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For: Kim S, Herazo-Maya JD, Kang DD, Juan-Guardela BM, Tedrow J, Martinez FJ, Sciurba FC, Tseng GC, Kaminski N. Integrative phenotyping framework (iPF): integrative clustering of multiple omics data identifies novel lung disease subphenotypes. BMC Genomics 2015;16:924. [PMID: 26560100 DOI: 10.1186/s12864-015-2170-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 10/31/2015] [Indexed: 12/15/2022]  Open
Number Cited by Other Article(s)
1
Boutanquoi PM, Pommerolle L, Dondaine L, Tanguy J, Bellaye PS, Biziorek L, Gautier-Isola M, Mari B, Masnikov D, Rocchi P, Finetti P, Korczak P, Vialet B, Barthelemy P, Garrido C, Bonniaud P, Burgy O, Goirand F. An antisense oligonucleotide targeting the heat-shock protein HSPB5 as an innovative therapeutic approach in pulmonary fibrosis. Br J Pharmacol 2025;182:2713-2729. [PMID: 40033950 DOI: 10.1111/bph.17470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 12/11/2024] [Accepted: 12/31/2024] [Indexed: 03/05/2025]  Open
2
Seasock MJ, Shafiquzzaman M, Ruiz-Echartea ME, Kanchi RS, Tran BT, Simon LM, Meyer MD, Erice PA, Lotlikar SL, Wenlock SC, Ochsner SA, Enright A, Carisey AF, Romero F, Rosas IO, King KY, McKenna NJ, Coarfa C, Rodriguez A. Let-7 restrains an epigenetic circuit in AT2 cells to prevent fibrogenic intermediates in pulmonary fibrosis. Nat Commun 2025;16:4353. [PMID: 40348760 PMCID: PMC12065893 DOI: 10.1038/s41467-025-59641-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 04/30/2025] [Indexed: 05/14/2025]  Open
3
Yi E, Li H, Liu Y, Li Q, Xie C, Sun R, Wu F, Deng Z, Zhou K, Wang H, Ran X, Zhou Y, Ran P. An integrated machine learning model of transcriptomic genes in multi-center chronic obstructive pulmonary disease reveals the causal role of TIMP4 in airway epithelial cell. Respir Res 2025;26:158. [PMID: 40269868 PMCID: PMC12020095 DOI: 10.1186/s12931-025-03238-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2024] [Accepted: 04/15/2025] [Indexed: 04/25/2025]  Open
4
Shao S, Cao S, Chen Y, Zhang Z, Zhaohui T. Immunological Features and Potential Biomarkers of Systemic Sclerosis-Associated Interstitial Lung Disease and Idiopathic Pulmonary Fibrosis. THE CLINICAL RESPIRATORY JOURNAL 2025;19:e70072. [PMID: 40165483 PMCID: PMC11959098 DOI: 10.1111/crj.70072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2024] [Revised: 03/01/2025] [Accepted: 03/17/2025] [Indexed: 04/02/2025]
5
Seasock MJ, Shafiquzzaman M, Ruiz-Echartea ME, Kanchi RS, Tran BT, Simon LM, Meyer MD, Erice PA, Lotlikar SL, Wenlock SC, Ochsner SA, Enright A, Carisey AF, Romero F, Rosas IO, King KY, McKenna NJ, Coarfa C, Rodriguez A. Let-7 restrains an oncogenic circuit in AT2 cells to prevent fibrogenic cell intermediates in pulmonary fibrosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.05.22.595205. [PMID: 38826218 PMCID: PMC11142151 DOI: 10.1101/2024.05.22.595205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
6
Zong W, Li D, Seney ML, Mcclung CA, Tseng GC. Model-based multifacet clustering with high-dimensional omics applications. Biostatistics 2024;26:kxae020. [PMID: 39002144 PMCID: PMC11823124 DOI: 10.1093/biostatistics/kxae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 05/08/2024] [Accepted: 06/02/2024] [Indexed: 07/15/2024]  Open
7
Bhargava M, Crouser ED. Application of laboratory models for sarcoidosis research. J Autoimmun 2024;149:103184. [PMID: 38443221 DOI: 10.1016/j.jaut.2024.103184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/12/2024] [Accepted: 02/15/2024] [Indexed: 03/07/2024]
