Bioinformatics

The Department of Bioinformatics is one of the three departments of the College of Animal Biotechnology. The focus of the department is towards in-silico analyses of genomes, parentage determination, and marker identification for molecular characterization of livestock and companion animals. The department also provides assistance and consultation on computational analysis of the biological data (genomics, transcriptomics, and proteomics) generated from other departments of the college and university. Additionally, the department is engaged in the development of therapeutic applications of stem cells and their products for livestock and pet animals using molecular biology and computational approaches. The department is newly venturing towards the development and application of Information and Communication Technology (ICT) and the Internet of Things (IoT), intended to be used for livestock by the farmers.


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. 


Faculty Detail

Back

Dr. Chandra Sekhar Mukhopadhay

Designation : Senior Scientist

Contact Address : Department of Bioinformatics, College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana-141004

Telephone :

Mobile : 9779541452

Email : csmbioinfo@gmail.com, csmukhopadhyay@gadvasu.in

Academic Credentials

  • B.V.Sc. & A.H. (WBUAFS, Kolkata): 2002
  • M.V.Sc. (Animal Genetics & Breeding, ICAR-NDRI, Karnal): 2004
  • Ph.D. (Animal Genetics & Breeding, ICAR-NDRI, Karnal): 2008
  • MSc (Information Technology) (PTU, Distance Education): 2013
  • One year online certificate masters course on Artificial Intelligence (from Simplilearn): 2020

Teaching appointments

  • Teaching: Bioinformatics, Animal Genomics, Genetics
    Training: Periodically organize online and offline trainings on Bioinformatics

Other appointments

  • In charge, Viral Research and Diagnostic Laboratory (COVID19 Diagnostics Lab, GADVASU, Ludhiana) (21st October 2020 till date)
  • Program Officer of National Service Scheme (NSS) wing of the B. Tech. (Biotechnology) students of the College of Animal Biotechnology, GADVASU, Ludhiana (2017 onward).
  • Member, RRC and PME Cell, College of Animal Biotechnology
  • Member, Disciplinary Committee of the College of Animal Biotechnology, GADVASU, Ludhiana
  • Nominee, Director of Research for Purchase
  • Nominee, Dean PGS  for verification of Program of Work of PG Students.
  • Member, Anti Ragging Committee
  • Member, Research Review Committee
  • Program Officer of National Service Scheme (NSS) of the College (2017 – till date)

Area of research

  • Bioinformatics
  • Artificial Intelligence
  • Genomics and Transcriptomics

Ongoing projects


SN

Name/ No of Project/ Scheme

Funding agency

Period

From To

Scientists involved

 

(PI/ Co-PI)

Total Funding

1.

Institutional Development Plan for Improved Learning Outcome, Skill and Entrepreneurship at GADVASU

ICAR, Govt. of India

2018-23

PI: Dr. P. S. Brar, Later Dr. SPS Ghuman

 

Member:

Dr. C.S. Mukhopadhyay

 

30 Crore

2.

Identification of Species-specific markers for parentage determination in livestock

RKVY

2021-23

PI:

Dr. CS Mukhopadhyay

Co-PI:

Dr. J S Arora

Dr. S Kaur

15 Lakh






Completed Projects

SN

Name/ No of Project/ Scheme

Funding Agency

Period

From   To

Total Funding

Scientist involved

(PI/ Co-PI)

1.                   

Parentage determination and cytogenetic profiling in dogs. “DBT-GADVASU Canine Research Centre and Network.”

DBT, New Delhi

2019-2021

Rs 39.7 lacs

PI: Dr. CS Mukhopadhyay

Co-PI:

 Dr. JS Arora,

Dr. RK Choudhary (Later Dr. RS Sethi),

Dr. S Mahajan,

Dr. CS Randhawa,

Dr. S Kota (TRPBV, Chennai )

2.                   

