Cai, Long

Combined from CaltechAUTHORS

• Polonsky, Michal and Gerhardt, Louisa M. S., el al. (2024) Spatial transcriptomics defines injury specific microenvironments and cellular interactions in kidney regeneration and disease; Nature Communications; Vol. 15; No. 1; 7010; PMCID PMC11377535; 10.1038/s41467-024-51186-z
• Jain, Sanjay and Pei, Liming, el al. (2024) Author Correction: Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP); Nature Cell Biology; Vol. 26; 10.1038/s41556-024-01384-0
• Polonsky, Michal and Gerhardt, Louisa M. S., el al. (2023) Spatial transcriptomics defines injury-specific microenvironments in the adult mouse kidney and novel cellular interactions in regeneration and disease; bioRxiv; 10.1101/2023.11.22.568217
• Lohoff, T. and Ghazanfar, S., el al. (2022) Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis; Nature Biotechnology; Vol. 40; No. 1; 74-85; 10.1038/s41587-021-01006-2
• Cable, Jennifer and Elowitz, Michael B., el al. (2021) Single cell biology—a Keystone Symposia report; Annals of the New York Academy of Sciences; Vol. 1506; 74-97; 10.1111/nyas.14692
• Takei, Yodai and Zheng, Shiwei, el al. (2021) Single-cell nuclear architecture across cell types in the mouse brain; Science; Vol. 374; No. 6567; 586-594; 10.1126/science.abj1966
• Dar, Daniel and Dar, Nina, el al. (2021) Spatial transcriptomics of planktonic and sessile bacterial populations at single-cell resolution; Science; Vol. 373; No. 6556; Art. No. eabi4882; PMCID PMC8454218; 10.1126/science.abi4882
• Takei, Yodai and Zheng, Shiwei, el al. (2021) Integrated spatial genomics in tissues reveals invariant and cell type dependent nuclear architecture; 10.1101/2021.04.26.441547
• Jang, Min Jee and Coughlin, Gerard M., el al. (2021) Deep Tropism Profiling of Barcoded AAV Capsid and Cargo Pools in Intact Tissue Using High-Throughput Ultrasensitive Sequential FISH; Molecular Therapy; Vol. 29; No. 4, S1; 142; 10.1016/j.ymthe.2021.04.019
• Chow, Ke-Huan K. and Budde, Mark W., el al. (2021) Imaging cell lineage with a synthetic digital recording system; Science; Vol. 372; No. 6538; Art. No. eabb3099; 10.1126/science.abb3099
• Dries, Ruben and Zhu, Qian, el al. (2021) Giotto: a toolbox for integrative analysis and visualization of spatial expression data; Genome Biology; Vol. 22; Art. No. 78; 10.1186/s13059-021-02286-2
• Takei, Yodai and Yun, Jina, el al. (2021) Integrated spatial genomics reveals global architecture of single nuclei; Nature; Vol. 590; No. 7845; 344-350; PMCID PMC7878433; 10.1038/s41586-020-03126-2
• Cai, L. (2020) Transcriptome-Scale Super-Resolved Imaging in Tissues by RNA SeqFISH; European Journal of Human Genetics; Vol. 28; No. S1; 10; 10.1038/s41431-020-00740-6
• Zhang, Yandong and Sohn, Changho, el al. (2020) Detecting protein and post-translational modifications in single cells with iDentification and qUantification sEparaTion (DUET); Communications Biology; Vol. 3; Art. No. 420; 10.1038/s42003-020-01132-8
• Polonsky, Michal and Round, Krista, el al. (2020) Analysis of luminal breast cancer tumor microenvironment using seqFISH; Cancer Epidemiology, Biomarkers and Prevention; Vol. 29; No. 6; Art. No. B117; 10.1158/1538-7755.disp18-b117
• Jang, Min Jee and Coughlin, Gerard M., el al. (2020) Method for High-Throughput, In Situ Characterization of AAV Variant Pools in Intact Tissue Using Ultrasensitive Sequential FISH; Molecular Therapy; Vol. 28; No. 4; 78-79; 10.1016/j.ymthe.2020.04.019
• Askary, Amjad and Sánchez-Guardado, Luis, el al. (2020) In situ readout of DNA barcodes and single base edits facilitated by in vitro transcription; Nature Biotechnology; Vol. 38; No. 1; 66-75; PMCID PMC6954335; 10.1038/s41587-019-0299-4
