Computational & Functional Genomics »
|Computational & Functional Genomics
Publications of Dr. Akash Ranjan
Ghosh DK, Ranjan A (2021). HYPK coordinates degradation of polyneddylated proteins by autophagy. Autophagy. 26:1-22.
Ghosh DK, Kumar A, Ranjan A (2021). Cellular targets of mefloquine. Toxicology. Dec;464:152995.
Deshpande D, Gupta SK, Sarma AS, Ranganath P, Jain S JMN, Sheth J, Mistri M, Gupta N, Kabra M, Phadke SR, Girisha KM, Dua Puri R, Aggarwal S, Datar C, Mandal K, Tilak P, Muranjan M, Bijarnia-Mahay S, Rama Devi A R, Tayade NB, Ranjan A, Dalal AB (2021). Functional characterization of novel variants in SMPD1 in Indian patients with acid sphingomyelinase deficiency. Hum Mutat. 42(10):1336-1350.
Kumar A, Ghosh DK, Ranjan A (2021). Differential Stabilities of Mefloquine-Bound Human and Plasmodium falciparum Acyl-CoA-Binding Proteins. ACS Omega. 6(3):1883-1893.
Ghosh DK, Ranjan A (2020). The metastable states of proteins. Protein Sci., 29(7):1559-1568.
Kumar A, Ghosh DK, Ranjan A (2020). Mefloquine binding to human acyl-CoA binding protein leads to redox stress-mediated apoptotic death of human neuroblastoma cells. Neurotoxicology., 77:169-180.
Gupta SK, Angara RK, Yousuf S, Reddy CG, Ranjan A (2020). Ectopic Expression of Rv0023 Mediates Isoniazid/Ethionamide Tolerance via Altering NADH/NAD+ Levels in Mycobacterium smegmatis. Front Microbiol., 11:3.
Ghosh DK, Kumar A, Ranjan A (2020). The metastable states of proteins. RSC Adv., 10, 10776-10788.
Kumar Ghosh D, Nanaji Shrikondawar A, Ranjan A (2020). Local structural unfolding at the edge-strands of beta sheets is the molecular basis for instability and aggregation of G85R and G93A mutants of superoxide dismutase 1. J Biomol Struct Dyn., 38(3):647-659.
Ghosh DK, Ranjan A (2019). An IRES-dependent translation of HYPK mRNA generates a truncated isoform of the protein that lacks the nuclear localization and functional ability. RNA Biol. , 16(11):1604-1621.
Kumar A, Ghosh DK, Ali J, Ranjan A (2019). Characterization of Lipid Binding Properties of Plasmodium falciparum Acyl-Coenzyme A Binding Proteins and Their Competitive Inhibition by Mefloquine. ACS Chem Biol., 14(5):901-915.
Ghosh DK, Kumar A, Ranjan A (2018). Metastable states of HYPK-UBA domain's seeds drive the dynamics of its own aggregation. Biochim Biophys Acta Gen Subj.,1862(12):2846-2861.
Ghosh DK, Roy A, Ranjan A (2018). The ATPase VCP/p97 functions as a disaggregase against toxic Huntingtin-exon1 aggregates. FEBS Lett., 592(16):2680-2692.
Ghosh DK, Roy A, Ranjan A (2018). Aggregation-prone regions in HYPK help it to form sequestration complex for toxic protein aggregates. J Mol Biol, 430:963-986.
Ghosh, DK, Roy, A, Ranjan A (2018). Disordered nanostructure in Huntigntin Interactinf Portein K acts as a stabilizing switch to prevent protein aggregation. Biochemistry, 53(13):2009-2023. (The April, 2018 issue of Biochemistry has the cover page from this article).
Yousuf S, Angara RK, Roy A, Gupta SK, Misra R, Ranjan A (2018). Mce2R/Rv0586 of Mycobacterium tuberculosis is the functional homologue of FadR(E. coli). Microbiology, 164(9):1133-1145
Angara RK, Yousuf S, Gupta SK, Ranjan A (2018). An IclR like protein from mycobacteria regulates leuCD operon and induces dormancy-like growth arrest in Mycobacterium smegmatis. Tuberculosis, 108:83-92.
Roy A, Reddi R, Sawhney B, Ghosh DK, Addlagatta A, Ranjan A (2016) Expression, Functional Characterization and X-ray Analysis of HosA, A Member of MarR Family of Transcription Regulator from Uropathogenic Escherichiacoli. Protein J.; 35(4):269-282.
Roy A, Ranjan A(2016) HosA, a MarR Family Transcriptional Regulator, Represses Nonoxidative Hydroxyarylic Acid Decarboxylase Operon and Is Modulated by 4-Hydroxybenzoic Acid. Biochemistry; 55(7):1120-34.
Sawhney B, Chopra K, Misra R, Ranjan A(2015) Identification of Plasmodium falciparum apicoplast-targeted tRNA-guanine transglycosylase and its potential inhibitors using comparative genomics, molecular modelling, docking and simulation studies. J Biomol Struct Dyn; 33(11):2404-20.
