Analysis codes, raw data, and source data to generate figures, extended data, and supplementary data for the manuscript titled: \"A train-and-assist device that upskills novices to strengthen the workforce and expand diagnostic access.\"
", "doi": "10.22002/qsx5j-53280", "publisher": "CaltechDATA", "publication_date": "2026-04-17" }, { "id": "data:wnh8n-mh110", "collection": "data", "collection_id": "wnh8n-mh110", "cite_using_url": "https://data.caltech.edu/records/wnh8n-mh110", "type": "dataset", "title": "A class of train-and-assist biomedical devices to strengthen the workforce and expand diagnostic access", "author": [ { "family_name": "Lee", "given_name": "Minkyo", "orcid": "0000-0002-2714-179X" }, { "family_name": "Pei", "given_name": "Xinyue (Penny)", "orcid": "0009-0003-9840-6243" }, { "family_name": "Jin", "given_name": "Si Hyung", "orcid": "0000-0003-3376-2549" }, { "family_name": "Shelby", "given_name": "Natasha", "orcid": "0000-0001-9097-3663" }, { "family_name": "Gera", "given_name": "Rani", "orcid": "0000-0003-1888-4337" }, { "family_name": "Viloria Winnett", "given_name": "Alexander", "orcid": "0000-0002-7338-5605" }, { "family_name": "Camerer", "given_name": "Colin F.", "orcid": "0000-0003-4049-1871" }, { "family_name": "Rahman", "given_name": "Mahbubur", "orcid": "0000-0003-0520-2683" }, { "family_name": "Pilotte", "given_name": "Nils", "orcid": "0000-0002-8447-7425" }, { "family_name": "Williams", "given_name": "Steven A.", "orcid": "0000-0002-4881-7496" }, { "family_name": "Ismagilov", "given_name": "Rustem F.", "orcid": "0000-0002-3680-4399" } ], "abstract": "Analysis codes, raw data, and source data to generate figures, extended data, and supplementary data for the manuscript titled: \"A class of train-and-assist biomedical devices to strengthen the workforce and expand diagnostic access.\"
", "doi": "10.22002/wnh8n-mh110", "publisher": "CaltechDATA", "publication_date": "2025-05-19" }, { "id": "data:c396r-v7t98", "collection": "data", "collection_id": "c396r-v7t98", "cite_using_url": "https://data.caltech.edu/records/c396r-v7t98", "type": "dataset", "title": "Instructional device assists and trains laboratory-na\u00efve users in sample pooling for high-performance, low-cost molecular testing", "author": [ { "family_name": "Lee", "given_name": "Minkyo", "orcid": "0000-0002-2714-179X" }, { "family_name": "Pei", "given_name": "Xinyue (Penny)", "orcid": "0009-0003-9840-6243" }, { "family_name": "Jin", "given_name": "Si Hyung", "orcid": "0000-0003-3376-2549" }, { "family_name": "Shelby", "given_name": "Natasha", "orcid": "0000-0001-9097-3663" }, { "family_name": "Gera", "given_name": "Rani", "orcid": "0000-0003-1888-4337" }, { "family_name": "Viloria Winnett", "given_name": "Alexander", "orcid": "0000-0002-7338-5605" }, { "family_name": "Camerer", "given_name": "Colin F.", "orcid": "0000-0003-4049-1871" }, { "family_name": "Rahman", "given_name": "Mahbubur", "orcid": "0000-0003-0520-2683" }, { "family_name": "Pilotte", "given_name": "Nils", "orcid": "0000-0002-8447-7425" }, { "family_name": "Williams", "given_name": "Steven A.", "orcid": "0000-0002-4881-7496" }, { "family_name": "Ismagilov", "given_name": "Rustem F.", "orcid": "0000-0002-3680-4399" } ], "abstract": "Analysis codes, raw data, and source data to generate figures, extended data, and supplementary data for the manuscript titled: \"Instructional device assists and trains laboratory-na\u00efve users in sample pooling for high-performance, low-cost molecular testing.\"
