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Gadvasu

Guru Angad Dev Veterinary And Animal Sciences University
ਗੁਰੂ ਅੰਗਦ ਦੇਵ ਵੈਟਨਰੀ ਐਂਡ ਐਨੀਮਲ ਸਾਇੰਸਜ਼ ਯੂਨੀਵਰਸਿਟੀ

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College of Animal Biotechnology

Bioinformatics
BIOINFORMATICS

Research Publications:

  • Singh J, Dhanoa JK, Choudhary RK, Singh A, Sethi RS, Kaur S and Mukhopadhyay CS*. 2020. MicroRNA expression profiling in PBMCs of Indian water Buffalo (Bubalus bubalis) infected with Brucella and Johne’s disease. ExRNA. 2: 1-13
  • Spitzer A, Tian Q, Choudhary RK and Zhao FQ. 2020. Bacterial endotoxin induces oxidative stress and reduces milk protein expression and hypoxia in the mammary gland. Oxidative Medicine and Cellular Longevity. https://doi.org/10.1155/2020/38943
  • Choudhary RK and Capuco AV. 2021. Expression of NR5A2, NUP153, HNF4A, USP15 and FNDC3B is consistent with their use as novel biomarkers for mammary stem/progenitor cells. Mol Histol. https://doi.org/10.1007/s10735-020-09948-8.
  • Shangraw E, Rodrigues R, Choudhary RK, Zhao FQ and McFadden TB. 2021. Hypogalactia in mammary quarters adjacent to LPS-infused quarters is associated with transcriptional changes in immune genes. Journal of Dairy Science. https://doi.org/10.3168/jds.2020-20048 
  • Shangraw E, Rodrigues R, Witzke M, Linder HF, Choudhary RK, Spitzer A, Zhao FQ, McFadden TB. 2020. Intramammary lipopolysaccharide infusion elicits local or systemic effects depending on milk component. Journal of Dairy Science. https://doi.org/10.3168/jds.2019-18022
  • Choudhary RK, Hundal JS, Wadhwa M, Choudhary S and Goyal N. 2020. Expression of lipogenic and milk protein genes in milk fat layer of goat after dietary supplementation of omega-3 rich linseed and chia oils. Small Animal Ruminants. 185:106083 https://doi.org/10.1016/j.smallrumres.2020.106083
  • Capuco AV and Choudhary RK. 2020. Invited Review: Determinants of milk production: Understanding population dynamics in the bovine mammary epithelium. J. Dairy Sci. 103(3):2928-2940. doi: https://doi.org/10.3168/jds.2019-17241
  • Saleem A, Singh SP, Kumar BVS, Arora JS and Choudhary RK. 2019. Analysis of lysyl oxidase as a marker for diagnosis of canine mammary tumors. Mol Biol Rep. https://doi.org/10.1007/s11033-019-04941-1.
  • Choudhary RK, Choudhary S, Mukhopadhyay CS, Pathak D and Verma R. 2019. Deciphering the transcriptome of prepubertal buffalo mammary glands using RNA sequencing. Functional & Integrative Genomics. doi: 10.1007/s10142-018-0645-5
  • Dhanoa JK, Singh J, Singh A, Arora JS, Sethi RS and Mukhopadhyay CS*. 2019. Discovery of isomiRs in PBMCs of diseased vis-à-vis healthy Indian water buffaloes. ExRNA. 1:12 https://doi.org/10.1186/s41544-019-0013-1
  • Grover J, Chhuneja P, Midha V, Ghia JE, Deka D, Mukhopadhyay CS, Sood N, Mahajan R, Singh A, Verma R, Bansal E and Sood A. 2019. Variable Immunogenic Potential of Wheat: Prospective for Selection of Innocuous Varieties for Celiac Disease Patients via in vitro Approach. Front. Immunol. 10: 84.
  • Choudhary S, Li W, Bickhart D, Verma R, Sethi RS, Mukhopadhyay CS and Choudhary RK. 2018. Examination of the xanthosine response on gene expression of mammary epithelial cells using RNA-seq technology. J. Anim Sci. Tech. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6045846/
  • Choudhary RK, Choudhary S, Pathak D, Udehiya R, Verma R, Kaswan S, Sharma A, Gupta D, Honparkhe M and Capuco AV. 2018. Evaluation of xanthosine treatment on gene expression of mammary glands in early lactating goat. J. Dairy Research. 85: 288-294. doi: 10.1017/S0022029918000493
  • Choudhary RK, Choudhary S and Verma R. 2018. In vivo response of xanthosine on gene expression of lactating Beetal goat. Molecular Biology Reports. https://doi.org/10.1007/s11033-018-4196-6
  • Choudhary S and Choudhary RK. 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. https://doi.org/10.1007/s40011-017-0955-8
  • Choudhary RK, Choudhary S, Pathak D and Verma R. 2017. Mucin 1 aberrantly expresses in goat mammary carcinoma. J Stem Cell Res Ther.; 2(4): 00072.
  • Manku HK, Dhanoa JK, Kaur S, Arora JS, Mukhopadhyay CS*. 2017. Biocomputational identification and validation of novel microRNAs predicted from bubaline whole genome shotgun sequences. Computational Biology and Chemistry, 70: 96-106.
  • Ahuja AK, Cheema RS, Narang D and Dhindsa SS. 2017. Bacterial pathogens and antibiotic susceptibility patterns of cervico-vaginal discharges in cross bred repeat breeding heifer cows. Int J Current Micro & Applied Sci, 6: 1769-1775.
  • Choudhary RK, Kaur H, Choudhary S and Verma R. 2017. Distribution and analysis of milk fat globule and milk fat globule with crescent in Murrah buffalo and crossbred cow. PNAS, India Section B: Biological Sciences. 87(1): 167–172.
  • Choudhary RK and Choudhary S. 2016. Quantitative analysis of anisotropy of mammary ductal epithelial cells of buffalo mammary gland. EC Veterinary Science. 2(4): 171-176.
  • Singh J, Mukhopadhyay CS, Kaur S, Malhotra P, Sethi RS and Choudhary RK. 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. doi: 10.1371/journal.pone.0156598
  • Baldwin RL, Capuco AV, Evock-Clover CM, Grossi P, Choudhary RK, Elsasser TH, Bertoni G, Trevisi E, Harmon RJ and McLeod KL. 2016. Consumption of endophyte-infected fescue during the dry period increases milk production in the subsequent lactation. J. Dairy Sci. 99 (9): 7574 – 7589. https://www.ncbi.nlm.nih.gov/pubmed/27320660
  • Choudhary RK, SChoudhary S and Verma R. 2016. CD10 is a marker of goat mammary cancer. 01 EC01O.01: 01-02.
  • Singh J, Mukhopadhyay CS, Kaur S, Malhotra P, Sethi RS and Choudhary RK. 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. https://doi.org/10.1371/journal.pone.0156598
  • Kaur H, Choudhary S, Pathak D, Singh O, Verma R and Choudhary RK. 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. https://link.springer.com/article/10.1007/s40011-016-0730-2.
  • Choudhary RK, Choudhary S, Kaur H and Pathak D. 2016. Expression of putative stem cell marker, Hepatocyte nuclear factor 4 alpha, in mammary gland of water buffalo. Animal Biotechnology. 27(3): 182-89. https://www.ncbi.nlm.nih.gov/pubmed/27092988.
  • Singh J, Mukhopadhyay CS*, Arora JS and Kaur S. 2015. Biocomputational Characterization and Evolutionary Analysis of Bubaline Dicer1 Enzyme. Asian Austr. J. Anim. Sci., 28(6): 876-887.
  • Kashyap N, Chakravarty AK and Deshmukh B. 2021. Novel heat index models for subtropical region based on daily milk production in crossbred Holstein cows. Turkish Journal of Veterinary and Animal Sciences. 45(3): 463-469.
  • Sharma N, Narang R, Kashyap N, Kumari S, Kaur S and Ratwan P. 2018. Genetic analysis of persistency in HF crossbred cattle at an organized farm of northern India. Tropical Animal Health and Production, 50:1219–1225.


