Taylor Adams
Research Assistant 1 MS
Research & Publications
Biography
News
Coauthors
Selected Publications
- VISTA (PD-1H) Is a Crucial Immune Regulator to Limit Pulmonary Fibrosis.Kim S, Adams T, Hu Q, Shin H, Chae G, Lee S, Sharma L, Kwon H, Lee F, Park H, Huh W, Manning E, Kaminski N, Sauler M, Chen L, Song J, Kim T, Kang M. VISTA (PD-1H) Is a Crucial Immune Regulator to Limit Pulmonary Fibrosis. American Journal Of Respiratory Cell And Molecular Biology 2023, 69: 22-33. PMID: 36450109, PMCID: PMC10324045, DOI: 10.1165/rcmb.2022-0219oc.
- microRNA-33 deficiency in macrophages enhances autophagy, improves mitochondrial homeostasis, and protects against lung fibrosisAhangari F, Price N, Malik S, Chioccioli M, Bärnthaler T, Adams T, Kim J, Pradeep S, Ding S, Cosme C, Rose K, McDonough J, Aurelien N, Ibarra G, Omote N, Schupp J, DeIuliis G, Nunez J, Sharma L, Ryu C, Dela Cruz C, Liu X, Prasse A, Rosas I, Bahal R, Fernandez-Hernando C, Kaminski N. microRNA-33 deficiency in macrophages enhances autophagy, improves mitochondrial homeostasis, and protects against lung fibrosis. JCI Insight 2023, 8: e158100. PMID: 36626225, PMCID: PMC9977502, DOI: 10.1172/jci.insight.158100.
- Lung Cell Atlases in Health and DiseaseAdams T, Marlier A, Kaminski N. Lung Cell Atlases in Health and Disease. Annual Review Of Physiology 2022, 85: 47-69. PMID: 36351366, DOI: 10.1146/annurev-physiol-032922-082826.
- Integrative analyses for the identification of idiopathic pulmonary fibrosis-associated genes and shared loci with other diseasesChen M, Zhang Y, Adams T, Ji D, Jiang W, Wain LV, Cho M, Kaminski N, Zhao H. Integrative analyses for the identification of idiopathic pulmonary fibrosis-associated genes and shared loci with other diseases. Thorax 2022, 78: 792-798. PMID: 36216496, PMCID: PMC10083187, DOI: 10.1136/thorax-2021-217703.
- Airway basal cells show a dedifferentiated KRT17highPhenotype and promote fibrosis in idiopathic pulmonary fibrosisJaeger B, Schupp JC, Plappert L, Terwolbeck O, Artysh N, Kayser G, Engelhard P, Adams TS, Zweigerdt R, Kempf H, Lienenklaus S, Garrels W, Nazarenko I, Jonigk D, Wygrecka M, Klatt D, Schambach A, Kaminski N, Prasse A. Airway basal cells show a dedifferentiated KRT17highPhenotype and promote fibrosis in idiopathic pulmonary fibrosis. Nature Communications 2022, 13: 5637. PMID: 36163190, PMCID: PMC9513076, DOI: 10.1038/s41467-022-33193-0.
- CINS: Cell Interaction Network inference from Single cell expression dataYuan Y, Cosme C, Adams TS, Schupp J, Sakamoto K, Xylourgidis N, Ruffalo M, Li J, Kaminski N, Bar-Joseph Z. CINS: Cell Interaction Network inference from Single cell expression data. PLOS Computational Biology 2022, 18: e1010468. PMID: 36095011, PMCID: PMC9499239, DOI: 10.1371/journal.pcbi.1010468.
- CD38 Mediates Lung Fibrosis by Promoting Alveolar Epithelial Cell Aging.Cui H, Xie N, Banerjee S, Dey T, Liu RM, Antony VB, Sanders YY, Adams TS, Gomez JL, Thannickal VJ, Kaminski N, Liu G. CD38 Mediates Lung Fibrosis by Promoting Alveolar Epithelial Cell Aging. American Journal Of Respiratory And Critical Care Medicine 2022, 206: 459-475. PMID: 35687485, DOI: 10.1164/rccm.202109-2151oc.
