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Reply to: Role of Transbronchial Cryobiopsy in Interstitial Lung Diseases - An Ongoing Tale.

Bourdin A, Suehs CM, Colby TV, Vachier I, Molinari N, Romagnoli M; all authors of “Poor Concordance between Sequential Transbronchial Lung Cryobiopsy and Surgical Lung Biopsy in the Diagnosis of Diffuse Interstitial Lung Diseases.”.

Am J Respir Crit Care Med. 2019 Sep 19. doi: 10.1164/rccm.201909-1736LE. [Epub ahead of print] No abstract available.


Severe lung disease characterized by lymphocytic bronchiolitis, alveolar ductitis, and emphysema (BADE) in industrial machine-manufacturing workers.

Cummings KJ, Stanton ML, Nett RJ, Segal LN, Kreiss K, Abraham JL, Colby TV, Franko AD, Green FHY, Sanyal S, Tallaksen RJ, Wendland D, Bachelder VD, Boylstein RJ, Park JH, Cox-Ganser JM, Virji MA, Crawford JA, Green BJ, LeBouf RF, Blaser MJ, Weissman DN.

Am J Ind Med. 2019 Nov;62(11):927-937. doi: 10.1002/ajim.23038. Epub 2019 Aug 28.


Cryobiopsy Compared with Surgical Lung Biopsy in ILD: Reply to Maldonado et al., Froidure et al., Bendstrup et al., Agarwal et al., Richeldi et al., Rajchgot et al., and Quadrelli et al.

Romagnoli M, Colby TV, Suehs CM, Vachier I, Molinari N, Bourdin A.

Am J Respir Crit Care Med. 2019 Oct 1;200(7):944-946. doi: 10.1164/rccm.201906-1252LE. No abstract available.


Before Freezing Out Cryobiopsy, We Need to Thaw Out Flaws in the Diagnosis of Interstitial Lung Disease.

Maldonado F, Wells A, Danoff S, Colby T, Ryu J, Poletti V, Rickman O, Herth F, Wahidi M, Hetzel J, Liberman M, Yarmus L.

Am J Respir Crit Care Med. 2019 Oct 1;200(7):937-938. doi: 10.1164/rccm.201903-0699LE. No abstract available.


Site-specific cleavage of bacterial MucD by secreted proteases mediates antibacterial resistance in Arabidopsis.

Wang Y, Garrido-Oter R, Wu J, Winkelmüller TM, Agler M, Colby T, Nobori T, Kemen E, Tsuda K.

Nat Commun. 2019 Jun 28;10(1):2853. doi: 10.1038/s41467-019-10793-x.


A 52-Year-Old Woman With an Abdominal Mass, Bilateral Pulmonary Nodules, and Mediastinal and Hilar Lymphadenopathy.

Van Treeck BJ, Gehlbach DA, Foster GH, Utz JP, Aubry MC, Colby TV, Yi ES.

Chest. 2019 Jun;155(6):e175-e178. doi: 10.1016/j.chest.2019.01.017.


Proteases Underground: Analysis of the Maize Root Apoplast Identifies Organ Specific Papain-Like Cysteine Protease Activity.

Schulze Hüynck J, Kaschani F, van der Linde K, Ziemann S, Müller AN, Colby T, Kaiser M, Misas Villamil JC, Doehlemann G.

Front Plant Sci. 2019 Apr 30;10:473. doi: 10.3389/fpls.2019.00473. eCollection 2019.


The Helpful Role of CD10 and Hormonal Receptors Co-Expression in the Histologic Diagnosis of Catamenial Pneumothorax.

Mataca E, Rossi G, Colby TV.

Int J Surg Pathol. 2019 Sep;27(6):593-597. doi: 10.1177/1066896919846386. Epub 2019 May 9.


Benign metastasizing leiomyoma presenting with miliary pattern and fatal outcome: Case report with molecular analysis & review of the literature.

