I pursued my post-graduation degrees in Bioinformatics from Orissa University of Agriculture and Technology, Bhubaneswar India. I did my PhD from ICAR-National Institute for Plant Biotechnology, New Delhi, India (2018), Just after completion of my PhD degree I got an opportunity for Post Doctoral position in one of the  best  lab in arena of plant genomics (Buckler Lab ) at Cornell University, USA (2019). 

Currently, I am working as Post Doctoral Scientist at Cornell University, USA. My research interests lie in genomics, proteomics and bioinformatics. I am especially interested in developing cost-effective, high throughput genotyping technologies for genetics and molecular breeding applications in diverse crops. These technologies will enable breeders to genotype a large number of samples in short span of time to implement genomic selection (GS) as a routine practice in breeding programs for fast track development of superior varieties. Additionally, I am researching how we can apply markers to the world and develop new avenues to evaluate variation at protein level.

Prior to Cornell University, I worked on genomic resource development of rice, wheat, pigeonpea, jute and mango at NIPB, IARI. During my PhD, I developed first genic 50K SNP genotyping chip “OsSNPnks”, a single copy gene based for genetics and molecular breeding applications in rice. This chip is being used to develop varieties of rice that can tolerate long durations of flooding and also help bridge the yield gap. I have also investigated the rice origin and domestication based on key agronomically important and domestication related genes.  

At the Buckler Lab, I am studying the cassava genome. Cassava suffers from a high level of inbreeding depression. I am interested in the identification of deleterious mutations and estimating the mutation burden in diverse cassava genotypes. I am employing different strategies to purge genetic load from cultivated cassava clones. Further, developing genomic selection models to incorporate mutational burden information to improve the prediction accuracy in Cassava.

In recognition of my scientific contributions, I have been awarded several prestigious awards including :- 

1) DST-Inspire Faculty award 2019 February. 

2) Best Oral Presentation award at International Conference Stewardship towards Sustainability (STS 2019) , Gurgaon, India. 

3) Young Biotechnologist award, JNU, New Delhi, April 2018. 

4) Young Scientist award, International Conference on Global Research Initiatives for Sustainable Agriculture & Allied Sciences (GRISAAS), Udaipur, Rajasthan, December 2017 

5) First prize in Oral Presentation (Rs. 10,000/-)  Rajasthan Science Congress, Jaipur Rajasthan, October 2017.

6) Scientific Associate Award, ICASS, Hyderabad, December 2016. 

Career Status:
Postdoctoral Scholar

Research Areas:
Computational Biology, Genomics, Systems Biology, Molecular Biology, Abiotic Interactions, Biotic Interactions


Patent - “A SINGLE COPY GENE BASED 50K SNP RICE DNA CHIP AND USES THERE OF” Nisha Singh, T. R. Sharma & N.K. Singh Application number 2280/DEL/2014 11.8.2014.

1.            Nisha Singh, Pawan Kumar Jayaswal, Kabita Panda, Paritra Mandal, Vinod Kumar, Balwant Singh, Shefali Mishra, Yashi Singh, Renu Singh, Vandna Rai, Anita Gupta, Tilak Raj Sharma & Nagendra Kumar Singh Single-copy gene based 50K SNP chip for genetic studies and molecular breeding in rice (2015) Nature Scientific Reports” 5:11600 | DOI: 10.1038/srep11600. IF-5.56 citations-70

2.            Nisha Singh, Neha Jain, Ram Kumar, Ajay Jain, Nagendra K Singh, Vandna Rai. A comparative method for protein extraction and 2-D gel electrophoresis from different tissues of Cajanus cajan (2015). Frontiers in Plant Science” 6, 606 DOI: 10.3389/fpls.2015.00606. IF-4.29 citations-11

3.            Nisha Singh, Balwant Singh, Vandna Rai, Sukhjeet Sidhu, A. K. Singh, and N. K. Singh. “Evolutionary Insights Based on SNP Haplotypes of Red Pericarp, Grain Size and Starch Synthase Genes in Wild and Cultivated Rice” (2017), Frontiers in Plant Science, DOI: 10.3389/fpls.2017.00972. I. F. 4.29  

