Faculty Details

Faculty Details

  • Name: Dr. Vivek
  • Mail: vivek22uohyd.ac.in
  • Contact: 04023134720
  • Area Of Research:Computational genomics

My research interest lies in:

  • Trait discovery related to C4 photosynthesis
  • Integration of omics data for knowledge mining of genes and genome annotation improvement
  • Taxonomic/Functional characterization of gut microbiota for nutrition and diseases
  • Taxonomic/Functional characterization of plant root microbiota for sustainable agriculture
  • Nutri-genomics for important crops

Professional Experience:

  • Assistant Professor, University of Hyderabad (Since July 2018)
  • Ramalingaswami Fellow, ICRISAT, Hyderabad (Jan 2017 - June 2018)
  • Research Associate/Guest faculty at JNU/Indraprastha University New Delhi (2016)
  • Postdoctoral Fellow in C4 Rice project at International Rice Research Institute (IRRI) (2010-2015)
  • Visiting Scientist, ICRISAT, Hyderabad (June 2008 - Dec 2009)

Education:

  • Ph.D. (Bioinformatics) at Jawaharlal Nehru University, New Delhi (2008)
  • Advanced PG Diploma in Bioinformatics at Jawaharlal Nehru University, New Delhi (2003)
  • M. Sc. in Medical Toxicology, Hamdard University, New Delhi (2002)
  • B. Sc. in Zoology, Delhi University, New Delhi (1999)
No Records Available

Students/Projects Trainees

Name Joined As Mail Contact
Nisha Chandel Ph.D. program --- ---
Padhma Preiya Ph.D. program --- ---
Angeo Saji MSc Project student --- ---
V Nandini MSc project student --- ---

