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Naftali Kaminski, MD

he/him/his

Boehringer Ingelheim Pharmaceuticals, Inc. Professor of Medicine (Pulmonary); Section Chief, Pulmonary, Critical Care & Sleep Medicine

Research & Publications
Biography
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Research Summary

Dr. Kaminski’s research is focused on improving our understanding, diagnosis and treatment of advanced lung diseases such as Idiopathic Pulmonary Fibrosis (IPF), using a combination of cutting-edge high throughput profiling technologies, advanced systems biology and disease modeling approaches. Among the key discoveries of his lab are reproducible outcome predictive peripheral blood biomarkers such as MMP7 and the 52 gene signature in IPF, the role of microRNAs in pulmonary fibrosis, the role of phosphatases in pulmonary fibrosis, the potential therapeutic role of thyroid hormone mimetics in pulmonary fibrosis and ARDS and most recently the identification of novel cell populations in IPF using single-cell profiling technologies.

Extensive Research Description

Dr. Kaminski’s team main ambition is to uncover the mechanisms, and thus have a significant impact on the management of advanced lung diseases with a specific focus on IPF, a chronic progressive interstitial lung disease that is currently incurable. To study these mechanisms Dr. Kaminski’s team applies systems biology approaches that incorporate a combination of traditional molecular biology methods, high-throughput genomic technologies such as transcript level profiling (single cell RNA sequencing and epigenomic profiling ) , genome scale analyses of gene variants, advanced bioinformatics approaches and targeted proteomic approaches. These studies have led to shifts in the perception of pulmonary fibrosis, the realization that aberrant activation of developmental pathways is at the core of lung fibrosis, the discovery of the role of microRNAs in IPF, the identification and validation of novel prognostic biomarkers in the bloodstream, as well many additional insights.

Mechanisms of pulmonary fibrosis and other chronic lung diseases

Understanding and identifying the genetic and molecular networks that determine the lung phenotype using high throughput high resolution genomic and proteomic technologies.
Role of miRNA in advanced lung disease (IPF, Emphysema).
Role of other non-coding RNAs (lincRNAs) in advanced lung disease
The IPF Cell Atlas (www.IPFCellAtlas.com)
The Normal Aging Lung Cell Atlas
The Pulmonary Fibrosis Connectome
Epigenomics of chronic lung disease.
Using computational approaches to Integrate clinical, biological, genomic and proteomic data to identify new molecular phenotypes of disease.

New molecular targets in Pulmonary Fibrosis

The role and regulation of microRNAs (let-7, mir-33, mir-29) in human pulmonary fibrosis and development of microRNA inhibitors and agonist for therapeutic interventions
The role of large non-coding RNAs in pulmonary fibrosis
The role of thyroid hormone signaling in epithelial cell protection in fibrosis
Novel lung resident cell specific therapeutic approaches in pulmonary fibrosis

Biomarker Discovery and Validation in chronic and progressive lung disease

Approaches to the development of liquid biopsy in human pulmonary fibrosis and other interstitial lung disease
Peripheral blood protein markers in lung fibrosis
Genetic predictors of outcome in lung fibrosis
Peripheral blood gene expression changes and disease progression

Coauthors

Research Interests

Emphysema; Fibrosis; Genetics, Medical; Lung Diseases; RNA; Gene Expression; Genomics; MicroRNAs; Metalloproteases; Biomarkers, Pharmacological

Public Health Interests

Aging; Bioinformatics; Biomarkers; Genetics, Genomics, Epigenetics; Respiratory Disease/Infections; Pollution