- Microenvironmental sensing by fibroblasts controls macrophage population sizeZhou X, Franklin RA, Adler M, Carter TS, Condiff E, Adams TS, Pope SD, Philip NH, Meizlish ML, Kaminski N, Medzhitov R. Microenvironmental sensing by fibroblasts controls macrophage population size. Proceedings Of The National Academy Of Sciences Of The United States Of America 2022, 119: e2205360119. PMID: 35930670, PMCID: PMC9371703, DOI: 10.1073/pnas.2205360119.
- Reduced Alveolar Type 2 Epithelial Expression of NUPR1 Is Associated with Severe COPD and Increases Susceptibility to Oxidative Stress and FerroptosisNouws J, Mcdonough J, Adams T, Werder R, Schupp J, Robertson M, Coarfa C, Poli De Frias S, Wilson A, Timshel P, Kaminski N, Rosas I, Sauler M. Reduced Alveolar Type 2 Epithelial Expression of NUPR1 Is Associated with Severe COPD and Increases Susceptibility to Oxidative Stress and Ferroptosis. 2022, a1040-a1040. DOI: 10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a1040.
- Leveraging Cell-Specific Disease Signatures to Predict New Drug Therapies for Idiopathic Pulmonary FibrosisAdams T, Song Q, Justet A, Mcdonough J, DeIuliis G, Yan X, Bar-Joseph Z, Kaminski N. Leveraging Cell-Specific Disease Signatures to Predict New Drug Therapies for Idiopathic Pulmonary Fibrosis. 2022, a2318-a2318. DOI: 10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a2318.
- GPR87 - a G-Coupled Protein Receptor Overexpressed in Human and Murine Pulmonary Fibrosis, Localizes to Aberrant Basaloid Cells in the IPF LungKhoury J, Ahangari F, Barnthaler T, McDonough J, Kothapalli N, Adams T, Schupp J, DeIuliis G, Gomez J, Kaminski N. GPR87 - a G-Coupled Protein Receptor Overexpressed in Human and Murine Pulmonary Fibrosis, Localizes to Aberrant Basaloid Cells in the IPF Lung. 2022, a2325-a2325. DOI: 10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a2325.
- Aberrant Mesenchymal Signaling in the COPD LungBrewster R, Neeharika N, Mcdonough J, Adams T, Schupp J, Niklason L, Raredon M, Kaminski N, Rosas I, Sauler M. Aberrant Mesenchymal Signaling in the COPD Lung. 2022, a4655-a4655. DOI: 10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a4655.
- Single Nuclei RNA Sequencing of Differentially Affected Regions in IPF Lungs Suggests a Central Role of Aberrant Basaloid Cells in Disease ProgressionSchupp J, Clair G, Adams T, Mcdonough J, Flint J, Kothapalli N, De Sadeleer L, Justet A, Melchior J, Paurus V, Olson H, Deluliis G, Ahangari F, Bar-Joseph Z, Yan X, Ding J, Wuyts W, Vanaudenaerde B, Kaminski N. Single Nuclei RNA Sequencing of Differentially Affected Regions in IPF Lungs Suggests a Central Role of Aberrant Basaloid Cells in Disease Progression. 2022, a4975-a4975. DOI: 10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a4975.
- Interactive Web-Based Lung Cell Atlases Lower Barriers to Transcriptomic Data Sharing, Mining and DisseminationCosme Jr. C, Flint J, Neumark N, Kothapalli N, Balayev A, Adams T, Schupp J, Mcdonough J, Yan X, Sauler M, Kaminski N. Interactive Web-Based Lung Cell Atlases Lower Barriers to Transcriptomic Data Sharing, Mining and Dissemination. 2022, a4978-a4978. DOI: 10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a4978.
- A Probabilistic Graphical Model for Understanding Cellular Dynamics in Idiopathic Pulmonary Fibrosis ProgressionDing J, Zheng Y, Schupp J, Adams T, Ahangari F, Yan X, Hasen P, Bar-Joseph Z, De Sadeleer L, Mcdonough J, Vanaudenaerde B, Wuyts W, Kaminski N. A Probabilistic Graphical Model for Understanding Cellular Dynamics in Idiopathic Pulmonary Fibrosis Progression. 2022, a4986-a4986. DOI: 10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a4986.
- Deconvolution of Spatial Transcriptomic Allows to Predict the Spatial Location of Each Cell Type of Interest in the Fibrotic LungJustet A, Adams T, Balayev A, Bärnthaler T, Cosme Jr C, Mcdonough J, Flint J, Schupp J, Zhao A, Deluliis J, Ahangari F, Yan X, Kaminski N. Deconvolution of Spatial Transcriptomic Allows to Predict the Spatial Location of Each Cell Type of Interest in the Fibrotic Lung. 2022, a4991-a4991. DOI: 10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a4991.
