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Please find here all publications of  Bioclues in PubMed


  • Editorial:  Do DN, Suravajhala P. Editorial: Role of Non-Coding RNAs in Animals. Animals
    (Basel). 2023 Feb 23;13(5):805. doi: 10.3390/ani13050805. PMID: 36899662; PMCID:
  • Research: Gupta S, Mathur P, Mishra AK, Medicherla KM, Bandapalli OR, Suravajhala P.
    Whole Exome-Trio Analysis Reveals Rare Variants Associated with Congenital Pouch
    Colon. Children (Basel). 2023 May 19;10(5):902. doi: 10.3390/children10050902.
    PMID: 37238450; PMCID: PMC10217150.
  • Research: Vidyasagar GVC, Reddy PVJ, Kumar S, Polipalli SK, Jaiswal RM, Venkateswarulu TC, Kishor PBK, Suravajhala P, Polavarapu R. Perspectives on Rapid Antigen Tests for Downstream Validation and Development of Theranostics. Adv Exp Med Biol. 2023;1412:285-310. doi: 10.1007/978-3-031-28012-2_16. PMID: 37378774.
  • Research:  Kumar S, Lomash A, Faruq M, Siddiqui O, Kumar S, Kapoor S, Suravajhala P, Polipalli SK. Amplicon-Based Nanopore Sequencing of Patients Infected by the SARS-CoV-2 Omicron (B.1.1.529) Variant in India. Adv Exp Med Biol. 2023;1412:271-283. doi: 10.1007/978-3-031-28012-2_15. PMID: 37378773.
  • Research:  Shukla N, Kour B, Sharma D, Vijayvargiya M, Sadasukhi TC, Medicherla KM, Malik B, Bissa B, Vuree S, Lohiya NK, Suravajhala P. Towards Understanding the Key Signature Pathways Associated from Differentially Expressed Gene Analysis in an Indian Prostate Cancer Cohort. Diseases. 2023 May 11;11(2):72. doi: 10.3390/diseases11020072. PMID: 37218885; PMCID: PMC10204445.


  • Research:  Rajagopal S, Sharma A, Simlot A, Mathur P, Mehta S, Mehta S, Naravula J,
    Medicherla KM, Kumar A, Kanga U, Suravajhala R, Bhandari RK, Nair BG, Kishor
    PBK, Suravajhala P. Inferring <i>bona fide</i> Differentially Expressed Genes
    and Their Variants Associated with Vitamin K Deficiency Using a Systems Genetics
    Approach. Genes (Basel). 2022 Nov 9;13(11):2078. doi: 10.3390/genes13112078.
    PMID: 36360315; PMCID: PMC9690332.
  • Research: Panchangam SS. BabyBoom: 3-Dimensional Structure-Based Ligand and Protein
    Interaction Prediction by Molecular Docking. Biomolecules. 2022 Nov
    3;12(11):1633. doi: 10.3390/biom12111633. PMID: 36358982; PMCID: PMC9687316.
  • Research:  Valadi J, Sundararajan VS, Bandapalli OR, Benso A, Suravajhala P. Editorial:
    Integrated systems genomic approaches for characterizing uncharacterized
    proteins. Front Genet. 2022 Sep 13;13:1000825. doi: 10.3389/fgene.2022.1000825.
    PMID: 36176288; PMCID: PMC9513579.
  • Editorial: Suravajhala P, Goltsov A. Three Grand Challenges in High Throughput Omics
    Technologies. Biomolecules. 2022 Sep 4;12(9):1238. doi: 10.3390/biom12091238.
    PMID: 36139077; PMCID: PMC9496467.
  • Research: Abbasi BA, Dharan A, Mishra A, Saraf D, Ahamad I, Suravajhala P, Valadi J.
    <i>In Silico</i> Characterization of Uncharacterized Proteins From Multiple
    Strains of <i>Clostridium Difficile</i>. Front Genet. 2022 Aug 11;13:878012.
    doi: 10.3389/fgene.2022.878012. PMID: 36035185; PMCID: PMC9403866.
  • Research:Rout M, Kour B, Vuree S, Lulu SS, Medicherla KM, Suravajhala P. Diabetes
    mellitus susceptibility with varied diseased phenotypes and its comparison with
    phenome interactome networks. World J Clin Cases. 2022 Jun 26;10(18):5957-5964.
    doi: 10.12998/wjcc.v10.i18.5957. PMID: 35949812; PMCID: PMC9254192.
  • Editorial:Khan AM, Ranganathan S, Suravajhala P. Editorial: Bioinformatics and the
    Translation of Data-Driven Discoveries. Front Genet. 2022 May 10;13:902940. doi:
    10.3389/fgene.2022.902940. PMID: 35620463; PMCID: PMC9127959.
  • Research: Suravajhala R, Gupta S, Kumar N, Suravajhala P. Deciphering LncRNA-protein
    interactions using docking complexes. J Biomol Struct Dyn. 2022
    May;40(8):3769-3776. doi: 10.1080/07391102.2020.1850354. Epub 2020 Dec 7. PMID:
  • Research: Parihar J, Parihar SP, Suravajhala P, Bagaria A. Spatial Metagenomic
    Analysis in Understanding the Microbial Diversity of Thar Desert. Biology
    (Basel). 2022 Mar 17;11(3):461. doi: 10.3390/biology11030461. PMID: 35336834;
    PMCID: PMC8945486.