8
Jin H, Park SY, Lee JE, Park H, Jeong M, Lee H, Cho J, Lee YS. GTSE1-driven ZEB1 stabilization promotes pulmonary fibrosis through the epithelial-to-mesenchymal transition. Mol Ther 2024;32:4138-4157. [PMID: 39342428 PMCID: PMC11573610 DOI: 10.1016/j.ymthe.2024.09.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 08/06/2024] [Accepted: 09/25/2024] [Indexed: 10/01/2024]  Open
9
Manuilova I, Bossenz J, Weise AB, Boehm D, Strantz C, Unberath P, Reimer N, Metzger P, Pauli T, Werle SD, Schulze S, Hiemer S, Ustjanzew A, Kestler HA, Busch H, Brors B, Christoph J. Identifications of Similarity Metrics for Patients With Cancer: Protocol for a Scoping Review. JMIR Res Protoc 2024;13:e58705. [PMID: 39230952 PMCID: PMC11411229 DOI: 10.2196/58705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/19/2024] [Accepted: 07/16/2024] [Indexed: 09/05/2024]  Open
10
Saha E, Ben Guebila M, Fanfani V, Fischer J, Shutta KH, Mandros P, DeMeo DL, Quackenbush J, Lopes-Ramos CM. Gene regulatory networks reveal sex difference in lung adenocarcinoma. Biol Sex Differ 2024;15:62. [PMID: 39107837 PMCID: PMC11302009 DOI: 10.1186/s13293-024-00634-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 07/04/2024] [Indexed: 08/10/2024]  Open
11
Li Q, Liu Y, Wang X, Xie C, Mei X, Cao W, Guan W, Lin X, Xie X, Zhou C, Yi E. The influence of CLEC5A on early macrophage-mediated inflammation in COPD progression. Cell Mol Life Sci 2024;81:330. [PMID: 39097839 PMCID: PMC11335254 DOI: 10.1007/s00018-024-05375-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 07/11/2024] [Accepted: 07/18/2024] [Indexed: 08/05/2024]
12
Saha E, Guebila MB, Fanfani V, Shutta KH, DeMeo DL, Quackenbush J, Lopes-Ramos CM. Aging-associated Alterations in the Gene Regulatory Network Landscape Associate with Risk, Prognosis and Response to Therapy in Lung Adenocarcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.02.601689. [PMID: 39005266 PMCID: PMC11244978 DOI: 10.1101/2024.07.02.601689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
13
Rakkar K, Thakker D, Portelli MA, Hall I, Schlüter H, Sayers I. Transcriptomics using lung resection material to advance our understanding of COPD and idiopathic pulmonary fibrosis pathogenesis. ERJ Open Res 2024;10:00061-2024. [PMID: 39104962 PMCID: PMC11299008 DOI: 10.1183/23120541.00061-2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 04/11/2024] [Indexed: 08/07/2024]  Open
14
Rodrigues Pereira RP, Mazzali Pessoa Martins AM, Mendes de Carvalho IT, Kel de Souza LD, Francao P, Gomes CM, Bernardes RDP, Meyer KF, Fonseca EMGOD, Machado MG, Tanaka C. Clinical phenotyping of children with nocturnal enuresis: A key classification to improve the approach. J Pediatr Urol 2024;20:384.e1-384.e9. [PMID: 38508980 DOI: 10.1016/j.jpurol.2024.01.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 12/01/2023] [Accepted: 01/19/2024] [Indexed: 03/22/2024]
15
Zheng Z, Peng F, Zhou Y. Biomarkers in idiopathic pulmonary fibrosis: Current insight and future direction. CHINESE MEDICAL JOURNAL PULMONARY AND CRITICAL CARE MEDICINE 2024;2:72-79. [PMID: 38962100 PMCID: PMC11221783 DOI: 10.1016/j.pccm.2024.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
16
