Current Ongoing Projects @ SCBB:

(A) Regulatory System Analysis with respect to microRNAs

Small but very effective: A thing which can be said easily about microRNAs. There was an era where reductionist approach hovered only around protein coding regions of the genome, and only those regions were called genes and everything else were called non-coding elements, a majority of which tagged as "Junk". With time, science matured and thus the definition of the gene and junk! Genes expanded and junks shrunk. Non-coding elements have gathered new found respectability as the king makers of genome and microRNAs fit the bill very well. The present project studies about the regulatory roles of microRNAs and how these microRNAs fit the modular system. The project aims to develop software to improve micorRNA target prediction, propose new theories and algorithms and finally develop a closely knitted system to put forward regulatory modules of various cell system. This all will benefit our understanding about cell response to stimulus and signaling as well as to look for possible therapeutic targets.

(B) Computational Epigenomics & Regulomics:

The science has evolved a very beautiful way. We would get contended with finding one gene in our labs after working for years. There came cloning, amplification and sequencing methods. Reductionist approach towards the metabolic disorders or diseases took the limelight till the realization of genomic level studies occurred opening new areas of genomics, proteomics and whole genome SNP studies. A huge realization toward TFBS based studies was sensed thereafter resulting into new software to detect TFBS and new promoter models. Now in present couple of years many studies have proved that alone genome, proteome sequencing and SNP mappings don't give enough information to elucidate the behavior of cell and development. Here comes the epigenetic control, which does not change nucleotide but methylation and related modification in DNA and histones determine the chromatin and DNA response to binding proteins. A combination of TFBS alongwith methylation pattern of DNA and histones decide the age, age stage and behavior of the regulatory system. In order to understand this combinatorial regulatory control, the Studio is pursuing research in that direction.

(C) Computational issues with Next Generation Sequencing:

Next generation sequencing approaches are changing the face of science in strong way. The dream of fast & affordable journey towards the paths of genome is achievable with this technology. It gives huge amount of reads in no period of time, giving high confidence for those covered areas producing the reads, minimizing the level of sequencing errors. Same time new challenges have emerged with these technologies regarding their de-novo assembling, scaffolding and new sequence generation. Also the process if image analysis and signal detection for base calling have ample scope for improvement. The Studio has initiated its project in this direction to standardize the process of de-novo sequence assembling and generate high confidence novel sequence out of short reads produced from next generation sequencers like Illumina Genome Analyzer.

Funded Project Grants:

1. Project titled "Computational investigation into the role of alternative splicing in cellular differentiation, tissue regeneration, diseases and evolution", sanctioned for funding by DBT, Govt. of India.
   PI: Dr. Ravi Shankar.

2. Project titled "National Network Project of CSIR-IHBT, Palampur", sanctioned for funding by DBT, Govt. of India.
   PI: Dr. Ravi Shankar.

3. Project titled "The Himalayan Centre for High-throughput Computational Biology (HiCHiCoB) - BIC at CSIR-IHBT, Palampur (HP)", sanctioned for funding by DBT, Govt. of India.
   PI: Dr. Ravi Shankar.

4. Project titled "iPRESS: Integrated Plant REgulomics Software & Server", sanctioned for funding by CSIR.
   PI: Dr. Ravi Shankar.

5. Project titled "Exploration of RBP-RNA interactions to reveal the post-transcriptional regulatory impact and development of related tools and resource server". sanctioned for funding by the DBT.
   PI: Dr. Ravi Shankar.

6. Project titled "Profiling and characterization of early phase differential mi-RNA(s) responsible for downstream development of insulin resistance in hMSC derived adipocytes". sanctioned for funding by DBT.
   PI: Dr. Ravi Shankar.

7. Project titled "Epigenetic and transcriptional regulation by small RNAs: a computational approach". sanctioned for funding by the "Department of Science and Technology".
   PI: Dr. Ravi Shankar.

8. Project titled "Identification of De-novo non-coding transcripts in Human Brain [HUNT]". Project Funded under "Encouraging and Motivating Pursuit of World Class Exploratory Research " [EMPOWER] CSIR, India.
   PI@IHBT: Dr. Ravi Shankar.

9. Project titled "Regulatory system Analysis with respect to microRNAs and development of related softwares and Servers", sanctioned for funding by DBT.
   PI: Dr. Ravi Shankar.

CSIR 12th FYP national projects(2012-17):

1. Project titled "Sequence Information & Regulomics Group(SIRG), under GENESIS project". A highly ambitious project to provide insights from Next generation sequencing projects and its application in wide level for open source solution provision for the research community..
   PI: Dr. Ravi Shankar.

2. Project titled "Computational Epigenomics and Tea Epigenetics (Under EpiHead project) ". An effort is being made to decode the epigenetic regulation at genome level, developing computational models and its application. Also study is being carried with wet-lab partners to study the impact of epigenetic regulation in Tea.
   PI: Dr. Ravi Shankar.