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Bridging the Gaps in Meta-Omic Analysis: Workflows and Reproducibility. OMICS (IF 3.3) Pub Date : 2023-11-29 João Vitor Ferreira Cavalcante,Iara Dantas de Souza,Diego Arthur de Azevedo Morais,Rodrigo Juliani Siqueira Dalmolin
The past few years have seen significant advances in the study of complex microbial communities associated with the evolution of sequencing technologies and increasing adoption of whole genome shotgun sequencing methods over the once more traditional Amplicon-based methods. Although these advances have broadened the horizon of meta-omic analyses in planetary health, human health, and ecology from simple
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Major Genetic Drivers of Statin Treatment Response in African Populations and Pharmacogenetics of Dyslipidemia Through a One Health Lens. OMICS (IF 3.3) Pub Date : 2023-11-14 Zizo Lusiki,Dirk Blom,Nyarai D Soko,Smangele Malema,Erika Jones,Brian Rayner,Jonathan Blackburn,Phumla Sinxadi,Michelle T Dandara,Collet Dandara
A One Health lens is increasingly significant to address the intertwined challenges in planetary health concerned with the health of humans, nonhuman animals, plants, and ecosystems. A One Health approach can benefit the public health systems in Africa that are overburdened by noncommunicable, infectious, and environmental diseases. Notably, the COVID-19 pandemic revealed the previously overlooked
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The Dynamic Landscapes of Circular RNAs in Axolotl, a Regenerative Medicine Model, with Implications for Early Phase of Limb Regeneration. OMICS (IF 3.3) Pub Date : 2023-11-10 Turan Demircan,Barış Ethem Süzek
Circular RNAs (circRNAs) are of relevance to regenerative medicine and play crucial roles in post-transcriptional and translational regulation of biological processes. circRNAs are a class of RNA molecules that are formed through a unique splicing process, resulting in a covalently closed-loop structure. Recent advancements in RNA sequencing technologies and specialized computational tools have facilitated
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Omics Analysis and Quality Control Pipelines in a High-Performance Computing Environment. OMICS (IF 3.3) Pub Date : 2023-11-10 Darrell O Ricke,Derek Ng,Adam Michaleas,Philip Fremont-Smith
Data quality is often an overlooked feature in the analysis of omics data. This is particularly relevant in studies of chemical and pathogen exposures that can modify an individual's epigenome and transcriptome with persistence over time. Portable, quality control (QC) pipelines for multiple different omics datasets are therefore needed. To meet these goals, portable quality assurance (QA) metrics
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From Microcosm to Macrocosm: The -Omics, Multiomics, and Sportomics Approaches in Exercise and Sports. OMICS (IF 3.3) Pub Date : 2023-11-09 Renan Muniz-Santos,Alexandre Magno-França,Igor Jurisica,L C Cameron
This article explores the progressive integration of -omics methods, including genomics, metabolomics, and proteomics, into sports research, highlighting the development of the concept of "sportomics." We discuss how sportomics can be used to comprehend the multilevel metabolism during exercise in real-life conditions faced by athletes, enabling potential personalized interventions to improve performance
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A Differential Transcriptional Regulome Approach to Unpack Cancer Biology: Insights on Renal Cell Carcinoma Subtypes. OMICS (IF 3.3) Pub Date : 2023-11-09 Aysegul Caliskan,Kazim Yalcin Arga
Cancer research calls for new approaches that account for the regulatory complexities of biology. We present, in this study, the differential transcriptional regulome (DIFFREG) approach for the identification and prioritization of key transcriptional regulators and apply it to the case of renal cell carcinoma (RCC) biology. Of note, RCC has a poor prognosis and the biomarker and drug discovery studies
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Feminism Is for Everyone: Scientists, Too. OMICS (IF 3.3) Pub Date : 2023-10-23 Vural Özdemir