- Single-Cell RNAseq Reveals Cell Composition and Gene Expression Patterns in the Peripheral Blood of Pediatric Obstructive Sleep ApneaCortese R, Adams T, Hohensee K, Kaminski N, Gozal L, Gozal D. Single-Cell RNAseq Reveals Cell Composition and Gene Expression Patterns in the Peripheral Blood of Pediatric Obstructive Sleep Apnea. 2022, a2565-a2565. DOI: 10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a2565.
- Single-Cell RNA Sequencing of Peripheral Blood Mononuclear Cells Reveals That T Cell Composition, Gene Expression, and Clonotype Significantly Distinguish Fibrotic Hypersensitivity Pneumonitis and Idiopathic Pulmonary FibrosisZhao A, Unterman A, Adams T, Yan X, Justet A, Deluliis G, Herzog E, Prasse A, BuendĂa-Roldán I, Pardo A, Selman M, Kaminski N. Single-Cell RNA Sequencing of Peripheral Blood Mononuclear Cells Reveals That T Cell Composition, Gene Expression, and Clonotype Significantly Distinguish Fibrotic Hypersensitivity Pneumonitis and Idiopathic Pulmonary Fibrosis. 2022, a3522-a3522. DOI: 10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a3522.
- Antifibrotic Effects of Sobetirome, a Thyroid Hormone Receptor Beta AgonistBaernthaler T, Ding S, Chioccioli M, Poli F, Justet A, Rose K, Cosme Jr. C, Adams T, Ahangari F, Rosas I, Kaminski N. Antifibrotic Effects of Sobetirome, a Thyroid Hormone Receptor Beta Agonist. 2022, a3722-a3722. DOI: 10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a3722.
- Changes in Immune Cell Populations in the Peripheral Blood of Individuals with Interstitial Lung AbnormalitiesZhao A, Unterman A, Adams T, Justet A, Yan X, Deluliis G, Herzog E, Prasse A, Buendia-Roldan I, Pardo A, Selman M, Kaminski N. Changes in Immune Cell Populations in the Peripheral Blood of Individuals with Interstitial Lung Abnormalities. 2022, a5273-a5273. DOI: 10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a5273.
- Computation and visualization of cell–cell signaling topologies in single-cell systems data using ConnectomeRaredon MSB, Yang J, Garritano J, Wang M, Kushnir D, Schupp JC, Adams TS, Greaney AM, Leiby KL, Kaminski N, Kluger Y, Levchenko A, Niklason LE. Computation and visualization of cell–cell signaling topologies in single-cell systems data using Connectome. Scientific Reports 2022, 12: 4187. PMID: 35264704, PMCID: PMC8906120, DOI: 10.1038/s41598-022-07959-x.
- Distinct roles of KLF4 in mesenchymal cell subtypes during lung fibrogenesisChandran RR, Xie Y, Gallardo-Vara E, Adams T, Garcia-Milian R, Kabir I, Sheikh AQ, Kaminski N, Martin KA, Herzog EL, Greif DM. Distinct roles of KLF4 in mesenchymal cell subtypes during lung fibrogenesis. Nature Communications 2021, 12: 7179. PMID: 34893592, PMCID: PMC8664937, DOI: 10.1038/s41467-021-27499-8.
- A Pulmonary Vascular Model From Endothelialized Whole Organ ScaffoldsYuan Y, Leiby KL, Greaney AM, Raredon MSB, Qian H, Schupp JC, Engler AJ, Baevova P, Adams TS, Kural MH, Wang J, Obata T, Yoder MC, Kaminski N, Niklason LE. A Pulmonary Vascular Model From Endothelialized Whole Organ Scaffolds. Frontiers In Bioengineering And Biotechnology 2021, 9: 760309. PMID: 34869270, PMCID: PMC8640093, DOI: 10.3389/fbioe.2021.760309.
- A Markov random field model for network-based differential expression analysis of single-cell RNA-seq dataLi H, Zhu B, Xu Z, Adams T, Kaminski N, Zhao H. A Markov random field model for network-based differential expression analysis of single-cell RNA-seq data. BMC Bioinformatics 2021, 22: 524. PMID: 34702190, PMCID: PMC8549347, DOI: 10.1186/s12859-021-04412-0.
