GANGE: Achieving Sequencing Without Sequencing With Diffusion Guided Generative Genomic Transformer
Sagar Gupta, Anchit Kumar, Umesh Bhati, Ravi Shankar*,
bioRxiv, 2026 Read the research article here

ProMaya: a hierarchical universal Deep Learning framework for accurate and interpretable Protein-Protein interaction identification
Umesh Bhati, Sagar Gupta, Veerbhan Kesarwani, Ravi Shankar*,
bioRxiv, 2026 Read the research article here

Explainable Deep-Learning on condition specific expression profiles reveals critical cytosines in gene regulation
Veerbhan Kesarwani, Anchit Kumar, Akanksha Sharma, Sagar Gupta, Kirti Pandey, Gaurav Zinta, Ravi Shankar*,
bioRxiv, 2026 Read the research article here

A comprehensive gene expression analysis of extensive cohorts from colon adenocarcinoma uncovered a set of genes regulated by DNA hypomethylation and predominantly influenced by lipid raft-mediated EGFR-RAS-MAPK signaling
Ankan Roy, Niharika, Veerbhan Kesarwani, Ravi Shankar, Samir Kumar Patra*,
Molecular Carcinogenesis, 2026 Read the research article here

Genome-wide identification, characterization, and expression pattern analysis of the glyoxalase gene family in Phyllostachys pubescens during abiotic stresses
Anita Kumari^†, Umesh Bhati^†, Ravi Shankar, Sudesh Kumar Yadav, Sudhir Kumar Sopory, Rohit Joshi*,
BMC Plant Biology, 2025 Read the research article here

PTF-Vāc: An explainable and generative deep co-learning encoders-decoders system for ab-initio discovery of plant transcription factor binding sites
Sagar Gupta, Jyoti, Umesh Bhati, Veerbhan Kesarwani, Akanksha Sharma, Ravi Shankar*,
Plant Communications, 2025 Read the research article here

Chemoinformatics exploration of synthetically accessible N-heterocycles: uncovering new antifungal lead candidates
Shiv Shankar Gupta, Veerbhan Kesarwani, Ravi Shankar*, Upendra Sharma*,
In Silico Pharmacology, 2025 Read the research article here

Transcriptional landscape illustrates the diversified adaptation of medicinal plants to multifactorial stress combinations linked with high altitude
Manglesh Kumari, Prakash Kumar, Vishal Saini, Rohit Joshi, Ravi Shankar*, Rajiv Kumar*,
Planta, 2025 Read the research article here

Decoding stress specific transcriptional regulation by causality aware Graph-Transformer deep learning
Umesh Bhati, Akanksha Sharma, Sagar Gupta, Anchit Kumar, Upendra Kumar Pradhan, Ravi Shankar*,
Current Plant Biology, 2025 Read the research article here

DMRU: Generative Deep-Learning to unravel condition specific cytosine methylation in plants
Sagar Gupta, Anchit Kumar, Veerbhan Kesarwani, Umesh Bhati, Ravi Shankar*,
Briefings in Bioinformatics, 2025 Read the research article here

Comprehensive analysis of computational approaches in plant transcription factors binding regions discovery
Jyoti, Ritu, Sagar Gupta, Ravi Shankar*,
Heliyon, 2024 Read the research article here

Genome wide identification of WUSHEL-related homeobox genes reveal their differential regulation during cold stress and in vitro organogenesis in Picrorhiza kurrooa
Jhilmil Nath, Shubham Joshi, Sagar Gupta, Veerbhan Kesarwani, Ravi Shankar and Rohit Joshi*,
In Vitro Cellular & Developmental Biology - Plant, 2024 Read the research article here

PTFSpot: deep co-learning on transcription factors and their binding regions attains impeccable universality in plants
Sagar Gupta, Veerbhan Kesarwani, Umesh Bhati, Jyoti, Ravi Shankar*,
Briefings in Bioinformatics, 2024 Read the research article here

Nutritional quality and microbial diversity of Chhurpe from different milk sources: An ethnic fermented food of high-altitude regions of the Western Himalayas
Sahdev Choudhary^†, Kumari Shanu^†, Athrinandan S Hegde^†, Raman Kumar, Veerbhan Kesarwani, Ravi Shankar*, Sarita Devi*, Vidyashankar Srivatsan*,
Discover Food, 2024 Read the research article here

