Profile
In planta, we are exploring the generation and function of novel components (e.g., non-coding RNAs and genes) of genome regulatory circuits by using both computational and experimental approaches. For this purpose, we are using multi-omics datasets, and our choice of molecules includes Transfer RNA (tRNA)-derived non-coding RNAs (tncRNAs), ribosomal RNA-derived fragments (e.g. rRFs), long non-coding RNAs, Fusion transcripts, and novel gene family in legume crops. In addition to this, we are also developing tools and databases for plant genomics research.
Current Focus Areas
To explore the generation and function of tRNA derived fragments (tRFs) and fusions transcripts for the understanding of genome regulatory circuits in plants. This includes the utilization of sequencing of small RNAs (for tRFs) and RNA-Seq (for fusion transcripts), and further experimental techniques.
Selected Publications
Singh A, Zahra S, Poddar N and Kumar S.* Transfer RNA-derived non-coding RNAs (tncRNAs): hidden regulation of plants transcriptional regulatory circuits. Computational and Structural Biotechnology Journal. Volume 19, 2021, Pages 5278-5291.
Zahra S, Singh A and Kumar S*. tncRNA Toolkit: a pipeline for convenient identification of RNA (tRNA)-derived non-coding RNAs. MethodsX, Volume 10, 2023, 101991.
Singh A, Zahra S, Das D and Kumar S.* AtFusionDB: A Database of Fusion Transcripts in Arabidopsis thaliana. Database (2018). Database (Oxford).Volume 2018 Jan 1.
Singh A, At V, Gupta K, Sharma S, Kumar S*. Long non-coding RNA and microRNA landscape of two major domesticated cotton species. Comput Struct Biotechnol J. 2023 May 12;21:3032-3044.
Gupta N, Singh A, Zahra S and Kumar S.* PtRFdb: a database for plant transfer RNA-derived fragments. Database (2018). Database (Oxford). 2018 Jan 1;2018. doi: 10.1093/database/bay063