4,282 results match your criteria incorporating genes


Hapo-G, haplotype-aware polishing of genome assemblies with accurate reads.

NAR Genom Bioinform 2021 Jun 3;3(2):lqab034. Epub 2021 May 3.

Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France.

Single-molecule sequencing technologies have recently been commercialized by Pacific Biosciences and Oxford Nanopore with the promise of sequencing long DNA fragments (kilobases to megabases order) and then, using efficient algorithms, provide high quality assemblies in terms of contiguity and completeness of repetitive regions. However, the error rate of long-read technologies is higher than that of short-read technologies. This has a direct consequence on the base quality of genome assemblies, particularly in coding regions where sequencing errors can disrupt the coding frame of genes. Read More

View Article and Full-Text PDF

Recovering Spatially-Varying Cell-Specific Gene Co-expression Networks for Single-Cell Spatial Expression Data.

Front Genet 2021 26;12:656637. Epub 2021 Apr 26.

Institute of Statistics and Big Data, Renmin University of China, Beijing, China.

Recent advances in single-cell technologies enable spatial expression profiling at the cell level, making it possible to elucidate spatial changes of cell-specific genomic features. The gene co-expression network is an important feature that encodes the gene-gene marginal dependence structure and allows for the functional annotation of highly connected genes. In this paper, we design a simple and computationally efficient two-step algorithm to recover spatially-varying cell-specific gene co-expression networks for single-cell spatial expression data. Read More

View Article and Full-Text PDF

scConnect: a method for exploratory analysis of cell-cell communication based on single cell RNA sequencing data.

Bioinformatics 2021 May 11. Epub 2021 May 11.

Department of Neuroscience, Uppsala University, 751 24 Uppsala, Sweden.

Motivation: Cell to cell communication is critical for all multicellular organisms, and single cell sequencing facilitates the construction of full connectivity graphs between cell types in tissues. Such complex data structures demand novel analysis methods and tools for exploratory analysis.

Results: We propose a method to predict the putative ligand-receptor interactions between cell types from single cell RNA-sequencing data. Read More

View Article and Full-Text PDF

Effective utilisation of influence maximization technique for the identification of significant nodes in breast cancer gene networks.

Comput Biol Med 2021 Apr 18;133:104378. Epub 2021 Apr 18.

School of Computer Science and Engineering, Vellore Institute of Technology, Vellore, India. Electronic address:

Background: Identifying the most important genes in a cancer gene network is a crucial step in understanding the disease's functional characteristics and finding an effective drug.

Method: In this study, a popular influence maximization technique was applied on a large breast cancer gene network to identify the most influential genes computationally. The novel approach involved incorporating gene expression data and protein to protein interaction network to create a customized pruned and weighted gene network. Read More

View Article and Full-Text PDF

Analysis of whole genome sequenced cases and controls shows that the association of variants in , , and with late onset Alzheimer's disease is driven by linkage disequilibrium with ε2/ε3/ε4 alleles.

Authors:
David Curtis

J Neurogenet 2021 May 10:1-8. Epub 2021 May 10.

UCL Genetics Institute, University College London, London, UK.

Variants in are associated with risk of late onset Alzheimer's disease (LOAD) but the magnitude of the effect has been reported to vary across ancestries. Also, other variants in the region have been reported to show association though it has been unclear whether this was secondary to their linkage disequilibrium with the variants rs429358 and rs7412. Previous analyses of exome-sequenced samples have identified other genes in which rare variants impact risk of disease. Read More

View Article and Full-Text PDF

Bayesian integrative analysis and prediction with application to atherosclerosis cardiovascular disease.

Biostatistics 2021 May 10. Epub 2021 May 10.

Division of Biostatistics, University of Minnesota, 20 Delaware St SE, Minneapolis, MN 55455, USA.

The problem of associating data from multiple sources and predicting an outcome simultaneously is an important one in modern biomedical research. It has potential to identify multidimensional array of variables predictive of a clinical outcome and to enhance our understanding of the pathobiology of complex diseases. Incorporating functional knowledge in association and prediction models can reveal pathways contributing to disease risk. Read More

View Article and Full-Text PDF

NEM-Tar: A Probabilistic Graphical Model for Cancer Regulatory Network Inference and Prioritization of Potential Therapeutic Targets From Multi-Omics Data.

Front Genet 2021 22;12:608042. Epub 2021 Apr 22.

Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China.

