<h1>Ismagilov, Rustem</h1> <h2>Combined from <a href="https://authors.library.caltech.edu">CaltechAUTHORS</a></h2> <ul> <li>Wu-Woods, Natalie J. and Barlow, Jacob T., el al. (2023) <a href="https://authors.library.caltech.edu/records/rjrx5-9bm15">Microbial-enrichment method enables high-throughput metagenomic characterization from host-rich samples</a>; Nature Methods; <a href="https://doi.org/10.1038/s41592-023-02025-4">10.1038/s41592-023-02025-4</a></li> <li>Ji, Jenny and Viloria Winnett, Alexander, el al. (2023) <a href="https://authors.library.caltech.edu/records/7j7m9-fec46">Index cases first identified by nasal-swab rapid COVID-19 tests had more transmission to household contacts than cases identified by other test types</a>; PLOS ONE; Vol. 18; No. 10; e0292389; PMCID PMC10553276; <a href="https://doi.org/10.1371/journal.pone.0292389">10.1371/journal.pone.0292389</a></li> <li>Poceviciute, Roberta and Bogatyrev, Said R., el al. (2023) <a href="https://authors.library.caltech.edu/records/4rjkx-r3m91">Quantitative whole-tissue 3D imaging reveals bacteria in close association with mouse jejunum mucosa</a>; npj Biofilms and Microbiomes; Vol. 9; 64; PMCID PMC10485000; <a href="https://doi.org/10.1038/s41522-023-00423-2">10.1038/s41522-023-00423-2</a></li> <li>Winnett, Alexander Viloria and Akana, Reid, el al. (2023) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20230628-344482000.1">Daily SARS-CoV-2 Nasal Antigen Tests Miss Infected and Presumably Infectious People Due to Viral Load Differences among Specimen Types</a>; Microbiology Spectrum; Vol. 11; No. 4; e01295-23; PMCID PMC10434058; <a href="https://doi.org/10.1128/spectrum.01295-23">10.1128/spectrum.01295-23</a></li> <li>Ji, Jenny and Winnett, Alexander Viloria, el al. (2023) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20230323-420614000.1">Index Cases First Identified by Nasal-Swab Rapid COVID-19 Tests Had More Transmission to Household Contacts Than Cases Identified by Other Test Types</a>; <a href="https://doi.org/10.1101/2023.03.09.23286855">10.1101/2023.03.09.23286855</a></li> <li>Winnett, Alexander Viloria and Akana, Reid, el al. (2023) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20230323-759607000.4">Extreme differences in SARS-CoV-2 viral loads among respiratory specimen types during presumed pre-infectious and infectious periods</a>; PNAS Nexus; Vol. 2; No. 3; pgad033; PMCID PMC10013338; <a href="https://doi.org/10.1093/pnasnexus/pgad033">10.1093/pnasnexus/pgad033</a></li> <li>Carter, Alyssa M. and Winnett, Alexander Viloria, el al. (2023) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20230130-263514000.2">Laboratory Evaluation Links Some False-Positive COVID-19 Antigen Test Results Observed in a Field Study to a Specific Lot of Test Strips</a>; Open Forum Infectious Diseases; Vol. 10; No. 1; Art. No. ofac701; PMCID PMC9887260; <a href="https://doi.org/10.1093/ofid/ofac701">10.1093/ofid/ofac701</a></li> <li>Earley, Zachary M. and Lisicka, Wioletta, el al. (2023) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20230130-262818000.1">GATA4 controls regionalization of tissue immunity and commensal-driven immunopathology</a>; Immunity; Vol. 56; No. 1; 43-57.e10; <a href="https://doi.org/10.1016/j.immuni.2022.12.009">10.1016/j.immuni.2022.12.009</a></li> <li>Winnett, Alexander Viloria and Porter, Michael K., el al. (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20221110-430693700.10">Morning SARS-CoV-2 Testing Yields Better Detection of Infection Due to Higher Viral Loads in Saliva and Nasal Swabs upon Waking</a>; Microbiology Spectrum; Vol. 10; No. 6; e03873-22; PMCID PMC9769854; <a