Bioinformatics Centre

Bioinformatics Centre at Centre for Plant Biotechnology and Molecular Biology (CPBMB), College of Agriculture, Kerala Agricultural University was established in 1995, as Distributed Information Sub-Centre (DISC) under DBT’s Bioinformatics Network programme. Main objective of the Centre is strengthening teaching, research and training in agricultural bioinformatics at Kerala Agricultural University. The performance of the Centre was evaluated and in 2004, the Centre has been declared as Distributed Information Centre (DIC). During this period, DBT-DIC at KAU has grown as a Centre facility assisting the entire research programmes in KAU in genome and sequence analysis, molecular docking and rational drug discovery, primer and probe designing etc. Recently, the Centre has completed the sequencing of two economically important microbes and published large number of phytocompounds with potential for drug development. Further, these molecules are being tested in vitro and in vivo. The facilities at the Centre include many computers including high performance computing cluster.

The Centre is currently running under a revolving fund scheme called as “Training Unit in Bioinformatics Centre”. In this, the students will be offered short term (one-three weeks) trainings as well as long term trainings or project works (one month or more).The Centre augments access to the global information in life sciences especially Plant Science and Plant Biotechnology involving students and scientists of the University and other S&T institutions. The Centre provide services to promote Biotechnological research and development in the specialized areas of Agriculture. The Centre also offers a (2+1) credit course in Bioinformatics to the Postgraduate students of Centre for Plant Biotechnology and Molecular Biology.

Support

Coordinator

Dr. Deepu Mathew

Professor & Coordinator

Bioinformatics Centre, College of Agriculture

Kerala Agricultural University, Vellanikkara, Thrissur

Research Associate

Mr. Ravisankar V

Areas: NGS data analysis, Molecular evolutionary analysis

 

Contact

Professor and Coordinator

Bioinformatics Centre, IT-BT Complex

Kerala Agricultural University, Vellanikkara,

KAU P.O, Thrissur, Kerala. PIN 680656.

E-mail – bic@kau.in, kaubioinfo@gmail.comdeepu.mathew@kau.in

 

Categories

Trainings

The Centre is offering short term (one-three weeks) trainings as well as long term trainings or project works (3-6 months) for the students from other institutions for a fees decided by the University. Students who are interested may send their applications to bic@kau.in along with their CV and details of training/project work required.

 

Selected publications (Last 5 years)

Devilekshmi S., Nazeem, P.A., Raghavamenon, A. C., Valsalan, R., Babu, T. D., James,P., Narayanankutty,A., Davis,S.P. and Shylaja, M. R. 2017. Coconut phytocompounds inhibits polyol pathway enzymes: Implication in prevention of microvascular diabetic complication. Prostaglandins, Leukotrienes and Essential Fatty Acids, 127:20-24.

 

Devilekshmi, S., Nazeem, P.A., Arunaksharan, N., Jeksy, J.M. and Achuthan C.R. 2016. In Silico and Wet Lab Studies Reveal the Cholesterol Lowering Efficacy of Lauric Acid, a Medium Chain Fat of Coconut Oil. Plant Foods in Human Nutrition, 71: 410-415.

 

Kumar, D.K., Mathew, D., Nazeem, P.A. Abida P.S., C. George Thomas. 2017. A comparative proteome assay on the quality of yard long bean pods as influenced by the organic and inorganic nourishment systems. Acta Physiologiae Plantarum, 39: 265-275.

 

John, J. K., Roy, Y. C., Krishnaraj, M. V., Nair, R. A., Deepu, M. and Bhat, K. V. A new subspecies of Momordicacochinchinensis (Lour.) Spreng. subsp. andamanica (Cucurbitaceae) endemic to Andaman Islands, India. Genetic Resources and Crop Evolution, 65(1): 103-112.

 

Roy,N., Nazeem, P.A., Babu, T. D.,Abida, P.S., Narayanankutty,A., Valsalan,R., Valsala, P. A. and Raghavamenon A.C.2017. EGFR gene regulation in colorectal cancer cells by garlic phytocompounds with special emphasis on S-allyl-L-cysteine sulfoxide. Interdisciplinary Sciences: Computational Life Sciences, 10: 686–693.

 

Roy, N., Nazeem, P.A., and Abida, P.S. 2017. Comparative docking studies to prove the accuracy of computational tools for recognizing the inhibitory action of garlic (Allium sativum L.) on diabetes. International Journal of Chemical Studies, 5(4): 342-345.

 

James,P., Davis,S.P., Valsalan,R., Nazeem,P.A. and Deepu, M., 2017. Novel Anti-diabetic Molecules from the Medicinal Plants of Western Ghats of India, Identified through Wide Spectrum In silico Analyses. Journal of Herbs, Spices and Medicinal Plants, 23 (3): 249-262.

