Sureshkumar V
PhD Scholar
Computational Biologist | Freelancer
No. of Publications: 14
Google Scholar - Citations: 297 h-index: 9 i10-index: 9
PhD Programme
Position: PhD Scholar
Organization: Regional Centre for Biotechnology, Faridabad, India - 121001
Period: Nov 2020 - Present
Experience
Position: ICAR - Young Professional II
Organization: ICAR - National Institute for Plant Biotechnology, New Delhi, India - 110012
Period: Nov 2017 - Oct 2020 (3 years)
Specialization
Bioinformatics
Biological Databases
NGS Analysis (Genome, Transcriptome, Metagenome, Single Cell, etc.),
Docking, Virtual Screening and MD Simulation
Computer Science
Database and Web-Server Development
Linux
R (Statistical Analysis and Visualization), Python, Shell scripting
Machine Learning (Scikit-Learn)
Databases/Servers Developed
RiceMetaSys (14.139.229.201/RiceMetaSys)
ClustergeneDB (14.139.229.201/ClustergeneDB)
EMSgardeN22 (14.139.229.201/EMSgardeN22)
RiceMetaSysB (14.139.229.201/RiceMetaSysB)
RiceMetaSys-HRG (14.139.229.201/RiceMetaSys/HRG)
PfPhospho (www.nii.ac.in/pfphospho.html)
PDBi - Biomolecular Structures in PDB from India (202.54.249.134/PDBi)
InTGS - Indian Tuberculosis Genomic Surveillance Consortium (intgs.nii.ac.in)
CovServer - Hosted at NII (Local server for Covid Nanopore Data Analysis)
Awards
Title: Best Poster Award (First Prize)
In: National Symposium on Database Development and Biocuration (NSDDB 2018), March 6-7, 2018
Conducted by: Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India.
Membership in the Scientific Soceity
Bioinformatics and Drug Discovery Society (BIDDS) - Life Member (https://bidds.org/)
Bachelor's Degree
Degree: B. Tech (Bioinformatics)
Year: 2013-2017
College: Agricultural College and Research Institute
University: Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India 641003
Master's Degree
Degree: M. Sc (Bioinformatics)
Year: 2018-2020
College: Faculty of Natural Sciences
University: Jamia Millia Islamia - Central University, New Delhi, India 110025
Internship Program (Bachelor's)
Institute: ICAR - National Institute for Plant Biotechnology, New Delhi, India 110012
Time Period: July 2016 to October 2016
Work Title: RiceMetaSys: A Web Database of Salt and Drought responsive genes in rice
Guide: Dr. Amitha CR Mithra SV, Scientist (SS), ICAR - NIPB, New Delhi
Bachelor's Degree Project
Work Title: Using Subtractive Genomics approach to identify potential drug targets for bacterial leaf blight disease in rice
Guide: Mrs. N. Bharathi (Assistant Professor), DPMB&B, TNAU, Coimbatore
Master's Degree Project
Work Title: Genome Assembly and Annotation of upland rice cultivar Nagina 22
Guide: Dr. Amitha CR Mithra SV (Sr. Scientist), ICAR - NIPB, New Delhi (External Supervisor)
Dr. Taran Singh Barti (Assistant Professor), DCS, JMI, New Delhi (Internal Supervisor)
Publications
2023
Malhotra, N., S. Khatri, A. Kumar, A. Arun, P. Daripa, S. Fatihi, S. Venkadesan, N. Jain, and L. Thukral. 2023. "AI-based AlphaFold2 significantly expands the structural space of the autophagy pathway." Autophagy:1-20. doi: 10.1080/15548627.2023.2238578. (IF: 13.3)
Singh BK, Venkadesan S, Ramkumar MK, Shanmugavadivel PS, Dutta B, Prakash C, Pal M, Solanke AU, Rai A, Singh NK, Mohapatra T, Sevanthi AM. Meta-Analysis of Microarray Data and Their Utility in Dissecting the Mapped QTLs for Heat Acclimation in Rice. Plants. 2023; 12(8):1697. doi: 10.3390/plants12081697 (IF: 4.5 - Equal contributing first author)
2022
Sidharthan, V.K., A.M. Sevanthi, S. Venkadesan, D. Diksha, and V.K. Baranwal. 2022. "Seasonal dynamics in leaf viromes of grapevines depicting leafroll syndrome under tropical condition." Tropical Plant Pathology. doi: 10.1007/s40858-022-00524-x. (IF: 2.404)
Pal, G., R. Bakade, S. Deshpande, V. Sureshkumar, S.S. Patil, A. Dawane, S. Agarwal, V. Niranjan, M.K. PrasannaKumar, and R.S. Vemanna. 2022. "Transcriptomic responses under combined bacterial blight and drought stress in rice reveal potential genes to improve multi-stress tolerance." BMC Plant Biology 22 (1):349. doi: 10.1186/s12870-022-03725-3. (IF: 5.260)