Research Images

The IPF Cell Atlas

Selected Publications

A lung targeted miR-29 mimic as a therapy for pulmonary fibrosisChioccioli M, Roy S, Newell R, Pestano L, Dickinson B, Rigby K, Herazo-Maya J, Jenkins G, Ian S, Saini G, Johnson SR, Braybrooke R, Yu G, Sauler M, Ahangari F, Ding S, DeIuliis J, Aurelien N, Montgomery RL, Kaminski N. A lung targeted miR-29 mimic as a therapy for pulmonary fibrosis. EBioMedicine 2022, 85: 104304. PMID: 36265417, PMCID: PMC9587275, DOI: 10.1016/j.ebiom.2022.104304.
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.
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.
Thyroid hormone inhibits lung fibrosis in mice by improving epithelial mitochondrial functionYu G, Tzouvelekis A, Wang R, Herazo-Maya JD, Ibarra GH, Srivastava A, de Castro JPW, DeIuliis G, Ahangari F, Woolard T, Aurelien N, Arrojo e Drigo R, Gan Y, Graham M, Liu X, Homer RJ, Scanlan TS, Mannam P, Lee PJ, Herzog EL, Bianco AC, Kaminski N. Thyroid hormone inhibits lung fibrosis in mice by improving epithelial mitochondrial function. Nature Medicine 2017, 24: 39-49. PMID: 29200204, PMCID: PMC5760280, DOI: 10.1038/nm.4447.
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.
Challenges and Opportunities for Commercializing Technologies in the Pulmonary Arena: An Official American Thoracic Society ReportVukmirovic M, Benam K, Rose J, Turner S, Magin C, Lagares D, Cohen A, Kaminski N, Hirota J, Maher T, Konigshoff M, Mallampalli R, Sheppard D, Tarran R, Gomer R, Kenyon N, Morris D, Hobbie S, Raju S, Petrache I, Watkins T, Kumar R, Lam W, Sherer T, Hecker L. Challenges and Opportunities for Commercializing Technologies in the Pulmonary Arena: An Official American Thoracic Society Report. Annals Of The American Thoracic Society 2024, 21: 1-11. PMID: 37903340, PMCID: PMC10867911, DOI: 10.1513/annalsats.202310-872st.
Somatic Mutations: The Next Frontier in Demystifying Chronic Obstructive Pulmonary Disease and Idiopathic Pulmonary Fibrosis?Yan X, Kaminski N. Somatic Mutations: The Next Frontier in Demystifying Chronic Obstructive Pulmonary Disease and Idiopathic Pulmonary Fibrosis? American Journal Of Respiratory And Critical Care Medicine 2023, 208: 1150-1151. PMID: 37856835, PMCID: PMC10868359, DOI: 10.1164/rccm.202310-1774ed.
Correction: iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjectsLiu Y, Zhao J, Adams T, Wang N, Schupp J, Wu W, McDonough J, Chupp G, Kaminski N, Wang Z, Yan X. Correction: iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects. BMC Bioinformatics 2023, 24: 394. PMID: 37858060, PMCID: PMC10588114, DOI: 10.1186/s12859-023-05523-6.
Fossil Industry and Respiratory Societies: Time for a Clear Stand.Piccari L, Kaminski N, Mann M. Fossil Industry and Respiratory Societies: Time for a Clear Stand. American Journal Of Respiratory And Critical Care Medicine 2023, 209: 245-247. PMID: 37796608, PMCID: PMC10840762, DOI: 10.1164/rccm.202308-1410vp.
Alveolar Vascular Remodeling in Nonspecific Interstitial Pneumonia: Replacement of Normal Lung Capillaries with COL15A1-Positive Endothelial Cells.Schupp J, Manning E, Chioccioli M, Kamp J, Christian L, Ryu C, Herzog E, Kühnel M, Prasse A, Kaminski N, Jonigk D, Homer R, Neubert L, Ius F, stringJustet A, Hariri L, Seeliger B, Welte T, Knipe R, Gottlieb J. Alveolar Vascular Remodeling in Nonspecific Interstitial Pneumonia: Replacement of Normal Lung Capillaries with COL15A1-Positive Endothelial Cells. American Journal Of Respiratory And Critical Care Medicine 2023, 208: 819-822. PMID: 37552025, PMCID: PMC10563189, DOI: 10.1164/rccm.202303-0544le.
SRC and TKS5 mediated podosome formation in fibroblasts promotes extracellular matrix invasion and pulmonary fibrosisBarbayianni I, Kanellopoulou P, Fanidis D, Nastos D, Ntouskou E, Galaris A, Harokopos V, Hatzis P, Tsitoura E, Homer R, Kaminski N, Antoniou K, Crestani B, Tzouvelekis A, Aidinis V. SRC and TKS5 mediated podosome formation in fibroblasts promotes extracellular matrix invasion and pulmonary fibrosis. Nature Communications 2023, 14: 5882. PMID: 37735172, PMCID: PMC10514346, DOI: 10.1038/s41467-023-41614-x.
When Development of the Alveolar Gas Exchange Unit Fails: Universal Single-Cell Lessons from Rare Monogenic DisordersSchupp J, Kaminski N. When Development of the Alveolar Gas Exchange Unit Fails: Universal Single-Cell Lessons from Rare Monogenic Disorders. American Journal Of Respiratory And Critical Care Medicine 2023, 208: 652-654. PMID: 37555730, PMCID: PMC10515565, DOI: 10.1164/rccm.202307-1271ed.
Identification of abnormal airway niches in the fibrotic lung using Spatial TranscriptomicsJustet A, Zhao J, Adams T, Balayev A, Barnthaler T, Raredon S, Poli De Frias F, Cala-Garcia J, Mcdonough J, Zhao A, Yunqing L, Ningshan L, Anita W, Rosas I, Yan X, Kaminski N. Identification of abnormal airway niches in the fibrotic lung using Spatial Transcriptomics. 2023, oa894. DOI: 10.1183/13993003.congress-2023.oa894.
iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjectsLiu Y, Zhao J, Adams T, Wang N, Schupp J, Wu W, McDonough J, Chupp G, Kaminski N, Wang Z, Yan X. iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects. BMC Bioinformatics 2023, 24: 318. PMID: 37608264, PMCID: PMC10463720, DOI: 10.1186/s12859-023-05432-8.
Integrative genetic and genomic networks identify microRNA associated with COPD and ILDPavel A, Garrison C, Luo L, Liu G, Taub D, Xiao J, Juan-Guardela B, Tedrow J, Alekseyev Y, Yang I, Geraci M, Sciurba F, Schwartz D, Kaminski N, Beane J, Spira A, Lenburg M, Campbell J. Integrative genetic and genomic networks identify microRNA associated with COPD and ILD. Scientific Reports 2023, 13: 13076. PMID: 37567908, PMCID: PMC10421936, DOI: 10.1038/s41598-023-39751-w.
A statistical framework to identify cell types whose genetically regulated proportions are associated with complex diseasesLiu W, Deng W, Chen M, Dong Z, Zhu B, Yu Z, Tang D, Sauler M, Lin C, Wain L, Cho M, Kaminski N, Zhao H. A statistical framework to identify cell types whose genetically regulated proportions are associated with complex diseases. PLOS Genetics 2023, 19: e1010825. PMID: 37523391, PMCID: PMC10414598, DOI: 10.1371/journal.pgen.1010825.
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.
An integrated cell atlas of the lung in health and diseaseSikkema L, Ramírez-Suástegui C, Strobl D, Gillett T, Zappia L, Madissoon E, Markov N, Zaragosi L, Ji Y, Ansari M, Arguel M, Apperloo L, Banchero M, Bécavin C, Berg M, Chichelnitskiy E, Chung M, Collin A, Gay A, Gote-Schniering J, Hooshiar Kashani B, Inecik K, Jain M, Kapellos T, Kole T, Leroy S, Mayr C, Oliver A, von Papen M, Peter L, Taylor C, Walzthoeni T, Xu C, Bui L, De Donno C, Dony L, Faiz A, Guo M, Gutierrez A, Heumos L, Huang N, Ibarra I, Jackson N, Kadur Lakshminarasimha Murthy P, Lotfollahi M, Tabib T, Talavera-López C, Travaglini K, Wilbrey-Clark A, Worlock K, Yoshida M, van den Berge M, Bossé Y, Desai T, Eickelberg O, Kaminski N, Krasnow M, Lafyatis R, Nikolic M, Powell J, Rajagopal J, Rojas M, Rozenblatt-Rosen O, Seibold M, Sheppard D, Shepherd D, Sin D, Timens W, Tsankov A, Whitsett J, Xu Y, Banovich N, Barbry P, Duong T, Falk C, Meyer K, Kropski J, Pe’er D, Schiller H, Tata P, Schultze J, Teichmann S, Misharin A, Nawijn M, Luecken M, Theis F. An integrated cell atlas of the lung in health and disease. Nature Medicine 2023, 29: 1563-1577. PMID: 37291214, PMCID: PMC10287567, DOI: 10.1038/s41591-023-02327-2.
PCSK6 and Survival in Idiopathic Pulmonary FibrosisOldham J, Allen R, Lorenzo-Salazar J, Molyneaux P, Ma S, Joseph C, Kim J, Guillen-Guio B, Hernández-Beeftink T, Kropski J, Huang Y, Lee C, Adegunsoye A, Pugashetti J, Linderholm A, Vo V, Strek M, Jou J, Muñoz-Barrera A, Rubio-Rodriguez L, Hubbard R, Hirani N, Whyte M, Hart S, Nicholson A, Lancaster L, Parfrey H, Rassl D, Wallace W, Valenzi E, Zhang Y, Mychaleckyj J, Stockwell A, Kaminski N, Wolters P, Molina-Molina M, Banovich N, Fahy W, Martinez F, Hall I, Tobin M, Maher T, Blackwell T, Yaspan B, Jenkins R, Flores C, Wain L, Noth I. PCSK6 and Survival in Idiopathic Pulmonary Fibrosis. American Journal Of Respiratory And Critical Care Medicine 2023, 207: 1515-1524. PMID: 36780644, PMCID: PMC10263132, DOI: 10.1164/rccm.202205-0845oc.
Vascular-Parenchymal Cross-Talk Promotes Lung Fibrosis through BMPR2 Signaling.Yanagihara T, Tsubouchi K, Zhou Q, Chong M, Otsubo K, Isshiki T, Schupp J, Sato S, Scallan C, Upagupta C, Revill S, Ayoub A, Chong S, Dvorkin-Gheva A, Kaminski N, Tikkanen J, Keshavjee S, Paré G, Guignabert C, Ask K, Kolb M. Vascular-Parenchymal Cross-Talk Promotes Lung Fibrosis through BMPR2 Signaling. American Journal Of Respiratory And Critical Care Medicine 2023, 207: 1498-1514. PMID: 36917778, DOI: 10.1164/rccm.202109-2174oc.
Medical Societies Must Choose Professional Meeting Locations Responsibly in a Post-Roe WorldLee A, Maley J, Hibbert K, Akgün K, Hauschildt K, Law A, Kaminski N, Hayes M, Gesthalter Y, Bosslet G, Santhosh L, Witkin A, Hills-Dunlap K, Çoruh B, Gershengorn H, Hardin C. Medical Societies Must Choose Professional Meeting Locations Responsibly in a Post-Roe World. Annals Of The American Thoracic Society 2023, 20: 781-784. PMID: 36812378, PMCID: PMC10257035, DOI: 10.1513/annalsats.202211-928ip.
A Picture Worth a Thousand Words, Created with One Sentence: Using Artificial Intelligence–created Art to Enhance Medical EducationHuston J, Kaminski N. A Picture Worth a Thousand Words, Created with One Sentence: Using Artificial Intelligence–created Art to Enhance Medical Education. ATS Scholar 2023, 4: 145-151. PMID: 37533539, PMCID: PMC10391737, DOI: 10.34197/ats-scholar.2022-0141ps.
MAVS Dependent Immune Responses in Cigarette Smoke Exposure and Influenza Viral InfectionGupta G, Cai C, Kim J, Kim S, Shin H, Kaminski N, Sharma L, Dela Cruz C, Kang M. MAVS Dependent Immune Responses in Cigarette Smoke Exposure and Influenza Viral Infection. 2023, a6747-a6747. DOI: 10.1164/ajrccm-conference.2023.207.1_meetingabstracts.a6747.
Morphometrics and Mucosal Immune Features in Lungs With End-stage Chronic Obstructive Pulmonary DiseaseDe Fays C, Beeckmans H, Kerckhof P, Geudens V, Vermaut A, Gyselinck I, Goos T, Vermant M, Kaes J, Van Slambrouck J, Mohamady Y, Willems L, Aversa L, Maes K, Aelbrecht C, Everaerts S, Mcdonough J, De Sadeleer L, Gohy S, Ambroise J, Wuyts W, Janssens W, Ceulemans L, Van Raemdonck D, Vos R, Hackett T, Hogg J, Kaminski N, Pilette C, Gayan-Ramirez G, Vanaudenaerde B. Morphometrics and Mucosal Immune Features in Lungs With End-stage Chronic Obstructive Pulmonary Disease. 2023, a6145-a6145. DOI: 10.1164/ajrccm-conference.2023.207.1_meetingabstracts.a6145.
Activation of Adam12-SDC4 and CCL22-CCR4 Pathways in the Airway in AsthmaChupp G, Liu Q, Adams T, Schupp J, Wilson G, Grant N, Gomez J, Cohn L, Kaminski N, Akuthota P, Weiss S, Glass K, Bleecker E, Meyers D, Tantisira K, Yan X. Activation of Adam12-SDC4 and CCL22-CCR4 Pathways in the Airway in Asthma. 2023, a5689-a5689. DOI: 10.1164/ajrccm-conference.2023.207.1_meetingabstracts.a5689.
Building Epithelial Barrier in Whole-lung Tissue EngineeringGreaney A, Raredon M, Adams T, Langer R, Kaminski N, Niklason L. Building Epithelial Barrier in Whole-lung Tissue Engineering. 2023, a6159-a6159. DOI: 10.1164/ajrccm-conference.2023.207.1_meetingabstracts.a6159.
Pulmonary Hypertension-related Changes in Structure and Function of the Human Proximal Pulmonary ArteryManning E, Ramachandra A, Cavinato C, Lee P, Heerdt P, Singh I, Tellides G, Kaminski N, Humphrey J. Pulmonary Hypertension-related Changes in Structure and Function of the Human Proximal Pulmonary Artery. 2023, a6133-a6133. DOI: 10.1164/ajrccm-conference.2023.207.1_meetingabstracts.a6133.
High-dimensional Analysis of Cell-cell Signaling in Pulmonary Biology and Disease Using NichesRaredon M, Yang J, Kothapalli N, Greaney A, Justet A, Adams T, Zhao A, Kim H, Manning E, Medzhitov R, Niklason L, Kaminski N, Kluger Y. High-dimensional Analysis of Cell-cell Signaling in Pulmonary Biology and Disease Using Niches. 2023, a4697-a4697. DOI: 10.1164/ajrccm-conference.2023.207.1_meetingabstracts.a4697.
Age-related Changes in Structure, Function, and Transcriptomics of the Human Proximal Pulmonary ArteryManning E, Ramachandra A, Cavinato C, Schupp J, Justet A, Lee P, Heerdt P, Singh I, Murphy T, Gill T, Tellides G, Kaminski N, Humphrey J. Age-related Changes in Structure, Function, and Transcriptomics of the Human Proximal Pulmonary Artery. 2023, a4656-a4656. DOI: 10.1164/ajrccm-conference.2023.207.1_meetingabstracts.a4656.
Common and Distinct Bronchoalveolar Lavage and Lung Immune Signatures in Fibrotic Hypersensitivity Pneumonitis and Idiopathic Pulmonary FibrosisZhao A, Yan X, Sharma P, Deluliis G, Buendia-Roldan I, Pardo A, Selman M, Kaminski N. Common and Distinct Bronchoalveolar Lavage and Lung Immune Signatures in Fibrotic Hypersensitivity Pneumonitis and Idiopathic Pulmonary Fibrosis. 2023, a3948-a3948. DOI: 10.1164/ajrccm-conference.2023.207.1_meetingabstracts.a3948.
Single Nuclear RNAseq of Differentially Affected IPF Lung Uncovers Potential Cellular Origins of Aberrant Basaloid CellsAdams T, Schupp J, Balayev A, Justet A, Sharma P, DeIuliis G, Yan X, Wuyts W, Vanaudenaerde B, Kaminski N. Single Nuclear RNAseq of Differentially Affected IPF Lung Uncovers Potential Cellular Origins of Aberrant Basaloid Cells. 2023, a2802-a2802. DOI: 10.1164/ajrccm-conference.2023.207.1_meetingabstracts.a2802.
The Extracellular Matrix of the Human Proximal Pulmonary Artery Regulates Gene Expression of Resident Cells Responsible for Remodeling During AgingYuan Y, Khoury J, Ramachandra A, Singh I, Tellides G, Humphrey J, Kaminski N, Manning E. The Extracellular Matrix of the Human Proximal Pulmonary Artery Regulates Gene Expression of Resident Cells Responsible for Remodeling During Aging. 2023, a2680-a2680. DOI: 10.1164/ajrccm-conference.2023.207.1_meetingabstracts.a2680.
Cellular Ageing and Senescence Transcriptional Modules in the Aged Human LungDe Man R, Mcdonough J, Adams T, Yan X, Kaminski N. Cellular Ageing and Senescence Transcriptional Modules in the Aged Human Lung. 2023, a2663-a2663. DOI: 10.1164/ajrccm-conference.2023.207.1_meetingabstracts.a2663.
The Therapeutic Gap in Idiopathic Pulmonary Fibrosis: Insights From Single Cell Transcriptional ProfilingMckenna N, Ochsner S, Moss B, Cala Garcia J, Cardenas Castillo R, Poli F, Poli De Frias S, Tsoyi K, Polverino F, Koenigshoff M, Kaminski N, Coarfa C, Rosas I. The Therapeutic Gap in Idiopathic Pulmonary Fibrosis: Insights From Single Cell Transcriptional Profiling. 2023, a2235-a2235. DOI: 10.1164/ajrccm-conference.2023.207.1_meetingabstracts.a2235.
Identification of Molecular Profiles Predictive of Outcome by RNA-Sequencing of Formalin-Fixed, Paraffin-Embedded (FFPE) Lung Tissue From Patients With Idiopathic Pulmonary FibrosisKarampitsakos T, Juan-Guardela B, Vukmirovic M, Perrot C, Zhang Y, Gibson K, Vamvakaris I, Tzouvelekis A, Yan X, Kaminski N, Herazo-Maya J. Identification of Molecular Profiles Predictive of Outcome by RNA-Sequencing of Formalin-Fixed, Paraffin-Embedded (FFPE) Lung Tissue From Patients With Idiopathic Pulmonary Fibrosis. 2023, a1505-a1505. DOI: 10.1164/ajrccm-conference.2023.207.1_meetingabstracts.a1505.
