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Publications:

† First Authors
* Corresponding Author

2023

Deep co-learning on transcription factors and their binding sites attains impeccable universality in plants
Sagar Gupta^†, Veerbhan Kesarwani, Umesh Bhati, Jyoti, Ravi Shankar*
bioRxiv, 2023 Read research article here
Comprehensive evaluation of plant transcription factors binding sites discovery tools
Jyoti^†, Ritu, Sagar Gupta, Ravi Shankar*
bioRxiv, 2023 Read 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 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 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 research article here

2022

De novo transcriptome based insights into secondary metabolite biosynthesis in Malaxis acuminata (Jeevak)âA 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 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 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 research article here

2021

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 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 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 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 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 research article here

2020

Comparative transcriptome analysis of Rheum australe, an endangered medicinal herb, 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 research article here
The dynamic aspects of RNA regulation (book chapter)
Ravi Shankar^†
RNA-based Regulation in Human Health and Disease. Elsevier (2020) Book link here

2019

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

2018

miR-876-3p regulates glucose homeostasis and insulin sensitivity by targeting adiponectin.
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*
Journal of Endocrinology, 2018 Read research article here
Transcriptome and Co-Expression Network Analyses Identify Key Genes Regulating Nitrogen Use Efficiency in Brassica juncea L.
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*
Scientific Reports, 2018 Read research article here

2017

Detecting the Molecular System Signatures of Idiopathic Pulmonary Fibrosis through Integrated Genomic Analysis
Indu Gangwar^†, Nitesh Kumar Sharma^†, Ganesh Panzade, Supriya Awasthi, Anurag Agrawal, and Ravi Shankar*
Scientific Reports, 2017 Read research article here

2016

Comparative Transcriptome Analysis of Chinary, Assamica and Cambod tea (Camellia sinensis) Types during Development and Seasonal Variation using RNA-seq Technology.
Ajay Kumar^†, Vandna Chawla^†, Eshita Sharma, Pallavi Mahajan, Ravi Shankar*, Sudesh Kumar Yadav*
Scientific Reports, 2016 Read research article here
Genome-wide regulatory dynamics of G-Quadruplexes in human malaria parasite Plasmodium falciparum.
Deeksha Bhartiya^†, Vandna Chawla^†, Sourav Ghosh, Ravi Shankar, Niti Kumar
Genomics, 2016 Read research article here.
Transcriptome Analysis Reveals Candidate Genes involved in Blister Blight defense in Tea (Camellia sinensis (L) Kuntze)
Kuldip Jayaswall, Pallavi Mahajan, Gagandeep Singh, Rajni Parmar, Romit Seth, Aparnashree Raina , Mohit k Swarnkar, Anil Singh, Ravi Shankar, Ram K Sharma
Scientific Reports, 2016 Read research article here
Identifying wrong assemblies in de novo short read primary sequence assembly contigs.
Vandna Chawla, Rajnish Kumar, and Ravi Shankar*.
Journal Of Biosciences, 2016 Read research article here
Global de novo protein-protein interactome elucidates interactions of drought responsive proteins in horsegram (Macrotyloma uniflorum).
Bhardwaj Jyoti^†, Gangwar Indu^†, Panzade Ganesh, Shankar Ravi*, Kumar Sudesh*.
Journal of proteome research, 2016 Read research article here
Transcriptome analysis of stem wood of Nothapodytes nimmoniana (Graham) Mabb. identifies genes associated with biosynthesis of camptothecin, an anti-carcinogenic molecule.
Manjunath BL, Singh HR, Ravikanth G, Karaba NN, Shankar R, Kumar S, Uma Shankeer R.
Journal of Biosciences, 2016 Read research article here

2015

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 Molecular Biology, 2015 Read research article here

A Deluge of Complex Repeats: The Solanum Genome.
Mrigaya Mehra, Indu Gangwar and Ravi Shankar*.
PLoS ONE, 2015
Read research article here

A legion of potential regulatory sRNAs exists beyond the typical microRNAs microcosm.,
Ashwani Jha, Ganesh Panzade, Rajesh Pandey and Ravi Shankar*.
Nucleic Acids Research, 2015 Read research article here

2014

Poster: Novel to Reference Free miRNA Discovery: NGS powered miRNA discovery with miR-BAG and miReader. Ashwani Jha, Jennifer Clancy, Thomas Preiss Ravi Shankar*. 35th Annual Lorne Genome Conference 2014 held in Lorne, Victoria, Australia, February 16â18, 2014
Related Reference : http://genomebiology.com/2014/15/4/304
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*.
Scientific Reports, 2014 Read research article here
miRNAting control of DNA methylation.
Ashwani Jha and Ravi Shankar*.
Journal of Biosciences, 2014 Read research article here.
Transcriptome sequencing of rhizome tissue of Sinopodophyllum hexandrum at two temperatures.
A Kumari, HR Singh, A Jha, MK Swarnkar, R Shankar, S KumarA Kumari, HR Singh, A Jha, MK Swarnkar, R Shankar*, S Kumar*.
BMC Genomics, 2014 Read research article here

2013

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. Read research article here
miReader: Discovering novel miRNAs in species without sequenced genome.
Ashwani Jha^† and Ravi Shankar*^†
PLoS ONE, 2013 Read research article here
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, 2013 Read research article here
(PLOS dedicated this article to mark the rise of Indian Science, celebrating National Science Day.)

2012

miR-BAG: Bagging Based Identification of MicroRNA Precursors.
Ashwani Jha^†, Rohit Chauhan^†, Mrigaya Mehra^†, Heikham Russiachand Singh, Ravi Shankar*
PLoS ONE, 2012 Read research article here
De novo sequencing and characterization of Picrorhiza kurrooa transcriptome at two temperatures showed major transcriptome adjustments.
Parul Gahlan^†, Heikham Russiachand Singh^†, Ravi Shankar*, Niharika Sharma, Anita Kumari, Vandna Chawla, Paramvir Singh Ahuja, Sanjay Kumar*.
BMC Genomics, 2012Read research article here

2011

Employing Machine Learning for Reliable miRNA target Identification in Plants.
Ashwani Jha and Ravi Shankar*.
BMC Genomics, 2011 Read research article here
The Regulatory Epicenter of microRNAs.
Ashwani Jha, Mrigaya Mehra, Ravi Shankar*.
Journal of Biosciences, 2011 Read research article here

2010

"The Bioinformatics of Next Generation Sequencing": A meeting report.
Ravi Shankar*
Journal of Molecular Cell Biology, 2010 Read article here

Flanking region sequence information to refine microRNA target predictions.
Heikham R and Shankar R*
Journal of Biosciences, 2010 Read research article here