Gupta, P., S. Venkadesan, and D. Mohanty. 2022. "Pf-Phospho: a machine learning-based phosphorylation sites prediction tool for Plasmodium proteins." Briefings in Bioinformatics. doi: 10.1093/bib/bbac249. (IF: 9.5)
Ramkumar, M.K., E. Mulani, V. Jadon, V. Sureshkumar, S.G. Krishnan, S. Senthil Kumar, M. Raveendran, A.K. Singh, A.U. Solanke, N.K. Singh, and A.M. Sevanthi. 2022. "Identification of major candidate genes for multiple abiotic stress tolerance at seedling stage by network analysis and their validation by expression profiling in rice (Oryza sativa L.)." 3 Biotech 12 (6):127. doi: 10.1007/s13205-022-03182-7. (IF: 2.893)
2021
Sevanthi, A.M., S.K. Sinha, Sureshkumar, V., M. Rani, M.R. Saini, S. Kumari, M. Kaushik, C. Prakash, V. K, G.P. Singh, T. Mohapatra, and P.K. Mandal. 2021. "Integration of Dual Stress Transcriptomes and Major QTLs from a Pair of Genotypes Contrasting for Drought and Chronic Nitrogen Starvation Identifies Key Stress Responsive Genes in Rice." Rice 14 (1):49. doi: 10.1186/s12284-021-00487-8. (IF: 5.638)
Kumar, V., P. Jain, S. Venkadesan, S.G. Karkute, J. Bhati, M.Z. Abdin, A.M. Sevanthi, D.C. Mishra, K.K. Chaturvedi, A. Rai, T.R. Sharma, and A.U. Solanke. 2021. "Understanding Rice-Magnaporthe Oryzae Interaction in Resistant and Susceptible Cultivars of Rice under Panicle Blast Infection Using a Time-Course Transcriptome Analysis." Genes 12 (2):301. (IF: 3.5)
2020
Kaushik, M., S. Rai, S. Venkadesan, S.K. Sinha, S. Mohan, and P.K. Mandal. 2020. "Transcriptome Analysis Reveals Important Candidate Genes Related to Nutrient Reservoir, Carbohydrate Metabolism, and Defence Proteins during Grain Development of Hexaploid Bread Wheat and Its Diploid Progenitors." Genes 11 (5):509. (IF: 3.5)
2019
Sureshkumar, V., B. Dutta, V. Kumar, G. Prakash, D.C. Mishra, K.K. Chaturvedi, A. Rai, A.M. Sevanthi, and A.U. Solanke. 2019. "RiceMetaSysB: a database of blast and bacterial blight responsive genes in rice and its utilization in identifying key blast-resistant WRKY genes." Database 2019:baz015. doi: 10.1093/database/baz015. (IF: 5.8)
2018
Sevanthi, A.M.V., P. Kandwal, P.B. Kale, C. Prakash, M.K. Ramkumar, N. Yadav, A.K. Mahato, V. Sureshkumar, M. Behera, R.K. Deshmukh, P. Jeyaparakash, M.K. Kar, S. Manonmani, R. Muthurajan, K.S. Gopala, S. Neelamraju, M.S. Sheshshayee, P. Swain, A.K. Singh, N.K. Singh, T. Mohapatra, and R.P. Sharma. 2018. "Whole Genome Characterization of a Few EMS-Induced Mutants of Upland Rice Variety Nagina 22 Reveals a Staggeringly High Frequency of SNPs Which Show High Phenotypic Plasticity Towards the Wild-Type." Frontiers in Plant Science 9. doi: 10.3389/fpls.2018.01179. (IF: 5.6)
Sinha, S.K., A.M. Sevanthi V., S. Chaudhary, P. Tyagi, S. Venkadesan, M. Rani, and P.K. Mandal. 2018. "Transcriptome Analysis of Two Rice Varieties Contrasting for Nitrogen Use Efficiency under Chronic N Starvation Reveals Differences in Chloroplast and Starch Metabolism-Related Genes." Genes 9 (4):206. (IF: 3.5)
2017
Sandhu, M., V. Sureshkumar, C. Prakash, R. Dixit, A.U. Solanke, T.R. Sharma, T. Mohapatra, and A.M. S. V. 2017. "RiceMetaSys for salt and drought stress responsive genes in rice: a web interface for crop improvement." BMC Bioinformatics 18 (1):432. doi: 10.1186/s12859-017-1846-y. (IF: 3.328 - Equal contributing first author)
Rawal, H.C., S. Kumar, A. Mithra S.V., A.U. Solanke, D. Nigam, S. Saxena, A. Tyagi, Sureshkumar V., N.R. Yadav, P. Kalia, N.P. Singh, N.K. Singh, T.R. Sharma, and K. Gaikwad. 2017. "High Quality Unigenes and Microsatellite Markers from Tissue Specific Transcriptome and Development of a Database in Clusterbean (Cyamopsis tetragonoloba, L. Taub)." Genes 8 (11):313. (IF: 3.5)
Book Chapter