G-coupled Protein 87 (GPR87) a Cell Surface Orphan Receptor Expressed in Aberrant Basaloid Cells in IPF Mediates LPA Induced Fibrotic Gene Expression in Human iPSC Derived Basal CellsKhoury J, Ahangari F, Barnthaler T, McDonough J, Justet A, Adams T, Schupp J, Alysandratos K, Beermann M, Kotton D, Gomez J, Kaminski N. G-coupled Protein 87 (GPR87) a Cell Surface Orphan Receptor Expressed in Aberrant Basaloid Cells in IPF Mediates LPA Induced Fibrotic Gene Expression in Human iPSC Derived Basal Cells. 2023, a6762-a6762. DOI: 10.1164/ajrccm-conference.2023.207.1_meetingabstracts.a6762.
Aberrant Basaloid Cells and Closely Connected Intermediate State Cells Are Involved in the Injury Repair Process of the Fibrotic Lungs in the Aftermath of Severe COVID-19Balayev A, Adams T, Justet A, Schupp J, Mcdonough J, Kaminski N. Aberrant Basaloid Cells and Closely Connected Intermediate State Cells Are Involved in the Injury Repair Process of the Fibrotic Lungs in the Aftermath of Severe COVID-19. 2023, a5667-a5667. DOI: 10.1164/ajrccm-conference.2023.207.1_meetingabstracts.a5667.
The Pulmonary Fibrosis Drug ConnectomeFlint J, Sharma P, Adams T, Lepe A, Kim H, Abu Hussein N, Schupp J, Cosme Jr. C, Mcdonough J, Sauler M, Yan X, Kaminski N. The Pulmonary Fibrosis Drug Connectome. 2023, a2234-a2234. DOI: 10.1164/ajrccm-conference.2023.207.1_meetingabstracts.a2234.
Online Cell Atlases Improve Interrogation of Lung Transcriptomic DataFlint J, Sharma P, Cosme Jr. C, Neumark N, Adams T, Kim H, Lepe A, Abu Hussein N, Schupp J, Mcdonough J, Sauler M, Yan X, Kaminski N. Online Cell Atlases Improve Interrogation of Lung Transcriptomic Data. 2023, a2223-a2223. DOI: 10.1164/ajrccm-conference.2023.207.1_meetingabstracts.a2223.
Spatial Transcriptomic Analysis Allow the Identification of Abnormal Airway Niches in the Fibrotic LungJustet A, Adams T, Balayev A, Baernthaler T, Poli F, Cala Garcia J, Mcdonough J, Flint J, Schupp J, Zhao A, Yunqing L, Ningshan L, Raredon M, Lepe A, Wang A, Abu Hussein N, Yan X, Rosas I, Kaminski N. Spatial Transcriptomic Analysis Allow the Identification of Abnormal Airway Niches in the Fibrotic Lung. 2023, a1033-a1033. DOI: 10.1164/ajrccm-conference.2023.207.1_meetingabstracts.a1033.
Rational engineering of lung alveolar epitheliumLeiby K, Yuan Y, Ng R, Raredon M, Adams T, Baevova P, Greaney A, Hirschi K, Campbell S, Kaminski N, Herzog E, Niklason L. Rational engineering of lung alveolar epithelium. Npj Regenerative Medicine 2023, 8: 22. PMID: 37117221, PMCID: PMC10147714, DOI: 10.1038/s41536-023-00295-2.
Thyroid hormone modulates hyperoxic neonatal lung injury and mitochondrial functionVamesu B, Nicola T, Li R, Hazra S, Matalon S, Kaminski N, Ambalavanan N, Kandasamy J. Thyroid hormone modulates hyperoxic neonatal lung injury and mitochondrial function. JCI Insight 2023, 8: e160697. PMID: 36917181, PMCID: PMC10243814, DOI: 10.1172/jci.insight.160697.
Emergence of division of labor in tissues through cell interactions and spatial cuesAdler M, Moriel N, Goeva A, Avraham-Davidi I, Mages S, Adams T, Kaminski N, Macosko E, Regev A, Medzhitov R, Nitzan M. Emergence of division of labor in tissues through cell interactions and spatial cues. Cell Reports 2023, 42: 112412. PMID: 37086403, PMCID: PMC10242439, DOI: 10.1016/j.celrep.2023.112412.
Genetic analyses of chr11p15.5 region identify MUC5AC-MUC5B associated with asthma-related phenotypesLi X, Li H, Christenson S, Castro M, Denlinger L, Erzurum S, Fahy J, Gaston B, Israel E, Jarjour N, Levy B, Mauger D, Moore W, Zein J, Kaminski N, Wenzel S, Woodruff P, Bleecker E, Meyers D, Program F. Genetic analyses of chr11p15.5 region identify MUC5AC-MUC5B associated with asthma-related phenotypes. Journal Of Asthma 2023, 60: 1824-1835. PMID: 36946148, PMCID: PMC10524756, DOI: 10.1080/02770903.2023.2193631.
Transbronchial Lung Cryobiopsy for the Diagnosis of Interstitial Lung DiseaseLow S, Kaminski N, Maldonado F. Transbronchial Lung Cryobiopsy for the Diagnosis of Interstitial Lung Disease. Journal Of Bronchology & Interventional Pulmonology 2023, 30: 93-95. PMID: 37005378, DOI: 10.1097/lbr.0000000000000882.
Single-Cell Rna Sequencing of the Mouse Isograft and Allograft Lung after Orthotopic Lung TransplantationHooft C, Kaes J, Heigl T, Beeckmans H, Kerckhof P, Vanstapel A, Jin X, Slambrouck J, Vandervelde C, Van Raemdonck D, Kaminski N, McDonough J, Ceulemans L, Vos R, Vanaudenaerde B. Single-Cell Rna Sequencing of the Mouse Isograft and Allograft Lung after Orthotopic Lung Transplantation. The Journal Of Heart And Lung Transplantation 2023, 42: s539. DOI: 10.1016/j.healun.2023.02.1473.
SH2 Domain-Containing Phosphatase-SHP2 Attenuates Fibrotic Responses through Negative Regulation of Mitochondrial Metabolism in Lung FibroblastsKarampitsakos T, Galaris A, Barbayianni I, DeIuliis G, Ahangari F, Sampsonas F, Sotiropoulou V, Aidinis V, Bennett A, Herazo-Maya J, Xylourgidis N, Bakakos P, Bouros D, Kaminski N, Tzouvelekis A. SH2 Domain-Containing Phosphatase-SHP2 Attenuates Fibrotic Responses through Negative Regulation of Mitochondrial Metabolism in Lung Fibroblasts. Diagnostics 2023, 13: 1166. PMID: 36980473, PMCID: PMC10047203, DOI: 10.3390/diagnostics13061166.
Ex vivo Testung der antifibrotischen Wirksamkeit von Medikamenten auf die Idiopathische Lungenfibrose mittels Langzeitkultur von humanen Lungengewebs-Präzisionsschnitte (PCLS)Artysh N, Jäger B, Terwolbeck O, Sewald K, Kaminski N, Zeug A, Prasse A. Ex vivo Testung der antifibrotischen Wirksamkeit von Medikamenten auf die Idiopathische Lungenfibrose mittels Langzeitkultur von humanen Lungengewebs-Präzisionsschnitte (PCLS). Pneumologie 2023, 77: s111-s111. DOI: 10.1055/s-0043-1761142.
A novel Bayesian framework for harmonizing information across tissues and studies to increase cell type deconvolution accuracyDeng W, Li B, Wang J, Jiang W, Yan X, Li N, Vukmirovic M, Kaminski N, Wang J, Zhao H. A novel Bayesian framework for harmonizing information across tissues and studies to increase cell type deconvolution accuracy. Briefings In Bioinformatics 2023, 24: bbac616. PMID: 36631398, PMCID: PMC9851324, DOI: 10.1093/bib/bbac616.
PD-1highCXCR5–CD4+ peripheral helper T cells promote CXCR3+ plasmablasts in human acute viral infectionAsashima H, Mohanty S, Comi M, Ruff W, Hoehn K, Wong P, Klein J, Lucas C, Cohen I, Coffey S, Lele N, Greta L, Raddassi K, Chaudhary O, Unterman A, Emu B, Kleinstein S, Montgomery R, Iwasaki A, Dela Cruz C, Kaminski N, Shaw A, Hafler D, Sumida T. PD-1highCXCR5–CD4+ peripheral helper T cells promote CXCR3+ plasmablasts in human acute viral infection. Cell Reports 2023, 42: 111895. PMID: 36596303, PMCID: PMC9806868, DOI: 10.1016/j.celrep.2022.111895.
Comprehensive visualization of cell–cell interactions in single-cell and spatial transcriptomics with NICHESRaredon M, Yang J, Kothapalli N, Lewis W, Kaminski N, Niklason L, Kluger Y. Comprehensive visualization of cell–cell interactions in single-cell and spatial transcriptomics with NICHES. Bioinformatics 2022, 39: btac775. PMID: 36458905, PMCID: PMC9825783, DOI: 10.1093/bioinformatics/btac775.
Single-cell RNA-seq uncovers cellular heterogeneity and provides a signature for paediatric sleep apnoea.Cortese R, Adams T, Cataldo K, Hummel J, Kaminski N, Kheirandish-Gozal L, Gozal D. Single-cell RNA-seq uncovers cellular heterogeneity and provides a signature for paediatric sleep apnoea. European Respiratory Journal 2022, 61: 2201465. PMID: 36356973, DOI: 10.1183/13993003.01465-2022.
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.
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.
From COVID to fibrosis: lessons from single-cell analyses of the human lungJustet A, Zhao AY, Kaminski N. From COVID to fibrosis: lessons from single-cell analyses of the human lung. Human Genomics 2022, 16: 20. PMID: 35698166, PMCID: PMC9189802, DOI: 10.1186/s40246-022-00393-0.
Soluble Signals to Improve Endothelial Integrity in the LungYuan Y, Raredon M, Yuan Q, Obata T, Qian H, Wu D, Kaminski N, Niklason L. Soluble Signals to Improve Endothelial Integrity in the Lung. 2022, a5749-a5749. DOI: 10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a5749.
Cigarette Smoke Exposure or Nigericin/LPS Stimulation Induces MAVS Aggregation, Which Is Further Augmented in NLRX1 DeficiencyGupta G, Kim S, Shin H, Wei L, Rosas I, Kaminski N, Sharma L, Dela Cruz C, Kang M. Cigarette Smoke Exposure or Nigericin/LPS Stimulation Induces MAVS Aggregation, Which Is Further Augmented in NLRX1 Deficiency. 2022, a1214-a1214. DOI: 10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a1214.
CD38 Mediates Lung Fibrosis by Promoting Alveolar Epithelial Cell AgingLiu G, Cui H, Xie N, Banerjee S, Liu R, Antony V, Sanders Y, Thannickal V, Kaminski N. CD38 Mediates Lung Fibrosis by Promoting Alveolar Epithelial Cell Aging. 2022, a2310-a2310. DOI: 10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a2310.
Integrating Gene Expression with Genome-Wide Association Summary Statistics to Identify Genes Associated with Idiopathic Pulmonary Fibrosis SurvivalHu X, Kim J, Ma S, Huang Y, Oldham J, Allen R, Molyneaux P, Joseph C, Guillen Guio B, Hernández Beeftink T, Kropski J, Lee C, Adegunsoye A, Pugashetti J, Linderholm A, Strek M, Hubbard R, Hart S, Nicholson A, Lancaster L, Lorenzo-Salazar J, Vo V, Hirani N, Whyte M, Parfrey H, Rassl D, Wallace W, Valenzi E, Zhang Y, Stockwell A, Kaminski N, Wolters P, Molina-Molina M, Martinez F, Hall I, Tobin M, Maher T, Blackwell T, Yaspan B, Jenkins R, Wain L, Flores C, Noth I, Manichaikul A. Integrating Gene Expression with Genome-Wide Association Summary Statistics to Identify Genes Associated with Idiopathic Pulmonary Fibrosis Survival. 2022, a2326-a2326. DOI: 10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a2326.
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, Buendía-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.
Toll-Like-Receptor 5 Protects Against Pulmonary Fibrosis by Reducing Lung DysbiosisSakamachi Y, Solis A, Johnson C, Hussain S, O'Dwyer D, Mehta S, Trempus C, Thomas S, Karmaus P, Schwartz D, Kaminski N, Zhang Y, Yang I, Molyneaux P, Kass D, Gibson K, Garantziotis S. Toll-Like-Receptor 5 Protects Against Pulmonary Fibrosis by Reducing Lung Dysbiosis. 2022, a4990-a4990. DOI: 10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a4990.
Structural, Functional, and Single Cell Transcriptomic Age-Related Remodeling of Mouse Proximal Pulmonary ArteryManning E, Ramachandra A, Cavinato C, Schupp J, Justet A, Singh I, Tellides G, Gill T, Kaminski N, Humphrey J. Structural, Functional, and Single Cell Transcriptomic Age-Related Remodeling of Mouse Proximal Pulmonary Artery. 2022, a5205-a5205. DOI: 10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a5205.
Differential RNAseq Analysis of an Ex-Vivo Human Fibrotic Tissue Slice Model Reveals Dysregulated Genes of Cellular Senescence and YAP/TAZ Signaling in FibrosisPineda R, Mitash N, Kohler K, Melo Narvaez M, Sembrat J, Fangping M, Lehmann M, Kaminski N, Koenigshoff M. Differential RNAseq Analysis of an Ex-Vivo Human Fibrotic Tissue Slice Model Reveals Dysregulated Genes of Cellular Senescence and YAP/TAZ Signaling in Fibrosis. 2022, a5229-a5229. DOI: 10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a5229.
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.
Live Imaging the Dynamic Spatiotemporal Behavior of Alveolar Type 2 Cells in Response to Bleomycin Induced Lung InjuryChioccioli M, Mcdonough J, Yang T, Gonzalez D, Rivera-Molina F, Kaminski N, Sauler M, DeIuliis G. Live Imaging the Dynamic Spatiotemporal Behavior of Alveolar Type 2 Cells in Response to Bleomycin Induced Lung Injury. 2022, a5477-a5477. DOI: 10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a5477.
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.
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.
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.
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.
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.
Decellularized Lung Tissue Proteomics Showed Decreased Surfactant and Increased Inflammatory Proteins in the Aged LungMcdonough J, Cosme Jr. C, Rupert C, Schupp J, Ahangari F, DeIuliis G, Yan X, Hagood J, Vanaudenaerde B, Niklason L, Hansen K, Kaminski N. Decellularized Lung Tissue Proteomics Showed Decreased Surfactant and Increased Inflammatory Proteins in the Aged Lung. 2022, a3903-a3903. DOI: 10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a3903.
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.
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.
New Insights on Idiopathic Pulmonary Fibrosis Revealed by Proteomics and Lipidomics Analysis of Human Tissue CoresClair G, Kyle J, Melchior J, Olson H, Paurus V, Bloodsworth K, Schupp J, Mcdonough J, Wuyts W, Vanaudenaerde B, Kaminski N. New Insights on Idiopathic Pulmonary Fibrosis Revealed by Proteomics and Lipidomics Analysis of Human Tissue Cores. 2022, a1972-a1972. DOI: 10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a1972.
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.
Single-cell multi-omics reveals dyssynchrony of the innate and adaptive immune system in progressive COVID-19Unterman A, Sumida TS, Nouri N, Yan X, Zhao AY, Gasque V, Schupp JC, Asashima H, Liu Y, Cosme C, Deng W, Chen M, Raredon MSB, Hoehn KB, Wang G, Wang Z, DeIuliis G, Ravindra NG, Li N, Castaldi C, Wong P, Fournier J, Bermejo S, Sharma L, Casanovas-Massana A, Vogels CBF, Wyllie AL, Grubaugh ND, Melillo A, Meng H, Stein Y, Minasyan M, Mohanty S, Ruff WE, Cohen I, Raddassi K, Niklason L, Ko A, Montgomery R, Farhadian S, Iwasaki A, Shaw A, van Dijk D, Zhao H, Kleinstein S, Hafler D, Kaminski N, Dela Cruz C. Single-cell multi-omics reveals dyssynchrony of the innate and adaptive immune system in progressive COVID-19. Nature Communications 2022, 13: 440. PMID: 35064122, PMCID: PMC8782894, DOI: 10.1038/s41467-021-27716-4.
Metagenomic sequencing of the bronchoalveolar lavage extracellular virome and cellular transcriptome of sarcoidosis patients does not detect rubella virusKeeler E, Vukmirovic M, Yan X, Gulino K, Ghedin E, Kaminski N, Sullivan K, Bushman F, Collman R, Rosenbach M. Metagenomic sequencing of the bronchoalveolar lavage extracellular virome and cellular transcriptome of sarcoidosis patients does not detect rubella virus. Sarcoidosis, Vasculitis, And Diffuse Lung Diseases 2022, 39: e2022040. PMID: 36533601, PMCID: PMC9798337, DOI: 10.36141/svdld.v39i4.13407.
T3 Integrated transcriptomic analysis of human tuberculosis granulomas and a biomimetic model identifies sphingosine kinase 1 as a potential therapeutic targetReichmann M, Tezera L, Vallejo A, Vukmirovic M, Xiao R, Jogai S, Wilson S, Marshall, Jones, Leslie A, D’Armiento J, Kaminski N, Polak M, Elkington P. T3 Integrated transcriptomic analysis of human tuberculosis granulomas and a biomimetic model identifies sphingosine kinase 1 as a potential therapeutic target. Thorax 2021, 76: a2-a3. DOI: 10.1136/thorax-2021-btsabstracts.3.