Critically informed engagement in politics and the knowledge of social theory help democratize knowledge production, and redress power asymmetries in science and society. A feminist lens is one of the many ways in which power asymmetries in science can be critically unpacked and interrupted. There are many strands of feminism and feminist theory that differ in their approaches to resist patriarchy
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One Health Lens for Antimicrobial Resistance Research and Funding: A Systematic Review. OMICS (IF 3.3) Pub Date : 2023-10-18 Issam Alsamara,Lesley Ogilvie,Ralf Sudbrak,Angela Brand
One Health (OH) offers conceptual and applied prospects to advance planetary health and integrative biology in the 21st century. For example, The World Health Organization (WHO) has declared antimicrobial resistance (AMR) one of humanity's top 10 health threats worldwide (AMR). The AMR research, as seen through the OH lens, recognizes the interdependence and the coproduction of the health of humans
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Identification of SARS-CoV-2 from Human Lung Formalin-Fixed Paraffin-Embedded Tissue Sections Using Mass Spectrometry. OMICS (IF 3.3) Pub Date : 2023-10-09 Kiran K Mangalaparthi,Smrita Singh,Kishore Garapati,Joaquin J Garcia,Benjamin R Kipp,Anja C Roden,Akhilesh Pandey
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A Comprehensive Bioinformatics Resource Guide for Genome-Based Antimicrobial Resistance Studies. OMICS (IF 3.3) Pub Date : 2023-10-01 Debyani Samantray,Ankit Singh Tanwar,Thokur Sreepathy Murali,Angela Brand,Kapaettu Satyamoorthy,Bobby Paul
The use of high-throughput sequencing technologies and bioinformatic tools has greatly transformed microbial genome research. With the help of sophisticated computational tools, it has become easier to perform whole genome assembly, identify and compare different species based on their genomes, and predict the presence of genes responsible for proteins, antimicrobial resistance, and toxins. These bioinformatics
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Maintaining High-Touch in High-Tech Digital Health Monitoring and Multi-Omics Prognostication: Ethical, Equity, and Societal Considerations in Precision Health for Palliative Care. OMICS (IF 3.3) Pub Date : 2023-10-01 John Noel Viana,Caitlin Pilbeam,Mark Howard,Brett Scholz,Zongyuan Ge,Carys Fisser,Imogen Mitchell,Sujatha Raman,Joan Leach
Advances in digital health, systems biology, environmental monitoring, and artificial intelligence (AI) continue to revolutionize health care, ushering a precision health future. More than disease treatment and prevention, precision health aims at maintaining good health throughout the lifespan. However, how can precision health impact care for people with a terminal or life-limiting condition? We
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Decoding Systems Biology of Inflammation Signatures in Cancer Pathogenesis: Pan-Cancer Insights from 12 Common Cancers. OMICS (IF 3.3) Pub Date : 2023-10-01 Beste Turanli
Chronic inflammation is an important contributor to tumorigenesis in many tissues. However, the underlying mechanisms of inflammatory signaling in the tumor microenvironment are not yet fully understood in various cancers. Therefore, this study aimed to uncover the gene expression signatures of inflammation-associated proteins that lead to tumorigenesis, and with an eye to discovery of potential system
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How Do Pharmacy Students Make Career Choices in Genomics? Gender and Other Key Determinants of Pharmacy Senior Students' Intentions to Pursue Postgraduate Training in Pharmacogenomics. OMICS (IF 3.3) Pub Date : 2023-10-01 Margarita-Ioanna Koufaki,Dimitra Makrygianni,George P Patrinos,Konstantinos Z Vasileiou
Pharmacists play a pivotal role in pharmacogenomic (PGx) implementation in clinical practice, and their university education is considered a strong driver in holding favorable intentions toward PGx adoption. Using a survey developed based on the Theory of Planned Behavior (TPB), this study aimed to evaluate the determinants of senior pharmacy students' intentions to pursue postgraduate training in
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Moving Research-Based Learning in Life Sciences Upstream, and Beyond Borders: An International Group Research Project for High School Youth. OMICS (IF 3.3) Pub Date : 2023-09-06 Gayane Ghukasyan,Mher Kurghinyan,Lusine Hovhannisyan,Vardges Tserunyan