- Aberrant endothelial CXCL signaling in COPDKothapalli N, Mcdonough J, Raredon M, Adams T, Schupp J, Niklason L, Kaminski N, Rosas I, Sauler M. Aberrant endothelial CXCL signaling in COPD. 2021, pa3623. DOI: 10.1183/13993003.congress-2021.pa3623.
- Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severityBui LT, Winters NI, Chung MI, Joseph C, Gutierrez AJ, Habermann AC, Adams TS, Schupp JC, Poli S, Peter LM, Taylor CJ, Blackburn JB, Richmond BW, Nicholson AG, Rassl D, Wallace WA, Rosas IO, Jenkins RG, Kaminski N, Kropski JA, Banovich NE. Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity. Nature Communications 2021, 12: 4314. PMID: 34262047, PMCID: PMC8280215, DOI: 10.1038/s41467-021-24467-0.
- Transcriptomics of bronchoalveolar lavage cells identifies new molecular endotypes of sarcoidosisVukmirovic M, Yan X, Gibson KF, Gulati M, Schupp JC, DeIuliis G, Adams TS, Hu B, Mihaljinec A, Woolard TN, Lynn H, Emeagwali N, Herzog EL, Chen ES, Morris A, Leader JK, Zhang Y, Garcia JGN, Maier LA, Collman RG, Drake WP, Becich MJ, Hochheiser H, Wisniewski SR, Benos PV, Moller DR, Prasse A, Koth LL, Kaminski N. Transcriptomics of bronchoalveolar lavage cells identifies new molecular endotypes of sarcoidosis. European Respiratory Journal 2021, 58: 2002950. PMID: 34083402, PMCID: PMC9759791, DOI: 10.1183/13993003.02950-2020.
- Fibroblasts positive for meflin have anti-fibrotic properties in pulmonary fibrosisNakahara Y, Hashimoto N, Sakamoto K, Enomoto A, Adams TS, Yokoi T, Omote N, Poli S, Ando A, Wakahara K, Suzuki A, Inoue M, Hara A, Mizutani Y, Imaizumi K, Kawabe T, Rosas IO, Takahashi M, Kaminski N, Hasegawa Y. Fibroblasts positive for meflin have anti-fibrotic properties in pulmonary fibrosis. European Respiratory Journal 2021, 58: 2003397. PMID: 34049947, DOI: 10.1183/13993003.03397-2020.
- Integrated Single-Cell Atlas of Endothelial Cells of the Human LungSchupp JC, Adams TS, Cosme C, Raredon MSB, Yuan Y, Omote N, Poli S, Chioccioli M, Rose KA, Manning EP, Sauler M, DeIuliis G, Ahangari F, Neumark N, Habermann AC, Gutierrez AJ, Bui LT, Lafyatis R, Pierce RW, Meyer KB, Nawijn MC, Teichmann SA, Banovich NE, Kropski JA, Niklason LE, Pe’er D, Yan X, Homer RJ, Rosas IO, Kaminski N. Integrated Single-Cell Atlas of Endothelial Cells of the Human Lung. Circulation 2021, 144: 286-302. PMID: 34030460, PMCID: PMC8300155, DOI: 10.1161/circulationaha.120.052318.
- Decreased NUPR1 in AT2 Cells Is Associated with Development of Emphysema in COPDMcDonough J, Adams T, Kothapalli N, Schupp J, Nouws J, Chioccioli M, Omote N, Cosme Jr. C, Poli De Frias S, Ayaub E, Chu S, Jensen K, Gomez J, Britto-Leon C, Raredon M, Niklason L, Timshel P, Kaminski N, Rosas I, Sauler M. Decreased NUPR1 in AT2 Cells Is Associated with Development of Emphysema in COPD. 2021, a4281-a4281. DOI: 10.1164/ajrccm-conference.2021.203.1_meetingabstracts.a4281.
- Single Cell RNA Velocity Analysis of Aberrant Basaloid Cells in Pulmonary Fibrosis Reveals Trajectory Towards an Alveolar Type I Like Cell StateSchupp J, Adams T, Ahangari F, McDonough J, DeIuliis G, Poli S, Rosas I, Yan X, Kaminski N. Single Cell RNA Velocity Analysis of Aberrant Basaloid Cells in Pulmonary Fibrosis Reveals Trajectory Towards an Alveolar Type I Like Cell State. 2021, a4350-a4350. DOI: 10.1164/ajrccm-conference.2021.203.1_meetingabstracts.a4350.
