Faculty Details

Faculty Details

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

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)


  • 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)

CV : Download CV

Title Details
Lab news

One new member joined the lab!

B. Gopikrishnan joined the lab in Aug 2022 for an MSc research project.

One member moved on after completing the project.

Manoj Kumar Chevella, who had joined the lab in Aug 2021 for MSc research project, moved on for career opportunities after the successful completion of the project.

Journal Club presentation
  • 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;

New publications


  • In this collaborative work, we were involved in analysis of metagenomic data to find out any alteration in the composition of gut microbiome of patients of amoebiasis, and the implications of the change.
    •  Lakshmi Rani Iyer,  Nisha Chandel,  Anil Kumar Verma,  Vivek Thakur,  Jaishree Paul,  Ashish Kumar Mandal,  Alok Bhattacharya,  Effect of Entamoeba histolytica infection on gut microbial diversity and composition in diarrhoeal patients from New Delhi  (under review) https://www.researchsquare.com/article/rs-1782339/v1


  •  In this collaborative work the objective was to find the mechanisms underlying the development of tolerance against cry toxin, our group analyzed the transcriptome data from mid-gut of castor semi-looper.
    • Dhania NK, Chauhan VK, Abhilash D, Thakur V, Chaitanya RK, Dutta-Gupta S, Dutta-Gupta A. Gut-specific arylphorin mediates midgut regenerative response against Cry-induced damage in Achaea janata. Compr Biochem Physiol Part B: Biochemistry and Molecular Biology, 255:110600 (2021) https://doi.org/10.1016/j.cbpb.2021.110600
  • 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

Students/Projects Trainees

Name Joined As Mail Contact
Nisha Chandel Ph.D. program --- ---
Padhma Preiya Ph.D. program --- ---
Angeo Saji MSc Project student --- ---
B. Gopikrishnan M. Sc. Project --- ---

Former Students/Projects Trainees

Name Joined As Working
Abhilash Dasari M. Sc. project PhD scholar at School of Bioengineering and Biotechnology, IIT Delhi
Pulkit Srivastava Summer Intern (from JUIT, HP) Innoplex
Hitesh Thakur Summer Intern (from JUIT, HP) Infosys
V Nandini MSc project student
Manoj Kumar Chevella M. Sc. Project
V Sai Samhitha Intern IISER Bhopal
Sowmomita Gharui Intern from Pondicherry University
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
Allele mining for the epigenetic regulator NGR5 and the yield associated genes (GID1 and GRF4) and their modulation using multiple genomic and molecular approaches to enhance rice yield under low nitrogen conditions 2022 3 60000000000 Co-PI
DBT-Centre for Microbial Informatics (DBT-CMI) 2021 5 176 Prof. H.A.Nagarajaram (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)
Characterization of human gut microbiota for micronutrient production and exploring metabolic potential for its enhancement (Funded by Uoh_IoE) 2021 3 400000000000 PI
Discovery of gene missing components of regulatory network underlying C4 pathway/anatomy for translational research (Funding agency: DBT-ramalingaswami grant)) 2017 5 880000000000 Vivek


Anyone interested in working on a problem on

  1. application of molecular evolution for gene discovery for plant developmental traits and
  2. Search for immunity-related genes in QTLs for resistance against fungal pathogen

may contact me at vivek22@uohyd.ac.in.


We will be advertising soon for a Bioinformatics JRF position in an ICAR project on Nitrogen use efficiency. Stay tuned!

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)

Some of the research problems that my group is currently working on are below.

Taxonomic/Functional characterization of gut microbiota for nutrition and diseases

One of the integral sources of micronutrients for human has been the gut microbiota, known to produce some of those essential micronutrients. However, behaviour of native gut microbiota in case of malnutrition has not been thoroughly investigated. So our hypothesis is whether altered abundance/composition of microbes contribute to the prevalence of deficiency of essential micronutrients? Several gut microbes may have metabolic capability for biosynthesis of some of the essential micronutrients, but they fail to do so due to lack of either one or a few genes. Such microbes can potentially be engineered or complemented in the form of pairs for in vivo or in vitro micronutrient production.

To address these gaps, we first want to survey the prevalence of B-vitamin producing microbes in population and key demographic groups. In case they happen to be prevalent, then how their abundance varies? To understand their role in malnutrition, we plan to sequence gut-metagenome for one or a few of the B-vitamin deficiencies in collaboration with community medicine scientists at ICMR-NIRTH and gut-metagenome researcher at UoH. Its analysis should answer if change in composition and dynamics of gut microbe(s) underlies micronutrient deficiency.

Overall, through this project we want to make discoveries for exploiting gut microbes for addressing the prevalent deficiency of essential B-vitamins. This may also lead to the development of new probiotic formulations.

Members involved: Nisha Chandel (JRF, UoH), Priyansh Patel (JRF, ICMR-NIRTH), Dr Anil Verma & Dr Suyash Srivastave (Co-PIs, ICMR-NIRTH)

Funding: UoH-Institute of Eminence

Trait discovery related to C4 anatomy/biochemistry

Driven by the challenge of food insecurity, some global projects are already underway to develop future crops by modifying the C 3 photosynthetic pathway to C 4 type, as the latter provides higher yield/biomass with reduced inputs. The major hurdle to these efforts has been incomplete knowledge of the genomic changes needed to operate the C 4 pathway. Attempts based on gene expression studies limit only to the genes and thus miss the regulatory elements involved, and also provide list of genes too long to be implementable.

In order to discover the missing genetic components as well as to address the limitations of current approach, I would like to take an alternate approach:

  •  Discover genome-wide changes in the genomes of C 4 species that associate with C4 phenotype.
  •  Obtain a comprehensive set of genetic components (regulatory elements, genes, etc.) that were recruited during establishment of C 4 features from their ancestral counterparts (C3 ).
  •  Discover trajectory of changes in the origin of C4 trait.
  •  Propose a module for the development of future crops with higher yields despite limited resources.

Members involved: Angeo Saji (Current), Manoj Kumar Chevella (Past)

Funding: DBT-Ramalingaswami grant

Integration of omics data for knowledge mining of genes and genome annotation improvement

The availability of draft genomes of the majority of crops has boosted forward genetics research for various agroeconomic traits. However, such studies often lead to multiple candidate genes, and narrowing down to causal gene becomes a challenging task. The challenges increase when the candidates happen to be partially annotated or even without annotation. To address these challenges we have developed a one-stop web-application, namely KYCg, that not only provides functional details from as many sources, but also makes use of public transcriptome data to predict functional information of the uncharacterized ones.

Members involved: Gopikrishnan (current), Hitesh Thakur, Pulkit Srivastava and Prasad Gandham (Past)

Genomics of Fe uptake/transport/storage

Members involved: Padhma Preiya