S63 Genome-wide sex-by-SNP interaction analysis of susceptibility to idiopathic pulmonary fibrosisLeavy O, Allen R, Oldham J, Guillen-Guio B, Stockwell A, Braybrooke R, Hubbard R, Ma S, Fingerlin T, Kaminski N, Zhang Y, Schwartz D, Yaspan B, Maher T, Molyneaux P, Flores C, Noth I, Jenkins R, Wain L. S63 Genome-wide sex-by-SNP interaction analysis of susceptibility to idiopathic pulmonary fibrosis. Thorax 2021, 76: a42-a42. DOI: 10.1136/thorax-2021-btsabstracts.69.
S65 Genome-wide association study of survival times after diagnosis of idiopathic pulmonary fibrosisAllen R, Oldham J, Lorenzo-Salazar J, Molyneaux P, Ma S, Stockwell A, Joseph C, Kim J, Guillen-Guio B, Hernandez-Beeftink T, Kropski J, Huang Y, Lee C, Adegunsoye A, Pugashetti J, Linderholm A, Vo V, Strek M, Hubbard R, Hirani N, Whyte M, Hart S, Nicholson A, Parfrey H, Rassl D, Wallace W, Fahy W, Valenzi E, Zhang Y, Kaminski N, Wolters P, Molina-Molina M, Martinez F, Hall I, Tobin, Maher T, Blackwell T, Yaspan B, Jenkins R, Flores C, Wain L, Noth I. S65 Genome-wide association study of survival times after diagnosis of idiopathic pulmonary fibrosis. Thorax 2021, 76: a43-a43. DOI: 10.1136/thorax-2021-btsabstracts.71.
S98 Dissecting human pleura at single-cell resolutionObacz J, Adams T, Schupp J, Kaminski N, Aresu G, Coonar A, Peryt A, Rassl D, Rintoul R, Marciniak S. S98 Dissecting human pleura at single-cell resolution. 2021, a63.1-a63. DOI: 10.1136/thorax-2021-btsabstracts.104.
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.
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.
Structural, Functional, and Single Cell Transcriptomic Changes in Mouse Pulmonary Artery Resulting from HypoxiaManning E, Ramachandra A, Schupp J, Cavinato C, Singh I, Kaminski N, Humphrey J. Structural, Functional, and Single Cell Transcriptomic Changes in Mouse Pulmonary Artery Resulting from Hypoxia. 2021, a3625-a3625. DOI: 10.1164/ajrccm-conference.2021.203.1_meetingabstracts.a3625.
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.
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.
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.
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.
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 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.
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.
Prediction of Survival after Chronic Lung Allograft Dysfunction in Lung Transplant Recipients by Blood Profiling Using a Predefined 52 Gene SignatureLuijk B, Krebber M, Li Q, Kardol-Hoefnagel T, Budding K, van Kessel D, Grutters J, Otten H, Kaminski N, Maya J. Prediction of Survival after Chronic Lung Allograft Dysfunction in Lung Transplant Recipients by Blood Profiling Using a Predefined 52 Gene Signature. The Journal Of Heart And Lung Transplantation 2021, 40: s155-s156. DOI: 10.1016/j.healun.2021.01.470.
Abstract 14125: An in vitro Pulmonary Vascular Platform From Endothelialized Whole Lung ScaffoldsYuan Y, Leiby K, Greaney A, Raredon M, Qian H, Baevova P, Admas T, Engler A, Kural M, Schupp J, Hong Y, Kaminski N, Niklason L. Abstract 14125: An in vitro Pulmonary Vascular Platform From Endothelialized Whole Lung Scaffolds. Circulation 2020, 142 DOI: 10.1161/circ.142.suppl_3.14125.
Retrograde signaling by a mtDNA-encoded non-coding RNA preserves mitochondrial bioenergeticsBlumental-Perry A, Jobava R, Bederman I, Degar A, Kenche H, Guan B, Pandit K, Perry N, Molyneaux N, Wu J, Prendergas E, Ye Z, Zhang J, Nelson C, Ahangari F, Krokowski D, Guttentag S, Linden P, Townsend D, Miron A, Kang M, Kaminski N, Perry Y, Hatzoglou M. Retrograde signaling by a mtDNA-encoded non-coding RNA preserves mitochondrial bioenergetics. Communications Biology 2020, 3: 626. PMID: 33127975, PMCID: PMC7603330, DOI: 10.1038/s42003-020-01322-4.
FK506-binding protein 11, a novel plasma cell specific antibody folding catalyst, is increased in idiopathic pulmonary fibrosisPreisendörfer S, Ishikawa Y, Knüppel L, Fernandez I, Binzenhöfer L, Juan-Guardela B, Hennen E, Ruppert C, Guenther A, Kneidinger N, Frankenberger M, Hatz R, Behr J, Schepers A, Hilgendorff A, Kaminski N, Bächinger H, Eickelberg O, Staab-Weijnitz C. FK506-binding protein 11, a novel plasma cell specific antibody folding catalyst, is increased in idiopathic pulmonary fibrosis. 2020, 2293. DOI: 10.1183/13993003.congress-2020.2293.
During the COVID-19 Pandemic, Lung Specialists of the World Implore You: Inhale Only Clean AirSanthosh L, Oh A, Alismail A, Breiburg A, Kaminski N, Carlos G, Jamil S. During the COVID-19 Pandemic, Lung Specialists of the World Implore You: Inhale Only Clean Air. American Journal Of Respiratory And Critical Care Medicine 2020 DOI: 10.1164/rccm.2020c13.
Exosomal Protein Signature for Non-Invasive Differential Diagnosis of Idiopathic Pulmonary FibrosisAdduri S, Alzate K, Iliuk A, Cai K, Miller J, Pal A, Poli De Frias S, Vasireddy R, Nicastro D, Kaminski N, Rosas I, Konduru N. Exosomal Protein Signature for Non-Invasive Differential Diagnosis of Idiopathic Pulmonary Fibrosis. 2020, a2568-a2568. DOI: 10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a2568.
T Cell Immunophenotypes in Sarcoidosis Identified by Cluster Analysis and a Transcriptomic IntegrationLiao S, Li L, Barkes B, Macphail K, Bowler R, Kaminski N, Wisniewski S, Hamzeh N, Maier L. T Cell Immunophenotypes in Sarcoidosis Identified by Cluster Analysis and a Transcriptomic Integration. 2020, a3630-a3630. DOI: 10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a3630.
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.
Genetic Analyses Identify IL1R2-IL1RL1-IL18R1 in Chr2q Region Associated with Asthma and COPDLi X, Christenson S, Kaminski N, Wenzel S, Woodruff P, Meyers D, Bleecker E, the Subpopulations and Intermediate Outcomes in CO P, the Severe Asthma Research Program (SARP). Genetic Analyses Identify IL1R2-IL1RL1-IL18R1 in Chr2q Region Associated with Asthma and COPD. 2020, a4218-a4218. DOI: 10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a4218.
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.
Retrograde Signaling by Mitochondria-Encoded Mito-ncR-805 Preserves Mitochondrial Function of Alveolar Epithelial Type 2 Cells During Exposure to Cigarette SmokeBlumental-Perry A, Jobava R, Guan B, Bederman I, Ye Z, Perry N, Molyneaux N, Wu J, Guttentag S, Townsend D, Miron A, Kang M, Shadel G, Kaminski N, Perry Y, Hatzoglou M. Retrograde Signaling by Mitochondria-Encoded Mito-ncR-805 Preserves Mitochondrial Function of Alveolar Epithelial Type 2 Cells During Exposure to Cigarette Smoke. 2020, a6384-a6384. DOI: 10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a6384.
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.
Unbiased RNA-Sequencing Analysis Demonstrates Common and Unique Features of Tuberculosis and Sarcoidosis Lymph Node SamplesReichmann M, Vukmirovic M, Vallejo A, Tezera L, Jones M, Kaminski N, Polak M, Elkington P. Unbiased RNA-Sequencing Analysis Demonstrates Common and Unique Features of Tuberculosis and Sarcoidosis Lymph Node Samples. 2020, a1048-a1048. DOI: 10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a1048.
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.
Single Cell RNA Sequencing of Peripheral Blood Mononuclear Cells in Idiopathic Pulmonary Fibrosis Reveals the Cellular Origin of the Outcome Predictive 52-Gene SignatureUnterman A, Neumark N, Zhao A, Schupp J, Ryu C, Antin-Ozerkis D, Winkler J, Herazo-Maya J, Herzog E, Kaminski N. Single Cell RNA Sequencing of Peripheral Blood Mononuclear Cells in Idiopathic Pulmonary Fibrosis Reveals the Cellular Origin of the Outcome Predictive 52-Gene Signature. 2020, a6211-a6211. DOI: 10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a6211.
Social Media Engagement During Pulmonary Disease National Health Observance Awareness MonthsPeabody Lever J, Carroll C, Kaminski N, Rowe S. Social Media Engagement During Pulmonary Disease National Health Observance Awareness Months. 2020, a6614-a6614. DOI: 10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a6614.
Gene Expression Patterns Distinctly Characterize Differentially Affected Regions in Human Fibrotic Hypersensitivity Pneumonitis LungsDe Sadeleer L, McDonough J, Schupp J, Yan X, Vanaudenaerde B, Verleden S, Kaminski N, Wuyts W. Gene Expression Patterns Distinctly Characterize Differentially Affected Regions in Human Fibrotic Hypersensitivity Pneumonitis Lungs. 2020, a2262-a2262. DOI: 10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a2262.
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.
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.
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.
SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across TissuesZiegler C, Allon S, Nyquist S, Mbano I, Miao V, Tzouanas C, Cao Y, Yousif A, Bals J, Hauser B, Feldman J, Muus C, Wadsworth M, Kazer S, Hughes T, Doran B, Gatter G, Vukovic M, Taliaferro F, Mead B, Guo Z, Wang J, Gras D, Plaisant M, Ansari M, Angelidis I, Adler H, Sucre J, Taylor C, Lin B, Waghray A, Mitsialis V, Dwyer D, Buchheit K, Boyce J, Barrett N, Laidlaw T, Carroll S, Colonna L, Tkachev V, Peterson C, Yu A, Zheng H, Gideon H, Winchell C, Lin P, Bingle C, Snapper S, Kropski J, Theis F, Schiller H, Zaragosi L, Barbry P, Leslie A, Kiem H, Flynn J, Fortune S, Berger B, Finberg R, Kean L, Garber M, Schmidt A, Lingwood D, Shalek A, Ordovas-Montanes J, Network H, Banovich N, Barbry P, Brazma A, Desai T, Duong T, Eickelberg O, Falk C, Farzan M, Glass I, Haniffa M, Horvath P, Hung D, Kaminski N, Krasnow M, Kropski J, Kuhnemund M, Lafyatis R, Lee H, Leroy S, Linnarson S, Lundeberg J, Meyer K, Misharin A, Nawijn M, Nikolic M, Ordovas-Montanes J, Pe’er D, Powell J, Quake S, Rajagopal J, Tata P, Rawlins E, Regev A, Reyfman P, Rojas M, Rosen O, Saeb-Parsy K, Samakovlis C, Schiller H, Schultze J, Seibold M, Shalek A, Shepherd D, Spence J, Spira A, Sun X, Teichmann S, Theis F, Tsankov A, van den Berge M, von Papen M, Whitsett J, Xavier R, Xu Y, Zaragosi L, Zhang K. SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues. Cell 2020, 181: 1016-1035.e19. PMID: 32413319, PMCID: PMC7252096, DOI: 10.1016/j.cell.2020.04.035.
Summary and Future Applications of Precision Medicine in Pulmonary, Critical Care, and Sleep MedicineGomez J, Kaminski N, Himes B. Summary and Future Applications of Precision Medicine in Pulmonary, Critical Care, and Sleep Medicine. 2020, 417-428. DOI: 10.1007/978-3-030-31507-8_28.
IntroductionGomez J, Kaminski N, Himes B. Introduction. 2020, 3-8. DOI: 10.1007/978-3-030-31507-8_1.
BAL Cell Gene Expression in Severe Asthma Reveals Mechanisms of Severe Disease and Influences of MedicationsWeathington N, O’Brien M, Radder J, Whisenant TC, Bleecker ER, Busse WW, Erzurum SC, Gaston B, Hastie A, Jarjour N, Meyers D, Milosevic J, Moore W, Tedrow J, Trudeau J, Wong H, Wu W, Kaminski N, Wenzel S, Modena B. BAL Cell Gene Expression in Severe Asthma Reveals Mechanisms of Severe Disease and Influences of Medications. American Journal Of Respiratory And Critical Care Medicine 2019, 200: 837-856. PMID: 31161938, PMCID: PMC6812436, DOI: 10.1164/rccm.201811-2221oc.
The Transciptome of BAL Cells at Acute Exacerbation of IPF reveals New InsightsCarleo A, Deluca D, Bargagli E, Wuyts W, Kaminski N, Prasse A. The Transciptome of BAL Cells at Acute Exacerbation of IPF reveals New Insights. 2019, pa597. DOI: 10.1183/13993003.congress-2019.pa597.
SH2 domain-containing Phosphatase-(SHP)-2 blunts fibrotic responses through regulation of fibroblast mitochondrial metabolism and autophagyTzouvelekis A, Yu G, Ahangari F, Bennett A, Karampitsakos T, Bouros D, Bouros E, Kaminski N. SH2 domain-containing Phosphatase-(SHP)-2 blunts fibrotic responses through regulation of fibroblast mitochondrial metabolism and autophagy. 2019, pa583. DOI: 10.1183/13993003.congress-2019.pa583.
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.
Role of dual-specificity protein phosphatase DUSP10/MKP-5 in pulmonary fibrosisXylourgidis N, Min K, Ahangari F, Yu G, Herazo-Maya JD, Karampitsakos T, Aidinis V, Binzenhöfer L, Bouros D, Bennett AM, Kaminski N, Tzouvelekis A. Role of dual-specificity protein phosphatase DUSP10/MKP-5 in pulmonary fibrosis. American Journal Of Physiology - Lung Cellular And Molecular Physiology 2019, 317: l678-l689. PMID: 31483681, PMCID: PMC6879900, DOI: 10.1152/ajplung.00264.2018.
The Human Lung Cell Atlas: A High-Resolution Reference Map of the Human Lung in Health and DiseaseSchiller HB, Montoro DT, Simon LM, Rawlins EL, Meyer KB, Strunz M, Braga F, Timens W, Koppelman GH, Budinger GRS, Burgess JK, Waghray A, van den Berge M, Theis F, Regev A, Kaminski N, Rajagopal J, Teichmann S, Misharin A, Nawijn M. The Human Lung Cell Atlas: A High-Resolution Reference Map of the Human Lung in Health and Disease. American Journal Of Respiratory Cell And Molecular Biology 2019, 61: 31-41. PMID: 30995076, PMCID: PMC6604220, DOI: 10.1165/rcmb.2018-0416tr.
The Prognostic Value of Monocyte Count in Idiopathic Pulmonary Fibrosis: A Multi-Omic Cohort StudyScott M, Quinn K, Li Q, Carroll R, Chen S, Carns M, Aren K, Sun J, Koloms K, Lee J, Kropski J, Zhao H, Herzog E, Martinez F, Moore B, Hinchcliff M, Denny J, Kaminski N, Herazo-Maya J, Shah N, Khatri P. The Prognostic Value of Monocyte Count in Idiopathic Pulmonary Fibrosis: A Multi-Omic Cohort Study. 2019, a7342-a7342. DOI: 10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a7342.
Profibrotic Effects of Mir-33 - Role of Autophagy and Mitochondrial Homeostasis in Macrophages, and Therapeutic ImplicationsAhangari F, Price N, Schupp J, Rose K, Ibarra G, DeIuliis G, Xylourgidis N, Prasse A, Fernandez-Hernando C, Kaminski N. Profibrotic Effects of Mir-33 - Role of Autophagy and Mitochondrial Homeostasis in Macrophages, and Therapeutic Implications. 2019, a7222-a7222. DOI: 10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a7222.
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.
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.
Deletion of Pou2af1 in Type II Alveolar Epithelial Cells Augments Bleomycin-Induced Pulmonary FibrosisLi Q, Omote N, Chen Z, DeIuliis G, Zhu Z, Herzog E, Shakya A, Tantin D, Herazo-Maya J, Kaminski N. Deletion of Pou2af1 in Type II Alveolar Epithelial Cells Augments Bleomycin-Induced Pulmonary Fibrosis. 2019, a5407-a5407. DOI: 10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a5407.
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.
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.
Alveolar and Fibroblast Foci Specific Genome-Wide Gene Expression Profiling Identifies Common Dysregulated Expression of CREB1, a Regulator Across Cell Types, in IPFVukmirovic M, Brereton C, Yan X, Xylourgidis N, Deluliis G, Woolard T, Hu B, Mihaljinec A, Homer R, Maya J, Ahangari F, Fabre A, Smart D, Conforti F, Marshall B, Alzetani A, Davies D, Richeldi L, Kaminski N, Jones M. Alveolar and Fibroblast Foci Specific Genome-Wide Gene Expression Profiling Identifies Common Dysregulated Expression of CREB1, a Regulator Across Cell Types, in IPF. 2019, a5262-a5262. DOI: 10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a5262.