- Integrated scRNAseq Analysis of Murine Lung Fibrosis Reveals Patterns in Composition and Gene Expression of LymphocytesAdams T, Schupp J, Mcdonough J, Chioccioli M, Rose K, DeIuliis G, Yan X, Kaminski N. Integrated scRNAseq Analysis of Murine Lung Fibrosis Reveals Patterns in Composition and Gene Expression of Lymphocytes. 2021, a4351-a4351. DOI: 10.1164/ajrccm-conference.2021.203.1_meetingabstracts.a4351.
- Single-Cell RNAseq of Aging Lungs from Nlrp3 -/- Mice Reveals Genotype- and Cell Type-Specific Effects of Aging on the Transcriptomes of Several Myeloid-Derived CellsCosme Jr. C, Adams T, Schupp J, Mcdonough J, Ahangari F, DeIuliis G, Omote N, Dixit V, Kaminski N. Single-Cell RNAseq of Aging Lungs from Nlrp3 -/- Mice Reveals Genotype- and Cell Type-Specific Effects of Aging on the Transcriptomes of Several Myeloid-Derived Cells. 2021, a4402-a4402. DOI: 10.1164/ajrccm-conference.2021.203.1_meetingabstracts.a4402.
- Macrophage Specific Regulatory Role of miR-33 in Pulmonary FibrosisAhangari F, Chioccioli M, Malik S, Baernthaler T, Price N, Ding S, Rose K, Mcdonough J, Omote N, Schupp J, Adams T, Sharma L, DeIuliis G, Dela Cruz C, Prasse A, Bahal R, Fernandez-Hernando C, Kaminski N. Macrophage Specific Regulatory Role of miR-33 in Pulmonary Fibrosis. 2021, a4452-a4452. DOI: 10.1164/ajrccm-conference.2021.203.1_meetingabstracts.a4452.
- IL-15 Is Independent of Pulmonary Sarcoid Granuloma Formation In VivoMinasyan M, Sharma L, Pivarnik T, Liu W, Adams T, Bermejo S, Peng X, Ishikawa G, Perry C, Kaminski N, Gulati M, Herzog E, Dela Cruz C, Ryu C. IL-15 Is Independent of Pulmonary Sarcoid Granuloma Formation In Vivo. 2021, a4263-a4263. DOI: 10.1164/ajrccm-conference.2021.203.1_meetingabstracts.a4263.
- Engineered Lung Reveals a Fibroblast-Endothelial Niche Supporting Alveolar Epithelial Type 2 Cell Growth and PhenotypeLeiby K, Yuan Y, Raredon M, Adams T, Kaminski N, Herzog E, Niklason L. Engineered Lung Reveals a Fibroblast-Endothelial Niche Supporting Alveolar Epithelial Type 2 Cell Growth and Phenotype. 2021, a1141-a1141. DOI: 10.1164/ajrccm-conference.2021.203.1_meetingabstracts.a1141.
- RNA-Seq Reveals Antifibrotic Effects of Sobetirome in Human Lung FibroblastsRose K, Adams T, Ahangari F, Ding S, DeIuliis G, Kaminski N. RNA-Seq Reveals Antifibrotic Effects of Sobetirome in Human Lung Fibroblasts. 2021, a4247-a4247. DOI: 10.1164/ajrccm-conference.2021.203.1_meetingabstracts.a4247.
- Comparative scRNA-seq Analysis of Peripheral Blood Mononuclear Cells from Patients with COVID-19 and Idiopathic Pulmonary Fibrosis Demonstrates Dissimilar Cell Shifts and Gene Expression ProfilesZhao A, Unterman A, Schupp J, Adams T, Sumida T, Ryu C, DeIuliis G, Yan X, Hafler D, Dela Cruz C, Herzog E, Kaminski N. Comparative scRNA-seq Analysis of Peripheral Blood Mononuclear Cells from Patients with COVID-19 and Idiopathic Pulmonary Fibrosis Demonstrates Dissimilar Cell Shifts and Gene Expression Profiles. 2021, a4361-a4361. DOI: 10.1164/ajrccm-conference.2021.203.1_meetingabstracts.a4361.