  • Book chapter: Manjari, K.S., Chakraborty, D., Kumar, A. and Singh, S. (2021). Biodiversity and Importance of Plant Bioprospecting in Cosmetics. In Bioprospecting of Plant Biodiversity for Industrial Molecules (eds S.K. Upadhyay and S.P. Singh). https://doi.org/10.1002/9781119718017.ch10
  • Editorial Perspective: Shukla N, Prasad A, Kanga U, Suravajhala R, Nigam VK, Kishor PK, Polavarapu R, Chaubey G, Singh KK, Suravajhala P. SARS-CoV-2 Transgressing LncRNAs Uncovers the Known Unknowns. Physiol Genomics. 2021 Sep 7. doi: 10.1152/physiolgenomics.00075.2021. Epub ahead of print. PMID: 34492207.
  • Review: Choudhary C, Sharma S, Meghwanshi KK, Patel S, Mehta P, Shukla N, Do DN, Rajpurohit S, Suravajhala P, Shukla JN. Long Non-Coding RNAs in Insects. Animals (Basel). 2021 Apr 14;11(4):1118. doi: 10.3390/ani11041118. PMID: 33919662; PMCID: PMC8069800.
  • Research: Suravajhala R, Parashar A, Choudhir G, Kumar A, Malik B, Nagaraj VA, Padmanaban G, Polavarapu R, Suravajhala P, Kishor PBK. Molecular docking and dynamics studies of curcumin with COVID-19 proteins. Netw Model Anal Health Inform Bioinform. 2021;10(1):44. doi: 10.1007/s13721-021-00312-8. Epub 2021 Jun 10. PMID: 34131556; PMCID: PMC8192041.


  • Research: Suravajhala R , Burri HR, Malik B. Selective targeted drug delivery mechanism via molecular imprinted polymers in cancer therapeutics [published online ahead of print, 2020 Jun 22]. Curr Top Med Chem. 2020;10.2174/1568026620666200622150710. doi:10.2174/1568026620666200622150710 . Link. 
  • Research: Suravajhala R, Gupta S, Kumar N, Suravajhala P. Deciphering LncRNA-protein interactions using docking complexes. J Biomol Struct Dyn. 2020 Dec 7:1-8. doi: 10.1080/07391102.2020.1850354. Epub ahead of print. PMID: 33280525.
  • Research:Katam R, Shokri S, Murthy N, Singh SK, Suravajhala P, Khan MN, Bahmani M, Sakata K, Reddy KR. Proteomics, physiological, and biochemical analysis of cross tolerance mechanisms in response to heat and water stresses in soybean. PLoS One. 2020 Jun 5;15(6):e0233905. doi: 10.1371/journal.pone.0233905. PMID: 32502194; PMCID: PMC7274410.
  • Research: Kumar A, Sharma M, Chaubey SN, Kumar A. Homology modeling and molecular dynamics based insights into Chalcone synthase and Chalcone isomerase in Phyllanthus emblica L. 3 Biotech. 2020 Aug;10(8):373. doi: 10.1007/s13205-020-02367-2. Epub 2020 Aug 4. PMID: 32832333; PMCID: PMC7403374.
  • Research: Katam R, Shokri S, Murthy N, et al. Proteomics, physiological, and biochemical analysis of cross tolerance mechanisms in response to heat and water stresses in soybean. PLoS One. 2020;15(6):e0233905. Published 2020 Jun 5. doi:10.1371/journal.pone.0233905.  Link