Review Articles:

  • Dhanoa JK, Verma R,Sethi RS, Arora JS and, Mukhopadhyay CS*. 2019. Biogenesis and biological implications of isomiRs in mammals- a review. ExRNA. 1: 3.
  • JK Dhanoa, RS Sethi, R Verma, JS Arora, Mukhopadhyay CS*. 2018. Long non-coding RNA: its evolutionary relics and biological implications in mammals: a review. Journal of Animal Science and Technology 60 (1), 25
  • Dhanoa JK, Mukhopadhyay CS*, Arora JS. 2016. Y-chromosomal genes affecting male fertility: A review. Vet World. 9(7):783-91. doi: 10.14202/vetworld.2016.783-791.
  • Hussain, S., Mukhopadhyay CS* and Arora, J S. 2014. Applications and Implications of Mammalian Antimicrobial peptides- A review. Agricultural Reviews. 35(4):299-306. DOI. 10.5958/0976-0741.2014.00918.0.
  • J. Tokas, Mukhopadhyay CS* and Archana Verma. 2011. Self-Renewal of Spermatogonial Stem Cells: the Most Promising Multipotent Cells- a Review. Veterinary world. 4(5): 234-240.
  • Mukhopadhyay CS*, J. Tokas and P. D. Mathur. 2011. Prospects and Ethical Concerns of Embryonic Stem Cells Research-- A Review. Veterinary world. 4(6): 281-286.
  • Mukhopadhyay CS*, G.V.P.P.S. Ravi Kumar and G. S. Brah. 2009. Gallinacin and Fowlicidin: Two Promising Antimicrobial Peptides in Chicken- A Review. Veterinary World. 3(6):297-300.

 Edited and authored books:

  • Basic Applied Bioinformatics-A Beginner's Guide for Students. 2017. CS Mukhopadhyay, RK Choudhary, MA Iquebal. John Wiley & Sons Limited; The Atrium, Southern Gate, Chichester, West Sussex, United Kingdom. ISBN: 9781119244332
  • Bioinformatic approaches for livestock genome analysis. 2015. Eds. U. Singh, S. Kumar, Mukhopadhyay CS, R. Deb, R. R. Alyethodi, R. Alex, K. Dhama, and I Ganguly. Satish Serial Publishing House, Delhi, India, ISBN: 9789384053017.

