@article{https://authors.library.caltech.edu/records/0j638-jx111,
    title = "Spatial transcriptomics defines injury specific microenvironments and cellular interactions in kidney regeneration and disease",
    journal = "Nature Communications",
    year = "2024",
    url = "https://authors.library.caltech.edu/records/0j638-jx111",
    id = "record",
    issn = "2041-1723",
    doi = "10.1038/s41467-024-51186-z",
    volume = "15",
    pmcid = "PMC11377535"
}


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    title = "Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis",
    journal = "Nature Biotechnology",
    year = "2022",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20201123-133350121",
    id = "record",
    issn = "1087-0156",
    doi = "10.1038/s41587-021-01006-2",
    volume = "40"
}


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    title = "Single cell biology—a Keystone Symposia report",
    journal = "Annals of the New York Academy of Sciences",
    year = "2021",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20211008-183538677",
    id = "record",
    issn = "0077-8923",
    doi = "10.1111/nyas.14692",
    volume = "1506"
}


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    title = "Single-cell nuclear architecture across cell types in the mouse brain",
    journal = "Science",
    year = "2021",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20211004-203742730",
    id = "record",
    issn = "0036-8075",
    doi = "10.1126/science.abj1966",
    volume = "374"
}


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    title = "Spatial transcriptomics of planktonic and sessile bacterial populations at single-cell resolution",
    journal = "Science",
    year = "2021",
    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",
    year = "2021",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20210527-161220137",
    id = "record",
    issn = "1525-0016",
    doi = "10.1016/j.ymthe.2021.04.019",
    volume = "29"
}


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    title = "Imaging cell lineage with a synthetic digital recording system",
    journal = "Science",
    year = "2021",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20200225-135944187",
    id = "record",
    issn = "0036-8075",
    doi = "10.1126/science.abb3099",
    volume = "372"
}


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    title = "Giotto: a toolbox for integrative analysis and visualization of spatial expression data",
    journal = "Genome Biology",
    year = "2021",
    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",
    year = "2021",
    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",
    year = "2020",
    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",
    year = "2020",
    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",
    year = "2020",
    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",
    year = "2020",
    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",
    year = "2020",
    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",
    year = "2019",
    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",
    year = "2019",
    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",
    year = "2019",
    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",
    year = "2019",
    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:20181023-084128561,
    title = "The adult human testis transcriptional cell atlas",
    journal = "Cell Research",
    year = "2018",
    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:20180821-132916530,
    title = "Identification of spatially associated subpopulations by combining scRNA-seq and sequential fluorescence in situ hybridization",
    journal = "Nature Biotechnology",
    year = "2018",
    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:20180607-101054915,
    title = "Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus",
    journal = "Cell",
    year = "2018",
    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",
    year = "2018",
    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",
    year = "2017",
    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",
    year = "2017",
    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",
    year = "2017",
    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",
    year = "2017",
    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",
    year = "2017",
    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",
    year = "2017",
    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",
    year = "2017",
    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",
    year = "2016",
    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",
    year = "2016",
    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",
    year = "2016",
    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",
    year = "2016",
    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",
    year = "2015",
    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",
    year = "2015",
    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",
    year = "2014",
    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",
    year = "2014",
    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",
    year = "2014",
    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",
    year = "2014",
    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:20140710-084044769,
    title = "Dynamic Gene Expression and Design Principles of Viral Infection Pathway",
    journal = "Biophysical Journal",
    year = "2014",
    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:20140710-095942704,
    title = "Imaging Chromosome Structure in Bacteria by Super-Resolution Microscopy",
    journal = "Biophysical Journal",
    year = "2014",
    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:20130507-073209344,
    title = "Turning single cells into microarrays by super-resolution barcoding",
    journal = "Briefings in Functional Genomics",
    year = "2013",
    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",
    year = "2013",
    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",
    year = "2012",
    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",
    year = "2009",
    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",
    year = "2008",
    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",
    year = "2008",
    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",
    year = "2006",
    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",
    year = "2006",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20120726-072703757",
    id = "record",
    issn = "0028-0836",
    doi = "10.1038/nature04599",
    volume = "440"
}