Chronic mesenteric ischemia (CMI) is a debilitating condition arising from intestinal malperfusion from mesenteric artery stenosis or occlusion. Mesenteric revascularization has been the standard of care but can result in substantial morbidity and mo... Read More
Bioinformatics Research Articles
Overview
5661 Articles
Published in last 50 years
Related Topics
Articles published on Bioinformatics
Journals
Select journals
Duration
Select duration
4159 Search results
Sort by Recency
Chronic mesenteric ischemia-induced intestinal dysbiosis resolved after revascularization
- Journal of Vascular Surgery Cases, Innovations and Techniques
- VOL. 9
on Jun 1, 2023
- CMI
- Number Of Operational Taxonomic Units
- Mesenteric Artery Stenosis
- Permutational Analysis Of Variance
- Intestinal Dysbiosis
- Stool Samples
- More +
Identification and analysis of the DNA content of small extracellular vesicles isolated from Leishmania parasites
- STAR Protocols
- VOL. 4
on Jun 1, 2023
- Ploidy Changes
- EVs
- DNA Content
- Pipeline For Visualization
- Content Of Vesicles
- Identification Of Content
- More +
Here, we focus on Leishmania extracellular vesicles (EVs) and their DNA content, detailing a protocol for the isolation of these nanoparticles and their subsequent genomic characterization. We describe a robust and comprehensive approach for obtainin... Read More
Minimal/Measurable Residual Disease Monitoring in Patients with Lymphoid Neoplasms by High-Throughput Sequencing of the T-Cell Receptor
- The Journal of Molecular Diagnostics
- VOL. 25
on Jun 1, 2023
- Burden In Patients
- T-cell Malignancies
- Disease Monitoring In Patients
- Custom Bioinformatics Pipeline
- Residual Disease Analysis
- Residual Disease Monitoring
- More +
High-throughput sequencing of the T-cell receptor beta (TRB) and gamma (TRG) loci is increasingly utilized due to its high sensitivity, specificity, and versatility in the diagnosis of various T-cell malignancies. Application of these technologies fo... Read More
Supervised machine learning classifies inflammatory bowel disease patients by subtype using whole exome sequencing data
- Journal of Crohn's and Colitis
on May 19, 2023
- Linear Support Vector Classifier
- CD
- UC
- Performing ML Model
- Supervised ML Method
- MethodsWhole Exome Sequencing
- More +
Abstract Background Inflammatory bowel disease (IBD) is a chronic inflammatory disorder with two main subtypes: Crohn’s disease (CD) and Ulcerative Colitis (UC). Prompt subtype diagnosis enables the... Read More
Census of exposed aggregation-prone regions in proteomes
- Briefings in Bioinformatics
on May 17, 2023
- Bioinformatics Pipeline
- Protein Aggregation
- Aggregation-prone Regions
- Large-scale Bioinformatics Analysis
- Presence Of Ears
- Linear Motifs
- More +
Abstract Loss of solubility usually leads to the detrimental elimination of protein function. In some cases, the protein aggregation is also required for beneficial functions. Given the duality of this phenomenon, it remains a fundamen... Read More
Surveillance of carbapenem-resistant organisms using next-generation sequencing
- Frontiers in Public Health
- VOL. 11
on May 15, 2023
- AMR Bacteria
- Differences In SNPs
- SNPs
- CRO
- NGS
- AMR
- More +
The genomic data generated from next-generation sequencing (NGS) provides nucleotide-level resolution of bacterial genomes which is critical for disease surveillance and the implementation of prevention strategies to interrupt the spread of antimicro... Read More
Spatial metabolomics reveals glycogen as an actionable target for pulmonary fibrosis
- Nature Communications
- VOL. 14
on May 13, 2023
- Spatial Metabolomics
- Human Lung Diseases
- Pulmonary Fibrosis
- Pulmonary Fibrosis Progression
- N-linked Glycan
- Metabolic Channeling
- More +