Ofori K, Fernandes H, Cummings M, Colby T, Saqi A.

Respir Med Case Rep. 2019 Mar 28;27:100831. doi: 10.1016/j.rmcr.2019.100831. eCollection 2019.


Use of a molecular classifier to identify usual interstitial pneumonia in conventional transbronchial lung biopsy samples: a prospective validation study.

Raghu G, Flaherty KR, Lederer DJ, Lynch DA, Colby TV, Myers JL, Groshong SD, Larsen BT, Chung JH, Steele MP, Benzaquen S, Calero K, Case AH, Criner GJ, Nathan SD, Rai NS, Ramaswamy M, Hagmeyer L, Davis JR, Gauhar UA, Pankratz DG, Choi Y, Huang J, Walsh PS, Neville H, Lofaro LR, Barth NM, Kennedy GC, Brown KK, Martinez FJ.

Lancet Respir Med. 2019 Jun;7(6):487-496. doi: 10.1016/S2213-2600(19)30059-1. Epub 2019 Apr 1.


The development of sarcoidosis in patients receiving daclizumab: A case series from multiple clinical trials.

Judson MA, Elicker BM, Colby TV, Kwon S, de Windt E, Chalkias S, Prada C, Smirnakis K, Singhal P.

Respir Med. 2019 Mar;149:23-27. doi: 10.1016/j.rmed.2019.01.015. Epub 2019 Feb 1.


Poor Concordance between Sequential Transbronchial Lung Cryobiopsy and Surgical Lung Biopsy in the Diagnosis of Diffuse Interstitial Lung Diseases.

Romagnoli M, Colby TV, Berthet JP, Gamez AS, Mallet JP, Serre I, Cancellieri A, Cavazza A, Solovei L, Dell'Amore A, Dolci G, Guerrieri A, Reynaud P, Bommart S, Zompatori M, Dalpiaz G, Nava S, Trisolini R, Suehs CM, Vachier I, Molinari N, Bourdin A.

Am J Respir Crit Care Med. 2019 May 15;199(10):1249-1256. doi: 10.1164/rccm.201810-1947OC.


Diagnostic yield and risk/benefit analysis of trans-bronchial lung cryobiopsy in diffuse parenchymal lung diseases: a large cohort of 699 patients.

Ravaglia C, Wells AU, Tomassetti S, Gurioli C, Gurioli C, Dubini A, Cavazza A, Colby TV, Piciucchi S, Puglisi S, Bosi M, Poletti V.

BMC Pulm Med. 2019 Jan 16;19(1):16. doi: 10.1186/s12890-019-0780-3.


IgG4-related disease presenting with combined pulmonary fibrosis and emphysema (CPFE).

Kono M, Nakamura Y, Oyama Y, Saito G, Koyanagi Y, Miyashita K, Tsutsumi A, Enomoto Y, Kobayashi T, Miki Y, Hashimoto D, Enomoto N, Colby TV, Suda T, Nakamura H.

Respir Med Case Rep. 2018 Oct 3;25:257-260. doi: 10.1016/j.rmcr.2018.09.017. eCollection 2018.


Interplay of Histone Marks with Serine ADP-Ribosylation.

Bartlett E, Bonfiglio JJ, Prokhorova E, Colby T, Zobel F, Ahel I, Matic I.

Cell Rep. 2018 Sep 25;24(13):3488-3502.e5. doi: 10.1016/j.celrep.2018.08.092.


Reprint of: Pathologic manifestations of Immunoglobulin(Ig)G4-related lung disease.

Yi ES, Sekiguchi H, Peikert T, Ryu JH, Colby TV.

Semin Diagn Pathol. 2018 Sep;35(5):347-351. doi: 10.1053/j.semdp.2018.09.004. Epub 2018 Sep 8.


Molecular and Ultrastructural Features of Diffuse Intrapulmonary Malignant Mesothelioma.

