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Article ; Online: Machine learning algorithms and computational validation of single-nucleotide polymorphisms of antioxidant enzymes and oxidative stress markers in neonates.

Sridharan, Kannan / Sekaran, Karthik / Doss C, George Priya / Jufairi, Mona Al

2023 Volume 17, Issue 7, Page(s) 369–378

Abstract: Aim: ...

Abstract	Aim:
MeSH term(s)	Infant, Newborn ; Humans ; Antioxidants/metabolism ; Polymorphism, Single Nucleotide ; Infant, Premature ; Bayes Theorem ; Oxidative Stress/genetics ; Respiratory Distress Syndrome, Newborn/genetics ; Respiratory Distress Syndrome
Chemical Substances	Antioxidants
Language	English
Publishing date	2023-06-29
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2481014-9
ISSN	1752-0371 ; 1752-0363
ISSN (online)	1752-0371
ISSN	1752-0363
DOI	10.2217/bmm-2023-0051
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Article ; Online: Bioinformatics investigation on blood-based gene expressions of Alzheimer's disease revealed ORAI2 gene biomarker susceptibility: An explainable artificial intelligence-based approach.

Sekaran, Karthik / Alsamman, Alsamman M / George Priya Doss, C / Zayed, Hatem

Metabolic brain disease

2023 Volume 38, Issue 4, Page(s) 1297–1310

Abstract: The progressive, chronic nature of Alzheimer's disease (AD), a form of dementia, defaces the adulthood of elderly individuals. The pathogenesis of the condition is primarily unascertained, turning the treatment efficacy more arduous. Therefore, ... ...

Abstract	The progressive, chronic nature of Alzheimer's disease (AD), a form of dementia, defaces the adulthood of elderly individuals. The pathogenesis of the condition is primarily unascertained, turning the treatment efficacy more arduous. Therefore, understanding the genetic etiology of AD is essential to identifying targeted therapeutics. This study aimed to use machine-learning techniques of expressed genes in patients with AD to identify potential biomarkers that can be used for future therapy. The dataset is accessed from the Gene Expression Omnibus (GEO) database (Accession Number: GSE36980). The subgroups (AD blood samples from frontal, hippocampal, and temporal regions) are individually investigated against non-AD models. Prioritized gene cluster analyses are conducted with the STRING database. The candidate gene biomarkers were trained with various supervised machine-learning (ML) classification algorithms. The interpretation of the model prediction is perpetrated with explainable artificial intelligence (AI) techniques. This experiment revealed 34, 60, and 28 genes as target biomarkers of AD mapped from the frontal, hippocampal, and temporal regions. It is identified ORAI2 as a shared biomarker in all three areas strongly associated with AD's progression. The pathway analysis showed that STIM1 and TRPC3 are strongly associated with ORAI2. We found three hub genes, TPI1, STIM1, and TRPC3, in the network of the ORAI2 gene that might be involved in the molecular pathogenesis of AD. Naive Bayes classified the samples of different groups by fivefold cross-validation with 100% accuracy. AI and ML are promising tools in identifying disease-associated genes that will advance the field of targeted therapeutics against genetic diseases.
MeSH term(s)	Humans ; Adult ; Aged ; Alzheimer Disease/metabolism ; Artificial Intelligence ; Bayes Theorem ; Computational Biology/methods ; Biomarkers ; Gene Expression ; ORAI2 Protein/genetics
Chemical Substances	Biomarkers ; ORAI2 protein, human ; ORAI2 Protein
Language	English
Publishing date	2023-02-21
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	632824-6
ISSN	1573-7365 ; 0885-7490
ISSN (online)	1573-7365
ISSN	0885-7490
DOI	10.1007/s11011-023-01171-0
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Article ; Online: Single-cell transcriptomic analysis reveals crucial oncogenic signatures and its associative cell types involved in gastric cancer.

Sekaran, Karthik / Varghese, Rinku Polachirakkal / Zayed, Hatem / El Allali, Achraf / George Priya Doss, C

Medical oncology (Northwood, London, England)

2023 Volume 40, Issue 10, Page(s) 305

Abstract: The intricate association of oncogenic markers negatively impacts accurate gastric cancer diagnosis and leads to the proliferation of mortality rate. Molecular heterogeneity is inevitable in determining gastric cancer's progression state with multiple ... ...