4.            Renu Singh, Yashi Singh, Suchit Xalaxo, S. Verulkar, Neera Yadav, Shweta Singh, Nisha Singh, K.S.N. Prasad K et al., From QTL to variety- harnessing the benefits of QTLs for drought, flood and salt tolerance in mega rice varieties of India through a multi-institutional network (2015). “Plant Sciences” DOI: 10.1016/j.plantsci.2015.08.008. IF-3.9 citations-72

5.            Bikram Pratap Singh, Pawan Kumar Jayaswal, Balwant Singh, Pankaj Kumar Singh , Vinod Kumar, Shefali Mishra, Nisha Singh, Kabita Panda, Nagendra Kumar Singh Natural allelic diversity in OsDREB1F gene in the Indian wild rice germplasm led to ascertain its association with drought tolerance (2015) Plant Cell Rep.  DOI 10.1007/s00299-015-1760-6. IF-2.9 citations-42

6.            Sonia Goel, Nisha Singh, Sapna Grewal, Shilpa D’souza, Ajay Mahato, N. K. Singh. Single nucleotide polymorphism in wheat triticin gene (Tri 1) among diverse wild wheat species. “Australian Journal of Crop Science” 9(12):1131-1138 (2015). IF-1.9

7.            Ram Kumar, Nisha Singh, Neha Jain, Nagendra K Singh, Vandna Rai. Phenomics approach in drought tolerant and sensitive cultivars of rice International journal of tropical agriculture 33, 2, 1559-1564 (2015).

8.            Shefali Mishra, Balwant Singh, Kabita Panda, Nisha Singh, Bikram Pratap Singh, Pragati Misra, Vandna Rai, Nagendra Kumar Singh “Association of SNP Haplotypes of HKT Family Genes with Salt Tolerance in Indian Wild Rice Germplasm” (2015). Rice” (2016) 9:15 DOI 10.1186/s12284-016-0083-8. IF-3.9 citations-10  

9.            Nagendra K. Singh, Ajay K. Mahato, Pawan K. Jayaswal, Akshay Singh, Sangeeta Singh, Nisha Singh, Vandna Rai et al., Origin, Diversity and Genome Sequence of Mango (Mangifera indica L.) (2016). Indian Journal of History of Science, 51.2.2

10.         Nisha Singh, Balwant Singh, Vandna Rai, Sukhjeet Kaur and Nagendra Kumar Singh. “Haplotype based phylogenetic analysis of black hull (Bh4) gene in wild and cultivated rice”, (2016), Progressive Research - An International Journal, Volume 11 (Special-VII): 5082-5084. citations-1

11.          Nagendra Kumar Singh, Balwant Singh, Shefali Mishra, Nisha Singh, Kabita Panda and Vandna Rai.Indian wild rice: diversity, population structure, trait value and relation with cultivated rice”, (2016), Indian J. Plant Genet. Resour. 29(3): 366-368 DOI 10.5958/0976-1926.2016.00072.3. citations-2

12.         Debabrata Sarkar, A. K. Mahato, Pratik Satya, Avijit Kundu, Sangeeta Singh, Nisha Singh, Pawan K Jaswal et al., “The draft genome of Corchorus olitorius cv. JRO-524 (Navin)”, (2017), Genomics Data, DOI: 10.1016/j.gdata.2017.05.007.

13.         Balwant Singh, Nisha Singh, Vandna Rai, Shefali Mishra, Kabita Panda, A. K. Singh, and N. K. Singh. “Morphological and molecular variations delineate species and population structure of Indian wild rice Oryza rufipogon Griff. species complex” (2018),  9, 123 Frontiers in Plant Science, DOI: 10.3389/fpls.2018.00123. I. F. 4.29.

14.         Pragya Mishra, Nisha Singh, Ajay Jain, Neha Jain, Vagish Mishra, Pushplatha G, Kiran P. Sandhya, Nagendra Kumar Singh, Vandna Rai “Co-expression gene interaction networks and common cis-regulatory elements for salinity and drought stress tolerance in rice” (2018) Bioinformation 14(3): 123-131.

15.         PoojaArchana Sahani1, Megha Ujinwal1, Sangeeta Singh2, Nisha Singh1* “Genome wide insilico characterization of dirigent protein family in flax (Linumu sitatissmum L)” (2018), Plant Archevies 18, 61-68, NAS IF-4.9.