href="https://doi.org/10.1128/spectrum.03873-22">10.1128/spectrum.03873-22</a></li> <li>Winnett, Alexander Viloria and Akana, Reid, el al. (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20220720-917402000">Extreme differences in SARS-CoV-2 viral loads among respiratory specimen types during presumed pre-infectious and infectious periods</a>; <a href="https://doi.org/10.1101/2022.07.13.22277113">10.1101/2022.07.13.22277113</a></li> <li>Winnett, Alexander Viloria and Akana, Reid, el al. (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20220720-917093000">Why Daily SARS-CoV-2 Nasal Rapid Antigen Testing Poorly Detects Infected and Infectious Individuals</a>; <a href="https://doi.org/10.1101/2022.07.13.22277513">10.1101/2022.07.13.22277513</a></li> <li>Poceviciute, Roberta and Bogatyrev, Said R., el al. (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20220706-965018000">Quantitative whole-tissue 3D imaging reveals bacteria in close association with mouse jejunum mucosa</a>; <a href="https://doi.org/10.1101/2022.06.17.496478">10.1101/2022.06.17.496478</a></li> <li>Mondragón-Palomino, Octavio and Poceviciute, Roberta, el al. (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20220428-203848852">Three-dimensional imaging for the quantification of spatial patterns in microbiota of the intestinal mucosa</a>; Proceedings of the National Academy of Sciences; Vol. 119; No. 18; Art. No. e2118483119; PMCID PMC9171773; <a href="https://doi.org/10.1073/pnas.2118483119">10.1073/pnas.2118483119</a></li> <li>Winnett, Alexander Viloria and Porter, Michael K., el al. (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20220307-188444000">Morning SARS-CoV-2 testing yields better detection of infection due to higher viral loads in saliva and nasal swabs upon waking</a>; <a href="https://doi.org/10.1101/2022.03.02.22271724">10.1101/2022.03.02.22271724</a></li> <li>Savela, Emily S. and Winnett, Alexander Viloria, el al. (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20210407-080559241">Quantitative SARS-CoV-2 Viral-Load Curves in Paired Saliva Samples and Nasal Swabs Inform Appropriate Respiratory Sampling Site and Analytical Test Sensitivity Required for Earliest Viral Detection</a>; Journal of Clinical Microbiology; Vol. 60; No. 2; Art. No. e01785-21; PMCID PMC8849374; <a href="https://doi.org/10.1128/JCM.01785-21">10.1128/JCM.01785-21</a></li> <li>Arrastia, Mary V. and Jachowicz, Joanna W., el al. (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200813-130113364">Single-cell measurement of higher-order 3D genome organization with scSPRITE</a>; Nature Biotechnology; Vol. 40; No. 1; 64-73; <a href="https://doi.org/10.1038/s41587-021-00998-1">10.1038/s41587-021-00998-1</a></li> <li>Barlow, Jacob T. and Leite, Gabriela, el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20211110-202208524">Quantitative sequencing clarifies the role of disruptor taxa, oral microbiota, and strict anaerobes in the human small-intestine microbiome</a>; Microbiome; Vol. 9; Art. No. 214; PMCID PMC8561862; <a href="https://doi.org/10.1186/s40168-021-01162-2">10.1186/s40168-021-01162-2</a></li> <li>Ji, Jenny and Winnett, Alexander, el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20220512-142847077">Modulating Factors of Household Transmission of SARS‑CoV‑2 in a Community-Based Study</a>; American Journal of Tropical Medicine and Hygiene; Vol. 105; No. 5; 313; <a href="https://doi.org/10.4269/ajtmh.abstract2021">10.4269/ajtmh.abstract2021</a></li> <li>Mondragón-Palomino, Octavio and Poceviciute, Roberta, el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20211015-222210959">3D imaging for the quantification of spatial