Sushma Naithani's blog

Notes from Biocuration 2017 conference

by Sushma Naithani and Parul Gupta

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Gramene webinar 11th April 2017: Overview, updates and new fireworks display in Plant Reactome

Plant Reactome (http://plantreactome.gramene.org/) is a freely available resource for comparative analyses of plant pathways. It features Oryza sativa (rice) as a reference species for the curation of cellular-level pathway networks by employing the Reactome data model. This reference set of curated rice pathways is being used to generate gene-orthology based pathway projections for 66 additional species.

Gramene Webinar Nov, 2016: Analysis and visualization of the plant gene Expression ATLAS data

The Gramene database is pleased to host another FREE 30-min webinar focused on "Analysis and visualization of the plant gene Expression ATLAS data using Gramene's Genome Browser and Plant Reactome." The plant gene Expression Atlas (https://www.ebi.ac.uk/gxa/plant/experiments) was developed by our collaborators at EMBL-EBI.

Highlights of 14th ISRFG Conference, 26-29 Sept 2016

From September 26-29th 2016, rice researchers from around the globe gathered in Montpellier, France to participate in the 14th International Symposium on Rice Functional Genomics (ISRFG) to discuss recent advances and exciting breakthroughs in rice genome biology and how this knowledge is being applied to improve the yield, and quality of rice, a major cereal crop.

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Gramene participating at the 14th ISRFG Conference, 26-29 Sept 2016

Representing Gramene, Dr. Sushma Naithani and Dr. Joshua Stein, will be available during the upcoming 14th International Symposium on Rice Functional Genomics in Montpellier, France on September 26-29, 2016. Dr. Naithani will present general updates to the Gramene Database and detailed navigation of the Plant Reactome database, a resource for comparative plant pathway analysis in the Bioinformatics Workshop ISRFG2016 on September 28th (Workshop Organizer: Dr. Francois Sabot).  Dr.

Gramene's impact on plant research in 2015-2016

Gramene database (www.gramene.org) offers resources for conducting comparative studies on plant genomes and pathways. Over the years, we have made efforts to reach out to the various communities of plant scientists and have assisted many individuals in using various tools/and resources available from the Gramene. We have also established connection between ours and other publicly available data sources. In year 2015 and 2016, Gramene has been cited ~90 times by various researchers.

2016 Basic DNA Biology and Bioinformatics STEM Camps

Dr. Pankaj Jaiswal (Co-PI of the NSF funded Gramene project) organized a basic DNA Biology and Bioinformatics STEM Summer Camps for 8-12 grade students from Jun 27th -July 1Ist.  To accomodate all applicants, two sessions of this camp were hosted.

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June 2016 Gramene Webinar: Tomato genomic resources and pathways

The Gramene database has the pleasure to invite you to a FREE 30-min webinar focused on tomato, an economically important crop of the family Solanaceae with a focus on the plant pathways. Plant Reactome (http://plantreactome.gramene.org), the pathway database of Gramene is a freely available online resource of plant metabolic, signaling, and regulatory pathways.

February 2016 Gramene Webinar: Updates on Plant Reactome

Register to join us online on Tuesday, February 16, 2016, at 2:00 pm EST/11:00 am PST.

Plant Reactome is a freely available resource of curated metabolic, signaling, and regulatory pathways from the reference species rice, and gene homology-based pathway projections for 58 other plants including Arabidopsis, maize, grape, strawberry, tomato, etc. Plant Reactome uses a eukaryotic cell model for pathway visualization, and allows uploading and analysis of omics data.

Gramene updates published in Jan, 2016 issue of Nucleic Acids Research

The recent updates in Gramene database have been summarized in the article “Gramene 2016: comparative plant genomics and pathway resources” published in the January 2016 issue of Nucleic Acids Research focused on biological databases.

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