Yousuf S, Angara R, Vindal V, Ranjan A (2015) Rv0494 is a starvation-inducible, auto-regulatory FadR-like regulator from Mycobacterium tuberculosis. Microbiology;161(Pt 3):463-76.
Pandey SD, Choudhury M, Yousuf S, Wheeler PR, Gordon SV, Ranjan A, Sritharan M (2014) Iron-regulated protein HupB of Mycobacterium tuberculosis positively regulates siderophore biosynthesis and is essential for growth in macrophages. J Bacteriol.;196(10):1853-65.
Muley VY, Ranjan A. Evaluation of physical and functional protein-protein interaction prediction methods for detecting biological pathways. PLoS One. 8(1):e54325.
Muley VY, Ranjan A (2012) Effect of reference genome selection on the performance of computational methods for genome-wide protein-protein interaction prediction. PLoS One. 7(7):e42057.
Ali J, Thummala SR, Ranjan A (2012) The parasite specific substitution matrices improve the annotation of apicomplexan proteins. BMC Genomics.13 Suppl 7:S19.**
Ali J, Paila U, Ranjan A(2011) ApicoAlign: an alignment and sequence search tool for apicomplexan proteins. BMC Genomics 12(Suppl 3):S6.**
Paila U, Kondam R, Ranjan A(2008) Genome bias influences amino acid choices: analysis of amino acid substitution and re-compilation of substitution matrices exclusive to an AT-biased genome. Nucleic Acids Res. 36 :6664-6675.
Rajesh V, Singamsetti VK, Vidya S, Gowrishankar M, Elamaran M, Tripathi J, Radhika NB, Kochar D, Ranjan A, Roy SK, Das A.(2008) Plasmodium falciparum: genetic polymorphism in apical membrane antigen-1 gene from Indian isolates. Exp Parasitol. 119:144-51.
Vindal V, Ashwantha Kumar E, Ranjan A.(2008)Identification of operator sites within the upstream region of the putative mce2R gene from mycobacteria.FEBS Lett. 582(7):1117-22.
Hussain MA, Naveed SA, Sechi LA, Ranjan S, Alvi A, Ahmed I, Ranjan A, Mukhopadhyay S, Ahmed N. (2008) Isocitrate dehydrogenase of Helicobacter pylori potentially induces humoral immune response in subjects with peptic ulcer disease and gastritis. PLoS ONE. 3(1):e1481.
Akhter Y, Yellaboina S, Farhana A, Ranjan A, Ahmed N, Hasnain SE.(2008) Genome scale portrait of cAMP-receptor protein (CRP) regulons in mycobacteria points to their role in pathogenesis.Gene.407:148-58.
Vindal V, Suma K, Ranjan A.(2007)GntR family of regulators in Mycobacterium smegmatis: a sequence and structure based characterization.BMC Genomics. 8:289.
Saxena V, Garg S, Ranjan S, Kochar D, Ranjan A, Das A.(2007) Analysis of elongation factor Tu (tuf A) of apicoplast from Indian Plasmodium vivax isolates. Infect Genet Evol. 7(5):618-26.
Ahmed N, Majeed AA, Ahmed I, Hussain MA, Alvi A, Devi SM, Rizwan M, Ranjan A, Sechi LA, Mégraud F. (2007) genoBASE pylori: a genotype search tool and database of the human gastric pathogen Helicobacter pylori. Infect Genet Evol. 7:463-8.
Vidyasagar, M. ..., Ranjan A. ... et al (2007) BioSuite: A comprehensive bioinformatics software package (A unique industry-academia collaboration) Current Science, 92, 29-38.
Ahmed N, Majeed AA, Ahmed I, Hussain MA, Alvi A, Manjulata Devi S, Rizwan M, Ranjan A, Sechi L A and Mraud F (2007) genoBASE pylori: A genotype search tool and database of the human gastric pathogen Helicobacter pylori Infection, Genetics and Evolution, 4:463-468.
Vindal V, Ranjan S and Ranjan A (2006) In silico Analysis and Classification of Mycobacterium tuberculosis putative GntR transcription regulators. Tuberculosis 87:242-247.
Ranjan S, Gundu RK and Ranjan A (2006) MycoperonDB: A database of computationally identified operons and transcriptional units in Mycobacteria. BMC Bioinformatics 7 (S2) : S5**
Ranjan S, Seshadri J, Vindal V, Yellaboina S and Ranjan A (2006) iCR: A web tool to identify conserved targets of a regulatory protein across the prokaryotic species. Nucleic Acids Res. 34, W584- W587.
Yellaboina S, Ranjan S, Vindal V, and Ranjan A (2006) Comparative analysis of Iron regulated genes in mycobacteria FEBS Letters, 580: 2567–2576.
Ranjan S, Yellaboina S, and Ranjan A (2006) IdeR: From target recognition to physiological functions Critical Reviews in Microbiology, 32: 69–75.
Prakash P, Yellaboina S, Ranjan A, and Hasnain S.E. (2005) Computational prediction and experimental verification of novel IdeR binding sites in the upstream sequences of Mycobacterium tuberculosis ORFs Bioinformatics 21: 2161-2166.