Flavonoids from Aerial Parts of Cissampelos pareira L. as Antimalarial Agents: Computational Validation of Ethnopharmacological Relevance
Patil Shivprasad Suresh^†, Veerbhan Kesarwani^†, Surekha Kumari, Ravi Shankar*, Upendra Sharma*,
South African Journal of Botany, 2023 Read the research article here

miWords: Transformers based composite deep-learning for highly accurate discovery of pre-miRNA regions across plant genomes
Sagar Gupta, Ravi Shankar*,
Briefings in Bioinformatics, 2023 Read the research article here

Bisbenzylisoquinolines from Cissampelos pareira L. as Antimalarial Agents: Molecular Docking, Pharmacokinetics Analysis, and Molecular Dynamic Simulation Studies
Patil Shivprasad Suresh^†, Veerbhan Kesarwani^†, Surekha Kumari, Ravi Shankar*, Upendra Sharma*,
Computational Biology and Chemistry, 2023 Read the research article here

De novo transcriptome based insights into secondary metabolite biosynthesis in Malaxis acuminata (Jeevak) - A therapeutically important orchid
Paromik Bhattacharyya^†, Tanvi Sharma^†, Abhinandan Yadav^†, Lucy Lalthafamkimi, Ritu, Mohit Kumar Swarnkar, Robin Joshi, Ravi Shankar*, Sanjay Kumar*,
Frontiers in Plant Science, 2022 Read the research article here

Time-series RNA-Seq transcriptome profiling reveals novel insights about cold acclimation and de-acclimation processes in an evergreen shrub of high altitude
Nikita Rathod^†, Prakash Kumar^†, Nandita Mehta, Mohit Kumar Swarnkar, Ravi Shankar*, Amit Chawla*,
Scientific Reports, 2022 Read the research article here

DeepPlnc: Bi-modal Deep Learning for Highly Accurate Plant lncRNA Discovery
Ritu^†, Sagar Gupta^†, Nitesh Kumar Sharma, Ravi Shankar*,
Genomics, 2022 Read the research article here

RBPSpot: Learning on Appropriate Contextual Information for RBP Binding Sites Discovery
Nitesh Kumar Sharma^†, Sagar Gupta, Ashwani Kumar, Prakash Kumar, Upendra Kumar Pradhan, Ravi Shankar*,
iScience, 2021 Read the research article here

In-depth assembly of organ and development dissected Picrorhiza kurroa proteome map using mass spectrometry
Manglesh Kumari^†, Upendra Kumar Pradhan, Robin Joshi, Ashwani Punia, Ravi Shankar, Rajiv Kumar*,
BMC Plant Biology, 2021 Read the research article here

miRbiom: Machine-Learning on Bayesian Causal Nets of RBP-miRNA interactions successfully predicts miRNA profiles
Upendra Kumar Pradhan^†, Nitesh Kumar Sharma^†, Prakash Kumar, Ashwani Kumar, Sagar Gupta, Ravi Shankar*,
PLoS ONE, 2021 Read the research article here

The first draft genome of Picrorhiza kurrooa, an endangered medicinal herb from Himalaya
Tanvi Sharma^†, Nitesh Kumar Sharma^†, Prakash Kumar, Ganesh Panzade, Tanuja Rana, Mohit Kumar Swarnkar, Anil Kumar Singh, Dharam Singh, Ravi Shankar*, Sanjay Kumar*,
Scientific Reports, 2021 Read the research article here

In Silico Approach for Identifying Natural Lead Molecules Against SARS-COV2
Shiv Shankar Gupta^†, Ashwani Kumar^†, Ravi Shankar*, Upendra Sharma*,
Journal of Molecular Graphics and Modelling, 2021 Read the research article here

Comparative transcriptome analysis of Rheum australe, an endangered medicinal herb, growing in its natural habitat and those grown in controlled growth chambers
Deep Mala^†, Supriya Awasthi^†, Nitesh Kumar Sharma, Mohit Kumar Swarnkar, Ravi Shankar & Sanjay Kumar
Scientific Reports, 2020 Read the research article here

The dynamic aspects of RNA regulation (book chapter)
Ravi Shankar*
RNA-Based Regulation in Human Health and Disease, 2020 Read book here

Plant Regulomics Portal (PRP): a comprehensive integrated regulatory information and analysis portal for plant genomes
Ganesh Panzade, Indu Gangwar, Supriya Awasthi, Nitesh Sharma, Ravi Shankar
Database, 2019 Read the research article here

Regulation of color transition in purple tea (Camellia sinensis)
Manglesh Kumari, Shweta Thakur, Ajay Kumar, Robin Joshi, Prakash Kumar, Ravi Shankar & Rajiv Kumar
Planta, 18 December 2019 Read the research article here