International cooperation beyond borders, institutions, and intergenerationally is an important aspect of science and research-based learning. Timing of learning also matters. Early exposure to group research-based learning can potentially have lasting positive impacts on youth and their careers in life sciences. Here, we report our work on the International Group Project (IGP), which builds on the
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Invasive Breast Cancer: miR-24-2 Targets Genes Associated with Survival and Sensitizes MDA-MB-231 Cells to Berberine. OMICS (IF 3.3) Pub Date : 2023-09-05 Mansoor Ali,Rameshwar N K Bamezai,Rana P Singh
MicroRNA aberrations including that of miR-24-2 have been reported in various cancers. However, the target genes for miR-24-2 are yet to be identified and validated in invasive breast cancer and the triple-negative breast cancer (TNBC). Using in silico approaches and gene expression analyses, we identified and validated the target genes of miR-24-2 in invasive breast cancer, majority of which were
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Upstream Engagement with High School Youth for Research-Based Learning in Life Sciences Beyond Nation-State Borders. OMICS (IF 3.3) Pub Date : 2023-09-05 Vural Özdemir,Gayane Ghukasyan,Vardges Tserunyan
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Toward Precision Oncology in Glioblastoma with a Personalized Cancer Genome Reporting Tool and Genetic Changes Identified by Whole Exome Sequencing. OMICS (IF 3.3) Pub Date : 2023-09-05 Onur Erdogan,Şeyma Çolakoğlu Özkaya,Can Erzik,Kaya Bilguvar,Kazım Yalçın Arga,Fatih Bayraklı
Precision/personalized medicine in oncology has two key pillars: molecular profiling of the tumors and personalized reporting of the results in ways that are clinically contextualized and triangulated. Moreover, neurosurgery as a field stands to benefit from precision/personalized medicine and new tools for reporting of the molecular findings. In this context, glioblastoma (GBM) is a highly aggressive
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Can Genome Sequencing Coupled to Flux Balance Analyses Offer Precision Guidance for Industrial Strain Development? The Lessons from Carbon Trafficking in Corynebacterium glutamicum ATCC 21573. OMICS (IF 3.3) Pub Date : 2023-09-01 Eldin Kurpejović,Daniel Wibberg,Gülsüm Merve Bastem,Arthur Burgardt,Tobias Busche,Fatma Ece Altinisik Kaya,Andreas Dräger,Volker F Wendisch,Berna Sariyar Akbulut
Systems biology tools offer new prospects for industrial strain selection. For bacteria that are significant for industrial applications, whole-genome sequencing coupled to flux balance analysis (FBA) can help unpack the complex relationships between genome mutations and carbon trafficking. This work investigates the l-tyrosine (l-Tyr) overproducing model system Corynebacterium glutamicum ATCC 21573
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A Proteomics Investigation of Cigarette Smoke Exposed Wistar Rats Revealed Improved Anti-Inflammatory Effects of the Cysteamine Nanoemulsions Delivered via Inhalation. OMICS (IF 3.3) Pub Date : 2023-08-11 Gautam Sharma,Swati Pund,Rajkumar Govindan,Mehar Un Nissa,Deeptarup Biswas,Sanniya Middha,Koustav Ganguly,Mahesh Padukudru Anand,Rinti Banerjee,Sanjeeva Srivastava
Cigarette smoking is the major cause of chronic inflammatory diseases such as chronic obstructive pulmonary disease (COPD). It is paramount to develop pharmacological interventions and delivery strategies against the cigarette smoke (CS) associated oxidative stress in COPD. This study in Wistar rats examined cysteamine in nanoemulsions to counteract the CS distressed microenvironment. In vivo, 28 days
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Urinary Proteomics for Discovery of Gastric Cancer Biomarkers to Enable Precision Clinical Oncology. OMICS (IF 3.3) Pub Date : 2023-08-09 Neha Joshi,Firdous Bhat,Anikha Bellad,Gajanan Sathe,Anu Jain,Sandip Chavan,Ravi Sirdeshmukh,Akhilesh Pandey
For precision in clinical oncology practice, detection of tumor-derived peptides and proteins in urine offers an attractive and noninvasive alternative for diagnostic or screening purposes. In this study, we report comparative quantitative proteomic profiling of urine samples from patients with gastric cancer and healthy controls using tandem mass tags-based multiplexed mass spectrometry approach.
