Areejit Samal

An integrated resource for systems-level analysis of aging hallmarks and associated genes

This paper introduces AgingHallmarksDB, a resource for systems-level analysis of aging hallmarks and associated genes, demonstrating its utility through various analyses of disease and transcriptome data.

NANHA - Neurostimulation in Atypical Neurodevelopment: a Harmonized Atlas

NANHA is a curated database of non-invasive brain stimulation studies in neurodevelopmental disorders, providing standardized data for analysis and protocol development.

Benchmarking Artificial Intelligence Models for Predicting Nuclear Receptor Activity from Tox21 Assays

This study benchmarks AI models for predicting nuclear receptor activity using Tox21 assays, finding that tree-based models perform better on imbalanced data while deep learning shows robustness on moderate imbalances.

TickMapKB: A FAIR Spatial Knowledgebase of Tick Species and Associated Pathogens in India

TickMapKB is a spatial knowledgebase compiling tick species, pathogens, and associated data in India to aid in disease surveillance and resistance management.

Sec and Tat mediated secretion safeguards Mycobacterium tuberculosis membrane homeostasis

This study identifies SecA1 and TatA as critical for Mycobacterium tuberculosis membrane integrity through multi-omics and functional genetics analyses.

Integrative network-based construction of ecologically relevant computational adverse outcome pathways for organic mercury-induced toxicity

This study constructs computational adverse outcome pathways for organic mercury toxicity in fish using an integrative network-based framework and curated toxicological data.

A comprehensive resource on chemicals used in aquaculture and their ecotoxicity

This paper introduces ReCAnt, a resource compiling data on 690 aquaculture chemicals and their ecotoxicity, highlighting regulatory gaps and environmental fate.

DEDuCT 3.0: An enhanced and expanded FAIR-compliant resource and toxicology knowledge graph for endocrine disrupting chemicals

This study updates the DEDuCT database with 1043 EDCs and 796 endpoints from 3269 articles, constructs a toxicology knowledge graph, and aligns it with FAIR principles for EDC research and regulation.

Node persistence from topological data analysis reveals changes in brain functional connectivity

The paper uses persistent homology to analyze brain functional connectivity changes in healthy aging and ASD, identifying clinically relevant regions with node persistence.

Network toxicology focused investigation on the impacts of inorganic arsenic and cadmium on human and ecosystem health

This study uses network toxicology to analyze the toxic effects of inorganic arsenic and cadmium on human and ecosystem health, identifying 51 and 78 adverse outcome pathways respectively.

TICToK: A comprehensive knowledgebase of tattoo ink chemicals and investigation of their associated toxicities and regulations

This paper creates a database of tattoo ink chemicals and their toxicities, identifying hazardous substances and regulatory coverage.

Simple threshold-based Boolean rules fall short in capturing biological regulatory network dynamics

This study evaluates threshold majority rules in gene regulatory network modeling, finding they lack biological realism and fail to capture key dynamics observed in empirical data.

Computational prediction of cyclotides from Viola odorata as potential inhibitors against the neuraminidase of Streptococcus pneumoniae

This study computationally identifies cyclotides from Viola odorata as potential inhibitors of Streptococcus pneumoniae neuraminidase, with five top candidates showing stability in molecular dynamics simulations.

sCentInDB: A database of essential oil chemical profiles of Indian medicinal plants

sCentInDB is a manually curated database of essential oil chemical profiles from 554 Indian medicinal plants, providing metadata and chemical space analysis for research and quality standards.

Choices of regulatory logic class modulate the dynamical regime in random Boolean networks

This study shows that biologically meaningful Boolean functions stabilize random Boolean network dynamics more than random functions, across varying network sizes and connectivities.

UVREK: Development and analysis of an expression profile knowledgebase of biomolecules induced by ultraviolet radiation exposure

UVREK compiles manually curated data on biomolecules induced by UV radiation exposure, revealing transcription-related processes and pathways involved in cancer and aging.

Network-based investigation of petroleum hydrocarbons-induced ecotoxicological effects and their risk assessment

This study uses network-based frameworks to assess the ecotoxicological effects of petroleum hydrocarbons and their risks to aquatic ecosystems.

Leveraging integrative toxicogenomic approach towards development of stressor-centric adverse outcome pathway networks for plastic additives

This study constructs a stressor-centric adverse outcome pathway network for plastic additives using toxicogenomic data, identifying 1287 additive-AOP associations and demonstrating their utility for risk assessment.

Biologically meaningful regulatory logic enhances the convergence rate in Boolean networks and bushiness of their state transition graph

The paper evaluates how different regulatory logic rules affect the structural features of Boolean network state transition graphs, finding that biologically meaningful rules improve bushiness and convergence.

Preponderance of generalized chain functions in reconstructed Boolean models of biological networks

The paper analyzes Boolean functions in biological networks and finds generalized chain functions are significantly enriched in NCFs across multiple datasets.

ViCEKb: Vitiligo-linked Chemical Exposome Knowledgebase

ViCEKb compiles 113 unique chemical triggers of vitiligo from literature, standardizes chemical data, and highlights their biological impacts and regulatory status.

T9GPred: A Comprehensive Computational Tool for the Prediction of Type 9 Secretion System, Gliding Motility and the Associated Secreted Proteins

T9GPred predicts Type 9 secretion system, gliding motility, and associated secreted proteins in Bacteroidetes strains using curated experimental data and signal domain analysis.

Discrete Ricci curvatures capture age-related changes in human brain functional connectivity networks

This study applies discrete Ricci curvatures to functional connectivity networks of young and older adults, finding age-related differences in brain regions associated with cognitive domains and behavioral scores.

Leveraging Developmental Landscapes for Model Selection in Boolean Gene Regulatory Networks

The paper develops a method to select Boolean gene regulatory network models by leveraging developmental landscapes and attractor stability, finding that a recent model fails to respect expected cell state hierarchies and proposing an algorithm to correct this.

EPEK: creation and analysis of an Ectopic Pregnancy Expression Knowledgebase

EPEK compiles and analyzes gene, metabolite, and SNP expression data from human ectopic pregnancy studies to identify potential diagnostic markers and cellular signaling processes involved.

Graph Ricci Curvatures Reveal Atypical Functional Connectivity in Autism Spectrum Disorder

This study applies graph Ricci curvatures to compare functional connectivity networks in ASD and typically developing individuals, finding region-specific differences associated with cognitive impairments and potential therapeutic targets.

Composition structures and biologically meaningful logics: plausibility and relevance in bipartite models of gene regulation

The paper investigates composition structures in bipartite Boolean network models of gene regulation, finding they are enriched in real biological networks but likely driven by nested canalyzing and read-once functions.

Minimum complexity drives regulatory logic in Boolean models of living systems

The paper analyzes Boolean functions in gene regulatory networks, finding that odd-biased and read-once functions are enriched due to their minimal Boolean complexity and average sensitivity.

MeFSAT: A curated natural product database specific to secondary metabolites of medicinal fungi

MeFSAT is a curated database of secondary metabolites from medicinal fungi, providing chemical and therapeutic information to aid drug discovery.

Broad substrate-specific phosphorylation events are associated with the initial stage of plant cell wall recognition in Neurospora crassa

The paper investigates substrate-specific phosphorylation events in Neurospora crassa during early plant cell wall recognition using phospho-proteomics and identifies key signaling pathways and proteins involved.