", "doi": "10.22002/c396r-v7t98", "publisher": "CaltechDATA", "publication_date": "2025-05-09" }, { "id": "data:wp1j8-k0j94", "collection": "data", "collection_id": "wp1j8-k0j94", "cite_using_url": "https://data.caltech.edu/records/wp1j8-k0j94", "type": "dataset", "title": "Instructional device assists and trains laboratory-na\u00efve users in sample pooling for high-performance, low-cost molecular testing", "author": [ { "family_name": "Lee", "given_name": "Minkyo", "orcid": "0000-0002-2714-179X" }, { "family_name": "Pei", "given_name": "Xinyue (Penny)", "orcid": "0009-0003-9840-6243" }, { "family_name": "Jin", "given_name": "Si Hyung", "orcid": "0000-0003-3376-2549" }, { "family_name": "Shelby", "given_name": "Natasha", "orcid": "0000-0001-9097-3663" }, { "family_name": "Gera", "given_name": "Rani", "orcid": "0000-0003-1888-4337" }, { "family_name": "Viloria Winnett", "given_name": "Alexander", "orcid": "0000-0002-7338-5605" }, { "family_name": "Camerer", "given_name": "Colin F.", "orcid": "0000-0003-4049-1871" }, { "family_name": "Rahman", "given_name": "Mahbubur", "orcid": "0000-0003-0520-2683" }, { "family_name": "Pilotte", "given_name": "Nils", "orcid": "0000-0002-8447-7425" }, { "family_name": "Williams", "given_name": "Steven A.", "orcid": "0000-0002-4881-7496" }, { "family_name": "Ismagilov", "given_name": "Rustem F.", "orcid": "0000-0002-3680-4399" } ], "abstract": "Analysis codes, raw data, and source data to generate figures, extended data, and supplementary data for the manuscript titled: \"Instructional device assists and trains laboratory-na\u00efve users in sample pooling for high-performance, low-cost molecular testing.\"
", "doi": "10.22002/wp1j8-k0j94", "publisher": "CaltechDATA", "publication_date": "2025-03-14" }, { "id": "data:gx69z-wec80", "collection": "data", "collection_id": "gx69z-wec80", "cite_using_url": "https://data.caltech.edu/records/gx69z-wec80", "type": "dataset", "title": "Microbial-enrichment method enables high-throughput metagenomic characterization from host-rich samples", "author": [ { "family_name": "Ismagilov", "given_name": "Rustem F.", "orcid": "0000-0002-3680-4399" }, { "family_name": "Barlow", "given_name": "Jacob", "orcid": "0000-0002-1842-4835" }, { "family_name": "Wu-Woods", "given_name": "Natalie", "orcid": "0000-0001-5070-9091" }, { "family_name": "Trigodet", "given_name": "Florian", "orcid": "0000-0002-4933-2896" }, { "family_name": "Shaw", "given_name": "Dustin", "orcid": "0000-0003-3961-7588" }, { "family_name": "Romano", "given_name": "Anna", "orcid": "0000-0002-7148-0668" }, { "family_name": "Jabri", "given_name": "Bana", "orcid": "0000-0001-7427-4424" }, { "family_name": "Eren", "given_name": "A. Murat", "orcid": "0000-0001-9013-4827" } ], "abstract": "Code, raw data, and source data to generate figures and extended data for the manuscript titled: \"Microbial-enrichment method enables high-throughput metagenomic characterization from host-rich samples\".
