Manikandan Narayanan
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View article: Delineating markers of disease-disease interaction: a systematic methodology and its application to multiple diabetes-helminth cohorts
Delineating markers of disease-disease interaction: a systematic methodology and its application to multiple diabetes-helminth cohorts Open
View article: Correlation of Serum Lipid Profile with Severity and Clinical Outcomes in Children with Dengue Fever – A Cross-Sectional Study
Correlation of Serum Lipid Profile with Severity and Clinical Outcomes in Children with Dengue Fever – A Cross-Sectional Study Open
View article: Dissecting the effect of single- and co-infection of TB and COVID-19 pathogens on the sputum microbiome
Dissecting the effect of single- and co-infection of TB and COVID-19 pathogens on the sputum microbiome Open
Tuberculosis (TB) and COVID-19 are both respiratory diseases and understanding their interaction is important for effective co-infection management. Although some studies have investigated TB and COVID-19 co-infection in terms of immune re…
View article: GViNC: an innovative framework for genome graph comparison reveals hidden patterns in the genetic diversity of human populations
GViNC: an innovative framework for genome graph comparison reveals hidden patterns in the genetic diversity of human populations Open
Genome graphs provide a powerful reference structure for representing genetic diversity. Their structure emphasizes the polymorphic regions in a collection of genomes, enabling network-based comparisons of population-level variation. Howev…
View article: Gene Symphony: Two-Layered Musification of Gene Expression Clusters with Functional Backgrounds
Gene Symphony: Two-Layered Musification of Gene Expression Clusters with Functional Backgrounds Open
Musification, the process of converting data into music, has found applications in scientific research as a novel medium for data representation and communication. However, in biology, its application has largely been limited to DNA and pr…
View article: Author Correction: Mapping genetic diversity with the GenomeIndia project
Author Correction: Mapping genetic diversity with the GenomeIndia project Open
View article: Demixer: a probabilistic generative model to delineate different strains of a microbial species in a mixed infection sample
Demixer: a probabilistic generative model to delineate different strains of a microbial species in a mixed infection sample Open
Motivation Multi-drug resistant or hetero-resistant tuberculosis (TB) hinders the successful treatment of TB. Hetero-resistant TB occurs when multiple strains of the TB-causing bacterium with varying degrees of drug susceptibility are pres…
View article: MultiPopPred: A Trans-Ethnic Disease Risk Prediction Method, and its Application to the South Asian Population
MultiPopPred: A Trans-Ethnic Disease Risk Prediction Method, and its Application to the South Asian Population Open
Genome-wide association studies (GWAS) have guided significant contributions towards identifying disease associated Single Nucleotide Polymorphisms (SNPs) in Caucasian populations, albeit with limited focus on other understudied low-resour…
View article: Beyond associations: A benchmark Causal Relation Extraction Dataset (CRED) of disease-causing genes, its comparative evaluation, interpretation and application
Beyond associations: A benchmark Causal Relation Extraction Dataset (CRED) of disease-causing genes, its comparative evaluation, interpretation and application Open
Information on causal relationships is essential to many sciences, including biomedical science, and beneficial (e.g., causative rather than merely associative gene-disease relations can lead to better treatments). Despite much work on Rel…
View article: GViNC: an innovative framework for genome graph comparison reveals hidden patterns in the genetic diversity of human populations
GViNC: an innovative framework for genome graph comparison reveals hidden patterns in the genetic diversity of human populations Open
Motivation Genome graphs represent genetic diversity by highlighting polymorphic regions, but current methods lack the ability to characterize and compare their complex structures effectively. Results Our study introduces GViNC: a framewor…
View article: Alzheimer’s disease rewires gene coexpression networks coupling different brain regions
Alzheimer’s disease rewires gene coexpression networks coupling different brain regions Open
View article: Demixer: A probabilistic generative model to delineate different strains of a microbial species in a mixed infection sample
Demixer: A probabilistic generative model to delineate different strains of a microbial species in a mixed infection sample Open
Motivation Multi-drug resistant or hetero-resistant Tuberculosis (TB) hinders the successful treatment of TB. Hetero-resistant TB occurs when multiple strains of the TB-causing bacterium with varying degrees of drug susceptibility are pres…
View article: SpecGMM: Integrating Spectral analysis and Gaussian Mixture Models for taxonomic classification and identification of discriminative DNA regions
SpecGMM: Integrating Spectral analysis and Gaussian Mixture Models for taxonomic classification and identification of discriminative DNA regions Open
Motivation Genomic signal processing (GSP), which transforms biomolecular sequences into discrete signals for spectral analysis, has provided valuable insights into DNA sequence, structure, and evolution. However, challenges persist with s…
View article: Delineating markers of disease-disease interaction: a systematic methodology and its application to multiple diabetes-helminth cohorts
Delineating markers of disease-disease interaction: a systematic methodology and its application to multiple diabetes-helminth cohorts Open
Understanding how the molecules in our body respond to the co-occurrence of two diseases in an individual (comorbidity) could lead to mechanistic insights into novel treatments for comorbid conditions. Studies have shown for instance that …