patterns in microbiota of the intestinal mucosa</a>; <a href="https://doi.org/10.1101/2021.10.07.463215">10.1101/2021.10.07.463215</a></li> <li>Olson, Christine A. and Iñiguez, Alonso J., el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20210908-171123816">Alterations in the gut microbiota contribute to cognitive impairment induced by the ketogenic diet and hypoxia</a>; Cell Host and Microbe; Vol. 29; No. 9; 1378-1392; PMCID PMC8429275; <a href="https://doi.org/10.1016/j.chom.2021.07.004">10.1016/j.chom.2021.07.004</a></li> <li>Wu, Wei-Li and Adame, Mark D., el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20210706-202344110">Microbiota regulate social behaviour via stress response neurons in the brain</a>; Nature; Vol. 595; No. 7867; 409-414; PMCID PMC8346519; <a href="https://doi.org/10.1038/s41586-021-03669-y">10.1038/s41586-021-03669-y</a></li> <li>Winnett, Alexander and Cooper, Matthew M., el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20201211-113537700">SARS-CoV-2 Viral Load in Saliva Rises Gradually and to Moderate Levels in Some Humans</a>; PMCID PMC7743094; <a href="https://doi.org/10.1101/2020.12.09.20239467">10.1101/2020.12.09.20239467</a></li> <li>Khazaei, Tahmineh and Williams, Rory L., el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200813-144241318">Metabolic multistability and hysteresis in a model aerobe-anaerobe microbiome community</a>; Science Advances; Vol. 6; No. 33; Art. No. eaba0353; PMCID PMC7423363; <a href="https://doi.org/10.1126/sciadv.aba0353">10.1126/sciadv.aba0353</a></li> <li>Barlow, Jacob T. and Bogatyrev, Said R., el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200303-103834329">A Quantitative Sequencing Framework for Absolute Abundance Measurements of Mucosal and Lumenal Microbial Communities</a>; Nature Communications; Vol. 11; Art. No. 2590; PMCID PMC7244552; <a href="https://doi.org/10.1038/s41467-020-16224-6">10.1038/s41467-020-16224-6</a></li> <li>Jue, Erik and Ismagilov, Rustem F. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200519-071416134">Commercial stocks of SARS-CoV-2 RNA may report low concentration values, leading to artificially increased apparent sensitivity of diagnostic assays</a>; <a href="https://doi.org/10.1101/2020.04.28.20077602">10.1101/2020.04.28.20077602</a></li> <li>Yu, Ziqing and Lyu, Weiyuan, el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200219-114918172">Self-partitioning SlipChip for slip-induced droplet formation and human papillomavirus viral load quantification with digital LAMP</a>; Biosensors and Bioelectronics; Vol. 155; Art. No. 112107; <a href="https://doi.org/10.1016/j.bios.2020.112107">10.1016/j.bios.2020.112107</a></li> <li>Rolando, Justin C. and Jue, Erik, el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200302-155937790">Real-time kinetics and high-resolution melt curves in single-molecule digital LAMP to differentiate and study specific and non-specific amplification</a>; Nucleic Acids Research; Vol. 48; No. 7; Art. No. e42; PMCID PMC7144905; <a href="https://doi.org/10.1093/nar/gkaa099">10.1093/nar/gkaa099</a></li> <li>Faber, Katherine T. and Kornfield, Julia A., el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20210201-150525983">Freeze-cast ceramic membrane for size based filtration</a></li> <li>Schoepp, Nathan G. and Liaw, Eric J., el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200320-065850359">Differential DNA accessibility to polymerase enables 30-minute phenotypic β-lactam antibiotic susceptibility testing of carbapenem-resistant Enterobacteriaceae</a>; PLoS Biology; Vol. 18; No. 3; Art. No. 3000652; PMCID PMC7081982; <a