TLR-Ligands: To Design Novel Vaccines Adjuvants Against New Castle Disease in Indigenous Chicken

DBT, New Delhi

2014-2018

26 Lacs

CC-PI: Dr. CS Mukhopadhyay

PI: Dr. TC Tolenkhomba (CAU, Imphal)

CC-Co-PI:

Dr. JS Arora

Dr. N. Singh

3.                   

Construction of miRNA library associated with Disease Resistance in Buffalo

SERB-DST

2012-2015

20.77 Lacs

PI:

Dr. CS Mukhopadhyay

4.                   

Characterization of Fecundity Gene in Assam Hill Goat

DBT, Govt. Of India

2017-2020

26.79 Lacs

PI: Dr. JS Arora

Co-PI: Dr. CS Mukhopadhyay

5.                   

Molecular characterization of canine distemper virus field isolates for selection of suitable vaccine candidate(s)

DBT, Govt. Of India

2018-2021

30 Lacs

PI: Dr. D Deka

Co-PI: Dr. CS Mukhopadhyay

Research honours awards

  • Appreciation award: by GADVASU for contributions towards establishment of COVID testing facility at GADVASU, Ludhiana; January 26, 2022.   (Date of Award: January 26, 2022)
  • “Best poster award” Award: Jaswinder Kaur, Kanwaljit Rana and C.S Mukhopadhyay* on the topic of “BOON OF COW CURD CONSUMPTION” in National webinar on CowPathy and animal health
  • on 16 December 2021
  • Best Researcher Award (for the College of Animal Biotechnology) of the Year 2018-19 given away by Guru Angad Dev Veterinary and Animal Sciences University on 29th may 2019
  • “Fulbright-Nehru Academic and Professional Excellence Fellowships” (FNAPE: Research-2016-17), an international educational exchange program sponsored by the USA Government, for conducting research at Iowa State University, USA, for 9 months (August 2016 to May 2017)
  • Punjab Farmers Commission funded Advanced Foreign Training on “Marker Assisted Selection and Functional Genomics” for 6 months (2011 to 2012) ate Iowa State University, USA.

No of publications

Research: 60Extension: 07     
Books: 07      
Manuals: 05

Publication

  • Sandhu Y, Mahajan S, Sethi RS, Arora, JS and Mukhopadhyay, CS*. 2021. Differential karyotype profiling of three popular breeds of dogs in India. The Indian Journal of Animal Sciences; 90(11): 0367-8318. http://epubs.icar.org.in/ejournal/index.php/IJAnS/article/view/111496 (IF: 0.33)
  • Mukhopadhyay CS*, Singh KP, Kashyap N, Sandhu Y, Singh S. 2020.SWOT analysis to identify important factors influencing dairy farming practices in Punjab. Agricultural Research Journal. 57(5):769-778. DOI : 10.5958/2395-146X.2020.00112.X (IF: UC)
  • Kaur B., Kaur J., Kashyap N., Arora J.S., and Mukhopadhyay C.S.* 2023. A comprehensive review of genomic perspectives of canine diseases as a model to study human disorders. The Canadian Journal of Veterinary Research. 87(1):3-8 (IF 0.45)
  • Malik, Y. S., Mukhopadhyay, C. S., Choudhary, R. K., Kashyap, N., and Sunil Kumar B.V. 2022. Short Course on Bioinformatics. Pp 108. (Editor).
  • Kalambhe, D., Bhanot, R., Malik, H., Mukhopadhyay, C.S. and Gill, J. P. S. 2022. The Indigenous Dogs of India: The Forgotten Treasure. Published by Project Monitoring Unit- DBT-GADVASU-CRC, Directorate of Research, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana (Editor)
  • Electronic Compendium Editing: e-Compendium of the online “Training on artificial intelligence for students”, organized during January to March 2022. Eds. D Kalambhe, H Panwar, SK Dash , A Sharma and C S Mukhopadhyay. 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).
  • Mukhopadhyay CS and Kaur B. 2022. Applications of Tag-SNPs in Quantitative Trait Loci (QTL) Identification. In Genomic, Proteomics, and Biotechnology. Eds. RC Sobti, M Mukesh, A Sobti. Chapter 6. 1st Edition. CRC Press- Taylor and Francis Group. Boca Raton. eBook ISBN 9781003220831

Invited Lectures:

  • More than 40 invited talks /hands on training in various Institutions in India.