Former Students/Projects Trainees

Name Joined As Working
Pulkit Srivastava Summer Intern (from JUIT, HP) Innoplex
Hitesh Thakur Summer Intern (from JUIT, HP) Infosys
22 Chatterjee, Jolly., Coe, Robert A., Acebron, Kelvin., Thakur, Vivek., Yennamalli, Ragothaman M., Danila, Florence., Lin, Hsiang-Chun., Balahadia, Christian Paolo., Bagunu, Efren., Padhmapreiya, POS., (2021) , Identification of a low CO2 responsive mutant from chemical mutagenesis of Setaria viridis shows that reduced carbonic anhydrase severely limits C4 photosynthesis , Journal of Experimental Botany, ,,,.
21 Bohra, Abhishek., Gandham, Prasad., Rathore, Abhishek., Thakur, Vivek., Saxena, Rachit K., Naik, SJ Satheesh., Varshney, Rajeev K., Singh, Narendra P., (2021) , Identification of microRNAs and their gene targets in cytoplasmic male sterile and fertile maintainer lines of pigeonpea , Planta, Springer,253,2,1-15.
20 Karki, Shanta., Lin, HsiangChun., Danila, Florence R., AbuJamous, Basel., Giuliani, Rita., Emms, David M., Coe, Robert A., Covshoff, Sarah., Woodfield, Helen., Bagunu, Efren., (2020) , A role for neutral variation in the evolution of C4 photosynthesis , BioRxiv, Cold Spring Harbor Laboratory,,,.
19 Subramaniam, Gopalakrishnan., Thakur, Vivek., Saxena, Rachit K., Vadlamudi, Srinivas., Purohit, Shilp., Kumar, Vinay., Rathore, Abhishek., Chitikineni, Annapurna., Varshney, Rajeev K., (2020) , Complete genome sequence of sixteen plant growth promoting Streptomyces strains , Scientific reports, Nature Publishing Group,10,1,1-13.
18 Chatterjee, Jolly., Thakur, Vivek., Nepomuceno, Robert., Coe, Robert A., Dionora, Jacqueline., Elmido-Mabilangan, Abigail., Llave, Abraham Darius., Reyes, Anna Mae Delos., Monroy, Apollo Neil., Canicosa, Irma., (2020) , Natural Diversity in Stomatal Features of Cultivated and Wild Oryza Species , Rice, SpringerOpen,13,1,1-20.
17 Thakur, Vivek., Wanchana, Samart., (2019) , Gene Discovery by Forward Genetic Approach in the Era of High‐Throughput Sequencing , OMICS‐Based Approaches in Plant Biotechnology, John Wiley & Sons, Inc. Hoboken, NJ, USA,,,75-89.
16 Naiyer, Sarah., Kaur, Devinder., Ahamad, Jamaluddin., Singh, Shashi Shekhar., Singh, Yatendra Pratap., Thakur, Vivek., Bhattacharya, Alok., Bhattacharya, Sudha., (2019) , Transcriptomic analysis reveals novel downstream regulatory motifs and highly transcribed virulence factor genes of Entamoeba histolytica , BMC genomics, BioMed Central,20,1,1-18.
15 BISWAL, AKSHAYA KUMAR., SINGH, ARUN KUMAR., THAKUR, VIVEK., MANGRAUTHIA, SATENDRA KUMAR., PONNUSWAMY, REVATHI., (2018) , Breeding Strategies to Convert C3 Plants into C4 Plants , Advanced Molecular Plant Breeding: Meeting the Challenge of Food Security, CRC Press,,,369.
14 Rizal, Govinda., Karki, Shanta., Thakur, Vivek., Wanchana, Samart., Alonso-Cantabrana, Hugo., Dionora, Jacque., Sheehy, John E., Furbank, Robert., von Caemmerer, Susanne., Quick, William Paul., (2017) , A sorghum (Sorghum bicolor) mutant with altered carbon isotope ratio , PloS one, Public Library of Science San Francisco, CA USA,12,6,e0179567.
13 Kelly, Steven., Covshoff, Sarah., Wanchana, Samart., Thakur, Vivek., Quick, W Paul., Wang, Yu., Ludwig, Martha., Bruskiewich, Richard., Fernie, Alisdair R., Sage, Rowan F., (2017) , Wide sampling of natural diversity identifies novel molecular signatures of C4 photosynthesis , BioRxiv, Cold Spring Harbor Laboratory,,,163097.
12 van Campen, Julia C., Yaapar, Muhammad N., Narawatthana, Supatthra., Lehmeier, Christoph., Wanchana, Samart., Thakur, Vivek., Chater, Caspar., Kelly, Steve., Rolfe, Stephen A., Quick, W Paul., (2016) , Combined chlorophyll fluorescence and transcriptomic analysis identifies the P3/P4 transition as a key stage in rice leaf photosynthetic development , Plant Physiology, American Society of Plant Biologists,170,3,1655-1674.
11 Wang, Fei., Coe, Robert A., Karki, Shanta., Wanchana, Samart., Thakur, Vivek., Henry, Amelia., Lin, Hsiang-Chun., Huang, Jianliang., Peng, Shaobing., Quick, William Paul., (2016) , Overexpression of OsSAP16 regulates photosynthesis and the expression of a broad range of stress response genes in rice (Oryza sativa L.) , PloS one, Public Library of Science San Francisco, CA USA,11,6,e0157244.
10 Chatterjee, Jolly., Dionora, Jacqueline., Elmido-Mabilangan, Abigail., Wanchana, Samart., Thakur, Vivek., Bandyopadhyay, Anindya., Brar, Darshan S., Quick, William Paul., (2016) , The evolutionary basis of naturally diverse rice leaves anatomy , PloS one, Public Library of Science San Francisco, CA USA,11,10,e0164532.
9 Rizal, Govinda., Thakur, Vivek., Dionora, Jacqueline., Karki, Shanta., Wanchana, Samart., Acebron, Kelvin., Larazo, Nikki., Garcia, Richard., Mabilangan, Abigail., Montecillo, Florencia., (2015) , Two forward genetic screens for vein density mutants in sorghum converge on a cytochrome P450 gene in the brassinosteroid pathway , The Plant Journal, ,84,2,257-266.
8 Azam, Sarwar., Thakur, Vivek., Ruperao, Pradeep., Shah, Trushar., Balaji, Jayashree., Amindala, BhanuPrakash., Farmer, Andrew D., Studholme, David J., May, Gregory D., Edwards, David., (2012) , Coverage‐based consensus calling (CbCC) of short sequence reads and comparison of CbCC results to identify SNPs in chickpea (Cicer arietinum; Fabaceae), a crop species without a reference genome , American journal of botany, Botanical Society of America,99,2,186-192.
7 Govinda Rizal, Shanta Karki, Vivek Thakur, Jolly, William Paul Quick., (2012) , Towards a C4 rice , Asian Journal of Cell Biology, ,7,2,13-31.
6 Thakur, Vivek., Wanchana, Samart., Xu, Mercedes., Bruskiewich, Richard., Quick, William Paul., Mosig, Axel., Zhu, Xin-Guang., (2011) , Characterization of statistical features for plant microRNA prediction , BMC genomics, BioMed Central,12,1,1-12.
5 Saxena, Rachit K., Cui, Xinping., Thakur, Vivek., Walter, Barbara., Close, Timothy J., Varshney, Rajeev K., (2011) , Single feature polymorphisms (SFPs) for drought tolerance in pigeonpea (Cajanus spp.) , Functional & integrative genomics, Springer-Verlag,11,4,651-657.
4 Thakur, Vivek., Varshney, RK., (2010) , Challenges and strategies for next generation sequencing (NGS) data analysis , Journal of Computer Science & Systems Biology, ,3,,40-42.
3 Kelkar, Ashwin., Thakur, Vivek., Ramaswamy, Ramakrishna., Deobagkar, Deepti., (2009) , Characterisation of inactivation domains and evolutionary strata in human X chromosome through Markov segmentation , PLoS One, Public Library of Science,4,11,e7885.
2 Thakur, Vivek., Azad, Rajeev K., Ramaswamy, Ram., (2007) , Markov models of genome segmentation , Physical Review E, APS,75,1,011915.
1 Azad, Rajeev K., Lawrence, J., Thakur, Vivek., Ramaswamy, Ram., (2007) , Segmentation of genomic DNA sequences , Pham TD, et al.(2007) Advanced Computational Methods in Biocomputing and Bioimaging. New York: Nova Science Publishers, ,,,107-126.
Title Year Duration Amount(In Lakhs) PI/I
DBT-Centre for Microbial Informatics (DBT-CMI) (approved by the Taskforce, DBT; awaiting financial sanction) 2020 5 200 Prof. H.A.Nagarajaram (Coordinator and PI), Prof. Appa Rao Podile (Co-PI), Prof. Dayananda Siddavattam (Co-PI), Prof. Ch Venkataramana (Co-PI), Dr. Pankaj Singh (Co-PI), Dr. Vivek (Co-PI), Dr. Manjari Kiran (Co-PI)
Discovery of gene missing components of regulatory network underlying C4 pathway/anatomy for translational research (Funding agency: DBT-ramalingaswami grant)) 2017 5 88 Vivek