Larsen BT, Smith ML, Roden AC, Sukov WR, Hornychová H, Thirumala S, Colby TV, Tazelaar HD.

Am J Surg Pathol. 2019 Jan;43(1):147-150. doi: 10.1097/PAS.0000000000001143. No abstract available.


Small airways disease in an Operation Desert Storm Deployer: Case report and review of the literature on respiratory health and inhalational exposures from Gulf War I.

Weiler BA, Colby TV, Floreth TJ, Hines SE.

Am J Ind Med. 2018 Oct;61(10):793-801. doi: 10.1002/ajim.22893. Epub 2018 Aug 16. Review.


Nonlocalized Searching of HCD Data for Fast and Sensitive Identification of ADP-Ribosylated Peptides.

Colby T, Bonfiglio JJ, Matic I.

Methods Mol Biol. 2018;1813:255-269. doi: 10.1007/978-1-4939-8588-3_18.


Smoking-Related Diffuse Cystic Lung Disease.

Gupta N, Colby TV, Meyer CA, McCormack FX, Wikenheiser-Brokamp KA.

Chest. 2018 Aug;154(2):e31-e35. doi: 10.1016/j.chest.2018.02.027.


Identification of usual interstitial pneumonia pattern using RNA-Seq and machine learning: challenges and solutions.

Choi Y, Liu TT, Pankratz DG, Colby TV, Barth NM, Lynch DA, Walsh PS, Raghu G, Kennedy GC, Huang J.

BMC Genomics. 2018 May 9;19(Suppl 2):101. doi: 10.1186/s12864-018-4467-6.


Distinctive characteristics and prognostic significance of interstitial pneumonia with autoimmune features in patients with chronic fibrosing interstitial pneumonia.

Yoshimura K, Kono M, Enomoto Y, Nishimoto K, Oyama Y, Yasui H, Hozumi H, Karayama M, Suzuki Y, Furuhashi K, Enomoto N, Fujisawa T, Nakamura Y, Inui N, Sumikawa H, Johkoh T, Colby TV, Sugimura H, Suda T.

Respir Med. 2018 Apr;137:167-175. doi: 10.1016/j.rmed.2018.02.024. Epub 2018 Mar 1.


An apoplastic peptide activates salicylic acid signalling in maize.

Ziemann S, van der Linde K, Lahrmann U, Acar B, Kaschani F, Colby T, Kaiser M, Ding Y, Schmelz E, Huffaker A, Holton N, Zipfel C, Doehlemann G.

Nat Plants. 2018 Mar;4(3):172-180. doi: 10.1038/s41477-018-0116-y. Epub 2018 Feb 26.


Diffuse Idiopathic Pulmonary Neuroendocrine Cell Hyperplasia (DIPNECH) Syndrome and Carcinoid Tumors With/Without NECH: A Clinicopathologic, Radiologic, and Immunomolecular Comparison Study.

Mengoli MC, Rossi G, Cavazza A, Franco R, Marino FZ, Migaldi M, Gnetti L, Silini EM, Ampollini L, Tiseo M, Lococo F, Fournel L, Spagnolo P, Cottin V, Colby TV.

Am J Surg Pathol. 2018 May;42(5):646-655. doi: 10.1097/PAS.0000000000001033.


Diagnostic criteria for idiopathic pulmonary fibrosis - Authors' reply.

Lynch DA, Sverzellati N, Travis WD, Colby TV, Inoue Y, Nicholson AG, Raoof S, Richeldi L, Ryerson CJ, Ryu JH.

Lancet Respir Med. 2018 Feb;6(2):e7. doi: 10.1016/S2213-2600(18)30021-3. No abstract available.


Transbronchial Cryobiopsies for the Diagnosis of Diffuse Parenchymal Lung Diseases: Expert Statement from the Cryobiopsy Working Group on Safety and Utility and a Call for Standardization of the Procedure.

