Ashutosh Singh | Department of Life Sciences

Profile

Dr. Ashutosh Singh
Ashutosh
Singh
Associate Professor
Department of Life Sciences
Center for Informatics
School of Natural Sciences (SoNS)
A321L
Block-A, Shiv Nadar University
GREATER NOIDA Uttar Pradesh
India
+911203819100
Extn: 
883
Profile Summary 

Translational Bioinformatics and Computational Genomics Lab

Our lab research goal is to identify and develop gene signatures for human diseases using underlying principles of gene expression and to explore how variations or defects in gene regulation cause phenotypic variation or diseases. We conduct our research using an integrative approach along with bioinformatics we also incorporate genomics, transcriptomics. Currently working on drug designing and Next generation sequencing of tropical region diseases and Cancer.

Cancer Genomics and Bioinformatics

Existing projects are emphasized on meta-analysis of cancer gene expression studies. This will provide information of significant genes and aberrant pathways with more confidence level observed to be involved in a specific cancer type or are present at exclusive stage of cancer. We along with my collaborators working towards development of colorectal cancer based drug resistance cell lines and identification of drug resistance mutations. We have made repositories exclusively for colorectal cancer like Colorectal Cancer Gene Database (CoReCG) has been developed (lms.snu.edu.in/corecg) which contain all validated colon-rectal cancer genes information.

Disease Genomics

Complete transcriptome sequencing of patient samples to analyze the expression of genes which are differentially regulated neglected tropical diseases. Further, the co-expression of microRNAs, lncRNAs and coding genes, will be deciphered to disentangle the molecular pathways that are triggered during the progression of these diseases from early stage to advance stages or malignancy. We also study comprehensive screening of variants frequency in the sample population and expression of alternative transcripts which will elucidate the reason for the heterogeneity observed in these patients. Moreover, we also work on plant transcriptome based big data to identify gene signatures for plant abiotic stress using meta-analysis and systems biology approaches.

Genome Sequencing Project

Group is also working on whole genome sequencing and Transcriptomic Profiling and data analysis of multi-centric National Agriculture Science Fund (NASF) funded ICAR research project on Pashmina goat. Consortium leader: Sher-e-Kashmir University of Agricultural Sciences and Technology, Division of Biotechnology, Shuhama, Srinagar.

Bioinformatics Tools, databases and Softwares

We have made few very significant tools and databases, some of them are: Colorectal Cancer Gene Database (CoReCG) has been developed (lms.snu.edu.in/corecg) which contain all validated colon-rectal cancer genes information.

TM-Aligner: Multiple sequence alignment tool for transmembrane proteins with reduced time and improved accuracy. TM-Aligner (https://lms.snu.edu.in/TM-Aligner/) is an unrestricted (in terms of length and number of sequences) tool which can align transmembrane proteins even at low level of sequence identity, accurate alignment is possible at low sequence identity because biological membrane proteins have a transmembrane between cytoplasmic and extracellular regions. TM-Aligner has been designed as a unique global, progressive alignment method, with the aim of high-quality alignment which has almost no limitation over input data-set size. TM-Aligner uses UPGMA method to create an initial guide tree that describes sequence relatedness. To identify transmembrane regions TMHMM  has been employed and alignment were made using dynamic programming and Wu-Manber string matching algorithm to calculate sequence distances and incorporate local matches in global alignment.

My research rely on the massive data production and analysis of large-scale data from high-throughput Next Generation Sequencing (NGS) or of microarray origin. Additionally, we are also interested in genetic linkage and association studies to identify disease associated genetic variants.

Educational Qualifications 
2011
Ph.D.
Banasthali University, Rajasthan
Work Experience 
01/12Present
Assistant Professor
Shiv Nadar University
Greater Noida
I currently work here
2012
Post Doctoral Fellow
Institute of Liver & Biliary Sciences
New Delhi
2011
Guest Faculty
TERI University
New Delhi
2010
Scientist
Mayar Biotech
Gurgaon
2009
Lecturer
Banasthali University
Banasthali, Rajasthan
Awards(Selected): 
  •  SHIV NADAR UNIVERSITY EXCELLENCE AWARD.
  • Young Scientist Gold Medal with Cash Prize for the Best Research Paper and Oral Presentation Award at National Conference Environmental Problems in India and Challenges to Plant Biologists (EPICPB) 4-5 Feb 2011 at Varanasi.
  • CSIR DIAMIOND JUBLIEE RESEARCH INETRNSHIP AWARD.
  • Best Paper Award at HIV/AIDS and TUBERCULOSIS 2006 International Conference/ CME, held at AIIMS, New Delhi, India.
  • CSIR Senior Research Fellowship (SRF) Award.
  • Award for University Minor Research Project for the facilitation of Research on “Potential Drug Target Identification for M.tuberculosis”.
  • Best Exhibitory Award at Bangalore Bio 2009.
  • DBT, BITP program coordinator.

Scholarly Activity

Journal Publications (accepted or published)

1. Singh, G., Bhat, B., Jayadev, M. S. K., Madhusudhan, C., & Singh, A*. (2018). mutTCPdb: a comprehensive database for genomic variants of a tropical country neglected disease—tropical calcific pancreatitis. Database2018.

2. Singh, G., Jayadev, M. S. K., Sharma, R., Bhat, B., Madhusudhan, C. H., & Singh, A.* (2018). Structural, functional and molecular dynamics analysis of cathepsin B gene SNPs associated with tropical calcific pancreatitis, a rare disease of tropics. bioRxiv, 308932. 