Bronchoalveolar Cell Transcriptome of Acute Exacerbation in Idiopathic Pulmonary FibrosisPrasse A, Jäger B, Schupp J, Kaminski N, Carleo A. Bronchoalveolar Cell Transcriptome of Acute Exacerbation in Idiopathic Pulmonary Fibrosis. 2019, a5259-a5259. DOI: 10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a5259.
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.
Conserved Role of High CO 2 in Regulating Gene Expression of Wnt Signaling PathwayShigemura M, Lecuona E, Angulo M, Edwards M, Welch L, Casalino-Matsuda M, Sporn P, Nader G, Vadasz I, Gruenbaum Y, Beitel G, Kaminski N, Berdnikovs S, Sznajder J. Conserved Role of High CO 2 in Regulating Gene Expression of Wnt Signaling Pathway. 2019, a4437-a4437. DOI: 10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a4437.
Viral Pneumonia Is an Independent Risk Factor for Pulmonary Fibrosis: Results of Large-Scale Longitudinal Population-Level DataShojaee A, Kaminski N, Siner J, Aryan Y, Yan X, Dela Cruz C. Viral Pneumonia Is an Independent Risk Factor for Pulmonary Fibrosis: Results of Large-Scale Longitudinal Population-Level Data. 2019, a4213-a4213. DOI: 10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a4213.
Evaluating the Role of Support Group Participation on Palliative Care Referral and Mortality in Idiopathic Pulmonary FibrosisZou R, Nouraie S, Rosenzweig M, Chen X, Kaminski N, Gibson K, Kass D, Lindell K. Evaluating the Role of Support Group Participation on Palliative Care Referral and Mortality in Idiopathic Pulmonary Fibrosis. 2019, a4093-a4093. DOI: 10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a4093.
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.
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.
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.
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.
Short-Term Longitudinal Gene Expression Changes Predict Forced Vital Capacity Decline in Idiopathic Pulmonary FibrosisHuang Y, Oldham J, Ma S, Hou P, Strek M, Molyneaux P, Maher T, Kaminski N, Herazo-Maya J, Martinez F, Noth I. Short-Term Longitudinal Gene Expression Changes Predict Forced Vital Capacity Decline in Idiopathic Pulmonary Fibrosis. 2019, a2426-a2426. DOI: 10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a2426.
Changes in Lung Histopathology from Diagnosis to Transplant in IPF PatientsUnterman A, Pertzov B, Kaminski N, Kramer M. Changes in Lung Histopathology from Diagnosis to Transplant in IPF Patients. 2019, a1460-a1460. DOI: 10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a1460.
Pink1 Mediates the Protective Effects of Thyroid Hormone T3 in Hyperoxia-Induced Lung InjuryZhang Y, Yu G, Kaminski N, Lee P. Pink1 Mediates the Protective Effects of Thyroid Hormone T3 in Hyperoxia-Induced Lung Injury. 2019, a7069-a7069. DOI: 10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a7069.
Role of Terra on Telomeric and Mitochondrial Functions in IPF PathogenesisYu G, Yang J, Zhao W, Iberra G, Chen X, Guo X, Kaminski N. Role of Terra on Telomeric and Mitochondrial Functions in IPF Pathogenesis. 2019, a1045-a1045. DOI: 10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a1045.
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.
Epigenetic Age Acceleration in Idiopathic Pulmonary FibrosisKurbanov D, Ahangari F, Xylourgidis N, McDonough J, Wuyts W, Vanaudenaerde B, Levine M, Kaminski N. Epigenetic Age Acceleration in Idiopathic Pulmonary Fibrosis. 2019, a5265-a5265. DOI: 10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a5265.
Evolving Genomics of Pulmonary FibrosisIbarra G, Herazo-Maya J, Kaminski N. Evolving Genomics of Pulmonary Fibrosis. 2018, 207-239. DOI: 10.1007/978-3-319-99975-3_9.
Club Cell Protein-16 modifies airway inflammation in asthma and is associated with significant clinical asthma outcomesKraft M, Ledford J, Gozdz J, Li X, Francisco D, Manne A, Guerra S, Martinez F, Kaminski N, Wenzel S, Meyers D, Bleecker E. Club Cell Protein-16 modifies airway inflammation in asthma and is associated with significant clinical asthma outcomes. 2018, pa5496. DOI: 10.1183/13993003.congress-2018.pa5496.
BPI Fold-Containing Family A Member 1 (BPIFA1) regulates lung neutrophil recruitment and interferon signaling during acute inflammationKhanal S, Niu N, Huleihel L, Herazo-Maya J, Kaminski N, Cohn L, Britto C. BPI Fold-Containing Family A Member 1 (BPIFA1) regulates lung neutrophil recruitment and interferon signaling during acute inflammation. 2018, pa4254. DOI: 10.1183/13993003.congress-2018.pa4254.
BAL cell transcriptome predicts survival in IPF and can be used to gauge and model treatment effects interfering with the TGF-beta pathwayPrasse A, Carleo A, Jaeger B, Schupp J, Rottoli P, Wuyts W, Kaminski N. BAL cell transcriptome predicts survival in IPF and can be used to gauge and model treatment effects interfering with the TGF-beta pathway. 2018, oa5359. DOI: 10.1183/13993003.congress-2018.oa5359.
MKP-5 inhibition blunts fibrotic responses in-vitro and in-vivo through negative regulation of TGFB1-induced smad3-signallingTzouvelekis A, Xylourgidis N, Min K, Karampitsakos T, Ninou I, Barbayianni I, Bennett A, Aidinis V, Kaminski N. MKP-5 inhibition blunts fibrotic responses in-vitro and in-vivo through negative regulation of TGFB1-induced smad3-signalling. 2018, oa5350. DOI: 10.1183/13993003.congress-2018.oa5350.
Role of Mitogen activated-kinase (MAPK)-phosphatase (MKP)-5 in pulmonary fibrosisTzouvelekis A, Karampitsakos T, Min K, Xylourgidis N, Yu G, Herazo-Maya J, Bizenhofer L, Bennett A, Kaminski N. Role of Mitogen activated-kinase (MAPK)-phosphatase (MKP)-5 in pulmonary fibrosis. 2018, lsc-1111. DOI: 10.1183/13993003.congress-2018.lsc-1111.
Fk506-binding protein 11, a plasma cell-specific protein folding catalyst, is increased in pulmonary fibrosisPreisendoerfer S, Knüppel L, Binzenhöfer L, Fernandez I, Juan-Guardela B, Hatz R, Behr J, Kaminski N, Schepers A, Eickelberg O, Staab-Weijnitz C. Fk506-binding protein 11, a plasma cell-specific protein folding catalyst, is increased in pulmonary fibrosis. Pneumologie 2018, 72: s115-s115. DOI: 10.1055/s-0037-1619433.
Insights from RNA-sequencing of bronchoalveolar lavage cells in a large sarcoidosis cohortVukmirovic M, Yan X, Gibson K, Gulati M, DeIuliis G, Woolard T, Adams T, Hu B, Zang W, Mihaljinec A, Luijk H, Aurelien N, O'Neal S, Becich M, Hochheiser H, Herzog E, Senior R, Chen E, Morris A, Leader J, Zhang Y, “Skip” Garcia J, Wisniewski S, Benos P, Maier L, Moller D, Drake W, Koth L, Kaminski N. Insights from RNA-sequencing of bronchoalveolar lavage cells in a large sarcoidosis cohort. 2017, oa2907. DOI: 10.1183/1393003.congress-2017.oa2907.
Consensus network analysis reveals pathways associated with lung function decline in both COPD and IPFMcdonough J, Vanaudenaerde B, Wuyts W, Kaminski N. Consensus network analysis reveals pathways associated with lung function decline in both COPD and IPF. 2017, pa3484. DOI: 10.1183/1393003.congress-2017.pa3484.
Feasibility, distribution, and efficacy of an inhaled oligonucleotide mimic of miR-29 for pulmonary fibrosis induced by bleomycin in ratsMontgomery R, Yu G, Ahangari F, Herazo-Maya J, Pestano L, Dalby C, Dickinson B, Nicholas C, Gallant-Behm C, Brower J, Kuehl P, McDonald J, Kaminski N. Feasibility, distribution, and efficacy of an inhaled oligonucleotide mimic of miR-29 for pulmonary fibrosis induced by bleomycin in rats. 2017, pa3480. DOI: 10.1183/1393003.congress-2017.pa3480.
LSC - 2017 - Hippo-YAP/TAZ signaling is deranged in IPFWagner D, Alsafadi H, Mutze K, Costa R, Stein M, Schiller H, Kaminski N, Koenigshoff M. LSC - 2017 - Hippo-YAP/TAZ signaling is deranged in IPF. 2017, oa475. DOI: 10.1183/1393003.congress-2017.oa475.
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.
Chapter 7 MicroRNAs in Idiopathic Pulmonary Fibrosis Partners in Health and DiseasePandit K, Kaminski N. Chapter 7 MicroRNAs in Idiopathic Pulmonary Fibrosis Partners in Health and Disease. 2017, 179-202. DOI: 10.1016/b978-0-12-800553-8.00007-x.
P049 Loss of Twist1 in Colα2(I)+ Cells Promotes Increased Fibrosis in Experimental Lung Injury Through C-X-C Motif Ligand 12 (CXCL12)Tan J, Tedrow J, Nouraie M, Dutta J, Chu Y, Ramani K, Biswas P, Juan-guardela B, Kaminski N, Zhang Y, Kass D. P049 Loss of Twist1 in Colα2(I)+ Cells Promotes Increased Fibrosis in Experimental Lung Injury Through C-X-C Motif Ligand 12 (CXCL12). QJM 2016, 109: s37-s38. DOI: 10.1093/qjmed/hcw124.021.
Thyroid hormone inhibits pulmonary fibrosis through enhancement of mitochondrial function in alveolar epithelial cellsTzouvelekis A, Yu G, Herazo-Maya J, Wang R, Werneck de Castro J, DeIuliis G, Ahangari F, Woolard T, Arrojo e Drigo R, Homer R, Srivastava A, Herzog E, Lee P, Bianco A, Kaminski N. Thyroid hormone inhibits pulmonary fibrosis through enhancement of mitochondrial function in alveolar epithelial cells. 2016, pa780. DOI: 10.1183/13993003.congress-2016.pa780.
SH2 domain-containing phosphatase-SHP-2 is a novel anti-fibrotic regulator in pulmonary fibrosisTzouvelekis A, Yu G, Herazo-Maya J, Woolard T, Zhang Y, Lee H, Lee P, Herzog E, Bennett A, Kaminski N. SH2 domain-containing phosphatase-SHP-2 is a novel anti-fibrotic regulator in pulmonary fibrosis. 2016, oa4979. DOI: 10.1183/13993003.congress-2016.oa4979.
Alterations in Gene Expression and DNA Methylation during Murine and Human Lung Alveolar SeptationCuna A, Halloran B, Faye-Petersen O, Kelly D, Crossman D, Cui X, Pandit K, Kaminski N, Bhattacharya S, Ahmad A, Mariani T, Ambalavanan N. Alterations in Gene Expression and DNA Methylation during Murine and Human Lung Alveolar Septation. Pediatrics 2016, 137: 434a-434a. DOI: 10.1542/peds.137.supplement_3.434a.
Novel Mechanisms of Disease: Network Biology and MicroRNA Signaling in Pulmonary HypertensionFares W, Pandit K, Kaminski N. Novel Mechanisms of Disease: Network Biology and MicroRNA Signaling in Pulmonary Hypertension. 2016, 123-133. DOI: 10.1007/978-3-319-23594-3_7.
Genomics of Lung Aging and Idiopathic Pulmonary FibrosisJuan-Guardela B, Kaminski N. Genomics of Lung Aging and Idiopathic Pulmonary Fibrosis. 2015, 389-408. DOI: 10.1142/9789814635011_0015.
Genomics of lung fibrosisSelman M, Pardo A, Sakamoto K, Kaminski N. Genomics of lung fibrosis. 2015, 6-20. DOI: 10.2217/fmeb2013.14.118.
Palliative Care and Location of Death in Decedents With Idiopathic Pulmonary FibrosisLindell KO, Liang Z, Hoffman LA, Rosenzweig MQ, Saul MI, Pilewski JM, Gibson KF, Kaminski N. Palliative Care and Location of Death in Decedents With Idiopathic Pulmonary Fibrosis. CHEST Journal 2015, 147: 423-429. PMID: 25187973, PMCID: PMC4314817, DOI: 10.1378/chest.14-1127.
T-RECS: STABLE SELECTION OF DYNAMICALLY FORMED GROUPS OF FEATURES WITH APPLICATION TO PREDICTION OF CLINICAL OUTCOMESAltman R, Dunker A, Hunter L, Ritchie M, Murray T, Klein T, HUANG G, TSAMARDINOS I, RAGHU V, KAMINSKI N, BENOS P. T-RECS: STABLE SELECTION OF DYNAMICALLY FORMED GROUPS OF FEATURES WITH APPLICATION TO PREDICTION OF CLINICAL OUTCOMES. Biocomputing 2014, 20: 431-42. PMID: 25592602, PMCID: PMC4299881, DOI: 10.1142/9789814644730_0041.
Bronchial Epithelial Cell Gene Expression In Relation To Exhaled Nitric Oxide Identifies New Molecular Asthma PhenotypesModena B, Tedrow J, Milosevic J, Kaminski N, Wenzel S. Bronchial Epithelial Cell Gene Expression In Relation To Exhaled Nitric Oxide Identifies New Molecular Asthma Phenotypes. Journal Of Allergy And Clinical Immunology 2014, 133: ab176. DOI: 10.1016/j.jaci.2013.12.632.
OmicsKass D, Kaminski N. Omics. 2013, 179-187. DOI: 10.1183/1025448x.10045712.
Erratum: Genome-wide association study identifies multiple susceptibility loci for pulmonary fibrosisFingerlin T, Murphy E, Zhang W, Peljto A, Brown K, Steele M, Loyd J, Cosgrove G, Lynch D, Groshong S, Collard H, Wolters P, Bradford W, Kossen K, Seiwert S, du Bois R, Garcia C, Devine M, Gudmundsson G, Isaksson H, Kaminski N, Zhang Y, Gibson K, Lancaster L, Cogan J, Mason W, Maher T, Molyneaux P, Wells A, Moffatt M, Selman M, Pardo A, Kim D, Crapo J, Make B, Regan E, Walek D, Daniel J, Kamatani Y, Zelenika D, Smith K, McKean D, Pedersen B, Talbert J, Kidd R, Markin C, Beckman K, Lathrop M, Schwarz M, Schwartz D. Erratum: Genome-wide association study identifies multiple susceptibility loci for pulmonary fibrosis. Nature Genetics 2013, 45: 1409-1409. DOI: 10.1038/ng1113-1409a.
A Peripheral Blood Biomarker Signature Potentially Identifies Smokers with Interstitial Lung AbnormalitiesPatel A, Doyle T, Liu Y, Hatabu H, Hatabu M, Okajima Y, Risquez C, Shi Y, Osorio J, Golzarri M, Lederer J, El-Chemaly S, Pinto-Plata V, Celli B, Hunninghake G, Washko G, Sciurba F, Kaminski N, Leader J, Siegfried J, Weissfeld J, Rosas I. A Peripheral Blood Biomarker Signature Potentially Identifies Smokers with Interstitial Lung Abnormalities. CHEST Journal 2013, 144: 1029a-1029b. DOI: 10.1378/chest.1778676.
Evolving Genomics of Pulmonary FibrosisHerazo-Maya J, Kaminski N. Evolving Genomics of Pulmonary Fibrosis. 2013, 379-402. DOI: 10.1007/978-1-62703-682-5_19.
Comprehensive genomic profiling of the lung transcriptome in emphysema and idiopathic pulmonary fibrosis using RNA-SeqKusko R, Brothers J, Liu G, Luo L, Guardela B, Tedrow J, Aleksyev Y, Yang I, Correll M, Geraci M, Quackenbush J, Sciurba F, Lenburg M, Schwartz D, Beane J, Kaminski N, Spira A. Comprehensive genomic profiling of the lung transcriptome in emphysema and idiopathic pulmonary fibrosis using RNA-Seq. BMC Proceedings 2012, 6: p21. PMCID: PMC3467575, DOI: 10.1186/1753-6561-6-s6-p21.
Characterizing the small RNA transcriptome associated with COPD and ILD using next-generation sequencingCampbell J, Luo L, Liu G, Xiao J, Gerrein J, Guardela B, Tedrow J, Aleksyev Y, Yang I, Correll M, Geraci M, Quackenbush J, Sciurba F, Schwartz D, Kaminski N, Lenburg M, Beane J, Spira A. Characterizing the small RNA transcriptome associated with COPD and ILD using next-generation sequencing. BMC Proceedings 2012, 6: p6. PMCID: PMC3467555, DOI: 10.1186/1753-6561-6-s6-p6.
Moving beyond gene expression: identification of lung-disease-associated novel transcripts and alternative splicing by RNA sequencingBrothers J, Kusko R, Liu G, Luo L, Guardela B, Tedrow J, Alekesyev Y, Yang I, Correll M, Geraci M, Quackenbush J, Sciurba F, Sebastiani P, Lenburg M, Kaminski N, Schwartz D, Spira A, Beane J. Moving beyond gene expression: identification of lung-disease-associated novel transcripts and alternative splicing by RNA sequencing. BMC Proceedings 2012, 6: p4. PMCID: PMC3467663, DOI: 10.1186/1753-6561-6-s6-p4.
The LIM Protein Zyxin Modulates TGF²1-Induced Alveolar Epithelial Cell Motility Via Integrin ±5²1Mise N, Yu H, Kaminski N, Eickelberg O. The LIM Protein Zyxin Modulates TGF²1-Induced Alveolar Epithelial Cell Motility Via Integrin ±5²1. 2012, a5563-a5563. DOI: 10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a5563.
