Research Publications

PUBLICATIONS @ CSIR-IHBT, Palampur

1. Neeraj Kumar, Vishal Acharya*, Advances in machine intelligence-driven virtual screening approaches for big-data Medicinal Research Reviews 2023;1–36 | doi: 10.1002/med.21995 (IF=13.33)

2. Aakriti Sharma#, Ekjot Kaur#, Robin Joshi, Pooja Kumari, Abhishek Khatri, Mohit K. Swarankar, Dinesh Kumar, Vishal Acharya*, Gireesh Nadda* "Systematic analyses with genomic and metabolomic insights reveal a new species, Ophiocordyceps indica sp. nov. from treeline area of Indian Western Himalayan region" Frontiers in Microbiology Volume 14 - 2023 | doi: 10.3389/fmicb.2023.1188649 (IF=5.2) #Joint First Authors

3. Abhishek Khatri, Aman Thakur,Ayush Lepcha, Vishal Acharya*, Rakshak Kumar*, IHM-DB: a curated collection of metagenomics data from the Indian Himalayan Region, and automated pipeline for 16S rRNA amplicon-based analysis (AutoQii2), Database (Oxford Journal) Volume 2023, 2023, baad039 https://doi.org/10.1093/database/baad039 (IF=5.8)

4. Ravi Kumar, Vishal Acharya*, Effector protein structures: a tale of evolutionary relationship, Trends in Plant Science, 2023,ISSN 1360-1385, https://doi.org/10.1016/j.tplants.2023.04.010. (IF=22.01)

5. Neeraj Kumar, Vishal Acharya*, Machine intelligence-guided selection of optimized inhibitor for human immunodeficiency virus (HIV) from natural products. Computers in Biology and Medicine Volume 153, February 2023, 106525 (IF=7.7)

6. Ravi Kumar, Vishal Acharya*, Deep learning based protocol to construct an immune-related gene network of host-pathogen interactions in plants. STAR Protocols, Cell Press 4,1 (2023). https://doi.org/10.1016/j.xpro.2022.101934

1. Neeraj Kumar, Vishal Acharya*, Machine intelligence-driven framework for optimized hit selection in virtual screening Journal of Cheminformatics 14, 48 (2022). https://doi.org/10.1186 (IF=8.48)

2. Shiv Rattan, Pankaj Kumar, Ekjot Kaur, Archit Sood, Vishal Acharya, Ashish R. Warghat Comparative transcriptome and tissue-specific expression analysis of genes reveal tissue-cultured plants as an alternative source for phenylethanoids and phenylpropanoids in Rhodiola imbricata (Edgew.) (2022) Gene 836 (2022) 146672 (IF=3.688)

3. Ravi Kumar, Abhishek Khatri Vishal Acharya*, Deep learning uncovers distinct behaviour of rice network to pathogens response. iScience, Cell Press (2022). (IF=6.107)

1. Meetal Sharma, Prince Anand, Yogendra Padwad*, Vivek Dogra*, Vishal Acharya*, DNA damage response proteins synergistically affect the cancer prognosis and resistance. Free radical Biology and medicine (2021) (IF=8.1)

2. Desh Raj, Vinesh Sharma, Ashwani Upadhyaya, Neeraj Kumar, Robin Joshi, Vishal Acharya, Dinesh Kumar,Vikram Patial Swertia purpurascens Wall ethanolic extract mitigates hepatic fibrosis and restores hepatic hepcidin levels via inhibition of TGFβ/SMAD/NFκB signaling in rats. Journal of Ethnopharmacology. (2021). (IF=5.195)

3. Jyoti Devi, Ekjot Kaur, Mohit Kumar Swarankar, Vishal Acharya*, Shashi Bhushan* De novo transcriptome analysis provides insights into formation of in vitro adventitious root from leaf explants of Arnebia euchroma. BMC Plant Biol 21, 414 (2021). (IF=5.260)

4. Narendra VijayTirpude*, Anamika Sharma, Robin Joshi, Monika Kumari, Vishal Acharya* Vitex negundo Linn. extract alleviates inflammatory aggravation and lung injury by modulating AMPK/PI3K/Akt/p38-NF-κB and TGF-β/Smad/Bcl2/Caspase/LC3 cascade and macrophages activation in murine model of OVA-LPS induced allergic asthma (2021) Journal of Ethnopharmacology 113894, ISSN 0378-8741 (IF =5.195)

5. Pankaj Kumar, Ashrita, Vishal Acharya, Ashish R. Warghat Comparative transcriptome analysis infers bulb derived in vitro cultures as a promising source for sipeimine biosynthesis in Fritillaria cirrhosa D. Don (Liliaceae, syn. Fritillaria roylei Hook.) - High value Himalayan medicinal herb, (2021) Phytochemistry, Volume 183, 2021, 112631, ISSN 0031-9422 (IF=4.004)

