@article{https://authors.library.caltech.edu/records/w9sxn-f7e77,
    title = "Commensal bacteria promote type I interferon signaling to maintain immune tolerance in mice",
    journal = "Journal of Experimental Medicine",
    url = "https://authors.library.caltech.edu/records/w9sxn-f7e77",
    id = "record",
    issn = "0022-1007",
    doi = "10.1084/jem.20230063",
    volume = "221",
    pmcid = "PMC10716256"
}


@article{https://authors.library.caltech.edu/records/e527q-6pq77,
    title = "Recovery of missing single-cell RNA-sequencing data with optimized transcriptomic references",
    journal = "Nature Methods",
    url = "https://authors.library.caltech.edu/records/e527q-6pq77",
    id = "record",
    issn = "1548-7091",
    doi = "10.1038/s41592-023-02003-w"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20230602-251540000.11,
    title = "Stem cell-derived synthetic embryos self-assemble by exploiting cadherin codes and cortical tension",
    journal = "Nature Cell Biology",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20230602-251540000.11",
    id = "record",
    issn = "1465-7392",
    doi = "10.1038/s41556-022-00984-y",
    volume = "24",
    pmcid = "PMC9481465"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20230628-344482000.1,
    title = "Daily SARS-CoV-2 Nasal Antigen Tests Miss Infected and Presumably Infectious People Due to Viral Load Differences among Specimen Types",
    journal = "Microbiology Spectrum",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20230628-344482000.1",
    id = "record",
    issn = "2165-0497",
    doi = "10.1128/spectrum.01295-23",
    volume = "11",
    pmcid = "PMC10434058"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20230628-257194000.34,
    title = "Spatio-temporal patterning of extensile active stresses in microtubule-based active fluids",
    journal = "PNAS Nexus",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20230628-257194000.34",
    id = "record",
    issn = "2752-6542",
    doi = "10.1093/pnasnexus/pgad130",
    volume = "2",
    pmcid = "PMC10165807"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20230323-759607000.4,
    title = "Extreme differences in SARS-CoV-2 viral loads among respiratory specimen types during presumed pre-infectious and infectious periods",
    journal = "PNAS Nexus",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20230323-759607000.4",
    id = "record",
    issn = "2752-6542",
    doi = "10.1093/pnasnexus/pgad033",
    volume = "2",
    pmcid = "PMC10013338"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20230510-982977000.2,
    title = "Motor processivity and speed determine structure and dynamics of microtubule-motor assemblies",
    journal = "eLife",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20230510-982977000.2",
    id = "record",
    issn = "2050-084X",
    doi = "10.7554/elife.79402",
    volume = "12",
    pmcid = "PMC10014072"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20230314-846690800.94,
    title = "Spin glasses, error correcting codes, and synchronization of human stem cell organoids",
    journal = "Cell",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20230314-846690800.94",
    id = "record",
    issn = "0092-8674",
    doi = "10.1016/j.cell.2023.01.006",
    volume = "186"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20221202-906989500.8,
    title = "A prebiotic diet modulates microglial states and motor deficits in α-synuclein overexpressing mice",
    journal = "eLife",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20221202-906989500.8",
    id = "record",
    issn = "2050-084X",
    doi = "10.7554/elife.81453",
    volume = "11",
    pmcid = "PMC9668333"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20220919-149101800,
    title = "Stem cell-derived synthetic embryos self-assemble by exploiting cadherin codes and cortical tension",
    journal = "Nature Cell Biology",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20220919-149101800",
    id = "record",
    issn = "1465-7392",
    doi = "10.1038/s41556-022-00984-y",
    volume = "24",
    pmcid = "PMC9481465"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20220720-918411000,
    title = "Mapping hormone-regulated cell-cell interaction networks in the human breast at single-cell resolution",
    journal = "Cell Systems",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20220720-918411000",
    id = "record",
    issn = "2405-4712",
    doi = "10.1016/j.cels.2022.06.005",
    volume = "13",
    pmcid = "PMC9590200"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20210707-155629727,
    title = "Localization of signaling receptors maximizes cellular information acquisition in spatially structured natural environments",
    journal = "Cell Systems",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20210707-155629727",
    id = "record",
    issn = "2405-4712",
    doi = "10.1016/j.cels.2022.05.004",
    volume = "13"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20220707-978247000,
    title = "Minimal gene set discovery in single-cell mRNA-seq datasets with ActiveSVM",
