Yokoi K, Tsubota T, Sun J, Joraku A, Sezutsu H, Bono H
bioRxiv 805978 Oct 2019
The silkworm Bombyx mori has long been used in the silk industry and utilized in studies of physiology, genetics, molecular biology, and pathology. We recently reported high quality reference genome data for B. mori. In the present study, we const...
Katayama T , Kawashima S , Micklem G , Kawano S , Kim J , Kocbek S , Okamoto S , Wang Y , Wu H , Yamaguchi A , Yamamoto Y , Antezana E , Aoki-Kinoshita KF , Arakawa K , Banno M , Baran J , Bolleman JT , Bonnal RJ , Bono H , Fernández-Breis JT , Buels R , Campbell MP , Chiba H , Cock PJA , Cohen KB , Dumontier M , Fujisawa T , Fujiwara T , Garcia L , Gaudet P , Hattori E , Hoehndorf R , Itaya K , Ito M , Jamieson D , Jupp S , Juty N , Kalderimis A , Kato F , Kawaji H , Kawashima T , Kinjo AR , Komiyama Y , Kotera M , Kushida T , Malone J , Matsubara M , Mizuno S , Mizutani S , Mori H , Moriya Y , Murakami K , Nakazato T , Nishide H , Nishimura Y , Ogishima S , Ohta T , Okuda S , Ono H , Perez-Riverol Y , Shinmachi D , Splendiani A , Strozzi F , Suzuki S , Takehara J , Thompson M , Tokimatsu T , Uchiyama I , Verspoor K , Wilkinson MD , Wimalaratne S , Yamada I , Yamamoto N , Yarimizu M , Kawamoto S , Takagi T
F1000Research Sep 2019 [Refereed]
Publishing databases in the Resource Description Framework (RDF) model is becoming widely accepted to maximize the syntactic and semantic interoperability of open data in life sciences. Here we report advancements made in the 6th and 7th annual Bi...
Ohno H, Sakamoto T, Okochi R, Nishiko M, Sasaki S, Bono H, Tabunoki H, Iwabuchi K
Developmental Biology Sep 2019 [Refereed]
Copidosoma floridanum is a polyembryonic, caste-forming, wasp species. The ratio of investment in different castes changes with environmental stressors (e.g. multi-parasitism with competitors). The vasa gene was first identified in Drosophila mela...
Nojima Y, Bono H, Yokoyama T, Iwabuchi K, Sato R, Arai K, Tabunoki H
Scientific Reports 9 14693 Oct 2019 [Refereed]
Perhaps, oxidative stress progresses pupation in some Lepidopteran insects; however, the reasons for this remain obscure. In our previous study, we clarified Bombyx mori SOD1 (BmSOD1) and B. mori SOD2 (BmSOD2) proteins respond in common to ultravi...
Ramilowski J , Yip CW , Agrawal S , Chang J , Ciani Y , Kulakovskiy IV , Mendez M , Ooi JLC , Ouyang JF , Parkinson N , Petri A , Roos L , Severin J , Yasuzawa K , Abugessaisa I , Akalin A , Antonov I , Arner E , Bonetti A , Bono H , Borsari B , Brombacher F , Cannistraci CV , Cardenas R , Cardon M , Chang H , Dostie J , Ducoli L , Favorov A , Fort A , Garrido D , Gil N , Gimenez J , Guler R , Handoko L , Harshbarger J , Hasegawa A , Hasegawa Y , Hashimoto K , Hayatsu N , Heutink P , Hirose T , Imada EL , Itoh M , Kaczkowski B , Kanhere A , Kawabata E , Kawaji H , Kawashima T , Kelly T , Kojima M , Kondo N , Koseki H , Kouno T , Kratz A , Kurowska-Stolarska M , Kwon ATJ , Leek J , Lennartsson A , Lizio M , Lopez F , Luginbühl J , Maeda S , Makeev V , Marchionni L , Medvedeva YA , Minoda A , Müller F , Aguirre MM , Murata M , Nishiyori H , Nitta K , Noguchi S , Noro Y , Nurtdinov R , Okazaki Y , Orlando V , Paquette D , Parr C , Rackham OJ , Rizzu P , Sanchez DF , Sandelin A , Sanjana P , Semple CA , Sharma H , Shibayama Y , Sivaraman D , Suzuki T , Szumowski S , Tagami M , Taylor MS , Terao C , Thodberg M , Thongjuea S , Tripathi V , Ulitsky I , Verardo R , Vorontsov I , Yamamoto C , Young RS , Baillie JK , Forrest AR , Guigó R , Hoffman MM , Hon CC , Kasukawa T , Kauppinen S , Kere J , Lenhard B , Schneider C , Suzuki H , Yagi K , de Hoon M , Shin JW , Carninci P , FANTOM consortium
bioRxiv 700864 Jul 2019
Long non-coding RNAs (lncRNAs) constitute the majority of transcripts in mammalian genomes and yet, their functions remain largely unknown. We systematically suppressed 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morpho...
Gene expression data have been archived as microarray and RNA-seq data in two public databases, Gene Expression Omnibus (GEO) and ArrayExpress (AE). In 2018, DNA DataBank of Japan started similar repository called Genomic Expression Archive (GEA)....
Kobayashi Y, Nojima Y, Sakamoto T, Iwabuchi K, Nakazato T, Bono H, Toyoda A, Fujiyama A, Kanost MR, Tabunoki H
Scientific Reports 9(1) 2170 Feb 2019 [Refereed]
Insects are well adapted to changing environmental conditions. They have unique systems for eliminating reactive oxygen species (ROS). Superoxide dismutase (SOD) is a key enzyme that plays a primary role in removing ROS. Bombyx mori is a lepidopte...
The possibility that anesthesia during cancer surgery may affect cancer recurrence, metastasis, and patient prognosis has become one of the most important topic of interest in cancer treatment. For example, the volatile anesthetic isoflurane was r...
A line of studies strongly suggest that the intravenous anesthetic, propofol, suppresses mitochondrial oxygen metabolism. It is also indicated that propofol induces the cell death in a reactive oxygen species (ROS)-dependent manner. Because hypoxi...
Molecular Targeted Therapy of Lung Cancer 97-115 Jan 2017 [Invited]
Improvement of next-generation sequencing (NGS) has revealed novel driver genes and new therapeutic targets for cancer patients. We summarize here the history of NGS development, current situation of typical analysis pipeline utilizing NGS – espec...
Basement membranes support proliferation, survival, and differentiation of epithelial/parenchymal cells through interaction with cell membrane receptors. Laminins, which have a heterotrimeric structure, are the major class of basement membrane gly...
RefEx: Dataset for Reference Gene Expression
Hiromasa Ono, Hidemasa Bono
Practical Guide to Life Science Databases in press [Invited]
Following
