Bioinformatics - Science topic

Current research highlights the importance of genomics in predicting tumor progression, identifying driver mutations, and informing personalized therapies in many types of cancer. This Special Issue will cover genomic alterations, driver mutations, tumor evolution metrics, and the integration of genomics with clinicopathological and artificial inte...

The koala (Phascolarctos cinereus) is an iconic Australian species that is listed as endangered in the northern parts of its range due to loss of habitat, disease, and road deaths. Diseases contribute significantly to the decline of koala populations, primarily Chlamydia and koala retrovirus. The distribution of these diseases across the species’ r...

Background The three-amino-acid-loop-extension (TALE) is a ubiquitous homeodomain transcription factor among plant species involved in regulating plant growth, development, and environmental responses. However, this has not been systematically analyzed or reported in sorghum. Results In this study, 23 SbTALE genes were identified using bioinformat...

Purpose This research probes into genes related to the risk of concurrent kidney injury in septic patients to provide reliable targets for early identification of sepsis-associated kidney injury and prognosis research. Methods Peripheral blood samples were isolated from 10 healthy individuals and 22 septic patients for RNA sequencing and different...

Backgrounds Distant metastasis in breast cancer patients contributes to increased breast cancer mortality, highlighting the urgent need for effective predictive strategies. Understanding metastasis mechanisms and identifying relevant biomarkers are crucial for improving patient outcomes and informing targeted therapies. This study employed a high-d...

Legionella pneumophila, the causative agent of Legionnaires' disease, is often found in the plumbing systems of buildings from where it can be transmitted to humans via inhalation or aspiration of contaminated water drops. Annual routine water sampling from the potable water system of an occupational healthcare building in Basel over 25 years was p...

Bioinformatics has played an important role in discovering medicine because whole-genome sequences can help to find out the many genetic diseases. Bioinformatics uses computational tools to manage, store and analyze the data. Multiple sequence alignment (MSA) seems to be a very useful process in molecular and evolutionary biology. There are a varie...

The process between 16S and shotgun are completely different regarding their downstream analysis. One of the advantages of 16S is that most downstream analysis is performed on one bioinformatics platform called QIIME2. Using QIIME 2 allows us to create the artifacts for data visualizations and statistical analysis. Another thing to remember is that...

Bioinformatics is a rapidly evolving field charged with cataloging, disseminating, and analyzing biological data. Bioinformatics started with genomics, but while genomics focuses more narrowly on the genes comprising a genome, bioinformatics now encompasses a much broader range of omics technologies. Overcoming barriers of scale and effort that pla...

Objectives To explore the role of radiomics in predicting the prognosis of proximal esophageal cancer and to investigate the biological underpinning of radiomics in identifying different prognoses. Methods A total of 170 patients with pathologically and endoscopically confirmed proximal esophageal cancer from two centers were enrolled. Radiomics m...

Background/Objectives: Gastric and lung adenocarcinomas are among the most common adenocarcinomas worldwide. Our research aimed to validate methylation biomarkers that differentiate gastric and lung adenocarcinomas from hepatocellular carcinoma, cholangiocarcinoma, colorectal carcinoma, pancreatic adenocarcinoma and paired healthy tissues. Methods:...

There is a very fine line between desired activity and unwanted toxicity. In general terms, the aim is to develop selective bioactives, which are active against microorganisms and not humans. To this end, it is intere sting to correlate predicted properties and experiments, whose results can both validate and improve bioinformatics programs, such a...

Although the prognosis of breast cancer has significantly improved compared to other types of cancer, there are still some patients who expire due to recurrence or metastasis. Therefore, it is necessary to develop a method to identify patients with poor prognosis at the early stages of cancer. In the process of discovering new prognostic markers fr...

Fusarium wilt in eggplant caused by F. oxysporum f. sp. melongenae is a major devastating soil-borne disease on a worldwide scale. Effectors play important roles in the interactions in pathogen–plant interactions. Identifying effectors is essential for elucidating the pathogenic mechanisms of phytopathogenic fungi. In this study, bioinformatic pred...

Machine learning (ML) and bioinformatics are catalyzing a new era in biomedical research, enabling unprecedented insights into the complex systems that govern human health and disease [...]