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

SN

Title of the project

Objectives

Investigators

Budget

Funding Agency

Duration of Project

1.

Modeling of indigenous diagnostics and immuno-potent vaccine candidates to combat African Swine Fever in India

1. Dual gene targeted real-time qPCR methods for detection and confirmation of ASFV

2. Development of protein-based diagnostics for detection of ASF at field and laboratory condition

CC PI: Dr. YPS Malik

 

CC Co-PI:

Dr. BV Sunil Kumar

Dr. NK Singh

Dr. Ratan K Choudhary

92.82 Lakh

(CC GADVASU: 39.56 Lakh)

DBT-NER

2021-2023

2.

Parentage determination vis-à-vis breed identification of indigenous canine through scanning the molecular signature panels

 

1. Parentage determination in Indian dog breeds using SSR-markers

 

2. Determining breed purity using microsatellite allele mining in indigenous dog-breeds

 

3. Molecular characterization through signature-paneling of indigenous canines

PI: Dr. CS Mukhopadhyay

 

Co-PI:

Dr. Neeraj Kashyap

Dr. Shashikant Mahajan

Dr. Asmita Narang

 

89 Lakh

DBT

 

 

 

 

 

 

 

2022-25

3.

Investigating the role of adipose tissue-derived stromal vascular fractions (SVFs) combined with Xanthosine in veterinary regenerative medicine

 

1. To establish adipose tissue-derived stromal vascular fractions (AT-SVFs) in dog.

2. To develop in vitro skin equivalent model of dog.

3. To evaluate effects of AT-SVFs in the presence/absence of xanthosine in skin equivalent.

4. To evaluate effects of AT-SVFs in the presence/absence of xanthosine in dog's surgical wounds.

PI: Dr. Ratan K Choudhary

 

Co-PI:

Dr. Yashpal Singh Malik

Dr. Devendra Pathak

 

50 Lakh

DBT

2022-25

4.

Enhancement of production and productivity potential of livestock poultry and fisheries sector for socio economic upliftment of the farmers of Punjab (2019-20) (RKVY-12-B1).

Establishment of Centralized Research Laboratory at GADVASU

Dr. Yashpal Singh Malik

 

256.0 Lakh

RKVY- 2020-21

2021-22

5.

Capacity Building in Veterinary Diagnostics and Specialized Services

 

RKVY-13B-1

Establishment of Centralized Research laboratory at GADVASU

Dr. Yashpal Singh Malik

 

44.0 Lakh

RKVY- 2020-21

2022-23

6.

Institutional Development Plan for Improved Learning Outcome, Skill, and Entrepreneurship at GADVASU

 

To support Participating Agricultural Universities and ICAR in providing more relevant and higher quality education to Agricultural University students

PI: Dr. P. S. Brar, Later Dr. SPS Ghuman

 

Member:

Dr. C.S. Mukhopadhyay

30 Crore

ICAR, Govt. of India

2018-23
Completed Research Projects

SN

Title of the project

Objectives

Investigators

Budget

Funding Agency

Duration of Project

1.

Elucidating the role of Cas6, Cas7 and Cas8 in spirochetes CRISPR adaptive immunity against alien genetic elements

1. Collection of serum and isolation of Leptospira for molecular epidemiology using CRISPR array from animals suspected for leptospirosis.

2. Generation of antibodies against recombinant Cas6, Cas7 and Cas8 proteins.

CPI: Dr. Ratan K Choudhary

Co-PI:

Dr. Satparkash Singh

68.72 Lakh (CC GADVASU 13.0 lakh)

DBT - NE Twinning

2018-2021

2.

Parentage Determination and Cytogenetic Profiling in Dogs

1. To determine the cytogenetic profiles of the three common dog breeds in India.

2. To identify a set of microsatellite and SNP markers that can be used to determine parentage and breed specific SNP/haplotypes in three most important dog-breeds.

