Research Articles
"In Nature's infinite book of secrecy, a little can I read"
- William Shakespeare
(39) Sarika Singh, Amresh Kumar Sharma, Anup Som, Valentina Gehlot, Shweta Mahant, Prateek Sharma, Kunal Das and Rajashree Das (2024). Molecular characterization and phylogenetic analysis of babA gene of Helicobacter pylori isolated from Indian patients with gastrointestinal diseases (Revised).
(38) Spriha Dutta, Surbhi Jain, Kunal Das, Prashant Verma, Anup Som and Rajashree Das (2024). Primary antibiotic resistance of Helicobacter pylori in India over the past two decades: A systematic review. Helicobacter 29(1): e13057. https://doi.org/10.1111/hel.13057.
(37) Khushboo, Priyanka Kumari, Bechan Sharma and Anup Som (2024). (2-Cyclohexyl-1-methylpropyl) cyclohexane isolated from garlic extract exhibits antidepressant-like activity: Extraction, docking, drug-like properties, molecular dynamics simulations and MM/GBSA studies. Journal of Biomolecular Structure and Dynamics 42(4): 1765–1777. https://doi.org/10.1080/07391102.2023.2202250.
(36) Arindam Ghosh and Anup Som (2024). Network analysis of transcriptomic data uncovers molecular signatures and the interplay of mRNAs, lncRNAs, and miRNAs in human embryonic stem cells. Differentiation 135: 100738. https://doi.org/10.1016/j.diff.2023.11.001.
(35) Vishal K. Singh, Priyanka Kumari, Anup Som, Richa Mishra, Shivangi Rai and Ramendra K. Singh. (2023). Design, synthesis and antimicrobial activity of novel quinoline derivatives: An in silico and in vitro study. Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2023.2236716.
(34) Amresh Kumar Sharma, Aparna Chaturvedi and Anup Som (2023). Host-Pathogen protein-protein interactions reveal the key mechanisms behind the endosymbiotic association of Wolbachia with Brugia malayi. Network Biology 13(4): 137-154.
(33) Amresh Kumar Sharma and Anup Som (2023). Assigning new supergroups V and W to the Wolbachia diversity. Bioinformation 19(3): 336-340.
(32) Sarika Singh, Prateek Sharma, Shweta Mahant, Kunal Das, Anup Som and Rajashree Das (2023). Analysis of Functional Status of Genetically Diverse OipA Gene in Indian Patients with Distinct Gastrointestinal Disease. Current Microbiology 80(1):35.
(31) Vishal Kumar Singh, Himani Chaurasia, Priyanka Kumari, Anup Som et al (2022). Design, synthesis and molecular dynamics simulation studies of quinoline derivatives as protease inhibitors against SARS-CoV-2. Journal of Biomolecular Structure and Dynamics 40(21): 10519–10542. https://doi.org/10.1080/07391102.2021.1946716.
(30) Aparna Chaturvedi and Anup Som (2022). The LCNetWork: An electronic representation of the mRNA-lncRNA-miRNA regulatory network underlying mechanisms of non-small cell lung cancer in humans, and its explorative analysis. Computational Biology and Chemistry 101: 107781.
(29) Anup Som, Amresh Kumar Sharma and Priyanka Kumari (2022). Recombination in sarbecovirus lineage and mutations/insertions in spike protein are linked to the emergence and adaptation of SARS-CoV-2. Bioinformation 18(10): 951-961.
(28) Vishal Kumar Singh, Richa Mishra, Priyanka Kumari, Anup Som et al (2022). In Silico Design, Synthesis and Anti-HIV Activity of Quinoline Derivatives as Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs). Computational Biology and Chemistry 98: 107675.
(27) Shweta Mahant, Amlan Chakraborty, Anup Som et al (2021).The synergistic role of Tip α, Nucleolin and Ras in Helicobacter pylori infection regulates the cell fate towards inflammation or apoptosis. Current Microbiology 78(10): 3720-3732.
(26) Rinki Singh and Anup Som (2021). Common miRNAs, candidate genes and their interaction network in four subtypes of epithelial ovarian cancer. Bioinformation 17(8): 748-759.
(25) Priyanka Kumari and Anup Som (2021). Comparative molecular dynamics simulation analysis of the docked c-di-GMP ligand with G20 and C92 mutants of the c-di-GMP I riboswitch. Bioinformation 17(8): 721-726.
(24) Priyanka Kumari, Surya Pratap Singh and Anup Som (2021). Insights into the dynamics of cyclic diguanosine monophosphate I riboswitch using molecular dynamics simulation. Indian Journal of Biochemistry & Biophysics 58(3) : 208-218.
