Mohammad Samir Farooqi
Mohammad Samir Farooqi

Research Interest

  • Bioinformatics
  • Data Warehousing and Data Mining
  • GIS and Remote Sensing Techniques
  • Information System
  • Decision Support System
  • Expert System


  • Data Analysis in Agriculture
  • System Analysis and Design
  • Modeling and Simulation
  • GIS and Remote Sensing techniques
  • Data Warehousing and Data Mining

Important Projects

  • Study of Synonymous Codon Usage and its Relation with Gene Expressivity in Halophilic Bacteria. (Aug 2011-Jan 2013), as Principal Investigator

  • Establishment of National Agricultural Bioinformatics Grid in ICAR (Apr 2010-Mar 2013), as Co- Investigator
  • Strengthening Statistical Computing for NARS. (Apr 2010- Mar 2013), as Co- Investigator
  • Microbial domain research projects on computational aspects.

  • Knowledge Data Warehouse for Agricultural Research

  • Study of Synonymous Codon Usage and its Relation with Gene Expressivity in Halophilic Bacteria

  • Platform or Integrated Genomics Warehouse

  • Computational biology approach for deciphering transcriptome and proteomic changes in rice-microbial interaction system.

  • Methodology for Trait Specific Genes Identification.

Awards and Honours

  • Appointed member of Board of Studies (Computer Application) of PG School, IARI.
  • Appointed reviewer by the journal Annals of Data Science to review the manuscript.
  • Appointed reviewer by the journal Biologia Plantarum to review the manuscript.

Training Organized

  • Lectures Delivered in trainings/Workshop: 120
  • Conference/Training/workshop/Kisan Mela attended: 35
  • Refresher Courses/Summer Institute attended: 2

Important Publications

  • Sonkusale, L., Chaturvedi, K.K., Sharma, A., Lama, A., Farooqi, M.S., Lal, S.B., Joshi, P., Mishra, D.C., and Kumar, M.(2023). Evaluating Text Preprocessing Methods for Discovering Quality Topics to Improve the Information Retrieval Mechanism. Acta Scientific COMPUTER SCIENCES, 5(9), pp. 03-08. iconpdf

  • Ahlawat, S., Arora, R., Sharma, R., Chhabra, P., Kumar, A., Kaur, M., Lal, S.B., Mishra, D.C.,Farooqi, M.S. and Srivastava, S. (2023). Revelation of genes associated with energy generating metabolic pathways in the fighter type Aseel chicken of India through skeletal muscle transcriptome sequencing. Animal Biotechnology iconpdf

  • Arora, R., Sharma, R., Ahlawat, S., Chhabra, P., Kumar, A., Kaur, M., Vijh, R.K., Lal, S.B., Mishra, D.C., Farooqi, M.S., and Srivastava, S., (2023). Transcriptomics reveals key genes responsible for functional diversity in pectoralis major muscles of native black Kadaknath and broiler chicken. 3 Biotech, 13, 253. iconpdf

  • Kumar, M., Ansari, W.A,. Zeyad, M.T. Singh, A., Chakdar, H., Kumar, A., Farooqi, M.S., Sharma, A. Srivastava, S., and Kumar. A.(2023) Core microbiota of wheat rhizosphere under Upper Indo-Gangetic plains and their response to soil physicochemical properties, Frontiers in Plant Science,VOLUME 14 iconpdf

  • Singh, D. P., Bisen, M. S., Prabha, R., Maurya, S., Yerasu, S. R., Shukla, R., Tiwari, J. K., Chaturvedi, K. K., Farooqi, M.S., Srivastava, S., Rai, A., Sarma, B. K., Rai, N., Singh, P. M., Behera, T. K., & Farag, M. A. (2023). Untargeted Metabolomics of Alternaria solani-Challenged Wild Tomato Species Solanum cheesmaniae Revealed Key Metabolite Biomarkers and Insight into Altered Metabolic Pathways. Metabolites, 13(5), 585. iconpdf

  • Priyadarshi, M.B., Sharma, A., Chaturvedi, K.K., Bhardwaj, R., Lal, S.B., Farooqi, M.S., Kumar, S., Mishra, D.C, Singh, M. (2023). Comparing various machine learning algorithms for sugar prediction in chickpea using near-infrared spectroscopy. Legume Research-An International Journal . Volume 46, Issues 02, Pages 251-256. iconpdf

  • Sharma, R., Arora, R., Ahlawat, S., Chhabra, P., Kumar, A., Kaur, M., Lal, S. B., Mishra, D. C., Farooqi, M.S., & Srivastava, S. (2023). Study on the muscle transcriptome of two diverse Indian backyard poultry breeds acclimatized to different agro-ecological conditions. Molecular biology reports, 10.1007/s11033-022-08223-1. Advance online publication. iconpdf

  • Priyadarshi, M. B., Sharma, A., Chaturvedi, K.K., Bhardwaj, R., Lal, S.B., Farooqi, M.S., Kumar, S., Mishra, D.C., Singh, M. (2022). Machine Learning Algorithms for Protein Physicochemical Component Prediction Using Near Infrared Spectroscopy in Chickpea Germplasm. Indian J. Plant Genet. Resour. 35(1): 44–48. iconpdf

