Sandeep Kumar Dhanda, Ph.D.

Our innate immune system recognizes a foreign RNA sequence of a pathogen and activates the immune system to eliminate the pathogen from our body. This immunomodulatory potential of RNA can be used to design RNA-based immunotherapy and vaccine adjuvants. In case of siRNA-based therapy, the immunomodulatory effect of an RNA sequence is unwanted as it may cause immunotoxicity. Thus, we developed a method for designing a single-stranded RNA (ssRNA) sequence with desired immunomodulatory potentials,… Show more

Our innate immune system recognizes a foreign RNA sequence of a pathogen and activates the immune system to eliminate the pathogen from our body. This immunomodulatory potential of RNA can be used to design RNA-based immunotherapy and vaccine adjuvants. In case of siRNA-based therapy, the immunomodulatory effect of an RNA sequence is unwanted as it may cause immunotoxicity. Thus, we developed a method for designing a single-stranded RNA (ssRNA) sequence with desired immunomodulatory potentials, for designing RNA-based therapeutics, immunotherapy and vaccine adjuvants. The dataset used for training and testing our models consists of 602 experimentally verified immunomodulatory oligoribonucleotides (IMORNs) that are ssRNA sequences of length 17 to 27 nucleotides and 520 circulating miRNAs as non-immunomodulatory sequences. We developed prediction models using various features that include composition-based features, binary profile, selected features, and hybrid features. All models were evaluated using five-fold cross-validation and external validation techniques; achieving a maximum mean Matthews Correlation Coefficient (MCC) of 0.86 with 93% accuracy. We identified motifs using MERCI software and observed the abundance of adenine (A) in motifs. Based on the above study, we developed a web server, imRNA, comprising of various modules important for designing RNA-based therapeutics (http://crdd.osdd.net/raghava/imrna/). Show less

Domestic cow, Bos taurus is one of the important species selected by humans for various traits, viz. milk yield, meat quality, draft ability, resistance to disease and pests and social and religious reasons. Since cattle domestication from Neolithic (8,000-10,000 years ago) today the population has reached 1.5 billion and further it’s likely to be 2.6 billion by 2050. High magnitude of numbers, breed management, market need of traceability of breed product, conservation prioritization and IPR… Show more

Domestic cow, Bos taurus is one of the important species selected by humans for various traits, viz. milk yield, meat quality, draft ability, resistance to disease and pests and social and religious reasons. Since cattle domestication from Neolithic (8,000-10,000 years ago) today the population has reached 1.5 billion and further it’s likely to be 2.6 billion by 2050. High magnitude of numbers, breed management, market need of traceability of breed product, conservation prioritization and IPR issues due to germplasm flow/exchange, has created a critical need for accurate and rapid breed identification. Since ages the defined breed descriptors has been used in identification of breed but due to lack of phenotypic description especially in ova, semen, embryos and breed products molecular approach is indispensable. Further the degree of admixture and non-descript animals characterization, needs of molecular approach is imperative. Till date breed identification methods based on molecular data analysis has great limitations like lack of reference data availability and need of computational expertise. To overcome these challenges we developed a web server for maintaining reference data and facility for breed identification. The reference data used for developing prediction model were obtained from8 cattle breeds and 18 microsatellite DNA markers yielding 18000 allele data. In this study various algorithms were used for reducing number of loci or for identification of important loci. Minimization up to 5 loci was achieved using memory-based learning algorithm without compromising with accuracy of 95%. This model approach and methodology can play immense role in all domestic animal species across globe in breed identification and conservation programme. This can also be modelled even for all flora and fauna to identify their respective variety or breed needed in germplasm management. Show less