Pathway "Gene-Swapper" Utility for PathVisio - available for download

Submitted by preecej on
Justin Preece and Mamatha Hanumappa have written a Perl utility application designed to map homologous genes from one species onto the PathVisio pathway diagram of another species. Requires only a GPML PathVisio document, a CSV file of homolog mappings, and a configuration file. The source code and documentation may be found here. Further enhancements and/or a collaboration with the PathVisio group on a plug-in version are likely forthcoming.

Welcome to the Jaiswal Lab

Welcome to the website for Jaiswal lab. My primary research focus is on studying the processes of flowering time and seed development in plants. These two developmental features of a plant determine how a plant reproduces on time and generate fruit/seeds thus contributing to our nutritional needs by way of quality and global food security by way of yield. We are interested in studying these two developmental features and their response to abiotic stresses like salt, drought and photoperiod.

Gramene database's 34th database build released

Submitted by pankaj on
The Gramene database team is happy to announce the 34th major release of the database and the website. The Jaiswal lab is a co-investigator on the Gramene project and several lab members contributed to this effort. Salient features of this release include:
  • Updates on Ensembl genome browser for six genomes

Jaiswal lab contributes to Global Profiling of Rice and Poplar Transcriptomes

Submitted by pankaj on
Jaiswal lab and Gramene team members Palitha Dharmawardhana and Pankaj Jaiswal contributed to a recent publication in PLoS ONE entitled "Global Profiling of Rice and Poplar Transcriptomes Highlights Key Conserved Circadian-Controlled Pathways and cis-Regulatory Modules". PLoS ONE 6(6): e16907. doi:10.1371/journal.pone.0016907.

Thanks to AMD and Advanced HPC for our new cluster node

Submitted by justin on
AMD has donated 4 12-core CPUs for a machine that was built by Advanced HPC that has been added to our cluster nodes. This 1U machine has singlehandedly doubled the number of processor cores available for our lab to do research. We have done some benchmarking on these new processors comparing them to the Intel Xeon 6-cores that make up the rest of our computing power. Stay tuned for these results.

Genome of brown algae Ectocarpus sequenced.

Submitted by pankaj on
Sequencing of the brown algae Ectocarpus siliculosus (Dillwyn) Lyngbye genome by Cock et. al. was published today in the journal Nature. Found in the rocky coastal environments, the brown algae possess a complex physiology and adaptation qualities. Of particular interest is the extended list of genes responsible for light harvesting and a new metabolic pathway on halide metabolism. In chemical terms 'halogen' is referred to ions such as fluorine, chlorine, iodine, or bromine.