Dr. Nisha Singh, PhD

About

I obtained my post-doctoral training from the Institute of Genomic Diversity, Cornell University, New York, USA (2018-2020), and then served as DST-Inspire Faculty at ICAR-National Institute for Plant Biotechnology, New Delhi (2020-2022). After my PhD thesis completion, I joined as Assistant Professor, Bioinformatics at Central University of Punjab, Bhatinda. My research interests lie in genomics, proteomics and bioinformatics, with a special interest in developing cost-effective, high throughput genotyping technologies for genetics and molecular breeding applications in diverse species. These technologies will enable breeders to genotype a large number of samples in a short span of time to implement genomic selection (GS) as a routine practice in breeding programs for fast-track development of superior breeds. I am interested in investigating how we can apply markers to the world and develop a new avenues to evaluate variation at protein level. I have developed the first patented genic 50K SNP genotyping chip “OsSNPnks”, a single copy gene based for genetics and molecular breeding applications in rice. This chip is being used very effectively to develop varieties of rice with good tolerance of long durations of flooding and also help bridge the yield gap. I have investigated the origin of rice and domestication based on key agronomically important and domestication related genes. I have identified seven genes responsible for resistance of root-knot nematode (Meloidogyne graminicola) in rice. Constructed the first Haplotype map (HapMap-1) of tea, and developed major genomics and bioinformatics tools and pipelines such as heterozygous genome assembly, gene-based haplotype pipelines, SNPs assay development tools. I worked on several international genome-sequencing projects (Wild rice, Wheat, Mango, Jute, Pigeonpea, and Tea), genome wide association mapping, haplotype analysis, synteny analysis, genic SNP chip development. I have made a significant contribution in Genomics, Transcriptomics and Proteomics resources development of several key crops, pigeonpea (62K CcSNPnks), Mango (80K MiSNPnks). Currently, my group is exploring tissue specific proteome atlas of pigeonpea.

Prior joining GBU I served as Assistant Professor in Department of Bioinformatics, CoABT, GADVASU, Ludhiana, developed HPC and bioinformatics facility, trained human resources and coordinated DBT sponsored Biotechnology PG program.

Background

• Post Doctoral, Institute of Genomic Diversity, Cornell University, New York, USA (2020)
• PhD. Biotechnology and Bioinformatics (NIPB, New Delhi) (2018)
• MSc. Bioinformatics (OUAT, Bhubaneswar) (2010)
• BSc. Biotechnology (Ranchi University) (2008)

Honours and Awards

• 2022 Fellow of Linnean Society of London, UK.
• 2022 Young Scientist Award for Outstanding contributions in the field of Bioinformatics on the occasion of 3 days International Conference AAVASILES-2022.
• 2022 Best Oral Presentation Award in the 7th International conference on OCAEBGD-2022, Goa.
• 2022 Young Biotechnologist Award 7th International conference on OCAEBGD-2022, Goa.
• 2022 Women Excellence Award (National Environmental Science Academy, New Delhi).
• 2022 Research Excellence Award, Institute of Science InSc, Government of India.
• 2022 Young Scientist Award (International Research Award on New Science Innovation, USA).
• 2020 Prestigious INSA-Medal for Young Scientist (Indian National Science Academy, New Delhi- India)
• 2020 Award of Excellence in Plant Biotechnology (Heredity Life Science, Bhubaneswar)
• 2020 Member of the American Society of Plant Biology, USA
• 2019 Prestigious DST-Inspire Faculty award and grant sponsored by DST, Govt. of India
• 2019 Best Oral Presentation Award, SGT, University Gurugram
• 2018 Young Biotechnologist award, JNU, New Delhi
• 2017 Young Scientist award, International Conference on Global Research Initiatives for Sustainable Agriculture & Allied Sciences (GRISAAS), Udaipur, Rajasthan.
• 2017 First prize in Oral Presentation in 5th Rajasthan Science Congress, Jaipur Rajasthan.
• 2016 Scientific Associate Award, ICASS, Hyderabad
• 2014 ICAR, ARS – National Eligibility Test
• 2011 Graduate Aptitude Test in Engineering award in the subject of life scienc
  Reviewer for journals including Nature, Springer, Elsevier, BMC Genomics, Bioinformatics, Frontier in Plant Science, Frontier in Genetics, Frontier in Bioinformatics, MDPI (Genes, Plants, agronomy) Journal of Food Science & Technology, omics group and PLOSOne.

Research Group Overview

• Identification of Novel Genes/QTLs for Seed Quality and Nutrition Traits in Pigeonpea Genome- Wide Association Mapping: Significant findings: Development of 62K genic SNP chip “CcSNPnks” genic from 48 diverse varieties of pigeonpea. This led to identification of the most effective genomic loci (genes) associated with seed quality and nutritional content in pigeonpea from diverse sets of wild and cultivated genetic backgrounds. I am also working on development of genome assembly and annotation pipeline for heterozygous crops; development and fine-tuning of machine learning model with feature engineering in multiomics data sets.
• Ongoing Project:
  PI (2019-2024) for project funded by DST, India: Identification of novel genes/ QTLs for seed quality and nutrition traits in pigeonpea using genome-wide association mapping.

Patents

• Patent granted:
  1. A single-copy gene based 50K SNP Rice DNA Chip and Uses thereof. Nisha Singh, T. R. Sharma & N.K. Singh Application number 2280/DEL/2014 11.8.2014, Patent grant No- 339438, grant year 25th June 2020.
  2. Negheri bao 1 of Rice (INGR21015), 2022.
  3. Saragphala-2 of Rice (INGR21016), 2022.

Publications

Top 5 Publications

• 
  Nisha Singh*, Hukam C Rawal, Ulavappa B Angadi, Tilak Raj Sharma, Nagendra Kumar Singh, Tapan Kumar Mondal, A first-generation Haplotype map (HapMap-1) of tea (Camellia sinensis L. O. Kuntz), Bioinformatics, 2021;, btab690,https://doi.org/10.1093/bioinformatics/btab690. I.F- 6.98
• 
  Megha Rohilla+, Nisha Singh+, Abhishek Mazumder, Priyabrata Sen, Priyanka Roy, Dhiren Chowdhury, Nagendra Kumar Singh, Tapan Kumar Mondal “Genome‑wide association studies using 50 K rice genic SNP chip unveil genetic architecture for anaerobic germination of deep‑water rice population of Assam, India” (2020) Molecular Genetics and Genomics: MGG 295:1211–1226.https://doi.org/10.1007/s00438-020-01690-w) IF 3.9.
• 
  Wang, Hai; Cimen, Emre; Singh, Nisha; Buckler, Edward S “Deep Learning for Plant Genomics and Crop Improvement” (2020) Current Opinion in Plant Biology 54:34-41https://doi.org/10.1016/j.pbi.2019.12.010 IF 8.43
• 
  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 |https://doi.org/10.1038/srep11600 . IF – 4.4
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  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, DOIhttps://doi.org/10.3389/fpls.2017.00972 IF – 5.7
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  Indian scientists’ new DNA chip for speeding up rice breeding July 5, 2015More
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  No match for mango’s diversity, July 17, 2016.More
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  Genome sequencing can spin disease-free jute, soon. May 8, 2017.More