16.         Kabita Tripathy, Balwant Singh, Nisha Singh, Vandna Rai, Gouri Mishra, Nagendra Singh “A database of Oryza rufipogon species complex wild rice germplasm collected from different agro-climatic zones of India” (2018), Oxford Database, bay058 I.F. 3.9. doi: 10.1093/database/bay058 IF 3.9.

17.         Mishra Pragya, Jain Ajay, Takabe Teruhiro, Tanaka Yoshito, Negi Manisha, Singh Nisha, Jain Neha, Mishra Vagish, Waditee-Sirisattha, Rungaroon Maniraj, R Krishanmurthy, S Sreevathsa, Rohini, Singh Nagendra, Rai Vandna. “Heterologous Expression of Serine Hydroxymethyltransferase-3 From Rice Confers Tolerance to Salinity Stress in E. coli and Arabidopsis”. (2019) 10, 217 IF 3.6

18.         Megha Ujinwal, Pooja Archana Sahani and Nisha Singh*  “Comparative sequence and structural analysis of lectin protein in  chickpea (Cicer crietinumn L.) and their relationship with fabaceae family”. accepted in International Journal of Proteomics and Bioinformatics (2019) IF 1.2.

19.         Sangeeta Singh , Ajay Mahato, Pawan Jayaswal , Nisha Singh , Meenakshi Dheer , Preeti Goel, Ranjeet Raje, Jeshima Khan Yasin, Rohini Sreevathsa, Vandna Rai, Kishor Gaikwad, N. K. Singh.  “A 62K genic-SNP chip for genetic studies and breeding applications in pigeonpea (Cajanus cajan L. Millsp.)”  2019 accepted in Scientific Reports IF 4.4.

20.         Aditi Bhandari, Pawan Jayaswal, Neera Yadav, Renu Singh, Yashi Singh, Balwant Singh, Nisha Singh, Sangeeta Singh, Amitha Sevanthi, Vandna Rai, Satish Verulkar “Genomics-assisted backcross breeding for infusing climate resilience in high-yielding green revolution varieties of rice” Indian J. Genet., 79(1) Suppl. 160-170 (2019) doi: 10.31742/IJGPB.79S.1.5. IF 1.2.

21.          Sufia Farhat, Neha Jain, Nisha Singh, Sandeep Yadav, Pramod Kumar, Rohini Sreevathsa, Prasanta Dash, Rhitu Rai, Ananda K Sarkar, Vandna Rai, Ajay Jain, Nagendra Kumar Singh “CRISPR-cas 9 directed genome engineering for enhancing salt stress tolerance in rice”. 2019 Seminars in Cell and Developmental Biology IF 6.9

22.         Wang, Hai; Cimen, Emre; Singh, Nisha; Buckler, Edward S “Deep Learning for Plant Genomics and Crop Improvement” Current Opinion in Plant Biology IF 7.8.


1.     Nisha Singh “Advances of NGS technologies to enhanced the Biofortifications in crops” Springer, Nature, Singapore 2019.

2.     Nisha Singh “Genetic diversity, population structure and Genome wide association studies (GWAS) in crop plant”, “CAFT- NGS applications in crop sciences”, published by ICAR- National research centre on plant Biotechnology, New Delhi, India, 2017.

3.     Nisha Singh “Applications of SNP genotyping using SNP chips”, “CAFT- NGS applications in crop sciences”, published by ICAR- National research centre on plant Biotechnology, New Delhi, India, 2017.

4.     Ram Kumar, Neha Jain, Vagish Mishra, Nisha Singh, Pragya Mishra, Sajad Majeed Zargar, Ajay Jain, Nagendra Kumar Singh, and Vandna Rai. Potentialities of Proteomics for Generating Abiotic Stress Tolerant Crop Species. “Plant OMICS and Crop Breeding” Apple Academic Press. USA, 2017.

Volunteer Activities

Reviewer of Frontier in Plant Sciences, Scientific Reports, PlosOne and International Journal of Genomics, Proteomics and Bioinformatics 

Teaching Courses for M.Sc. (Life Science specialization in Bioinformatics)

·       System Biology, Course Code-LB1.621 (Credits: 4)

·       Molecular Evolution, Course Code-LB1.622 (Credits: 4)

·       Sequence Analysis, Course Code-LB1.522 (Credits: 3)

STUDENT GUIDED- 3 MSc Bioinformatics thesis, 1 MPhil. Biotechnology

Current Affiliations
Experience & Education