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Compound-protein Interaction Prediction with End-to-end Learning of Neural Networks for Graphs and Sequences.

Tsubaki M, Tomii K, Sese J.

Bioinformatics. 2018 Jul 6. doi: 10.1093/bioinformatics/bty535. [Epub ahead of print]


Clinical Characteristics and Prognosis of Patients With Advanced Non-Small-cell Lung Cancer Who Are Ineligible for Clinical Trials.

Kawachi H, Fujimoto D, Morimoto T, Ito M, Teraoka S, Sato Y, Nagata K, Nakagawa A, Otsuka K, Tomii K.

Clin Lung Cancer. 2018 May 26. pii: S1525-7304(18)30134-7. doi: 10.1016/j.cllc.2018.05.014. [Epub ahead of print]


Chemoradiotherapy in Elderly Patients With Non-Small-Cell Lung Cancer: Long-Term Follow-Up of a Randomized Trial (JCOG0301).

Atagi S, Mizusawa J, Ishikura S, Takahashi T, Okamoto H, Tanaka H, Goto K, Nakagawa K, Harada M, Takeda Y, Nogami N, Fujita Y, Kasai T, Kishi K, Sawa T, Takeda K, Tomii K, Satouchi M, Seto T, Ohe Y.

Clin Lung Cancer. 2018 May 5. pii: S1525-7304(18)30100-1. doi: 10.1016/j.cllc.2018.04.018. [Epub ahead of print]


Erratum: AIG1 affects in vitro and in vivo virulence in clinical isolates of Entamoeba histolytica.

Nakada-Tsukui K, Sekizuka T, Sato-Ebine E, Escueta-de Cadiz A, Ji DD, Tomii K, Kuroda M, Nozaki T.

PLoS Pathog. 2018 May 31;14(5):e1007091. doi: 10.1371/journal.ppat.1007091. eCollection 2018 May.


Programmed Cell Death Ligand 1 Expression in Non-Small-cell Lung Cancer Patients With Interstitial Lung Disease: A Matched Case-control Study.

Fujimoto D, Sato Y, Morimoto T, Uehara K, Ito M, Otsuka K, Nagata K, Sakanoue I, Hamakawa H, Nakagawa A, Takahashi Y, Imai Y, Tomii K.

Clin Lung Cancer. 2018 May 5. pii: S1525-7304(18)30094-9. doi: 10.1016/j.cllc.2018.04.012. [Epub ahead of print]


The clinical practice of high-flow nasal cannula oxygen therapy in adults: A Japanese cross-sectional multicenter survey.

Ito J, Nagata K, Sato S, Shiraki A, Nishimura N, Izumi S, Tachikawa R, Morimoto T, Tomii K.

Respir Investig. 2018 May;56(3):249-257. doi: 10.1016/j.resinv.2018.02.002. Epub 2018 Mar 10.


Successful oral desensitization with osimertinib following osimertinib-induced fever and hepatotoxicity: a case report.

Hirabayashi R, Fujimoto D, Satsuma Y, Hirabatake M, Tomii K.

Invest New Drugs. 2018 May 2. doi: 10.1007/s10637-018-0608-7. [Epub ahead of print]


Efficacy and safety of nivolumab in previously treated patients with non-small cell lung cancer: A multicenter retrospective cohort study.

Fujimoto D, Yoshioka H, Kataoka Y, Morimoto T, Kim YH, Tomii K, Ishida T, Hirabayashi M, Hara S, Ishitoko M, Fukuda Y, Hwang MH, Sakai N, Fukui M, Nakaji H, Morita M, Mio T, Yasuda T, Sugita T, Hirai T.

Lung Cancer. 2018 May;119:14-20. doi: 10.1016/j.lungcan.2018.02.017. Epub 2018 Mar 2.


Clinical spectrum and prognostic factors of possible UIP pattern on high-resolution CT in patients who underwent surgical lung biopsy.

Kondoh Y, Taniguchi H, Kataoka K, Furukawa T, Shintani A, Fujisawa T, Suda T, Arita M, Baba T, Ichikado K, Inoue Y, Kishi K, Kishaba T, Nishiyama O, Ogura T, Tomii K, Homma S.

PLoS One. 2018 Mar 28;13(3):e0193608. doi: 10.1371/journal.pone.0193608. eCollection 2018.


AIG1 affects in vitro and in vivo virulence in clinical isolates of Entamoeba histolytica.

