A. Paul

Explainable machine learning reveals an RBP regulatory logic of exon skipping

The paper uses explainable machine learning to uncover RBP binding patterns that predict exon skipping and reveals biologically interpretable regulatory logic.

STARTER : A Stand-Alone Reconfigurable and TranslationalOoC Platorm based on Modularity and Open Design Principles

The paper introduces a modular microfluidic platform for Organ-on-Chips that supports interoperability, reconfigurability, and open design to enhance collaboration and translation.

Bacterial Protein Signatures Identified in Porphyromonas gingivalis Containing-Autophagic Vacuoles Reveal Co-Evolution Between Oral Red/Orange Complex Bacteria and Gut Bacteria

The paper identifies shared protein signatures between oral and gut bacteria, revealing co-evolutionary relationships through phylogenetic analysis and mass spectrometry.

FUSION: A web-based application for in-depth exploration of multi-omics data with brightfield histology

FUSION is a web-based tool that integrates spatial -omics data with histology to analyze tissue states and identify spatial linkages between molecular and histopathologic features.

SWEET family transporters act as water conducting carrier proteins in plants

This study shows SWEET family transporters in plants act as water-conducting carrier proteins through multiple mechanisms, validated by simulations and experiments.

Rosettes in a matrix: Predicting spatial variation in density of a large felid in a forest-production mosaic

This study estimates leopard densities in a tea-plantation and forest mosaic, finding higher densities in tea plantations than in forests, suggesting multi-use landscapes may support large felids better than protected areas.

Developing Bioactive Hydrogels Containing Cell-derived Extracellular Matrix: Implications in Drug and Cell-free Bone and Cartilage Repair

This study develops bioactive hydrogels containing cell-derived extracellular matrix for drug-free and cell-free bone and cartilage repair, showing induction of stem cell differentiation.

Dynamics of aqueous suspension of short Hyaluronic acid chains near DPPC bilayer

This study uses molecular dynamics simulations to investigate the dynamics of short HA chains near a DPPC bilayer, revealing subdiffusive behavior and concentration-dependent diffusion.

Assessing the capacity of high-resolution commercial satellite imagery for grapevine downy mildew detection and surveillance in New York state

This study evaluates the effectiveness of high-resolution satellite imagery for detecting grapevine downy mildew using spectral data and vegetation indices.

Endothelial stiffening induced by CD36-mediated lipid uptake leads to endothelial barrier disruption and contributes to atherosclerotic lesions

This study shows that CD36-mediated lipid uptake causes endothelial stiffening, leading to barrier disruption and atherosclerosis in mouse models, with sex-dependent effects.

Nucleo-cytoplasmic environment modulates spatio-temporal p53 phase separation

This study shows that p53 phase separation and condensate formation are modulated by the nucleo-cytoplasmic environment and cancer-associated mutations affect condensate stability and DNA binding.

Phosphatidylinositol (PI) Lipids Modulate the Binding of Tau Fibrils on Lipid Bilayers

This study uses molecular dynamics simulations to show that PI lipids bind more strongly to tau fibrils than PC/PG lipids, revealing docking sites and aggregation mechanisms.

VapC12 ribonuclease toxin modulates host immune response during Mycobacterium tuberculosis infection

This study shows that the VapC12 toxin in Mycobacterium tuberculosis modulates host immune responses, promoting pathogen survival by altering T-cell and neutrophil responses.

p53 amyloid pathology with cancer grades and p53 mutations

The paper shows p53 amyloid load correlates with cancer grades and shows both mutant and wild-type p53 form amyloids in cancer tissues.

Biotic Assessment of Crowdsourced Data Defines Four Ecoregions in Thar: A Novel Approach for Citizen Engagement in Conservation

This study uses crowdsourced bird data to identify four distinct ecoregions in Thar, highlighting anthropogenic impacts and the need for conservation.

Temporal modification of H3K9/14ac and H3K4me3 histone marks mediates mechano-responsive gene expression during the accommodation process in poplar.

This study shows that histone modifications H3K9/14ac and H3K4me3 mediate mechano-responsive gene expression in poplar, with H3K4me3 playing a key role in desensitization and resensitization phases.

Decoding Proteoforms with Single Acid Resolution Using a Sub-nanometer Diameter Pore

The paper demonstrates that sub-nanopore assays can decode proteoforms with single acid resolution by analyzing current fluctuations correlated with amino acid volumes and PTMs.

Interaction of the Tau fibrils with the neuronal membrane

This study uses molecular dynamics simulations to investigate how tau fibrils interact with neuronal membranes, finding that membrane-bound tau is more compact and that lipid interactions influence fibril structure.

Elevator-type Mechanism of the Cyanobacterial Bicarbonate Transporter

This study uses molecular dynamics simulations to elucidate the conformational dynamics of the cyanobacterial bicarbonate transporter BicA and identify mutations that lower the free energy barrier for transport.

Comparing lipid remodeling in mouse adipose and liver tissue with quantitative Raman microscopy

This study compares lipid remodeling in mouse adipose and liver tissue after one week of high-fat diet intervention using quantitative Raman microscopy, finding faster lipid changes in brown adipose tissue.

Babesia divergens egress from host cells is orchestrated by essential and druggable kinases and proteases

This study identifies essential kinases and proteases involved in Babesia divergens egress and invasion, suggesting potential drug targets.

Biomechanical dependence of SARS-CoV-2 infections

This study investigates how lung biomechanical changes with age affect SARS-CoV-2 infection rates using hydrogels and fiber matrices, finding higher infection rates on softer scaffolds resembling younger lungs.

The Effect of Lipid Composition on the Dynamics of Tau Fibrils

This study shows how lipid composition affects tau fibril structure and dynamics through molecular dynamics simulations.

Long-Range Electrostatic Interactions Significantly Modulate the Affinity of Dynein for Microtubules

This study shows that long-range electrostatic interactions significantly modulate dynein's microtubule binding affinity, affecting its processivity.

Calculating the force-dependent unbinding rate of biological macromolecular bonds from the force-ramp optical trapping assays

This paper introduces a new analytical method to calculate force-dependent unbinding rates from optical trapping assays, demonstrating its benefits and limitations through simulations.

Co-aggregation and secondary nucleation in the life cycle of human prolactin/galanin functional amyloids

This study investigates co-aggregation and cross-seeding between prolactin and galanin in rat lactotrophs, revealing a novel mechanism of heterologous amyloid formation with implications for functional and pathological amyloids.

Selective MAP1LC3C (LC3C) autophagy requires noncanonical initiation regulators and the paralog-specific C-terminal peptide

This study identifies noncanonical regulators and a C-terminal peptide essential for LC3C-mediated selective autophagy targeting PDMBs in cancer stem cells.

Effects of genetic variability of CYP2D6 on neural substrates of sustained attention during on-task activity

This study investigates how CYP2D6 genetic variants affect neural activity during attention tasks, finding that rapid metabolizers show reduced cognitive efficiency compared to poor metabolizers.

Detection and genetic analysis of infectious spleen and kidney necrosis virus (ISKNV) in ornamental fish from non-clinical cases: First report from India

The paper detects ISKNV in ornamental fish from India using PCR and sequence analysis, identifies it as genotype I, and finds it more stable than other genotypes.

Thermodynamics and kinetics of the amyloid-β peptide revealed by Markov state models based on MD data in agreement with experiment

This study uses 30-microsecond MD simulations with seven force fields to analyze the thermodynamics and kinetics of Aβ40, identifying suitable force fields and equilibrium times.