Targeted therapy has been widely adopted as an effective treatment strategy to battle against cancer. However, cancers are not single disease entities, but comprising multiple molecularly distinct subtypes, and the heterogeneity nature prevents precise selection of patients for optimized therapy. Dissecting cancer subtype-specific signaling pathways is crucial to pinpointing dysregulated genes for the prioritization of novel therapeutic targets. Read More

View Article and Full-Text PDF

Development of a multiplex assay to determine the expression of mitochondrial genes in human skeletal muscle.

Exp Physiol 2021 May 7. Epub 2021 May 7.

Physical Education and Sports Sciences, University of Limerick, Limerick, Ireland.

New Findings: What is the central question of this study? Description and testing of a custom-designed multiplex gene expression assay to quantitate expression levels of a targeted group of mitochondrial genes in human skeletal muscle. What is the main finding and its importance? This study describes the development of a custom-designed GeXP multiplex assay and demonstrates the ability to accurately quantitate expression of a targeted set of mitochondrial genes in human skeletal muscle, while holding distinct methodological and practical advantages over other commonly used quantitation methods.

Abstract: Skeletal muscle is an important endocrine tissue demonstrating plasticity in response to external stimuli, including exercise and nutrition. Read More

View Article and Full-Text PDF

Protocol for a prospective, observational, deep phenotyping study on adipose epigenetic and lipidomic determinants of metabolic homoeostasis in South Asian Indians: the Indian Diabetes and Metabolic Health (InDiMeT) study.

BMJ Open 2021 May 6;11(5):e043644. Epub 2021 May 6.

Division of Nutrition, St John's National Academy of Health Sciences, Bangalore, Karnataka, India

Introduction: We describe the rationale and broad study design of the Indian Diabetes and Metabolic Health (InDiMeT) study, a new prospective, observational study incorporating extensive epigenetic (DNA methylation) and lipidomic signatures to examine their association with the dysregulation of adipose de novo lipogenesis (DNL) in South Asian Indians. The InDiMeT study aims to use a case-control design to identify genetic and modifiable-environmental-lifestyle associated determinants of (1) epigenomic (DNA methylome) dysregulation of adipose DNL in type 2 diabetes mellitus (T2DM) adipose tissue, (2) identify correlates of epigenomic (DNA methylome) dysregulation of adipose DNL in peripheral blood mononuclear cells (PBMCs) from T2DM subjects and (3) elucidate plasma lipidomic correlates of adipose DNL in T2DM that can be used as biomarkers of adipose tissue dysfunction.

Methods And Analysis: The InDiMeT study will involve recruitment of 176 normoglycaemic and T2DM individuals who will be undergoing laparoscopic surgery for clinical conditions. Read More

View Article and Full-Text PDF

Systematic interrogation of mutation groupings reveals divergent downstream expression programs within key cancer genes.

BMC Bioinformatics 2021 May 6;22(1):233. Epub 2021 May 6.

Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA.

Background: Genes implicated in tumorigenesis often exhibit diverse sets of genomic variants in the tumor cohorts within which they are frequently mutated. For many genes, neither the transcriptomic effects of these variants nor their relationship to one another in cancer processes have been well-characterized. We sought to identify the downstream expression effects of these mutations and to determine whether this heterogeneity at the genomic level is reflected in a corresponding heterogeneity at the transcriptomic level. Read More

View Article and Full-Text PDF

Group B Streptococcus chimeric capsular polysaccharides as novel multivalent vaccine candidates.

Glycoconj J 2021 May 6. Epub 2021 May 6.

GSK, Siena, Italy.

The capsular polysaccharide of the human pathogen Group B Streptococcus is a key virulence factor and vaccine candidate that induces protective antibodies when conjugated to carrier proteins. It consists of long polymeric chains of oligosaccharide repeating units, and each of the ten capsular serotypes described so far presents a unique chemical structure with distinct antigenic properties; therefore, broad protection against this pathogen could be achieved by a combination of ten glycoconjugates. Capsular polysaccharide biosynthesis and assembly follow a polymerase-dependent pathway that is widespread in encapsulated bacteria and is encoded by a polycistronic operon. Read More

View Article and Full-Text PDF

Using Genomics Feature Selection Method in Radiomics Pipeline Improves Prognostication Performance in Locally Advanced Esophageal Squamous Cell Carcinoma-A Pilot Study.

Cancers (Basel) 2021 Apr 29;13(9). Epub 2021 Apr 29.

Department of Diagnostic Radiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong.