Cartilage Oligomeric Matrix Protein Is Upregulated And Modulates TGF-² Signaling In Idiopathic Pulmonary FibrosisLouis V, Milosevic J, Pandit K, Ben-Yehudah A, Richards T, Choi J, Sciurba J, Zhang Y, Myerburg M, Parwani A, Gibson K, Kaminski N. Cartilage Oligomeric Matrix Protein Is Upregulated And Modulates TGF-² Signaling In Idiopathic Pulmonary Fibrosis. 2012, a5560-a5560. DOI: 10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a5560.
Identification Of Biomarkers To Monitor The Activity Of STX-100, A Humanized Anti-±v²6 Antibody, In A Phase 2a Trial In Idiopathic Pulmonary FibrosisViolette S, Sheppard D, Rosas I, Arjomandi M, Rice T, Gilman M, Kaminski N, Prasse A, Maroni B. Identification Of Biomarkers To Monitor The Activity Of STX-100, A Humanized Anti-±v²6 Antibody, In A Phase 2a Trial In Idiopathic Pulmonary Fibrosis. 2012, a2659-a2659. DOI: 10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a2659.
Defective DNA Repair On The Ercc1-/Mice Causes Accelerated Aging And Increased Susceptibility To Lung Injury And FibrosisBustos M, Bueno M, Robison A, Sciurba J, Mroz L, Niedernhofer L, Mora A, Kaminski N, Rojas M. Defective DNA Repair On The Ercc1-/Mice Causes Accelerated Aging And Increased Susceptibility To Lung Injury And Fibrosis. 2012, a5283-a5283. DOI: 10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a5283.
Changes In Expression Of Argonaut Proteins In IPFRabinovich E, Yu G, Kapetanaki M, Schneider F, Kaminski N. Changes In Expression Of Argonaut Proteins In IPF. 2012, a3473-a3473. DOI: 10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a3473.
Characterizing The Small RNA Transcriptome Associated With COPD And ILD Using Next Generation SequencingCampbell J, Luo L, Xiao J, Liu G, Gerrein J, Juan-Guardela B, Tedrow J, Aleksyev Y, Yang I, Correll M, Geraci M, Quackenbush J, Sciurba F, Schwartz D, Kaminski N, Lenburg M, Beane J, Spira A. Characterizing The Small RNA Transcriptome Associated With COPD And ILD Using Next Generation Sequencing. 2012, a5001-a5001. DOI: 10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a5001.
Role Of DIO2 In Idiopathic Pulmonary FibrosisYu G, Tedrow J, Rabinovich E, Drigo R, Gibson K, Yousem S, Richards T, Chensny L, Bianco A, Kaminski N. Role Of DIO2 In Idiopathic Pulmonary Fibrosis. 2012, a4932-a4932. DOI: 10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a4932.
Global Gene Expression Of Bronchoalveolar Lavage (BAL) Cells And Peripheral Blood Mononuclear Cells (PBMCs) In IPF PatientsVuga L, Richards T, Tedrow J, Sciurba J, Autore K, Kaminski N, Prasse A. Global Gene Expression Of Bronchoalveolar Lavage (BAL) Cells And Peripheral Blood Mononuclear Cells (PBMCs) In IPF Patients. 2012, a2661-a2661. DOI: 10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a2661.
Genome-Wide DNA Methylation Patterns In Interstitial Lung Disease (ILD) And Chronic Obstructive Lung Disease (COPD)Yang I, Pedersen B, Hennessy C, Davidson E, Bonney M, Leach S, Brown J, Turner J, Guardela B, Tedrow J, Correll M, Geraci M, Kaminski N, Quackenbush J, Sciurba F, Spira A, Schwartz D. Genome-Wide DNA Methylation Patterns In Interstitial Lung Disease (ILD) And Chronic Obstructive Lung Disease (COPD). 2012, a2667-a2667. DOI: 10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a2667.
Over Expression Of MiRNA In Mesenchymal Stem Cells Alters Their Anti-Fibrotic PropertiesHuleihel L, Bustos M, DeIuliis G, Manor E, Chensny L, Mora A, Rojas M, Kaminski N. Over Expression Of MiRNA In Mesenchymal Stem Cells Alters Their Anti-Fibrotic Properties. 2012, a3513-a3513. DOI: 10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a3513.
Does The Oxygen Prescription Match The Study Results?: A Prospective Study Of Patients In A Speciality Interstitial Lung Disease CenterPagnotta E, MacPherson M, Gibson K, Kaminski N, Lindell K. Does The Oxygen Prescription Match The Study Results?: A Prospective Study Of Patients In A Speciality Interstitial Lung Disease Center. 2012, a1490-a1490. DOI: 10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a1490.
Age-Related Changes In The Relative Expression Of Functional Genes In Mesenchymal Stem CellsBustos M, Kapetanaki M, Meyer M, Donnenberg A, Donnenberg V, Sciurba J, Mroz L, Kaminski N, Rojas M. Age-Related Changes In The Relative Expression Of Functional Genes In Mesenchymal Stem Cells. 2012, a5289-a5289. DOI: 10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a5289.
Translational Value Of The Bleomycin Rat Model For The Treatment Of Patients With Idiopathic Pulmonary Fibrosis (IPF)Bauer Y, Gibson K, Guardella B, Hess P, Klenk A, Lindell K, Renault B, Rey M, Tedrow J, Weber E, Kaminski N, Nayler O. Translational Value Of The Bleomycin Rat Model For The Treatment Of Patients With Idiopathic Pulmonary Fibrosis (IPF). 2012, a6241-a6241. DOI: 10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a6241.
CLF1 Gene Expression Is Increased In Lung Injury And DevelopmentKass D, Yu G, Kahloon R, Scheller E, Huleihel L, Deiuliis G, Tedrow J, Guardela B, Leader J, Pandit K, Milosevic J, Alcorn J, Kaminski N. CLF1 Gene Expression Is Increased In Lung Injury And Development. 2012, a5546-a5546. DOI: 10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a5546.
Smoke-Induced MiRNA Expression Profiles Of Type II Cells Differ From Total Lung And MacrophagesDegar A, Pandit K, Kenche H, Perry Y, Kaminski N, Blumental-Perry A. Smoke-Induced MiRNA Expression Profiles Of Type II Cells Differ From Total Lung And Macrophages. 2012, a2016-a2016. DOI: 10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a2016.
Evidence For A Th2 Phenotype Across The Spectrum Of Asthma SeverityBhakta N, Solberg O, Nguyen C, Peng J, Wang T, Nguyen C, Arron J, Fahy J, Bleecker E, Meyers D, Erzurum S, Busse W, Kaminski N, Wenzel S, Woodruff P. Evidence For A Th2 Phenotype Across The Spectrum Of Asthma Severity. 2012, a2193-a2193. DOI: 10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a2193.
Hypomethylation Of LINE-1 Repeats Is A Predictor Of Carcinogenic Transformation In Normal Histology Lung TissueRabinovich E, Tedrow J, Schwartz D, Spira A, Quackenbush J, Geraci M, Sciurba F, Guardela B, Pandit K, Zhang Y, Kaminski N. Hypomethylation Of LINE-1 Repeats Is A Predictor Of Carcinogenic Transformation In Normal Histology Lung Tissue. 2012, a3487-a3487. DOI: 10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a3487.
Epithelial Microarray Studies From The Severe Asthma Research Program (SARP)Wenzel S, Kang D, Kaminski N, Milosevic J, Trudeau J, Meyers D, Bleecker E, Busse W, Erzurum S, Woodruff P. Epithelial Microarray Studies From The Severe Asthma Research Program (SARP). 2012, a2510-a2510. DOI: 10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a2510.
Gender Effects On Pre- And Post-Transplant Survival In Idiopathic Pulmonary FibrosisRichards T, Kass D, Lindell K, Kaminski N, Gibson K. Gender Effects On Pre- And Post-Transplant Survival In Idiopathic Pulmonary Fibrosis. 2012, a3766-a3766. DOI: 10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a3766.
Mimicry Of MiR-29 Attenuates Pulmonary Fibrosis Induced By Bleomycin In MiceYu G, Pandit K, Milosevic J, Montgomery R, Rooij E, Chensny L, Kaminski N. Mimicry Of MiR-29 Attenuates Pulmonary Fibrosis Induced By Bleomycin In Mice. 2012, a4986-a4986. DOI: 10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a4986.
Association Of Plasma Levels Of PTX3 With Clinical Phenotypes Of Chronic Obstructive Pulmonary DiseaseZhang Y, Tedrow J, Zeng Q, Bon J, Chu Y, Duncan S, Weissfeld J, Leader K, Fuhrman C, Branch R, Porter M, Kaminski N, Sciurba F. Association Of Plasma Levels Of PTX3 With Clinical Phenotypes Of Chronic Obstructive Pulmonary Disease. 2012, a2670-a2670. DOI: 10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a2670.
Comprehensive Genomic Profiling Of The Lung Transcriptome In Emphysema And IPF Using RNA-SeqKusko R, Brothers J, Liu G, Luo L, Guardela B, Tedrow J, Aleksyev Y, Yang I, Correll M, Geraci M, Quackenbush J, Sciurba F, Lenburg M, Schwartz D, Beane J, Kaminski N, Spira A. Comprehensive Genomic Profiling Of The Lung Transcriptome In Emphysema And IPF Using RNA-Seq. 2012, a2664-a2664. DOI: 10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a2664.
The Expression Of Long Intergenic Noncoding RNAs In Idiopathic Pulmonary Fibrosis And Their Possible Role As Suppressors Of ProliferationGuardela B, Herazo J, Tedrow J, Chensny L, Richards T, Spira A, Correll M, Quackenbush J, Geraci M, Schwartz D, Sciurba F, Gibson K, Pandit K, Kaminski N. The Expression Of Long Intergenic Noncoding RNAs In Idiopathic Pulmonary Fibrosis And Their Possible Role As Suppressors Of Proliferation. 2012, a3507-a3507. DOI: 10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a3507.
Elevated PTX3 Expression Is Specific For Emphysema Severity In Lung Tissue And Plasma Of Patients With COPDTedrow J, Juan-Guardela B, Zhang Y, Kass D, Kahloon R, Leader J, Shapiro S, Geraci M, Quackenbush J, Schwartz D, Spira A, Sciurba F, Kaminski N. Elevated PTX3 Expression Is Specific For Emphysema Severity In Lung Tissue And Plasma Of Patients With COPD. 2012, a1002-a1002. DOI: 10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a1002.
Molecular Pathways Associated With Autoimmunity In Patients With Idiopathic Pulmonary FibrosisVij R, Huang Y, Ma S, Broderick S, White S, Strek M, Kaminski N, Garcia J, Noth I. Molecular Pathways Associated With Autoimmunity In Patients With Idiopathic Pulmonary Fibrosis. 2012, a5175-a5175. DOI: 10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a5175.
Gene Expression Of BAL Cells And PBMCs Predicts Survival Via Different Pathways In IPFPrasse A, Vuga L, Richards T, Kaminski N. Gene Expression Of BAL Cells And PBMCs Predicts Survival Via Different Pathways In IPF. 2012, a2660-a2660. DOI: 10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a2660.
Identification Of Lung Disease-Associated Novel Transcripts And Alternative Splicing By RNA-SequencingBrothers J, Kusko R, Liu G, Luo L, Guardela B, Tedrow J, Alekseyev Y, Yang I, Correll M, Geraci M, Quackenbush J, Sciurba F, Sebastiani P, Lenburg M, Kaminski N, Schwartz D, Spira A, Beane J. Identification Of Lung Disease-Associated Novel Transcripts And Alternative Splicing By RNA-Sequencing. 2012, a4892-a4892. DOI: 10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a4892.
High Fat Diet Protects Mice From Cigarette Smoke-Induced Emphysema In Part By Altering Let 7b MicroRNA And Subsequent Oncostatin SignalingTakahashi S, Pandit K, Kaminski N, Shapiro S. High Fat Diet Protects Mice From Cigarette Smoke-Induced Emphysema In Part By Altering Let 7b MicroRNA And Subsequent Oncostatin Signaling. 2012, a3754-a3754. DOI: 10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a3754.
The Wnt Co-Receptors, LRP5/6, Contribute To Fibrosis In Mice And MenLam A, Sennello J, Herazo-Maya J, Flozak A, Russell S, Kaminski N, Gottardi C. The Wnt Co-Receptors, LRP5/6, Contribute To Fibrosis In Mice And Men. 2012, a3919-a3919. DOI: 10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a3919.
Abstract 4937: Factors in NSCLC stage and outcome: Integrated genome-wide studyPancoska P, Romkes M, Nukui T, Buch S, Herazo-Maya J, Kaminski N, Dacic S, Weissfeld J, Bigbee W, Siegfried J. Abstract 4937: Factors in NSCLC stage and outcome: Integrated genome-wide study. Cancer Research 2012, 72: 4937-4937. DOI: 10.1158/1538-7445.am2012-4937.
Abstract 1722: Prognostic markers in early stage non small-cell lung cancer (NSCLC)Romkes M, Nukui T, Buch S, Pancoska P, Herazo-Maya J, Kaminski N, Dacic S, Weissfeld J, Bigbee W, Shapiro S, Siegfried J. Abstract 1722: Prognostic markers in early stage non small-cell lung cancer (NSCLC). Cancer Research 2012, 72: 1722-1722. DOI: 10.1158/1538-7445.am2012-1722.
Abstract 1720: Validation of a 15-gene prognostic signature in stage IB non small-cell lung cancer (NSCLC)Pancoska P, Romkes M, Nukui T, Buch S, Herazo-Maya J, Kaminski N, Dacic S, Weissfeld J, Bigbee W, Shapiro S, Siegfried J. Abstract 1720: Validation of a 15-gene prognostic signature in stage IB non small-cell lung cancer (NSCLC). Cancer Research 2012, 72: 1720-1720. DOI: 10.1158/1538-7445.am2012-1720.
The LIM protein zyxin modulates TGF-β1-induced cell migrationMiše N, Yu H, Kaminski N, Eickelberg O. The LIM protein zyxin modulates TGF-β1-induced cell migration. Pneumologie 2011, 65 DOI: 10.1055/s-0031-1296127.
Peripheral Blood Monuclear Cells Gene Expression Patterns Predict Mortality In Patients With Idiopathic Pulmonary FibrosisHerazo J, Gibson K, Juan-Guardela B, Ma S, Richards T, Lussier Y, Duncan S, Tseng G, Lindell K, Garcia J, Noth I, Kaminski N. Peripheral Blood Monuclear Cells Gene Expression Patterns Predict Mortality In Patients With Idiopathic Pulmonary Fibrosis. 2011, a5306-a5306. DOI: 10.1164/ajrccm-conference.2011.183.1_meetingabstracts.a5306.
Decreased Survival Of Idiopathic Pulmonary Fibrosis Patients With Heat Shock Protein 70 AutoreactivityXue J, Kahloon R, Bhargava A, Banga G, Gochuico B, Dacic S, Gibson K, Kaminski N, Sciurba F, Rosas I, Otterbein L, Zhang Y, Duncan S. Decreased Survival Of Idiopathic Pulmonary Fibrosis Patients With Heat Shock Protein 70 Autoreactivity. 2011, a4275-a4275. DOI: 10.1164/ajrccm-conference.2011.183.1_meetingabstracts.a4275.
Pulmonary Fibroblast Thy-1 Expression Modulates Elastin Expression During Alveolarization - In Part Via Rhoa Activation Of JNKVarisco B, Hagood J, Kaminski N, Whitsett J. Pulmonary Fibroblast Thy-1 Expression Modulates Elastin Expression During Alveolarization - In Part Via Rhoa Activation Of JNK. 2011, a3492-a3492. DOI: 10.1164/ajrccm-conference.2011.183.1_meetingabstracts.a3492.
Characterizing The Lung Disease Transcriptome With Next Generation Rna-SequencingKusko R, Beane J, Brothers J, Liu G, Luo L, Guardela B, Tedrow J, Aleksyev Y, Yang I, Correll M, Geraci M, Quackenbush J, Sciurba F, Lenburg M, Schwartz D, Kaminski N, Spira A. Characterizing The Lung Disease Transcriptome With Next Generation Rna-Sequencing. 2011, a5539-a5539. DOI: 10.1164/ajrccm-conference.2011.183.1_meetingabstracts.a5539.
Whole Transcriptome Study Of Mesenchymal Stem Cell Response To TGF-Beta 1Kapetanaki M, Gupta N, Chensny L, Rojas M, Benos P, Kaminski N. Whole Transcriptome Study Of Mesenchymal Stem Cell Response To TGF-Beta 1. 2011, a6007-a6007. DOI: 10.1164/ajrccm-conference.2011.183.1_meetingabstracts.a6007.
Genome Wide Association Study In Idiopathic Pulmonary Fibrosis Identifies LCLAT1 As A Novel Candidate GeneNoth I, Zhang Y, Barber M, Gibson K, Ma S, Lindell K, Kaminski N, Hysi P, Nicolae D, Garcia J. Genome Wide Association Study In Idiopathic Pulmonary Fibrosis Identifies LCLAT1 As A Novel Candidate Gene. 2011, a2266-a2266. DOI: 10.1164/ajrccm-conference.2011.183.1_meetingabstracts.a2266.