Matrix assisted laser desorption/ionization imaging has greatly improved our understanding of spatial biology, however a robust bioinformatic pipeline for data analysis is lacking. Here, we demonstrate the application of high-dimensionality reduction... Read More
Development and Validation of a High-Throughput Sequencing Test for Mitogenome and rDNA Assembly and Annotation, and Its Use in Support of Nematode Identification of Regulatory Concern
- PhytoFrontiersTM
on May 11, 2023
- HTS Test
- Annotation Of Mitochondrial Genomes
- Use Of Sequence Data
- Reliable Species Identification
- Sanger Sequencing
- Terms Of Individuals
- More +
Nematoda is a diverse phylum, and representatives are found in most habitats, including in and on animals and plants. Nematodes are regarded as the most abundant group in terms of individuals in marine and terrestrial sediments. Plant-parasitic nema... Read More
Downregulation of lncRNA SNHG1 in hypoxia and stem cells is associated with poor disease prognosis in gliomas
- Cell Cycle
- VOL. 22
on May 3, 2023
- Prognostic Biomarkers
- Glioma Stem Cells
- Outcomes In Gliomas
- Hypoxic Tumor Microenvironment
- HRE
- SNHG1 Expression
- More +
ABSTRACT Gliomas are brain tumors associated with high morbidity, relapse and lethality despite improvement in therapeutic regimes. The hypoxic tumor microenvironment is a key feature associated with such poor outcomes in gliomas. The Hypoxia Inducib... Read More
Draft genome of clinical isolate Salmonella enterica Typhimurium ms204 from Odisha, India, reveals multi drug resistance and decreased virulent gene expression
- Gene
- VOL. 863
on May 1, 2023
- Bioinformatics Pipeline
- SPI
- Pathogenic Island
- Gastroenteritis Patients
- Single Plasmid
- Draft Genome
- More +
Salmonellosis, a food-borne illnesses caused by enteropathogenic bacterium Salmonella spp., is a continuous concern in both developed and developing countries. This study was carried out to perform an in-depth examination of an MDR Salmonella strain ... Read More
Using low-coverage whole genome sequencing (genome skimming) to delineate three introgressed species of buffalofish (Ictiobus)
- Molecular Phylogenetics and Evolution
- VOL. 182
on May 1, 2023
- Bioinformatics Pipeline
- Genome Skimming
- Ictiobus Cyprinellus
- Ictiobus Bubalus
- Ictiobus Niger
- UCEs
- More +
Consumption of buffalofish has been sporadically associated with Haff disease-like illnesses involving sudden onset muscle pain and weakness due to skeletal muscle rhabdomyolysis, but determination of precisely which species are associated with these... Read More
First Whole-Genome Sequence and Flow Cytometry Genome Size Data for the Lichen-Forming Fungus Ramalina farinacea (Ascomycota)
- Genome Biology and Evolution
- VOL. 15
on May 1, 2023
- Bioinformatic Pipelines
- Genome Size
- Lichen-forming Fungus
- Lichen Thalli
- Coefficients Of Variation
- Accurate Size Measurements
- More +
Abstract Lichen-forming fungi are a diverse and ecologically important group of obligate mutualistic symbionts. Due to difficulties with maintaining them in culture and their extremely slow growth, lichenologists are increasingly optin... Read More
Abstract A22: Complete mutation concordance with amplicon-based NGS between peripheral blood and bone marrow at 0.5% VAF threshold
- Blood Cancer Discovery
- VOL. 4
on May 1, 2023
- Complete Concordance
- BM Samples
- VAF
- VAF Threshold
- PPA
- Amplicon-based NGS
- More +
Abstract Background: Acute myeloid leukemia (AML) is a hematological malignancy characterized by genomic heterogeneity throughout disease progression and between patients. Traditionally, both multiparameter flow cytometry (MFC) and nex... Read More
Accurate subspecies-level identification of clinically significant Mycobacterium avium and Mycobacterium intracellulare by whole-genome sequencing
