D. Chakraborty

Discovering Novel Prognostic Biomarkers of Hepatocellular Carcinoma using eXplainable Artificial Intelligence

This study uses explainable AI to identify novel genetic biomarkers for HCC prognosis, showing improved accuracy over AFP and highlighting demographic-specific relevance.

Structural insights into viral hijacking of p53 by E6 and E6AP

The paper uses cryo-EM to study the E6AP-E6-p53 complex, revealing new interaction interfaces and stoichiometry.

Competition between stacking and divalent cation mediated electrostatic interactions determines the conformations of short DNA sequences

The paper develops a computational model to study ion-DNA interactions and shows it accurately predicts experimental results without parameter tuning.

Alcohol Responsive Genes in the Neutrophils of Acute-On-Chronic Liver Failure Reveal Modulation of Intracellular Calcium, ROS, and Phagocytosis

The paper identifies alcohol-responsive genes in neutrophils of ACLF patients, showing alcohol modulates ROS, phagocytosis, and intracellular calcium, while retaining inflammatory gene expression.

Brewing COFFEE: a sequence-specific coarse-grained energy function for simulations of DNA-protein complexes

The paper introduces COFFEE, a sequence-specific coarse-grained energy function for simulating DNA-protein complexes, showing it accurately reproduces experimental data and explains nucleosome behavior.

Sizes, conformational fluctuations, and SAXS profiles for Intrinsically Disordered Proteins

This paper develops a transferable model to predict biophysical properties of IDPs, showing agreement with experimental data on size, conformation, and SAXS profiles.

Enhanced protective efficacy of a novel, thermostable, RBD-S2 fusion immunogen against SARS-CoV-2 and its variants

This study evaluates a novel RBD-S2 fusion immunogen that shows enhanced protection against SARS-CoV-2 and its variants in animal models.

Mutations in S2 subunit of SARS-CoV-2 Omicron spike strongly influence its conformation, fusogenicity and neutralization sensitivity

This study investigates how mutations in the S2 subunit of SARS-CoV-2 Omicron spike affect its structure, fusogenicity, and neutralization sensitivity.

Energy landscapes of Aβ monomers are sculpted in accordance with Ostwald's rule of stages

The paper shows that N* states in Aβ40 and Aβ42 monomers follow Ostwald's rule of stages, influencing aggregation and dimer formation.

Molecular characterization of carbapenem resistant Klebsiella pneumoniae clinical isolates: Preliminary experience from a tertiary care teaching hospital in the Himalayas

This study uses whole-genome sequencing to characterize carbapenem-resistant Klebsiella pneumoniae isolates from a hospital in Uttarakhand, India, identifying common sequence types, virulence factors, and plasmid replicons.

Direct and indirect interactions promote complexes of the lipoprotein LbcA, the CtpA protease and its substrates, and other cell wall proteins in Pseudomonas aeruginosa

This study identifies LbcA as a scaffold promoting CtpA protease activity and reveals its role in facilitating proteolysis and cell wall remodeling in Pseudomonas aeruginosa.

Sequence Determines the Switch in the Fibril Forming Regions in the Low-Complexity FUS Protein and Its Variants

The paper shows that sequence determines the fibril-forming structure in FUS-LC and its variants, with core-1 forming more readily than core-2.

Phylodynamic assessment of control measures for highly pathogenic avian influenza epidemics in France

This study uses phylodynamic analysis to assess the impact of control measures on H5N8 avian influenza spread in France, finding that culling reduced inter-departmental spread but transport within departments increased local transmission.

On the emergence of orientational order in folded proteins with implications for allostery

The paper shows that folded proteins exhibit orientational order through nematic droplets, which may enable allosteric function by resisting mechanical stress in some regions while allowing flexibility in others.

Immunogenicity and protective efficacy of a highly thermotolerant, trimeric SARS-CoV-2 receptor binding domain derivative

This study designs a thermotolerant trimeric RBD vaccine candidate that elicits strong neutralizing antibodies against multiple SARS-CoV-2 variants in animal models.

Inferring within-flock transmission dynamics of highly pathogenic avian influenza (H5N8) in France, 2020

This study uses a stochastic epidemic model and ABC-SMC to estimate H5N8 transmission dynamics in ducks, revealing key parameters and latent threats in France in 2020.

Differences in the free energies between the excited states of Aβ40 and Aβ42 monomers encode their distinct aggregation propensities

This paper explains the faster aggregation rate of Aβ42 compared to Aβ40 by showing that their distinct populations of high free energy excited states encode their aggregation propensities.

Pharmacological and fasting-induced activation of SIRT1/LXRα signaling alleviates diabetes-induced retinopathy.

This study shows that activating SIRT1 signaling through fasting or pharmacology reduces diabetes-induced retinopathy by improving cholesterol metabolism, reducing inflammation, and preserving neural function.

TUTase mediated site-directed access to clickable chromatin employing CRISPR-dCas9

This paper develops sgRNA-Click (sgR-CLK), a method to site-directly display synthetic molecules on chromatin using CRISPR-dCas9 and bioorthogonal click chemistry.

Land Use Change Increases Wildlife Parasite Diversity in Anamalai Hills, Western Ghats, India

The paper examines how land use change and habitat fragmentation affect gastrointestinal parasite diversity in wild mammals in the Anamalai Hills, finding increased parasite diversity with plantations and livestock but no significant effect from fragmentation.

Enhanced autophagic-lysosomal activity and increased BAG3-mediated selective macroautophagy as adaptive response of neuronal cells to chronic oxidative stress

Sequence effects on size, shape, and structural heterogeneity in Intrinsically Disordered Proteins

This study uses simulations to analyze how sequence and length affect the structural properties of intrinsically disordered proteins, showing sequence-dependent conformational heterogeneity despite polymer-like scaling behavior.

Charge fluctuation effects on the shape of flexible polyampholytes with applications to Intrinsically disordered proteins

The paper investigates charge fluctuation effects on flexible polyampholytes, showing non-monotonic size dependence and implications for intrinsically disordered proteins.

Sequence-dependent Three Interaction Site (TIS) Model for Single and Double-stranded DNA

The paper develops a TIS model for DNA that accurately reproduces experimental data on melting temperatures, ssDNA size, and persistence lengths without parameter tuning.