Bioproductivity Informatics Research Team

Accomplishments

2019

Original Paper

Mochida K, Koda S, Inoue K, Hirayama T, Tanaka S, Nishii R, Melgani F. (2019) Computer vision-based phenotyping for improvement of plant productivity: a machine learning perspective. Gigascience. 8(1)
https://www.ncbi.nlm.nih.gov/pubmed/30520975

2018

Original Paper

Chu HD, Nguyen KH, Watanabe Y, Le DT, Pham, Mochida K, Tran LP. (2018) Identification, Structural Characterization and Gene Expression Analysis of Members of the Nuclear Factor-Y Family in Chickpea (Cicer arietinum L.) under Dehydration and Abscisic Acid Treatments. Int J Mol Sci. 19(11)
https://www.ncbi.nlm.nih.gov/pubmed/30360493

Takahagi K, Inoue K, Mochida K. (2018) Gene Co-expression Network Analysis Suggests the Existence of Transcriptional Modules Containing a High Proportion of Transcriptionally Differentiated Homoeologs in Hexaploid Wheat. Front Plant Sci. 9(9):1163
https://www.ncbi.nlm.nih.gov/pubmed/30135697

Ogita S, Nomura T, Kato Y, Uehara-Yamaguchi Y, Inoue K, Yoshida T, Sakurai T, Shinozaki K, Mochida K. (2018) Transcriptional alterations during proliferation and lignification in Phyllostachys nigra cells. Sci Rep. 8(1):11347
https://www.ncbi.nlm.nih.gov/pubmed/30054534

Kouzai Y, Noutoshi Y, Inoue K, Shimizu M, Onda Y, Mochida K. (2018) Benzothiadiazole, a plant defense inducer, negatively regulates sheath blight resistance in Brachypodium distachyon. Sci Rep. 8(1):17358
https://www.ncbi.nlm.nih.gov/pubmed/30478396

Tamura K, Yoshida K, Hiraoka Y, Sakaguchi D, Chikugo A, Mochida K, Kojoma M, Mitsuda N, Saito K, Muranaka T, Seki H. (2018) The Basic Helix-Loop-Helix Transcription Factor GubHLH3 Positively Regulates Soyasaponin Biosynthetic Genes in Glycyrrhiza uralensis. Plant Cell Physiol. 59(4):783-796
https://www.ncbi.nlm.nih.gov/pubmed/29648666

Onda Y, Takahagi K, Shimizu M, Inoue K, Mochida K. (2018) Multiplex PCR Targeted Amplicon Sequencing (MTA-Seq): Simple, Flexible, and Versatile SNP Genotyping by Highly Multiplexed PCR Amplicon Sequencing. Front Plant Sci. 9(201):201
https://www.ncbi.nlm.nih.gov/pubmed/29628929

Takahagi K, Inoue K, Shimizu M, Uehara-Yamaguchi Y, Onda Y, Mochida K. (2018) Homoeolog-specific activation of genes for heat acclimation in the allopolyploid grass Brachypodium hybridum. Gigascience. 7(4)
https://www.ncbi.nlm.nih.gov/pubmed/29697823

Review Paper

Mochida K, Koda S, Inoue K, Nishii R. (2018) Statistical and Machine Learning Approaches to Predict Gene Regulatory Networks From Transcriptome Datasets. Front Plant Sci. 9(9):1770
https://www.ncbi.nlm.nih.gov/pubmed/30555503

2017

Original Paper

Koda S, Onda Y, Matsui H, Takahagi K, Yamaguchi-Uehara Y, Shimizu M, Inoue K, Yoshida T, Sakurai T, Honda H, Eguchi S, Nishii R, Mochida K. (2017) Diurnal Transcriptome and Gene Network Represented through Sparse Modeling in Brachypodium distachyon. Front Plant Sci. 8(8):2055
https://www.ncbi.nlm.nih.gov/pubmed/29234348

Ren Y, Sekine-Kondo E, Shibata R, Kato-Itoh M, Umino A, Yanagida A, Satoh M, Inoue K, Yamaguchi T, Mochida K, Nakae S, Van Kaer L, Iwabuchi K, Nakauchi H, Watarai H. (2017) A Novel Mouse Model of iNKT Cell-deficiency Generated by CRISPR/Cas9 Reveals a Pathogenic Role of iNKT Cells in Metabolic Disease. Sci Rep. 7(12765)
https://www.ncbi.nlm.nih.gov/pubmed/28986544

Mochida K, Shinozaki K. (2017) Information Resources for Functional Genomics Studies in Brachypodium distachyon. Methods Mol Biol. 1667:87-99
https://www.ncbi.nlm.nih.gov/pubmed/29039006

Kouzai Y, Kimura M, Watanabe M, Kusunoki K, Osaka D, Suzuki T, Matsui H, Yamamoto M, Ichinose Y, Toyoda K, Matsuura T, Mori IC, Hirayama T, Minami E, Nishizawa Y, Inoue K, Onda Y, Mochida K, Noutoshi Y. (2017) Salicylic acidā€dependent immunity contributes to resistance against Rhizoctonia solani, a necrotrophic fungal agent of sheath blight, in rice and Brachypodium distachyon. New Phytol. 217(2):771-783
https://www.ncbi.nlm.nih.gov/pubmed/29048113

