Bioinformatics

Prof (Dr) Yashpal Singh Malik

Address : Head, Department of Bioinformatics, College of Animal Biotechnology, Guru Angad Dev Veterinary & Animal Sciences University, Ludhiana

Email: malikyps@gmail.com

Call: +91-7500777999

Brief Introduction :

Prof (Dr) Yashpal Singh Malik Dean, College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University (GADVASU), Ludhiana, Punjab is also serving as the current head of the department. Previously, he served as ICAR-National Fellow at ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar India (Nov 2014 to Oct 2020). Prof Malik served as Assistant Professor/Scientist (June 2001- August 2008), Associate Professor/Senior Scientist (May 2008-September 2008) at the College of Veterinary Sciences, JN Krishi Vishwa Vidyalaya, Jabalpur, Madhya Pradesh, and later joined ICAR-IVRI as Senior Scientist (September 2008-May 2014) and Principal Scientist (May 2014-November 2014). He is having rich experience in the field of Virology and Biotechnology. His major research achievements include contributions to viral disease epidemiology, virus-host interactions, microbial biodiversity, and characterization and diagnosis of animal pathogens. He has worked on rotavirus, astrovirus, picobirnavirus, picornaviruses, coronaviruses, and many other zoonotic viruses.

Prof Malik obtained his bachelor’s degree in 1995 in Veterinary Sciences and Animal Husbandry; his master's in 1997 and his Ph.D. (2000) in Microbiology from Haryana. Prof Malik did his postdoctoral research in Molecular Virology at the University of Minnesota, Saint Paul, USA (2001-2002). He acquired advanced training in Molecular Virology from the University of Minnesota, Saint Paul, USA (2005), Division of Virology, Ontario Research Institute, University of Ottawa, Ontario, Canada 2013, and Wuhan Institute of Virology, China 2019. Prof Malik has been to The United States of America, Canada, the United Arab Emirates, Malaysia, Belarus, Belgium, Sweden, and the People’s Republic of China representing India in the scientific arena.

Prof. Malik is a recipient of several prestigious awards/honors including the Jawaharlal Nehru Award (2001). Dr. Malik has the honor to receive a Fellowship from the National Academy of Dairy Sciences (India), Associate Fellowships from the National Academy of Agricultural Sciences (2010), and the National Academy of Veterinary Sciences (2010). Prof Malik has been endowed with Fellowships from several national professional academies and societies including the Academy of Microbiological Sciences, National Academy of Biological Sciences, Indian Virology Society, Indian Association of Veterinary Microbiologists, Immunologists and Specialists in Infectious Diseases, Indian Society of Veterinary Immunologists and Biotechnologists, Society for Immunology and Immunopathology, Biotechnology Research Society India, and many others.

Prof Malik is a member of the Committee for Control and Supervision of Experiments on Animals (CPCSEA), a statutory Committee of the Department of Animal Husbandry and Dairying (DAHD), Ministry of Fisheries, Animal Husbandry and Dairying for three years (2021-2023). In the international arena, he is a member of the International Committee on Taxonomy of Viruses (ICTV) on Birnaviridae and Picobirnaviridae study group, an executive council member of the World Society for Virology (USA), a member of the One-Health Group of Federation of Asian Veterinary Association (FAVA) (2021-2025), and a member of Pharmaceutical Stewardship Group of World Veterinary Association (WVA).

He has developed several technologies and diagnostic kits and has two National patents to his credit. He has authored 8 books by reputed publishers including ICAR, Elsevier, and Springer Nature, and has contributed over 60 book chapters. His h index is 48 with citations of more than 9400 and an RG score of 41. Prof Malik has supervised 7 Ph.D. and 20 Master’s degree students for their thesis research.

