@article{https://resolver.caltech.edu/CaltechAUTHORS:20201123-133350121, title = "Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis", journal = "Nature Biotechnology", url = "https://resolver.caltech.edu/CaltechAUTHORS:20201123-133350121", id = "record", issn = "1087-0156", doi = "10.1038/s41587-021-01006-2", volume = "40" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20211008-183538677, title = "Single cell biology—a Keystone Symposia report", journal = "Annals of the New York Academy of Sciences", url = "https://resolver.caltech.edu/CaltechAUTHORS:20211008-183538677", id = "record", issn = "0077-8923", doi = "10.1111/nyas.14692", volume = "1506" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20211004-203742730, title = "Single-cell nuclear architecture across cell types in the mouse brain", journal = "Science", url = "https://resolver.caltech.edu/CaltechAUTHORS:20211004-203742730", id = "record", issn = "0036-8075", doi = "10.1126/science.abj1966", volume = "374" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20210226-074209469, title = "Spatial transcriptomics of planktonic and sessile bacterial populations at single-cell resolution", journal = "Science", url = "https://resolver.caltech.edu/CaltechAUTHORS:20210226-074209469", id = "record", issn = "0036-8075", doi = "10.1126/science.abi4882", volume = "373", pmcid = "PMC8454218" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20210527-161220137, title = "Deep Tropism Profiling of Barcoded AAV Capsid and Cargo Pools in Intact Tissue Using High-Throughput Ultrasensitive Sequential FISH", journal = "Molecular Therapy", url = "https://resolver.caltech.edu/CaltechAUTHORS:20210527-161220137", id = "record", issn = "1525-0016", doi = "10.1016/j.ymthe.2021.04.019", volume = "29" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20200225-135944187, title = "Imaging cell lineage with a synthetic digital recording system", journal = "Science", url = "https://resolver.caltech.edu/CaltechAUTHORS:20200225-135944187", id = "record", issn = "0036-8075", doi = "10.1126/science.abb3099", volume = "372" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20190716-114136984, title = "Giotto: a toolbox for integrative analysis and visualization of spatial expression data", journal = "Genome Biology", url = "https://resolver.caltech.edu/CaltechAUTHORS:20190716-114136984", id = "record", issn = "1465-6906", doi = "10.1186/s13059-021-02286-2", volume = "22" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20201207-124413570, title = "Integrated spatial genomics reveals global architecture of single nuclei", journal = "Nature", url = "https://resolver.caltech.edu/CaltechAUTHORS:20201207-124413570", id = "record", issn = "0028-0836", doi = "10.1038/s41586-020-03126-2", volume = "590", pmcid = "PMC7878433" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20210120-154339392, title = "Transcriptome-Scale Super-Resolved Imaging in Tissues by RNA SeqFISH", journal = "European Journal of Human Genetics", url = "https://resolver.caltech.edu/CaltechAUTHORS:20210120-154339392", id = "record", issn = "1018-4813", doi = "10.1038/s41431-020-00740-6", volume = "28" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20200803-104852533, title = "Detecting protein and post-translational modifications in single cells with iDentification and qUantification sEparaTion (DUET)", journal = "Communications Biology", url = "https://resolver.caltech.edu/CaltechAUTHORS:20200803-104852533", id = "record", issn = "2399-3642", doi = "10.1038/s42003-020-01132-8", volume = "3" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20201103-105218022, title = "Analysis of luminal breast cancer tumor microenvironment using seqFISH", journal = "Cancer Epidemiology, Biomarkers and Prevention", url = "https://resolver.caltech.edu/CaltechAUTHORS:20201103-105218022", id = "record", issn = "1055-9965", doi = "10.1158/1538-7755.disp18-b117", volume = "29" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20200604-074008042, title = "Method for High-Throughput, In Situ Characterization of AAV Variant Pools in Intact Tissue Using Ultrasensitive Sequential FISH", journal = "Molecular Therapy", url = "https://resolver.caltech.edu/CaltechAUTHORS:20200604-074008042", id = "record", issn = "1525-0016", doi = "10.1016/j.ymthe.2020.04.019", volume = "28" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20190920-163128957, title = "In situ readout of DNA barcodes and single base edits facilitated by in vitro transcription", journal = "Nature Biotechnology", url = "https://resolver.caltech.edu/CaltechAUTHORS:20190920-163128957", id = "record", issn = "1087-0156", doi = "10.1038/s41587-019-0299-4", volume = "38", pmcid = "PMC6954335" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20191016-124948167, title = "Single-Cell Analysis Reveals Regulatory Gene Expression Dynamics Leading to Lineage Commitment in Early T Cell Development", journal = "Cell Systems", url = "https://resolver.caltech.edu/CaltechAUTHORS:20191016-124948167", id = "record", issn = "2405-4712", doi = "10.1016/j.cels.2019.09.008", volume = "9", pmcid = "PMC6932747" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20191017-094121433, title = "Multimodal Analysis of Cell Types in a Hypothalamic Node Controlling Social Behavior", journal = "Cell", url = "https://resolver.caltech.edu/CaltechAUTHORS:20191017-094121433", id = "record", issn = "0092-8674", doi = "10.1016/j.cell.2019.09.020", volume = "179", pmcid = "PMC7534821" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20191009-112519199, title = "The human body at cellular resolution: the NIH Human Biomolecular Atlas Program", journal = "Nature", url = "https://resolver.caltech.edu/CaltechAUTHORS:20191009-112519199", id = "record", issn = "0028-0836", doi = "10.1038/s41586-019-1629-x", volume = "574" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20190129-144119260, title = "Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+", journal = "Nature", url = "https://resolver.caltech.edu/CaltechAUTHORS:20190129-144119260", id = "record", issn = "0028-0836", doi = "10.1038/s41586-019-1049-y", volume = "568", pmcid = "PMC6544023" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20180821-132916530, title = "Identification of spatially associated subpopulations by combining scRNA-seq and sequential fluorescence in situ hybridization", journal = "Nature Biotechnology", url = "https://resolver.caltech.edu/CaltechAUTHORS:20180821-132916530", id = "record", issn = "1087-0156", doi = "10.1038/nbt.4260", volume = "36", pmcid = "PMC6488461" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20181023-084128561, title = "The adult human testis transcriptional cell atlas", journal = "Cell Research", url = "https://resolver.caltech.edu/CaltechAUTHORS:20181023-084128561", id = "record", issn = "1001-0602", doi = "10.1038/s41422-018-0099-2", volume = "28", pmcid = "PMC6274646" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20180607-101054915, title = "Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus", journal = "Cell", url = "https://resolver.caltech.edu/CaltechAUTHORS:20180607-101054915", id = "record", issn = "0092-8674", doi = "10.1016/j.cell.2018.05.024", volume = "174", pmcid = "PMC6548320" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20180607-131657607, title = "Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH", journal = "Cell", url = "https://resolver.caltech.edu/CaltechAUTHORS:20180607-131657607", id = "record", issn = "0092-8674", doi = "10.1016/j.cell.2018.05.035", volume = "174", pmcid = "PMC6046268" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20171002-110633228, title = "Profiling the transcriptome with RNA SPOTs", journal = "Nature Methods", url = "https://resolver.caltech.edu/CaltechAUTHORS:20171002-110633228", id = "record", issn = "1548-7091", doi = "10.1038/nmeth.4500", volume = "14", pmcid = "PMC5819366" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20171128-101613048, title = "Identification of a neural crest stem cell niche by Spatial Genomic Analysis", journal = "Nature Communications", url = "https://resolver.caltech.edu/CaltechAUTHORS:20171128-101613048", id = "record", issn = "2041-1723", doi = "10.1038/s41467-017-01561-w", volume = "8", pmcid = "PMC5705662" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20170519-092429585, title = "seqFISH Accurately Detects Transcripts in Single Cells and Reveals Robust Spatial Organization in the Hippocampus", journal = "Neuron", url = "https://resolver.caltech.edu/CaltechAUTHORS:20170519-092429585", id = "record", issn = "0896-6273", doi = "10.1016/j.neuron.2017.05.008", volume = "94" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20170424-085453982, title = "Multiplexed Dynamic Imaging of Genomic Loci by Combined CRISPR Imaging and DNA Sequential FISH", journal = "Biophysical Journal", url = "https://resolver.caltech.edu/CaltechAUTHORS:20170424-085453982", id = "record", issn = "0006-3495", doi = "10.1016/j.bpj.2017.03.024", volume = "112", pmcid = "PMC5425380" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20170515-103755842, title = "Challenges and emerging directions in single-cell analysis", journal = "Genome Biology", url = "https://resolver.caltech.edu/CaltechAUTHORS:20170515-103755842", id = "record", issn = "1474-760X", doi = "10.1186/s13059-017-1218-y", volume = "18", pmcid = "PMC5421338" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20170307-082231020, title = "Directed Evolution of a Bright Near-Infrared Fluorescent Rhodopsin Using a Synthetic Chromophore", journal = "Cell Chemical Biology", url = "https://resolver.caltech.edu/CaltechAUTHORS:20170307-082231020", id = "record", issn = "2451-9456", doi = "10.1016/j.chembiol.2017.02.008", volume = "24", pmcid = "PMC5357175" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20161102-141950462, title = "Synthetic recording and in situ readout of lineage information in single cells", journal = "Nature", url = "https://resolver.caltech.edu/CaltechAUTHORS:20161102-141950462", id = "record", issn = "0028-0836", doi = "10.1038/nature20777", volume = "541", pmcid = "PMC6487260" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20161021-132836401, title = "In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus", journal = "Neuron", url = "https://resolver.caltech.edu/CaltechAUTHORS:20161021-132836401", id = "record", issn = "0896-6273", doi = "10.1016/j.neuron.2016.10.001", volume = "92", pmcid = "PMC5087994" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20160628-085406782, title = "Single-molecule RNA detection at depth via hybridization chain reaction and tissue hydrogel embedding and clearing", journal = "Development", url = "https://resolver.caltech.edu/CaltechAUTHORS:20160628-085406782", id = "record", issn = "0950-1991", doi = "10.1242/dev.138560", volume = "143", pmcid = "PMC5004914" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20160509-170833016, title = "Dense transcript profiling in single cells by image correlation decoding", journal = "Nature Methods", url = "https://resolver.caltech.edu/CaltechAUTHORS:20160509-170833016", id = "record", issn = "1548-7091", doi = "10.1038/nmeth.3895", volume = "13", pmcid = "PMC4965285" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20160907-080424816, title = "Noncommutative Biology: Sequential Regulation of Complex Networks", journal = "PLoS Computational Biology", url = "https://resolver.caltech.edu/CaltechAUTHORS:20160907-080424816", id = "record", issn = "1553-734X", doi = "10.1371/journal.pcbi.1005089", volume = "12", pmcid = "PMC4999240" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20150805-144646254, title = "Combinatorial gene regulation by modulation of relative pulse timing", journal = "Nature", url = "https://resolver.caltech.edu/CaltechAUTHORS:20150805-144646254", id = "record", issn = "0028-0836", doi = "10.1038/nature15710", volume = "527", pmcid = "PMC4870307" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20150914-123933415, title = "Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping", journal = "Nature Protocols", url = "https://resolver.caltech.edu/CaltechAUTHORS:20150914-123933415", id = "record", issn = "1754-2189", doi = "10.1038/nprot.2015.122", volume = "10", pmcid = "PMC4917295" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20140909-172029209, title = "Pulsatile Dynamics in the Yeast Proteome", journal = "Current Biology", url = "https://resolver.caltech.edu/CaltechAUTHORS:20140909-172029209", id = "record", issn = "0960-9822", doi = "10.1016/j.cub.2014.07.076", volume = "24", pmcid = "PMC4203654" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20140801-121634734, title = "Single-Cell Phenotyping within Transparent Intact Tissue through Whole-Body Clearing", journal = "Cell", url = "https://resolver.caltech.edu/CaltechAUTHORS:20140801-121634734", id = "record", issn = "0092-8674", doi = "10.1016/j.cell.2014.07.017", volume = "158", pmcid = "PMC4153367" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20140729-074318148, title = "Dynamic Heterogeneity and DNA Methylation in Embryonic Stem Cells", journal = "Molecular Cell", url = "https://resolver.caltech.edu/CaltechAUTHORS:20140729-074318148", id = "record", issn = "1097-2765", doi = "10.1016/j.molcel.2014.06.029", volume = "55", pmcid = "PMC4104113" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20140228-201820558, title = "Single-cell in situ RNA profiling by sequential hybridization", journal = "Nature Methods", url = "https://resolver.caltech.edu/CaltechAUTHORS:20140228-201820558", id = "record", issn = "1548-7091", doi = "10.1038/nmeth.2892", volume = "11", pmcid = "PMC4085791" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20140710-095942704, title = "Imaging Chromosome Structure in Bacteria by Super-Resolution Microscopy", journal = "Biophysical Journal", url = "https://resolver.caltech.edu/CaltechAUTHORS:20140710-095942704", id = "record", issn = "0006-3495", doi = "10.1016/j.bpj.2013.11.2120", volume = "106" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20140710-084044769, title = "Dynamic Gene Expression and Design Principles of Viral Infection Pathway", journal = "Biophysical Journal", url = "https://resolver.caltech.edu/CaltechAUTHORS:20140710-084044769", id = "record", issn = "0006-3495", doi = "10.1016/j.bpj.2013.11.2111", volume = "106" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20130507-073209344, title = "Turning single cells into microarrays by super-resolution barcoding", journal = "Briefings in Functional Genomics", url = "https://resolver.caltech.edu/CaltechAUTHORS:20130507-073209344", id = "record", issn = "2041-2649", doi = "10.1093/bfgp/els054", volume = "12", pmcid = "PMC3609437" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20130429-080544935, title = "Towards Single-Cell Systems Biology through Super-Resolution Imaging and Molecular Barcoding", journal = "Biophysical Journal", url = "https://resolver.caltech.edu/CaltechAUTHORS:20130429-080544935", id = "record", issn = "0006-3495", doi = "10.1016/j.bpj.2012.11.2062", volume = "104" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20120801-094824257, title = "Single-cell systems biology by super-resolution imaging and combinatorial labeling", journal = "Nature Methods", url = "https://resolver.caltech.edu/CaltechAUTHORS:20120801-094824257", id = "record", issn = "1548-7091", doi = "10.1038/nmeth.2069", volume = "9", pmcid = "PMC3418883" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20100720-094603442, title = "Stochasticity in Gene Expression as Observed by Single-molecule Experiments in Live Cells", journal = "Israel Journal of Chemistry", url = "https://resolver.caltech.edu/CaltechAUTHORS:20100720-094603442", id = "record", issn = "0021-2148", doi = "10.1560/IJC.49.3-4.333", volume = "49" } @article{https://resolver.caltech.edu/CaltechAUTHORS:CHOsci08, title = "A Stochastic Single-Molecule Event Triggers Phenotype Switching of a Bacterial Cell", journal = "Science", url = "https://resolver.caltech.edu/CaltechAUTHORS:CHOsci08", id = "record", issn = "0036-8075", doi = "10.1126/science.1161427", volume = "322", pmcid = "PMC2819113" } @article{https://resolver.caltech.edu/CaltechAUTHORS:CAInat08, title = "Frequency-modulated nuclear localization bursts coordinate gene regulation", journal = "Nature", url = "https://resolver.caltech.edu/CaltechAUTHORS:CAInat08", id = "record", issn = "0028-0836", doi = "10.1038/nature07292", volume = "455", pmcid = "PMC2695983" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20120726-073337126, title = "Linking Stochastic Dynamics to Population Distribution: An Analytical Framework of Gene Expression", journal = "Physical Review Letters", url = "https://resolver.caltech.edu/CaltechAUTHORS:20120726-073337126", id = "record", issn = "0031-9007", doi = "10.1103/PhysRevLett.97.168302", volume = "97" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20120726-072703757, title = "Stochastic protein expression in individual cells at the single molecule level", journal = "Nature", url = "https://resolver.caltech.edu/CaltechAUTHORS:20120726-072703757", id = "record", issn = "0028-0836", doi = "10.1038/nature04599", volume = "440" }