    journal = "Nature Computational Science",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20220707-978247000",
    id = "record",
    issn = "2662-8457",
    doi = "10.1038/s43588-022-00263-8",
    volume = "2"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20220422-296339700,
    title = "Measuring energy consumption through space and time in an active matter system of cytoskeletal motors and filaments",
    journal = "Biophysical Journal",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20220422-296339700",
    id = "record",
    issn = "0006-3495",
    doi = "10.1016/j.bpj.2021.11.2745",
    volume = "121"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20220422-225704323,
    title = "Reconstituting the nonequilibrium biophysics of the LECA cytoskeleton in active matter",
    journal = "Biophysical Journal",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20220422-225704323",
    id = "record",
    issn = "0006-3495",
    doi = "10.1016/j.bpj.2021.11.2744",
    volume = "121"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20211221-866382000,
    title = "Reinforcement learning reveals fundamental limits on the mixing of active particles",
    journal = "Soft Matter",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20211221-866382000",
    id = "record",
    issn = "1744-683X",
    doi = "10.1039/d1sm01400e",
    volume = "18"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20210629-153450418,
    title = "Deep Parallel Characterization of AAV Tropism and AAV-Mediated Transcriptional Changes via Single-Cell RNA Sequencing",
    journal = "Frontiers in Immunology",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20210629-153450418",
    id = "record",
    issn = "1664-3224",
    doi = "10.3389/fimmu.2021.730825",
    volume = "12",
    pmcid = "PMC8574206"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20201110-143708446,
    title = "Persistent fluid flows defined by active matter boundaries",
    journal = "Communications Physics",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20201110-143708446",
    id = "record",
    issn = "2399-3650",
    doi = "10.1038/s42005-021-00703-3",
    volume = "4"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20210726-193944737,
    title = "A DNA repair pathway can regulate transcriptional noise to promote cell fate transitions",
    journal = "Science",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20210726-193944737",
    id = "record",
    issn = "0036-8075",
    doi = "10.1126/science.abc6506",
    volume = "373",
    pmcid = "PMC8667278"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20200811-074939566,
    title = "Phenomenological model of motility by spatiotemporal modulation of active interactions",
    journal = "New Journal of Physics",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20200811-074939566",
    id = "record",
    issn = "1367-2630",
    doi = "10.1088/1367-2630/ac1144",
    volume = "23"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20210503-102948566,
    title = "Identifying Enthalpic Barriers to Entropically-Driven Structural Disruption in Breast Cancers",
    journal = "Biophysical Journal",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20210503-102948566",
    id = "record",
    issn = "0006-3495",
    doi = "10.1016/j.bpj.2020.11.1347",
    volume = "120"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20200212-084819179,
    title = "Developmental clock and mechanism of de novo polarization of the mouse embryo",
    journal = "Science",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20200212-084819179",
    id = "record",
    issn = "0036-8075",
    doi = "10.1126/science.abd2703",
    volume = "370",
    pmcid = "PMC8210885"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20201130-100709314,
    title = "Single cell profiling of capillary blood enables out of clinic human immunity studies",
    journal = "Scientific Reports",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20201130-100709314",
    id = "record",
    issn = "2045-2322",
    doi = "10.1038/s41598-020-77073-3",
    volume = "10",
    pmcid = "PMC7688970"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20180927-114224716,
    title = "Dissecting heterogeneous cell populations across drug and disease conditions with PopAlign",
    journal = "Proceedings of the National Academy of Sciences of the United States of America",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20180927-114224716",
    id = "record",
    issn = "0027-8424",
    doi = "10.1073/pnas.2005990117",
    volume = "117",
    pmcid = "PMC7682438"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20200929-102516984,
    title = "Bimodal function of chromatin remodeler Hmga1 in neural crest induction and Wnt-dependent emigration",
    journal = "eLife",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20200929-102516984",
    id = "record",
    issn = "2050-084X",
    doi = "10.7554/elife.57779",
    volume = "2020",