Nakada-Tsukui K, Sekizuka T, Sato-Ebine E, Escueta-de Cadiz A, Ji DD, Tomii K, Kuroda M, Nozaki T.

PLoS Pathog. 2018 Mar 19;14(3):e1006882. doi: 10.1371/journal.ppat.1006882. eCollection 2018 Mar. Erratum in: PLoS Pathog. 2018 May 31;14 (5):e1007091.


Identification of new abscisic acid receptor agonists using a wheat cell-free based drug screening system.

Nemoto K, Kagawa M, Nozawa A, Hasegawa Y, Hayashi M, Imai K, Tomii K, Sawasaki T.

Sci Rep. 2018 Mar 9;8(1):4268. doi: 10.1038/s41598-018-22538-9.


Parallelization of MAFFT for large-scale multiple sequence alignments.

Nakamura T, Yamada KD, Tomii K, Katoh K.

Bioinformatics. 2018 Jul 15;34(14):2490-2492. doi: 10.1093/bioinformatics/bty121.


Reduced Tumour Proportion Scores for Programmed Cell Death Ligand 1 in Stored Paraffin Tissue Sections.

Sato Y, Fujimoto D, Uehara K, Kawachi H, Nagata K, Nakagawa A, Otsuka K, Sakanoue I, Hamakawa H, Takahashi Y, Imai Y, Tomii K.

Anticancer Res. 2018 Mar;38(3):1401-1405.


What Is the Impact of Mildly Altered Consciousness on Acute Hypoxemic Respiratory Failure with Non-invasive Ventilation?

Kogo M, Nagata K, Morimoto T, Ito J, Fujimoto D, Nakagawa A, Otsuka K, Tomii K.

Intern Med. 2018 Jun 15;57(12):1689-1695. doi: 10.2169/internalmedicine.9355-17. Epub 2018 Feb 9.


Exacerbation of autoimmune hemolytic anemia induced by the first dose of programmed death-1 inhibitor pembrolizumab: a case report.

Ogawa K, Ito J, Fujimoto D, Morita M, Yoshizumi Y, Ariyoshi K, Tomii K, Katakami N.

Invest New Drugs. 2018 Jun;36(3):509-512. doi: 10.1007/s10637-018-0561-5. Epub 2018 Jan 16.


Domiciliary High-Flow Nasal Cannula Oxygen Therapy for Patients with Stable Hypercapnic Chronic Obstructive Pulmonary Disease. A Multicenter Randomized Crossover Trial.

Nagata K, Kikuchi T, Horie T, Shiraki A, Kitajima T, Kadowaki T, Tokioka F, Chohnabayashi N, Watanabe A, Sato S, Tomii K.

Ann Am Thorac Soc. 2018 Apr;15(4):432-439. doi: 10.1513/AnnalsATS.201706-425OC.


Carcinoembryonic Antigen as a Predictive Biomarker of Response to Nivolumab in Non-small Cell Lung Cancer.

Kataoka Y, Hirano K, Narabayashi T, Hara S, Fujimoto D, Tanaka T, Ebi N, Tomii K, Yoshioka H.

Anticancer Res. 2018 Jan;38(1):559-563.


Predictive Performance of Four Programmed Cell Death Ligand 1 Assay Systems on Nivolumab Response in Previously Treated Patients with Non-Small Cell Lung Cancer.

Fujimoto D, Sato Y, Uehara K, Ishida K, Fukuoka J, Morimoto T, Kawachi H, Mori R, Ito M, Teraoka S, Nagata K, Nakagawa A, Otsuka K, Imai Y, Tomii K.

J Thorac Oncol. 2018 Mar;13(3):377-386. doi: 10.1016/j.jtho.2017.11.123. Epub 2017 Dec 9.


Concordance between the response evaluation criteria in solid tumors version 1.1 and the immune-related response criteria in patients with non-small cell lung cancer treated with nivolumab: a multicenter retrospective cohort study.

Kataoka Y, Hirano K, Narabayashi T, Hara S, Fujimoto D, Tanaka T, Ebi N, Tomii K, Yoshioka H.

Cancer Chemother Pharmacol. 2018 Feb;81(2):333-337. doi: 10.1007/s00280-017-3498-z. Epub 2017 Dec 11.


Identification of patterns of factors preceding severe or life-threatening asthma exacerbations in a nationwide study.

Tanaka H, Nakatani E, Fukutomi Y, Sekiya K, Kaneda H, Iikura M, Yoshida M, Takahashi K, Tomii K, Nishikawa M, Kaneko N, Sugino Y, Shinkai M, Ueda T, Tanikawa Y, Shirai T, Hirabayashi M, Aoki T, Kato T, Iizuka K, Fujii M, Taniguchi M.

