon et al.   eLife

Modern Raman Imaging: Vibrational Spectroscopy on the Micrometer and Nanometer Scales

(2013) Lothar Opilik et al.   Annual Review of Analytical Chemistry

Review: Alternative Splicing (AS) of Genes As An Approach for Generating Protein Complexity

(2013) Bishakha Roy et al.   CURRENT GENOMICS

mRNA on the Move: The Road to Its Biological Destiny

(2013) Carolina Eliscovich et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

In situ sequencing for RNA analysis in preserved tissue and cells

(2013) Rongqin Ke et al.   NATURE METHODS

Second harmonic generation correlation spectroscopy for single molecule experiments

(2013) Jing Liu et al.   OPTICS EXPRESS

Spherical Nucleic Acid Nanoparticle Conjugates as an RNAi-Based Therapy for Glioblastoma

(2013) S. A. Jensen et al.   Science Translational Medicine

Surface-enhanced Raman scattering imaging using noble metal nanoparticles

(2013) Andrew J. Wilson et al.   Wiley Interdisciplinary Reviews-Nanomedicine and Nanobiotechnology

Live-Cell Visualization of Pre-mRNA Splicing with Single-Molecule Sensitivity

(2013) Robert M. Martin et al.   Cell Reports

Function of alternative splicing

(2012) Olga Kelemen et al.   GENE

Spherical Nucleic Acids

(2012) Joshua I. Cutler et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome

(2012) Zhiyu Peng et al.   NATURE BIOTECHNOLOGY

Single-cell systems biology by super-resolution imaging and combinatorial labeling

(2012) Eric Lubeck et al.   NATURE METHODS

The Local Transcriptome in the Synaptic Neuropil Revealed by Deep Sequencing and High-Resolution Imaging

(2012) Iván J. Cajigas et al.   NEURON

Surface-enhanced Raman spectroscopy at single-molecule scale and its implications in biology

(2012) Y. Wang et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

DNA-based plasmonic nanoarchitectures: from structural design to emerging applications

(2012) Yi Chen et al.   Wiley Interdisciplinary Reviews-Nanomedicine and Nanobiotechnology

DNA−Gold Nanoparticle Reversible Networks Grown on Cell Surface Marker Sites: Application in Diagnostics

(2011) Kyuwan Lee et al.   ACS Nano

Single-Molecule Imaging of Transcriptionally Coupled and Uncoupled Splicing

(2011) Diana Y. Vargas et al.   CELL

Cell-to-cell variability of alternative RNA splicing

(2011) Z. Waks et al.   Molecular Systems Biology

Toxicity and cellular uptake of gold nanoparticles: what we have learned so far?

(2010) Alaaldin M. Alkilany et al.   JOURNAL OF NANOPARTICLE RESEARCH

Hairpin DNA-Functionalized Gold Colloids for the Imaging of mRNA in Live Cells

(2010) Ashwath Jayagopal et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Making the message clear: visualizing mRNA localization

(2010) Timothy T. Weil et al.   TRENDS IN CELL BIOLOGY

Nano-flares for mRNA Regulation and Detection

(2009) Andrew E. Prigodich et al.   ACS Nano

Super-Resolution Fluorescence Microscopy

(2009) Bo Huang et al.   Annual Review of Biochemistry

Imaging Transcription in Living Cells

(2009) Xavier Darzacq et al.   Annual Review of Biophysics

Quantitative Surface-Enhanced Raman for Gene Expression Estimation

(2009) Lan Sun et al.   BIOPHYSICAL JOURNAL

PCR-Free Quantification of Multiple Splice Variants in a Cancer Gene by Surface-Enhanced Raman Spectroscopy

(2009) Lan Sun et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A FRET-based assay for characterization of alternative splicing events using peptide nucleic acid fluorescence in situ hybridization

(2009) Ana M. Blanco et al.   NUCLEIC ACIDS RESEARCH

Raman Multiplexers for Alternative Gene Splicing

(2008) Lan Sun et al.   ANALYTICAL CHEMISTRY

Polyvalent DNA Nanoparticle Conjugates Stabilize Nucleic Acids

(2008) Dwight S. Seferos et al.   NANO LETTERS

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS

Label-Free Biomedical Imaging with High Sensitivity by Stimulated Raman Scattering Microscopy

(2008) Christian W. Freudiger et al.   SCIENCE