Sakamachi Y, Wiley E, Solis A, Johnson CG, Meng X, Hussain S, Lipinski JH, O'Dwyer DN, Randall T, Malphurs J, Papas B, Wu BG, Li Y, Kugler M, Mehta S, Trempus CS, Thomas SY, Li JL, Zhou L, Karmaus PW, Fessler MB, McGrath JA, Gibson K, Kass DJ, Gleiberman A, Walts A, Invernizzi R, Molyneaux PL, Yang IV, Zhang Y, Kaminski N, Segal LN, Schwartz DA, Gudkov AV, Garantziotis S. Toll-Like-Receptor 5 protects against pulmonary fibrosis by reducing lung dysbiosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.30.591719. [PMID: 39605370 PMCID: PMC11601505 DOI: 10.1101/2024.04.30.591719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2024]
17
Xu F, Tong Y, Yang W, Cai Y, Yu M, Liu L, Meng Q. Identifying a survival-associated cell type based on multi-level transcriptome analysis in idiopathic pulmonary fibrosis. Respir Res 2024;25:126. [PMID: 38491375 PMCID: PMC10941445 DOI: 10.1186/s12931-024-02738-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 02/19/2024] [Indexed: 03/18/2024]  Open
18
Wang W, Ren W, Zhu L, Hu Y, Ye C. Identification of genes and key pathways underlying the pathophysiological association between sarcopenia and chronic obstructive pulmonary disease. Exp Gerontol 2024;187:112373. [PMID: 38320732 DOI: 10.1016/j.exger.2024.112373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/09/2024]
19
Bahudhanapati H, Tan J, Apel RM, Seeliger B, Schupp J, Li X, Sullivan DI, Sembrat J, Rojas M, Tabib T, Valenzi E, Lafyatis R, Mitash N, Hernandez Pineda R, Jawale C, Peroumal D, Biswas P, Tedrow J, Adams T, Kaminski N, Wuyts WA, McDyer JF, Gibson KF, Alder JK, Königshoff M, Zhang Y, Nouraie M, Prasse A, Kass DJ. Increased expression of CXCL6 in secretory cells drives fibroblast collagen synthesis and is associated with increased mortality in idiopathic pulmonary fibrosis. Eur Respir J 2024;63:2300088. [PMID: 37918852 DOI: 10.1183/13993003.00088-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 10/09/2023] [Indexed: 11/04/2023]
20
Karampitsakos T, Galaris A, Chrysikos S, Papaioannou O, Vamvakaris I, Barbayianni I, Kanellopoulou P, Grammenoudi S, Anagnostopoulos N, Stratakos G, Katsaras M, Sampsonas F, Dimakou K, Manali ED, Papiris S, Tourki B, Juan-Guardela BM, Bakakos P, Bouros D, Herazo-Maya JD, Aidinis V, Tzouvelekis A. Expression of PD-1/PD-L1 axis in mediastinal lymph nodes and lung tissue of human and experimental lung fibrosis indicates a potential therapeutic target for idiopathic pulmonary fibrosis. Respir Res 2023;24:279. [PMID: 37964265 PMCID: PMC10648728 DOI: 10.1186/s12931-023-02551-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/02/2023] [Indexed: 11/16/2023]  Open
21
He J, Wang B, Chen M, Song L, Li H. Machine learning-based metabolism-related genes signature, single-cell RNA sequencing, and experimental validation in hypersensitivity pneumonitis. Medicine (Baltimore) 2023;102:e34940. [PMID: 37800807 PMCID: PMC10553120 DOI: 10.1097/md.0000000000034940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 08/04/2023] [Indexed: 10/07/2023]  Open
22
Saha E, Guebila MB, Fanfani V, Fischer J, Shutta KH, Mandros P, DeMeo DL, Quackenbush J, Lopes-Ramos CM. Gene regulatory Networks Reveal Sex Difference in Lung Adenocarcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.22.559001. [PMID: 37790409 PMCID: PMC10543009 DOI: 10.1101/2023.09.22.559001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
23
Chen Y, Wang Y, Li Z, Jing J, Jiang D, Yuan X, Li F. Exploration of the Mechanism of Shengxian Decoction Against Chronic Obstructive Pulmonary Disease Based on Network Pharmacology and Experimental Verification. Assay Drug Dev Technol 2023;21:258-272. [PMID: 37682969 DOI: 10.1089/adt.2023.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/10/2023]  Open