Identifying Novel Transcripts And Alternative Splicing Associated With The ILD And COPD Lung Transcriptome Using MRNA-SeqBrothers J, Kusko R, Luo L, Liu G, Guardela B, Tedrow J, Alekseyev Y, Yang I, Correll M, Geraci M, Quackenbush J, Sciurba F, Sebastiani P, Lenburg M, Kaminski N, Schwartz D, Spira A, Beane J. Identifying Novel Transcripts And Alternative Splicing Associated With The ILD And COPD Lung Transcriptome Using MRNA-Seq. 2011, a5540-a5540. DOI: 10.1164/ajrccm-conference.2011.183.1_meetingabstracts.a5540.
A Variant In The Promoter Of MUC5B Is Associated With Idiopathic Pulmonary Fibrosis And Not Chronic Obstructive Pulmonary DiseaseZhang Y, Noth I, Gibson K, Ma S, Richards T, Bon J, Lindell K, Branch R, Nicolae D, Sciurba F, Garcia A, Kaminski N. A Variant In The Promoter Of MUC5B Is Associated With Idiopathic Pulmonary Fibrosis And Not Chronic Obstructive Pulmonary Disease. 2011, a6395-a6395. DOI: 10.1164/ajrccm-conference.2011.183.1_meetingabstracts.a6395.
The HLA Class II Allele DRB1*1501 Is Over-Represented In Patients With Idiopathic Pulmonary FibrosisXue J, Gochuico B, Feghali-Bostwick C, Noth I, Nathan S, Rosen G, Rosas I, Gibson K, Kaminski N, Sciurba F, Zhang Y, Duncan S. The HLA Class II Allele DRB1*1501 Is Over-Represented In Patients With Idiopathic Pulmonary Fibrosis. 2011, a4272-a4272. DOI: 10.1164/ajrccm-conference.2011.183.1_meetingabstracts.a4272.
High-Throughput Sequencing Of MicroRNA In Idiopathic Pulmonary FibrosisRakova I, Kapetanaki M, Pandit K, Chensny L, Gibson K, Ghedin E, Kaminski N. High-Throughput Sequencing Of MicroRNA In Idiopathic Pulmonary Fibrosis. 2011, a5538-a5538. DOI: 10.1164/ajrccm-conference.2011.183.1_meetingabstracts.a5538.
Divergent And Convergent Gene Expression Patterns In Well Phenotyped Patients With COPD And IPFTedrow J, Juan-Guardela B, Gur D, Leader J, Schwartz D, Spira A, Geraci M, Quackenbush J, Correll M, Richards T, Chensny L, Shapiro S, Vuga L, Sciurba F, Kaminski N. Divergent And Convergent Gene Expression Patterns In Well Phenotyped Patients With COPD And IPF. 2011, a2274-a2274. DOI: 10.1164/ajrccm-conference.2011.183.1_meetingabstracts.a2274.
Microrna Expression Profiles In EmphysemaTedrow J, Juan-Guardela B, Pandit K, Gur D, Leader J, Landreneau R, Schwartz D, Geraci M, Quackenbush J, Correll M, Richards T, Chensny L, Spira A, Sciurba F, Kaminski N. Microrna Expression Profiles In Emphysema. 2011, a4099-a4099. DOI: 10.1164/ajrccm-conference.2011.183.1_meetingabstracts.a4099.
Global Microrna Profiles Of Idiopathic Pulmonary Fibrosis Lungs Indicate Reversal Of Lung DifferentiationPandit K, Milosevic J, Benos P, Coronello C, Ben-Yehudah A, Hagood J, Ambalavanan N, Kaminski N. Global Microrna Profiles Of Idiopathic Pulmonary Fibrosis Lungs Indicate Reversal Of Lung Differentiation. 2011, a5528-a5528. DOI: 10.1164/ajrccm-conference.2011.183.1_meetingabstracts.a5528.
Lysocardiolipin Acyltransferase (lycat) Is A Novel Candidate Gene In Radiation-Induced Pulmonary FibrosisMathew B, huang L, Noth I, Ma S, Kaminski N, Zhao Y, Wade M, Berdyshev E, Siegler J, Jacobson J, Weishelbaum R, Natarajan V, Garcia J. Lysocardiolipin Acyltransferase (lycat) Is A Novel Candidate Gene In Radiation-Induced Pulmonary Fibrosis. 2011, a6146-a6146. DOI: 10.1164/ajrccm-conference.2011.183.1_meetingabstracts.a6146.
Cytokine-Like Factor I (CLF1) Expression Is Increased In Idiopathic Pulmonary Fibrosis (IPF) And Promotes Inflammation But Decreases Fibrosis In Bleomycin InjuryKass D, Loh K, Borczuk A, Tedrow J, Guardela B, Kaminski N, Greenberg S. Cytokine-Like Factor I (CLF1) Expression Is Increased In Idiopathic Pulmonary Fibrosis (IPF) And Promotes Inflammation But Decreases Fibrosis In Bleomycin Injury. 2011, a2710-a2710. DOI: 10.1164/ajrccm-conference.2011.183.1_meetingabstracts.a2710.
Pulmonary Fibrosis In Response To Pharmaceutical Grade Bleomycin Is Independent Of IL-17Pociask D, Chen K, Kaminski N, Kolls J. Pulmonary Fibrosis In Response To Pharmaceutical Grade Bleomycin Is Independent Of IL-17. 2011, a5982-a5982. DOI: 10.1164/ajrccm-conference.2011.183.1_meetingabstracts.a5982.
Mir 30b As A Potential Modifier Of Fibroblasts Phenotypes In Lung FibrosisHuleihel L, Ben-Yehudah A, Manor E, Milosevic J, Benos P, Chensny L, Kaminski N. Mir 30b As A Potential Modifier Of Fibroblasts Phenotypes In Lung Fibrosis. 2011, a3528-a3528. DOI: 10.1164/ajrccm-conference.2011.183.1_meetingabstracts.a3528.
Emphysema Gene Expression SignaturesTedrow J, Juan-Guardela B, Gur D, Leader J, Schwartz D, Spira A, Geraci M, Quackenbush J, Correll M, Richards T, Chensny L, Shapiro S, Sciurba F, Kaminski N. Emphysema Gene Expression Signatures. 2011, a2271-a2271. DOI: 10.1164/ajrccm-conference.2011.183.1_meetingabstracts.a2271.
Does Ambient Air Pollution Exposure Modify Longitudinal Disease Outcomes In A Cohort Of Patients With Idiopathic Pulmonary Fibrosis?Richards T, Kuhlengel T, Choi J, Kaminski N, Bascom R. Does Ambient Air Pollution Exposure Modify Longitudinal Disease Outcomes In A Cohort Of Patients With Idiopathic Pulmonary Fibrosis? 2011, a5433-a5433. DOI: 10.1164/ajrccm-conference.2011.183.1_meetingabstracts.a5433.
Genome-Wide Analysis Of Somatic Genetic Alterations In Severe Lung DiseaseColdren C, Gao B, Rice J, Leach S, Yang I, Murphy E, Kaminski N, Quackenbush J, Schwartz D, Sciurba F, Spira A, Geraci M. Genome-Wide Analysis Of Somatic Genetic Alterations In Severe Lung Disease. 2011, a5529-a5529. DOI: 10.1164/ajrccm-conference.2011.183.1_meetingabstracts.a5529.
Differential Expression Of Microrna In Mesenchymal Stem Cell Derived ExosomesDeIuliis G, Di Giuseppe M, Phinney D, Sala E, Kaminski N, Ortiz L. Differential Expression Of Microrna In Mesenchymal Stem Cell Derived Exosomes. 2011, a3769-a3769. DOI: 10.1164/ajrccm-conference.2011.183.1_meetingabstracts.a3769.
Somatic Mutations In The Lungs Of Patients With Idiopathic Pulmonary FibrosisYang I, Leach S, Turner J, Kummer N, Brown J, Murphy E, Farias-Hesson E, Sisneros N, Wang Z, Coldren C, Correll M, Geraci M, Kaminski N, Quackenbush J, Sciurba F, Spira A, Schwartz D. Somatic Mutations In The Lungs Of Patients With Idiopathic Pulmonary Fibrosis. 2011, a5537-a5537. DOI: 10.1164/ajrccm-conference.2011.183.1_meetingabstracts.a5537.
MRNA And MicroRNA Expression Profiles Indicate Disease Severity In Patients With Idiopathic Pulmonary FibrosisJuan-Guardela B, Tedrow J, Herazo J, Aboud C, Pandit K, Chensny L, Gur D, Leader J, Benos P, Richards T, Correll M, Quackenbush J, Geraci M, Spira A, Schwartz D, Sciurba F, Kaminski N. MRNA And MicroRNA Expression Profiles Indicate Disease Severity In Patients With Idiopathic Pulmonary Fibrosis. 2011, a6005-a6005. DOI: 10.1164/ajrccm-conference.2011.183.1_meetingabstracts.a6005.
Genome-Wide DNA Methylation Patterns In Interstitial Lung Disease (ild) And Chronic Obstructive Lung Disease (COPD)Yang I, Hennessy C, Davidson E, Bonney M, Leach S, Brown J, Turner J, Guardela B, Tedrow J, Correll M, Geraci M, Kaminski N, Quackenbush J, Sciurba F, Spira A, Schwartz D. Genome-Wide DNA Methylation Patterns In Interstitial Lung Disease (ild) And Chronic Obstructive Lung Disease (COPD). 2011, a1049-a1049. DOI: 10.1164/ajrccm-conference.2011.183.1_meetingabstracts.a1049.
Gene Expression Of Pneumocystis Jirovecii Infection In COPD LungsFitzpatrick M, Tedrow J, Hillenbrand M, Lucht L, Richards T, Zhang Y, Kaminski N, Sciurba F, Morris A. Gene Expression Of Pneumocystis Jirovecii Infection In COPD Lungs. 2011, a4144-a4144. DOI: 10.1164/ajrccm-conference.2011.183.1_meetingabstracts.a4144.
Unsupervised Combination Of Clinical And Gene Expression Data Elucidates Intermediate Phenotypes In Ild And COPDKang D, Tedrow J, Richards T, Schwartz D, Schwarz M, Martinez F, Limper A, Quackenbush J, Geraci M, Bartholmai B, Spira A, Tseng G, Sciurba F, Kaminski N. Unsupervised Combination Of Clinical And Gene Expression Data Elucidates Intermediate Phenotypes In Ild And COPD. 2011, a4087-a4087. DOI: 10.1164/ajrccm-conference.2011.183.1_meetingabstracts.a4087.
Characterization of Microrna Expression Profile In Platelets In Sickle Cell DiseaseJain S, Raghavachari N, Woodhouse K, Kaminski N, Gladwin M. Characterization of Microrna Expression Profile In Platelets In Sickle Cell Disease. Blood 2010, 116: 2030. DOI: 10.1182/blood.v116.21.2030.2030.
miR-21 mediates fibrogenic activation of pulmonary fibroblasts and lung fibrosisLiu G, Friggeri A, Yang Y, Milosevic J, Ding Q, Thannickal V, Kaminski N, Abraham E. miR-21 mediates fibrogenic activation of pulmonary fibroblasts and lung fibrosis. Journal Of Cell Biology 2010, 190: i3-i3. DOI: 10.1083/jcb1902oia3.
Gene Expression Profiles Differentiate Human Airway From Parenchymal FibroblastsZhou X, Wu W, Hu H, Konishi K, Milosevic J, Kaminski N, Wenzel S. Gene Expression Profiles Differentiate Human Airway From Parenchymal Fibroblasts. 2010, a3978-a3978. DOI: 10.1164/ajrccm-conference.2010.181.1_meetingabstracts.a3978.
Characterization Of Airway- And Distal Lung Fibroblasts Using Systems Biology ApproachesWu W, Zhou X, Hu H, Konishi K, Milosevic J, Kaminski N, Wenzel S. Characterization Of Airway- And Distal Lung Fibroblasts Using Systems Biology Approaches. 2010, a6409-a6409. DOI: 10.1164/ajrccm-conference.2010.181.1_meetingabstracts.a6409.
Gene Expression Profiles Of Pulmonary Fibrosis Reveal Developmental Functions As Determinants That Distinguish NSIP And UIP In Interstitial PneumoniasKonishi K, Richards T, Song J, Chensny L, Lindell K, Herazo J, Zhang Y, Gibson K, Kaminski N, Kim D. Gene Expression Profiles Of Pulmonary Fibrosis Reveal Developmental Functions As Determinants That Distinguish NSIP And UIP In Interstitial Pneumonias. 2010, a2492-a2492. DOI: 10.1164/ajrccm-conference.2010.181.1_meetingabstracts.a2492.
Candidate Susceptibility Genes Identified By Genomewide Analysis Of Chloride-induced Acute Lung Injury In MiceLeikauf G, Pope-Varsalona H, Concel V, Liu P, Bein K, Brant K, Dopico R, Di Y, Jang A, Medvedovic M, Li Q, Vega L, Kaminski N, You M, Prows D. Candidate Susceptibility Genes Identified By Genomewide Analysis Of Chloride-induced Acute Lung Injury In Mice. 2010, a5370-a5370. DOI: 10.1164/ajrccm-conference.2010.181.1_meetingabstracts.a5370.
Regulation Telomerase and Telomere Length In IPF By MicroRNAs.Singh M, Tzfati Y, Chensny L, Benos P, Kaminski N. Regulation Telomerase and Telomere Length In IPF By MicroRNAs. 2010, a2297-a2297. DOI: 10.1164/ajrccm-conference.2010.181.1_meetingabstracts.a2297.
Alternatively Activated Macrophage (M2) Marker Expression In Leukocytes During Acute Exacerbation Of COPD (AECOPD)Cornwell W, Grabianowski C, Chensny L, Gaughan J, Sciurba F, Kaminski N, Richards T, Rogers T, Criner G. Alternatively Activated Macrophage (M2) Marker Expression In Leukocytes During Acute Exacerbation Of COPD (AECOPD). 2010, a5342-a5342. DOI: 10.1164/ajrccm-conference.2010.181.1_meetingabstracts.a5342.
Extent And Impact Of Pulmonary Fibrosis In A Regional Health SystemLindell K, Hoffman K, Black T, Richards T, Choi J, Saul M, Kaminski N, Gibson K. Extent And Impact Of Pulmonary Fibrosis In A Regional Health System. 2010, a2966-a2966. DOI: 10.1164/ajrccm-conference.2010.181.1_meetingabstracts.a2966.
Peripheral Blood Biomarkers Predict Disease Progression And Mortality In IPFRichards T, Lindell K, Klesen M, Kaminski N, Zhang Y, Gibson K. Peripheral Blood Biomarkers Predict Disease Progression And Mortality In IPF. 2010, a1120-a1120. DOI: 10.1164/ajrccm-conference.2010.181.1_meetingabstracts.a1120.
Ambient Air Pollution Exposure of Patients In The Pennsylvania Idiopathic Pulmonary Fibrosis (PA-IPF) State RegistryKuhlengel T, Bascom R, Qian Z, Kaminski N, Lindell K, Tino G, Criner G, Simonelli P, Cordova F, Patel N, Gibson K. Ambient Air Pollution Exposure of Patients In The Pennsylvania Idiopathic Pulmonary Fibrosis (PA-IPF) State Registry. 2010, a4618-a4618. DOI: 10.1164/ajrccm-conference.2010.181.1_meetingabstracts.a4618.
The Pennsylvania Idiopathic Pulmonary Fibrosis (PA-IPF) State RegistryLindell K, Black T, Hoffman K, Richards T, Kaminski N, Gibson K, Tino G, Simonelli P, Bascom R, Cordova F, Patel N, Criner G. The Pennsylvania Idiopathic Pulmonary Fibrosis (PA-IPF) State Registry. 2010, a2964-a2964. DOI: 10.1164/ajrccm-conference.2010.181.1_meetingabstracts.a2964.
The Warm Autopsy Program For Patients With Idiopathic Pulmonary FibrosisLindell K, Zellem E, Hoffman L, Richards T, Gibson K, Dhir R, Bisceglia M, Yousem S, Nichols L, Kaminski N. The Warm Autopsy Program For Patients With Idiopathic Pulmonary Fibrosis. 2010, a4016-a4016. DOI: 10.1164/ajrccm-conference.2010.181.1_meetingabstracts.a4016.
A Potential Role Of MMP19 In The Development And Progression Of Human Lung CancerYu G, Pandit K, Parwani A, Gilbert S, Ei-Hefnawy T, Richards T, Rosas I, Chensny L, Kaminski N. A Potential Role Of MMP19 In The Development And Progression Of Human Lung Cancer. 2010, a4983-a4983. DOI: 10.1164/ajrccm-conference.2010.181.1_meetingabstracts.a4983.
Bronchial And Alveolar Epithelium Differentiated From Embryonic Stem CellsBen-Yehudah A, Castro C, Eisinger V, Kinney T, Kaminski N, Schatten G, Carlisle D. Bronchial And Alveolar Epithelium Differentiated From Embryonic Stem Cells. 2010, a4916-a4916. DOI: 10.1164/ajrccm-conference.2010.181.1_meetingabstracts.a4916.
Combinatorial Analysis Of Secreted Plasma Proteins Is Associated With Long-term Outcome In Lung Transplant RecipientsRichards T, Choi J, Zhang Y, Kaminski N, Studer S. Combinatorial Analysis Of Secreted Plasma Proteins Is Associated With Long-term Outcome In Lung Transplant Recipients. 2010, a1006-a1006. DOI: 10.1164/ajrccm-conference.2010.181.1_meetingabstracts.a1006.
Peripheral Blood Biomarkers Of Acute Exacerbation In Idiopathic Pulmonary FibrosisZhang Y, Song J, Richards T, Porter M, Kaminski N, Hagerty S, Choi A, Kim D. Peripheral Blood Biomarkers Of Acute Exacerbation In Idiopathic Pulmonary Fibrosis. 2010, a1118-a1118. DOI: 10.1164/ajrccm-conference.2010.181.1_meetingabstracts.a1118.
MMP activation peptide detection in biological samples as a diagnostic marker of idiopathic pulmonary fibrosisVoeghtly L, Kaminski N, Oury T. MMP activation peptide detection in biological samples as a diagnostic marker of idiopathic pulmonary fibrosis. The FASEB Journal 2009, 23: 572.11-572.11. DOI: 10.1096/fasebj.23.1_supplement.572.11.
Regulation of microRNA let-7d Expression in Idiopathic Pulmonary Fibrosis.Singh M, Patel J, Majister M, Kaminski N. Regulation of microRNA let-7d Expression in Idiopathic Pulmonary Fibrosis. 2009, a3016. DOI: 10.1164/ajrccm-conference.2009.179.1_meetingabstracts.a3016.
Early Interstitial Lung Disease in Smokers from the PLuSS Study.Rosas I, Weissfeld J, Furman C, Gibson K, Leader J, Gur D, Tedrow J, Kaminski N, Sciurba F. Early Interstitial Lung Disease in Smokers from the PLuSS Study. 2009, a1125. DOI: 10.1164/ajrccm-conference.2009.179.1_meetingabstracts.a1125.
Gene Expression Patterns of Peripheral Blood Mononuclear Cells in Patients with Idiopathic Pulmonary Fibrosis.Herazo J, Juan B, Chensny L, Richards T, Konishi K, leJeune M, Ravinovich E, Lindell K, Gibson K, Kaminski N. Gene Expression Patterns of Peripheral Blood Mononuclear Cells in Patients with Idiopathic Pulmonary Fibrosis. 2009, a2731. DOI: 10.1164/ajrccm-conference.2009.179.1_meetingabstracts.a2731.