href="https://doi.org/10.1371/journal.pbio.3000652">10.1371/journal.pbio.3000652</a></li> <li>Savela, Emily S. and Schoepp, Nathan G., el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200319-141031875">Surfactant-enhanced DNA accessibility to nuclease accelerates phenotypic β-lactam antibiotic susceptibility testing of Neisseria gonorrhoeae</a>; PLoS Biology; Vol. 18; No. 3; Art. No. 3000651; PMCID PMC7081974; <a href="https://doi.org/10.1371/journal.pbio.3000651">10.1371/journal.pbio.3000651</a></li> <li>Khazaei, Tahmineh and Williams, Rory L., el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200303-084602692">Metabolic multi-stability and hysteresis in a model aerobe-anaerobe microbiome community</a>; <a href="https://doi.org/10.1101/2020.02.28.968941">10.1101/2020.02.28.968941</a></li> <li>Bogatyrev, Said R. and Rolando, Justin C., el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200212-152816065">Self-reinoculation with fecal flora changes microbiota density and composition leading to an altered bile-acid profile in the mouse small intestine</a>; Microbiome; Vol. 8; Art. No. 19; PMCID PMC7017497; <a href="https://doi.org/10.1186/s40168-020-0785-4">10.1186/s40168-020-0785-4</a></li> <li>Jue, Erik and Witters, Daan, el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200206-125057522">Two-phase wash to solve the ubiquitous contaminant-carryover problem in commercial nucleic-acid extraction kits</a>; Scientific Reports; Vol. 10; Art. No. 1940; PMCID PMC7004994; <a href="https://doi.org/10.1038/s41598-020-58586-3">10.1038/s41598-020-58586-3</a></li> <li>Bogatyrev, Said R. and Ismagilov, Rustem F. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200123-094353991">Quantitative microbiome profiling in lumenal and tissue samples with broad coverage and dynamic range via a single-step 16S rRNA gene DNA copy quantification and amplicon barcoding</a>; <a href="https://doi.org/10.1101/2020.01.22.914705">10.1101/2020.01.22.914705</a></li> <li>Zhukov, Dmitriy V. and Khorosheva, Eugenia M., el al. (2019) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20190823-090755927">Microfluidic SlipChip device for multistep multiplexed biochemistry on a nanoliter scale</a>; Lab on a Chip; Vol. 19; No. 19; 3200-3211; <a href="https://doi.org/10.1039/c9lc00541b">10.1039/c9lc00541b</a></li> <li>Porter, Michael K. and Steinberg, Asher Preska, el al. (2019) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20190823-085722494">Interplay of motility and polymer-driven depletion forces in the initial stages of bacterial aggregation</a>; Soft Matter; Vol. 15; No. 35; 7071-7079; <a href="https://doi.org/10.1039/c9sm00791a">10.1039/c9sm00791a</a></li> <li>Yu, Mengchao and Chen, Xiaoying, el al. (2019) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20190523-142111730">Multistep SlipChip for the Generation of Serial Dilution Nanoliter Arrays and Hepatitis B Viral Load Quantification by Digital Loop Mediated Isothermal Amplification</a>; Analytical Chemistry; Vol. 91; No. 14; 8751-8755; <a href="https://doi.org/10.1021/acs.analchem.9b01270">10.1021/acs.analchem.9b01270</a></li> <li>Preska Steinberg, Asher and Wang, Zhen-Gang, el al. (2019) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20190619-091518942">Food Polyelectrolytes Compress the Colonic Mucus Hydrogel by a Donnan Mechanism</a>; Biomacromolecules; Vol. 20; No. 7; 2675-2683; <a href="https://doi.org/10.1021/acs.biomac.9b00442">10.1021/acs.biomac.9b00442</a></li> <li>Poceviciute, Roberta and Ismagilov, Rustem F. (2019) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20190710-125335706">Human-gut-microbiome on a chip</a>; Nature Biomedical Engineering; Vol. 