Endometrial cancer is a common malignant tumor in women, with rising incidence rates and an unoptimistic prognosis. DSN1 is a kinetochore protein-coding gene that affects centromere assembly and progression in cell cycles, which is associated with adverse predictions for many cancers. However, the role of DSN1 in UCEC has not yet been reported. We...

The prevalence and mortality rates of colorectal cancer (CRC) are increasing worldwide. Radiation resistance hinders radiotherapy, a standard treatment for advanced CRC, leading to local recurrence and metastasis. Elucidating the molecular mechanisms underlying radioresistance in CRC is critical to enhance therapeutic efficacy and patient outcomes....

Background Dynamin 2 (DNM2) is aberrantly expressed in different malignancies and exerts a function in tumor progression. Aims This study, for the first time, aimed to evaluate the clinical and prognostic value of DNM2 in the pathophysiology of bladder cancer using bioinformatics analysis and experimental evaluation. Methods and Results We analyz...

Abdominal aortic aneurysm (AAA) is a severe vascular condition, marked by the progressive dilation of the abdominal aorta, leading to rupture if untreated. The objective of this study was to identify key biomarkers and decipher the immune mechanisms underlying AAA utilising multi‐omics data analysis and machine learning techniques. Single‐cell RNA...

Within Polynoidae, a diverse aphroditiform family, the subfamily Macellicephalinae comprises anchialine cave-dwelling and deep-sea scaleworms. In this study, Lepidonotopodinae is synonymized with Macellicephalinae, and the tribe Lepidonotopodini is applied to a well-supported clade inhabiting deep-sea chemosynthetic-based ecosystems. Newly sequence...

Purpose The aim of this study is to investigate the underlying molecular mechanism of oxidative stress (OS) involved in aortic dissection (AD). Methods Datasets of AD and OS-related genes were obtained from the Gene Expression Omnibus (GEO) and the GeneCards database, respectively. Differential expression analysis and weighted gene correlation net...

Citation: Artemyev, V.; Gubaeva, A.; Paremskaia, A.I.; Dzhioeva, A.A.; Deviatkin, A.; Feoktistova, S.G.; Mityaeva, O.; Volchkov, P.Y. Synthetic Promoters in Gene Therapy: Design Approaches, Features and Applications. Abstract: Gene therapy is a promising approach to the treatment of various inherited diseases, but its development is complicated by...

The rapid advancements in biomedical sciences, including genomics, microbiome research, and bioinformatics, underscore the need for dental education to evolve to meet future challenges in public oral health and healthcare delivery. The integration of basic sciences into dental curricula is crucial to ensure that dental professionals are thoroughly...

Stuttering is a common neurodevelopmental condition characterized by disfluencies in speech, such as blocks, prolongations, and repetitions. While most children who stutter do so only transiently, there are some for whom stuttering persists into adulthood. Rare-variant screens in families including multiple relatives with persistent stuttering have...

Background: HER2-positive breast cancer is an aggressive subtype where innate/acquired resistance to targeted drugs remains a challenge. This study aims to uncover the underlying mechanisms of HER2 drug resistance through miRNA analysis and target identification. Methods: MiRNA datasets were systematically retrieved from the GEO database, and diffe...

The interaction of transcription factors (TFs) with DNA precisely regulates gene transcription. In mammalian cells, thousands of TFs often interact with DNA cis‐regulatory elements in a combinatorial manner rather than act alone. The identification of cooperativity between TFs can help to explore the mechanism of transcriptional regulation. However...

Hepatocellular carcinoma (HCC) with complex molecular carcinogenesis represents a kind of prevalent neoplasm occurring in the liver. The objective of this study is to illustrate the function of baculoviral inhibitor of apoptosis repeat containing 5 (BIRC5) and underlying action mechanisms in HCC progression. Comprehensive bioinformatics methods wer...

Rosemary (Salvia rosmarinus) is a world-famous plant frequently subjected to various environmental stresses. Heat Shock Transcription Factor (HSF) has been shown to be essential for plant growth and for resistance to environmental stresses. This study utilized bioinformatics techniques to identify the SrHSF gene family in the rosemary genome. A tot...