De novo transcriptome provides insights into the growth behaviour and resveratrol and trans-stilbenes biosynthesis in Dactylorhiza hatagirea - An endangered alpine terrestrial orchid of western Himalaya
Nisha Dhiman^†, Nitesh Kumar Sharma^†, Pooja Thapa^†, Isha Sharma, Mohit Kumar Swarnkar, Amit Chawla, Ravi Shankar & Amita Bhattacharya
Scientific Reports, 2019 Read the research article here

miR-876-3p regulates glucose homeostasis and insulin sensitivity by targeting adiponectin.
Journal of Endocrinology, 2 July 2018 Read the research article here
Sujith Rajan, Ganesh Panzade, Ankita Srivastava, Kripa Shankar, Rajesh Pandey, Abhishek Gupta, Durgesh Kumar, Salil Varshney, Muheeb beg, Raj Kumar Mishra, Ravi Shankar* and Anil Gaikwad*.

Transcriptome and Co-Expression Network Analyses Identify Key Genes Regulating Nitrogen Use Efficiency in Brassica juncea L.
Scientific Reports, 2018;doi:10.1038/s41598-018-25826-6 Read the research article here
Parul Goel^†, Nitesh Kumar Sharma^†, Monika Bhuria, Vishal Sharma, Rohit Chauhan, Shivalika Pathania, Mohit Kumar Swarnkar, Vandna Chawla, Vishal Acharya, Ravi Shankar* and Anil Kumar Singh*.

Detecting the Molecular System Signatures of Idiopathic Pulmonary Fibrosis through Integrated Genomic Analysis
Scientific Reports, 2017;doi:10.1038/s41598-017-01765-6 Read the research article here
Indu Gangwar^†, Nitesh Kumar Sharma^†, Ganesh Panzade, Supriya Awasthi, Anurag Agrawal and Ravi Shankar*.

Comparative Transcriptome Analysis of Chinary, Assamica and Cambod tea (Camellia sinensis) Types during Development and Seasonal Variation using RNA-seq Technology.
Scientific Reports, 2016
Ajay Kumar^†, Vandna Chawla^†, Eshita Sharma, Pallavi Mahajan, Ravi Shankar* and Sudesh Yadav*.

Genome-wide regulatory dynamics of G-Quadruplexes in human malaria parasite Plasmodium falciparum.
Genomics, Oct 2016
Deeksha Bhartiya^†, Vandna Chawla^†, Sourav Ghosh, Ravi Shankar, Niti Kumar

Transcriptome Analysis Reveals Candidate Genes involved in Blister Blight defense in Tea (Camellia sinensis (L) Kuntze).
Scientific Reports, Jul 2016
Kuldip Jayaswall, Pallavi Mahajan, Gagandeep Singh, Rajni Parmar, Romit Seth, Aparnashree Raina , Mohit k Swarnkar, Anil Singh, Ravi Shankar, Ram K Sharma.

Identifying wrong assemblies in de novo short read primary sequence assembly contigs.
Journal Of Biosciences, September 2016
Vandna Chawla, Rajnish Kumar and Ravi Shankar*.

Global de novo protein-protein interactome elucidates interactions of drought responsive proteins in horsegram (Macrotyloma uniflorum).
Journal of proteome research; May 10, 2016
Bhardwaj Jyoti^†, Gangwar Indu^†, Panzade Ganesh, Ravi Shankar*, Kumar Sudesh*.

Transcriptome analysis of stem wood of Nothapodytes nimmoniana (Graham) Mabb. identifies genes associated with biosynthesis of camptothecin, an anti-carcinogenic molecule.
J Bioscience, Mar 2016
Manjunath BL, Singh HR, Ravikanth G, Karaba NN, Shankar R, Kumar S, Uma Shankeer R

A legion of potential regulatory sRNAs exists beyond the typical microRNAs microcosm.
(Nucleic Acids Research[NAR]), 2015
Ashwani Jha, Ganesh Panzade, Rajesh Pandey and Ravi Shankar*.

A Deluge of Complex Repeats: The Solanum Genome.
PLOS ONE, 2015
Mrigaya Mehra, Indu Gangwar, Ravi Shankar*.

