Published in bioRxiv, 2024
In this manuscript, we used brain organoids to investigate how different cell types and environmental contexts influence gene regulation.
Recommended citation: Benjamin D Umans and Yoav Gilad (2024). "Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids" bioRxiv. 2024.09.03.611030.
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Published in bioRxiv, 2024
In this manuscript, we extended prior work investigating the roles of vagal TRPV1+ neurons in pulmonary infections, looking here at roles in organizing the immune response to influenza.
Recommended citation: Daping Yang, Nicole Almanzar, Jingya Xia, Swalpa Udit, Stephen T Yeung, Camille Khairallah, Daisy A Hoagland, Benjamin D Umans, Nicole Sarden, Ozge Erdogan, Nadia Baalbaki, Anna Beekmayer-Dhillon, Juhyun Lee, Kimberly A Meerschaert, Stephen D Liberles, Bryan G Yipp, Ruth A Franklin, Kamal M Khanna, Pankaj Baral, Adam L Haber, Isaac M Chiu. (2024). "Vagal TRPV1+ sensory neurons regulate myeloid cell dynamics and protect against influenza virus infection" bioRxiv. 2024.08.21.609013.
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Published in Trends in Genetics, 2021
In this review, we discuss current challenges and potential future strategies for identifying gene regulatory effects contributing to human complex traits.
Recommended citation: B. D. Umans, A. Battle, and Y. Gilad. (2021). "Where Are the Disease-Associated eQTLs?" Trends in Genetics. 37(2) 109-124.
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Published in Cell, 2020
In this paper, we identified and characterized a defined subset of sensory neurons that detects chemical stimuli in the larynx to evoke protective reflexes.
Recommended citation: S. L. Prescott*, B. D. Umans*, E. K. Williams, R. D. Brust, and S. D. Liberles. (2020). "An Airway Protection Program Revealed by Sweeping Genetic Control of Vagal Afferents." Cell. 181(3) 574-589.e14.
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Published in Trends in Neurosciences, 2018
In this review, we discuss neural mechanisms of volume sensing across three organ systems.
Recommended citation: B. D. Umans and S. D. Liberles. (2018). "Neural Sensing of Organ Volume." Trends in Neurosciences. 41(12) 911-924.
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Published in Nature Medicine, 2018
In this paper, we used a cell type-specific ablation strategy to demonstrate an essential role for subsets of vagal sensory neurons in the response to lung bacterial infection.
Recommended citation: P. Baral, B. D. Umans, L. Li, A. Wallrapp, M. Bist, T. Kirschbaum, Y. Wei, Y. Zhou, V. K. Kuchroo, P. R. Burkett, B. G. Yipp, S. D. Liberles, and I. M. Chiu. (2018). "Nociceptor sensory neurons suppress neutrophil and γδ T cell responses in bacterial lung infections and lethal pneumonia." Nature Medicine. 24(4) 417-426.
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Published in PLoS ONE, 2017
In this paper, we used chromatin conformation capture (Hi-C) to examine features of Drosophila genome organization.
Recommended citation: S. El-Sharnouby, B. Fischer, J. P. Magbanua, B. Umans, R. Flower, S. W. Choo, S. Russell, and R. White. (2017). "Regions of very low H3K27me3 partition the Drosophila genome into topological domains." PLoS ONE. 12(3) e0172725.
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Published in Antimicrobial Agents and Chemotherapy, 2016
In this paper, we continued our prior investigation of Vibrio cholerae outer membrane assembly and integrity by applying Tn-seq to a post-antibiotic recovery paradigm.
Recommended citation: A. I. Weaver, S. G. Murphy, B. D. Umans, S. Tallavajhala, I. Onyekwere, S. Wittels, J.-H. Shin, M. VanNieuwenhze, M. K. Waldor, and T. Dörr. (2016). "Genetic Determinants of Penicillin Tolerance in Vibrio cholerae." Antimicrobial Agents and Chemotherapy. 62(10):e01326-18
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Published in Antimicrobial Agents and Chemotherapy, 2016
In this paper, we implemented a Tn-seq screening strategy to identify proteins required for bacterial outer membrane function.
Recommended citation: T. Dörr, F. Delgado, B. D. Umans, M. A. Gerding, B. M. Davis, and M. K. Waldor. (2016). "A Transposon Screen Identifies Genetic Determinants of Vibrio cholerae Resistance to High-Molecular-Weight Antibiotics." Antimicrobial Agents and Chemotherapy. 60(8) 4757-4763.
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Published in Skeletal Radiology, 2016
In this paper, we designed and executed a study to identify simple MRI features that would accurately predict plantar plate tear injuries and help prioritize patients that would benefit from targeted diagnostic follow-up.
Recommended citation: R. L. Umans, B. D. Umans, H. Umans, and E. Elsinger. (2016). "Predictive MRI correlates of lesser metatarsophalangeal joint plantar plate tear." Skeletal Radiology. 45(7) 969-975.
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Published in Cell, 2016
In this paper, we identified genetically defined vagal sensory neuron subtypes that innervate the stomach and small intestine, respond to gastrointestinal chemical and mechanical stimuli, and evoke gastrointestinal motor control outputs.
Recommended citation: E. K. Williams, R. B. Chang, D. E. Strochlic, B. D. Umans, B. B. Lowell, and S. D. Liberles. (2016). "Sensory Neurons that Detect Stretch and Nutrients in the Digestive System." Cell. 166(1) 209-221.
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Published in International Journal of Circumpolar Health, 2015
In this paper, we used genetic data, measured blood analytes, and survey data to disentangle contributions to cardiovascular disease risk.
Recommended citation: S. O. E. Ebbesson, V. S. Voruganti, P. B. Higgins, R. R. Fabsitz, L. O. Ebbesson, S. Laston, W. S. Harris, J. Kennish, B. D. Umans, H. Wang, R. B. Devereux, P. M. Okin, N. J. Weissman, J. W. MacCluer, J. G. Umans, and B. V. Howard. (2015). “"Fatty acids linked to cardiovascular mortality are associated with risk factors." International Journal of Circumpolar Health 74(1).
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Published in Cell, 2015
In this paper, we identified genetically defined vagal sensory neuron subtypes that innervate the lung and control breathing.
Recommended citation: R. B. Chang, D. E. Strochlic, E. K. Williams, B. D. Umans, and S. D. Liberles. (2015). "Vagal Sensory Neuron Subtypes that Differentially Control Breathing." Cell. 161(3) 622–633.
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