IntroductionWe studied the predictive and prognostic influences of hypertension (HT), type 2 diabetes (T2D), weight, and p53 mutations in metastatic colorectal cancer (CRC) patients.Patients and methodsT2D was diagnosed according to the ADA criteria.... Read More
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Hypertension, type 2 diabetes, obesity, and p53 mutations negatively correlate with metastatic colorectal cancer patients’ survival
- Frontiers in Medicine
- VOL. 10
on Jan 23, 2023
- P53 Mutated
- Metastatic CRC Patients
- P53 Mutations
- T2D
- Occurrence Of P53 Mutations
- BMI
- More +
A large scale 16S ribosomal RNA gene amplicon dataset of hand, foot and mouth patients and healthy individuals
- Scientific Data
- VOL. 10
on Jan 21, 2023
- HFMD
- HFMD Patient
- ASV
- Genus Prevotella
- Table Generation
- Large Dataset Of Patients
- More +
There is evidence linking hand, foot and mouth disease (HFMD) to gut microbiota dysbiosis, and this relationship was corroborated in a large HFMD patient population in our previous study. Here, we present a bacterial 16S rRNA gene dataset from faecal... Read More
Benchmarking of two bioinformatic workflows for the analysis of whole-genome sequenced Staphylococcus aureus collected from patients with suspected sepsis
- BMC Infectious Diseases
- VOL. 23
on Jan 20, 2023
- Phenotypic AST
- Western Region Of Sweden
- Bioinformatic Workflows
- Septic Shock In Adults
- AST
- AST Results
- More +
BackgroundThe rapidly growing area of sequencing technologies, and more specifically bacterial whole-genome sequencing, could offer applications in clinical microbiology, including species identification of bacteria, prediction of genetic antibiotic ... Read More
Cancer detection in clinical practice and using blood‐based liquid biopsy: A retrospective audit of over 350 dogs
- Journal of Veterinary Internal Medicine
on Jan 20, 2023
- Liquid Biopsy
- Wellness Visit
- Detection In Clinical Practice
- Definitive Cancer Diagnosis
- Cancer Detection
- Onset Of Clinical Signs
- More +
Guidelines-driven screening protocols for early cancer detection in dogs are lacking, and cancer often is detected at advanced stages. To examine how cancer typically is detected in dogs and whether the addition of a next-generation sequencing-based ... Read More
MedMNIST v2 - A large-scale lightweight benchmark for 2D and 3D biomedical image classification
- Scientific Data
- VOL. 10
on Jan 19, 2023
- 2D Images
- Biomedical Image
- Lightweight 2D
- Biomedical Image Analysis
- Large-scale Collection Of Images
- 2D Image Classification
- More +
We introduce MedMNIST v2, a large-scale MNIST-like dataset collection of standardized biomedical images, including 12 datasets for 2D and 6 datasets for 3D. All images are pre-processed into a small size of 28 × 28 (2D) or 28 × 28 × 28 (3D) with the ... Read More
Whole genome sequencing provides comprehensive genetic testing in childhood B-cell acute lymphoblastic leukaemia
- Leukemia
on Jan 19, 2023
- B-ALL
- Childhood B-ALL
- WGS Results
- WGS
- Key Genetic Changes
- Recurrent Genetic Abnormalities
- More +
AbstractChildhood B-cell acute lymphoblastic leukaemia (B-ALL) is characterised by recurrent genetic abnormalities that drive risk-directed treatment strategies. Using current techniques, accurate detection of such aberrations can be challenging, due... Read More
Best Practices in Designing, Sequencing, and Identifying Random DNA Barcodes
- Journal of Molecular Evolution
on Jan 18, 2023
- UMIs
- Raw Sequencing Reads
- Barcode Design
- Barcode Data
- Preparation Of Sequencing Libraries
- DNA Barcodes
- More +
AbstractRandom DNA barcodes are a versatile tool for tracking cell lineages, with applications ranging from development to cancer to evolution. Here, we review and critically evaluate barcode designs as well as methods of barcode sequencing and initi... Read More
Genome-wide measurement of DNA replication fork directionality and quantification of DNA replication initiation and termination with Okazaki fragment sequencing
- Nature Protocols
on Jan 18, 2023
- Replication Termination
- Replication In Mammalian Cells
- Epigenome Maintenance
- Okazaki Fragment
- Replication Program
- Location Of Initiation
- More +
Studying the dynamics of genome replication in mammalian cells has been historically challenging. To reveal the location of replication initiation and termination in the human genome, we developed Okazaki fragment sequencing (OK-seq), a quantitative ... Read More
JBrowse Jupyter: A Python interface to JBrowse 2
- Bioinformatics
on Jan 17, 2023
- Web-based Genome Browsers
- Jupyter Notebooks
- Python Programming
- End Of Pipelines
- Source Code
- Rapid Cycle
- More +
Abstract Motivation JBrowse Jupyter is a package that aims to close the gap between Python programming and genomic visualization. Web-based genome browsers are routinely used for publishing and insp... Read More
Nano‐RECall provides an integrated pipeline for HIV ‐1 drug resistance testing from Oxford Nanopore sequence data
- Tropical Medicine & International Health
on Jan 13, 2023
- ONT Sequencing
- ONT
- HIV Drug Resistance
- Stanford HIV Drug Resistance Database
- Sanger Sequencing
- HIV Drug Resistance Mutations
- More +
Low-capital-layout sequencing options from Oxford Nanopore Technologies (ONT) could assist in expanding HIV drug resistance testing to resource-limited settings. HIV drug resistance mutations often occur as mixtures, but current ONT pipelines provide... Read More
Next Generation Sequencing for the Analysis of Parvovirus B19 Genomic Diversity
