Sushma Naithani's blog

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.

Follow up on Nov 2015 Webinar: Variant Effect Prediction using the standalone perl scripts

In  November 2015 Gramene Webinar, Matt Geniza, (a graduate student, Jaiswal Lab at Oregon State University) presented how to use standalone Perl script and command line protocols for Variant Effect Predictor (VEP) analysis. This option is for advanced users who are familiar with the Unix/Linux command line. Also, users are expected to have a SNP DATA file before proceeding for this exercise.

The 13th International Symposium on Rice Functional Genomics

The 13th International Symposium on Rice Functional Genomics (ISRFG) conference was organized by the National Key Laboratory of Crop Genetic Improvement at Huazhong Agricultural University in Wuhan, China, from the 21st to the 24th of September 2015.

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Prof. QIFA ZHANG welcoming 13th ISRFG participants (Photo credit : Organizers of 13th ISFRG)

Recent Advances in Plant Reactome - PAG 2015

Plant Reactome is a resource for plant metabolic and regulatory pathways built using the Reactome model. At present, Plant Reactome has curated metabolic and regulatory pathways from rice and Arabidopsis, and the orthology-based projections of pathways for additional 33 plant species including several Oryza species, and maize. We are developing tools that can support analysis and visualization of user-defined expression data.

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