Structural variants (SVs) are important contributors to human disease. Their characterization remains however difficult due to their size and association with repetitive regions. Long-read sequencing (LRS) and optical genome mapping (OGM) can aid as their molecules span multiple kilobases and capture SVs in full. In this study, we selected six indi...

Shenmai injection (SMI) is widely used in the clinical treatment of sepsis, but its mechanism is not yet clear. This study aimed to explore the molecular mechanism through network pharmacology, bioinformatics, and molecular docking technologies. The active ingredients and targets of SMI were screened through traditional Chinese medicine databases a...

Circular RNA (circRNA) serves as a competitive endogenous RNA (ceRNA) that plays a pivotal role in the initiation and progression of breast cancer (BC). However, compared to other noncoding RNAs (ncRNAs), research on circRNA in BC is still in its infancy. Through the analysis of circRNA datasets in the GEO database, hsa_circ_0001314, which is upreg...

Intracranial haemorrhage (ICH) is an urgent and potentially fatal medical condition caused by brain blood vessel rupture, leading to blood accumulation in the brain tissue. Due to the pressure and damage it causes to brain tissue, ICH results in severe neurological impairment or even death. Recently, deep neural networks have been widely applied to...

Parkinson’s Disease (PD) is a debilitating neurodegenerative disorder, characterized by motor and cognitive impairments, that affects >1% of the population over the age of 60. The pathogenesis of PD is complex and remains largely unknown. Due to the cellular heterogeneity of the human brain and changes in cell type composition with disease progress...

Background Advances in high-throughput technologies have originated an ever-increasing availability of omics datasets. The integration of multiple heterogeneous data sources is currently an issue for biology and bioinformatics. Multiple kernel learning (MKL) has shown to be a flexible and valid approach to consider the diverse nature of multi-omics...

Background The intricate interplay between stemness markers and cell death pathways significantly influences the pathophysiology of cervical cancer. SOX2, a pivotal regulator of stem cell pluripotency, has recently been implicated in the modulation of ferroptosis, a specialized form of iron-dependent cell death, in cancer dynamics. This study delin...

Matrix Gla protein (MGP) is a vitamin K-dependent γ-carboxylated protein that was initially identified as a physiological inhibitor of ectopic calcification, primarily affecting cartilage and the vascular system. Mutations in the MGP gene were found to be responsible for the Keutel syndrome, a condition characterized by abnormal calcifications in t...

Counting distinct permutations with replacement, especially when involving multiple subwords, is a longstanding challenge in combinatorial analysis, with critical applications in cryptography, bioinformatics, and statistical modeling. This paper introduces a novel framework that presents closed-form formulas for calculating distinct permutations wi...

Sepsis is a severe systemic inflammatory syndrome triggered by infection and is a leading cause of morbidity and mortality in intensive care units (ICUs). Immune dysfunction is a hallmark of sepsis. In this study, the authors investigated cell‐cell communication among lymphoid‐derived leucocytes using single‐cell RNA sequencing (scRNA‐seq) to gain...

Background Improper expression of long noncoding RNAs (lncRNAs) can cause various cancers. Single nucleotide polymorphisms (SNPs) affect the expression and function of several key lncRNAs. We assessed the associations of MEG3, PVT1, and H19 lncRNA polymorphisms with susceptibility to gastric cancer (GC). Methods In Ardabil (a high-risk area in Nor...

In the current study, the expression of the Kirsten rat sarcoma virus oncogene (KRAS) in esophageal carcinoma (ESCA) was examined for its medical and therapeutic relevance. ESCA has a 20% five-year survival rate, placing it seventh in the world in terms of overall rate of mortality. GEPIA2, UALCAN, OncoDB, cBioPortal, STRING, DAVID, and TIMER2 data...

Drug side effects have become paramount concerns in drug safety research, ranking as the fourth leading cause of mortality following cardiovascular diseases, cancer, and infectious diseases. Simultaneously, the widespread use of multiple prescription and over-the-counter medications by many patients in their daily lives has heightened the occurrenc...

Circular RNA (circRNA) is a covalently closed RNA molecule formed by back splicing. The role of circRNAs in posttranscriptional gene regulation provides new insights into several types of cancer and neurological diseases. CircRNAs are associated with multiple diseases and are emerging biomarkers in cancer diagnosis and treatment. The associations p...