PI: Dr. CS Mukhopadhyay

Co-PI:

 Dr. JS Arora,

Dr. RK Choudhary (Later Dr. RS Sethi),

Dr. S Mahajan,

Dr. CS Randhawa,

Dr. S Kota (TRPBV, Chennai)

Rs. 39.12 Lakh

DBT, India

2018-2021

3.

TLR-Ligands: To Design Novel Vaccines Adjuvants Against Newcastle Disease in Indigenous Chicken

1. To investigate the effect of TLR ligand (Poly I: C, LPS, and CpG ODN) on enhancing the immune response against Newcastle disease in indigenous chicken (Aseel Breed).

2. To study the impact of the alum based as well as an emulsion-based delivery system to be used with the TLR ligands on immune response against Newcastle disease

3. To study the longevity of the immune response following administration of the TLR ligands

CC-PI: Dr. CS Mukhopadhyay

CC-Co-PI:

Dr. NK Singh

Dr. JS Arora

26 Lakh

DBT, in collaboration with CAU, Imphal

2014-2018

4.

Xanthosine treatment: A novel strategy to increase milk production and mammary stem cells

1. Evaluate the effect of xanthosine in increasing total milk production in goat.

2. Evaluate the role of xanthosine in increasing stem cell population in goat mammary tissue.

3. Analyze changes in global gene expression of goat mammary tissue induced by xanthosine, way towards identifying pathways of increased milk production and stem cell population.

PI: Dr. Ratan K Choudhary

Co-PI:

Dr. Ramneek Verma,

Dr. RS Sethi

Dr. Dipak Deka

66.3 Lakh

DBT, India

2014-17

5.

Construction of miRNA Library Associated with Disease Resistance in Buffalo

1. To screen and characterize the array of endogenous miRNA (associated with disease resistance in Murrah buffalo) by high throughput sequencing of total RNA in cultured cells.

2. To construct miRNA library in buffalo for comparative bioinformatic analysis between healthy and disease susceptible ones.

3. Cloning, sequencing vis-à-vis to study the bubaline Dicer Enzyme.

PI: Dr. CS Mukhopadhyay

Co-PI: NA

 

 

20.77 Lakh

DST-SERB, India

2012-15

Bioinformatics

  • Reported the maiden atlas of the differentially expressed miRNAs in TLR ligand stimulated vis-à-vis control bubaline PBMCs (DST-SERB Young Scientist Project).
  • Displayed miRNA library by GADVASU for disseminating the information to the research community. http://gadvasu.in/noticedetails.asp?J=0&id=785 
  • Sequencing of Gaddi dog genome and identification of protein-coding and non-coding genes
  • Mammary stem cell expression and in vivo manipulation using xanthosine have been shown in Beetal goats.
  • Established a non-invasive method of isolating RNA from milk and RNA sequencing of the milk fat layer.
  • Early pregnancy diagnosis in water buffalo using probe-based duplex qPCR assay
  • Fine-needle aspiration-based gene expression analysis for diagnosing canine mammary tumor

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:

