Publications

Please find here all publications of Bioclues in PubMed

2022:

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 bona fide 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.
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.
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.
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.
Abbasi BA, Dharan A, Mishra A, Saraf D, Ahamad I, Suravajhala P, Valadi J.
In Silico Characterization of Uncharacterized Proteins From Multiple
Strains of Clostridium Difficile. Front Genet. 2022 Aug 11;13:878012.
doi: 10.3389/fgene.2022.878012. PMID: 36035185; PMCID: PMC9403866.
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.
Selvaraj C, Chandra I, Singh SK. Artificial intelligence and machine learning
approaches for drug design: challenges and opportunities for the pharmaceutical
industries. Mol Divers. 2022 Jun;26(3):1893-1913. doi:
10.1007/s11030-021-10326-z. Epub 2021 Oct 23. PMID: 34686947; PMCID: PMC8536481.
Sheoran S, Arora S, Samsonraj R, Govindaiah P, Vuree S. Lipid-based
nanoparticles for treatment of cancer. Heliyon. 2022 May 13;8(5):e09403. doi:
10.1016/j.heliyon.2022.e09403. PMID: 35663739; PMCID: PMC9160046.
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.
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:
33280525.
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.

2021:

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.

2020:

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

2019:

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

2018:

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

2017:

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

2016:

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

2015:

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

2014:

Research Article: PR Shidhi et al., Making novel proteins from pseudogenes. Bioinformatics (Oxford). 2014. Link
Short Communication: Prashanth Suravajhala et al., Eur. Chem. Bull. 2014, 3(8), 809-810. Link
Book: PB. Kavi Kishor, Rajib Bandyopadhyay and Prashanth Suravajhala. Agricultural Bioinformatics. Springer Book.June 2014.
Database/Webserver: Anil Kumar, P et al., PSPDB: Plant Stress Protein Database. Plant Molecular Biology Reporter. February 2014
Research Article: Sameera Panchangam et al., . Androgenesis in chickpea: Anther culture and expressed sequence tags derived annotation. Indian Journal of Experimental biology. 52(2): 181-188.
Article: Singhania RR et al., (2014). The Making of the Women in Biology Forum (WiB) at Bioclues. PLoS Comput Biol 10(1): e1003436.
Correspondence: Prashanth Suravajhala (2014). Two Freds’ no more: the legacies of two scientists Current Science 106 (1): 9.
Book Chapter: Renuka Suravajhala et al., Springer: Agricultural Bioinformatics 2014.

2013:

Research Article: Alfredo Benso et al., A combined approach for genome wide protein function annotation/prediction. Proteome Science 2013, 11(Suppl 1):S1
Correspondence: Mohanalatha Chandrasekharan et al., Women Biologists in India: Challenges. Current Science 105 (8): 1034.
Mini Review: Tiratha Raj Singh et al., Challenges in the miRNA research. International Journal of Bioinformatics Research and Applications. 2013: 9(6):576-583.
Book: Prashanth Suravajhala. Your Passport to a career in Bioinformatics. Springer. August 2013.

Until 2012:

Commentary: Silvia Vasquez et al., ISSN 1684-1662.
Research Article: Suravajhala P and Sundararajan VS. A classification scoring schema to validate protein interactors. 2012;8(1):34-9. Epub 2012 Jan 6. Free PMC Article
Database: Bolser DM et al., MetaBase–the wiki-database of biological databases. Nucleic Acids Res. 2012 Jan;40(Database issue):D1250-4. doi: 10.1093/nar/gkr1099. Epub 2011 Dec 1. Free PMC Article
Research Article: Katam R et al., Analysis of peanut leaf proteome.J Proteome Res. 2010 May 7;9(5):2236-54. doi: 10.1021/pr901009n.
Correspondence: Suravajhala P et al., Influence of virtual conferences on bioinformatics in India and developing nations. Current Science 2010.98 (11),1429.
Editorial: Gichora NN et al., Ten simple rules for organizing a virtual conference–anywhere.PLoS Comput Biol. 2010 Feb 26;6(2):e1000650. doi: 10.1371/journal.pcbi.1000650. Free PMC Article
Challenges: Gudimella R et al., Fungome: Annotating proteins implicated in fungal pathogenesis. 2010 Nov 1; 5(5):202-7. Free PMC Article.
Book: Prashanth Suravajhala. Biotoons. Frog Publishers. 2006. Link