1.Srijana Mukhia#, Abhishek Khatri#, Vishal Acharya*, Rakshak Kumar* Comparative genomics and molecular adaptational analysis of Arthrobacter from Sikkim Himalaya provided insights into its survivability under multiple high-altitude stress Genomics (2020) https://doi.org/10.1016/j.ygeno.2020.12.001 (IF=4.31)
#Joint First Author

2.Supriya Sharma#¸ Meetal Sharma#¸ Anil Kumar Rana¸ Robin Joshi¸ Mohit Swarnkar¸ Vishal Acharya*¸ Damanpreet Singh* Deciphering key regulators involved in epilepsy-induced cardiac damage through whole transcriptome and proteome analysis in a rat model Epilepsia (2020) Accepted (IF=6.74)
#Joint First Author

3. Anil Kumar, Srijana Mukhia, Neeraj Kumar, Vishal Acharya, Sanjay Kumar and Rakshak Kumar (2020) A Broad Temperature Active Lipase Purified From a Psychrotrophic Bacterium of Sikkim Himalaya With Potential Application in Detergent Formulation. Front. Bioeng. Biotechnol. 8:642. doi: 10.3389/fbioe.2020.00642 (IF=6.06)

1. Rakshak Kumar, Vishal Acharya, Srijana Mukhia, Dharam Singh, Sanjay Kumar (2019) Complete genome sequence of Pseudomonas frederiksbergensis ERDD5:01 revealed genetic bases for survivability at high altitude ecosystem and bioprospection potential Genomics   Volume 111, Issue 3, May 2019, Pages 492-499 (IF=4.31)

1. Parul Goel, Nitesh Kumar Sharma, Monika Bhuria, Vishal Sharma, Rohit Chauhan,Shivalika Pathania , Mohit Kumar Swarnkar , Vandna Chawla , Vishal Acharya , Ravi Shankar & Anil Kumar Singh (2018) Transcriptome and Co-Expression Network Analyses Identify Key Genes Regulating Nitrogen Use Efficiency in Brassica juncea L. Scientific Reports 8, Article number: 7451 (IF= 4.996)

2. Rakshak Kumar#, Vishal Acharya#, Dharam Singh, Sanjay Kumar (2018) Strategies for high-altitude adaptation revealed from high quality draft genome of non-violacein producing Janthinobacterium lividum ERGS5:01 Environmental Microbiome 13:11 (IF=6.36) # Joint First Author

Book Chapters

1. Neeraj Kumar, Vishal Acharya* (2018) Metabolomics Resources: An Introduction of Databases and Their Future Prospective Recent Trends and Techniques in Plant Metabolic Engineering Springer DOI (Editors: Sudesh Kumar Yadav, Vinay Kumar, Sudhir P Singh) Online ISBN 978-981-13-2251-8

1. Preeti Arya & Vishal Acharya* (2017) Plant STAND P-loop NTPases: A current perspective of genome distribution, evolution, and function. Molecular Genetics and Genomics  Volume 293, Issue 1, pp 17–31 (IF = 2.98)

2. Shailender Kumar Verma, Ankita Sharma, Padmani Sandhu, Neha Choudhary, Shailaja Sharma, Vishal Acharya, Yusuf Akhter (2017) Proteome scale identification, classification and structural analysis of iron-binding proteins in bread wheat Journal of Inorganic Biochemistry Volume 170, , Pages 63-74 (IF =4.366)

1. Preeti Arya & Vishal Acharya* (2016) Computational identification raises a riddle for distribution of putative NACHT NTPases in the genome of early green plants PLoS ONE 11(3): e0150634 (IF =3.752)

2. Gulshan Kumar#, Preeti Arya#, Khushboo Gupta, Vinay Randhawa, Vishal Acharya, and Anil Kumar Singh (2016) Comparative phylogenetic analysis and transcriptional profiling of MADS-box gene family identified DAM and FLC-like genes in apple (Malus x domestica) Scientific Reports (Nature Publishing Group) (# Equal first authorship) (IF = 4.996)

3. Geetika Sirhindi, Poonam Sharma, Preeti Arya, Parul Goel, Gulshan Kumar, Vishal Acharya, Anil Kumar Singh (2016) Genome-Wide Characterization and Expression Profiling of TIFY Gene Family in Pigeonpea (Cajanus cajan (L.) Millsp.) under Copper Stress Journal of Plant Biochemistry and Biotechnology Volume 25, Issue 3, pp 301–310 (IF = 1.175)