- Targeting the IPF-Expanded Macrophages: Identification and Drug Discovery via scRNAseq and CyTOFPoli De Frias S, Ayaub E, Adams T, Schupp J, Ng J, Quesada L, Martinez J, Planchart M, Robertson M, Chu S, Coarfa C, El-Chemaly S, Perrella M, Washko G, Raby B, Kaminski N, Rosas I. Targeting the IPF-Expanded Macrophages: Identification and Drug Discovery via scRNAseq and CyTOF. 2021, a4435-a4435. DOI: 10.1164/ajrccm-conference.2021.203.1_meetingabstracts.a4435.
- The Thyroid Hormone Receptor Beta Agonist Sobetirome Exerts Beneficial Effects in Pulmonary FibrosisBaernthaler T, Ahangari F, Chioccioli M, Adams T, Rose K, Ding S, Kaminski N. The Thyroid Hormone Receptor Beta Agonist Sobetirome Exerts Beneficial Effects in Pulmonary Fibrosis. 2021, a4449-a4449. DOI: 10.1164/ajrccm-conference.2021.203.1_meetingabstracts.a4449.
- Single-cell characterization of a model of poly I:C-stimulated peripheral blood mononuclear cells in severe asthmaChen A, Diaz-Soto MP, Sanmamed MF, Adams T, Schupp JC, Gupta A, Britto C, Sauler M, Yan X, Liu Q, Nino G, Cruz CSD, Chupp GL, Gomez JL. Single-cell characterization of a model of poly I:C-stimulated peripheral blood mononuclear cells in severe asthma. Respiratory Research 2021, 22: 122. PMID: 33902571, PMCID: PMC8074196, DOI: 10.1186/s12931-021-01709-9.
- Elevated IL-15 concentrations in the sarcoidosis lung are independent of granuloma burden and disease phenotypesMinasyan M, Sharma L, Pivarnik T, Liu W, Adams T, Bermejo S, Peng X, Liu A, Ishikawa G, Perry C, Kaminski N, Gulati M, Herzog EL, Dela Cruz CS, Ryu C. Elevated IL-15 concentrations in the sarcoidosis lung are independent of granuloma burden and disease phenotypes. American Journal Of Physiology - Lung Cellular And Molecular Physiology 2021, 320: l1137-l1146. PMID: 33851886, PMCID: PMC8285626, DOI: 10.1152/ajplung.00575.2020.
- Long noncoding RNA TINCR is a novel regulator of human bronchial epithelial cell differentiation stateOmote N, Sakamoto K, Li Q, Schupp JC, Adams T, Ahangari F, Chioccioli M, DeIuliis G, Hashimoto N, Hasegawa Y, Kaminski N. Long noncoding RNA TINCR is a novel regulator of human bronchial epithelial cell differentiation state. Physiological Reports 2021, 9: e14727. PMID: 33527707, PMCID: PMC7851438, DOI: 10.14814/phy2.14727.
- Gene coexpression networks reveal novel molecular endotypes in alpha-1 antitrypsin deficiencyChu JH, Zang W, Vukmirovic M, Yan X, Adams T, DeIuliis G, Hu B, Mihaljinec A, Schupp JC, Becich MJ, Hochheiser H, Gibson KF, Chen ES, Morris A, Leader JK, Wisniewski SR, Zhang Y, Sciurba FC, Collman RG, Sandhaus R, Herzog EL, Patterson KC, Sauler M, Strange C, Kaminski N. Gene coexpression networks reveal novel molecular endotypes in alpha-1 antitrypsin deficiency. Thorax 2020, 76: 134-143. PMID: 33303696, PMCID: PMC10794043, DOI: 10.1136/thoraxjnl-2019-214301.
- Single-Cell RNAseq of Aging Mouse Lungs Reveals Global and Cell-Specific Inflammatory AberrationsCosme Jr. C, McDonough J, Adams T, Schupp J, Omote N, Ahangari F, DeIuliis G, Sakamoto K, Kaminski N. Single-Cell RNAseq of Aging Mouse Lungs Reveals Global and Cell-Specific Inflammatory Aberrations. 2020, a4389-a4389. DOI: 10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a4389.
- Low Surfactant Type II Alveolar Epithelial Cells Are an Enriched Cell Population in the Aged LungMcDonough J, Adams T, Schupp J, DeIuliis G, Yan X, Cosme jr C, Kaminski N. Low Surfactant Type II Alveolar Epithelial Cells Are an Enriched Cell Population in the Aged Lung. 2020, a4390-a4390. DOI: 10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a4390.