Abstract	The intricate association of oncogenic markers negatively impacts accurate gastric cancer diagnosis and leads to the proliferation of mortality rate. Molecular heterogeneity is inevitable in determining gastric cancer's progression state with multiple cell types involved. Identification of pathogenic gene signatures is imperative to understand the disease's etiology. This study demonstrates a systematic approach to identifying oncogenic gastric cancer genes linked with different cell types. The raw counts of adjacent normal and gastric cancer samples are subjected to a quality control step. The dimensionality reduction and multidimensional clustering are performed using Principal Component Analysis (PCA) and Uniform Manifold Approximation and Projection (UMAP) techniques. The adjacent normal and gastric cancer sample cell clusters are annotated with the Human Primary Cell Atlas database using the "SingleR." Cellular state transition between the distinct groups is characterized using trajectory analysis. The ligand-receptor interaction between Vascular Endothelial Growth Factor (VEGF) and cell clusters unveils crucial molecular pathways in gastric cancer progression. Chondrocytes, Smooth muscle cells, and fibroblast cell clusters contain genes contributing to poor survival rates based on hazard ratio during survival analysis. The GC-related oncogenic signatures are isolated by comparing the gene set with the DisGeNET database. Twelve gastric cancer biomarkers (SPARC, KLF5, HLA-DRB1, IGFBP3, TIMP3, LGALS1, IGFBP6, COL18A1, F3, COL4A1, PDGFRB, COL5A2) are linked with gastric cancer and further validated through gene set enrichment analysis. Drug-gene interaction found PDGFRB, interacting with various anti-cancer drugs, as a potential inhibitor for gastric cancer. Further investigations on these molecular signatures will assist the development of precision therapeutics, promising longevity among gastric cancer patients.
MeSH term(s)	Humans ; Stomach Neoplasms/genetics ; Receptor, Platelet-Derived Growth Factor beta ; Transcriptome ; Vascular Endothelial Growth Factor A
Chemical Substances	Receptor, Platelet-Derived Growth Factor beta (EC 2.7.10.1) ; Vascular Endothelial Growth Factor A
Language	English
Publishing date	2023-09-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	1201189-7
ISSN	1559-131X ; 0736-0118 ; 1357-0560
ISSN (online)	1559-131X
ISSN	0736-0118 ; 1357-0560
DOI	10.1007/s12032-023-02174-8
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Article ; Online: A systematic review of artificial intelligence-based COVID-19 modeling on multimodal genetic information.

Sekaran, Karthik / Gnanasambandan, R / Thirunavukarasu, Ramkumar / Iyyadurai, Ramya / Karthik, G / George Priya Doss, C

Progress in biophysics and molecular biology

2023 Volume 179, Page(s) 1–9

Abstract: This study systematically reviews the Artificial Intelligence (AI) methods developed to resolve the critical process of COVID-19 gene data analysis, including diagnosis, prognosis, biomarker discovery, drug responsiveness, and vaccine efficacy. This ... ...

Abstract	This study systematically reviews the Artificial Intelligence (AI) methods developed to resolve the critical process of COVID-19 gene data analysis, including diagnosis, prognosis, biomarker discovery, drug responsiveness, and vaccine efficacy. This systematic review follows the guidelines of Preferred Reporting for Systematic Reviews and Meta-Analyses (PRISMA). We searched PubMed, Embase, Web of Science, and Scopus databases to identify the relevant articles from January 2020 to June 2022. It includes the published studies of AI-based COVID-19 gene modeling extracted through relevant keyword searches in academic databases. This study included 48 articles discussing AI-based genetic studies for several objectives. Ten articles confer about the COVID-19 gene modeling with computational tools, and five articles evaluated ML-based diagnosis with observed accuracy of 97% on SARS-CoV-2 classification. Gene-based prognosis study reviewed three articles and found host biomarkers detecting COVID-19 progression with 90% accuracy. Twelve manuscripts reviewed the prediction models with various genome analysis studies, nine articles examined the gene-based in silico drug discovery, and another nine investigated the AI-based vaccine development models. This study compiled the novel coronavirus gene biomarkers and targeted drugs identified through ML approaches from published clinical studies. This review provided sufficient evidence to delineate the potential of AI in analyzing complex gene information for COVID-19 modeling on multiple aspects like diagnosis, drug discovery, and disease dynamics. AI models entrenched a substantial positive impact by enhancing the efficiency of the healthcare system during the COVID-19 pandemic.
MeSH term(s)	Humans ; COVID-19/diagnosis ; Artificial Intelligence ; SARS-CoV-2/genetics ; Pandemics/prevention & control
Language	English
Publishing date	2023-02-19
Publishing country	England
Document type	Systematic Review ; Letter ; Research Support, Non-U.S. Gov't
ZDB-ID	209302-9
ISSN	1873-1732 ; 0079-6107
ISSN (online)	1873-1732
ISSN	0079-6107
DOI	10.1016/j.pbiomolbio.2023.02.003
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Article ; Online: Unraveling the Dysbiosis of Vaginal Microbiome to Understand Cervical Cancer Disease Etiology-An Explainable AI Approach.