• Zhou, Wen and Yui, Mary A., el al. (2019) Single-Cell Analysis Reveals Regulatory Gene Expression Dynamics Leading to Lineage Commitment in Early T Cell Development; Cell Systems; Vol. 9; No. 4; 321-337; PMCID PMC6932747; 10.1016/j.cels.2019.09.008
• Kim, Dong-Wook and Yao, Zizhen, el al. (2019) Multimodal Analysis of Cell Types in a Hypothalamic Node Controlling Social Behavior; Cell; Vol. 179; No. 3; 713-728; PMCID PMC7534821; 10.1016/j.cell.2019.09.020
• Snyder, Michael P. and Cai, Long, el al. (2019) The human body at cellular resolution: the NIH Human Biomolecular Atlas Program; Nature; Vol. 574; No. 7777; 187-192; 10.1038/s41586-019-1629-x
• Eng, Chee-Huat Linus and Lawson, Michael, el al. (2019) Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+; Nature; Vol. 568; No. 7751; 235-239; PMCID PMC6544023; 10.1038/s41586-019-1049-y
• Zhu, Qian and Shah, Sheel, el al. (2018) Identification of spatially associated subpopulations by combining scRNA-seq and sequential fluorescence in situ hybridization; Nature Biotechnology; Vol. 36; No. 12; 1183-1190; PMCID PMC6488461; 10.1038/nbt.4260
• Guo, Jingtao and Grow, Edward J., el al. (2018) The adult human testis transcriptional cell atlas; Cell Research; Vol. 28; No. 12; 1141-1157; PMCID PMC6274646; 10.1038/s41422-018-0099-2
• Zhu, Qian and Shah, Sheel, el al. (2018) Decomposing spatially dependent and cell type specific contributions to cellular heterogeneity; 10.1101/275156
• Quinodoz, Sofia A. and Ollikainen, Noah, el al. (2018) Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus; Cell; Vol. 174; No. 3; 744-757; PMCID PMC6548320; 10.1016/j.cell.2018.05.024
• Shah, Sheel and Takei, Yodai, el al. (2018) Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH; Cell; Vol. 174; No. 2; 363-376; PMCID PMC6046268; 10.1016/j.cell.2018.05.035
• Eng, Chee-Huat Linus and Shah, Sheel, el al. (2017) Profiling the transcriptome with RNA SPOTs; Nature Methods; Vol. 14; No. 12; 1153-1155; PMCID PMC5819366; 10.1038/nmeth.4500
• Lignell, Antti and Kerosuo, Laura, el al. (2017) Identification of a neural crest stem cell niche by Spatial Genomic Analysis; Nature Communications; Vol. 8; Art. No. 1830; PMCID PMC5705662; 10.1038/s41467-017-01561-w
• Shah, Sheel and Lubeck, Eric, el al. (2017) seqFISH Accurately Detects Transcripts in Single Cells and Reveals Robust Spatial Organization in the Hippocampus; Neuron; Vol. 94; No. 4; 752-758; 10.1016/j.neuron.2017.05.008
• Takei, Yodai and Shah, Sheel, el al. (2017) Multiplexed Dynamic Imaging of Genomic Loci by Combined CRISPR Imaging and DNA Sequential FISH; Biophysical Journal; Vol. 112; No. 9; 1773-1776; PMCID PMC5425380; 10.1016/j.bpj.2017.03.024
• Yuan, Guo-Cheng and Cai, Long, el al. (2017) Challenges and emerging directions in single-cell analysis; Genome Biology; Vol. 18; No. 1; Art. No. 84; PMCID PMC5421338; 10.1186/s13059-017-1218-y
• Herwig, Lukas and Rice, Austin J., el al. (2017) Directed Evolution of a Bright Near-Infrared Fluorescent Rhodopsin Using a Synthetic Chromophore; Cell Chemical Biology; Vol. 24; No. 3; 415-425; PMCID PMC5357175; 10.1016/j.chembiol.2017.02.008
• Frieda, Kirsten L. and Linton, James M., el al. (2017) Synthetic recording and in situ readout of lineage information in single cells; Nature; Vol. 541; No. 7635; 107-111; PMCID PMC6487260; 10.1038/nature20777
• Shah, Sheel and Lubeck, Eric, el al. (2016) In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus; Neuron; Vol. 92; No. 2; 342-357; PMCID PMC5087994; 10.1016/j.neuron.2016.10.001
• Shah, Sheel and Lubeck, Eric, el al. (2016) Single-molecule RNA detection at depth via hybridization chain reaction and tissue hydrogel embedding and clearing; Development; Vol. 143; No. 15; 2862-2867; PMCID PMC5004914; 10.1242/dev.138560