  • Choudhary, S., Malik, Y. S., & Choudhary, R. K. (2022). Therapeutic potential of stem cell secretome, in Recent Advances in Stem Cell Biology and Therapeutics. Bhartiya, D. & Chandra, V. (Eds.) Issue 29, Publishers: Indian Society for the Study of Reproduction and Fertility. Page 21-23. ISSN 2395-2806
  • Choudhary, R. K. (2021). Overview of Stem Cells and Their Applications in Veterinary Medicine. In: R. K. Choudhary & S. Choudhary (eds.) Stem Cells in Veterinary Science. Springer, Singapore. https://doi.org/10.1007/978-981-16-3464-2_1
  • Kaur, T. P., Verma, R. & Choudhary, R. K. (2021). Introduction to Mammary Gland and Its Cell Types. In: R. K. Choudhary & S. Choudhary (eds.) Stem Cells in Veterinary Science. Springer, Singapore. https://doi.org/10.1007/978-981-16-3464-2_2
  • Choudhary R. K. (2021). Milk and Milk-Derived Stem Cells. In: R. K. Choudhary & S. Choudhary (eds.) Stem Cells in Veterinary Science. Springer, Singapore. https://doi.org/10.1007/978-981-16-3464-2_8
  • Choudhary R.K. 2021 Identification of Species-Specific Stem Cells and Challenges. In: R. K. Choudhary & S. Choudhary (eds.) Stem Cells in Veterinary Science. Springer, Singapore. https://doi.org/10.1007/978-981-16-3464-2_19
  • Choudhary R. K. & Choudhary, S. (2021). Regulations of Animal Cell-Based Drugs in Veterinary Regenerative Medicine. In: R. K. Choudhary & S. Choudhary (eds.) Stem Cells in Veterinary Science. Springer, Singapore. https://doi.org/10.1007/978-981-16-3464-2_20
  • Mukhopadhyay, C. S., Kumar, A. & Deb. R. (2020). Cattle genomics: genome projects, current status, and future applications. In: Y. S. Malik, D. Barh, V. Azevedo & S. M. P. Khurana (eds.). Genomics and Biotechnological Advances in Veterinary, Poultry, and Fisheries. Academic Press, Elsevier. First Edition. ISBN: 9780128163528. PP. 3-28
  • Deb, R., Mukhopadhyay, C. S., Sengar, G. S., da Cruz, A. S., Silva, D. C., Pinto, I. P., Minasi, L. B., Costa, E. O. A. & da Cruz, A. D. (2020). Genetic markers for improving farm animals. In: Y. S. Malik, D. Barh, V. Azevedo & S. M. P. Khurana (eds.). Genomics and Biotechnological Advances in Veterinary, Poultry, and Fisheries. Academic Press, Elsevier. First Edition. ISBN: 9780128163528. PP. 107-129
  • Chawla, R., Arora, J, Dubey, R. K, Mukhopadhyay, C. S. (2018). Omics approaches and applications in dairy and food processing technology. In: D. Barh & V. Azevedo (eds.). Omics Technologies and Bio-Engineering. Elsevier Science & Technology Publishers. 271-295. ISBN: 9780128046593
  • Mukhopadhyay, C. S., Verma, R., & Singh, J. (2017). Extraction and qPCR-based detection of miRNAs from cultured PBMCs of bubaline origin. [Mossman, Karen] In: Innate Antiviral Immunity: Methods and Protocols. Humana Press, Springer New York, USA; Series Vol. 1656; pp. 89-102 eBook ISBN: 978-1-4939-7237-1, Hardcover ISBN: 978-1-4939-7236-4, DOI 10.1007/978-1-4939-7237-1; Series ISSN: 1064-3745.
  • Iquebal, M. A., Jaiswal, S., Mukhopadhyay, C. S., Sarkar, C., Rai, A. & Kumar, D. (2015). Applications of Bioinformatics in Plant and Agriculture. In: D. Barh, M.S. Khan & E. Davies. PlantOmics: The Omics of Plant Science, Edition: First, Springer Publications. pp.755-789 DOI: 10.1007/978-81-322-2172-2_27. ISBN 978-81-322-2172-2
  • Mukhopadhyay, C. S. (2015). Designing and In-silico quality checking of PCR primers. In: U. Singh, S. Kumar, C. S. Mukhopadhyay, R. Deb, R. R. Alyethodi, R. Alex, K. Dhama, & I. Ganguly (eds.). Bioinformatic Approaches for Livestock Genome Analysis. Satish Serial Publishing House, Delhi, India. Pp. 23-76. ISBN: 9789384053017.
  • Mukhopadhyay, C. S. & Osahan, S.S. (2015). Sequence alignment: concepts and methods. In: U. Singh, S. Kumar, C. S. Mukhopadhyay, R. Deb, R. R. Alyethodi, R. Alex, K. Dhama, & I. Ganguly (eds.). Bioinformatic Approaches for Livestock Genome Analysis. Satish Serial Publishing House, Delhi, India. Pp. 77-112. ISBN: 9789384053017.
  • Mukhopadhyay, C. S. (2015). Submitting Nucleotide sequence to Bankit. In: U. Singh, S. Kumar, C. S. Mukhopadhyay, R. Deb, R. R. Alyethodi, R. Alex, K. Dhama, & I. Ganguly (eds.). Bioinformatic Approaches for Livestock Genome Analysis. Satish Serial Publishing House, Delhi, India. Pp. 113-136. ISBN: 9789384053017.
  • Mukhopadhyay, C. S. & Osahan, S.S. (2015). Molecular phylogeny: basics, methods, and applications. In: U. Singh, S. Kumar, C. S. Mukhopadhyay, R. Deb, R. R. Alyethodi, R. Alex, K. Dhama, & I. Ganguly (eds.). Bioinformatic Approaches for Livestock Genome Analysis. Satish Serial Publishing House, Delhi, India. Pp. 137-156. ISBN: 9789384053017.
  • Sarika, M., Iquebal, A., Mukhopadhyay, C. S., Koringa, P. G., Rai, A., Joshi, C. G. & Kumar, D. (2015). Genome annotation in Prokaryotes and Eukaryotes. In: U. Singh, S. Kumar, C. S. Mukhopadhyay, R. Deb, R. R. Alyethodi, R. Alex, K. Dhama, & I. Ganguly (eds.). Bioinformatic Approaches for Livestock Genome Analysis. Satish Serial Publishing House, Delhi, India. Pp. 247-278. ISBN: 9789384053017.
  • Mukhopadhyay, C. S. & Kumar, D. (2013). Applications of SNP-Chip in Bovine Selection. In: U. Singh, S. Kumar, A. Kumar, R. Deb & A. Sharma (eds.). Advances in Cattle Research. Satish Serial Publishing House, Delhi-110033, India. Pp. 1-18. ISBN: 9789381226421
  • Mukhopadhyay, C. S., Dubey, P.P. & Gupta, A. K. (2013). Assessment of Sperm Chromatin Compactness and Integrity in Mammalian Semen Sample. In. C. V. Singh & R. S. Barwhal (eds.). Genetic Improvement of Livestock and Poultry. New India Publishing Agency, New Delhi. Pp. 275-283. ISBN: 9381450821; 9789381450826.