Allergy. 2018 May;73(5):1110-1118. doi: 10.1111/all.13374. Epub 2017 Dec 19.


Template-based quaternary structure prediction of proteins using enhanced profile-profile alignments.

Nakamura T, Oda T, Fukasawa Y, Tomii K.

Proteins. 2018 Mar;86 Suppl 1:274-282. doi: 10.1002/prot.25432. Epub 2017 Dec 5.


Tyrosine phosphorylation of the GARU E3 ubiquitin ligase promotes gibberellin signalling by preventing GID1 degradation.

Nemoto K, Ramadan A, Arimura GI, Imai K, Tomii K, Shinozaki K, Sawasaki T.

Nat Commun. 2017 Oct 17;8(1):1004. doi: 10.1038/s41467-017-01005-5.


Early Immune-Related Adverse Events and Association with Outcome in Advanced Non-Small Cell Lung Cancer Patients Treated with Nivolumab: A Prospective Cohort Study.

Teraoka S, Fujimoto D, Morimoto T, Kawachi H, Ito M, Sato Y, Nagata K, Nakagawa A, Otsuka K, Uehara K, Imai Y, Ishida K, Fukuoka J, Tomii K.

J Thorac Oncol. 2017 Dec;12(12):1798-1805. doi: 10.1016/j.jtho.2017.08.022. Epub 2017 Sep 20.


KRAS mutation-positive mucinous adenocarcinoma originating in the thymus.

Sakanoue I, Hamakawa H, Fujimoto D, Imai Y, Minami K, Tomii K, Takahashi Y.

J Thorac Dis. 2017 Aug;9(8):E694-E697. doi: 10.21037/jtd.2017.07.11.


Successful Treatment of Herpes Simplex Virus (HSV)-1-associated Hemophagocytic Lymphohistiocytosis (HLH) with Acyclovir: A Case Report and Literature Review.

Yabushita T, Yoshioka S, Koba Y, Ono Y, Hiramoto N, Tabata S, Itou M, Shimizu N, Tomii K, Ishikawa T.

Intern Med. 2017 Nov 1;56(21):2919-2923. doi: 10.2169/internalmedicine.8490-16. Epub 2017 Sep 15.


Rituximab for nivolumab plus ipilimumab-induced encephalitis in a small-cell lung cancer patient.

Ito M, Fujiwara S, Fujimoto D, Mori R, Yoshimura H, Hata A, Kohara N, Tomii K.

Ann Oncol. 2017 Sep 1;28(9):2318-2319. doi: 10.1093/annonc/mdx252. No abstract available.


Alteration of PD-L1 expression and its prognostic impact after concurrent chemoradiation therapy in non-small cell lung cancer patients.

Fujimoto D, Uehara K, Sato Y, Sakanoue I, Ito M, Teraoka S, Nagata K, Nakagawa A, Kosaka Y, Otsuka K, Imai Y, Hamakawa H, Takahashi Y, Kokubo M, Tomii K.

Sci Rep. 2017 Sep 12;7(1):11373. doi: 10.1038/s41598-017-11949-9.


Designing better diffracting crystals of biotin carboxyl carrier protein from Pyrococcus horikoshii by a mutation based on the crystal-packing propensity of amino acids.

Yamada KD, Kunishima N, Matsuura Y, Nakai K, Naitow H, Fukasawa Y, Tomii K.

Acta Crystallogr D Struct Biol. 2017 Sep 1;73(Pt 9):757-766. doi: 10.1107/S2059798317010932. Epub 2017 Aug 15.


A pilot trial of nivolumab treatment for advanced non-small cell lung cancer patients with mild idiopathic interstitial pneumonia.

Fujimoto D, Morimoto T, Ito J, Sato Y, Ito M, Teraoka S, Otsuka K, Nagata K, Nakagawa A, Tomii K.

Lung Cancer. 2017 Sep;111:1-5. doi: 10.1016/j.lungcan.2017.06.008. Epub 2017 Jun 17.


Hinge-Deficient IgG1 Fc Fusion: Application to Human Lactoferrin.

Shiga Y, Murata D, Sugimoto A, Oshima Y, Tada M, Ishii-Watabe A, Imai K, Tomii K, Takeuchi T, Kagaya S, Sato A.