- Viruses
- VOL. 15
on Jan 12, 2023
- Application Of NGS Techniques
- Sequence Heterogeneity
- NGS
- Analysis Of Sequence Variation
- NGS Analysis
- Parvovirus B19
- More +
Parvovirus B19 (B19V) is a ssDNA human virus, responsible for an ample range of clinical manifestations. Sequencing of B19V DNA from clinical samples is frequently reported in the literature to assign genotype (genotypes 1–3) and for finer molecular ... Read More
First proficiency testing for NGS ‐based and combined NGS ‐ and FISH ‐based detection of FGFR2 fusions in intrahepatic cholangiocarcinoma
- The Journal of Pathology: Clinical Research
on Jan 12, 2023
- FISH
- Round Robin Test
- Detection Of Fusions
- NGS
- Unknown Fusion Partners
- Academic Pathology Departments
- More +
Intrahepatic cholangiocarcinoma harbours druggable genetic lesions including FGFR2 gene fusions. Reliable and accurate detection of these fusions is becoming a critical component of the molecular work-up, but real-world data on the performance of flu... Read More
Software update: Interpreting killer‐cell immunoglobulin‐like receptors from whole genome sequence data with PING
- HLA
on Jan 10, 2023
- Bioinformatic Pipeline
- WGS Data
- Genome Sequence Data
- KIR
- Sequencing Data
- WGS
- More +
Here, we demonstrate improvements to our bioinformatic pipeline, PING, which provides high-resolution genotyping of killer-cell immunoglobulin-like receptor (KIR) sequencing data, that expand the method to provide KIR interpretation from whole genome... Read More
Dimorphic glioblastoma with glial and epithelioid phenotypes: Clonal evolution and immune selection
- Frontiers in Neurology
- VOL. 13
on Jan 10, 2023
- Epithelioid Glioblastoma
- Tumor Immune Microenvironment
- Tumor Cell Content
- Typical Glioblastoma
- Epithelioid Phenotypes
- Mutations In PTEN
- More +
PurposeEpithelioid glioblastoma is an unusual histologic variant of malignant glioma. The present study investigates both the genomic and transcriptomic determinants that may promote the development of this tumor.MethodsWhole-exome sequencing (WES) a... Read More
Improving Protein–Ligand Interaction Modeling with cryo-EM Data, Templates, and Deep Learning in 2021 Ligand Model Challenge
- Biomolecules
- VOL. 13
on Jan 9, 2023
- cryo-EM Maps
- Protein Ligand Interaction
- cryo-EM Data
- cryo-EM Density Maps
- Prior Structural Information
- Deep Learning
- More +
Elucidating protein–ligand interaction is crucial for studying the function of proteins and compounds in an organism and critical for drug discovery and design. The problem of protein–ligand interaction is traditionally tackled by molecular docking a... Read More
Bioinformatics and In silico approaches to identify novel biomarkers and key pathways for cancers that are linked to the progression of female infertility: A comprehensive approach for drug discovery
- PLOS ONE
- VOL. 18
on Jan 6, 2023
- FI
- MCC
- Hub Proteins
- Carcinogenic Risk Factors
- EC
- TC
- More +
Despite modern treatment, infertility remains one of the most common gynecologic diseases causing severe health effects worldwide. The clinical and epidemiological data have shown that several cancerous risk factors are strongly linked to Female Infe... Read More
Association between inflammation, lipopolysaccharide binding protein, and gut microbiota composition in a New Hampshire Bhutanese refugee population with a high burden of type 2 diabetes
- Frontiers in Nutrition
- VOL. 9
on Jan 6, 2023
- LBP
- Gut Microbiota Composition
- Bhutanese Refugee
- Glycemic Status
- Gut Microbiome Alpha Diversity
- Gut Microbiota
- More +
IntroductionSouth Asian refugees experience a high risk of obesity and diabetes yet are often underrepresented in studies on chronic diseases and their risk factors. The gut microbiota and gut permeability, as assessed through circulating lipopolysac... Read More
Lung Cancer Gene Regulatory Network of Transcription Factors Related to the Hallmarks of Cancer
- Current Issues in Molecular Biology
- VOL. 45
on Jan 5, 2023
- Regulatory Network Of Transcription Factors
- Transcriptional Regulatory Network
- Lung Cancer
- Transcription Factors
- Lung Cancer Patients
- Type Of Lung Cancer
- More +
The transcriptomic analysis of microarray and RNA-Seq datasets followed our own bioinformatic pipeline to identify a transcriptional regulatory network of lung cancer. Twenty-six transcription factors are dysregulated and co-expressed in most of the ... Read More
Abstract IA025: Utilizing Visium spatial transcriptomics to investigate prostate cancer disparity in men of African descent
- Cancer Epidemiology, Biomarkers & Prevention
- VOL. 32
on Jan 1, 2023
- Men Of African Descent
- Spatial Transcriptomics
- Prostate Cancer
- Cause Of Death
- Mortality Rate Of Prostate Cancer
- SEER
- More +
Abstract People of African descent suffer more from cancer compared to other racial groups in terms of morbidity and mortality. Surveillance, Epidemiology, and End Results (SEER) reports Black men and women to have the highest diagnose... Read More
UPP2: fast and accurate alignment of datasets with fragmentary sequences
- Bioinformatics
- VOL. 39
on Jan 1, 2023
- Bioinformatics Pipelines
- Ensemble Of Hidden Markov Models
- Accurate Alignments
- Large Datasets
- Basic Step
- Full-length Sequences
- More +
Abstract Motivation Multiple sequence alignment (MSA) is a basic step in many bioinformatics pipelines. However, achieving highly accurate alignments on large datasets, especially those with sequenc... Read More