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Idiopathic Pulmonary Fibrosis Molecular Substrates Revealed by Competing Endogenous RNA Regulatory Networks. OMICS (IF 3.3) Pub Date : 2023-08-04 Muhammed Fatih Kircali,Beste Turanli
Idiopathic pulmonary fibrosis (IPF) is a chronic progressive fibrotic disease of the lung with poor prognosis. Fibrosis results from remodeling of the interstitial tissue. A wide range of gene expression changes are observed, but the role of micro RNAs (miRNAs) and circular RNAs (circRNA) is still unclear. Therefore, this study aimed to establish an messenger RNA (mRNA)-miRNA-circRNA competing endogenous
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Genome-Wide Analysis of Kidney Renal Cell Carcinoma: Exploring Differentially Expressed Genes for Diagnostic and Therapeutic Targets. OMICS (IF 3.3) Pub Date : 2023-08-01 Yash Mathur,Alaa Shafie,Bandar Alharbi,Amal Adnan Ashour,Waleed Abu Al-Soud,Hassan H Alhassan,Salem Hussain Alharethi,Farah Anjum
Kidney renal cell carcinoma (KIRC) is the most common type of renal cancer. Kidney malignancies have been ranked in the top 10 most frequently occurring cancers. KIRC is a prevalent malignancy with a poor prognosis. The disease has risen for the last 40 years, and robust biomarkers for KIRC are needed for precision/personalized medicine. In this bioinformatics study, we utilized genomic data of KIRC
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A Splicing Transcriptome-Wide Association Study Identifies Candidate Altered Splicing for Prostate Cancer Risk. OMICS (IF 3.3) Pub Date : 2023-07-25 Yanfa Sun,Ye Eun Bae,Jingjing Zhu,Zichen Zhang,Hua Zhong,Chunmei Cheng,Youping Deng,Chong Wu,Lang Wu
Prostate cancer (PCa) represents a huge public health burden among men. Many susceptibility genetic factors for PCa still remain unknown. In this study, we performed a large splicing transcriptome-wide association study (spTWAS) using three modeling strategies to develop alternative splicing genetic prediction models for identifying novel susceptibility loci and splicing introns for PCa risk by assessing
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Whole Exome Sequencing Reveals Novel Variants in Unexplained Erythrocytosis. OMICS (IF 3.3) Pub Date : 2023-07-11 Harshit Khurana,Babylakshmi Muthusamy,Uday Yanamandra,Kishore Garapati,Harikrishnan Premdeep,Shankar Subramanian,Akhilesh Pandey
Erythrocytosis is characterized by an increase in red cells in peripheral blood. Polycythemia vera, the commonest primary erythrocytosis, results from pathogenic variants in JAK2 in ∼98% of cases. Although some variants have been reported in JAK2-negative polycythemia, the causal genetic variants remain unidentified in ∼80% of cases. To discover genetic variants in unexplained erythrocytosis, we performed
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Idiopathic Pulmonary Arterial Hypertension: Network-Based Integration of Multi-Omics Data Reveals New Molecular Signatures and Candidate Drugs. OMICS (IF 3.3) Pub Date : 2023-07-06 Ceyda Kasavi
Idiopathic pulmonary arterial hypertension (IPAH) is a progressive disease that affects the pulmonary arteries, resulting in increased pulmonary vascular resistance and right ventricular dysfunction, which can ultimately lead to heart failure and death. The molecular substrates of IPAH are poorly understood while diagnostics and therapeutics innovation remain as unmet needs for this debilitating disease
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A Robust Machine Learning Framework Built Upon Molecular Representations Predicts CYP450 Inhibition: Toward Precision in Drug Repurposing. OMICS (IF 3.3) Pub Date : 2023-07-04 Sotiris Ouzounis,Vasilis Panagiotopoulos,Vivi Bafiti,Panagiotis Zoumpoulakis,Dionisis Cavouras,Ioannis Kalatzis,Minos-Timotheos Matsoukas,Theodora Katsila
Human cytochrome P450 (CYP450) enzymes play a crucial role in drug metabolism and pharmacokinetics. CYP450 inhibition can lead to toxicity, in particular when drugs are co-administered with other drugs and xenobiotics or in the case of polypharmacy. Predicting CYP450 inhibition is also important for rational drug discovery and development, and precision in drug repurposing. In this overarching context
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Characterization of Lipid Alterations by Oncogenic PIK3CA Mutations Using Untargeted Lipidomics in Breast Cancer. OMICS (IF 3.3) Pub Date : 2023-07-01 Jae Hun Jung,Da-Qing Yang,Hongming Song,Xiangyu Wang,Xinyan Wu,Kwang Pyo Kim,Akhilesh Pandey,Seul Kee Byeon
Lipids play crucial biological roles in health and disease, including in cancers. The phosphatidylinositol 3-kinase (PI3K) signaling pathway is a pivotal promoter of cell growth and proliferation in various types of cancer. The somatic mutations in PIK3CA, the gene coding for the catalytic subunit p110α of PI3K, are frequently present in cancer cells, including breast cancer. Although the most prominent
