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Advances in Omics and Bioinformatics Tools for Systems Analyses of Plant Functions

K. Mochida, K. Shinozaki
2011 Plant and Cell Physiology  
Omics and bioinformatics are essential to understanding the molecular systems that underlie various plant functions.  ...  Recent game-changing sequencing technologies have revitalized sequencing approaches in genomics and have produced opportunities for various emerging analytical applications.  ...  Acknowledgments The authors thank Tetsuya Sakurai, Takuhiro Yoshida, Lam-Son Phan Tran and Yuji Sawada of the RIKEN Plant Science Center, and Kei Iida of RIKEN BASE for their valuable suggestions and comments  ... 
doi:10.1093/pcp/pcr153 pmid:22156726 pmcid:PMC3233218 fatcat:5p4m7xlrknflrfbjfb4pwdug4u

Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era

Luca Ambrosino, Chiara Colantuono, Gianfranco Diretto, Alessia Fiore, Maria Luisa Chiusano
2020 Plants  
Integrated multilevel approaches, based on molecular investigations at genomics, transcriptomics, proteomics and metabolomics levels, are now feasible, expanding the opportunities to clarify key molecular  ...  To this aim, bioinformatics has become fundamental for data production, mining and integration, and necessary for extracting valuable information and for comparative efforts, paving the way to the modeling  ...  Acknowledgments: This work is in the frame of the Cost Action FA1106, CA15136 and CA18210, and of the Genopom Pro (PON02_00395_3082360) and HORT (PON02_00395_3215002) Projects (Ministero dell'Istruzione  ... 
doi:10.3390/plants9050591 pmid:32384671 pmcid:PMC7285221 fatcat:oapvn52yhjh6lbuejhd53vygpu

Intriguing Interaction of Bacteriophage-Host Association: An Understanding in the Era of Omics

Krupa M. Parmar, Saurabh L. Gaikwad, Prashant K. Dhakephalkar, Ramesh Kothari, Ravindra Pal Singh
2017 Frontiers in Microbiology  
This review highlights various concepts such as genomics, transcriptomics, proteomics, and metabolomics to infer the phylogenetic affiliation and function of bacteriophages and their impact on diverse  ...  The interplay between bacteriophages and their host has created a significant influence on the biogeochemical cycles, microbial diversity, and bacterial population regulation.  ...  ACKNOWLEDGMENTS The authors are thankful to Agharkar Research Institute, John Innes Center and Saurashtra University for support and encouragement.  ... 
doi:10.3389/fmicb.2017.00559 pmid:28439260 pmcid:PMC5383658 fatcat:rnusv5tteje5tihvlbrjdikk6y

Genomics and Bioinformatics Resources for Crop Improvement

K. Mochida, K. Shinozaki
2010 Plant and Cell Physiology  
A combinatorial approach using multiple omics platforms and integration of their outcomes is now an effective strategy for clarifying molecular systems integral to improving plant productivity.  ...  Recent remarkable innovations in platforms for omics-based research and application development provide crucial resources to promote research in model and applied plant species.  ...  Center for their valuable suggestions and comments.  ... 
doi:10.1093/pcp/pcq027 pmid:20208064 pmcid:PMC2852516 fatcat:7kkmabdhpfer5a6b5b3pp6u4pe

Unlocking Triticeae genomics to sustainably feed the future

K. Mochida, K. Shinozaki
2013 Plant and Cell Physiology  
Innovative approaches and tools such as analysis of next-generation populations, evolutionary genomics and systems approaches with mathematical modeling are new strategies that will help us discover alleles  ...  In this review, we provide an update on genomic tools for use with Triticeae plants and Brachypodium and describe emerging approaches toward crop improvements in Triticeae.  ...  The authors also thank Daisuke Saisho of Okayama University for his valuable comments and discussions on this manuscript. Disclosures The authors have no conflicts of interest to declare.  ... 
doi:10.1093/pcp/pct163 pmid:24204022 pmcid:PMC3856857 fatcat:uuepryp45rhk3etegnzb3sedka