Amitha Mithra SV, Solanke AU, Prakash C, Sureshkumar V., Ramkumar MK, Sandhu M, Shanmugavadivel PS (2018) Integrating expression data in rice: An effort towards deciphering biotic and abiotic stress tolerance. Proceeding of PSMB Edited by Ahmad J, Tomar RS and Tiwari S. pp. 9-13. (ISBN-978-93-5321-456-2)
Sevanthi A. M. V., Kale, P., Chandra Prakash, Ramkumar M. K., Yadav N., Sureshkumar V., Poli Y., Grover N., Behera M., Khandual A., Jeyaparakash P., Kar M. K., Muthurajan Raveendran, Manonmani S., Krishnan S. G., Mangrauthia S. K., Sarla N., Sheshshayee M. S., Mohapatra T., Singh A. K., Singh N. K., Sharma R. P. (2021) National repository of EMS induced mutants of an upland rice cultivar Nagina 22: progress update on characterization and utilization. Mutation breeding, genetic diversity and crop adaptation to climate change. (ISBN: 9781789249095)
National Conferences
S.V. Amitha Mithra, Amolkumar U. Solanke, Chandra Prakash, Sureshkumar V, Ramkumar MK, Manninder Sandhu, Shanmugavadivel PS. Integrating Expression data in Rice: An Effort towards deciphering biotic and abiotic stress tolerance. In: National Conference Current trends in Plant Science and Molecular Biology for Food Security and Climate Resilient Agriculture. February 15-16, 2018, Gwalior, India.
Sureshkumar V, SV Amitha Mithra and Amolkuamr U. Solanke (2018). RiceMetaSys (Biotic Stress): A comprehensive database of rice blast and bacterial leaf blight disease responsive genes in rice. In: National Symposium on Database Development and Biocuration. March 6-7, 2018, New Delhi, India.(Best Poster Award)
Prakash C, Sureshkumar V, Shanmugavadivel PS, Ramkumar MK, Amolkumar U Solanke and Amitha Mithra SV (2018). RiceMetaSys (HRG): An open source database of heat responsive genes and markers for comparative genomics and molecular breeding in rice for heat tolerance. In: National Symposium on Database Development and Biocuration. March 6-7, 2018, New Delhi, India.
MK Ramkumar, V. Sureshkumar, Prashant B. Kale, Chandra Prakash, Nera Yadav, A. K. Singh, S. Gopalakrishnan, P.Jeyaprakash, M.K. kar, M.S. Sheeshayee, Satendra Kumar Mangrauthia, S. SenthilKumar, R. P. Sharma, N. K. Singh and S. V. Amitha Mithra (2018). Evaluation and expression profiling of stay-green mutants of upland rice cv. N22 under drought. In: National Genetics Congress. December 14-16, 2018, New Delhi, India.
MK Ramkumar, V. Sureshkumar, Chandra Prakash, Neera Yadav, S. Gopalakrishnan, AK Singh, MK Kar, MS Sheshshyaee, Satendra Kumar Mangrauthiam, S Senthil Kumar, AK Singh, RP Sharma, NK Singh and SV Amitha Mithra (2019). NGS based TILLING of leaf senescence genes in stay-green mutantsof upland rice cv. Nagina22. In: Indian PlantScience Congress 2019, January 23-25, 2019, Chennai, India.
Lalitha Hari Dharani D, Kavitha S, Sureshkumar V and Anandhi V (2019). TNRiceBase–Exhaustive and user-friendly genomics web portal for rice cultivars. In: Bioconcorrenza’19 National Level Technical Symposium, March 1-2, 2019, Coimbatore, India.
International Conferences
Amitha CR Mithra SV, Ashok K Singh, Chandra Prakash, Gopalakrishnan S., Jeyaprakash P., Meera Kumari Kar, NagendraK Singh, Neera Yadav, Padmini Swain, Prashant Kale, Rameshwar P. Sharma, M.K. Ramkumar, M. Raveendran, N. Sarla, Satendra Kumar Mangrauthia, M.S. Sheshashayee, V. Sureshkumar, Trilochan Mohapatra. National repository of rice ems mutants of an upland rice cultivar nagina22: progress update on characterization and utilization. In: International Symposium on Plant Mutation Breeding and Biotechnology. August 27-31, 2018, Vienna, Austria.
Ashish Kumar Singh, Antara Das, Kuldeep Kumar, Sureshkumar Venkadesan, Ila Joshi, Deshika Kohli, Ramanna Koulagi, Animesh Kumar, Harsha Srivastava, Kishor Gaikwad, Pradeep Kumar Jain, K.K. Mishara, Anil Sirohi. Announcement of draft genome of the seed gali nematode Angunia tritici. In: 7th International Cereal Nematodes Symposium, September 2019, New Delhi, India.