Sano N, Kim JS, Onda Y, Nomura T, Mochida K, Okamoto M, Seo M. (2017) RNA-Seq using bulked recombinant inbred line populations uncovers the importance of brassinosteroid for seed longevity after priming treatments. Sci Rep. 7(8095)
https://www.ncbi.nlm.nih.gov/pubmed/28808238

Nasr Esfahani M, Inoue K, Chu HD, Nguyen KH, Van Ha C, Watanabe Y, Burritt DJ, Herrera-Estrella L, Mochida K, Tran LP. (2017) Comparative transcriptome analysis of nodules of two Mesorhizobium-chickpea associations with differential symbiotic efficiency under phosphate deficiency. Plant J.91(5):911-926
https://www.ncbi.nlm.nih.gov/pubmed/28628240

2016

Original Paper

Mochida K, Sakurai T, Seki H, Yoshida T, Takahagi K, Sawai S, Uchiyama H, Muranaka T, Saito K. (2016) Draft genome assembly and annotation of Glycyrrhiza uralensis, a medicinal legume. Plant J. 89(2):181-194
https://www.ncbi.nlm.nih.gov/pubmed/27775193

Takahagi K, Uehara-Yamaguchi Y, Yoshida T, Sakurai T, Shinozaki K, Mochida K, Saisho D. (2016) Analysis of single nucleotide polymorphisms based on RNA sequencing data of diverse bio-geographical accessions in barley. Sci Rep. 6(6):33199
https://www.ncbi.nlm.nih.gov/pubmed/27616653

Utsumi Y, Tanaka M, Kurotani A, Yoshida T, Mochida K, Matsui A, Ishitani M, Sraphet S, Whankaew S, Asvarak T, Narangajavana J, Triwitayakorn K, Sakurai T, Seki M. (2016) Cassava (Manihot esculenta) transcriptome analysis in response to infection by the fungus Colletotrichum gloeosporioides using an oligonucleotide-DNA microarray. J Plant Res. 129(4):771-726
https://www.ncbi.nlm.nih.gov/pubmed/27138000

Kouzai Y, Kimura M, Yamanaka Y, Watanabe M, Matsui H, Yamamoto M, Ichinose Y, Toyoda K, Onda Y, Mochida K, Noutoshi Y. (2016) Expression profiling of marker genes responsive to the defence-associated phytohormones salicylic acid, jasmonic acid and ethylene in Brachypodium distachyon. BMC Plant Biol. 16(16):59
https://www.ncbi.nlm.nih.gov/pubmed/6935959

Review Paper

Onda Y, Mochida K. (2016) Exploring Genetic Diversity in Plants Using High-Throughput Sequencing Techniques. Curr Genomics. 17(4):358-367
https://www.ncbi.nlm.nih.gov/pubmed/27499684

2015

Original Paper

Onda, Y., Hashimoto, K., Yoshida, T., Sakurai, T., Sawada, Y., Hirai, M. Y., Toyooka, K., Mochida, K. and Shinozaki, K. (2015a) Determination of growth stages and metabolic profiles in Brachypodium distachyon for comparison of developmental context with Triticeae crops. Proc Biol Sci, 282, 1811.
http://www.ncbi.nlm.nih.gov/pubmed/26156770

Onda Y, Mochida K, Yoshida T, Sakurai T, Seymour RS, Umekawa Y, Pirintsos SA, Shinozaki K and Ito K (2015) Transcriptome analysis of thermogenic Arum concinnatum reveals the molecular components of floral scent production. Sci Rep., 5, 8753.
http://www.ncbi.nlm.nih.gov/pubmed/25736477

Kakei, Y., Mochida, K., Sakurai, T., Yoshida, T., Shinozaki, K. and Shimada, Y. (2015) Transcriptome analysis of hormone-induced gene expression in Brachypodium distachyon. Sci Rep, 5, 14476.
http://www.ncbi.nlm.nih.gov/pubmed/26419335

Review Paper

Mochida K, Saisho D, Hirayama T. (2015) Crop improvement using life cycle datasets acquired under field conditions. Front Plant Sci. 22, 740.
http://www.ncbi.nlm.nih.gov/pubmed/26442053

Book

Mochida K. and Tran L-S. P. (2015) The Jatropha Genome. Transcription factors in Jatropha in press.

2014

Original Paper

Miyazaki Y, Maruyama Y, Chiba Y, Kobayashi MJ, Joseph B, Shimizu KK, Mochida K, Hiura T, Kon H, Satake A. (2014) Nitrogen as a key regulator of flowering in Fagus crenata: understanding the physiological mechanism of masting by gene expression analysis. Ecol Lett, 17, 1299-1309.
http://www.ncbi.nlm.nih.gov/pubmed/25103959

Chien Van Ha, Maryam Nasr Esfahani, Watanabe Y, Uyen Thi Tran, Sulieman S, Mochida K, Dong Van Nguyen, Tran L-S P (2014) Genome-Wide Identification and Expression Analysis of the CaNAC Family Members in Chickpea during Development, Dehydration and ABA Treatments. Plos One, 9, e114107.
http://www.ncbi.nlm.nih.gov/pubmed/25479253