Purpose: To evaluate the prognostic value of baseline and restaging CT-based radiomics with features associated with gene expression in esophageal squamous cell carcinoma (ESCC) patients receiving neoadjuvant chemoradiation (nCRT) plus surgery.

Methods: We enrolled 106 ESCC patients receiving nCRT from two institutions. Gene expression profiles of 28 patients in the training set were used to detect differentially expressed (DE) genes between patients with and without relapse. Read More

View Article and Full-Text PDF

Mutational landscape of chronic myeloid leukemia: more than a single oncogene leukemia.

Leuk Lymphoma 2021 May 4:1-15. Epub 2021 May 4.

Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.

The fusion gene, which causes aberrant kinase activity and uncontrolled cell proliferation, is the hallmark of chronic myeloid leukemia (CML). The development of tyrosine kinase inhibitors (TKI) that target the BCR-ABL oncoprotein has led to dramatic improvement in CML management. However, some challenges remain to be addressed in the TKI era, including patient stratification and the selection of frontline TKIs and CML progression. Read More

View Article and Full-Text PDF

Uranium accumulation and toxicokinetics in the crustacean Daphnia magna provide perspective to toxicodynamic responses.

Aquat Toxicol 2021 Jun 20;235:105836. Epub 2021 Apr 20.

Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), P.O. Box 5003, N-1432 Ås, Norway; Norwegian University of Life Sciences (NMBU), Faculty of Environmental Sciences and Natural Resource Management (MINA), P.O. Box 5003, N-1432 Ås, Norway.

The importance of incorporating kinetic approaches in order to gain information on underlying physiological processes explaining species sensitivity to environmental stressors has been highlighted in recent years. Uranium is present in the aquatic environment worldwide due to naturally occurring and anthropogenic sources, posing a potential risk to freshwater taxa in contaminated areas. Although literature shows that organisms vary widely with respect to susceptibility to U, information on toxicokinetics that may explain the variation in toxicodynamic responses is scarce. Read More

View Article and Full-Text PDF

ChrNet: A re-trainable chromosome-based 1D convolutional neural network for predicting immune cell types.

Genomics 2021 Apr 28;113(4):2023-2031. Epub 2021 Apr 28.

Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada; Department of Computer Science, University of Manitoba, Winnipeg, MB, Canada; Research Institute in Oncology and Hematology, CancerCare Manitoba, University of Manitoba, Winnipeg, MB, Canada. Electronic address:

Cells from our immune system detect and kill pathogens to protect our body against various diseases. However, current methods for determining cell types have some major limitations, such as being time-consuming and with low throughput, etc. Immune cells that are associated with cancer tissues play a critical role in revealing tumor development. Read More

View Article and Full-Text PDF

IBDDB: a manually curated and text-mining-enhanced database of genes involved in inflammatory bowel disease.

Database (Oxford) 2021 Apr;2021

School of Molecular and Cell Biology, University of the Witwatersrand, Private Bag 3, Johannesburg, Gauteng WITS-2050, South Africa.

To date, research on inflammatory bowel disease (IBD, encompassing Crohn's disease and ulcerative colitis), a chronic complex disorder, has generated a large amount of data scattered across published literature (1 06 333) listed in PubMed on 14 October 2020, and no dedicated database currently exists that catalogues information on genes associated with IBD. We aimed to manually curate 289 genes that are experimentally validated to be linked with IBD and its known phenotypes. Furthermore, we have developed an integrated platform providing information about different aspects of these genes by incorporating several resources and an extensive text-mined knowledgebase. Read More

View Article and Full-Text PDF

Toll-Like Receptor 4 Mediated Oxidized Low-Density Lipoprotein-Induced Foam Cell Formation in Vascular Smooth Muscle Cells via Src and Sirt1/3 Pathway.

Mediators Inflamm 2021 9;2021:6639252. Epub 2021 Apr 9.

Department of Vascular & Cardiology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China.

Oxidized low-density lipoprotein (oxLDL) induced a foam-cell-like phenotype of the vascular smooth muscle cells (VSMCs), leading to the inflammatory responses incorporating Toll-like receptor- (Tlr-) mediated cellular alterations. However, the role of Tlr4 in foam cell formation and underlying molecular pathways has not been comprehensively elucidated. To further investigate the mechanism, VSMCs were incubated with different doses of oxLDL, and then, the lipid, reactive oxygen species (ROS) accumulation, Tlr family genes, and the foam cell phenotype were explored. Read More

View Article and Full-Text PDF

Incidence of Gibelio Gill Hemorrhagic Disease Caused by CyHV-2 Infection Can Be Reduced by Vaccination with Polyhedra Incorporating Antigens.