Background Advances in transcriptional profiling methods have enabled the discovery of molecular subtypes within and across traditional tissue-based cancer classifications. Such molecular subgroups hold potential for improving patient outcomes by guiding treatment decisions and revealing physiological distinctions and targetable pathways. Computati...

Background/Objectives: There exist significant challenges for lung adenocarcinoma (LUAD) due to its poor prognosis and limited treatment options, particularly in the advanced stages. It is crucial to identify genetic biomarkers for improving outcome predictions and guiding personalized therapies. Methods: In this study, we utilize a multi-step appr...

Accumulating evidence has shown that tRNA-derived small RNAs (tsRNAs) play crucial roles in malignant tumor development. However, whether serum tsRNAs can act as potential biological markers for hepatocellular carcinoma (HCC) are still largely unknown. In the current study, a novel tsRNA, namely tsRNA-Thr-5-0015, was prominently elevated in the ser...

Introdução: a docagem cega consiste em uma investigação inicial em busca de cavidades de uma proteína que possam atuar como sítio ativo para um determinado ligante. Sua aplicação é importante especialmente no desenvolvimento e estudo inicial de novos fármacos, antes da realização de outros estudos de docagem molecular. Objetivo: apresentar uma anál...

Background CD147 belongs to the immunoglobulin superfamily, also known as Basigin (BSG), and is a highly glycosylated single transmembrane glycoprotein present in various tissues. Meta and bioinformatic analyses were used to explore the correlation between CD147 expression and the clinicopathological characteristics prognosis of breast cancer. Met...

Background While high-grade serous ovarian cancer (HGSC) has proven largely resistant to immunotherapy, sporadic incidents of partial and complete response have been observed in clinical trials and case reports. These observations suggest that a molecular basis for effective immunity may exist within a subpopulation of HGSC. Herein, we developed an...

Time series are ubiquitous in numerous science and engineering domains, e.g., signal processing, bioinformatics, and astronomy. Previous work has verified the efficacy of symbolic time series representation in a variety of engineering applications due to its storage efficiency and numerosity reduction. The most recent symbolic aggregate approximati...

Quantum machine learning (QML) is one of the most promising applications of quantum computation. Despite the theoretical advantages, it is still unclear exactly what kind of problems QML techniques can be used for, given the current limitation of noisy intermediate-scale quantum devices. In this work, we apply the well-studied quantum support vecto...

Background Skin cutaneous melanoma (SKCM) ranks among the most prevalent malignant tumors, highlighting the significance of identifying new research targets. In this study, our objective was to pinpoint pivotal genes implicated in SKCM pathogenesis and ascertain their potential as prognostic biomarkers. Methods Leveraging data from 1809 normal ski...

In this work, we describe the implementation of an infrastructure of conversational chatbots by using natural language processing and training within the Rasa framework. We use this infrastructure to create a chatbot assistant for the users of a bioinformatics suite. This suite provides a customized interface solution for omic pipelines and workflo...

Amino acids are the main form of nitrogen in plants, and their transport across cell membranes relies on amino acid transporters (AATs). Among the plant AATs, the TaATLa subfamily comprises 18 members, yet the bioinformatics characteristics and functions of TaATLa genes in common wheat remain poorly understood due to their complex genomes. This stu...

Background: The association of overall cardiovascular health (CVH) with changes in DNA methylation (DNAm) has not been well characterized. Methods: We calculated the American Heart Association's Life's Essential 8 (LE8) score to reflect CVH in five cohorts with diverse ancestry backgrounds. Epigenome-wide association studies (EWAS) for LE8 score we...

Recent technological advancements, including computer-assisted drug discovery, gene-editing techniques, and high-throughput screening approaches, have greatly expanded the palette of methods for the discovery of peptides available to researchers. These emerging strategies, driven by recent advances in bioinformatics and multi-omics, have significan...

Gliomas are among the most common malignant tumors of the central nervous system. Despite surgical resection followed by postoperative radiotherapy and chemotherapy, their prognosis remains unfavorable. The present study aimed to assess new mechanisms and explore promising prognostic biomarkers for patients with glioma using comprehensive bioinform...