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Breast Cancer Therapeutics and Hippo Signaling Pathway: Novel MicroRNA-Gene-Protein Interaction Networks. OMICS (IF 3.3) Pub Date : 2023-06-01 Shradheya R R Gupta,Garima Nagar,Pooja Mittal,Shweta Rana,Harpreet Singh,Rajeev Singh,Archana Singh,Indrakant K Singh
The Hippo signaling pathway is a master regulator of development, cell proliferation, and apoptosis in particular, and it plays an important role in tissue regeneration, controlling organ size, and cancer suppression. Dysregulation of the Hippo signaling pathway has been implicated in breast cancer, a highly prevalent cancer affecting 1 out of every 15 women worldwide. While the Hippo signaling pathway
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The Versatility of Plectin in Cancer: A Pan-Cancer Analysis on Potential Diagnostic and Prognostic Impacts of Plectin Isoforms. OMICS (IF 3.3) Pub Date : 2023-06-01 Hulya Gundesli,Medi Kori,Kazim Yalcin Arga
Plectin, encoded by PLEC, is a cytoskeletal and scaffold protein with a number of unique isoforms that act on various cellular functions such as cell adhesion, signal transduction, cancer cell invasion, and migration. While plectin has been shown to display high expression and mislocalization in tumor cells, our knowledge of the biological significance of plectin and its isoforms in tumorigenesis remain
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Gastric Cancer Biomarker Candidates Identified by Machine Learning and Integrative Bioinformatics: Toward Personalized Medicine. OMICS (IF 3.3) Pub Date : 2023-05-25 Vigneshwar Suriya Prakash Sinnarasan,Dahrii Paul,Rajesh Das,Amouda Venkatesan
Gastric cancer (GC) is among the leading causes of cancer-related deaths worldwide. The discovery of robust diagnostic biomarkers for GC remains a challenge. This study sought to identify biomarker candidates for GC by integrating machine learning (ML) and bioinformatics approaches. Transcriptome profiles of patients with GC were analyzed to identify differentially expressed genes between the tumor
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Digital Transformation, Omics and Society: Industry 4.0 and Industry 5.0. OMICS (IF 3.3) Pub Date : 2023-05-19 Vural Özdemir
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Emerging Pathogens in Planetary Health and Lessons from Comparative Genome Analyses of Three Clostridia Species. OMICS (IF 3.3) Pub Date : 2023-05-16 Ankit Singh Tanwar,Padival Shruptha,Apoorva Jnana,Angela Brand,Mamatha Ballal,Kapaettu Satyamoorthy,Thokur Sreepathy Murali
Clostridioides difficile (CD) is a major planetary health burden. A Gram-positive opportunistic pathogen, CD, colonizes the large intestine and is implicated in sepsis, pseudomembranous colitis, and colorectal cancer. C. difficile infection typically following antibiotic exposure results in dysbiosis of the gut microbiome, and is one of the leading causes of diarrhea in the elderly population. While
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Breast Cancer Prognostic Hub Genes Identified by Integrated Transcriptomic and Weighted Network Analysis: A Road Toward Personalized Medicine. OMICS (IF 3.3) Pub Date : 2023-05-08 Prithvi Singh,Aanchal Rathi,Rashmi Minocha,Anuradha Sinha,Mohammad Mahfuzul Haque,Md Imtaiyaz Hassan,Ravins Dohare
Breast cancer (BC) is the second-most common type and among the leading causes of worldwide cancer-related deaths. There is marked person-to-person variability in susceptibility to, and phenotypic expression and prognosis of BC, a predicament that calls for personalized medicine and individually tailored therapeutics. In this study, we report new observations on prognostic hub genes and key pathways
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Gene Set Based Integrated Methylome and Transcriptome Analysis Reveals Potential Molecular Mechanisms Linking Cigarette Smoking and Related Diseases. OMICS (IF 3.3) Pub Date : 2023-05-05 Pashupati P Mishra,Binisha H Mishra,Emma Raitoharju,Nina Mononen,Jorma Viikari,Markus Juonala,Nina Hutri-Kähönen,Mika Kähönen,Olli T Raitakari,Terho Lehtimäki
Advanced integrative analysis of DNA methylation and transcriptomics data may provide deeper insights into smoke-induced epigenetic alterations, their effects on gene expression and related biological processes, linking cigarette smoking and related diseases. We hypothesize that accumulation of DNA methylation changes in CpG sites across genomic locations of different genes might have biological significance