View article: A Cluster-Based Energy-Efficient Secure Optimal Path-Routing Protocol for Wireless Body-Area Sensor Networks
A Cluster-Based Energy-Efficient Secure Optimal Path-Routing Protocol for Wireless Body-Area Sensor Networks Open
Recently, research into Wireless Body-Area Sensor Networks (WBASN) or Wireless Body-Area Networks (WBAN) has gained much importance in medical applications, and now plays a significant role in patient monitoring. Among the various operatio…
View article: Alzheimer’s disease perturbs gene‐gene correlation networks across brain regions
Alzheimer’s disease perturbs gene‐gene correlation networks across brain regions Open
Background Functional imaging has revealed how Alzheimer’s disease (AD) disrupts functional connectivity between brain regions, but the molecular basis of such changes has been less explored 1 . Genomic studies can reveal molecular/gene bi…
View article: Robust discovery of causal gene networks via measurement error estimation and correction
Robust discovery of causal gene networks via measurement error estimation and correction Open
Discovering causal relations among genes from observational data is a fundamental problem in systems biology, especially in humans where direct gene interventions or perturbations are unethical/infeasible. Furthermore, causality is emergin…
View article: MultiCens: Multilayer network centrality measures to uncover molecular mediators of tissue-tissue communication
MultiCens: Multilayer network centrality measures to uncover molecular mediators of tissue-tissue communication Open
With the evolution of multicellularity, communication among cells in different tissues and organs became pivotal to life. Molecular basis of such communication has long been studied, but genome-wide screens for genes and other biomolecules…
View article: Using Signal Processing in Tandem With Adapted Mixture Models for Classifying Genomic Signals
Using Signal Processing in Tandem With Adapted Mixture Models for Classifying Genomic Signals Open
Genomic signal processing has been used successfully in bioinformatics to analyze biomolecular sequences and gain varied insights into DNA structure, gene organization, protein binding, sequence evolution, etc. But challenges remain in fin…
View article: Predicting cross-tissue hormone–gene relations using balanced word embeddings
Predicting cross-tissue hormone–gene relations using balanced word embeddings Open
Motivation Inter-organ/inter-tissue communication is central to multi-cellular organisms including humans, and mapping inter-tissue interactions can advance system-level whole-body modeling efforts. Large volumes of biomedical literature h…
View article: Alzheimer’s disease rewires gene coexpression networks coupling different brain regions
Alzheimer’s disease rewires gene coexpression networks coupling different brain regions Open
Connectome studies have revealed how neurodegenerative diseases like Alzheimer’s disease (AD) disrupt functional and structural connectivity among brain regions, but the molecular basis of such disruptions is less studied, with most genomi…
View article: MultiCens: Multilayer network centrality measures to uncover molecular mediators of tissue-tissue communication
MultiCens: Multilayer network centrality measures to uncover molecular mediators of tissue-tissue communication Open
With the evolution of multicellularity, communication among cells in different organs/tissues became pivotal to life. Molecular basis of such communication has long been studied, but genome-wide screens for biomolecules/genes mediating tis…
View article: Parameterized Algorithms for the Steiner Tree Problem on a Directed Hypercube.
Parameterized Algorithms for the Steiner Tree Problem on a Directed Hypercube. Open
We address the problem of computing a Steiner Arborescence on a directed hypercube. The directed hypercube enjoys a special connectivity structure among its node set $\{0,1\}^m$, but its exponential in $m$ size renders traditional Steiner …
View article: Parameterized Algorithms for the Steiner Arborescence Problem on a Hypercube
Parameterized Algorithms for the Steiner Arborescence Problem on a Hypercube Open
Motivated by a phylogeny reconstruction problem in evolutionary biology, we study the minimum Steiner arborescence problem on directed hypercubes (MSA-DH). Given $m$, representing the directed hypercube $\vec{Q}_m$, and a set of terminals …
View article: Predicting cross-tissue hormone-gene relations using balanced word embeddings
Predicting cross-tissue hormone-gene relations using balanced word embeddings Open
Motivation Large volumes of biomedical literature present an opportunity to build whole-body human models comprising both within-tissue and across-tissue interactions among genes. Current studies have mostly focused on identifying within-t…
View article: Effect of Inter-layer Coupling on Multilayer Network Centrality Measures
Effect of Inter-layer Coupling on Multilayer Network Centrality Measures Open
View article: Shared mechanisms among neurodegenerative diseases: from genetic factors to gene networks
Shared mechanisms among neurodegenerative diseases: from genetic factors to gene networks Open
View article: Environment Tunes Propagation of Cell-to-Cell Variation in the Human Macrophage Gene Network
Environment Tunes Propagation of Cell-to-Cell Variation in the Human Macrophage Gene Network Open
View article: Equilibrative nucleoside transporter ENT1 as a biomarker of Huntington disease
Equilibrative nucleoside transporter ENT1 as a biomarker of Huntington disease Open
View article: Robust Inference of Cell-to-Cell Expression Variations from Single- and K-Cell Profiling
Robust Inference of Cell-to-Cell Expression Variations from Single- and K-Cell Profiling Open
Quantifying heterogeneity in gene expression among single cells can reveal information inaccessible to cell-population averaged measurements. However, the expression level of many genes in single cells fall below the detection limit of eve…