1. Vinay Randhawa, Anil Kumar Singh & Vishal Acharya* (2015) A systematic approach to prioritize drug targets using machine learning, a molecular descriptor-based classification model, and high-throughput screening of plant derived molecules: a case study in oral cancer Molecular omics, 2015, 11, 3362-3377, DOI: 10.1039/C5MB00468C (IF= 3.743)

2. Vinay Randhawa & Vishal Acharya* (2015) Integrated network analysis and logistic regression modeling identify stage-specific genes in Oral Squamous Cell Carcinoma BMC Medical Genomics 8:39, DOI: 10.1186/s12920-015-0114-0 (IF = 3.622) (Highly accessed article; 7th Most Viewed in August Issue)

3. Shivalika Pathania & Vishal Acharya* (2015) Computational analysis of "-omics" data to identify transcription factors regulating secondary metabolism in Rauvolfia serpentine Plant Molecular Biology Reporter DOI: 10.1007/s11105-015-0919-1 (IF = 1.816)

4. Arun Kumar, Vinay Randhawa, Vishal Acharya, Kashmir Singh, Sanjay Kumar (2015) Amino acids flanking the central core of Cu,Zn superoxide dismutase are important in retaining enzyme activity after autoclaving Journal of Bimolecular Structure & Dynamics 10.1080/07391102.2015.1049551 (IF = 3.392)

1. Preeti Arya, Gulshan Kumar, Vishal Acharya*, Anil Kumar Singh* (2014) Genome-wide identification and expression analysis of NBS-encoding genes in Malus x domestica and expansion of NBS genes family in Rosaceae PLoS ONE 9(9): e107987. doi:10.1371/journal.pone.0107987 (IF = 3.752)

1. Anil Kumar Singh, Vishal Sharma, Awadhesh Kumar Pal, Vishal Acharya and Paramvir Singh Ahuja (2013) Genome-Wide Organization and Expression Profiling of NAC Transcription Factor Family in Potato (Solanum tuberosum L.) DNA Research doi 10.1093/dnares/dst019 (IF =4.477) (This article has been ranked 8th among 50 Most Read Articles in DNA Research in July Issue of 2013)

2. Pradeep Kumar Bhardwaj, Ritu kapoor, Deep Mala, Geetika Bhagwat, Vishal Acharya, Anil Kumar Singh, Surender K Vats, Paramvir S. Ahuja & Sanjay Kumar (2013): Braving the attitude of altitude: Caragana jubata at work in cold desert of Himalaya, Scientific Reports (Nature Publishing Group) 01/2013; DOI:DOI:10.1038/srep01022 (IF =4.996)

PREVIOUS PUBLICATIONS @(CDFD,Hyderabad & MKU, Madurai)

1. Acharya, V. and Nagarajaram, H. A. (2013), Response to: Statistical Analysis of Missense Mutation Classifiers. Human Mutation, 34: 407. doi: 10.1002/ humu.22250 (IF=4.7)

2. Acharya V, Nagarajaram HA. (2012) Hansa: an automated method for discriminating disease and neutral human nsSNPs Human Mutation Feb;33(2):332-7. doi: 10.1002/humu.21642. Epub 2011 Dec 9 (IF =4.7). (This article is also part of the annual virtual issue of Human Mutation entitled "Evaluating Mutation Pathogenicity" Edited by Sean V. Tavtigian and Marc S. Greenblatt) (Also see a brief description of Hansa at ).

3. Bashyam MD, Chaudhary AK, Reddy EC, Reddy V, Acharya V, Nagarajaram HA, Devi AR, Bashyam L, Dalal AB, Gupta N, Kabra M, Agarwal M, Phadke SR, Tainwala R, Kumar R, Hariharan SV. (2012) A founder ectodysplasin A receptor (EDAR) mutation results in a high frequency of the autosomal recessive form of hypohidrotic ectodermal dysplasia in India British Journal of Dermatology Apr;166(4):819-29. doi: 10.1111/j.1365-2133.2011.10707.x. Epub 2012 Mar 5. (IF =6.129)

4. Bashyam MD, Purushotham G, Chaudhary AK, Rao KM, Acharya V, Mohammad TA, Nagarajaram HA, Hariram V, Narasimhan C. (2012) A low prevalence of MYH7/MYBPC3 mutations among familial hypertrophic cardiomyopathy patients in India Molecular and Cellular Biochemistry Jan;360(1-2):373-82. Epub 2011 Sep 29. (IF 2.569)

5. Alaguraj Veluchamy, Sujitha Mary, Vishal Acharya, Preethi Mehta, Taru Deva, and Sankaran Krishnaswamy (2009)HNHDb: A database on pattern based classification of HNH domains reveals functional relevance of sequence patterns and domain associations Bioinformation.; 4(2): 80–83