Sekaran, Karthik / Varghese, Rinku Polachirakkal / Gopikrishnan, Mohanraj / Alsamman, Alsamman M / El Allali, Achraf / Zayed, Hatem / Doss C, George Priya

Genes

2023 Volume 14, Issue 4

Abstract: Microbial Dysbiosis is associated with the etiology and pathogenesis of diseases. The studies on the vaginal microbiome in cervical cancer are essential to discern the cause and effect of the condition. The present study characterizes the microbial ... ...

Abstract	Microbial Dysbiosis is associated with the etiology and pathogenesis of diseases. The studies on the vaginal microbiome in cervical cancer are essential to discern the cause and effect of the condition. The present study characterizes the microbial pathogenesis involved in developing cervical cancer. Relative species abundance assessment identified
MeSH term(s)	Humans ; Female ; Uterine Cervical Neoplasms ; Dysbiosis ; Microbiota ; Artificial Intelligence
Language	English
Publishing date	2023-04-18
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes14040936
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Article ; Online: Airway and Oral microbiome profiling of SARS-CoV-2 infected asthma and non-asthma cases revealing alterations-A pulmonary microbial investigation.

Sekaran, Karthik / Varghese, Rinku Polachirakkal / Doss C, George Priya / Alsamman, Alsamman M / Zayed, Hatem / El Allali, Achraf

PloS one

2023 Volume 18, Issue 8, Page(s) e0289891

Abstract: New evidence strongly discloses the pathogenesis of host-associated microbiomes in respiratory diseases. The microbiome dysbiosis modulates the lung's behavior and deteriorates the respiratory system's effective functioning. Several exogenous and ... ...

Abstract	New evidence strongly discloses the pathogenesis of host-associated microbiomes in respiratory diseases. The microbiome dysbiosis modulates the lung's behavior and deteriorates the respiratory system's effective functioning. Several exogenous and environmental factors influence the development of asthma and chronic lung disease. The relationship between asthma and microbes is reasonably understood and yet to be investigated for more substantiation. The comorbidities such as SARS-CoV-2 further exacerbate the health condition of the asthma-affected individuals. This study examines the raw 16S rRNA sequencing data collected from the saliva and nasopharyngeal regions of pre-existing asthma (23) and non-asthma patients (82) infected by SARS-CoV-2 acquired from the public database. The experiment is designed in a two-fold pattern, analyzing the associativity between the samples collected from the saliva and nasopharyngeal regions. Later, investigates the microbial pathogenesis, its role in exacerbations of respiratory disease, and deciphering the diagnostic biomarkers of the target condition. LEfSE analysis identified that Actinobacteriota and Pseudomonadota are enriched in the SARS-CoV-2-non-asthma group and SARS-CoV-2 asthma group of the salivary microbiome, respectively. Random forest algorithm is trained with amplicon sequence variants (ASVs) attained better classification accuracy, ROC scores on nasal (84% and 87%) and saliva datasets (93% and 97.5%). Rothia mucilaginosa is less abundant, and Corynebacterium tuberculostearicum showed higher abundance in the SARS-CoV-2 asthma group. The increase in Streptococcus at the genus level in the SARS-CoV-2-asthma group is evidence of discriminating the subgroups.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; RNA, Ribosomal, 16S/genetics ; COVID-19 ; Asthma ; Nose ; Microbiota/genetics ; Lung
Chemical Substances	RNA, Ribosomal, 16S
Language	English
Publishing date	2023-08-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0289891
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Article ; Online: In silico network pharmacology study on Glycyrrhiza glabra: Analyzing the immune-boosting phytochemical properties of Siddha medicinal plant against COVID-19.

Sekaran, Karthik / Karthik, Ashwini / Varghese, Rinku Polachirakkal / Sathiyarajeswaran, P / Shree Devi, M S / Siva, R / George Priya Doss, C

Advances in protein chemistry and structural biology

2023 Volume 138, Page(s) 233–255

Abstract: Immunosenescence is a pertinent factor in the mortality rate caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The changes in the immune system are strongly associated with age and provoke the deterioration of the individual's ... ...