3. Sharma, R., Singh, G., Bhattacharya, S., & Singh, A.* (2018). Comparative transcriptome meta-analysis of Arabidopsis thaliana under drought and cold stress. PloS one13(9), e0203266

4. Bhat, Basharat, Nazir A. Ganai, Syed Mudasir Andrabi, Riaz A. Shah, and Ashutosh Singh*. "TM-Aligner: Multiple sequence alignment tool for transmembrane proteins with reduced time and improved accuracy." Scientific reports 7, no. 1 (2017): 12543.

5. G Singh, A K Agarwal, J Prosek, M S K Jayadev, Ashutosh Singh* (2017), Can killers be saviors? Lupus. DOI: 10.1177/0961203316688783. [Impact Factor: 2.1]

6. Hati S, Tripathy S, Dutta PK, Agarwal R, Srinivasan R, Singh Ashutosh , Singh S, Sen (2016) S.Spiro[pyrrolidine-3, 3´-oxindole] as potent anti-breast cancer compounds: Their design, synthesis, biological evaluation and cellular target identification.          Scientific Reports. (Nature Publishing Group) 6:32213 PMID: 27573798,        DOI: 10.1038/srep32213    [Impact Factor: 5.5]

7. Akansha Gupta, Rahul Agarwal, Ashutosh Singh, Bhatnagar, Sonika (2016), Calcium Induced Conformational Changes of Thrombospondin-1 Signature Domain: Implications for Vascular Disease. Journal of Receptors and Signal Transduction, DOI: 10.1080/10799893.2016.1212377. [Impact Factor: 1.7]

8. Singh, A., Raghav, D., Msk, J., Agarwal, R., Kumar, B. CoReCG: a comprehensive database of genes associated with colon-rectal cancer. Database (2016) Vol. 2016: article ID bav059; doi:10.1093/database/bav059  [Impact Factor: 3.3]

9. S Hati · S M Madurkar · C Bathula · C Thulluri · R Agarwal · F A Siddiqui · P Dangi · U Adepally · Singh  A · S Singh · S Sen (2015) Design, synthesis and biological evaluation of small molecules as potent glucosidase inhibitors. European Journal of Medicinal Chemistry 04/2015; 100. DOI:10.1016/j.ejmech.2015.04.059 ·[Impact Factor: 3.447]

10. Majumdar P, Bathula C, Basu SM, Das SK, Agarwal R, Hati S, Singh A, Sen S, Das BB.(2015) Design, synthesis and evaluation of thiohydantoin derivatives as potent topoisomerase I (Top1) inhibitors with anticancer activity. Eur J Med Chem. 2015 Sep 18;102:540-51. doi: 10.1016/j.ejmech.2015.08.032. [Impact Factor: 3.447] 8. Bathula C,   Dangi P,   Hati S,   Agarwal R,  Munshi P,  Singh A,   Singh S and   Sen S.(2015) Diverse synthesis of natural product inspired fused and spiro-heterocyclic scaffolds via ring distortion and ring construction strategies. New J. Chem., doi: 10.1039/C5NJ01858G. [Impact Factor: 3.086]

11. Bathula C, Mamidala R,Thulluri C, Agarwal R, Kumar K, Munshi P,Adepally U, Singh A, Thirumala M C and Sen S (2015), Substituted furopyridinediones as novel inhibitors of a-glucosidase. RSC Adv., 5, 90374, doi: 10.1039/c5ra19255b. [Impact Factor: 3.84]

12. P. Guptaa, N. Bairagi, R. Priyadarshini, Singh A., D. Chauhan, D. Gupta (2016), Bacterial contamination of nurses' white coats after 1st and 2nd shift. American Journal of Infection Control. [Impact Factor: 2.1]

13. P. Gupta, N. Bairagi, R. Priyadarshini, Singh A., D. Chauhan, D. Gupta (2016), Bacterial contamination of nurses' white coats made from polyester and polyester cotton blend fabrics.  Journal of Hospital Infection, doi: 10.1016/j.jhin.2016.05.016. [Impact Factor: 2.7]

14. Katara P, Singh A, Ragav D, Sharma V (2010) Analysis of Regulatory Genomics and Gene Expression Pattern of Medicinal Importance Genes of Helicobacter Pylori. J Comput Sci Syst Biol 3: 010-015. doi:10.4172/jcsb.1000049

15. Shanker A., Singh A. and Sharma V. (2007). In silico mining in expressed sequences of Neurospora crassa for identification and abundance of microsatellites. Microbiological Research 162: 250-256. [Impact Factor: 2.7]

16. Shanker A., Tripathi D., Khandelwal G., Sharma G., Agrawal S., Singh A. and Sharma V. (2006). Data mining and database development for simple sequence repeats of Takifugu rubripes (Japanese Pufferfish).Biochem. Cell. Arch. 6: 1-12.

17. Singh Ashutosh, Mishra Shruti, Raghav Dhwani, Shanker Asheesh and Sharma Vinay, 2008. In Silico Method for the Identification of Mycobacterial sp.Potential Drug Targets. ICCES, TECH SCIENCE PRESS, USA,  vol.6, no.2, pp.119-123.

18. Singh Ashutosh, Katara Pramod and Sharma Vinay, 2009. Drug Discovery Process: An Overview. (Invited Review) DBT Newsletter BIOBYTES .

19. Tripathi B.N, Kasana Rohini, Singh Vijeta, Singh Ashutosh, Sharma Vinay and Gaur J.P, 2009, Carotenoids and pH of the culture medium play important role in displaying metal stress in batch and semi-continuous cultures of Anabaena doliolum. Annals de limnologie, vol. 45, II, 119-125 . [Impact Factor: 1.1]

20. Singh.A, Sharma.S.A, Mishra.S, Sharma.A, Shasany.K.A, 2005.In Silico Mining and Classification of Monoterpene synthase Genes. ISBN 0- 9717880-0-6, ICCES, Tech       Science Press, 1787-1791.