 Book Chapters:

  • Mukhopadhyay CS, Amit Kumar, Rajib Deb. 2020. Cattle genomics: genome projects, current status, and future applications. Genomics and Biotechnological Advances in Veterinary, Poultry, and Fisheries. Eds.YS Malik, D Barh, V Azevedo and SMP Khurana. Academic Press, Elsevier. First Ediction. ISBN: 9780128163528. PP. 3-28
  • R Deb, Mukhopadhyay CS, GS Sengar, AS da Cruz, DC Silva, IP Pinto, LB Minasi, EOA Costa, and AD da Cruz. 2020 Genetic markers for improving farm animals. Genomics and Biotechnological Advances in Veterinary, Poultry, and Fisheries. Eds.YS Malik, D Barh, V Azevedo and SMP Khurana. Academic Press, Elsevier. First Ediction. ISBN: 9780128163528. PP. 107-129
  • R Chawla, JS Arora, RK Dubey, Mukhopadhyay CS. 2018. Omics Approaches and Applications in Dairy and Food Processing Technology. Eds. Debmalya Barh, Vasco Azevedo. In Omics Technologies and Bio-Engineering. Elsevier Science & Technology Publishers. 271-295. ISBN: 9780128046593
  • Mukhopadhyay CS, 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”. Publisher 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 CS, Sarkar, C., Rai, A. and Kumar, D. 2015. Applications of Bioinformatics in Plant and Agriculture. [Editors Barh,D., Khan M.S., Davies, E.] In: PlantOmics: The Omics of Plant Science, Edition: First, Chapter: Applications of Bioinformatics in Plant and Agriculture, Springer Publications. pp.755-789 DOI: 10.1007/978-81-322-2172-2_27. ISBN 978-81-322-2172-2
  • Mukhopadhyay CS 2015. Designing and In silico quality checking of PCR primers. In Bioinformatic Approaches for Livestock Genome Analysis. Eds. U. Singh, S. Kumar, Mukhopadhyay CS, R. Deb, R. R. Alyethodi, R. Alex, K. Dhama, and I. Ganguly. Satish Serial Publishing House, Delhi, India. Pp. 23-76. ISBN: 9789384053017.
  • Mukhopadhyay CS and S.S. Osahan. 2015. Sequence alignment: concepts and methods. In Bioinformatic Approaches for Livestock Genome Analysis. Eds. U. Singh, S. Kumar, Mukhopadhyay CS, R. Deb, R. R. Alyethodi, R. Alex, K. Dhama, and I. Ganguly. Satish Serial Publishing House, Delhi, India. Pp. 77-112. ISBN: 9789384053017.
  • Mukhopadhyay CS 2015. Submitting Nucleotide sequence to Bankit. In Bioinformatic Approaches for Livestock Genome Analysis. Eds. U. Singh, S. Kumar, Mukhopadhyay CS, R. Deb, R. R. Alyethodi, R. Alex, K. Dhama, and I. Ganguly. Satish Serial Publishing House, Delhi, India. Pp. 113-136. ISBN: 9789384053017.
  • Mukhopadhyay CS and S.S. Osahan. 2015. Molecular phylogeny: basics, methods and applications. In Bioinformatic Approaches for Livestock Genome Analysis. Eds. U. Singh, S. Kumar, Mukhopadhyay CS, R. Deb, R. R. Alyethodi, R. Alex, K. Dhama, and I. Ganguly. Satish Serial Publishing House, Delhi, India. Pp. 137-156. ISBN: 9789384053017.
  • Sarika, M.A. Iquebal, Mukhopadhyay CS, P. G. Koringa, A. Rai, C.G. Joshi and D. Kumar. 2015. Genome annotation in Prokaryotes and Eukaryotes. In Bioinformatic Approaches for Livestock Genome Analysis. Eds. U. Singh, S. Kumar, Mukhopadhyay CS, R. Deb, R. R. Alyethodi, R. Alex, K. Dhama, and I. Ganguly. Satish Serial Publishing House, Delhi, India. Pp. 247-278. ISBN: 9789384053017.
  • Mukhopadhyay CS and Dinesh Kumar. 2013. Applications of SNP-Chip in Bovine Selection. In. Advances in Cattle Research [Eds. U. Singh, S. Kumar, A. Kumar, R. Deb and A. Sharma]. Satish Serial Publishing House, Delhi-110033, India. Pp. 1-18. ISBN: 9789381226421
  • Mukhopadhyay CS, P.P. Dubey and A.K. Gupta. 2013. Assessment of Sperm Chromatin Compactness and Integrity in Mammalian Semen Sample. In. Genetic Improvement of Livestock and Poultry [Eds. Singh, C.V.& Barwhal R.S.]. New India Publishing Agency, New Delhi. Pp. 275-283. ISBN: 9381450821; 9789381450826.