Vaccines (Basel) 2021 Apr 16;9(4). Epub 2021 Apr 16.

School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China.

Encapsulation of antigens within protein microcrystals (polyhedra) is a promising approach for the stable delivery of vaccines. In this study, a vaccine was encapsulated into polyhedra against cyprinid herpesvirus II (CyHV-2). CyHV-2 typically infects gibel carp, gibelio, causing gill hemorrhagic disease. Read More

View Article and Full-Text PDF

The Development of Bacteriophage Resistance in Depends on a Complex Metabolic Adaptation Strategy.

Viruses 2021 04 10;13(4). Epub 2021 Apr 10.

Laboratory of Molecular Biology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 1855 Athens, Greece.

Lytic bacteriophages have been well documented to play a pivotal role in microbial ecology due to their complex interactions with bacterial species, especially in aquatic habitats. Although the use of phages as antimicrobial agents, known as phage therapy, in the aquatic environment has been increasing, recent research has revealed drawbacks due to the development of phage-resistant strains among Gram-negative species. Acquired phage resistance in marine has been proven to be a very complicated process utilizing biochemical, metabolic, and molecular adaptation strategies. Read More

View Article and Full-Text PDF

Proteomic Identification and Meta-Analysis in RNA-Seq de novo Assemblies.

Plants (Basel) 2021 Apr 14;10(4). Epub 2021 Apr 14.

Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa.

While proteomics has demonstrated its value for model organisms and for organisms with mature genome sequence annotations, proteomics has been of less value in nonmodel organisms that are unaccompanied by genome sequence annotations. This project sought to determine the value of RNA-Seq experiments as a basis for establishing a set of protein sequences to represent a nonmodel organism, in this case, the pseudocereal chia. Assembling four publicly available chia RNA-Seq datasets produced transcript sequence sets with a high BUSCO completeness, though the number of transcript sequences and Trinity "genes" varied considerably among them. Read More

View Article and Full-Text PDF

Next-Generation Sequencing Identifies Potential Actionable Targets in Paediatric Sarcomas.

J Pers Med 2021 Apr 3;11(4). Epub 2021 Apr 3.

Paediatric Oncology and Hematology Unit, Hospital U I P La Fe, Av. Fernando Abril Martorell, 106, 46026 Valencia, Spain.

Bone and soft-tissue sarcomas represent 13% of all paediatric malignancies. International contributions to introduce next-generation sequencing (NGS) approaches into clinical application are currently developing. We present the results from the Precision Medicine program for children with sarcomas at a reference centre. Read More

View Article and Full-Text PDF

Toxicity, inflammatory and antioxidant genes expression, and physiological changes of green synthesis silver nanoparticles on Nile tilapia (Oreochromis niloticus) fingerlings.

Comp Biochem Physiol C Toxicol Pharmacol 2021 Apr 26;247:109068. Epub 2021 Apr 26.

Animal and Fish Production Department, College of Agricultural and Food Sciences, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia; Fish and Animal Production Department, Faculty of Agriculture (Saba Basha), Alexandria University, 21531 Alexandria, Egypt. Electronic address:

The rapid increase of incorporating silver nanoparticles (Ag-NPs) in different anthropogenic and industrial activities increased the discharge of these particles in the aquatic ecosystem. The environmental impact of Ag-NPs, especially the green synthesized is still not completely understood on fish. Therefore, this study aimed to investigate the effects of exposure to graded series of starch-mediated Ag-NPs at levels of 0, 3. Read More

View Article and Full-Text PDF

Predicting gene phenotype by multi-label multi-class model based on essential functional features.

Mol Genet Genomics 2021 Apr 29. Epub 2021 Apr 29.

School of Life Sciences, Shanghai University, Shanghai, 200444, People's Republic of China.

Phenotype is one of the most significant concepts in genetics, which is used to describe all the characteristics of a research object that can be observed. Considering that phenotype reflects the integrated features of genotype and environment factors, it is hard to define phenotype characteristics, even difficult to predict unknown phenotypes. Restricted by current biological techniques, it is still quite expensive and time-consuming to obtain sufficient structural information of large-scale phenotype-associated genes/proteins. Read More

View Article and Full-Text PDF

Australian bush medicines harbour diverse microbial endophytes with broad-spectrum antibacterial activity.

J Appl Microbiol 2021 Apr 27. Epub 2021 Apr 27.