Prof Malik is the Chief Editor of the Journal of Immunology and Immunopathology and Bhartiya Krishi Anusandhan Patrika, the UGC/NAAS-rated journals. At the international platform, serving as Associate Editor in Frontiers in Microbiology and Frontiers in Veterinary Sciences, the high-impact international journals. Prof Malik is on the advisory board of several professional academic societies including the Indian Virological Society where he is serving as “Secretary General”, “Secretary” in the World Society for Virology, “Joint Secretary” in the Indian Society of Veterinary Immunology, and Biotechnology and served as Joint Secretary in the Indian Association of Veterinary Microbiologists, Immunologists and Specialists of Infectious Diseases. 

Bioinformatics

Picture	Name	Designation	Superannuation/ Transfer/ Promotion	Date of Superannuation/ Relieving
	Dr. GVPPS Ravi Kumar	Assistant Scientist	Selected and joined as Senior Scientist at IVRI, Izatnagar	Relieved on 21-01-2010
	Dr. Ranjana S. Cheema	Professor and Head, Department of Bioinformatics	Superannuated	Retired on 31-01-2021

Bioinformatics

Bioinformatics

Bioinformatics

The Department has prepared questionnaires for dairy farmers and collected input through direct questioning at 'Pashu Palan Melas' (at GADVASU) & online survey (through Google form). The research output is in form of a publication in the Agriculture Research Journal [(57(5): 769-778)] (NAAS 2022: 5.44)

Extension Publications:

• Mukhopadhyay, C.S.*, Singh, K., Kashyap N., Sandhu Y. & Singh, S. (2020). SWOT Analysis to Identify Important Factors Influencing Dairy Farming Practices in Punjab. Agric Res J., 57(5): 769-778. DOI No. 10.5958/2395-146X.2020.00112.X (NAAS 2022: 5.44)
  
• Tewari, S. & Mukhopadhyay, C. S. (2022). Dairy farm data recording impact analysis on socio-economic aspects of business Pashudhan Praharee. Published online on 17th March 2022. URL: http://www.pashudhanpraharee.com/
• Mukhopadhyay, C. S. & Kaur, B. (2021). Kheti bari da Bhavik: Smart Kheti-bari (In Punjabi). Vaigyanik Pashupalan. 16(1), 13-14. 
• Choudhary, R. K. & Zhao, F-Q. (2021). Editorial: Re-Evaluation of Milk Components & Stem Cells. Acta Scientific Veterinary Sciences 3(1), 01-02. (IF-0.581).
• Sharma, P. & Choudhary, R K. (2021). Pregnancy diagnosis is key for the better management of dairy farms. Vet Alumnus 43(1&2): 22-24.
• Kashyap N. & Deshmukh, B. (2020). Efficient poultry farming with bio-security measures. Poultry World; 05; 20-22.
• Kashyap N., Deshmukh, B. & Bansal, B. K. (2020). Santati parikshan ke madhyam se dudharu pashuon ka aanuvanshik sudhar. Krishi Kiran 2020; 60-64.
• Kashyap N. & Deshmukh, B. (2019). Livestock record keeping: A key to efficient genetic improvement. Vet Alumnus: 41; 45-48.
• Kashyap N. & Deshmukh, B. (2019). Varsha ritu mein murgiyon mein hone wale ushmagat tanaw ke dushparinam evam nivaran. Poultry Technology, 14(5); 74-75.
• Kashyap N. & Deshmukh, B. (2019). Dudharu pashuon mein Thanaila Rog Pratirodhakata ki Aanuvanshik Samiksha. Kheti Duniya 2019: 11.
• Kashyap N. & Deshmukh, B. (2019). Bhartiya govanshiya pashudhan mein taap sahanshilta. Kheti Duniya 2019; 6.
• Kashyap, N., Malhotra, P. & Kaur, R. (2017). Deyri pashuan te vadhere tapas de prabhaw ate dhakviyan naslan. in: Booklet 'Vadhdi aalmi tapas anusaar pashu aahar ate prabandh'. Published by: GADVASU, Ludhiana, pp 11-14.
  