Abstract	Immunosenescence is a pertinent factor in the mortality rate caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The changes in the immune system are strongly associated with age and provoke the deterioration of the individual's health. Traditional medical practices in ancient India effectively deal with COVID-19 by boosting natural immunity through medicinal plants. The anti-inflammatory and antiviral properties of Glycyrrhiza glabra are potent in fighting against COVID-19 and promote immunity boost against the severity of the infection. Athimadhura Chooranam, a polyherbal formulation containing Glycyrrhiza glabra as the main ingredient, is recommended as an antiviral Siddha herb by the Ministry of AYUSH. This paper is intended to identify the phytoconstituents of Glycyrrhiza glabra that are actively involved in preventing individuals from COVID-19 transmission. The modulated pathways, enrichment study, and drug-likeness are calculated from the target proteins of the phytoconstituents at the pharmacological activity (Pa) of more than 0.7. Liquiritigenin and Isoliquiritin, the natural compounds in Glycyrrhiza glabra, belong to the flavonoid class and exhibit ameliorative effects against COVID-19. The latter compound displays a higher protein interaction to a maximum of six, out of which HMOX1, PLAU, and PGR are top-hub genes. ADMET screening further confirms the significance of the abovementioned components containing better drug-likeness. The molecular docking and molecular dynamics method identified liquiritigenin as a possible lead molecule capable of inhibiting the activity of the major protease protein of SARS-CoV-2. The findings emphasize the importance of in silico network pharmacological assessments in delivering cost-effective, time-bound clinical drugs.
MeSH term(s)	Humans ; Plants, Medicinal ; Network Pharmacology ; Molecular Docking Simulation ; COVID-19 ; SARS-CoV-2 ; Glycyrrhiza/chemistry ; Glycyrrhiza/genetics ; Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use ; Phytochemicals/pharmacology ; Phytochemicals/therapeutic use
Chemical Substances	Antiviral Agents ; Phytochemicals
Language	English
Publishing date	2023-06-17
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2473077-4
ISSN	1876-1631 ; 1876-1623
ISSN (online)	1876-1631
ISSN	1876-1623
DOI	10.1016/bs.apcsb.2023.04.003
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Article ; Online: In silico network pharmacology analysis and molecular docking validation of Swasa Kudori tablet for screening druggable phytoconstituents of asthma.

Sekaran, Karthik / Varghese, Rinku Polachirakkal / Karthik, Ashwini / Sasikumar, K / Shree Devi, M S / Sathiyarajeswaran, P / George Priya Doss, C

Advances in protein chemistry and structural biology

2023 Volume 138, Page(s) 257–274

Abstract: Traditional medicines are impactful in treating a cluster of respiratory-related illnesses. This paper demonstrates screening active, druggable phytoconstituents from a classical Siddha-based poly-herbal formulation called Swasa Kudori Tablet to treat ... ...

Abstract	Traditional medicines are impactful in treating a cluster of respiratory-related illnesses. This paper demonstrates screening active, druggable phytoconstituents from a classical Siddha-based poly-herbal formulation called Swasa Kudori Tablet to treat asthma. The phytoconstituents of Swasa Kudori are identified as Calotropis gigantea, Piper nigrum, and (Co-drug) Abies webbiana. Active chemical compounds are extracted with the Chemical Entities of Biological Interest (ChEBI) database. The gene targets of each compound are identified based on the pharmacological activity using the DIGEP-Pred database. Thirty-two genes showing P
MeSH term(s)	Humans ; Molecular Docking Simulation ; Network Pharmacology ; Asthma/drug therapy ; Computer Simulation ; Databases, Factual
Language	English
Publishing date	2023-08-10
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2473077-4
ISSN	1876-1631 ; 1876-1623
ISSN (online)	1876-1631
ISSN	1876-1623
DOI	10.1016/bs.apcsb.2023.07.001
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Article ; Online: Unraveling the Dysbiosis of Vaginal Microbiome to Understand Cervical Cancer Disease Etiology—An Explainable AI Approach

Sekaran, Karthik / Varghese, Rinku Polachirakkal / Gopikrishnan, Mohanraj / Alsamman, Alsamman M. / El Allali, Achraf / Zayed, Hatem / Doss C, George Priya

