Sagar Gupta

CSIR - Institute of Himalayan Bioresource Technology | IHBT · Bioinformatics Research Area

Identifying RBP binding sites and mechanistic factors determining the interactions remain a big challenge. Besides the sparse binding motifs across the RNAs, it also requires a suitable sequence context for binding. The present work describes an approach to detect RBP binding sites while using an ultra-fast BWT/FM-indexing coupled inexact k-mer spe...

Formation of mature miRNAs and their expression is a highly controlled process. It is very much dependent upon the post-transcriptional regulatory events. Recent findings suggest that several RNA binding proteins beyond Drosha/Dicer are involved in the processing of miRNAs. Deciphering of conditional networks for these RBP-miRNA interactions may he...

Identifying the factors determining the RBP-RNA interactions remains a big challenge. It involves sparse binding motifs and a suitable sequence context for binding. The present work describes an approach to detect RBP binding sites in RNAs using an ultra-fast inexact k-mers search for statistically significant seeds. The seeds work as an anchor to...

s Various noncoding elements of genome have gained attention for their regulatory roles where the lncRNAs are very recent and most intriguing for their possible functions. Due to limited information about lncRNAs, their characterization remains a big challenge, especially in plants. Plant lncRNAs differ a lot from others even in the mode of transcr...

We present here a bi-modal CNN based deep-learning system, DeepPlnc, to identify plant lncRNAs with high accuracy while using sequence and structural properties. Unlike most of the existing software, it works accurately even in conditions with ambiguity of boundaries and incomplete sequences. It scored consistently high for performance metrics whil...

Transcription factors (TFs) are regulatory proteins which bind to a specific DNA region known as the transcription factor binding regions (TFBRs) to regulate the rate of transcription process. The identification of TFBRs has been made possible by a number of experimental and computational techniques established during the past few years. The proces...

WUSCHEL-related homeobox (WOX) genes are plant-specific homeobox transcription factors and are known to play a key role during in vitro embryogenesis and organogenesis. To decipher the structural basis and genetic diversification of WOX family genes, this study performed a genome-wide analysis in Plantaginaceae. In the current study, Picrorhiza kur...

Unlike animals, variability in transcription factors (TFs) and their binding regions (TFBRs) across the plants species is a major problem that most of the existing TFBR finding software fail to tackle, rendering them hardly of any use. This limitation has resulted into underdevelopment of plant regulatory research and rampant use of Arabidopsis-lik...

Discovery of transcription factors (TFs) binding sites (TFBS) and their motifs in plants pose significant challenges due to high cross-species variability. The interaction between TFs and their binding sites is highly specific and context dependent. Most of the existing TFBS finding software tools are not accurate enough to discover these binding s...

Unlike animals, variability in transcription factors (TF) and their binding sites (TFBS) across the plants is a major problem which most of the existing TFBS finding software fail to tackle, rendering them hardly of any use. This limitation has resulted into underdevelopment of plant regulatory research and rampant misuse of Arabidopsis models, gen...

Transcription factors (TFs) are regulatory proteins that bind to a specific DNA sequence, known as the transcription factor binding site (TFBS), to regulate the rate of transcription process. For a better understanding of these regulatory proteins, it is crucial to identify these TFBSs across the genomic sequences. The identification of TFBS has be...

Discovering pre-microRNAs (miRNAs) is the core of miRNA discovery. Using traditional sequence/structural features, many tools have been published to discover miRNAs. However, in practical applications like genomic annotations, their actual performance has been very low. This becomes more grave in plants where unlike animals pre-miRNAs are much more...

miRNAs are major post-transcriptional regulators. Discovering pre-miRNAs is the core of locating miRNAs and their genomic annotations. Using traditional sequence/structural features many tools have been published to discover miRNAs. However, in practical applications like genomic annotation, their actual performance has been far away from acceptabl...

Improvement and acceleration in sequencing technology and the discovery of metagenomic and bioinformatics concepts have opened up a few modern gates to understand the microorganisms living in the human bowel. They play an essential role in wellness and several disease condition of the human body are being found to extend beyond the gastrointestinal...

The rapid exponential growth of biological data including genome structure and functionalities, encouraged by the advent of Next Generation Sequencing (NGS) technologies, expands the golden chance to highlight still hidden molecular perspectives in several fields. One such field is plant genomics which uses bioinformatics based data repositories, t...

Next-Generation sequencing(NGS) revolutionizes the era of biological fields. The low-cost next-generation sequencing has made it possible to understand and manipulate DNA, cells and systems biology as never before. Analysis of big data reveals mystical patterns, correlations, and different insights from the study of high-throughput NGS data sets. W...