- Journal of Microbiological Methods
- VOL. 208
on May 1, 2023
- MAC Isolates
- MAC
- Clinical Isolates
- Subspecies Identification
- MAC Infections
- Lower Respiratory Tract Infections
- More +
Whole genome sequencing (WGS) of Mycobacterium avium complex (MAC) isolates in the clinical laboratory setting allows for rapid and reliable subspecies identification of a closely related complex of human pathogens. We developed a bioinformatics pipe... Read More
Phase-specific signatures of wound fibroblasts and matrix patterns define cancer-associated fibroblast subtypes
- Matrix Biology
- VOL. 119
on May 1, 2023
- Late Wound
- Early Wound
- Time-course Of Healing
- RUNX2 Transcription Factor
- Skin Cancer
- CAF
- More +
Healing wounds and cancers present remarkable cellular and molecular parallels, but the specific roles of the healing phases are largely unknown. We developed a bioinformatics pipeline to identify genes and pathways that define distinct phases across... Read More
The Mighty NUMT: Mitochondrial DNA Flexing Its Code in the Nuclear Genome
- Biomolecules
- VOL. 13
on Apr 27, 2023
- NUMTs
- VAF
- Low Variant Allele Frequency
- False Positive Variants
- mtDNA Copy Number
- Nuclear Genome
- More +
Nuclear-mitochondrial DNA segments (NUMTs) are mitochondrial DNA (mtDNA) fragments that have been inserted into the nuclear genome. Some NUMTs are common within the human population but most NUMTs are rare and specific to individuals. NUMTs range in ... Read More
Detection of multiple types of cancer driver mutations using targeted RNA sequencing in nonsmall cell lung cancer
- Cancer
on Apr 25, 2023
- DNA Panel Sequencing
- DNA Panel
- RNA Panel
- Paraffin-embedded Samples
- MET Exon 14-skipping Mutations
- Multiple Types Of Mutations
- More +
DNA-based next-generation sequencing has been widely used in the selection of target therapies for patients with nonsmall cell lung cancer (NSCLC). RNA-based next-generation sequencing has been proven to be valuable in detecting fusion and exon-skipp... Read More
Non-invasive prenatal diagnosis of single gene disorders with enhanced relative haplotype dosage analysis for diagnostic implementation
- PLOS ONE
- VOL. 18
on Apr 24, 2023
- RHDO
- Prenatal Diagnosis For Single-gene Disorders
- Diagnosis Of Single Gene Disorders
- F8 Mutations
- Concordance Score
- Non-invasive Diagnosis
- More +
Non-invasive prenatal diagnosis of single-gene disorders (SGD-NIPD) has been widely accepted, but is mostly limited to the exclusion of either paternal or de novo mutations. Indeed, it is still difficult to infer the inheritance of the maternal allel... Read More
A novel SNP panel developed for targeted genotyping-by-sequencing (GBS) reveals genetic diversity and population structure of Musa spp. germplasm collection
- Molecular Genetics and Genomics
on Apr 21, 2023
- SNP Panel
- DAPC
- Germplasm Collection
- Heterozygous Calls
- Marker-based Approach
- Germplasm Management
- More +
The Philippines is situated in the geographic region regarded as the center of diversity of banana and its wild relatives (Musa spp.). It holds the most extensive collection of B-genome germplasm in the world along with A-genome groups and several na... Read More
A Core Genome Multilocus Sequence Typing Scheme for Proteus mirabilis.
- Biomedical and environmental sciences : BES
- VOL. 36
on Apr 20, 2023
- cgMLST Scheme
- CGs
- Core Genome Multilocus Sequence Typing
- Unique Antibiotic Resistance Genes
- Severe Urinary Tract Infections
- Regional Distribution Characteristics
- More +
A core genome multilocus sequence typing (cgMLST) scheme to genotype and identify potential risk clonal groups (CGs) in Proteus mirabilis. In this work, we propose a publicly available cgMLST scheme for P. mirabilis using chewBBACA. In total 72 compl... Read More