    pmcid = "PMC7591248"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20200604-075354300,
    title = "In-Depth Parallel Profiling of Tissue and Cell-Type Tropism of AAV Variants by Single-Cell RNA Sequencing",
    journal = "Molecular Therapy",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20200604-075354300",
    id = "record",
    issn = "1525-0016",
    doi = "10.1016/j.ymthe.2020.04.019",
    volume = "28"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20200604-102237108,
    title = "A Computational and Experimental Platform for Detecting Full Transcriptome Cell Type Tropism of Lowly Expressed Barcoded and Pooled AAV Variants via Single-Cell RNA Sequencing",
    journal = "Molecular Therapy",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20200604-102237108",
    id = "record",
    issn = "1525-0016",
    doi = "10.1016/j.ymthe.2020.04.019",
    volume = "28"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20200210-111806006,
    title = "Bridging Kinesin Properties with System-scale Characteristics of Microtubule-Motor Assemblies",
    journal = "Biophysical Journal",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20200210-111806006",
    id = "record",
    issn = "0006-3495",
    doi = "10.1016/j.bpj.2019.11.1081",
    volume = "118"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20181030-145533155,
    title = "Highly multiplexed single-cell RNA-seq by DNA oligonucleotide tagging of cellular proteins",
    journal = "Nature Biotechnology",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20181030-145533155",
    id = "record",
    issn = "1087-0156",
    doi = "10.1038/s41587-019-0372-z",
    volume = "38"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20190102-092232993,
    title = "Controlling Organization and Forces in Active Matter Through Optically-Defined Boundaries",
    journal = "Nature",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20190102-092232993",
    id = "record",
    issn = "0028-0836",
    doi = "10.1038/s41586-019-1447-1",
    volume = "572",
    pmcid = "PMC6719720"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20180910-090801725,
    title = "Integrated measurement of intracellular proteins and transcripts in single cells",
    journal = "Lab on a Chip",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20180910-090801725",
    id = "record",
    issn = "1473-0197",
    doi = "10.1039/c8lc00639c",
    volume = "18",
    pmcid = "PMC6752714"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20180212-080247041,
    title = "Diffusion as a Ruler: Modeling Kinesin Diffusion as a Length Sensor for Intraflagellar Transport",
    journal = "Biophysical Journal",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20180212-080247041",
    id = "record",
    issn = "0006-3495",
    doi = "10.1016/j.bpj.2017.11.3784",
    volume = "114",
    pmcid = "PMC5985012"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20180523-145718338,
    title = "Diffusion as a Ruler: Modeling Kinesin Diffusion as a Lenth Sensor for Intraflagellar Transport",
    journal = "Biophysical Journal",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20180523-145718338",
    id = "record",
    issn = "0006-3495",
    doi = "10.1016/j.bpj.2017.11.1877",
    volume = "114"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20180202-090924087,
    title = "Adult Neurogenesis Is Sustained by Symmetric Self-Renewal and Differentiation",
    journal = "Cell Stem Cell",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20180202-090924087",
    id = "record",
    issn = "1934-5909",
    doi = "10.1016/j.stem.2018.01.003",
    volume = "22",
    pmcid = "PMC5802882"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20180321-144810107,
    title = "Diffusion as a ruler: Modeling kinesin diffusion as a length sensor for intraflagellar transport",
    journal = "Molecular Biology of the Cell",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20180321-144810107",
    id = "record",
    issn = "1059-1524",
    doi = "10.1091/mbc.E17-10-0618",
    volume = "28"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20170612-083933304,
    title = "Transient Thresholding: A Mechanism Enabling Noncooperative Transcriptional Circuitry to Form a Switch",
    journal = "Biophysical Journal",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170612-083933304",
    id = "record",
    issn = "0006-3495",
    doi = "10.1016/j.bpj.2017.05.002",
    volume = "112",
    pmcid = "PMC5474885"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20161121-084221387,
    title = {Signaling Boundary Conditions Drive Self-Organization of Human "Gastruloids"},
    journal = "Developmental Cell",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20161121-084221387",
    id = "record",
    issn = "1534-5807",
    doi = "10.1016/j.devcel.2016.10.016",
    volume = "39"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20170203-145417665,
    title = "Low Dimensionality in Gene Expression Data Enables the Accurate Extraction of Transcriptional Programs from Shallow Sequencing",