Plant systems biology: insights, advances and challenges

Bhavisha P. Sheth, Vrinda S. Thaker
2014 Planta  
In this review, we discuss the basics of systems biology including the various 'omics' approaches and their integration, the modeling aspects and the tools needed for the plant systems research.  ...  A particular emphasis is given to the recent analytical advances, updated published examples of plant systems biology studies and the future trends.  ...  Acknowledgements The authors would like to thank Centre for Advanced Studies in Plant Biotechnology and Genetic engineering (CPBGe), Govt. of Gujarat and Department of Biosciences, Saurashtra University  ... 
doi:10.1007/s00425-014-2059-5 pmid:24671625 fatcat:5krvjspz65dera6elsq3oznhh4

Web-Based Arabidopsis Functional and Structural Genomics Resources

Yan Lu, Robert L. Last
2008 The Arabidopsis Book  
Web MicroRNA Designer (WMD) http://wmd2.weigelworld.org This site has a web-based tool for design of plasmids that encode artificial microRNAs (amiRNAs), which are useful for targeted gene inactivation  ...  Instead, a subset of Arabidopsis-centric web tools were selected that we and our colleagues find to be useful.  ... 
doi:10.1199/tab.0118 pmid:22303243 pmcid:PMC3243351 fatcat:swsrfjpxszaobflnda7udjizwa

Innovative in Silico Approaches for Characterization of Genes and Proteins

Gh. Rasool Bhat, Itty Sethi, Bilal Rah, Rakesh Kumar, Dil Afroze
2022 Frontiers in Genetics  
Till now several online tools have been developed to analyze the genomic, transcriptomic, proteomics, epigenomics and metabolomics data.  ...  Thus, the tool is helpful in predicting the effect of mutations on splicing signals and can provide data even for better understanding of the intronic mutations that can be further validated experimentally  ...  Despite the fact that ESEfinder is a tool for RNA analysis, it only accepts normal DNA nomenclature (A, C, G, and T, not U).  ... 
doi:10.3389/fgene.2022.865182 pmid:35664302 pmcid:PMC9159363 fatcat:mbz7ci3s25eudn7qmqch5xghci

Web-Queryable Large-Scale Data Sets for Hypothesis Generation in Plant Biology

S. M. Brady, N. J. Provart
2009 The Plant Cell  
This review provides an overview of several such genomic, epigenomic, transcriptomic, proteomic, and metabolomic data sets and describes Web-based tools for querying them in the context of hypothesis generation  ...  to gain new insights into their own biological systems of interest, often at a mouse click through a Web browser.  ...  assembled genome sequence for grass species and for A. thaliana, A. lyrata, V. vinifera, and P. trichocarpa.  ... 
doi:10.1105/tpc.109.066050 pmid:19401381 pmcid:PMC2685637 fatcat:4ofi6mrjwnde7eqpuf4j7mmq4e

Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences

Claudia Manzoni, Demis A Kia, Jana Vandrovcova, John Hardy, Nicholas W Wood, Patrick A Lewis, Raffaele Ferrari
2016 Briefings in Bioinformatics  
While genomics, transcriptomics and proteinomics, coupled with bioinformatics and biostatistics, are gaining momentum, they are still, for the most part, assessed individually with distinct approaches  ...  This review cuts across the boundaries between genomics, transcriptomics and proteomics, summarizing how omics data are generated, analysed and shared, and provides an overview of the current strengths  ...  Fox Foundation, Parkinson's UK and the Rosetrees Trust.  ... 
doi:10.1093/bib/bbw114 pmid:27881428 pmcid:PMC6018996 fatcat:u5p5ojgitng6ndp4uetyr2u4ay

De-novo RNA Sequencing and Metabolite Profiling to Identify Genes Involved in Anthocyanin Biosynthesis in Korean Black Raspberry (Rubus coreanus Miquel)