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New Ways to Protect the Host from SARS-CoV-2? Lung Microbiome Metabolites Inhibit STAT3 and Modulate the Immunological Network. OMICS (IF 3.3) Pub Date : 2023-05-04 Jency Roshni,Mahema Sivakumar,Faris Ahmed Bahammam,Shilpa Bhandi,Shankargouda Patil,Manjunath Kamath,Ali Abusharha,Shiek S S J Ahmed
COVID-19 caused by the SARS-CoV-2 infection is a systemic disease that affects multiple organs, biological pathways, and cell types. A systems biology approach would benefit the study of COVID-19 in the pandemic as well as the endemic state. Notably, patients with COVID-19 have dysbiosis of lung microbiota whose functional relevance to the host is largely unknown. We carried out a systems biology investigation
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miR-433 Inhibits Glioblastoma Progression by Suppressing the PI3K/Akt Signaling Pathway Through Direct Targeting of ERBB4. OMICS (IF 3.3) Pub Date : 2023-05-01 Huawei Jiang,Zhiwei Su,Wangxiong Hu,Xianggui Yuan,Teng Yu,Jing Yang,Xibin Xiao,Shu Zheng,Biaoyang Lin
Glioblastoma multiforme (GBM) is a highly malignant brain tumor where new biomarkers and drug targets are much needed in the oncology clinic. miR-433 was identified as a tumor-suppressing miRNA in several different types of human cancer. However, the integrative biology of miR-433 in GBM is still largely unknown. By analyzing the expression profiles of miR-433 in 198 patients with glioma at The Cancer
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Identification of Common Dysregulated Genes in COVID-19 and Hypersensitivity Pneumonitis: A Systems Biology and Machine Learning Approach. OMICS (IF 3.3) Pub Date : 2023-04-14 Sanjukta Dasgupta,Sankha Subhra Das,Sankalp Patidar,Vaibhav Kajaria,Sushmita Roy Chowdhury,Koel Chaudhury
A comprehensive knowledge on systems biology of severe acute respiratory syndrome coronavirus 2 is crucial for differential diagnosis of COVID-19. Interestingly, the radiological and pathological features of COVID-19 mimic that of hypersensitivity pneumonitis (HP), another pulmonary fibrotic phenotype. This motivated us to explore the overlapping pathophysiology of COVID-19 and HP, if any, and using
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Signal Transducer and Activator of Transcription 6 Changes and Protein Frustration by Single Amino Acid Substitutions: Implications for Cancer Progression. OMICS (IF 3.3) Pub Date : 2023-04-01 Salem Hussain Alharethi,Tahseen Kamal,Bandar Alharbi,Hassan H Alhassan,Mohammed Ageeli Hakami,Bader Saud Alotaibi,Malik Abdul Rub,Hadi M Marwani,Khalid A Alamry,Abdullah M Asiri,Naved Azum
Signal transducer and activator of transcription 6 (STAT6) is a multifunctional protein that plays critical functions in cell proliferation, apoptosis, differentiation, and angiogenesis. Mutations in STAT6 may contribute to the development of certain complex diseases such as cancer. This study examined single amino acid substitutions in STAT6 to pinpoint deleterious variants and their related structural
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Harnessing Deep Learning for Omics in an Era of COVID-19. OMICS (IF 3.3) Pub Date : 2023-04-01 Bahareh Jahanyar,Hamid Tabatabaee,Alireza Rowhanimanesh
Omics data are multidimensional, heterogeneous, and high throughput. Robust computational methods and machine learning (ML)-based models offer new prospects to accelerate the data-to-knowledge trajectory. Deep learning (DL) is a powerful subset of ML inspired by brain structure and has created unprecedented momentum in bioinformatics and computational biology research. This article provides an overview
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One Health and Planetary Health Omics: New Intersections and Call for Papers. OMICS (IF 3.3) Pub Date : 2023-03-24 Vural Özdemir
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Oral Microbiome, Mental Health, and Sleep Outcomes During the COVID-19 Pandemic: An Observational Study in Chinese and Korean American Immigrants. OMICS (IF 3.3) Pub Date : 2023-03-22 Brianna N Richardson,Hye In Noh,Caitlin I Webster,Wenhui Zhang,Sangmi Kim,Irene Yang,Jinbing Bai
COVID-19 is a systemic disease whose effects are not limited to the respiratory system. The oral microbiome (OM)-brain axis is of growing interest in understanding the broader, neuropsychiatric, impacts of the COVID-19 pandemic through a systems biology lens. In this context, mental health and sleep disturbance are often reported by Asian Americans. In a cross-sectional observational study design,
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Global Catastrophic Biological Risks in the Post-COVID-19 World: Time to Act Is Now. OMICS (IF 3.3) Pub Date : 2023-03-21 Manousos E Kambouris