- Deconvolution of Bulk RNAseq Datasets Confirms Substantial Cellular Population Shifts in the Distal Lung in IPFAdams T, Schupp J, McDonough J, Ahangari F, DeIuliis G, Yan X, Rosas I, Kaminski N. Deconvolution of Bulk RNAseq Datasets Confirms Substantial Cellular Population Shifts in the Distal Lung in IPF. 2020, a2248-a2248. DOI: 10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a2248.
- Single Cell RNA Sequencing Reveals Altered T-Cell Repertoire and Gene Expression in the Peripheral Blood and Lungs of Patients with Idiopathic Pulmonary FibrosisUnterman A, Neumark N, Zhao A, Schupp J, Adams T, Antin-Ozerkis D, Winkler J, Banovich N, Kropski J, Herzog E, Kaminski N. Single Cell RNA Sequencing Reveals Altered T-Cell Repertoire and Gene Expression in the Peripheral Blood and Lungs of Patients with Idiopathic Pulmonary Fibrosis. 2020, a2516-a2516. DOI: 10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a2516.
- Background Contamination Correction in Human Lung Single-Cell RNA Sequencing DataZang W, Schupp J, Kane M, Adams T, Poli De Frias S, Rosas I, Kaminski N, Chu J. Background Contamination Correction in Human Lung Single-Cell RNA Sequencing Data. 2020, a4024-a4024. DOI: 10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a4024.
- Long Non-Coding RNA TINCR Is a Novel Regulator of Human Bronchial Epithelial Cell DifferentiationOmote N, Sakamoto K, Li Q, Schupp J, Adams T, Ahangari F, Chioccioli M, Hashimoto N, Hasegawa Y, Kaminski N. Long Non-Coding RNA TINCR Is a Novel Regulator of Human Bronchial Epithelial Cell Differentiation. 2020, a5987-a5987. DOI: 10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a5987.
- Saracatinib Is a Potential Novel Therapeutic for Pulmonary FibrosisAhangari F, Becker C, Foster D, Chioccioli M, Nelson M, Beke K, Meador C, Wang X, Corell K, Roybal H, DeIuliis G, Rose K, Schupp J, Li Q, Adams T, Aschner Y, Lilli L, Readhead B, Cousens L, Dudley J, Kaminski N, Downey G. Saracatinib Is a Potential Novel Therapeutic for Pulmonary Fibrosis. 2020, a2784-a2784. DOI: 10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a2784.
- Single Cell Transcriptomics Reveals Novel COL15A1+ Endothelial Population in Pulmonary Fibrosis and Lung CancerSchupp J, Adams T, Ahangari F, Poli De Frias S, DeIuliis G, Yan X, Rosas I, Homer R, Kaminski N. Single Cell Transcriptomics Reveals Novel COL15A1+ Endothelial Population in Pulmonary Fibrosis and Lung Cancer. 2020, a6142-a6142. DOI: 10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a6142.
- Characterization of Sputum Single Cell Transcriptomes in AsthmaYan X, Liu Q, Adams T, Schupp J, Grant N, Gomez J, Cohn L, Chupp G. Characterization of Sputum Single Cell Transcriptomes in Asthma. 2020, a3046-a3046. DOI: 10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a3046.
- Single Cell RNA Sequencing profiles Distinct BAL Cell Subpopulations in SarcoidosisSchupp J, Adams T, Jäger B, Deluiis G, Ahangari F, Kaminski N, Prasse A. Single Cell RNA Sequencing profiles Distinct BAL Cell Subpopulations in Sarcoidosis. 2019, oa5154. DOI: 10.1183/13993003.congress-2019.oa5154.
- Cross-Species scRNAseq Systems Biology Analysis of Cell-Cell Signaling in LungRaredon M, Adams T, Schupp J, Suhail Y, Leiby K, Greaney A, Boffa D, Levchenko A, Kaminski N, Niklason L. Cross-Species scRNAseq Systems Biology Analysis of Cell-Cell Signaling in Lung. 2019, a6073-a6073. DOI: 10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a6073.
