Bioinformatics - Science topic

Dear Colleagues, After the great success of the first two editions, we are pleased to inform you that Molecules will launch the third edition of the Special Issue “Computational Approaches: Drug Discovery and Design in Medicinal Chemistry and Bioinformatics”. https://www.mdpi.com/journal/molecules/special_issues/ comput_appr_drug_dis_des_med_chem_b...

Phylogenomic analysis of 48 Actinobacillus suis isolates from pigs in the United States using whole genome sequencing (WGS) and bioinformatic pipelines.

Exploration of avian gametologous genes, i.e., homologous genes located on both the Z and W chromosomes, provides a crucial information about the underlying mechanism pertaining to the evolution of these chromosomes. The domestic chicken (Gallus gallus (Linnaeus 1758); GGA) traditionally serves as the primary reference subject of these comparative...

Cancer is one of the most common causes of mortality today. This disease's complications impose many costs on the human community's health, care, and well-being sectors. Solving complex biological problems requires advanced computational methods, and bioinformatics was created to solve such complex problems with the active interaction of several fi...

Fungal specialized metabolites are a major source of beneficial compounds that are routinely isolated, characterized, and manufactured as pharmaceuticals, agrochemical agents, and industrial chemicals. The production of these metabolites is encoded by biosynthetic gene clusters that are often silent under standard growth conditions. There are limit...

The genus Ceratocystis includes many phytopathogenic fungi that affect different plant species. One of these is Ceratocystis cacaofunesta, which is pathogenic to the cocoa tree and causes Ceratocystis wilt, a lethal disease for the crop. However, little is known about how this pathogen interacts with its host. The knowledge and identification of po...

The protein interaction network is a network composed of the interactions between all proteins in living organisms. The use of computational methods to prove that the functional modules in the PPI network is an important research topic in bioinformatics. With the development of technologies for detecting protein interactions, the available data on...

Background SINE-VNTR- Alu (SVA) retrotransposons are hominid-specific elements which have been shown to play important roles in processes such as chromatin structure remodelling and regulation of gene expression demonstrating that these repetitive elements exert regulatory functions. We have previously shown that the presence or absence of a specif...

Identifying protein sequences with common ancestry is a core task in bioinformatics and evolutionary biology. However, methods for inferring and aligning such sequences in annotated genomes have not kept pace with the increasing scale and complexity of the available data. Thus, in this work we implemented several improvements to the traditional met...

Marine fungal metabolites often exhibit antioxidant activity, but their effects on the Keap1/Nrf2 cellular system are rarely studied, possibly due to insufficient isolated amounts. In this work, we used a bioinformatics approach to evaluate the ability of some promising cytoprotective compounds to bind Kelch domain of Keap1 protein, and thus inhibi...

Background Recently we developed a gene orthology inference tool based on genome rearrangements (Journal of Bioinformatics and Computational Biology 19:6, 2021). Given a set of genomes our method first computes all pairwise gene similarities. Then it runs pairwise ILP comparisons to compute optimal gene matchings, which minimize, by taking the simi...

Computer programming is a fundamental tool for life scientists, allowing them to carry out essential research tasks. However, despite various educational efforts, learning to write code can be a challenging endeavor for students and researchers in life-sciences disciplines. Recent advances in artificial intelligence have made it possible to transla...

Many machine learning applications in bioinformatics currently rely on gene identities extracted from input gene signatures, and fail to take advantage of preexisting knowledge about gene functions. We developed the Functional Representation of Gene Signatures (FRoGS) approach by training a deep learning model. FRoGS represents gene signatures proj...

During the SARS-CoV-2 pandemic, wastewater-based genomic surveillance (WWGS) emerged as an efficient viral surveillance tool that takes into account asymptomatic cases and can identify known and novel mutations and offers the opportunity to assign known virus lineages based on the detected mutations profiles. WWGS can also hint towards novel or cry...

Cell type classification serves as one of the most fundamental analyses in bioinformatics. It helps recognizing various cells in cancer microenvironment, discovering new cell types and facilitating other downstream tasks. Single-cell RNA-sequencing (scRNA-seq) technology can profile the whole transcriptome of each cell, thus enabling cell type clas...

The majority of hepatocellular carcinoma (HCC) cases are diagnosed at an advanced stage. Currently, there are only a few therapeutic methods available for patients with advanced HCC and extrahepatic metastasis (EHM). Systemic chemotherapy, such as FOLFOX4 (infusions of fluorouracil, leucovorin, and oxaliplatin), has been reported for treating advan...

Purpose As a member of the ubiquitin‐conjugating enzyme (E2) family, UBE2V2 demonstrates significant tumorigenicity in many cancers. However, the relationship between UBE2V2 expression and the morbidity of lung adenocarcinoma (LUAD) is still unknown. Methods We detected the mRNA and protein expression of UBE2V2 and analyzed its relationship with c...