Global Catastrophic Biological Risks (GCBRs) refer to events with biological agents that can result in unprecedented or catastrophic disasters that are beyond the collective response-abilities of nation-states and the existing governance instruments of global governance and international affairs. This article offers a narrative review, with a view to new hypothesis development to rethink GCBRs after
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Integration of Human and Viral miRNAs in Epstein-Barr Virus-Associated Tumors and Implications for Drug Repurposing. OMICS (IF 3.3) Pub Date : 2023-03-01 Anamika Thakur,Manoj Kumar
Epstein-Barr virus (EBV) is associated with several tumors, and has substantial relevance for public health. Therapeutics innovation for EBV-related disorders is much needed. In this context, miRNAs are noncoding RNA molecules that play vital roles in EBV infection. miRNA-Seq and RNA-Seq data for EBV-associated clinical samples and cell lines have been generated, but their detailed integrative analyses
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The Promises of Proteomics and Metabolomics for Unravelling the Mechanism and Side Effect Landscape of Beta-Adrenoceptor Antagonists in Cardiovascular Therapeutics. OMICS (IF 3.3) Pub Date : 2023-02-28 Shreyayukta Chakraborty,Arpita Kannihalli,Abhishek Mohanty,Sandipan Ray
Cardiovascular medicine witnessed notable advances for the past decade. Multiomics research offers a new lens for precision/personalized medicine for existing and emerging drugs used in the cardiovascular clinic. Beta-blockers are vital in treating hypertension and chronic heart failure. However, clinical use of beta-blockers is also associated with side effects and person-to-person variations in their
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An Omics Strategy for Translational Bioinformatics and Rapid COVID-19 Drug Repurposing. OMICS (IF 3.3) Pub Date : 2023-02-28 Amjesh Revikumar
As COVID-19 continues to evolve around the world, there are unmet needs for rapid discovery, repurposing, and development of antiviral drugs. COVID-19 drug development is relevant for acute/pandemic context as well as the endemic disease with SARS-CoV-2 going forward. In the present study, the transcriptome data of the SARS-CoV-2-infected human lung cell lines were used to identify the signature genes
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Systems Biomarkers, Artificial Intelligence, and One Health Vision Can Help Fight Antimicrobial Resistance. OMICS (IF 3.3) Pub Date : 2023-02-28 Ceyda Kula,Kazım Yalçın Arga
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Can Water-Only DNA Extraction Reduce the Logistical Footprint of Biosurveillance and Planetary Health Diagnostics? Toward a New Method. OMICS (IF 3.3) Pub Date : 2023-02-20 Stavroula Goudoudaki,Manousos E Kambouris,Stavroula Siamoglou,Georgia Gioula,Maria Kantzanou,Marianna Manoussopoulou,George P Patrinos,Yiannis Manoussopoulos
The coronavirus disease-2019 (COVID-19) pandemic has raised the stakes for planetary health diagnostics. Because pandemics pose enormous burdens on biosurveillance and diagnostics, reduction of the logistical burdens of pandemics and ecological crises is essential. Moreover, the disruptive effects of catastrophic bioevents impact the supply chains in both highly populated urban centers and rural communities
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A Transcriptomic and Reverse-Engineering Strategy Reveals Molecular Signatures of Arachidonic Acid Metabolism in 12 Cancers. OMICS (IF 3.3) Pub Date : 2023-02-17 Elif Kubat Oktem,Busra Aydin,Gizem Gulfidan,Kazim Yalcin Arga
Cancer and arachidonic acid (AA) have important linkages. For example, AA metabolites regulate several critical biological functions associated with carcinogenesis: angiogenesis, apoptosis, and cancer invasion. However, little is known about the comparative changes in metabolite expression of the arachidonic acid pathway (AAP) in carcinogenesis. In this study, we examined transcriptome data from 12
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How Can Omics Inform Diabetic Foot Ulcer Clinical Management? A Whole Genome Comparison of Four Clinical Strains of Staphylococcus aureus. OMICS (IF 3.3) Pub Date : 2023-02-08 Ankit Singh Tanwar,Padival Shruptha,Bobby Paul,Thokur Sreepathy Murali,Angela Brand,Kapaettu Satyamoorthy
Foot ulcers and associated infections significantly contribute to morbidity and mortality in diabetes. While diverse pathogens are found in the diabetes-related infected ulcers, Staphylococcus aureus remains one of the most virulent and widely prevalent pathogens. The high prevalence of S. aureus in chronic wound infections, especially in clinical settings, is attributed to its ability to evolve and