  •  Review:  Madduru D et al., Systems Challenges of Hepatic Carcinomas: A Review. J Clin Exp Hepatol. 2019 Mar-Apr;9(2):233-244. Link 
  •  Methodology: Ijaq J and Malik G et al., A model to predict the function of hypothetical proteins through a nine-point classification scoring schema.  BMC Bioinformatics. 2019 Jan 8;20(1):14. Link


  • Commentary Preprint: Das PS and Poddar R et al., (2018Twelve years of BIOinformatics CLUb for Experimenting Scientists (Bioclues) PeerJ Preprints6:e26503v1. Link.


  • Research:  M.Nagaraju et al.,  Genome-wide in silico analysis of dehydrins in Sorghum bicolor, Setaria italica and Zea mays and quantitative analysis of dehydrin gene expressions under abiotic stresses in Sorghum bicolor. Plant Gene. 13: 64-75. Link


  • Review/Challenges: Iddamalgoda L et al.,   Data Mining and Pattern Recognition Models for Identifying Inherited Diseases: Challenges and Implications.  Front Genet. 2016 Aug 10;7:136. Link

  • Review: Sameera Panchangam et al.,  Saffron’omics’: The Challenges of Integrating Omic Technologies. Avicenna Journal of Phytomedicine.  In Press. Link
  • Perspective: Pranathi Pappu et al.,  Next Generation Sequencing Analysis of Lung Cancer Datasets: A Functional Genomics Perspective.  Indian Journal of Cancer. 2016: 53(1):1-7.  Link
  • Research: Sade H et al.,  Toxicity and tolerance of aluminum in plants: tailoring plants to suit to acid soils. Biometals. 2016 Jan 21. Link


  • Research Commentary:  Deepti Chachra et al., Syst Synth Biol. 2015 Dec;9(Suppl 1):57-62..  Link
  • Editorial: Prashanth Suravajhala, Alfredo Benso and Jayaraman Valadi. (Challenges in characterizing the uncharacterized) Annotation and curation of uncharacterized proteins: systems biology approaches. Front Genet. 2015 Jun 30;6:224. Link
  • Research Commentary:  Prashanth Suravajhala and Tiratha Raj singh. Is HNF4A a candidate to study zinc finger protein slug? International Journal of Bioinformatics Research and Applications 11(4):366-373 Link
  • Review Article:  Johny Ijaq et al.,  (2015) Annotation and curation of uncharacterized proteins- challenges. Front. Genet., 31 March 2015 | Link
  • Review Article:  Anil Kumar S et al.,  Osmotin: a plant sentinel and a possible agonist of mammalian adiponectin.  Plant Sci. Link
  • Research Article:  Sai Kumar Kompelli et al.,   Genome-wide identification of miRNAs in pigeonpea (Cajanus cajan ).  Link
  • Protocol: Prashanth Suravajhala and Jeff W Bizzaro. A Conceptual Outline for ‘Omics Experiments Using Bioinformatics Analogies. BioProtocol 2015; 5(3).Link
  • Obituary: Prashanth Suravajhala, Renuka Suravajhala: Brian F C Clark. Current science 01/2015; 108(2):287. Link
  • Perspective: Srikanth Chiliveru et al., . On Brucella pathogenesis: looking for the unified challenge in systems and synthetic biology. Syst Synth Biol. 2015 Jun;9(1-2):73-5. Link



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