Mol Pharm. 2017 Sep 5;14(9):3025-3035. doi: 10.1021/acs.molpharmaceut.7b00221. Epub 2017 Aug 18.


Enteral Nutrition During Noninvasive Ventilation: We Should Go Deeper in the Investigation-Reply.

Kogo M, Nagata K, Morimoto T, Ito J, Sato Y, Teraoka S, Fujimoto D, Nakagawa A, Otsuka K, Tomii K.

Respir Care. 2017 Aug;62(8):1119-1120. doi: 10.4187/respcare.05684. No abstract available.


Natural history and clinical characteristics of multiple pulmonary nodules with ground glass opacity.

Sato Y, Fujimoto D, Morimoto T, Uehara K, Nagata K, Sakanoue I, Hamakawa H, Takahashi Y, Imai Y, Tomii K.

Respirology. 2017 Nov;22(8):1615-1621. doi: 10.1111/resp.13089. Epub 2017 Jun 13.


Bevacizumab for ramucirumab refractory malignant pleural effusion in non-small cell lung cancer: a case report and review of the literature.

Mori R, Fujimoto D, Ito M, Tomii K.

Oncotarget. 2017 Jul 18;8(29):48521-48524. doi: 10.18632/oncotarget.17952. Review.


Comparison of Different Disease-Specific Health-Related Quality of Life Measurements in Patients with Long-Term Noninvasive Ventilation.

Oga T, Taniguchi H, Kita H, Tsuboi T, Tomii K, Ando M, Kojima E, Tomioka H, Taguchi Y, Kaji Y, Maekura R, Hiraga T, Sakai N, Kimura T, Mishima M, Windisch W, Chin K.

Can Respir J. 2017;2017:8295079. doi: 10.1155/2017/8295079. Epub 2017 May 15.


Simple adjustment of the sequence weight algorithm remarkably enhances PSI-BLAST performance.

Oda T, Lim K, Tomii K.

BMC Bioinformatics. 2017 Jun 2;18(1):288. doi: 10.1186/s12859-017-1686-9.


Aprepitant for refractory nivolumab-induced pruritus.

Ito J, Fujimoto D, Nakamura A, Nagano T, Uehara K, Imai Y, Tomii K.

Lung Cancer. 2017 Jul;109:58-61. doi: 10.1016/j.lungcan.2017.04.020. Epub 2017 Apr 27.


Biliary Pneumonia due to the Presence of a Bronchobiliary Fistula.

Matsumoto T, Otsuka K, Kaihara S, Tomii K.

Intern Med. 2017;56(11):1451-1452. doi: 10.2169/internalmedicine.56.8066. Epub 2017 Jun 1. No abstract available.


Thoracic aortitis and aortic dissection following pegfilgrastim administration.

Sato Y, Kaji S, Ueda H, Tomii K.

Eur J Cardiothorac Surg. 2017 Nov 1;52(5):993-994. doi: 10.1093/ejcts/ezx165.


Origin and Evolutionary Alteration of the Mitochondrial Import System in Eukaryotic Lineages.

Fukasawa Y, Oda T, Tomii K, Imai K.

Mol Biol Evol. 2017 Jul 1;34(7):1574-1586. doi: 10.1093/molbev/msx096.


Prior radiotherapy does not predict nivolumab response in non-small-cell lung cancer: a retrospective cohort study.

Kataoka Y, Ebi N, Fujimoto D, Hara S, Hirano K, Narabayashi T, Tanaka T, Tomii K, Yoshioka H.

Ann Oncol. 2017 Jun 1;28(6):1402. doi: 10.1093/annonc/mdx114. No abstract available.


IL4Rα and ADAM33 as genetic markers in asthma exacerbations and type-2 inflammatory endotype.

Sunadome H, Matsumoto H, Petrova G, Kanemitsu Y, Tohda Y, Horiguchi T, Kita H, Kuwabara K, Tomii K, Otsuka K, Fujimura M, Ohkura N, Tomita K, Yokoyama A, Ohnishi H, Nakano Y, Oguma T, Hozawa S, Nagasaki T, Ito I, Oguma T, Inoue H, Tajiri T, Iwata T, Izuhara Y, Ono J, Ohta S, Hirota T, Tamari M, Yokoyama T, Niimi A, Izuhara K, Mishima M.

Clin Exp Allergy. 2017 Aug;47(8):998-1006. doi: 10.1111/cea.12927. Epub 2017 Apr 21.


Validation of the Japanese Severe Respiratory Insufficiency Questionnaire in hypercapnic patients with noninvasive ventilation.