Bioinformatics

Extension Publications:

• Mukhopadhyay, C.S.*, Singh, K., Kashyap N., Sandhu Y. & Singh, S. (2020). SWOT Analysis to Identify Important Factors Influencing Dairy Farming Practices in Punjab. Agric Res J., 57(5): 769-778. DOI No. 10.5958/2395-146X.2020.00112.X (NAAS 2022: 5.44)
• Tewari, S. & Mukhopadhyay, C. S. (2022). Dairy farm data recording impact analysis on socio-economic aspects of business Pashudhan Praharee. Published online on 17th March 2022. URL: http://www.pashudhanpraharee.com/
• Mukhopadhyay, C. S. & Kaur, B. (2021). Kheti bari da Bhavik: Smart Kheti-bari (In Punjabi). Vaigyanik Pashupalan. 16(1), 13-14. 
• Choudhary, R. K. & Zhao, F-Q. (2021). Editorial: Re-Evaluation of Milk Components & Stem Cells. Acta Scientific Veterinary Sciences 3(1), 01-02. (IF-0.581).
• Sharma, P. & Choudhary, R K. (2021). Pregnancy diagnosis is key for the better management of dairy farms. Vet Alumnus 43(1&2): 22-24.
• Kashyap N. & Deshmukh, B. (2020). Efficient poultry farming with bio-security measures. Poultry World; 05; 20-22.
• Kashyap N., Deshmukh, B. & Bansal, B. K. (2020). Santati parikshan ke madhyam se dudharu pashuon ka aanuvanshik sudhar. Krishi Kiran 2020; 60-64.
• Kashyap N. & Deshmukh, B. (2019). Livestock record keeping: A key to efficient genetic improvement. Vet Alumnus: 41; 45-48.
• Kashyap N. & Deshmukh, B. (2019). Varsha ritu mein murgiyon mein hone wale ushmagat tanaw ke dushparinam evam nivaran. Poultry Technology, 14(5); 74-75.
• Kashyap N. & Deshmukh, B. (2019). Dudharu pashuon mein Thanaila Rog Pratirodhakata ki Aanuvanshik Samiksha. Kheti Duniya 2019: 11.
• Kashyap N. & Deshmukh, B. (2019). Bhartiya govanshiya pashudhan mein taap sahanshilta. Kheti Duniya 2019; 6.
• Kashyap, N., Malhotra, P. & Kaur, R. (2017). Deyri pashuan te vadhere tapas de prabhaw ate dhakviyan naslan. in: Booklet 'Vadhdi aalmi tapas anusaar pashu aahar ate prabandh'. Published by: GADVASU, Ludhiana, pp 11-14.    
  

Research Publications:

• Choudhary, R. K., & Zhao, F. Q. (2022). Stem cells in mammary health and milk production. Current Stem Cell Research & Therapy, 17(3), 207-213. (NAAS-9.83)
• Rana, H., Luhach, P., Singh, S., Sharma, P., Choudhary, S. & Choudhary, R. K. (2022). Caprine Cancer: Etiology, Types, and Metanalysis of 21-Years of Case Reports. EC Veterinary Science, 7, 1-9. (NAAS- awaited)
• Kaur, H., Malik, Y. S, Mukhopadhyay, C. S. (2022). Biocomputational analysis of spike proteins to identify evolutionary divergence of beta-CoVs with focusing on SARS-CoV2. Indian Veterinary Journal, 98(12):22-29. (NAAS-awaited)
• Kaur, M., Mukhopadhyay, C. S., Sethi, R. S, Deka, D., & Dubey, P. P.. (2022). Selecting the best combination of adjuvant and the delivery vehicle for optimizing the th1 and th2 biased responses of NDV live vaccine in indigenous Aseel chicken. Bhartiya Krishi Anusandhan Patrika, 36(3): 215-223. DOI: 10.18805/BKAP304 (NAAS-awaited)
• Sandhu, Y,, Mahajan. S,, Sethi, R. S., Arora, J. S. & Mukhopadhyay, C. S. (2021). Differential karyotype profiling of three popular breeds of dogs in India. The Indian Journal of Animal Sciences, 90(11): 0367-8318. (NAAS- 6.32)
• Singh, J., Dhanoa, J. K., Choudhary, R. K., Singh, A., Sethi, R. S., Kaur, S. & Mukhopadhyay, C. S. 2020. MicroRNA expression profiling in PBMCs of Indian water Buffalo (Bubalus bubalis) infected with Brucella and Johne’s disease. ExRNA, 2: 1-13 (NAAS-awaited)
• Choudhary, R. K., Hundal, J. S., Wadhwa, M., Choudhary, S. & Goyal, N. (2020). Expression of lipogenic and milk protein genes in milk fat layer of a goat after dietary supplementation of omega-3 rich linseed and chia oils. Small Animal Ruminants, 185,106083 (NAAS-7.611).
• Capuco, A. V. & Choudhary, R. K. (2020). Invited Review: Determinants of milk production: Understanding population dynamics in the bovine mammary epithelium. Journal of Dairy Science, 103(3):2928-2940. (NAAS- 10.03).
• Saleem, A., Singh, S. P., Kumar, B. V. S., Arora, J. S., & Choudhary, R. K. (2019). Analysis of lysyl oxidase as a marker for diagnosis of canine mammary tumors. Molecular Biology Reports. 46(5): 4909-4919. (NAAS- 8.316).
• Choudhary, R. K., Choudhary, S., Mukhopadhyay, C. S., Pathak, D. & Verma, R. (2019). Deciphering the transcriptome of prepubertal buffalo mammary glands using RNA sequencing. Functional & Integrative Genomics.19(2):349-362 (NAAS- 9.41).
• Choudhary, S., Li, W., Bickhart, D., Verma, R., Sethi, R. S., Mukhopadhyay, C. S. & Choudhary R. K. (2018). Examination of the xanthosine response on gene expression of mammary epithelial cells using RNA-seq technology. Journal of Animal Science and Technology. 60(18); 1-12. (NAAS- 8.23).
  
• Kaur, H., Choudhary, S., Pathak, D., Singh, O., Verma, R. & Choudhary, R. K. (2018). Immunolocalization of Musashi 1 and Fibronectin Type III Domain Containing 3B in Water Buffalo Mammary Glands. Proc. Natl. Acad. Sci., India, Sect. B Biol. Sci. 88(1); 23–32. (NAAS- NA).
• Choudhary R. K., Choudhary, S., Pathak, D., Udehiya, R., Verma, R., Kaswan, S., Sharma, A., Gupta, D., Honparkhe, M. & Capuco, A. V. (2018). Evaluation of xanthosine treatment on gene expression of mammary glands in early lactating goat. Journal of Dairy Research. 85; 288-294. (NAAS- 7.90).
• Choudhary, R. K., Choudhary, S. & Verma, R. (2018). In vivo response of xanthosine on gene expression of lactating Beetal goat. Molecular Biology Reports. 45(4); 581-590. (NAAS- 8.32).
• Choudhary, S. & Choudhary, R. K. (2018). Rapid and efficient method of total RNA isolation from milk fat for transcriptome analysis of mammary gland. Proc. Natl. Acad. Sci., India, Sect. B Biol. Sci.89, 455–460. NAAS- awaited) (Scopus IF 1.40).
• Choudhary, R. K., Choudhary, S., Pathak, D. & Verma, R. (2017). Mucin 1 aberrantly expresses in goat mammary carcinoma. Journal of Stem Cell Research & Therapeutics. 2(4): 00072. (NAAS- NA).
• Manku, H. K.., Dhanoa, J. K., Kaur, S., Arora, J. S. & Mukhopadhyay, C. S. (2017). Biocomputational identification and validation of novel microRNAs predicted from bubaline whole genome shotgun sequences. Computational Biology and Chemistry, 70; 96-106. (NAAS- 8.88)
• Choudhary, R. K., Kaur, H., Choudhary, S. & Verma, R. (2017). Distribution and analysis of milk fat globule and milk fat globule with crescent in Murrah buffalo and crossbred cow. Proc. Natl. Acad. Sci., India, Sect. B Biol. Sci., 87(1): 167–172. (NAAS- NA) (Scopus IF 1.40).
• Choudhary, R. K. & Choudhary, S. (2016). Quantitative analysis of anisotropy of mammary ductal epithelial cells of buffalo mammary gland. EC Veterinary Science. 2(4): 171-176. (NAAS-awaited).
• Singh, J., Mukhopadhyay, C. S., Kaur, S., Malhotra, P., Sethi, R. S., & Choudhary, R. K. (2016). Identification of the MicroRNA Repertoire in TLR-Ligand Challenged Bubaline PBMCs as a Model of Bacterial and Viral Infection. PLoS One. 11(6); e0156598. (NAAS- 9.24).
  