Vijay Kumar S, Ranjan S, Saxena V, Rajesh V, Roy SK, Kochar D, Ranjan A, Das A. (2005) Plasmodium falciparum: genetic diversity of C-terminal region of MSP-1 in isolates from Indian sub-continent. Exp Parasitol. 110: 384-388.
Yellaboina S., Ranjan S., Chakhaiyar P., Hasnain SE., and Ranjan A. (2004) Prediction of DtxR regulon: Identification of binding sites and operons controlled by Diphtheria toxin repressor in Corynebacterium diphtheriae. BMC Microbiology 4:38
Yellaboina S., Seshadri J., Senthil Kumar M and Ranjan A. (2004) Predictregulon: A webserver for the prediction of the regulatory protein binding sites and operons in prokaryote genomes. Nucleic Acids Research 32, W318-320.
Yellaboina S., Chakhaiyar P., Hasnain SE., and Ranjan A. (2003) Computational prediction of DtxR regulon-A Dissection of physiological process controlled by DtxR in Corynebacterium species. Proceedings of IEEE Computational System Bioinformatics Conference 442-443.**
Singh S., Pandey K., Chatopadhya R., Yazdani S.S., Lynn A., Bharadwaj A., Ranjan A., and Chitnis C. (2001) Biochemical, biophysical and functional characterization of bacterially expressed and refolded receptor binding domain of Plasmodium vivax Duffy Binding protein. J. Biol. Chem. 276, 17111-17116.
Ranjan A., and Chitnis C. (1999) Mapping of receptor binding site within the erythrocyte binding domain of Plasmodium vivax and Plasmodium knowlesi proteins involved in erythrocyte invasion. Proc. Nat. Acad of Sc., USA, 96, 14067-14072.
Chitnis C., Chatopadhya R., Okoyeh,J.N., Pandey K., Ranjan A. and Singh S., (1998).A superfamily of Plasmodium proteins involved in erythrocyte invasion and cytoadherence: implications for malariavaccine development The Immunologist , Suppl 1, 193
Hasnain, S.E., Jain, A., Habib, S., Ghosh, S., Chatterji, U., Ramachandran, A., Das, P., Venkaiah, B., Pandey, S., Liang, B., Ranjan, A., Natrajan, K., Azim, C.A. (1997) Involvement of host factors in transcription from baculovirus very late gene promoters. Gene, 190, 113-118.
Awasthi, A.K., Jha, P.K., Ranjan, A. and Hasnain, S.E. (1997) Monitoring.recombinant baculovirus replication in Spodoptera litura (Lepidoptera:Noctuidae) larvae using firefly luciferase gene as reporter. Annuls of Entomology Society of America 90, 832-835.
Ranjan, A., and Hasnain, S.E. (1995). Codon usage in the prototype baculovirus- Autographa Californica Nuclear polyhedrosis virus. Ind. J. Biochem. Biophys., 32, 424-428.
Mishra, N., Habib, S., Ranjan, A., Hasnain S.E. and Nath, I. (1996). Cloning and expression of Mycobacterium lepraeclpC gene. Gene, 172, 99-104.
Ranjan, A., and Hasnain, S.E. (1994). Influence of codon usage and translation initiation codon context in the AcNPV-based expression system: Computer analysis using homologous and heterologous genes. Virus Genes, 09, 149-153.
Hasnain, S.E., Nakhai, B., Ehtesham, N.Z., Sridhar, P., Ranjan, A., Talwar, G.P., and Jha, P.K. (1994). ß-Subunit of human chorionic gonadotropin hormone and firefly luciferase simultaneously synthesised in insect cells using a recombinant baculovirus are differentially expressed and transported. DNA and Cell Biology 13, 275-282.
Sridhar, P., Azim, C.A., Burma, S., Habib, S., Jain, A., Mukherjee, B., Ranjan, A., and Hasnain, S.E. (1994) Baculovirus vector-mediated expression of heterologous genes in insect cells. J. Biosciences, 19, 603-614.
|Articles in Books
Jain, A., Ranjan, A., Chatterji, U., Das, P., Ghosh, S., Habib, S., Pandey, S., Ramachandran, A., Venkaiah, B., and Hasnain, S.E. (1998) High level expression of heterologous genes in insect cells is not dependent on promoter alone in Invertebrate cell culture: Novel Direction and Biotechnological Applications (Eds: Maramorosch K and Mitsuhashi J) Science Publishers, Inc (USA) New Hampshire, p221-227.*
Habib, S., Burma, S., Chatterji, U., Das, P., Jain, A., Mukherjee, B., Natarajan, K., Ranjan, A. and Hasnain S.E . (1996) Transcriptional regulation of the AcNPV polyhedrin gene promoter in Current Developments in Animal Virology (Ed Wagner and S Jameel eds) Oxford and IBH Publishing Co. Pvt Ltd, New Delhi, India.*
|* Book Chapters
** Non peer-reviewed journals / supplements / proceedings
|Last updated on: Thursday, 17thFeb, 2022.