    journal = "Cell Systems",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170203-145417665",
    id = "record",
    issn = "2405-4712",
    doi = "10.1016/j.cels.2016.04.001",
    volume = "2",
    pmcid = "PMC4856162"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20170217-152208931,
    title = "SOX2O-GlcNAcylation alters its protein-protein interactions and genomic occupancy to modulate gene expression in pluripotent cells",
    journal = "eLife",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170217-152208931",
    id = "record",
    issn = "2050-084X",
    doi = "10.7554/eLife.10647",
    volume = "5",
    pmcid = "PMC4841768"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20170217-155108197,
    title = "Engineering Customized Cell Sensing and Response Behaviors Using Synthetic Notch Receptors",
    journal = "Cell",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170217-155108197",
    id = "record",
    issn = "0092-8674",
    doi = "10.1016/j.cell.2016.01.012",
    volume = "164",
    pmcid = "PMC4752866"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20170206-125245319,
    title = "Transcription Factor Competition Allows Embryonic Stem Cells to Distinguish Authentic Signals from Noise",
    journal = "Cell Systems",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170206-125245319",
    id = "record",
    issn = "2405-4712",
    doi = "10.1016/j.cels.2015.08.001",
    volume = "1",
    pmcid = "PMC4576702"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20170217-155108581,
    title = "Transcriptome-wide Analysis Reveals Hallmarks of Human Intestine Development and Maturation In Vitro and In Vivo",
    journal = "Stem Cell Reports",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170217-155108581",
    id = "record",
    issn = "2213-6711",
    doi = "10.1016/j.stemcr.2015.04.010",
    volume = "4",
    pmcid = "PMC4471827"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20170206-125245656,
    title = "A strategy for tissue self-organization that is robust to cellular heterogeneity and plasticity",
    journal = "Proceedings of the National Academy of Sciences of the United States of America",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170206-125245656",
    id = "record",
    issn = "0027-8424",
    doi = "10.1073/pnas.1410776112",
    volume = "112",
    pmcid = "PMC4343104"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20170217-150644261,
    title = "Environmental Statistics and Optimal Regulation",
    journal = "Biophysical Journal",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170217-150644261",
    id = "record",
    issn = "0006-3495",
    doi = "10.1016/j.bpj.2014.11.1999",
    volume = "108"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20170206-153034371,
    title = "Environmental Statistics and Optimal Regulation",
    journal = "PLOS Computational Biology",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170206-153034371",
    id = "record",
    issn = "1553-7358",
    doi = "10.1371/journal.pcbi.1003826",
    volume = "10",
    pmcid = "PMC4177669"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20170127-224411366,
    title = "Pluripotency Factors in Embryonic Stem Cells Regulate Differentiation into Germ Layers",
    journal = "Cell",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170127-224411366",
    id = "record",
    issn = "0092-8674",
    doi = "10.1016/j.cell.2011.05.017",
    volume = "145"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20170206-154848264,
    title = "The rational parameterisation theorem for multisite post-translational modification systems",
    journal = "Journal of Theoretical Biology",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170206-154848264",
    id = "record",
    issn = "0022-5193",
    doi = "10.1016/j.jtbi.2009.09.003",
    volume = "261",
    pmcid = "PMC2800989"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20170206-154848538,
    title = "Unlimited multistability in multisite phosphorylation systems",
    journal = "Nature",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170206-154848538",
    id = "record",
    issn = "0028-0836",
    doi = "10.1038/nature08102",
    volume = "460",
    pmcid = "PMC2859978"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20170206-154848804,
    title = "Programming with models: modularity and abstraction provide powerful capabilities for systems biology",
    journal = "Journal of the Royal Society Interface",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170206-154848804",
    id = "record",
    issn = "1742-5689",
    doi = "10.1098/rsif.2008.0205",
    volume = "6",
    pmcid = "PMC2659579"
}


@article{https://resolver.caltech.edu/CaltechAUTHORS:20170217-132836548,
    title = "An embryonic stem cell–like gene expression signature in poorly differentiated aggressive human tumors",
    journal = "Nature Genetics",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170217-132836548",
    id = "record",
    issn = "1061-4036",
    doi = "10.1038/ng.127",
    volume = "40",
    pmcid = "PMC2912221"
}