24
Zhang YH, Cho MH, Morrow JD, Castaldi PJ, Hersh CP, Midha MK, Hoopmann MR, Lutz SM, Moritz RL, Silverman EK. Integrating Genetics, Transcriptomics, and Proteomics in Lung Tissue to Investigate Chronic Obstructive Pulmonary Disease. Am J Respir Cell Mol Biol 2023;68:651-663. [PMID: 36780661 PMCID: PMC10257075 DOI: 10.1165/rcmb.2022-0302oc] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 02/13/2023] [Indexed: 02/15/2023]  Open
25
Ruan P, Todd JL, Zhao H, Liu Y, Vinisko R, Soellner JF, Schmid R, Kaner RJ, Luckhardt TR, Neely ML, Noth I, Porteous M, Raj R, Safdar Z, Strek ME, Hesslinger C, Palmer SM, Leonard TB, Salisbury ML. Integrative multi-omics analysis reveals novel idiopathic pulmonary fibrosis endotypes associated with disease progression. Respir Res 2023;24:141. [PMID: 37344825 PMCID: PMC10283254 DOI: 10.1186/s12931-023-02435-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 04/26/2023] [Indexed: 06/23/2023]  Open
26
Hobbs BD, Morrow JD, Wang XW, Liu YY, DeMeo DL, Hersh CP, Celli BR, Bueno R, Criner GJ, Silverman EK, Cho MH. Identifying chronic obstructive pulmonary disease from integrative omics and clustering in lung tissue. BMC Pulm Med 2023;23:115. [PMID: 37041558 PMCID: PMC10091624 DOI: 10.1186/s12890-023-02389-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 03/15/2023] [Indexed: 04/13/2023]  Open
27
Yi E, Cao W, Zhang J, Lin B, Wang Z, Wang X, Bai G, Mei X, Xie C, Jin J, Liu X, Li H, Wu F, Lin Z, Sun R, Li B, Zhou Y, Ran P. Genetic screening of MMP1 as a potential pathogenic gene in chronic obstructive pulmonary disease. Life Sci 2023;313:121214. [PMID: 36442527 DOI: 10.1016/j.lfs.2022.121214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 11/27/2022]
28
Zhang J, Zhang Y, Wang Z, Zhao J, Li Z, Wang K, Tian L, Yao B, Wu Q, Wang T, Wang J. Genes related to N6-methyladenosine in the diagnosis and prognosis of idiopathic pulmonary fibrosis. Front Genet 2023;13:1102422. [PMID: 36685949 PMCID: PMC9846232 DOI: 10.3389/fgene.2022.1102422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 12/12/2022] [Indexed: 01/05/2023]  Open
29
He J, Zhang J, Ren X. Krebs von den lungen-6 as a clinical marker for hypersensitivity pneumonitis: A meta-analysis and bioinformatics analysis. Front Immunol 2022;13:1041098. [PMID: 36532009 PMCID: PMC9748086 DOI: 10.3389/fimmu.2022.1041098] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 11/14/2022] [Indexed: 12/05/2022]  Open
30
Zhang L, Tang C, Zhang M, Tong X, Xie Y, Yan R, Wang X, Zhang X, Liu D, Li S. Single cell meta-analysis of EndMT and EMT state in COVID-19. Front Immunol 2022;13:976512. [PMID: 36248845 PMCID: PMC9558222 DOI: 10.3389/fimmu.2022.976512] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022]  Open
31
Tebani A, Bekri S. [The promise of omics in the precision medicine era]. Rev Med Interne 2022;43:649-660. [PMID: 36041909 DOI: 10.1016/j.revmed.2022.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 07/12/2022] [Indexed: 10/15/2022]
32
Mostafaei S, Borna H, Emamvirdizadeh A, Arabfard M, Ahmadi A, Salimian J, Salesi M, Azimzadeh Jamalkandi S. Causal Path of COPD Progression-Associated Genes in Different Biological Samples. COPD 2022;19:290-299. [PMID: 35696265 DOI: 10.1080/15412555.2022.2081541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
33
