Expression profiling of luminal B breast tumor in Indian women.

Purpose: In this study, we aimed at profiling of luminal B breast cancer specific gene expression pattern in Indian women using mRNA-seq and validation based on TCGA expression data.

Methods: RNA isolated from luminal B tumor and adjacent normal tissues was used for library construction and sequencing. Reference-based assemblies of these reads were used for differential gene expression analysis using DeSeq2.

Assembly of genomic reads of elite indica rice cultivar onto 2101 reference bacterial genomes for identification of co-sequenced endophytic bacteria.

Reference based assembly of genomic reads of the elite indica rice cultivar RP Bio-226 was carried out against 2101 reference bacterial genomes using Bowtie-2 genome assembly tool. Five types of data: Number of paired end reads concordantly aligned exactly only once, number of paired end reads concordantly aligned more than once, number of mates that make the pairs aligned exactly only once, number of mates that make the pairs aligned more than once and overall percentage of alignment were collected. Interpretation of the results and identification of endophytes based on these alignment statistics are described in detail in our research article "L.

Genome inside genome: NGS based identification and assembly of endophytic Sphingopyxis granuli and Pseudomonas aeruginosa genomes from rice genomic reads.

The interactions between crop plants and the endophytic bacteria colonizing them are poorly understood and experimental methods were found to be inadequate to meet the complexities associated with the interaction. Moreover, research on endophytic bacteria was focused at host plant species level and not at cultivar level which is essential for understanding the role played by them on the productivity of specific crop genotype. High throughput genomics offers valuable tools for identification, characterization of endophytic bacteria and understand their interaction with host plants.

miRNA regulation during cardiac development and remodeling in cardiomyopathy.

miRNAs have been found to play a major role in cardiomyopathy, a heart muscle disorder characterized by cardiac dysfunction. Several miRNAs including those involved in heart development are found to be dysregulated in cardiomyopathy. These miRNAs act either directly or indirectly by controlling the genes involved in normal development and functioning of the heart.

Genome-wide analyses of rice root development QTLs and development of an online resource, Rootbrowse.

Unlabelled: Genetic control of root development in rice is complex and the underlying mechanisms (constitutive and adaptive) are poorly understood. Lowland and upland varieties of indica and japonica rice with contrasting root development characteristics have been crossed, mapping populations developed and a number of QTLs in different chromosomes were identified. As these studies have used different sets of markers and many of the QTLs identified are long, it is difficult to exploit the varietal difference for improved root traits by marker assisted selection and for identification of concerned alleles.