  • Sinha, D., Sharma, A., Mishra, D.C., Rai, A., Lal, S.B., Kumar, S.,Farooqi, M.S., Chaturvedi, K.K.(2022). MetaConClust - Unsupervised Binning of Metagenomics Data Using Consensus Clustering. Current Genomicsiconpdf

  • Kumar, V., Sharma, A., Lal, S.B., Chaturvedi, K.K., Farooqi, M.S., Mishra, D.C., Sonkusale, L. and Kumar, R. Comparative analysis of genome browser for visualization of genetic variants. The Pharma Innovation Journal. AP-11(3):384-388. iconpdf

  • Mishra, D.C., Arora, D., Budhlakoti, N., Solanke, A.U., Mithra, S., Kumar, A., Pandey, P.S., Srivastava, S., Kumar, S., Farooqi, M.S., Lal, S.B., Rai, A., & Chaturvedi, K.K. (2022). Identification of Potential Cytokinin Responsive Key Genes in Rice Treated With Trans-Zeatin Through Systems Biology Approach. Frontiers in genetics, 12, 780599.iconpdf

  • Kumar, S., Bhati, J., Saha, A., Lal, S.B., Pandey, P.K., Mishra, D.C., Farooqi, M.S., Kumar, A., Chaturvedi, K.K., Rai, A.(2022). CerealESTDb: A comprehensive resource for abiotic stress responsive annotated ESTs with predicted genes, gene ontology and metabolic pathways in major cereal crops. Frontiers in Genetics, section Plant Genomics. doi: iconpdf

  • Sharma, N.K., Mishra, D.C., Farooqi, M.S., Budhlakoti, N., Chaturvedi, K.K., Das, S., Kumar, A. and Rai, A., (2021). Algorithm for selection of informative genes using gene expression data. International Journal of Agricultural and Statistical Sciences. iconpdf

  • Farooqi, M.S., Kumar, D., Mishra, D.C., Rai, A. and Singh, N.K. (2021) ‘A hybrid method for differentially expressed genes identification and ranking from RNA-Seq data’, Int. J. Bioinformatics Research and Applications, Vol. 17, No. 1, pp.38–52 iconpdf

  • Farooqi, M.S, and Kumar, D., (2020), “Moments Properties Of Exponentiated Exponential-Geometric Distribution Based On Generalized Order Statistics ", Journal of Applied Probability and Statistics, Vol. 15, No. 2, pp. 01-18.

  • Farooqi M S, Mishra DC, Chaturvedi KK, Rai Anil, Lal SB, Kumar Sanjeev, Bhati Jyotika and Sharma Anu. (2019) A Review on Recent Statistical Models for RNA-Seq. Journal of Applied Bioinformatics & Computational Biology. 8:1 DOI: 10.4172/2329-9533.1000162.iconpdf

  • Islam, S., Sharma, A.K., Sharma, K., Farooqi, M.S., Chaturvedi, K.K. (2018). Diagnosing wheat disease using expert system. Journal of the Indian Society of Agricultural Statistics. 72(3):255-259.

  • Farooqi, M. S., and Kumar, D., (2018), "On Dagum Distribution Based on Dual Generalized Order Statistics with Applications", Int. J. Agricult. Stat. Sci. Vol. 14, No. 2, pp. 833-841

  • अनु शर्मा, ज्योतिका भाटी, शशि भूषण लाल, कृष्ण कुमार चतुर्वेदी, मोहम्मद समीर फ़ारूकी और अनिल राय (2018). संगणनात्मक विधियों के द्वारा अरहर में माइक्रो-आर.एन.ए. की पहचान एवं उसका विवरण, भारतीय कृषि अनुसंधान पत्रिका, 33(1), 51-57.

  • Farooqi, M. S. and Kumar, D. (2018) Moment generating functions of generalized exponential distribution based on lower generalized order statistics, International Journal of Agricultural and Statistical Sciences, 14 (1), 165-174

  • Kumar A, Farooqi MS, Mishra DC, Kumar S, Rai A, Chaturvedi KK, Lal SB, Sharma, A. (2018). Prediction of miRNA and Identification of their Relationship Network Related to Late Blight Disease of Potato. Microrna. 7(1):11-19. doi: 10.2174/2211536607666171213123038. PubMed PMID: 29237394.

  • Kumar Devendra and Farooqi Mohammad Samir (2017). The Type I Generalized Half Logistic Distribution Based On Generalized Order Statistics, International Journal of Agricultural and Statistical Sciences, 13 (1), 337-344

  • Mishra, DC, Smita, S, Singh I, Devi, MN, Kumar S, Farooqi, MS, Chaturvedi, KK, Rai, A (2017). Prediction of novel putative miRNAs and their targets in buffalo. Indian Journal of Animal Sciences, 87(1), 59–63.

  • Lal, S. B., Sharma, A., Chaturvedi, K. K., Farooqi, M. S., Kumar, S, Mishra, D. C. (2017).State-of-the-Art Information Retrieval Tools for Biological Resources. Web Semantics for Textual and Visual Information Retrieval, A volume in the Advances in Data Mining and Database Management (ADMDM) Book Series, IGI-Global, Pp. 203-226.

