Plant Omics

Hajime Ohyanagi (Edited By) Dr. Hajime Ohyanagi is the director of JCRAC Data Center at National Center for Global Health and Medicine, Japan. He has received a BSc and a MS from University of Tokyo and PhD from SOKENDAI (The Graduate University for Advanced Studies). He has been working on plant omics (genomics, transcriptomics, and proteomics) and plant domestication. His current project is focusing on the molecular evolution of human pathogenic virus, and the general clinical bioinformatics. Eiji Yamamoto (Edited By) Dr. Eiji Yamamoto received a BSc from Osaka Prefecture University, Japan, and MSc and PhD degrees in agriculture from Nagoya University, Japan. He worked as a Researcher at National Agriculture and Food Research Organization, Japan and at Kazusa DNA Research Institute, Japan before recruited as a Project Lecturer at Meiji University, Japan. His research interests include genetics and genomics of crop plants such as genome-wide association study and genomic selection. Currently he is working on application of advanced genetics and genomics to practical plant breeding. Ai Kitazumi (Edited By) Dr. Ai Kitazumi is a research associate of computational biology for the De los Reyes laboratory at Texas Tech University. She has received a BA from College of the Atlantic, a MS from University of Maine and PhD from Texas Tech University. Her current research is addressing the genomic basis of transgressive segregation in plants by combining genomics, transcriptome, methylome, and prediction of recombination sites and chromatin confirmation. Kentaro Yano (Edited By) Dr. Kentaro Yano is a professor in the School of Agriculture at Meiji University, Japan. After receiving a PhD degree from Graduate School of Agriculture, Kyoto University, he has been working on big data integration to advance the plant omics research. His group has developed knowledge-based databases (e.g., TOMATOMICS, PODC) that integrates high-quality expression data from re-analysis of public datasets and the literature curated information on genes in crops and model plants through natural language processing.

Chapter 1: Plant Genomics. Masalu Bamba, Kenta Shirasawa, Sachiko Isobe, Nadia Kamal, Klaus Mayer and Shusei Sato Chapter 2: Plant Transcriptomics: Data-driven Global Approach to Understand Cellular Processes and their Regulation in Model and Non-Model Plants. Ai Kitazumi, Isaiah C.M. Pabuayon, Kevin R. Cushman, Kentaro Yano and Benildo G. de los Reyes Chapter 3: Plant Proteomics. Setsuko Komatsu and Ghazala Mustafa Chapter 4: Plant Metabolomics: The Great Potential of Plant Metabolomics in Big Data Biology. Miyako Kusano and Atsushi Fukushima Chapter 5: Plant Phenomics. Wei Guo and Jiangsan Zhao Chapter 6: Plant Non-coding Transcriptomics: Overview of lncRNAs in Abiotic Stress Responses. Akihiro Matsui and Motoaki Seki Chapter 7: Plant Epigenomics. Taiko Kim To and Jong-Myong Kim Chapter 8: Plant Organellar Omics. Masatake Kanai, Kentaro Tamura, Katarzyna Tarnawska-Glatt, Shino Goto-Yamada, Kenji Yamada and Shoji Mano Chapter 9: Plant Cis-elements and Transcription Factors. Chi-Nga Chow, Kuan-Chieh Tseng and Wen-Chi Chang Chapter 10: Plant Gene Expression Network.Miyu Asari, Ai Kitazumi, Eiji Nambara, Benildo G. de los Reyes and Kentaro Yano Chapter 11: Plant Hormones: Gene Family Organization and Homeolog Interactions of Genes for Gibberellin Metabolism and Signaling in Allotetraploid Brassica napus. Eiji Nambara, Dawei Yan, Jing Wen, Arjun Sharma, Frederik Nguyen, Ange Yan, Karin Uruma and Kentaro Yano Chapter 12: Plant–Pathogen Interaction: New Era of Plant–Pathogen Interaction Studies: “Omics” Perspectives. Shu’an Zheng and Ryohei Terauchi Chapter 13: Plant GWAS. Matthew Shenton Chapter 14: Plant Genomic Selection: a Concept that uses genomics data in plant breeding. Eiji Yamamoto Chapter 15: Plant Genome Editing. Naoki Wada, Yuriko Osakabe and Keishi Osakabe Chapter 16: Introduction of Deep Learning Approaches in Plant Omics Research. Eli Kaminuma Chapter 17: Deep Learning on Images and Genetic Sequences in Plants: Classifications and Regressions. Kanae Masuda and Takashi Akagi Chapter 18: Deep Learning in Plant Omics: Object Detection and Image Segmentation. Wei Guo and Akshay L. Chandra Chapter 19: Plant Experimental Resources. Masatomo Kobayashi Chapter 20: Plant Omics Databases: an Online Resource Guide. Feng Li, Yingtian Deng, Eiji Yamamoto and Zhenya Liu