Oga T, Taniguchi H, Kita H, Tsuboi T, Tomii K, Ando M, Kojima E, Tomioka H, Taguchi Y, Kaji Y, Maekura R, Hiraga T, Sakai N, Kimura T, Mishima M, Windisch W, Chin K.

Respir Investig. 2017 Mar;55(2):166-172. doi: 10.1016/j.resinv.2016.12.003. Epub 2017 Feb 6.


Comparison of clinical and pathological features of lung lesions of systemic IgG4-related disease and idiopathic multicentric Castleman's disease.

Terasaki Y, Ikushima S, Matsui S, Hebisawa A, Ichimura Y, Izumi S, Ujita M, Arita M, Tomii K, Komase Y, Owan I, Kawamura T, Matsuzawa Y, Murakami M, Ishimoto H, Kimura H, Bando M, Nishimoto N, Kawabata Y, Fukuda Y, Ogura T; Tokyo Diffuse Lung Diseases Study Group.

Histopathology. 2017 Jun;70(7):1114-1124. doi: 10.1111/his.13186. Epub 2017 Apr 3.


Pemetrexed-related interstitial lung disease reported from post marketing surveillance (malignant pleural mesothelioma/non-small cell lung cancer).

Tomii K, Kato T, Takahashi M, Noma S, Kobashi Y, Enatsu S, Okubo S, Kobayashi N, Kudoh S.

Jpn J Clin Oncol. 2017 Apr 1;47(4):350-356. doi: 10.1093/jjco/hyx010.


An Atypical Clinical Course of Anti-MDA5 Antibody-positive Interstitial Lung Disease in a Patient with Three Deteriorations in 9 years.

Sato Y, Otsuka K, Tamai K, Ono Y, Hamaguchi Y, Tomii K.

Intern Med. 2017;56(3):341-346. doi: 10.2169/internalmedicine.56.6856. Epub 2017 Feb 1.


Protein sequence-similarity search acceleration using a heuristic algorithm with a sensitive matrix.

Lim K, Yamada KD, Frith MC, Tomii K.

J Struct Funct Genomics. 2016 Dec;17(4):147-154. doi: 10.1007/s10969-016-9210-4. Epub 2017 Jan 12.


Staphylococcus aureus enterotoxin sensitization involvement and its association with the CysLTR1 variant in different asthma phenotypes.

Matsumoto H, Kanemitsu Y, Nagasaki T, Tohda Y, Horiguchi T, Kita H, Kuwabara K, Tomii K, Otsuka K, Fujimura M, Ohkura N, Tomita K, Yokoyama A, Ohnishi H, Nakano Y, Oguma T, Hozawa S, Izuhara Y, Ito I, Oguma T, Inoue H, Tajiri T, Iwata T, Ono J, Ohta S, Hirota T, Kawaguchi T, Tamari M, Yokoyama T, Tabara Y, Matsuda F, Izuhara K, Niimi A, Mishima M.

Ann Allergy Asthma Immunol. 2017 Feb;118(2):197-203. doi: 10.1016/j.anai.2016.11.013. Epub 2016 Dec 27.


The Japanese Respiratory Society Noninvasive Positive Pressure Ventilation (NPPV) Guidelines (second revised edition).

Akashiba T, Ishikawa Y, Ishihara H, Imanaka H, Ohi M, Ochiai R, Kasai T, Kimura K, Kondoh Y, Sakurai S, Shime N, Suzukawa M, Takegami M, Takeda S, Tasaka S, Taniguchi H, Chohnabayashi N, Chin K, Tsuboi T, Tomii K, Narui K, Hasegawa N, Hasegawa R, Ujike Y, Kubo K, Hasegawa Y, Momomura SI, Yamada Y, Yoshida M, Takekawa Y, Tachikawa R, Hamada S, Murase K.

Respir Investig. 2017 Jan;55(1):83-92. doi: 10.1016/j.resinv.2015.11.007. Epub 2016 Nov 9. No abstract available.


Characteristics and Prognostic Impact of Pneumonitis during Systemic Anti-Cancer Therapy in Patients with Advanced Non-Small-Cell Lung Cancer.

Fujimoto D, Kato R, Morimoto T, Shimizu R, Sato Y, Kogo M, Ito J, Teraoka S, Nagata K, Nakagawa A, Otsuka K, Tomii K.

PLoS One. 2016 Dec 22;11(12):e0168465. doi: 10.1371/journal.pone.0168465. eCollection 2016.


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