The MicroRNA Let7d Causes Mesenchymal to Epithelial Transition in Human Lung Fibroblasts.Ben-Yehudah A, Yousef H, LeJeune M, Huleihel L, Takac E, Chensny L, Kaminski N. The MicroRNA Let7d Causes Mesenchymal to Epithelial Transition in Human Lung Fibroblasts. 2009, a2490. DOI: 10.1164/ajrccm-conference.2009.179.1_meetingabstracts.a2490.
Expression and Role of miR-30 in Idiopathic Pulmonary Fibrosis.Pandit K, Corcoran D, Konishi K, Benos P, Kaminski N. Expression and Role of miR-30 in Idiopathic Pulmonary Fibrosis. 2009, a5310. DOI: 10.1164/ajrccm-conference.2009.179.1_meetingabstracts.a5310.
Molecular Characterization of Early Interstitial Lung Disease in Familial Pulmonary Fibrosis.Konishi K, Gochuico B, Herazo J, Richards T, MacDonald S, Kaminski N, Rosas I. Molecular Characterization of Early Interstitial Lung Disease in Familial Pulmonary Fibrosis. 2009, a3494. DOI: 10.1164/ajrccm-conference.2009.179.1_meetingabstracts.a3494.
Positive Feedback Loop Regulates Transcription of Syndecan-2 and Multiple TGF-beta Target Genes in HL-60 Cells.Yu G, Konishi K, Herazo J, Hanley D, Pacheco G, Richards T, Kaminski N, Rosas I. Positive Feedback Loop Regulates Transcription of Syndecan-2 and Multiple TGF-beta Target Genes in HL-60 Cells. 2009, a1876. DOI: 10.1164/ajrccm-conference.2009.179.1_meetingabstracts.a1876.
Cartilage Oligomeric Matrix Protein Is a Potential Biomarker for Idiopathic Pulmonary Fibrosis.Vuga L, Ben-Yehudah A, Pandit K, Zheng Y, Sciurba J, Milosevic J, Chensny L, Konishi K, Gibson K, Kaminski N. Cartilage Oligomeric Matrix Protein Is a Potential Biomarker for Idiopathic Pulmonary Fibrosis. 2009, a3487. DOI: 10.1164/ajrccm-conference.2009.179.1_meetingabstracts.a3487.
Altered Immune Competence of Peripheral Blood Leukocytes during AECOPD.Cunanan, Rogers T, Ciccolella D, Grabianowski C, Chensny L, Crookshank A, Gaughan J, Sciurba F, Kaminski N, Richards T, Mamary A, Chatila W, Criner G. Altered Immune Competence of Peripheral Blood Leukocytes during AECOPD. 2009, a2975. DOI: 10.1164/ajrccm-conference.2009.179.1_meetingabstracts.a2975.
Expression of Alpha-Defensins in the Lungs and Peripheral Blood of Patients with Acute Exacerbations of Idiopathic Pulmonary Fibrosis.Konishi K, Gibson K, Richards T, Lindell K, Chensny L, Zhang Y, Kaminski N, Kim D. Expression of Alpha-Defensins in the Lungs and Peripheral Blood of Patients with Acute Exacerbations of Idiopathic Pulmonary Fibrosis. 2009, a3020. DOI: 10.1164/ajrccm-conference.2009.179.1_meetingabstracts.a3020.
The Role of miR-154 microRNA Family in IPF.Milosevic J, Pandit K, Jacobs R, Benos P, Yakhini Z, Chensny L, Kaminski N. The Role of miR-154 microRNA Family in IPF. 2009, a2732. DOI: 10.1164/ajrccm-conference.2009.179.1_meetingabstracts.a2732.
Association of Radiographic COPD Phenotypes with Differential Gene Expression.Tedrow J, Konishi K, Landreneau R, Luketich J, Kaminski N, Sciurba F. Association of Radiographic COPD Phenotypes with Differential Gene Expression. 2009, a2996. DOI: 10.1164/ajrccm-conference.2009.179.1_meetingabstracts.a2996.
Decreased Expression of Cholesterol and Fatty Acid Synthesis Genes in Lungs of Patients with Pulmonary Fibrosis.Geyer A, Gochuico B, Kaminski N, Morse D, Rosas I. Decreased Expression of Cholesterol and Fatty Acid Synthesis Genes in Lungs of Patients with Pulmonary Fibrosis. 2009, a1912. DOI: 10.1164/ajrccm-conference.2009.179.1_meetingabstracts.a1912.
Contrasts between IPF and Mouse Models of Pulmonary Fibrosis.Kliment C, Gochuico B, Kaminski N, Rosas I, Oury T. Contrasts between IPF and Mouse Models of Pulmonary Fibrosis. 2009, a2716. DOI: 10.1164/ajrccm-conference.2009.179.1_meetingabstracts.a2716.
Effects of Exercise Training on Quadriceps Muscle Gene Expression in Chronic Obstructive Pulmonary Disease.RadomAizik S, Kaminski N, Hayek S, Halkin H, Cooper D, BenDov I. Effects of Exercise Training on Quadriceps Muscle Gene Expression in Chronic Obstructive Pulmonary Disease. Cardiopulmonary Physical Therapy Journal 2007, 18: 26-27. DOI: 10.1097/01823246-200718030-00009.
331: Gene expression profiles in peripheral blood for the noninvasive diagnosis of chronic lung allograft rejectionStuder S, Richards T, Wu W, McCurry K, Kaminski N. 331: Gene expression profiles in peripheral blood for the noninvasive diagnosis of chronic lung allograft rejection. The Journal Of Heart And Lung Transplantation 2007, 26: s179. DOI: 10.1016/j.healun.2006.11.351.
Systemic Biomarker Pattern in Different Chronic Obstructive Pulmonary Disease Phenotypes Independent of Smoking StatusPatel S, Choi A, Zhang Y, Kaminski N, Lokshin A, Weissfeld J, Sciurba F. Systemic Biomarker Pattern in Different Chronic Obstructive Pulmonary Disease Phenotypes Independent of Smoking Status. Annals Of The American Thoracic Society 2006, 3: 551-551. DOI: 10.1513/pats.200603-083ms.
RAGE: A beneficial role in pulmonary fibrosisOury T, Hanford L, Kaminski N, Fattman C, Tan R, Tobloewski J, Kasper M, Bierhaus A. RAGE: A beneficial role in pulmonary fibrosis. The FASEB Journal 2006, 20: a213-a213. DOI: 10.1096/fasebj.20.4.a213.
A Patient-Gene Model for Temporal Expression Profiles in Clinical StudiesKaminski N, Bar-Joseph Z. A Patient-Gene Model for Temporal Expression Profiles in Clinical Studies. 2006, 3909: 69-82. DOI: 10.1007/11732990_6.
S.16.04 Peripheral gene expression in PTSDShalev A, Segman R, Friedman N, Kaminski N, Sheffi N, Goltser-Dubner T. S.16.04 Peripheral gene expression in PTSD. European Neuropsychopharmacology 2006, 16: s188. DOI: 10.1016/s0924-977x(06)70081-5.
Erratum: Peripheral blood mononuclear cell gene expression profiles identify emergent post-traumatic stress disorder among trauma survivorsSegman R, Shefi N, Goltser-Dubner T, Friedman N, Kaminski N, Shalev A. Erratum: Peripheral blood mononuclear cell gene expression profiles identify emergent post-traumatic stress disorder among trauma survivors. Molecular Psychiatry 2005, 10: 514-514. DOI: 10.1038/sj.mp.4001654.
Training Reverses Age-Related Gene Expression Changes In Skeletal Muscle Of Elderly MenRadom-Aizik S, Hayek S, Rechavi G, Amariglio N, Halkin H, Kaminski N, Ben-Dov I. Training Reverses Age-Related Gene Expression Changes In Skeletal Muscle Of Elderly Men. Medicine & Science In Sports & Exercise 2005, 37: s243. DOI: 10.1249/00005768-200505001-01259.
Training Reverses Age-Related Gene Expression Changes In Skeletal Muscle Of Elderly MenRadom-Aizik S, Hayek S, Rechavi G, Amariglio N, Halkin H, Kaminski N, Ben-Dov I. Training Reverses Age-Related Gene Expression Changes In Skeletal Muscle Of Elderly Men. Medicine & Science In Sports & Exercise 2005, 37: s243. DOI: 10.1097/00005768-200505001-01259.
Peripheral blood mononuclear cell gene expression profiles identify emergent post-traumatic stress disorder among trauma survivorsSegman R, Shefi N, Goltser-Dubner T, Friedman N, Kaminski N, Shalev A. Peripheral blood mononuclear cell gene expression profiles identify emergent post-traumatic stress disorder among trauma survivors. Molecular Psychiatry 2005, 10: 425-425. DOI: 10.1038/sj.mp.4001676.
The mechanisms of idiopathic pulmonary fibrosis: can we see the elephant?Gibson K, Kaminski N. The mechanisms of idiopathic pulmonary fibrosis: can we see the elephant? Drug Discovery Today Disease Mechanisms 2004, 1: 117-122. DOI: 10.1016/j.ddmec.2004.08.002.
Effects of Exercise Training on Quadriceps Muscle Gene Expression in Chronic Obstructive Pulmonary Disease.RadomAizik S, Kaminski N, Hayek S, Halkin H, Cooper D, BenDov I. Effects of Exercise Training on Quadriceps Muscle Gene Expression in Chronic Obstructive Pulmonary Disease. Cardiopulmonary Physical Therapy Journal 2004, 18: 26-27. DOI: 10.1097/01823246-200418030-00009.
Functional Genomics of Lung DiseaseWhitsett J, Bachurski C, Barnes K, Bunn P, Case L, Cook D, Crooks D, Duncan M, Dwyer-Nield L, Elston R, Fessler M, Franklin W, Friedman N, Garcia J, Geraci M, Glasgow C, Glasser S, Hardie W, Henning L, Johnson G, Kawkitinarong K, Keith R, Korfhagen T, Leikauf G, Liggett S, Malcolm K, Malkinson A, Mariani T, McDowell S, McGraw D, Medvedovic M, Moss J, Nogee L, Nonas S, Pacheco-Rodriguez G, Palmer L, Peters D, Prows D, Redline S, Regev A, Sartor M, Schwartz D, Silverman E, Steagall W, Stearman R, Taveira-DaSilva A, Tichelaar J, Tomlinson C, Tsukada K, Weaver T, Wert S, Wesselkamper S, Worthen G, Xu Y, Zerbe L, Zhang Y, Zhang Y, Choi A, Kaminski N. Functional Genomics of Lung Disease. American Journal Of Respiratory Cell And Molecular Biology 2004, 31: s1-s81. PMID: 15269003, DOI: 10.1165/rcmb.2004-0071su.
Idiopathic Pulmonary FibrosisKaminski N, Belperio J, Bitterman P, Chen L, Chensue S, Choi A, Dacic S, Dauber J, du Bois R, Enghild J, Fattman C, Grutters J, Haegens A, Hanford L, Heintz N, Henson P, Hogaboam C, Kagan V, Keane M, Kunkel S, Land S, Loyd J, Lukacs N, MacPherson M, Manning B, Manning N, Martinelli M, Moller D, Morse D, Mossman B, Noble P, Nowak N, Oury T, Pardo A, Perez A, Petty T, Phan S, Ramos-Nino M, Ray P, Rogers R, Sato H, Scapoli L, Schaefer L, Selman M, Stern M, Strollo D, Tyurin V, Valnickova Z, Welsh K, Witzmann F, Yousem S, Strieter R. Idiopathic Pulmonary Fibrosis. American Journal Of Respiratory Cell And Molecular Biology 2003, 29: s1-s105. PMID: 12936907, DOI: 10.1165/rcmb.2003-0159su.
Use of Oligonucleotide Microarrays to Analyze Gene Expression Patterns in Pulmonary Fibrosis Reveals Distinct Patterns of Gene Expression in Mice and HumansKaminski N. Use of Oligonucleotide Microarrays to Analyze Gene Expression Patterns in Pulmonary Fibrosis Reveals Distinct Patterns of Gene Expression in Mice and Humans. CHEST Journal 2002, 121: 31s-a-32. DOI: 10.1378/chest.121.3_suppl.31s-a.
Lung inflammation induced by mixed T cell responses: Critical mediatorsHwang J, Yen D, Shahar I, Rennick D, Donaldson D, Kaminski N, Grunig G. Lung inflammation induced by mixed T cell responses: Critical mediators. Journal Of Allergy And Clinical Immunology 2002, 109: s317. DOI: 10.1016/s0091-6749(02)82112-1.
Interleukin-13 Induces Dramatically Different Transcriptional Programs in Three Human Airway Cell TypesLee J, Kaminski N, Dolganov G, Grunig G, Koth L, Solomon C, Erle D, Sheppard D. Interleukin-13 Induces Dramatically Different Transcriptional Programs in Three Human Airway Cell Types. American Journal Of Respiratory Cell And Molecular Biology 2001, 25: 474-485. PMID: 11694453, DOI: 10.1165/ajrcmb.25.4.4522.
TGF-β is a critical mediator of acute lung injuryPittet J, Griffiths M, Geiser T, Kaminski N, Dalton S, Huang X, Brown L, Gotwals P, Koteliansky V, Matthay M, Sheppard D. TGF-β is a critical mediator of acute lung injury. Journal Of Clinical Investigation 2001, 107: 1537-1544. PMID: 11413161, PMCID: PMC200192, DOI: 10.1172/jci11963.
DNA microarray analysis of genes involved in p53 mediated apoptosis: activation of Apaf-1Kannan K, Kaminski N, Rechavi G, Jakob-Hirsch J, Amariglio N, Givol D. DNA microarray analysis of genes involved in p53 mediated apoptosis: activation of Apaf-1. Oncogene 2001, 20: 3449-3455. PMID: 11423996, DOI: 10.1038/sj.onc.1204446.
DNA microarrays identification of primary and secondary target genes regulated by p53Kannan K, Amariglio N, Rechavi G, Jakob-Hirsch J, Kela I, Kaminski N, Getz G, Domany E, Givol D. DNA microarrays identification of primary and secondary target genes regulated by p53. Oncogene 2001, 20: 2225-2234. PMID: 11402317, DOI: 10.1038/sj.onc.1204319.
A composite genomic profile of lung cancer in smokers and nonsmokersKaminski N, Pilzer D, Cojocaru G, Margalit O, Friedman N, Reinstein S, Simansky D, Yaron P, Ninnete A, Yellin A, Rechavi G, Friedman E, Krupsky M. A composite genomic profile of lung cancer in smokers and nonsmokers. Nature Genetics 2001, 27: 63-63. DOI: 10.1038/87144.
Primary and secondary target genes regulated by p53 identified by DNA microarraysKannan K, Amariglio N, Rechavi G, Yaakov Y, Kaminski N, Getz G, Domany E, Givol D. Primary and secondary target genes regulated by p53 identified by DNA microarrays. Nature Genetics 2001, 27: 63-63. DOI: 10.1038/87146.
BioinformaticsKaminski N. Bioinformatics. American Journal Of Respiratory Cell And Molecular Biology 2000, 23: 705-711. PMID: 11104721, DOI: 10.1165/ajrcmb.23.6.4291.
Use of Oligonucleotide Arrays to Analyze Drug ToxicityKAMINSKI N, ALLARD J, HELLER R. Use of Oligonucleotide Arrays to Analyze Drug Toxicity. Annals Of The New York Academy Of Sciences 2000, 919: 1-8. PMID: 11083091, DOI: 10.1111/j.1749-6632.2000.tb06861.x.
Global analysis of gene expression in pulmonary fibrosis reveals distinct programs regulating lung inflammation and fibrosisKaminski N, Allard J, Pittet J, Zuo F, Griffiths M, Morris D, Huang X, Sheppard D, Heller R. Global analysis of gene expression in pulmonary fibrosis reveals distinct programs regulating lung inflammation and fibrosis. Proceedings Of The National Academy Of Sciences Of The United States Of America 2000, 97: 1778-1783. PMID: 10677534, PMCID: PMC26512, DOI: 10.1073/pnas.97.4.1778.
A Mechanism for Regulating Pulmonary Inflammation and Fibrosis: The Integrin αvβ6 Binds and Activates Latent TGF β1Munger J, Huang X, Kawakatsu H, Griffiths M, Dalton S, Wu J, Pittet J, Kaminski N, Garat C, Matthay M, Rifkin D, Sheppard D. A Mechanism for Regulating Pulmonary Inflammation and Fibrosis: The Integrin αvβ6 Binds and Activates Latent TGF β1. Cell 1999, 96: 319-328. PMID: 10025398, DOI: 10.1016/s0092-8674(00)80545-0.
Right-Sided Endocarditis Due to Staphylococcus aureusSchwaber M, Lossos I, Goldberg Y, Jaffe R, Kaminski N. Right-Sided Endocarditis Due to Staphylococcus aureus. Infectious Diseases In Clinical Practice 1995, 4: 453-455. DOI: 10.1097/00019048-199511000-00023.
Regression of Kaposi's sarcoma after intravenous immunoglobulin treatment for polymyositisCarmeli Y, Mevorach D, Kaminski N, Raz E. Regression of Kaposi's sarcoma after intravenous immunoglobulin treatment for polymyositis. Cancer 1994, 73: 2859-2861. PMID: 8194027, DOI: 10.1002/1097-0142(19940601)73:11<2859::aid-cncr2820731132>3.0.co;2-p.
Effects of Perfusion Pressure and Renal Flow upon Albumin Excretion in Isolated Perfused KidneysRaz E, Kaminski N, Brezis M. Effects of Perfusion Pressure and Renal Flow upon Albumin Excretion in Isolated Perfused Kidneys. Nephron 1990, 56: 396-398. PMID: 2079998, DOI: 10.1159/000186182.

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Naftali Kaminski, MD

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The IPF Cell Atlas

Thyroid Hormone effects on Mitochondria in Type II Epithelial Cells

Dr. Kaminski receiving the ERS gold Medal in London in 2017

Dr. Kaminski Receiving the Helmholtz International Award from Dr. Eickelberg in Munich, June 2013

52 Gene Signature Predictive of Outcome in 6 Cohorts of IPF Patients

Transcriptional Regulatory networks of Fibrosis Progression within the Human Lung

Cell regulatory Networks in the IPF lung

Selected Publications