Genetics

Analysis of Single Nuclei in a Microfluidic Cytometer Towards Metaphase Enrichment.

Identifying analyzable metaphase chromosomes is crucial for karyotyping, a common procedure used by clinicians to diagnose genetic disorders and some forms of cancer. This task is often laborious and time-consuming, making it essential to develop automated, efficient, and reliable methods to assist clinical technicians. In this work, an original label-free microfluidic approach to identify potenti...

Preoperative radiomics models using CT and MRI for microsatellite instability in colorectal cancer: a systematic review and meta-analysis.

OBJECTIVE: Microsatellite instability (MSI) is a novel predictive biomarker for chemotherapy and immunotherapy response, as well as prognostic indicator in colorectal cancer (CRC). The current standard for MSI identification is polymerase chain reaction (PCR) testing or the immunohistochemical analysis of tumor biopsy samples. However, tumor heterogeneity and procedure complications pose challenge...

Global intraspecific diversity of marine forests of brown macroalgae predicted by past climate conditions.

Global patterns of intraspecific genetic diversity are key to understanding evolutionary and ecological processes. However, insights into the distribu...

Emerging biomarkers for pancreatic cancer: from early detection to personalized therapy.

Pancreatic cancer (PC) remains one of the most lethal malignancies, primarily due to its poor prognosis and late diagnosis. Biomarkers are essential i...

FastDup: a scalable duplicate marking tool using speculation-and-test mechanism

Duplicate marking is a critical preprocessing step in gene sequence analysis to flag redundant reads arising from polymerase chain reaction(PCR) amp...

Data-driven consideration of genetic disorders for global genomic newborn screening programs.

PURPOSE: Over 30 international studies are exploring newborn sequencing (NBSeq) to expand the range of genetic disorders included in newborn screening...

Image2Reg: Linking chromatin images to gene regulation using genetic and chemical perturbation screens.

Representation learning provides an opportunity to uncover the link between 3D genome organization and gene regulatory networks, thereby connecting th...

NetLnc: A Network-Based Computational Framework to Identify Immune Checkpoint-Related lncRNAs for Immunotherapy Response in Melanoma.

Long non-coding RNAs (lncRNAs) could alter the tumor immune microenvironment and regulate the expression of immune checkpoints (ICPs) by regulating ta...

Value of Bioinformatics Models for Predicting Translational Control of Angiogenesis.

Angiogenesis, the formation of new blood vessels, is a fundamental biological process with implications for both physiological functions and pathologi...

Model-to-crop conserved NUE Regulons enhance machine learning predictions of nitrogen use efficiency.

Systems biology aims to uncover gene regulatory networks (GRNs) for agricultural traits, but validating them in crops is challenging. We addressed thi...

Using machine learning models to predict the impact of template mismatches on polymerase chain reaction assay performance.

Molecular assays are critical tools for the diagnosis of infectious diseases. These assays have been extremely valuable during the COVID pandemic, use...

PCVR: a pre-trained contextualized visual representation for DNA sequence classification.

BACKGROUND: The classification of DNA sequences is pivotal in bioinformatics, essentially for genetic information analysis. Traditional alignment-base...

ChromActivity: integrative epigenomic and functional characterization assay based annotation of regulatory activity across diverse human cell types.

We introduce ChromActivity, a computational framework for predicting and annotating regulatory activity across the genome through integration of multi...

Endometrial tumorigenesis involves epigenetic plasticity demarcating non-coding somatic mutations and 3D-genome alterations.

BACKGROUND: The incidence and mortality of endometrial cancer (EC) is on the rise. Eighty-five percent of ECs depend on estrogen receptor alpha (ERα) ...

Transforming beef quality through healthy breeding: a strategy to reduce carcinogenic compounds and enhance human health: a review.

The presence of carcinogenic substances in beef poses a significant risk to public health, with far-reaching implications for consumer safety and the ...

Current updates in the epidemiology and comorbidities of atopic dermatitis.

Atopic dermatitis (AD) is a chronic, inflammatory skin disorder that affects individuals across the lifespan, with significant implications for both p...

Hippocampal-prefrontal functional neural networks in a rat model of fragile X syndrome are poorly organized with limited resiliency.

Fragile X Syndrome (FXS) is a common cause of autism spectrum symptoms. The genetic mutation results in multiple molecular alterations that are hypoth...

Facilitating crRNA Design by Integrating DNA Interaction Features of CRISPR-Cas12a System.

The CRISPR-Cas12a system has gained significant attention as a rapid nucleic acid diagnostic tool due to its crRNA-guided trans-cleavage activity. Acc...

Identifying Molecular Properties of Ataxin-2 Inhibitors for Spinocerebellar Ataxia Type 2 Utilizing High-Throughput Screening and Machine Learning.

Spinocerebellar ataxia type 2 (SCA2) is an autosomal dominant neurodegenerative disorder marked by cerebellar dysfunction, ataxic gait, and progressiv...

Machine Learning-Based Ensemble Feature Selection and Nested Cross-Validation for miRNA Biomarker Discovery in Usher Syndrome.

Usher syndrome (USH) is a rare genetic disorder affecting vision, hearing, and balance. Identifying reliable biomarkers is crucial for early diagnosis...