Tae Kyung Hyun, Sarah Lee, Yeonggil Rim, Ritesh Kumar, Xiao Han, Sang Yeol Lee, Choong Hwan Lee, Jae-Yean Kim, Christos A. Ouzounis
2014 PLoS ONE  
to provide the gene resources for improving plant nutrition and pigmentation.  ...  To analyze biochemical changes during fruit ripening process at molecular level, firstly, we have sequenced, assembled, and annotated the transcriptome of KB fruits.  ...  Pill-Jae Park (Gochang Black Raspberry Research Institute) for supporting plant materials. Author Contributions Conceived and designed the experiments: TKH SL SYL CHL JYK.  ... 
doi:10.1371/journal.pone.0088292 pmid:24505466 pmcid:PMC3914977 fatcat:2xuibzgpyvgitmv7crgaeq5uju

An Omics Analysis Search and Information System (OASIS) for Enabling Biological Discovery in the Old Order Amish [article]

James A Perry, Brady J Gaynor, Braxton D Mitchell, Jeffrey R O'Connell
2021 bioRxiv   pre-print
OASIS provides this unique capability with a web-based, scientist-friendly search system and a variety of real-time analysis tools (linkage disequilibrium calculations, conditional analysis, and direct  ...  The OASIS application has been used to enable discovery from whole-exome, whole-genome, metabolome, transcriptome and methylome association results for Old Order Amish studies at the University of Maryland  ...  The copyright holder for this preprint (which this version posted May 3, 2021.  ... 
doi:10.1101/2021.05.02.442370 fatcat:xhhkjtomqjhn3ivlwi3leb5qnq

Soybean Functional Genomics: Bridging the Genotype-to-Phenotype Gap [chapter]

Jamie A. O'Rourke, Michelle A. Graham, Steven A. Whitham
2017 The Soybean Genome  
In this chapter, we review the current approaches, tools, and resources that are being applied for functional genomics research in soybean.  ...  In this chapter, we review the current approaches, tools, and resources that are being applied for functional genomics research in soybean.  ...  The USDA is an equal opportunity provider and employer. Mention of trade names or commercial products in this article is solely for the purpose of  ... 
doi:10.1007/978-3-319-64198-0_10 fatcat:ot46i3mhuvfhlkkltel6csyfee

ECOMICS:Ecosystem Trans-OMICS Tools and Methods for Complex Environmental Samples and Datasets

Jun Kikuchi, Yoshiyuki Ogata
2013 Journal of Ecosystem & Ecography  
, and HetMap for identifying and viewing correlations between heterogeneous trans-omics data sets that are produced by such web tools.  ...  ECOMICS comprises the E-class web tool for taxonomic (metagenomic) classification based on prokaryotic and eukaryotic ribosomal sequences and selected functional (enzymatic) classification based on sequential  ...  tools.  ... 
doi:10.4172/2157-7625.s2-001 fatcat:id7adngokvgljeh7rhj7pweqje

De novo assembly and functional annotation of Myrciaria dubia fruit transcriptome reveals multiple metabolic pathways for L-ascorbic acid biosynthesis

Juan C. Castro, J. Dylan Maddox, Marianela Cobos, David Requena, Mirko Zimic, Aureliano Bombarely, Sixto A. Imán, Luis A. Cerdeira, Andersson E. Medina
2015 BMC Genomics  
Conclusions: This study describes the first next-generation sequencing effort and transcriptome annotation of a non-model Amazonian plant that is relevant for AsA production and other bioactive phytochemicals  ...  The goals of this research, therefore, were to assemble, characterize, and annotate the fruit transcriptome of M. dubia in order to reconstruct metabolic pathways and determine if multiple pathways contribute  ...  The novel assembly methods [36] [37] [38] [39] have made short read assembly to be a cost-effective and reliable tool for gene discovery and molecular markers development in non-model plant species.  ... 
doi:10.1186/s12864-015-2225-6 pmid:26602763 pmcid:PMC4658800 fatcat:7zzka7a3ivfg5gdt7zmqm3iyqm
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