School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia.

Aims: Microbial endophytes produce specialized metabolites, including antibiotics and other compounds of pharmaceutical and agricultural value. This study aimed to investigate the diversity and bioactivity of endophytes from medicinal plants used by the Dharawal People of Gamay (Botany Bay), Australia.

Methods And Results: Of the 48 endophytes isolated, 19 tested positive for polyketide synthase or non-ribosomal peptide synthetase genes via a PCR incorporating degenerate primers. Read More

View Article and Full-Text PDF

Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences.

Environ Microbiome 2020 May 18;15(1):11. Epub 2020 May 18.

Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.

Background: Sequencing of 16S rRNA genes has become a powerful technique to study microbial communities and their responses towards changing environmental conditions in various ecosystems. Several tools have been developed for the prediction of functional profiles from 16S rRNA gene sequencing data, because numerous questions in ecosystem ecology require knowledge of community functions in addition to taxonomic composition. However, the accuracy of these tools relies on functional information derived from genomes available in public databases, which are often not representative of the microorganisms present in the studied ecosystem. Read More

View Article and Full-Text PDF

Controlling for cellular heterogeneity using single-cell deconvolution of gene expression reveals novel markers of colorectal tumors exhibiting microsatellite instability.

Oncotarget 2021 Apr 13;12(8):767-782. Epub 2021 Apr 13.

Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA.

Approximately 15% of colorectal cancer (CRC) cases present with high levels of microsatellite instability (MSI-H). Bulk RNA-sequencing approaches have been employed to elucidate transcriptional differences between MSI-H and microsatellite stable (MSS) CRC tumors. These approaches are frequently confounded by the complex cellular heterogeneity of tumors. Read More

View Article and Full-Text PDF

Epicardial placement of human MSC-loaded fibrin sealant films for heart failure: preclinical efficacy and mechanistic data.

Mol Ther 2021 Apr 20. Epub 2021 Apr 20.

William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK. Electronic address:

Mesenchymal stromal cell (MSC) transplantation has been investigated as an advanced treatment of heart failure; however, further improvement of the therapeutic efficacy and mechanistic understanding are needed. Our previous study has reported that epicardial placement of fibrin sealant films incorporating rat amniotic membrane-derived (AM)-MSCs (MSC-dressings) could address limitations of traditional transplantation methods. To progress this finding toward clinical translation, this current study aimed to examine the efficacy of MSC-dressings using human AM-MSCs (hAM-MSCs) and the underpinning mechanism for myocardial repair. Read More

View Article and Full-Text PDF

Molecular Pathology of Urothelial Carcinoma.

Hum Pathol 2021 Apr 19. Epub 2021 Apr 19.

Department of Pathology and Laboratory Medicine; Department of Urology, Indiana University School of Medicine, Indianapolis, IN, USA. Electronic address:

The current personalized oncology era has witnessed significant efforts to integrate clinical, pathological, and molecular classifications. The growing need for molecular biomarkers to feed personalized oncology, together with the unprecedented wealth of knowledge on the molecular basis of bladder cancer, has led to a novel approach to this disease, incorporating molecularly generated data in clinical practice for locally advanced or metastatic disease. Translational research allows better understanding of the early events in the development of urothelial carcinoma in the urinary bladder. Read More

View Article and Full-Text PDF

Intraspecies Transcriptional Profiling Reveals Key Regulators of Candida albicans Pathogenic Traits.

mBio 2021 04 20;12(2). Epub 2021 Apr 20.

Department of Microbiology, The Ohio State University, Columbus, Ohio, USA

The human commensal and opportunistic fungal pathogen displays extensive genetic and phenotypic variation across clinical isolates. Here, we performed RNA sequencing on 21 well-characterized isolates to examine how genetic variation contributes to gene expression differences and to link these differences to phenotypic traits. adapts primarily through clonal evolution, and yet hierarchical clustering of gene expression profiles in this set of isolates did not reproduce their phylogenetic relationship. Read More

View Article and Full-Text PDF

A pilot study of differential gene expressions in patients with cough variant asthma and classic bronchial asthma.

J Asthma 2021 May 14:1-9. Epub 2021 May 14.

Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, Sichuan, P. R. China.

Background: Despite extensive exploration of asthma, the mechanism of asthma has not been fully elucidated. Cough variant asthma (CVA) is considered as precursor to classical asthma (CA). Comparative study between CA and CVA may be helpful in further understanding the pathogenesis of asthma. Read More

View Article and Full-Text PDF