Hetzel J, Maldonado F, Ravaglia C, Wells AU, Colby TV, Tomassetti S, Ryu JH, Fruchter O, Piciucchi S, Dubini A, Cavazza A, Chilosi M, Sverzellati N, Valeyre D, Leduc D, Walsh SLF, Gasparini S, Hetzel M, Hagmeyer L, Haentschel M, Eberhardt R, Darwiche K, Yarmus LB, Torrego A, Krishna G, Shah PL, Annema JT, Herth FJF, Poletti V.

Respiration. 2018;95(3):188-200. doi: 10.1159/000484055. Epub 2018 Jan 9.


Reply to Wijmans et al.: Optical Coherence Tomography: A Valuable Novel Tool for Assessing the Alveolar Compartment in Interstitial Lung Disease?

Hariri LP, Adams DC, Wain JC, Lanuti M, Muniappan A, Sharma A, Colby TV, Mino-Kenudson M, Mark EJ, Kradin RL, Goulart H, Suter MJ.

Am J Respir Crit Care Med. 2018 May 1;197(9):1232-1233. doi: 10.1164/rccm.201711-2347LE. No abstract available.


Incidental iatrogenic form of collagenized organizing pneumonia.

Mengoli MC, Colby TV, Cavazza A, Zanelli M, De Marco L, Casolari R, Lococo F, Rossi G.

Hum Pathol. 2018 Mar;73:192-193. doi: 10.1016/j.humpath.2017.10.035. Epub 2017 Dec 5. No abstract available.


Clinical diagnosis of idiopathic pleuroparenchymal fibroelastosis: A retrospective multicenter study.

Enomoto Y, Nakamura Y, Satake Y, Sumikawa H, Johkoh T, Colby TV, Yasui H, Hozumi H, Karayama M, Suzuki Y, Furuhashi K, Fujisawa T, Enomoto N, Inui N, Iwashita T, Kuroishi S, Yokomura K, Koshimizu N, Toyoshima M, Imokawa S, Yamada T, Shirai T, Hayakawa H, Suda T.

Respir Med. 2017 Dec;133:1-5. doi: 10.1016/j.rmed.2017.11.003. Epub 2017 Nov 6.


Diagnostic criteria for idiopathic pulmonary fibrosis: a Fleischner Society White Paper.

Lynch DA, Sverzellati N, Travis WD, Brown KK, Colby TV, Galvin JR, Goldin JG, Hansell DM, Inoue Y, Johkoh T, Nicholson AG, Knight SL, Raoof S, Richeldi L, Ryerson CJ, Ryu JH, Wells AU.

Lancet Respir Med. 2018 Feb;6(2):138-153. doi: 10.1016/S2213-2600(17)30433-2. Epub 2017 Nov 15. Review.


Lymphangioleiomyomatosis Diagnosis and Management: High-Resolution Chest Computed Tomography, Transbronchial Lung Biopsy, and Pleural Disease Management. An Official American Thoracic Society/Japanese Respiratory Society Clinical Practice Guideline.

Gupta N, Finlay GA, Kotloff RM, Strange C, Wilson KC, Young LR, Taveira-DaSilva AM, Johnson SR, Cottin V, Sahn SA, Ryu JH, Seyama K, Inoue Y, Downey GP, Han MK, Colby TV, Wikenheiser-Brokamp KA, Meyer CA, Smith K, Moss J, McCormack FX; ATS Assembly on Clinical Problems.

Am J Respir Crit Care Med. 2017 Nov 15;196(10):1337-1348. doi: 10.1164/rccm.201709-1965ST.


The prognostic significance of pneumothorax in patients with idiopathic pulmonary fibrosis.

Nishimoto K, Fujisawa T, Yoshimura K, Enomoto Y, Enomoto N, Nakamura Y, Inui N, Sumikawa H, Johkoh T, Colby TV, Suda T.