T cell leukemia homeobox 2 (TLX2) plays an important role in some tumors. Bioinformatics and experimental validation represent a useful way to explore the mechanisms and functions of TLX2 gene in the cancer disease process from a pan cancer perspective. TLX2 was aberrantly expressed in pan cancer and cell lines and correlated with clinical stage. H...

Motivation: Many bioinformatics problems can be approached as optimization or controlled sampling tasks, and solved exactly and efficiently using Dynamic Programming (DP). However, such exact methods are typically tailored towards specific settings, complex to develop, and hard to implement and adapt to problem variations. Methods: We introduce...

Colorectal cancer (CRC) remains a primary cause of cancer mortality globally, necessitating precise prognostic indicators for effective clinical management. Our study introduces the Senescence Risk Score (SRRS), based on several senescence-related genes (SRGs), a potent prognostic tool designed to measure cellular senescence in CRC. The higher SRRS...

Differentiated thyroid cancer is the most common malignancy of the endocrine system. Although most thyroid nodules are benign, given the high incidence of thyroid nodules in the population, it is important to understand the differences between benign and malignant thyroid cancer and the molecular alterations associated with malignancy to improve de...

Whole genome sequencing of bacterial isolates is increasingly becoming routine in clinical microbiology; however, subsequent analysis often needs to be started by a bioinformatician even for comprehensive pipelines. With the RSYD-BASIC pipeline, we present a reads-to-results analysis pipeline operated by non-expert users that has already yielded cl...

Gliomas are the most prevalent primary tumor in the central nervous system, with an abysmal 5-year survival rate and alarming mortality. The current standard management of glioma is maximum resection of tumors followed by postoperative chemotherapy with temozolomide (TMZ) or radiotherapy. Low chemosensitivity of TMZ in glioma treatment eventuates l...

Recent technical breakthroughs in genotyping and bioinformatics techniques have greatly facilitated the translation of genomics into clinical care [...]

Membrane proteins are critical mediators for tumor progression and present enormous therapeutic potentials. Although gene profiling can identify their cancer-specific signatures, systematic correlations between protein functions and tumor-related mechanisms are still unclear. We present here the CrMP-Sol database (https://bio-gateway.aigene.org.cn/...

Background Renal clear cell carcinoma (RCC) is a common cancer in urinary system with increasing incidence. At present, targeted therapy and immunotherapy are the main therapeutic programs in clinical therapy. To develop novel drugs and provide new ideas for clinical therapy, the identification of potential ccRCC subtypes and potential target genes...

Mobile genetic elements (MGEs) are relevant agents in bacterial adaptation and evolutionary diversification. Stable appropriation of these DNA elements depends on host factors, among which are the nucleoid-associated proteins (NAPs). NAPs are highly abundant proteins that bind and bend DNA, altering its topology and folding, thus affecting all know...

This study built a prognostic model for CRC-diabetes and analyzed whether quercetin could be used for CRC-diabetes treatment through a network of pharmacology, molecular dynamics simulation, bioinformatics, and in vitro experiments. First, multivariate Cox proportional hazards regression was used to construct the prognosis modelof CRC-diabetes. The...

In the rapidly evolving field of bioinformatics, the analysis of Next-Generation Sequencing (NGS) data has become increasingly intricate, with a plethora of specialized tools addressing specific aspects of this domain. However, the fragmented nature of these tools often hinders comprehensive data mining. Introducing PipenGeneX, a pioneering framewo...

In this study, bioinformatic analyses were carried out according to the fully coded CP and MP gene regions of the agent, using six novel tomato brown rugose fruit virus (ToBRFV) variants obtained from the production greenhouses in Antalya, where the infection was first detected in Turkey and global variants. Molecular evolutionary analyses using...

In this webinar titled "Introduction to Bioinformatics and Its Applications," we embark on a journey to understand the essential concepts and profound implications of bioinformatics in the modern scientific landscape.

Motivation The winner’s curse is a form of selection bias that arises when estimates are obtained for a large number of features, but only a subset of most extreme estimates is reported. It occurs in large scale significance testing as well as in rank-based selection, and imperils reproducibility of findings and follow-up study design. Several meth...

Phylogenetic profiling is a common bioinformatics approach used to study the distribution of traits across species or, more broadly, along the topology of a phylogenetic tree. Originally proposed as a technique for establishing functional relationships between various genes through their correlated presence/absence patterns, phylogenetic profiling...

Background: Social isolation and loneliness pose significant public health challenges globally. The objective of this study is to investigate the association between social isolation, loneliness, and the risk of type 2 diabetes mellitus (T2DM). Methods: 423,503 UK adults from the UK Biobank (UKB) and 13,800 Chinese adults from the China Health and...