3; No. 7; 500-501; <a href="https://doi.org/10.1038/s41551-019-0425-0">10.1038/s41551-019-0425-0</a></li> <li>Savela, Emily and Schoepp, Nathan G., el al. (2019) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200127-080528197">Cell Envelope Damage of N. gonorrhoeae after 15-min Beta-Lactam Exposure Enables Rapid Antimicrobial Susceptibility Testing</a>; Sexually Transmitted Infections; Vol. 95; No. S1; A291; <a href="https://doi.org/10.1136/sextrans-2019-sti.729">10.1136/sextrans-2019-sti.729</a></li> <li>Preska Steinberg, Asher and Datta, Sujit S., el al. (2019) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20181210-140412486">High-molecular-weight polymers from dietary fiber drive aggregation of particulates in the murine small intestine</a>; eLife; Vol. 8; Art. No. e40387; PMCID PMC6342521; <a href="https://doi.org/10.7554/eLife.40387">10.7554/eLife.40387</a></li> <li>Rolando, Justin C. and Jue, Erik, el al. (2019) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20181221-105356677">Real-Time, Digital LAMP with Commercial Microfluidic Chips Reveals the Interplay of Efficiency, Speed, and Background Amplification as a Function of Reaction Temperature and Time</a>; Analytical Chemistry; Vol. 91; No. 1; 1034-1042; PMCID PMC6322147; <a href="https://doi.org/10.1021/acs.analchem.8b04324">10.1021/acs.analchem.8b04324</a></li> <li>Khazaei, Tahmineh and Barlow, Jacob T., el al. (2018) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20180802-093834589">RNA markers enable phenotypic test of antibiotic susceptibility in Neisseria gonorrhoeae after 10 minutes of ciprofloxacin exposure</a>; Scientific Reports; Vol. 8; Art. No. 11606; PMCID PMC6072703; <a href="https://doi.org/10.1038/s41598-018-29707-w">10.1038/s41598-018-29707-w</a></li> <li>Schoepp, Nathan G. and Schlappi, Travis S., el al. (2017) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20161213-131157930">Rapid pathogen-specific phenotypic antibiotic susceptibility testing using digital LAMP quantification in clinical samples</a>; Science Translational Medicine; Vol. 9; No. 410; Art. No. eaal3693; PMCID PMC6765391; <a href="https://doi.org/10.1126/scitranslmed.aal3693">10.1126/scitranslmed.aal3693</a></li> <li>Pompano, Rebecca R. and Chiang, Andrew H., el al. (2017) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170628-083437438">Conceptual and Experimental Tools to Understand Spatial Effects and Transport Phenomena in Nonlinear Biochemical Networks Illustrated with Patchy Switching</a>; Annual Review of Biochemistry; Vol. 86; 333-356; PMCID PMC10852032; <a href="https://doi.org/10.1146/annurev-biochem-060815-014207">10.1146/annurev-biochem-060815-014207</a></li> <li>Selck, David A. and Ismagilov, Rustem F. (2016) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20161031-113924216">Instrument for Real-Time Digital Nucleic Acid Amplification on Custom Microfluidic Devices</a>; PLOS ONE; Vol. 11; No. 10; Art. No. e0163060; PMCID PMC5070811; <a href="https://doi.org/10.1371/journal.pone.0163060">10.1371/journal.pone.0163060</a></li> <li>Schoepp, Nathan G. and Khorosheva, Eugenia M., el al. (2016) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20160705-083001025">Digital Quantification of DNA Replication and Chromosome Segregation Enables Determination of Antimicrobial Susceptibility after only 15 Minutes of Antibiotic Exposure</a>; Angewandte Chemie International Edition in English; Vol. 55; No. 33; 9557-9561; PMCID PMC5215780; <a href="https://doi.org/10.1002/ange.201602763">10.1002/ange.201602763</a></li> <li>Schlappi, Travis S. and McCalla, Stephanie E., el al. 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