Shubhada R. Kulkarni

The paper introduces circtools 2.0, an enhanced software for circRNA detection and analysis, with new features for improved detection, probe design, conservation analysis, and support for Oxford Nanopore sequencing.

The paper evaluates motif mapping tools for Arabidopsis, showing that an ensemble approach improves gene regulatory network reconstruction from chromatin data.

TF2Network predicts transcription factor regulators and gene regulatory networks in Arabidopsis using binding site data and co-expressed genes, achieving 75-92% accuracy in validation.