• Letsou, William and Cai, Long (2016) Noncommutative Biology: Sequential Regulation of Complex Networks; PLoS Computational Biology; Vol. 12; No. 8; Art. No. e1005089; PMCID PMC4999240; 10.1371/journal.pcbi.1005089
• Coskun, Ahmet F. and Cai, Long (2016) Dense transcript profiling in single cells by image correlation decoding; Nature Methods; Vol. 13; No. 8; 657-660; PMCID PMC4965285; 10.1038/nmeth.3895
• Lin, Yihan and Sohn, Chang Ho, el al. (2015) Combinatorial gene regulation by modulation of relative pulse timing; Nature; Vol. 527; No. 7576; 54-58; PMCID PMC4870307; 10.1038/nature15710
• Treweek, Jennifer B. and Chan, Ken Y., el al. (2015) Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping; Nature Protocols; Vol. 10; No. 11; 1860-1896; PMCID PMC4917295; 10.1038/nprot.2015.122
• Dalal, Chiraj K. and Cai, Long, el al. (2014) Pulsatile Dynamics in the Yeast Proteome; Current Biology; Vol. 24; No. 18; 2189-2194; PMCID PMC4203654; 10.1016/j.cub.2014.07.076
• Yang, Bin and Treweek, Jennifer B., el al. (2014) Single-Cell Phenotyping within Transparent Intact Tissue through Whole-Body Clearing; Cell; Vol. 158; No. 4; 945-958; PMCID PMC4153367; 10.1016/j.cell.2014.07.017
• Singer, Zakary S. and Yong, John, el al. (2014) Dynamic Heterogeneity and DNA Methylation in Embryonic Stem Cells; Molecular Cell; Vol. 55; No. 2; 319-331; PMCID PMC4104113; 10.1016/j.molcel.2014.06.029
• Lubeck, Eric and Coskun, Ahmet F., el al. (2014) Single-cell in situ RNA profiling by sequential hybridization; Nature Methods; Vol. 11; No. 4; 360-361; PMCID PMC4085791; 10.1038/nmeth.2892
• Cai, Long (2014) Imaging Chromosome Structure in Bacteria by Super-Resolution Microscopy; Biophysical Journal; Vol. 106; No. 2; 375A; 10.1016/j.bpj.2013.11.2120
• Chen, Yi-Ju and Zhiyentayev, Timur, el al. (2014) Dynamic Gene Expression and Design Principles of Viral Infection Pathway; Biophysical Journal; Vol. 106; No. 2; 373A; 10.1016/j.bpj.2013.11.2111
• Cai, Long (2013) Turning single cells into microarrays by super-resolution barcoding; Briefings in Functional Genomics; Vol. 12; No. 2; 75-78; PMCID PMC3609437; 10.1093/bfgp/els054
• Lubeck, Eric and Cai, Long (2013) Towards Single-Cell Systems Biology through Super-Resolution Imaging and Molecular Barcoding; Biophysical Journal; Vol. 104; No. 2; 371A; 10.1016/j.bpj.2012.11.2062
• Lubeck, Eric and Cai, Long (2012) Single-cell systems biology by super-resolution imaging and combinatorial labeling; Nature Methods; Vol. 9; No. 7; 743-748; PMCID PMC3418883; 10.1038/nmeth.2069
• Friedman, Nir and Cai, Long, el al. (2009) Stochasticity in Gene Expression as Observed by Single-molecule Experiments in Live Cells; Israel Journal of Chemistry; Vol. 49; No. 3-4; 333-342; 10.1560/IJC.49.3-4.333
• Choi, Paul J. and Cai, Long, el al. (2008) A Stochastic Single-Molecule Event Triggers Phenotype Switching of a Bacterial Cell; Science; Vol. 322; No. 5900; 442-446; PMCID PMC2819113; 10.1126/science.1161427
• Cai, Long and Dalal, Chiraj K., el al. (2008) Frequency-modulated nuclear localization bursts coordinate gene regulation; Nature; Vol. 455; No. 7212; 485-491; PMCID PMC2695983; 10.1038/nature07292
• Friedman, Nir and Cai, Long, el al. (2006) Linking Stochastic Dynamics to Population Distribution: An Analytical Framework of Gene Expression; Physical Review Letters; Vol. 97; No. 16; Art. No. 168302; 10.1103/PhysRevLett.97.168302
• Cai, Long and Friedman, Nir, el al. (2006) Stochastic protein expression in individual cells at the single molecule level; Nature; Vol. 440; No. 7082; 358-362; 10.1038/nature04599