• Choudhary, R. K., Choudhary, S., & Verma, R., (2016). CD10 is a marker of goat mammary cancer. EC Veterinary Science. 01 EC01O.01: 01-02. (NAAS: NA).
• Choudhary, R. K., Choudhary, S., Kaur, H. & Pathak, D. (2016). Expression of putative stem cell marker, Hepatocyte nuclear factor 4 alpha, in the mammary gland of water buffalo. Animal Biotechnology, 27(3): 182-89. (NAAS- 8.28).
  

Review Articles:

• Choudhary, R. K. (2022). Caprine Cancer: Etiology, Types, and Metanalysis of 21-Years of Case Reports. EC Veterinary Science, 7, 2000-2021. (NAAS- awaited)
• Sahoo, B., Choudhary, R. K., Sharma, P., Choudhary, S. & Gupta, M. K. (2021). Significance and relevance of spermatozoal RNAs to male fertility in livestock. Frontiers in Genetics, 12; 7681-7696. (IF-4.599).
• Choudhary, R. K. & Zhao, F. Q. (2022). Invited Review: Stem cells in mammary health and milk production. Current Stem Cell Research & Therapy. 17(3); 207-213. (IF-3.828)
• Choudhary, R. K. & Zhao, F-Q. (2021). Editorial: Re-Evaluation of Milk Components and Stem Cells. Acta Scientific Veterinary Sciences 3.1; 01-02. (IF-0.581)
• Dhanoa, J. K., Verma, R., Sethi, R. S., Arora, J. S. & Mukhopadhyay, C. S. (2019). Biogenesis and biological implications of isomiRs in mammals-a review. ExRNA, 1(1); 1-8. (NAAS- NA)
• Dhanoa, J. K., Sethi, R. S., Verma, R., Arora, J. S. & Mukhopadhyay, C. S. (2018). Long non-coding RNA: its evolutionary relics and biological implications in mammals: a review. Journal of animal science and technology, 60(1); 1-10. (NAAS- 8.23)
• Dhanoa, J. K., Mukhopadhyay, C. S. & Arora, J. S. (2016). Y-chromosomal genes affecting male fertility: A review. Veterinary World, 9(7), 783. DOI: 10.14202/vetworld.2016.783-791. (NAAS- 4.83)
• Hussain, S., Mukhopadhyay, C. S. & Arora, J. S. (2014). Applications and implications of mammalian antimicrobial peptides-a review. Agricultural Reviews, 35(4). DOI. 10.5958/0976-0741.2014.00918.0. (NAAS- 4.63)
• Tokas, J., Mukhopadhyay, C. S., & Verma, A. (2011). Self-renewal of spermatogonial stem cells: the most promising multipotent cells-a review. Veterinary World, 4(5); 234. (NAAS- 4.83)
• Mukhopadhyay, C. S., Tokas, J., & Mathur, P. D. (2011). Prospects and ethical concerns of embryonic stem cells research-a review. Veterinary World, 4(6); 281. (NAAS- 4.83)
• Mukhopadhyay, C. S., Kumar, R., & Brah, G. S. (2010). Gallinacin and fowlicidin: two promising antimicrobial peptides in chickens: a review. Veterinary World, 3(6), 297-300. (NAAS- 4.83)
  