- Single Cell RNA Sequencing of Human Lung Explants Identifies the Cell-Specific Contributions of Extracellular Matrix-Related Gene ExpressionPoli De Frias S, Adams T, Schupp J, Chu S, Neumark N, Ahangari F, Waskho G, Raby B, Kaminski N, Rosas I. Single Cell RNA Sequencing of Human Lung Explants Identifies the Cell-Specific Contributions of Extracellular Matrix-Related Gene Expression. 2019, a2550-a2550. DOI: 10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a2550.
- Pou2af1 Is a Novel Regulator of Airway EpithelialCells Differentiation and Response to Fibrotic InjuryLi Q, Omote N, Adams T, Chioccioli M, Shakya A, DeIuliis G, Herzog E, Tantin D, Herazo-Maya J, Kaminski N. Pou2af1 Is a Novel Regulator of Airway EpithelialCells Differentiation and Response to Fibrotic Injury. 2019, a2827-a2827. DOI: 10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a2827.
- Whole Lung Single Cell RNAseq Reveals a Unique IPF-Specific Epithelial Cell PopulationSchupp J, Adams T, Neumark N, Poli De Frias S, Ahangari F, Omote N, Chioccioli M, Xylourgidis N, DeIuliis G, Chu S, Yan X, Rosas I, Kaminski N. Whole Lung Single Cell RNAseq Reveals a Unique IPF-Specific Epithelial Cell Population. 2019, a4017-a4017. DOI: 10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a4017.
- Archetype Analysis Reveals Distinct Disease-Specific Archetypes of Fibroblast and Myofibroblast Co-Occurring Within the IPF LungAdams T, Schupp J, Neumark N, Poli De Frias S, Ahangari F, DeIuliis G, Chu S, Raredon M, Yan X, Rosas I, Kaminski N. Archetype Analysis Reveals Distinct Disease-Specific Archetypes of Fibroblast and Myofibroblast Co-Occurring Within the IPF Lung. 2019, a4018-a4018. DOI: 10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a4018.
- Macrophage Programs in BAL and Lung Parenchyma of the Healthy and in IPF PatientsSchupp J, Adams T, Neumark N, Poli De Frias S, Ahangari F, DeIuliis G, Chu S, Yan X, Kaminski N, Prasse A, Rosas I. Macrophage Programs in BAL and Lung Parenchyma of the Healthy and in IPF Patients. 2019, a5247-a5247. DOI: 10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a5247.
- Loss of lncRNA FENDRR Induces Senescence in Adult Mouse LungsXylourgidis N, Sakamoto K, Schupp J, Adams T, DeIuliis G, Omote N, Hashimoto N, Hasegawa Y, Kaminski N. Loss of lncRNA FENDRR Induces Senescence in Adult Mouse Lungs. 2019, a5274-a5274. DOI: 10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a5274.
- TINCR, a Long Intergenic Noncoding RNA Decreased in IPF, Is a Novel Regulator of Airway Epithelial Cell DifferentiationOmote N, Sakamoto K, Li Q, Schupp J, Adams T, Ahangari F, Chioccioli M, Xylourgidis N, DeIuliis G, Hashimoto N, Hasegawa Y, Kaminski N. TINCR, a Long Intergenic Noncoding RNA Decreased in IPF, Is a Novel Regulator of Airway Epithelial Cell Differentiation. 2019, a5406-a5406. DOI: 10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a5406.
- Basal Epithelial Progenitor Cells for Pulmonary Engineering as Evaluated by Single-Cell TranscriptomicsGreaney A, Raredon M, Adams T, Schupp J, Kaminski N, Niklason L. Basal Epithelial Progenitor Cells for Pulmonary Engineering as Evaluated by Single-Cell Transcriptomics. 2019, a5890-a5890. DOI: 10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a5890.
- A Novel Interface for Sharing the Human Cell IPF AtlasNeumark N, Adams T, Schupp J, Yan X, Poli De Frias S, Kaminski N. A Novel Interface for Sharing the Human Cell IPF Atlas. 2019, a6076-a6076. DOI: 10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a6076.
- Decreased expression of FENDRR, a lung mesenchymal long non-coding RNA, regulates fibroblast phenotypes in IPF through NOX4Sakamoto K, Xylourgidis N, Omote N, Adams T, Yu G, Ahangari F, Herazo-Maya J, Kaminski N, Homer R. Decreased expression of FENDRR, a lung mesenchymal long non-coding RNA, regulates fibroblast phenotypes in IPF through NOX4. 2017, oa2909. DOI: 10.1183/1393003.congress-2017.oa2909.