A. Gupta

A Machine Learning-Enabled Pipeline for Large-Scale Virtual Drug Screening

The paper develops a machine learning pipeline for virtual drug screening that reduces compound libraries and classifies hits as true or false positives using a dense neural network.

Robust Brain State Decoding using Bidirectional Long Short Term Memory Networks in functional MRI

This paper uses bidirectional LSTM to decode brain states from fMRI data, achieving 18% higher accuracy than unidirectional LSTM on working memory tasks.

Evaluation of Antibiotic Tolerance in Pseudomonas aeruginosa for Aminoglycosides and its Predicted Gene Regulations Through In-silico Transcriptomic Analysis

This study evaluates antibiotic tolerance in Pseudomonas aeruginosa to aminoglycosides and identifies gene expression changes, finding tobramycin shows superior in vitro response and potential for combating resistance.

Development of a rapid LC-MS/MS method for the simultaneous quantification of various flavonoids and phytohormones extracted from Medicago Truncatula leaves

The paper develops and validates an HPLC-MS/MS method to rapidly quantify nine flavonoids and two phytohormones in Medicago truncatula leaf extracts.

Characterization of transcript enrichment and detection bias in single-nuclei RNA-seq for mapping of distinct human adipocyte lineages

This study compares snRNA-seq and scRNA-seq in adipose tissue, showing snRNA-seq can identify cell types but has transcript enrichment and detection biases that require normalization.

Copper dependent ERK1/2 phosphorylation is essential for the viability of neurons and not glia

This study shows that copper-dependent ERK1/2 phosphorylation is essential for neuronal viability but not glial cells during differentiation.

Phenotypic shifts of tumor associated macrophages and STAT3 mediated suppression of myeloid derived suppressor cells drive sensitization of HER2+ tumor immunity.

The paper uses single-cell RNA-sequencing to show entinostat shifts tumor microenvironment cell states, reducing immunosuppression and enhancing immune checkpoint inhibitor responses in HER2+ breast tumors.

The novel leishmanial Copper P-type ATPase plays a vital role in intracellular parasite survival

This study identifies and characterizes the Leishmania major Cu-ATPase, LmATP7, and demonstrates its role in copper stress resistance and parasite survival within macrophages.

Nucleoid associated proteins and their effect on E. coli chromosome

The paper uses Hi-C simulations to study how nucleoid associated proteins affect E. coli chromosome organization, revealing scale-dependent structural changes.

Leapfrog dynamics in phage-bacteria coevolution revealed by joint analysis of cross-infection phenotypes and whole genome sequencing

The paper analyzes phage-bacteria coevolution using phenotypic and genomic data, finding that coevolution does not follow expected arms race dynamics but instead exhibits leapfrog dynamics.

PRAK-03202: A triple antigen VLP vaccine candidate against SARS CoV-2

This paper develops a triple antigen VLP vaccine candidate, PRAK-03202, against SARS-CoV-2 and shows it induces neutralizing antibodies and Th1 immune responses in mice.

A skyline birth-death process for inferring the population size from a reconstructed tree with occurrences

This paper introduces a skyline birth-death process to infer population size changes over time using occurrence data and phylogenetic trees, applied to epidemiology and macroevolution.

Downregulation of miR-17-92 cluster by PERK fine-tunes unfolded protein response mediated apoptosis

The paper shows that PERK-mediated repression of miR-17-92 cluster promotes ER stress-induced apoptosis through NRF2.

Mechanism of bacterial adhesion and embedment in a DNA biofilm matrix:Evidence that binding of outer membrane lipopolysaccharide (LPS) to HU is key

The paper identifies HU's role in bacterial adhesion to DNA in biofilms by binding LPS to HU's DNA-binding sites, facilitating bacterium-bacterium and bacterium-DNA interactions.

Using protein interaction networks to identify cancer dependencies from tumor genome data

This paper develops an algorithm to predict cancer dependencies from tumor genomes by analyzing protein interaction networks and validates its predictions using CRISPR screens.

Antigen-specific induction of CD4+CD8αα+ intraepithelial T lymphocytes byBacteroidetes species

This study identifies Bacteroidetes species that induce CD4+CD8αα+ intraepithelial T lymphocytes, which provide protective immunity against colitis.

Does visitation dictate animal welfare in captivity? A case study of tigers and leopards from National Zoological Park, New Delhi

This study examines the impact of visitor density on stereotypic behaviors in tigers and leopards at a zoo, finding significant associations with visitor numbers but not ambient noise.

Receptor-independent membrane mediated pathways of serotonin action

This study shows serotonin can directly modulate membrane properties and cellular processes without acting through receptors.

Mapping the Multiscale Organisation of Escherichia Coli Chromosome in a Hi-C-integrated Model

The paper develops a Hi-C-integrated model to map the multiscale organization of E. coli chromosome, revealing a helical structure with macrodomains and chromosomal interaction domains.

Compartment-specific opioid receptor signaling is selectively modulated by Dynorphin subtypes

The paper shows that different Dynorphin subtypes modulate KOR signaling by directing it to distinct subcellular compartments and altering its post-endocytic fate.

Enhancing the Antiviral Efficacy of RNA-Dependent RNA Polymerase Inhibition by Combination with Modulators of Pyrimidine Metabolism

The paper identifies DHODH as a target of GSK983 and shows that combining it with pyrimidine salvage inhibitors like CPU enhances antiviral efficacy against dengue virus.

Pervasive promoter hypermethylation of silenced TERT alleles in human cancers

The paper investigates TERT promoter methylation in cancer cells and finds that hypermethylation represses TERT expression, explaining modest telomerase activation in most cancers.

JAK Inhibitors Suppress Colon Cancer Cachexia-Associated Anorexia and Adipose Wasting in Mice

This study shows JAK inhibitors reduce cachexia-associated anorexia and adipose wasting in colon cancer models by blocking cytokine-induced pathways.

Retromer retrieves the Wilson Disease protein, ATP7B from lysosomes in a copper-dependent mode

The paper shows that retromer facilitates the recycling of the copper transporter ATP7B from lysosomes to the Trans Golgi Network in a copper-dependent manner.

Heterogeneity and targeted therapy-induced adaptations in lung cancer revealed by longitudinal single-cell RNA sequencing

This study uses longitudinal single-cell RNA sequencing to reveal therapy-induced adaptations in lung cancer, identifying cell state transitions and pathways associated with treatment response and resistance.

Porous upconversion nanostructures as bimodal biomedical imaging contrast agents

This study designs core-porous shell upconversion nanoparticles to enhance both fluorescent and MRI signals for dual-modal biomedical imaging.

CXCR4 intracellular protein regulates drug resistance and tumorigenic potential via modulating the expression of Death Receptor 5

The paper shows that intracellular CXCR4 protein, not its signaling, promotes drug resistance and tumorigenicity by downregulating DR5 through transcription factor modulation.

Human Rotavirus Diarrhea Is Associated with Altered Trafficking and Expression of Apical Membrane Transport Proteins

Analysing plasma membrane asymmetry of lipid organisation by fluorescence lifetime and correlation spectroscopy

The paper uses FLIM and ITIR-FCS to study lipid asymmetry in mammalian cell membranes, revealing distinct dynamics in the outer and inner leaflets.

Kinomorphs: Shape-shifting tissues for developmental engineering

This paper introduces kinomorphs, dynamic scaffolds that guide large-scale tissue assembly through programmed shape changes, enabling the creation of structurally mature epithelial tubules.