Interns

We work on solving various biological problems through computational approach. If any of the problem interest you, or have got any interesting problem to work on, then please contact through my emai (vivek22@uohyd.ac.in.

UPDATE: For 2021's summer internship the position are already full.  



University of Hyderabad
  • July-Dec 2019: Comparative Systems Modeling (1 out of 2 credits; IMSc-SB IXth sem)
  • July-Dec 2019: Comparative Systems Modeling LAB (1 out of 2 credits; IMSc-SB IXth sem)
  • July-Dec 2019: Computers and Programming (1 out of 2 credits; IMSc-SB Vth sem)
  • July-Dec 2019: Computers and Programming  LAB(1 out of 2 credits; IMSc-SB Vth sem)
  • Jan-May 2019: Genomics (3 credits; IMSc-SB VIIIth sem)
  • Jan-May 2019: Genomics LAB (2 credits; IMSc-SB VIIIth sem)
  • Jan-May 2019: Evolution and Diversity (1 out of 2 credits course; IMSc-SB IVth Sem )
  • July-Dec 2018: Metagenomics (1 out of 4 credits Computational Systems Modeling to IMSc. IXth sem)

Indraprastha University, New Delhi

  • Sep-Dec 2016: Bio-statistics (4 credit theory course)
  • Sep-Dec 2016: Computer based statistical analysis (2 credit Lab)


New publications in 2021 (from collaborations)!

  • The whole genome sequence analysis of S. viridis mutant for compensation point led to discovery of an ABC transporter which is crucial for transsport of a cell wall component of the C4 plants namely, monomers of Suberin.
    •  Danila F, Thakur V, et al. “Bundle sheath suberisation is required for C4 photosynthesis in a Setaria viridis mutant" Nature Comm. Biol. (2021) (In press)
  • Whole genome sequence analysis of S. viridis another mutant for compensation point led to discovery that loss of function of beta Carbonic Anhydrase enzyme does affect the C4 photosynthesis.
    •  Chatterjee J, Coe RA, Acebron K, Thakur V, …., Quick WP. Identification of a low CO2 responsive mutant from chemical mutagenesis of Setaria viridis shows that reduced carbonic anhydrase severely limits C4 photosynthesis. Journal of Experimental Botany, erab039 (2021), https://doi.org/10.1093/jxb/erab039
  • Analysis of sequencing of small RNA fraction to discover if any of them are involved in male sterility in Pigeonpea.
    • Bohra, A., Gandham, P., Rathore, A., Thakur V.,  et al. Identification of microRNAs and their gene targets in cytoplasmic male sterile and fertile maintainer lines of pigeonpea. Planta 253, 59 (2021). https://doi.org/10.1007/s00425-021-03568-6

Journal Club presentation (Jan 2021)

  • Presenter: Angeo Saji
  • Article: Brassinosteroid signaling and auxin transport are required to establish the periodic pattern of Arabidopsis shoot vascular bundles Marta Ibañes, Norma Fàbregas, Joanne Chory, and Ana I. Caño-Delgado PNAS August 11, 2009 106 (32) 13630-13635;

Two new members joined lab!

For MSc research project, Angeo and Nandini joined the lab in Sep 2020