Respirology. 2018 May;23(5):519-525. doi: 10.1111/resp.13219. Epub 2017 Nov 12.


Reply: Improving Care for Patients with Interstitial Lung Disease, Using Machine Learning, Requires Transparency and Reproducibility.

Kennedy GC, Barth NM, Walsh PS, Huang J, Pankratz DG, Choi Y, Fedorowicz GM, Anderson JD, Raghu G, Martinez FJ, Colby TV, Lynch DA, Brown KK, Groshong SD, Myers JL, Flaherty KR, Steele MP.

Ann Am Thorac Soc. 2017 Dec;14(12):1864-1865. doi: 10.1513/AnnalsATS.201708-654LE. No abstract available.


BRAF and NRAS mutations in circulating Langerhans-like CD1a+ cells in a patient with pulmonary Langerhans' cell histiocytosis.

Zhang L, Pacheco-Rodriguez G, Steagall WK, Kato J, Colby TV, Haughey M, Moss J.

Eur Respir J. 2017 Oct 12;50(4). pii: 1700521. doi: 10.1183/13993003.00521-2017. Print 2017 Oct. No abstract available.


Endobronchial Optical Coherence Tomography for Low-Risk Microscopic Assessment and Diagnosis of Idiopathic Pulmonary Fibrosis In Vivo.

Hariri LP, Adams DC, Wain JC, Lanuti M, Muniappan A, Sharma A, Colby TV, Mino-Kenudson M, Mark EJ, Kradin RL, Goulart H, Tager AM, Suter MJ.

Am J Respir Crit Care Med. 2018 Apr 1;197(7):949-952. doi: 10.1164/rccm.201707-1446LE. No abstract available.


Mitotic post-translational modifications of histones promote chromatin compaction in vitro.

Zhiteneva A, Bonfiglio JJ, Makarov A, Colby T, Vagnarelli P, Schirmer EC, Matic I, Earnshaw WC.

Open Biol. 2017 Sep;7(9). pii: 170076. doi: 10.1098/rsob.170076.


Transbronchial cryobiopsy for diffuse parenchymal lung disease: a state-of-the-art review of procedural techniques, current evidence, and future challenges.

Lentz RJ, Argento AC, Colby TV, Rickman OB, Maldonado F.

J Thorac Dis. 2017 Jul;9(7):2186-2203. doi: 10.21037/jtd.2017.06.96. Review.


Guidelines for Pathologic Diagnosis of Malignant Mesothelioma 2017 Update of the Consensus Statement From the International Mesothelioma Interest Group.

Husain AN, Colby TV, Ordóñez NG, Allen TC, Attanoos RL, Beasley MB, Butnor KJ, Chirieac LR, Churg AM, Dacic S, Galateau-Sallé F, Gibbs A, Gown AM, Krausz T, Litzky LA, Marchevsky A, Nicholson AG, Roggli VL, Sharma AK, Travis WD, Walts AE, Wick MR.

Arch Pathol Lab Med. 2018 Jan;142(1):89-108. doi: 10.5858/arpa.2017-0124-RA. Epub 2017 Jul 7.


Radiologic pleuroparenchymal fibroelastosis-like lesion in connective tissue disease-related interstitial lung disease.

Enomoto Y, Nakamura Y, Colby TV, Johkoh T, Sumikawa H, Nishimoto K, Yoshimura K, Matsushima S, Oyama Y, Hozumi H, Kono M, Fujisawa T, Enomoto N, Inui N, Iwashita T, Suda T.

PLoS One. 2017 Jun 30;12(6):e0180283. doi: 10.1371/journal.pone.0180283. eCollection 2017.


Usual Interstitial Pneumonia Can Be Detected in Transbronchial Biopsies Using Machine Learning.