", "doi": "10.22002/gx69z-wec80", "publisher": "CaltechDATA", "publication_date": "2023-07-05" }, { "id": "data:zg1d3-k3b49", "collection": "data", "collection_id": "zg1d3-k3b49", "cite_using_url": "https://data.caltech.edu/records/zg1d3-k3b49", "type": "dataset", "title": "Quantitative whole-tissue 3D imaging reveals bacteria in close association with mouse jejunum mucosa", "author": [ { "family_name": "Poceviciute", "given_name": "Roberta", "orcid": "0000-0002-6649-2170" }, { "family_name": "Bogatyrev", "given_name": "Said R.", "orcid": "0000-0003-0486-9451" }, { "family_name": "Romano", "given_name": "Anna E.", "orcid": "0000-0002-7148-0668" }, { "family_name": "Dilmore", "given_name": "Amanda H.", "orcid": "0000-0001-6493-7116" }, { "family_name": "Mondrag\u00f3n-Palomino", "given_name": "Octavio", "orcid": "0000-0003-1129-4932" }, { "family_name": "Takko", "given_name": "Heli", "orcid": "0000-0003-2544-409X" }, { "family_name": "Ismagilov", "given_name": "Rustem F.", "orcid": "0000-0002-3680-4399" } ], "abstract": "Raw and processed data and imaging files [0.42 TB total] for the bioRxiv preprint \"Quantitative whole-tissue 3D imaging reveals bacteria in close association with mouse jejunum mucosa\"", "doi": "10.22002/zg1d3-k3b49", "publisher": "CaltechDATA", "publication_date": "2023-06-16" }, { "id": "data:tds5b-9rs75", "collection": "data", "collection_id": "tds5b-9rs75", "cite_using_url": "https://data.caltech.edu/records/tds5b-9rs75", "type": "dataset", "title": "The ratio between SARS-CoV-2 RNA viral load and culturable viral titer differs depending on stage of infection", "author": [ { "family_name": "Porter", "given_name": "Michael Koizumi", "orcid": "0000-0002-0777-7563" }, { "family_name": "Alexander", "given_name": "Viloria Winnett", "orcid": "0000-0002-7338-5605" }, { "family_name": "Hao", "given_name": "Linhui", "orcid": "0000-0002-7325-1009" }, { "family_name": "Shelby", "given_name": "Natasha", "orcid": "0000-0001-9097-3663" }, { "family_name": "Reyes", "given_name": "Jessica A", "orcid": "0000-0002-5507-7633" }, { "family_name": "Schlenker", "given_name": "Noah W", "orcid": "0000-0002-8581-4403" }, { "family_name": "Romano", "given_name": "Anna E" }, { "family_name": "Tognazzini", "given_name": "Colton", "orcid": "0000-0002-2754-3588" }, { "family_name": "Feaster", "given_name": "Matthew", "orcid": "0000-0001-9966-2845" }, { "family_name": "Goh", "given_name": "Ying-Ying", "orcid": "0000-0001-5136-7214" }, { "family_name": "Gale, Jr.", "given_name": "Michael", "orcid": "0000-0002-6332-7436" }, { "family_name": "Ismagilov", "given_name": "Rustem F.", "orcid": "0000-0002-3680-4399" } ], "abstract": "Data for the manuscript: The ratio between SARS-CoV-2 RNA viral load and culturable viral titer differs depending on stage of infection
", "doi": "10.22002/tds5b-9rs75", "publisher": "CaltechDATA", "publication_date": "2023" }, { "id": "data:5vng7-8ne78", "collection": "data", "collection_id": "5vng7-8ne78", "cite_using_url": "https://data.caltech.edu/records/5vng7-8ne78", "type": "dataset", "title": "Quantitative whole-tissue 3D imaging reveals bacteria in close association with mouse jejunum mucosa", "author": [ { "family_name": "Poceviciute", "given_name": "Roberta", "orcid": "0000-0002-6649-2170" }, { "family_name": "Bogatyrev", "given_name": "Said R.", "orcid": "0000-0003-0486-9451" }, { "family_name": "Romano", "given_name": "Anna E.", "orcid": "0000-0002-7148-0668" }, { "family_name": "Dilmore", "given_name": "Amanda H.", "orcid": "0000-0001-6493-7116" }, { "family_name": "Mondrag\u00f3n-Palomino", "given_name": "Octavio", "orcid": "0000-0003-1129-4932" }, { "family_name": "Takko", "given_name": "Heli", "orcid": "0000-0003-2544-409X" }, { "family_name": "Ismagilov", "given_name": "Rustem F.", "orcid": "0000-0002-3680-4399" } ], "abstract": "Raw and processed data and imaging files [0.42 TB total] for the bioRxiv preprint \"Quantitative whole-tissue 3D imaging reveals bacteria in close association with mouse jejunum mucosa\"", "doi": "10.22002/D1.20199", "publisher": "CaltechDATA", "publication_date": "2022-06-16" }, { "id": "data:daw89-7qg52", "collection": "data", "collection_id": "daw89-7qg52", "cite_using_url": "https://data.caltech.edu/records/daw89-7qg52", "type": "dataset", "title": "[dataset] Commercial