Pancreatic cancer (PC) is a malignant tumor with insidious clinical manifestations and dismal prognosis. Emerging reports have demonstrated that circRNAs exert pivotal biological function in PC. Here, we investigated the crucial biological role and underlying regulatory mechanisms of differentially expressed circ_103809 in PC. In this study, hsa_ci...

Background Intracranial aneurysms (IAs) pose a significant and intricate challenge. Elucidating the interplay between DNA methylation and IA pathogenesis is paramount to identify potential biomarkers and therapeutic interventions. Methods We employed a comprehensive bioinformatics investigation of DNA methylation in IA, utilizing a transcriptomics...

Biological agents known as anti-tumor necrosis factor (TNF) drugs are frequently utilized in the treatment of inflammatory bowel disease (IBD). In this study, we analyzed the shared processes of pyroptosis in Ulcerative colitis (UC) and Crohn's disease (CD), as well as explored the correlation between the burden of pyroptosis and the results of ant...

Context Environmental heterogeneity across species distributions creates diverse conditions that individual populations encounter. As a result, local selective pressures vary across a species range, leading to individual populations becoming locally adapted and therefore better suited to their environment. Recent advances in genomics and bioinforma...

Background Alzheimer’s disease (AD) represents profound degenerative conditions of the brain that cause significant deterioration in memory and cognitive function. Despite extensive research on the significant contribution of lipid metabolism to AD progression, the precise mechanisms remain incompletely understood. Hence, this study aimed to identi...

The use of short-read metabarcoding for classifying microeukaryotes is challenged by the lack of comprehensive 18S rRNA reference databases. While recent advances in high-throughput long-read sequencing provide the potential to greatly increase the phylogenetic coverage of these databases, the performance of different sequencing technologies and su...

Asthma is a “common chronic disorder that affects the lungs causing variable and recurring symptoms like repeated episodes of wheezing, breathlessness, chest tightness and underlying inflammation. The interaction of these features of asthma determines the clinical manifestations and severity of asthma and the response to treatment" [cited from: Nat...

Background It is now understood that APOBEC3 family proteins (A3s) are essential in tumor progression, yet their involvement in tumor immunity and stemness across diverse cancer types remains poorly understood. Methods In the present study, comprehensive genome-wide statistical and bioinformatic analyses were conducted to elucidate A3 family expre...

The biofilm lifestyle is critical for bacterial survival and proliferation in the fluctuating marine environment. Cyclic diguanylate (c-di-GMP) is a key second messenger during bacterial adaptation to various environmental signals, which has been identified as a master regulator of biofilm formation. However, little is known about whether and how c...

In higher organisms, individual cells respond to signals and perturbations by epigenetic regulation or transcriptional adaptation. However, in addition to shifting the expression level of individual genes, the adaptive response of cells can also lead to shifts in the proportions of different cell types. Recent methods such as scRNA-seq allow for th...

Many important aspects of biological knowledge at the molecular level can be represented by pathways . Through their analysis, we gain mechanistic insights and interpret lists of interesting genes from experiments (usually omics and functional genomic experiments). As a result, pathways play a central role in the development of bioinformatics metho...

Recent studies have found a link between deep vein thrombosis and inflammatory reactions. N6-methyladenosine (m6A), a crucial element in immunological regulation, is believed to contribute to the pathophysiology of venous thromboembolism (VTE). However, how the m6A-modified immune microenvironment is involved in VTE remains unclear. In the present...

Targeting peptides or presequences are N-terminal extensions of proteins that encode information about their cellular localization. They include signal peptides (SP), which target proteins to the endoplasmic reticulum, and transit peptides (TP) directing proteins to the organelles of endosymbiotic origin: chloroplasts and mitochondria. TPs were hyp...

En el estudio del cáncer, los perfiles de expresión génica tienen gran relevancia dado que permiten conocer la actividad de genes de interés en el tejido en análisis. El avance biotecnológico y la disminución de costos de secuenciación han permitido producir grandes volúmenes de datos moleculares incluidos los perfiles de expresión génica, que pued...

Due to the development of sequence technology and decreased cost, many whole genome sequences have been obtained. As a result, extensive genetic variations have been discovered from many populations and germplasms to understand the genetic diversity of soybean (Glycine max [L.] Merr.). However, assessing the quality of variation is essential becaus...

Renal hypouricemia (RHUC) is a rare hereditary disorder caused by loss-of-function mutations in the SLC22A12 (RHUC type 1) or SLC2A9 (RHUC type 2) genes, encoding urate transporters URAT1 and GLUT9, respectively, that reabsorb urate in the renal proximal tubule. The characteristics of this disorder are low serum urate levels, high renal fractional...