  • Islam, S., Sharma, R.K., Chhokar, R.S., Dhar, S., Sabir, N., Chaturvedi, K.K., Singh, R., Farooqi, M.S. and Sharma, K. (2017). Expert system for the identification and control of weeds in wheat crop. Annals of Agricultural Research, New Series. 38(2):1-9.

  • Rai, N, Mishra, DC, Kumar, S, Rai, A, Chaturvedi, KK, Lal, SB, Kumar, A, Farooqi, MS, Majumdar, PG, and Archak, S. (2016). Genome analysis of Rhizobium species using codon usage bias tools International Conference on Bioinformatics and Systems Biology (BSB, 2016). IEEE Xplore digital library, Page(s):1 – 4.

  • Ngaki, MN, Wang, B, Sahu, BB, Srivastava, SK, Farooqi, MS and Kambakam, S, etal. (2016) Tanscriptomic Study of the Soybean- Fusarium virguliforme Interaction Revealed a Novel Ankyrin-Repeat Containing Defense Gene, Expression of Whose during Infection Led to Enhanced Resistance to the Fungal Pathogen in Transgenic Soybean Plants. PLoS ONE, 11(10): e0163106. DOI:10.1371/ journal.pone.0163106.

  • Md. Samir Farooqi, DC Mishra, Niyati Rai, DP Singh, Anil Rai, Chaturvedi, K.K., Ratna Prabha and Manjeet Kaur (2016). Genome-wide relative analysis of codon usage bias and codon context pattern in the bacteria Salinibacter ruber, Chromohalobacter salexigens and Rhizobium etli. in Biochemistry and Analytical Biochemistry. 5:257. doi:10.4172/2161-1009.1000257.

  • Kumar Devendra and Md. Samir Farooqi (2015). On Generalized Order Statistics from Marshall-Olkin Log-Logistic Distribution. Global Journal of Pure and Applied Mathematics. ISSN 0973-1768 Volume 11, Number 5 (2015), pp. 3513-3528. .

  • Sharma Naveen,Md. Samir Farooqi, Chaturvedi Krishna Kumar, Lal Shashi Bhushan, Grover Monendra, Rai Anil, and Pandey Pankaj (2014). The Halophile Protein Database, Database (Oxford). 2014; doi:10.1093/database/bau114.

  • Md. Samir Farooqi, Rajkumari Sanjukta, Naveen Sharma, Anil Rai, Dwijesh Chandra Mishra Dhananjaya P Singh & K K Chaturvedi (2013). Statistical and computational methods for detection of synonymous codon usage patterns and gene expression. International Journal of Agricultural and Statistical Sciences, 9(1): 303-310.

  • RK Sanjukta, Md. Samir Farooqi, Niyati Rai, Anil Rai, Naveen Sharma, Dwijesh C Mishra and Dhananjaya P Singh (2013). Expression analysis of genes responsible for amino acid biosynthesis in extremely halophilic bacterium, Salinibacter ruber. Indian Journal of Biochemistry and Biophysics, Vol. 50, pp. 177-185.

  • Sanjukta RK, Md. Samir Farooqi, Sharma N, Rai N, Mishra DC, Rai A, Singh DP, Chaturvedi KK (2013). Statistical Analysis of codon usage in extremely halophilic bacterium, Salinibacter ruber DSM 13855. Online J Bioinform., 14(1): 15-31.

  • Sanjeev Panwar, Anil Kumar, K.N. Singh, Md. Samir Farooqi, and Abhishek Rathore (2012). Nonlinear regression techniques for analysis of onion (Allium cepa) production in India. Indian Journal of Agricultural Sciences, 82(12): 1051-4.

  • Rajkumari Sanjukta, Md. Samir Farooqi, Naveen Sharma, Anil Rai, Dwijesh Chandra Mishra, and Dhananjaya P Singh (2012). Trends in the codon usage patterns of Chromohalobacter salexigens genes. Bioinformation, 8(22): 1087-1095.

  • Ratna Prabha, Dhananjaya P. Singh, Shailendra K. Gupta, Md. Samir Farooqi and Anil Rai (2012). Synonymous codon usage in Thermosynechococcus elongatus (cyanobacteria) identifies the factors shaping codon usage variation. Bioinformation, 8(13): 622-628.

  • Islam Shahnawazul, Kundu Sushila, Shoran Jag, Sabir Naved, Sharma Kirti, Md. Samir Farooqi, Singh Randhir, Agarwal Hari Om, Chaturvedi K.K., Sharma R.K. and Sharma A.K. (2012) Selection of wheat (Triticum aestivum) variety through expert system. Indian Journal of Agricultural Sciences, 82(1): 43–7.

  • Md. Samir Farooqi, Arora Alka, Dahiya Shashi, Rai Anil and Singh Balbir (2011). PERMISnet-II: Personnel Management Information System Network - II for Indian Council of Agricultural Research. Journal of the Indian Society of Agricultural Statistics, 65(1), 105-113.

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