 Edited and authored books:

• Mukhopadhyay, C. Sekharx, Choudhary, R. Kumar, & Iquebal, M. Asif. (2018). Basic applied bioinformatics: a beginner's guide for students. First edition. Hoboken, New Jersey: Wiley. ISBN: 9781119244332
• Singh, U., & Kumar, S., Mukhopadhyay, C. S., Deb, R., Alyethodi, R. R., Alex, R., Dhama, K. & Ganguly, I. (2015). Bioinformatic Approaches for Livestock Genome Analysis. Satish Serial Publishing House.
  
• Choudhary, R. K. & Choudhary, S. (2021). Stem Cells in Veterinary Science. Springer Singapore Hard Cover ISBN: 978-981-16-3463-5. 

Compendium:

• E-Compendium Editing: e-Compendium of the online “Training on artificial intelligence for students”, organized during January to March 2022. Eds. Kalambhe, D., Panwar, H., Dash, S.K., Sharma, A. & Mukhopadhyay, C. S. 2022. Published under Institutional Development Plan (IDP), Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab. Edition: I. ISBN: 978-93-5636-707-4 (Editor)
• Choudhary R. K. & Malik, Y. S. (2021). Biotechnological Approaches in Animal Research and Disease Diagnosis. College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University Ludhiana, Punjab. ISBN 978-93-5566-112-8. Pp. 106- (Editor)
• Malik, Y. P. S., Sethi, R. S. Narang, D., Choudhary, R. K., Pathak, D., Mehta, N. & Shanthanagouda, A. H. (2022). Transforming Livestock Economy through Innovations in Immunology and Biotechnology: A Souvenir-cum-Compendium. College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University Ludhiana, Punjab. ISBN 978-93-5619-958-3. Pp. 250. (Editor)
• Malik, Y. S., Mukhopadhyay, C. S., Choudhary, R. K., Kashyap, N. & Sunil Kumar, B. V. (2022). Training manual for a six-weeks short course on Bioinformatics held at the College of Animal Biotechnology in hybrid mode in July 2022. Pp. 108 (Editor)
  

Book Chapters:

Bioinformatics

The following facilities are available in the Department:

• High Performance Computing for Big Data Analysis
  
• Bioinformatic tools and software  for molecular data analysis
• Statistical Tools and software for research data analysis
• Equipment and instruments required for molecular genetic studies
• Nano-pore Sequencer (under purchase)

State-of-the-art facilities are available in the department, such as:

• High Power Computing analysis
• Gel Documentation System (Syngene)
• Veriti 96-well PCR Machine (Applied Biosystems Inc.)
• Refrigerated Centrifuge (Thermo Scientific)
• Microscope (Olympus)
• MultiSkan FC ELISA Plate Reader (Thermo Scientific)
• NanoDrop (Thermo Scientific)
• Shaking Water Bath (Thermo Scientific)
• UV Illuminator (Wealtec)
• Real time PCR

Bioinformatics

Faculty awards/ recognition

• Dr. CS Mukhopadhyay was awarded the prestigious "Fulbright-Nehru Academic and Professional Excellence Fellowships" (FNAPE: Research-2016-17), an international educational exchange program sponsored by the USA government, for 9 months (August 2016 to May 2017) to conduct research at the Department of Animal Science, Iowa State University, Ames, USA.
• Dr. Ratan Choudhary received Postdoctoral associateship training at the USDA project at the University of Vermont, Burlington, USA (Aug 2018-July 2020)
• Dr. Ratan Choudhary is a reviewer of USDA Israel BARD grant proposals and the French Animal National Research proposal.