Browse Papers
Search the literature by keyword, topic, or author. Filter to articles with full text available.
2701 results
Retention of embryonic positional identity signatures in the adult sheep tail: evidence from HOXB13 spatial RNA expression gradients
Body axis patterning in vertebrates is controlled by HOX genes during embryogenesis, with their expression gradients defining spatial identity along the anterior-posterior axis. While the developmental roles of HOX genes in axial patterning are well …
Read PDFRNA binding protein YWHAZ mediates specific mRNA translation and regulates cell proliferation and apoptosis in diabetic foot ulcer
<h4>Background</h4>Diabetic foot ulcer (DFU), a condition marked by high rates of recurrence, amputation, and mortality, represents one of the major challenges in diabetes management. RNA-binding proteins (RBPs) are pivotal for post-transcriptional regulation in diabetic complications. …
Read PDFMulti-omics driven computational framework for cancer molecular subtype classification
Cancer molecular subtype classification is an essential component of precision oncology which provides insights into cancer prognosis and guides targeted therapy. Despite the growing applications of AI for cancer molecular subtype classification, challenges persist due …
Read PDFEvolutionary dynamics of FoxQ2 transcription factors across metazoans reveals three ancient paralogs
FoxQ2 is a highly conserved Forkhead-box transcription factor expressed anteriorly in cnidarians and bilaterians, yet its evolution is marked by rapid divergence and lineage-specific duplications or losses. Moreover, its presence and localization in vertebrate groups …
Read PDFMitigation of multi-scale biases in cell-type deconvolution for spatially resolved transcriptomics using HarmoDecon
<h4>Motivation</h4>The advent of spatially resolved transcriptomics (SRT) has revolutionized our understanding of tissue molecular microenvironments by enabling the study of gene expression in its spatial context. However, many SRT platforms lack single-cell resolution, necessitating cell-type …
Read PDFDifferential Gene Expression Across Species Following Spinal Cord Injury: A Systematic Review and Meta-Analysis
The limited regenerative capacity of human nervous tissue compared to other species has long fascinated researchers. Remarkably, non-mammalian vertebrates such as teleost fish and axolotls possess robust regenerative abilities, capable of regenerating entire limbs and …
Read PDFExpressed mutated genes in Sezary syndrome and their potential prognostic value in patients treated with extracorporeal photopheresis
<h4>Background</h4>Sézary syndrome (SS) is an aggressive and leukemic variant of Cutaneous T-cell Lymphoma (CTCL) with an incidence of 1 case per million people per year. It is characterized by a complex and heterogeneous profile of …
Read PDFRapamycin treatment ameliorates HLA-B27-mediated gut inflammation and alters the microbiome in experimental spondyloarthritis
<h4>Objective</h4>To determine whether rapamycin affects HLA-B27-mediated gut inflammation in experimental spondyloarthritis (SpA).<h4>Methods</h4>HLA-B27/human β<sub>2</sub>-microglobulin transgenic (B27-Tg) rats with gut inflammation were treated with rapamycin (1.5 mg/kg intraperitoneally, 3 times a week) or vehicle for 5 weeks. …
Read PDFIntegration of RNA Editing into Multiomics Machine Learning Models for Predicting Drug Responses in Breast Cancer Patients
<b>Background</b>: The integration of multi-omics data, such as genomics and transcriptomics, into artificial intelligence models has advanced precision medicine. However, their clinical applicability remains limited due to model complexity. We integrated DNA mutation, RNA expression, …
Read PDFRNA-Seq of Cultured Peripheral Blood Lymphocytes Improves Identification of Cryptic Splicing Defects in Rare Disease Diagnostics
Accurate identification of the genetic determinants of rare diseases is essential for effective recurrence-risk management and informed reproductive decision-making. Although whole-exome sequencing (WES) and whole-genome sequencing (WGS) have significantly improved diagnostic capabilities, a subset of …
Read PDFComplementary ROC-Derived Indices for Screening Improper Expression Profiles in RNA-Seq Differential Expression Analysis
<h4>Background</h4>Differential expression (DE) analysis of RNA sequencing (RNA-Seq) data are cornerstone of transcriptomic research. Widely used statistical frameworks are primarily optimized to detect monotonic mean shifts between conditions and may therefore overlook genes or microRNAs …
Read PDFA multivariate cell-based liquid biopsy for lung nodule risk stratification: Analytical validation and early clinical evaluation
<h4>Background</h4>The Indicator Cell Assay Platform (iCAP) is a novel tool for blood-based diagnostics that uses living cells as biosensors to integrate and amplify weak, multivalent disease signals present in patient serum. In the platform, standardized …
Read PDFMulti-omics whole-genome characterization of the copy number landscape of metastatic pancreatic ductal adenocarcinoma
Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive disease with limited therapeutic options. While genome profiling has benefitted clinical decision-making in many cancer types, PDAC remains among the most lethal solid cancers and has relatively …
Read PDFElucidation of the <i>ty-5</i> resistance network in tomato against tomato yellow leaf curl virus reveals the involvement of AP2/ERF gene
<h4>Introduction</h4>Tomato yellow leaf curl virus (TYLCV, <i>Begomovirus coheni</i>), a whitefly-transmitted begomovirus, causes serious economic losses to tomato crops globally. Over the past three decades, several genetic sources of TYLCV resistance have been identified and incorporated …
Read PDFCancer-associated fibroblast driven paracrine IL-6/STAT3 signaling promotes migration and dissemination in invasive lobular carcinoma
<h4>Background</h4>Invasive lobular carcinoma (ILC) is the second most common histological subtype of breast cancer after invasive ductal carcinoma of no special type (NST), accounting for 10-15% of diagnoses. Despite the myriad molecular, histological and clinical …
Read PDFDouble stranded RNA sensing is silenced during early embryonic development
The type I interferon response is inactive during early mammalian development and becomes functional only after gastrulation. As a result, the totipotent and pluripotent embryonic stages remain susceptible to pathogens, including viruses. Here, we demonstrate …
Read PDF