stocks of SARS-CoV-2 RNA may report low concentration values, leading to artificially increased apparent sensitivity of diagnostic assays", "author": [ { "family_name": "Jue", "given_name": "Erik", "orcid": "0000-0001-7585-3794" }, { "family_name": "Ismagilov", "given_name": "Rustem F.", "orcid": "0000-0002-3680-4399" } ], "abstract": "Full dataset for \"Commercial stocks of SARS-CoV-2 RNA may report low concentration values, leading to artificially increased apparent sensitivity of diagnostic assays \" published as pre-print in medrxiv", "doi": "10.22002/D1.1424", "publisher": "CaltechDATA", "publication_date": "2020-04-29" }, { "id": "data:88yzp-h0n85", "collection": "data", "collection_id": "88yzp-h0n85", "cite_using_url": "https://data.caltech.edu/records/88yzp-h0n85", "type": "dataset", "title": "Self-reinoculation with fecal flora changes microbiota density and composition leading to an altered bile-acid profile in the mouse small intestine", "author": [ { "family_name": "Bogatyrev", "given_name": "Said R.", "orcid": "0000-0003-0486-9451" }, { "family_name": "Rolando", "given_name": "Justin C.", "orcid": "0000-0001-8948-319X" }, { "family_name": "Ismagilov", "given_name": "Rustem F.", "orcid": "0000-0002-3680-4399" } ], "abstract": "Background: The upper gastrointestinal tract plays a prominent role in human physiology as the primary site for enzymatic digestion and nutrient absorption, immune sampling, and drug uptake. Alterations to the small-intestine microbiome have been implicated in various human diseases, such as non-alcoholic steatohepatitis and inflammatory bowel conditions. Yet, the physiological and functional roles of the small-intestine microbiota in humans remain poorly characterized because of the complexities associated with its sampling. Rodent models are used extensively in microbiome research and enable the spatial, temporal, compositional, and functional interrogation of the gastrointestinal microbiota and its effects on the host physiology and disease phenotype. Classical, culture-based studies have documented that fecal microbial self-reinoculation (via coprophagy) affects the composition and abundance of microbes in the murine proximal gastrointestinal tract. This pervasive self-reinoculation behavior could be a particularly relevant study factor when investigating small-intestine microbiota. Modern microbiome studies either do not take self-reinoculation into account, or assume that approaches such as single housing mice or housing on wire mesh floors eliminate it. These assumptions have not been rigorously tested with modern tools. Here, we used quantitative 16S rRNA gene amplicon sequencing, quantitative microbial functional gene content inference, and metabolomic analyses of bile acids to evaluate the effects of self-reinoculation on microbial loads, composition, and function in the murine upper gastrointestinal tract.\n\nResults: In coprophagic mice, continuous self-exposure to the fecal flora had substantial quantitative and qualitative effects on the upper gastrointestinal microbiome. These differences in microbial abundance and community composition were associated with an altered profile of the small-intestine bile acid pool, and, importantly, could not be inferred from analyzing large-intestine or stool samples. Overall, the patterns observed in the small intestine of non-coprophagic mice (reduced total microbial load, low abundance of anaerobic microbiota, and bile acids predominantly in the conjugated form) resemble those typically seen in the human small intestine. \nConclusions: Future studies need to take self-reinoculation into account when using mouse models to evaluate gastrointestinal microbial colonization and function in relation to xenobiotic transformation and pharmacokinetics or in the context of physiological states and diseases linked to small-intestine microbiome and to small-intestine dysbiosis.", "doi": "10.22002/D1.1295", "publisher": "CaltechDATA", "publication_date": "2019-10-14" } ]