Preisendörfer S, Ishikawa Y, Hennen E, Winklmeier S, Schupp JC, Knüppel L, Fernandez IE, Binzenhöfer L, Flatley A, Juan-Guardela BM, Ruppert C, Guenther A, Frankenberger M, Hatz RA, Kneidinger N, Behr J, Feederle R, Schepers A, Hilgendorff A, Kaminski N, Meinl E, Bächinger HP, Eickelberg O, Staab-Weijnitz CA. FK506-Binding Protein 11 Is a Novel Plasma Cell-Specific Antibody Folding Catalyst with Increased Expression in Idiopathic Pulmonary Fibrosis. Cells 2022;11:1341. [PMID: 35456020 PMCID: PMC9027113 DOI: 10.3390/cells11081341] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 02/01/2023]  Open
34
Vahabi N, Michailidis G. Unsupervised Multi-Omics Data Integration Methods: A Comprehensive Review. Front Genet 2022;13:854752. [PMID: 35391796 PMCID: PMC8981526 DOI: 10.3389/fgene.2022.854752] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 02/28/2022] [Indexed: 12/26/2022]  Open
35
Kim J, Yoon Y, Park HJ, Kim YH. Comparative Study of Classification Algorithms for Various DNA Microarray Data. Genes (Basel) 2022;13:494. [PMID: 35328048 PMCID: PMC8951024 DOI: 10.3390/genes13030494] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 03/07/2022] [Indexed: 12/19/2022]  Open
36
Lin J, Xue Y, Su W, Zhang Z, Wei Q, Huang T. Identification of Dysregulated Mechanisms and Candidate Gene Markers in Chronic Obstructive Pulmonary Disease. Int J Chron Obstruct Pulmon Dis 2022;17:475-487. [PMID: 35281477 PMCID: PMC8904782 DOI: 10.2147/copd.s349694] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/27/2022] [Indexed: 11/23/2022]  Open
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Sauler M, McDonough JE, Adams TS, Kothapalli N, Barnthaler T, Werder RB, Schupp JC, Nouws J, Robertson MJ, Coarfa C, Yang T, Chioccioli M, Omote N, Cosme C, Poli S, Ayaub EA, Chu SG, Jensen KH, Gomez JL, Britto CJ, Raredon MSB, Niklason LE, Wilson AA, Timshel PN, Kaminski N, Rosas IO. Characterization of the COPD alveolar niche using single-cell RNA sequencing. Nat Commun 2022;13:494. [PMID: 35078977 PMCID: PMC8789871 DOI: 10.1038/s41467-022-28062-9] [Citation(s) in RCA: 121] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 12/14/2021] [Indexed: 12/16/2022]  Open
38
Ma C, Wu M, Ma S. Analysis of cancer omics data: a selective review of statistical techniques. Brief Bioinform 2022;23:6510158. [PMID: 35039832 DOI: 10.1093/bib/bbab585] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022]  Open
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Vukmirovic M, Yan X, Gibson KF, Gulati M, Schupp JC, DeIuliis G, Adams TS, Hu B, Mihaljinec A, Woolard TN, Lynn H, Emeagwali N, Herzog EL, Chen ES, Morris A, Leader JK, Zhang Y, Garcia JGN, Maier LA, Collman RG, Drake WP, Becich MJ, Hochheiser H, Wisniewski SR, Benos PV, Moller DR, Prasse A, Koth LL, Kaminski N. Transcriptomics of bronchoalveolar lavage cells identifies new molecular endotypes of sarcoidosis. Eur Respir J 2021;58:2002950. [PMID: 34083402 PMCID: PMC9759791 DOI: 10.1183/13993003.02950-2020] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 04/20/2021] [Indexed: 11/05/2022]
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Fanidis D, Moulos P, Aidinis V. Fibromine is a multi-omics database and mining tool for target discovery in pulmonary fibrosis. Sci Rep 2021;11:21712. [PMID: 34741074 PMCID: PMC8571330 DOI: 10.1038/s41598-021-01069-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/21/2021] [Indexed: 11/22/2022]  Open
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Fließer E, Birnhuber A, Marsh LM, Gschwandtner E, Klepetko W, Olschewski H, Kwapiszewska G. Dysbalance of ACE2 levels - a possible cause for severe COVID-19 outcome in COPD. J Pathol Clin Res 2021;7:446-458. [PMID: 33978304 PMCID: PMC8239572 DOI: 10.1002/cjp2.224] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/22/2021] [Accepted: 04/21/2021] [Indexed: 12/23/2022]