Pankratz DG, Choi Y, Imtiaz U, Fedorowicz GM, Anderson JD, Colby TV, Myers JL, Lynch DA, Brown KK, Flaherty KR, Steele MP, Groshong SD, Raghu G, Barth NM, Walsh PS, Huang J, Kennedy GC, Martinez FJ.

Ann Am Thorac Soc. 2017 Nov;14(11):1646-1654. doi: 10.1513/AnnalsATS.201612-947OC.


Mass spectrometry for serine ADP-ribosylation? Think o-glycosylation!

Bonfiglio JJ, Colby T, Matic I.

Nucleic Acids Res. 2017 Jun 20;45(11):6259-6264. doi: 10.1093/nar/gkx446.


Endobronchial solitary fibrous tumor.

Oliveira CC, de Moraes MP, Colby T, Oliveira GF, Hasimoto EN, Cataneo DC, Cataneo AJ, De Faveri J.

Autops Case Rep. 2016 Dec 30;6(4):35-40. doi: 10.4322/acr.2016.053. eCollection 2016 Oct-Dec.


Serine ADP-Ribosylation Depends on HPF1.

Bonfiglio JJ, Fontana P, Zhang Q, Colby T, Gibbs-Seymour I, Atanassov I, Bartlett E, Zaja R, Ahel I, Matic I.

Mol Cell. 2017 Mar 2;65(5):932-940.e6. doi: 10.1016/j.molcel.2017.01.003. Epub 2017 Feb 9.


Amyloidosis of the Lung.

Khoor A, Colby TV.

Arch Pathol Lab Med. 2017 Feb;141(2):247-254. doi: 10.5858/arpa.2016-0102-RA. Review.


Phosphoribosylation of Ubiquitin Promotes Serine Ubiquitination and Impairs Conventional Ubiquitination.

Bhogaraju S, Kalayil S, Liu Y, Bonn F, Colby T, Matic I, Dikic I.

Cell. 2016 Dec 1;167(6):1636-1649.e13. doi: 10.1016/j.cell.2016.11.019.


Angiosarcoma in the chest: radiologic-pathologic correlation: Case report.

Piciucchi S, Dubini A, Tomassetti S, Sanna S, Ravaglia C, Carloni A, Gurioli C, Gurioli C, Colby TV, Poletti V.

Medicine (Baltimore). 2016 Nov;95(48):e5348.


Disruption of Macrodomain Protein SCO6735 Increases Antibiotic Production in Streptomyces coelicolor.

Lalić J, Posavec Marjanović M, Palazzo L, Perina D, Sabljić I, Žaja R, Colby T, Pleše B, Halasz M, Jankevicius G, Bucca G, Ahel M, Matić I, Ćetković H, Luić M, Mikoč A, Ahel I.

J Biol Chem. 2016 Oct 28;291(44):23175-23187. Epub 2016 Sep 15.


Serine is a new target residue for endogenous ADP-ribosylation on histones.

Leidecker O, Bonfiglio JJ, Colby T, Zhang Q, Atanassov I, Zaja R, Palazzo L, Stockum A, Ahel I, Matic I.

Nat Chem Biol. 2016 Dec;12(12):998-1000. doi: 10.1038/nchembio.2180. Epub 2016 Oct 10.


The Value of Biomarkers as Predictors of Outcome in Patients with Rheumatoid Arthritis-Associated Usual Interstitial Pneumonia.

Lee YS, Kim HC, Lee BY, Lee CK, Kim MY, Jang SJ, Lee HS, Moon J, Colby TV, Kim DS.

Sarcoidosis Vasc Diffuse Lung Dis. 2016 Oct 7;33(3):216-223.


Role of fibrogenesis of gastroesophageal reflux and microaspiration in a patient with 12 years of radiologic follow-up.

Piciucchi S, Tomassetti S, Colby TV, Poletti V.

Hum Pathol. 2017 Jan;59:152-153. doi: 10.1016/j.humpath.2016.06.025. Epub 2016 Oct 5. No abstract available.


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