Genes (Basel). 2023 Apr. 18, v. 14, no. 4

2023

Abstract	Microbial Dysbiosis is associated with the etiology and pathogenesis of diseases. The studies on the vaginal microbiome in cervical cancer are essential to discern the cause and effect of the condition. The present study characterizes the microbial pathogenesis involved in developing cervical cancer. Relative species abundance assessment identified Firmicutes, Actinobacteria, and Proteobacteria dominating the phylum level. A significant increase in Lactobacillus iners and Prevotella timonensis at the species level revealed its pathogenic influence on cervical cancer progression. The diversity, richness, and dominance analysis divulges a substantial decline in cervical cancer compared to control samples. The β diversity index proves the homogeneity in the subgroups’ microbial composition. The association between enriched Lactobacillus iners at the species level, Lactobacillus, Pseudomonas, and Enterococcus genera with cervical cancer is identified by Linear discriminant analysis Effect Size (LEfSe) prediction. The functional enrichment corroborates the microbial disease association with pathogenic infections such as aerobic vaginitis, bacterial vaginosis, and chlamydia. The dataset is trained and validated with repeated k-fold cross-validation technique using a random forest algorithm to determine the discriminative pattern from the samples. SHapley Additive exPlanations (SHAP), a game theoretic approach, is employed to analyze the results predicted by the model. Interestingly, SHAP identified that the increase in Ralstonia has a higher probability of predicting the sample as cervical cancer. New evidential microbiomes identified in the experiment confirm the presence of pathogenic microbiomes in cervical cancer vaginal samples and their mutuality with microbial imbalance.
Keywords	Actinobacteria ; Enterococcus ; Lactobacillus ; Prevotella ; Pseudomonas ; Ralstonia ; algorithms ; data collection ; discriminant analysis ; dysbiosis ; etiology ; microbiome ; models ; neoplasm progression ; prediction ; probability ; species abundance ; uterine cervical neoplasms ; vaginitis
Language	English
Dates of publication	2023-0418
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article ; Online
ZDB-ID	2527218-4
ISSN	2073-4425
ISSN	2073-4425
DOI	10.3390/genes14040936
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Molecular modeling of C1-inhibitor as SARS-CoV-2 target identified from the immune signatures of multiple tissues: An integrated bioinformatics study.

Sekaran, Karthik / Polachirakkal Varghese, Rinku / Gnanasambandan, R / Karthik, G / Ramya, I / George Priya Doss, C

Cell biochemistry and function

2022 Volume 41, Issue 1, Page(s) 112–127

Abstract: The expeditious transmission of the severe acute respiratory coronavirus 2 (SARS-CoV-2), a strain of COVID-19, crumbled the global economic strength and caused a veritable collapse in health infrastructure. The molecular modeling of the novel coronavirus ...

Abstract	The expeditious transmission of the severe acute respiratory coronavirus 2 (SARS-CoV-2), a strain of COVID-19, crumbled the global economic strength and caused a veritable collapse in health infrastructure. The molecular modeling of the novel coronavirus research sounds promising and equips more evidence about the pragmatic therapeutic options. This article proposes a machine-learning framework for identifying potential COVID-19 transcriptomic signatures. The transcriptomics data contains immune-related genes collected from multiple tissues (blood, nasal, and buccal) with accession number: GSE183071. Extensive bioinformatics work was carried out to identify the potential candidate markers, including differential expression analysis, protein interactions, gene ontology, and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment studies. The overlapping investigation found SERPING1, the gene that encodes a glycosylated plasma protein C1-INH, in all three datasets. Furthermore, the immuno-informatics study was conducted on the C1-INH protein. 5DU3, the protein identifier of C1-INH, was fetched to identify the antigenicity, major histocompatibility (MHC) Class I and II binding epitopes, allergenicity, toxicity, and immunogenicity. The screening of peptides satisfying the vaccine-design criteria based on the metrics mentioned above is performed. The drug-gene interaction study reported that Rhucin is strongly associated with SERPING1. HSIC-Lasso (Hilbert-Schmidt independence criterion-least absolute shrinkage and selection operator), a model-free biomarker selection technique, was employed to identify the genes having a nonlinear relationship with the target class. The gene subset is trained with supervised machine learning models by a leave-one-out cross-validation method. Explainable artificial intelligence techniques perform the model interpretation analysis.
MeSH term(s)	Humans ; Artificial Intelligence ; Complement C1 Inhibitor Protein/genetics ; Computational Biology ; COVID-19/genetics ; COVID-19/immunology ; SARS-CoV-2/drug effects ; COVID-19 Drug Treatment ; Gene Expression Profiling ; Machine Learning ; Immunity/genetics ; COVID-19 Vaccines/genetics ; COVID-19 Vaccines/immunology
Chemical Substances	Complement C1 Inhibitor Protein ; SERPING1 protein, human ; COVID-19 Vaccines
Language	English
Publishing date	2022-12-14
Publishing country	England
Document type	Journal Article
ZDB-ID	283643-9
ISSN	1099-0844 ; 0263-6484
ISSN (online)	1099-0844
ISSN	0263-6484
DOI	10.1002/cbf.3769
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