Genetics

Reliable detection of Host-Microbe Signatures in cancer using PRISM.

Recent controversy in the cancer microbiome field highlights the need for more reliable microbial detection from human genomic data. Here, we develop PRISM, an efficient computational framework for precise microorganism identification and decontamination from low-biomass sequencing data. PRISM achieves robust performance when benchmarked on 230 independent datasets with known true-positive and con...

Concordant and Discordant Transcriptomic Signatures of Twin Placentas in the Setting of Preeclampsia.

BACKGROUND: Multifetal pregnancies have increased preeclampsia risk, but the underlying pathogenesis may differ from that of singletons. It remains unclear whether twin placentas show molecular signs of preeclampsia synchronously. METHODS: We performed RNA sequencing on 32 individual placental samples from twin gestations grouped by preeclampsia status: 24 dichorionic twin (DT) and 8 monochorionic...

Integrative bioinformatics and machine learning approaches identify novel diagnostic signatures for oxaliplatin-resistant colorectal cancer.

BACKGROUND: Oxaliplatin resistance significantly impairs therapeutic outcomes in colorectal cancer. However, reliable diagnostic markers for early det...

Extracellular vesicles in colorectal cancer: immunomodulation, diagnostics, and therapeutic perspectives.

Colorectal cancer (CRC) remains a significant global health concern and is among the leading causes of cancer-related mortality. The disease often pro...

Enhancing Transcription Factor Regulatory Network Analysis through Data Balancing and Representation Learning.

Transcription factor (TF) and target gene interactions are pivotal in gene regulatory networks, influencing molecular biology and disease mechanisms, ...

A hybrid feature extraction framework combining PCA and mutual information for gene expression based lung cancer classification.

Lung cancer remains a leading cause of cancer-related mortality worldwide, with early and accurate diagnosis posing a critical challenge for improving...

Variant calling in genomics: A comparative performance analysis and decision guide.

The accurate detection of genetic variants is critical for advancing genomics research and precision medicine. However, this task remains challenging ...

MYB: A potential therapeutic target in triple-negative breast cancer based on the PI3K/AKT signaling pathway.

BACKGROUND: Compared to non-triple-negative breast cancer (Non-TNBC), triple-negative breast cancer (TNBC) exhibits significantly poorer prognosis. Pr...

Forensic inference in Africa: Evaluating population structure, databases, and regional assignment accuracy.

This study reports novel 21 aSTR (autosomal Short Tandem Repeats) allele frequencies from 538 individuals, as well as 11 triallelic profiles, represen...

CRISPR-initiated exponential amplification on fluorescently-barcoded microspheres for deep learning-assisted multiplexed HPV detection.

Rapid, low-cost, and multiplexed nucleic acid testing is essential for human health but remains challenging. Although CRISPR-Cas systems offer high sp...

Biological aging across the metabolic dysfunction-associated steatotic liver disease spectrum: A systematic review.

BACKGROUND AND AIMS: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a growing global health burden. Geroscience posits that accel...

Integrated single-cell analyses of affinity-tested B cells enable the identification of a gene signature to predict antibody affinity.

Advancements in single-cell technologies and deep sequencing have expanded the B cell repertoire available for antibody discovery. However, selecting ...

Hopfield Networks as Models of Emergent Function in Biology.

Hopfield models, originally developed to study memory retrieval in neural networks, have become versatile tools for modeling diverse biological system...

Machine-Learning Ice Spectra: From 1 to 256 Features.

The study explores how well machine learning and structural fingerprints can predict spectroscopic properties of ice (OH vibrational frequencies and 1...

Applying biotechnology to overcome cancer drug resistance and improve public health outcomes.

This review examines how biotechnology advances (CRISPR/Cas9, next-generation targeted therapies, nanotechnology-based drug delivery, and immunotherap...

Advances in multi-omics for esophageal squamous cell carcinoma: Diagnostic, prognostic, and therapeutic perspectives.

Esophageal squamous cell carcinoma (ESCC) remains a major health burden, particularly in Asia, with poor patient prognosis despite advancements in rad...

Forensic Transcriptomics: Research Progress of the Past Two Decades.

Over the last two decades, advancements in sequencing technology and data science have significantly deepened the study of transcriptomics, especially...

Sharing approaches in predictive genomics across animals, plants and humans.

Genomic prediction has become central to human, animal and plant biology, enabling quantitative inference of how genetic variation shapes complex trai...

Regulatory grammar in human promoters uncovered by MPRA-based deep learning.

Promoters are the core regulatory elements of all genes. Their activity ensures the correct transcription level of each individual gene, which is esse...

Transcriptomic analyses reveal regulatory plasticity and metabolic reprogramming underlying genotype-specific microspore embryogenesis in wheat.

Embryogenic efficiency in wheat microspores is driven by epigenetic regulation, homoeolog expression bias, and genotype-specific genomic variation, wi...