Expression of SOD and APX genes positively regulates secondary cell wall biosynthesis and promotes plant growth and yield in Arabidopsis under salt stress.
Amrina Shafi, Rohit Chauhan, Tejpal Gill, Mohit K. Swarnkar, Yelam Sreenivasulu, Sanjay Kumar, Neeraj Kumar, Ravi Shankar, Paramvir Singh Ahuja, Anil Kumar Singh
Plant Mol. Biol., April 2015, Volume 87, Issue 6, pp 615-631

RNA-seq-mediated transcriptome analysis of actively growing and winter dormant shoots identifies non-deciduous habit of evergreen tree tea during winters.
Asosii Paul^†, Ashwani Jha^†, Shruti Bhardwaj, Sewa Singh, Ravi Shankar*, Sanjay Kumar*. Sci. Rep., 2014. doi:10.1038/srep05932

miRNAting control of DNA methylation. Ashwani Jha and Ravi Shankar*. J biosci. 39 365-380.

Comprehensive Transcriptomic Study on horse gram (Macrotyloma uniflorum): De novo Assembly, Functional Characterization and Comparative Analysis in Relation to Drought Stress.
Jyoti Bhardwaj^†, Rohit Chauhan^†, Mohit Swarnkar, R Chahota, R Shankar* and S Yadav*.BMC Genomics. 2013 14:647, September 2013.

Transcriptome sequencing of rhizome tissue of Sinopodophyllum hexandrum at two temperatures.
A Kumari^†, HR Singh^†, A Jha, MK Swarnkar, R Shankar*, S Kumar*.
BMC Genomics, 15 (1), 871.

miReader: Discovering novel miRNAs in species without sequenced genome.
Ashwani Jha^† and Ravi Shankar*^† PLoS ONE 8(6): e66857. doi:10.1371/journal.pone.0066857

De-novo sequence assembly and transcriptome analysis of Venturia inaequalis, the deadly apple scab pathogen.
Karnika Thakur^†, Vandna Chawla^†, Shammi Bhatti, Mohit Kumar Swarnkar, Jagdeep Kaur, Ravi Shankar*, Gopaljee Jha*.
PLoS ONE 8(1): e53937. doi:10.1371/journal.pone.0053937.

miR-BAG: Bagging Based Identification of MicroRNA Precursors.
Ashwani Jha^†, Rohit Chauhan^†, Mrigaya Mehra^†, Heikham Russiachand Singh, Ravi Shankar* PLOS ONE 2012 7(9): e45782. doi:10.1371/journal.pone.0045782.

De novo sequencing and characterization of Picrorhiza kurrooa transcriptome at two temperatures showed major transcriptome adjustments.
Parul Gahlan^†, Heikham Russiachand Singh^†, Ravi Shankar¹*, Niharika Sharma, Anita Kumari, Vandna Chawla, Paramvir Singh Ahuja, Sanjay Kumar²*.
BMC Genomics, 13:126, March, 2012.

Employing machine learning for reliable miRNA target identificaiton in plants.
Ashwani Jha and Ravi Shankar*.
BMC Genomics,12:636, December, 2011.

The Regulatory Epicenter of microRNAs.
Ashwani Jha, Mrigaya Mehra, Ravi Shankar*.
J Biosci. 2011 Sep;36(4):621-38.

EGLN1 involvement in high-altitude adaptation revealed through genetic analysis of extreme constitution types defined in Ayurveda.
Aggarwal et al.
PNAS, 107, 44, 2010

"The Bioinformatics of Next Generation Sequencing": A meeting report.
Journal of Mol. Cell Biol. (Oxford University Press) 2010.
Ravi Shankar*.

Flanking region sequence information to improve microRNA target prediction.
Journal of Biosciences, Springer, 35(1), March 2010, 105-118
Russiachand Heikham and Ravi Shankar*.

Involvement of repeats in non-random genomic divergence in 5' upstream regions of Human and Chimpanzee genes of different biological processes.
HUGO's 13th international meeting on the Human Genome.
The HUGO Journal (Genomic Medicine) (2008) 2:401-413.
Chaurasia A, Shankar R, Mukerji M

Non-random genomic divergence in repetitive sequences of human and chimpanzee in genes of different functional categories.
Mol Genet Genomics.2007 Apr;277(4):441-55.
Shankar R, Chaurasia A, Ghosh B, Chekmenev D, Cheremushkin E, Kel A, Mukerji M

Evolution and distribution of RNA polymerase II regulatory sites from RNA polymerase III dependant mobile Alu elements.
BMC Evolutionary Biology, BMC Evol Biol. 2004 Oct 4;4(1):37
Shankar R, Grover D, Brahmachari S K, Mukerji M.

Repbase Reports. 2006, Vol. 6, Issue 10.
Shankar R & Jerzy Jurka.