    • 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

    Following trainings have been organized recently in the department

    SN

    Name of Training

    Dates

    Funding Agency

    Course Director/

    Organizing secretary

    1

    Artificial Intelligence for Students

    16 Days (divided into 4 modules) during January to March 2022.

    NAHEP-IDP (In collaboration with COVS)

    Dr. CS Mukhopadhyay

    2

    Setting up real time qPCR for disease diagnosis and gene expression studies

    11th March 2022

    ICAR scheduled class sub plan (SCSP) scheme

    Dr. RK Choudhary

    3

    Sensitization on basic bioinformatics for molecular data analysis

    22nd to 24th December 2021

    Institutional

    Dr. CS Mukhopadhyay

    4

    SNP data analysis for detecting parentage in animals

    23rd September 2021

    DBT, Govt. Of India

    Dr. CS Mukhopadhyay

    5

    Skill development on advanced bioinformatics in genome analysis of livestock and pets

    5th to 25th March 2021

    DBT, Govt. Of India

    Dr. CS Mukhopadhyay

    6

    Training on biotechnological approaches in animal research and disease diagnosis

    1st to 12th February 2021

    COABT

    Dr. RK Choudhary

    7

    Training on molecular diagnostics techniques: PCR and qPCR

    28th – 30th October 2021

     

    COABT

    Dr. RK Choudhary

    8

    Biocomputational interventions to analyze canine & livestock genomes

    6th - 9th October 2020

    DBT, Govt. Of India

    Dr. CS Mukhopadhyay


    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.

    © 2024 www.gadvasu.in, All Rights Reserved  |  Developed & Hosted by: Cyberframe