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Gong M, Liu P, Sciurba FC, Stojanov P, Tao D, Tseng GC, Zhang K, Batmanghelich K. Unpaired data empowers association tests. Bioinformatics 2021;37:785-792. [PMID: 33070196 PMCID: PMC8098021 DOI: 10.1093/bioinformatics/btaa886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 09/07/2020] [Accepted: 10/05/2020] [Indexed: 11/25/2022]  Open
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Watson NF, Fernandez CR. Artificial intelligence and sleep: Advancing sleep medicine. Sleep Med Rev 2021;59:101512. [PMID: 34166990 DOI: 10.1016/j.smrv.2021.101512] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 02/07/2023]
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Wu M, Yi H, Ma S. Vertical integration methods for gene expression data analysis. Brief Bioinform 2021;22:bbaa169. [PMID: 32793970 PMCID: PMC8138889 DOI: 10.1093/bib/bbaa169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/18/2020] [Accepted: 07/04/2020] [Indexed: 12/12/2022]  Open
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Lung gene expression and single cell analyses reveal two subsets of idiopathic pulmonary fibrosis (IPF) patients associated with different pathogenic mechanisms. PLoS One 2021;16:e0248889. [PMID: 33755690 PMCID: PMC7987152 DOI: 10.1371/journal.pone.0248889] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 03/07/2021] [Indexed: 12/13/2022]  Open
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Nouws J, Wan F, Finnemore E, Roque W, Kim SJ, Bazan I, Li CX, Skold CM, Dai Q, Yan X, Chioccioli M, Neumeister V, Britto CJ, Sweasy J, Bindra R, Wheelock ÅM, Gomez JL, Kaminski N, Lee PJ, Sauler M. MicroRNA miR-24-3p reduces DNA damage responses, apoptosis, and susceptibility to chronic obstructive pulmonary disease. JCI Insight 2021;6:134218. [PMID: 33290275 PMCID: PMC7934877 DOI: 10.1172/jci.insight.134218] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 12/02/2020] [Indexed: 12/27/2022]  Open
47
López-Agudelo VA, Gómez-Ríos D, Ramirez-Malule H. Clavulanic Acid Production by Streptomyces clavuligerus: Insights from Systems Biology, Strain Engineering, and Downstream Processing. Antibiotics (Basel) 2021;10:84. [PMID: 33477401 PMCID: PMC7830376 DOI: 10.3390/antibiotics10010084] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 12/16/2022]  Open
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Walentek P. Xenopus epidermal and endodermal epithelia as models for mucociliary epithelial evolution, disease, and metaplasia. Genesis 2021;59:e23406. [PMID: 33400364 DOI: 10.1002/dvg.23406] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 11/08/2022]
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Wu M, Jiang Y, Ma S. Integration of Proteomics and Other Omics Data. Methods Mol Biol 2021;2361:307-324. [PMID: 34236669 DOI: 10.1007/978-1-0716-1641-3_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
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Zhu K, Xu A, Xia W, Li P, Han R, Wang E, Zhou S, Wang R. Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis. Int J Med Sci 2021;18:3412-3424. [PMID: 34522168 PMCID: PMC8436110 DOI: 10.7150/ijms.61309] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/30/2021] [Indexed: 12/29/2022]  Open
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