(23) Arindam Ghosh and Anup Som (2021). Decoding molecular markers and transcriptional circuitry of naive and primed states of human pluripotency. Stem Cell Research 53 : 102334.
(22) Arindam Ghosh and Anup Som (2020). RNA-Seq analysis reveals pluripotency-associated genes and their interaction networks in human embryonic stem cells. Computational Biology and Chemistry. 85 : 107239.
(21) Rinki Singh and Anup Som (2020). Identification of common candidate genes and pathways for progression of ovarian, cervical and endometrial cancers. Meta Gene 23(2020): 1006343.
(20) Shweta Mahant, Amresh Kumar Sharma, …, Anup Som et al. (2019). Geographically distinct North-East Indian Helicobacter pylori strains are highly sensitive to Clarithromycin but are Levofloxacin resistant. Indian Journal of Medical Microbiology 37(3): 337-344.
(19) Priyanka Kumari and Anup Som (2019). In silico identification of riboswitches in the human gut microbiome for therapeutic applications. Journal of RNA and Genomics 15: 610-618.
(18) Anup Som, P. Kumari and A. Ghosh (2019). Advancing India’s bioinformatics education and research: an assessment and outlook. Journal of Proteins Proteomics 10(3): 257-267.
(17) P. Narad, K. C. Upadhyaya, Anup Som (2017). Reconstruction, visualization and explorative analysis of human pluripotency network. Network Biology 7(3): 57-75.
(16) Anup Som (2015). Causes, consequences and solutions of phylogenetic incongruence. Briefings in Bioinformatics 16(3), 536-548.
(15) Anup Som (2013). Genome-scale approach and the accuracy of phylogenetic methods. Journal of Phylogenetics and Evolutionary Biology 1(3): 1000116.
(14) Anup Som, M. Luštrek, N. K. Singh, G. Fuellen (2012). Derivation of an interaction/regulation network describing pluripotency in human. Gene 502, 99-107.
(13) Anup Som, C. Harder, B. Greber, M. Siatkowski, et al. (2010). The PluriNetWork: An Electronic Representation of the Network Underlying Pluripotency in Mouse, and Its Applications. PLoS One 5(12), e15165.
(12) G. Warsow, B.Greber, S. Falk, C. Harder, M. Siatkowski, Anup Som, et al. (2010). ExprEssence - Revealing the essence of differential experimental data in the context of an interaction/regulation network. BMC Systems Biology 4(64).
(11) Anup Som (2009). ML or NJ-MCL? A comparison between two robust phylogenetic methods. Computational Biology & Chemistry 33(5), 373-378.
(10) Anup Som and G. Fuellen (2009). The effect of heterotachy in multigene analysis using the neighbor joining method. Molecular Phylogenetics and Evolution 52, 846-851.
(9) Anup Som (2007). A new approach for estimating the efficiencies of the nucleotide substitution models. Theory in Biosciences 125(2), 133-145.
(8) Anup Som (2006). Theoretical foundation to estimate the relative efficiencies of the JC+Γ model and the JC model in obtaining the correct phylogenetic tree. Gene 385, 103-110.
(7) I. Mukhopadhyay , Anup Som , and S. Sahoo (2006). Word Organization in Coding DNA: A Mathematical Model. Theory in Biosciences 125: 1-17.
(6) Anup Som, S. Sahoo, I. Mukhopadhyay, and J. Chakrabarti (2003). Scaling Violations in Coding DNA. Europhysics Letters 62(2): 271-277.
(5) Anup Som, S. Sahoo, and J. Chakrabarti (2003). Coding DNA sequences: Statistical distributions. Mathematical Biosciences 183: 49-61.
(4) Anup Som, S. Chattopadhyay, J. Chakrabarti, and D. Bandhyopadhyay (2001). Codon distributions in DNA. Physical Review E 63(5): 51908-51915.
(3) S. Chattopadhyay, J. Chakrabarti, D. Bondhapadhyay, and Anup Som (2001). Identification of human proteins using the linguist's tools. Indian Journal of Biochemistry & Biophysics 38(1 & 2): 124-127.
(2) S. Chattopadhyay, Anup Som, S. Sahoo, and J. Chakrabarti (2000). Order and fluctuations in DNA sequences. Indian Journal of Physics 74B(1): 1-39.
(1) S. Tarafdar, P. Nandy, S. Sahoo, Anup Som, J. Chakrabarti, and A. Nandy (1999). Self-similarity and scaling exponent for DNA walk model in two and four dimensions. Indian Journal of Physics 73B(2): 337-343.