The term new genomic techniques (NGTs), is an umbrella term to describe a variety of techniques that can alter the genetic material of an organism and that have emerged or have been developed since 2001, when the existing genetically modified organism (GMO) legislation was adopted. The analytical framework to detect GMOs in Europe is a established...

We published a paper in BMC Bioinformatics comprehensively evaluating the performance of structural variation (SV) calling with long-read SV detection methods based on simulated error-prone long-read data under various sequencing settings. Recently, C.Y.T. et al. wrote a correspondence claiming that the performance of NanoVar was underestimated in...

As Proteínas são cadeias de aminoácidos com capacidade de regular a maioria das atividades biológicas nos organismos. A pesquisa de proteínas em bioinformática surge com a necessidade de dar resposta aos problemas de Predição da Estrutura de Proteínas (PPEP), pois conhecendo a estrutura de uma proteína é possível identificar o tipo de atividade que...

Myocardial infarction (MI) is a leading cause of mortality. To better understand its molecular and cellular mechanisms, we used bioinformatic tools and molecular experiments to explore the pathogenesis and prognostic markers. Differential gene expression analysis was conducted using GSE60993 and GSE66360 datasets. Hub genes were identified through...

We present CCPlotR—an R package that generates visualisations of cell-cell interactions. CCPlotR is designed to work with the output of tools that predict cell-cell interactions from single-cell gene expression data and requires only a table of predicted interactions as input. The package can generate a comprehensive set of publication-ready figure...

Acidithiobacillus caldus plays an important role in bioleaching of low-grade metal ore. It can promote the release of heavy metals in mining-associated habitats and survive in high concentrations of heavy metals. Functions of glutathione reductase (GR) in cell defense against reactive oxygen species caused by heavy metals have been elucidated in so...

A recent paper by Jiang et al. in BMC Bioinformatics presented guidelines on long-read sequencing settings for structural variation (SV) calling, and benchmarked the performance of various SV calling tools, including NanoVar. In their simulation-based benchmarking, NanoVar was shown to perform poorly compared to other tools, mostly due to low SV re...

Although obesity in the domestic dog ( Canis lupus familiaris) is known to decrease well-being and shorten lifespan, the genetic risk variants associated with canine obesity remain largely unknown. In our study, which focused on the obesity-prone Labrador Retriever breed, we conducted a genome-wide analysis to identify structural variants linked to...

Objective We aim to use the microRNA (miRNA, micro-ribonucleic acid) data of lung cancer tissues to establish a miRNA biomarker database for lung cancer that can be used for marker screening and analysis of lung cancer prognosis. Methods We obtained lung cancer-related data from The Cancer Genome Atlas (TCGA) and analyzed the miRNA expression prof...

The JADE family comprises three members encoded by individual genes and roles for these proteins have been identified in chromatin remodeling, cell cycle progression, cell regeneration and the DNA damage response. JADE family members, and in particular JADE2 have not been studied in any great detail in cancer. Using a series of standard biological...

Background Osteoarthritis (OA) is the most common chronic joint disease and how ferroptosis contributes to OA has garnered much attention recently. Bioinformatics promoted the discovery of ferroptosis-related biomarkers for OA. But since OA is a whole-joint disease, sensitive biomarkers for OA are still limited. We herein focused on subchondral bon...

水稻 (Oryza sativa L.) 是主要的粮食作物，也是单子叶植物研究的模式植物。面对日益严峻的环境和人口压力，培育高产、优质、环境适性强的水稻品种是解决当前粮食安全问题的有效途径。随着多组学技术的快速发展，积累了海量的水稻遗传育种相关的数据。生物信息数据库和在线分析工具是存储这些数据的载体，用来整合、可视化和共享数据，并为数据的深入挖掘和利用提供工具，从而为育种决策提供数据支撑。本综述系统梳理了近二十年来开发的水稻生物信息数据库和在线分析工具，并基于内置数据集和功能对它们进行了分类和总结。最后，讨论了现有的水稻生物信息数据库和在线分析工具的问题与不足，并对它们在大数据和人工智能时代的发展方向进行了展望。 Rice (Oryza sativa L.) is both a major...

Artificial intelligence (AI) with machine learning tools are used to search, store, and analyze medical data to benefit both phy�sicians and the health of patients in various ways. With the advancement in machine learning algorithms and bioinformatics techniques, AI has become an essential part of modern healthcare society. AI algorithms and deep...

Absent in animals and with only seven enzymatic reactions toward the synthesis of chorismate and aromatic amino acids, the shikimate pathway is a crucial target for developing antimicrobial agents and herbicides. Although this pathway has been extensively studied in microorganisms related to human health, it reveals complexities in plants, as it ta...