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Protein Therapeutic Target Candidates Against Acinetobacter baumannii, a Pathogen of Concern to Planetary Health: A Network-Based Integrative Omics Drug Discovery Approach OMICS (IF 3.3) Pub Date : 2023-02-03 Aishwarya Swain, Archana Pan
Acinetobacter baumannii, an opportunistic gram-negative pathogen responsible for several nosocomial infections, has developed resistance to various antibiotics. Proteins involved in the two-component system (TCS), virulence, and antibiotic resistance (AR), help this pathogen in regulating antibiotic susceptibility and virulence mechanisms. The present study reports a network-based integrative omics
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Colon Adenocarcinoma Quantitative Proteomics Reveals Dysregulation in Key Cancer Signaling Pathways and a Candidate Protein Marker Panel OMICS (IF 3.3) Pub Date : 2023-02-01 Abhilash Barpanda, Ankit Halder, Ayushi Dhote, Shashwati Parihari, Chetan Kantharia, Sanjeeva Srivastava
Colorectal cancer (CRC) is reportedly the second leading cause of cancer death worldwide. By the end of the decade, there will likely be more than one million fatalities worldwide from this cancer, with an estimated 2.2 million additional cases. We need new ways of thinking about cancer research. One approach is to deploy systems science using quantitative proteomics to obtain postgenomic and functional
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Is Public Engagement in Bioengineering and Synthetic Biology Improving Research Outcomes? OMICS (IF 3.3) Pub Date : 2023-01-27 Lucy Carter, Aditi Mankad, Elizabeth V. Hobman
Engaging diverse publics on the acceptability of large-scale biology applications such as gene drives is held in high regard by the international research community. The development of gene drives to suppress invasive and pest species and improvements to the sustainability of food systems are examples of integrative biology applications in engineering and ecology with the potential for large-scale
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Public Engagement and Global Governance of Science: Beyond Instrumentalism. OMICS (IF 3.3) Pub Date : 2023-01-25 Vural Özdemir
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Systems Biology of COVID-19 and Human Diseases: Beyond a Bird's Eye View, and Toward One Health OMICS (IF 3.3) Pub Date : 2023-01-17 Srishti Banerjee, Shreyayukta Chakraborty, Sandipan Ray
As we gaze into the future beyond the current coronavirus disease 2019 (COVID-19) pandemic, there is a need to rethink our priorities in planetary health, research funding, and, importantly, the concepts and unchecked assumptions by which we attempt to understand health and prevent illness. Next-generation quantitative omics technologies promise a more profound and panoptic understanding of the dynamic
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Theranostics for COVID-19 Antiviral Drugs: Prospects and Challenges for Worldwide Precision/Personalized Medicine OMICS (IF 3.3) Pub Date : 2023-01-17 Caíque Manóchio, Sabrina Torres-Loureiro, Mariana M. Scudeler, Bruno Miwa, Fernanda C. Souza-Santos, Fernanda Rodrigues-Soares
Coronavirus disease 2019 (COVID-19) is a systemic disease that impacts multiple organ systems with a complex clinical presentation and outcomes that can vary from person to person and between populations. To optimize COVID-19 treatment outcomes, and in light of the availability of antiviral drugs, there is a need for greater attention to the field of theranostics, the fusion of therapeutics and diagnostics
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Pathogenesis of Human Immunodeficiency Virus and Mycobacterium tuberculosis Infection as Revealed by Transcriptome and Interactome Data OMICS (IF 3.3) Pub Date : 2023-01-17 Pooja Wakchoure, Khizra Momin, Abdul Arif Khan
Tuberculosis (TB) among patients with human immunodeficiency virus (HIV) is a major global health burden and contributes to a high mortality rate due to HIV-mediated immunosuppression and subsequent susceptibility to TB. It is imperative to understand the pathogenesis of the association between HIV and TB for therapeutic innovation and preventive medicine. In the present study, we employed transcriptomic
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Multiomics Integration at Single-Cell Resolution Using Bayesian Networks: A Case Study in Hepatocellular Carcinoma OMICS (IF 3.3) Pub Date : 2023-01-17 Muntadher Jihad, İdil Yet
Multiomics data integration is one of the leading frontiers of complex disease research and integrative biology. The advances in single-cell sequencing technologies offer yet another crucial dimension in multiomics research. The single-cell studies enable the study and integration of multiomics data simultaneously in the same cell. We report in this study multiomics data integration in single-cell