 

Pradhan, D., Deepu Mathew, Mathew, S. K. and Nazeem, P. A., 2018, Identifying the markers and tagging a leucine-rich repeat receptor-like kinase gene for resistance to anthracnose disease in vegetable cowpea [Vigna unguiculata (L.) Walp.]. The Journal of Horticultural Science and Biotechnology, 93(3): 225-231. doi: 10.1080/14620316.2017.1362962.

 

Manjesh, S., Abida, P.S., Valsala, P.A., Rosemary, F. and George, T. 2017. Identification and characterization of differentially expressed genes responsible for drought tolerance in rice mediated by Pseudomonas fluorescens. Rice Science, 24(5): 291-298.

 

Mathew, D., John, P. L., Manila, T. M., Divyasree, P., Rajan, V. T. K. S., 2017, Therapeutic molecules for multiple human diseases identified from pigeon pea (Cajanus cajan L. Millsp.) through GC-MS and molecular docking. Food Science and Human Wellness, 6(4): 202-216 doi: 10.1016/j.fshw.2017.09.003.

 

Radha T., Priyanka James, Simi S., Sangeetha P. Davis, Nazeem P. A., Shylaja M. R. and Deepu Mathew, 2018 MangoDB: A Database of Mango Varieties and Landraces of Indian Subcontinent. Current Science 114(10): 2022-2025

 

Sheela DL, Narayanankutty A, Nazeem PA, Raghavamenon AC, Muthangaparambil SR, 2019 Lauric acid induce cell death in colon cancer cells mediated by the epidermal growth factor receptor downregulation: An in silico and in vitro study. Human Experimental Toxicology 38(7): 753-761

 

Brinda O. P., Deepu Mathew, Shylaja M. R., Sangeetha P. Davis, Anita Cherian K.and

Valsala P. A. 2019, Isovaleric acid and Avicequinone C are Chikungunya Virus Resistance Principles in Glycosmispentaphylla (Retz.) Correa . Journal of Vector Borne Diseases 56(2): 111-121

 

Owens, B., Deepu Mathew, Diepenbrock, C., Tiede, T., Wu, D., Mateos-Hernandez,

M., Gore, M. and Rocheford, T. 2019, Genome-Wide Association Study and pathway-

level analysis of kernel color in maize. G3: Genes|Genomes|Genetics, 9: 1945-

1955

 

Harish, E. R., Chellappan, M. K., Makeshkumar, T., Deepu Mathew, Ranjith, M. T.

and Girija, D. 2019 , Next generation sequencing reveals endosymbiont variability in cassava whitefly, Bemisiatabaci, across the agro-ecological zones of Kerala, India. Genome,

62: 571-584.

 

Paul BB, Mathew D, Beena S, Shylaja MR. 2019, Comparative transcriptome analysis reveals the signal proteins and defence genes conferring foot rot (Phytophthora capsici sp. nov.) resistance in black pepper (Piper nigrum L.). Physiological and Molecular Plant Pathology. 1(108): 101436.

 

Mathew D, Anju PS, Tom A, Johnson N, Lidia George M, Davis SP, Ravisankar V, Asha KN. 2020, Genome-wide microsatellites and species specific markers in genus Phytophthora revealed through whole genome analysis. 3 Biotech. 10(10): 1-8.

 

Valsalan R, Mathew D. 2020, Draft genome of Meyerozyma guilliermondii strain vka1: a yeast strain with composting potential. Journal of Genetic Engineering and Biotechnology. 18(1):1-6.

 

Mathew D. 2020, Analysis of QTL Bw1 and marker CAMS451 associated with the bacterial wilt resistance in hot pepper (Capsicum annuum L.). Plant Gene. 1(24): 100260.

 

Mathew D, Ramesh GA. 2020, A universal system for matK gene based diagnostic markers to identify the species in Cucurbitaceae. Indian Journal of Horticulture 77(4): 733-5.

 

Saakre M, Mathew D, Ravisankar V. 2021, Perspectives on plant flavonoid quercetin-based drugs for novel SARS-CoV-2. Beni-Suef University Journal of Basic and Applied Sciences. 10(1): 1-3.

 

Ramesh GA, Mathew D, John KJ, Ravisankar V. 2022, Chloroplast gene matK holds the barcodes for identification of Momordica (Cucurbitaceae) species from Indian subcontinent. Horticultural Plant Journal. 8(1): 89-98.

 

Varghese B, Valsalan R and Mathew D. 2022, Novel MicroRNAs and their Functional Targets from Phytophthora infestans and Phytophthora cinnamomi. Current Genomics 23(1).

 

Ajinath LS, Mathew D. 2022, Genome-wide mining of potentially-hypervariable microsatellites and validation of markers in Momordica charantia L. Genetica. 150(1): 77-85.

 

 

Databases

Repeat Library for genome analysis is available publicly in the following link:

https://kau.in/repeat-libraries