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DNMT3A p.R882C driven proliferation and anti-apoptotic effects in pancreatic cancer cells
Pancreatic cancer, one of the most lethal malignancies, is characterized by insidious onset, frequent late-stage diagnosis, rapid progression, and limited surgical opportunities. Pancreatic ductal adenocarcinoma (PDAC), accounting for over 90% of pancreatic cancer cases, remains …
Read PDFZoon0PredV: Potential Virus Species Crossover Prediction Using Convolutional Neural Networks and Viral Protein Sequence Patterns
Biomedical science has made substantial progress toward diagnosing, understanding the pathogenesis, and treating various causative agents of infectious disease. However, novel microbial pathogens continue to emerge, and existing pathogens continue to evolve alternative strategies to …
Read PDFXhetRel: a pipeline for X heterozygosity and relatedness analysis of sequencing data
<h4>Motivation</h4>Verification of sample sex is an essential quality control step in next-generation sequencing studies, typically assessed from genomic data. Clustering individuals by X chromosome heterozygosity (Xhet) and incorporating relatedness estimates offers a practical first-pass screen …
Read PDFDraft genome of extended-spectrum β-lactamase-producing multidrug-resistant <i>Salmonella enterica</i> serovar Brandearup strain DE0603 from an urban river in South Africa
We report the draft genome of multidrug-resistant <i>Salmonella enterica</i> serovar Braenderup strain DE0603, isolated from an urban river in Johannesburg, South Africa. The isolate was identified as sequence type 22 and carries multiple resistance genes, …
Read PDFASPM promotes the progression of ovarian endometriosis by modulating the cell cycle and activating the Wnt/β-catenin signaling pathway
<h4>Background</h4>Endometriosis (EMs) is a common gynecological disorder associated with impaired fertility and reduced quality of life. This study investigated abnormal spindle-like microcephaly-associated protein (ASPM), identified as a hub gene in EMs pathogenesis, and explored its …
Read PDFMorpheus: a fragment-based algorithm to predict fold-switching behaviour in proteins across proteomes
<h4>Motivation</h4>Functionally important 'fold-switching' proteins, which do not obey the classical folding dogma, are now thought to be widespread. Algorithms that can accurately annotate fold-switching proteins from sequence information can help uncover the true extent of …
Read PDFLive triatomine bug, vector of Trypanosoma cruzi , found engorged in Lisbon hotel room: A first for Portugal and for Europe
Triatomine bugs are blood feeding insects that transmit the parasite Trypanosoma cruzi, causative agent of Chagas disease. The bugs are found primarily in the Americas with a few species in Asia and Africa. Here, we …
Read PDFGeoGAD: geometry-aware antibody design framework for complementarity-determining region precision engineering
<h4>Motivation</h4>Antibodies, as pivotal effector molecules of the immune system, neutralize pathogens through specific binding to antigens mediated by complementarity-determining regions (CDRs), highlighting the critical importance of precise antibody design in diagnostics and therapeutics. Despite significant …
Read PDFValidation and Functional Exploration of Exosome-Derived ITGA9-AS1 and WNT5A-AS1 as Candidate Diagnostic Biomarkers for Schizophrenia
<h4>Objective</h4>Schizophrenia lacks objective biomarkers, and its complex aetiology demands epigenetic insight. Given the regulatory roles of long non-coding RNAs (lncRNAs) in the nervous system and brain-relevant signals in peripheral exosomes, we evaluated lncRNA expression in …
Read PDFSARS-CoV-2 wastewater genomic surveillance: approaches, challenges, and opportunities
Wastewater-based genomic surveillance (WWGS) has proven effective for monitoring SARS-CoV-2 and other viruses within communities. It enables rapid detection of known and emerging mutations and provides insights into circulating lineages. Despite its advantages, WWGS faces …
Read PDFSketchbook: logical model inference from Boolean network sketches
<h4>Summary</h4>Sketchbook is a tool for design and analysis of <i>Boolean network sketches</i>, a framework for partial specification of Boolean network models combining static and dynamic logical constraints. The tool combines an intuitive graphical interface with …
Read PDFBIWT: a bioinformatics walkthrough for embedding spatial multiomics in agent-based models for virtual cells
<h4>Summary</h4>Whereas transcriptomic and spatial profiling offer static snapshots of tissue structure, mechanistic models use biological rules to predict how tissues evolve. We present the BioInformatics WalkThrough (BIWT) software to directly initialize spatial agent-based models from …
Read PDFIdentification of hub targets involved in carotid atherosclerosis through bioinformatics and machine learning approaches
BACKGROUND: Carotid atherosclerosis is a kind of systemic atherosclerosis in the carotid arteries. It remains one of the leading causes of ischemic stroke. However, the efficiency of treatment is insufficient. Thus, it is urgent to …
Read PDFPSMB8 as a Core Target Mediating the Anti-Hepatocellular Carci-Noma Activity of Lingonberry (<i>Vaccinium vitis-idaea</i> L.) Extract in HepG2 Cells
Hepatocellular carcinoma (HCC) is a highly malignant tumour with a poor prognosis and few effective treatment options. Development of resistance to conventional therapies and occurrence of severe side effects highlight the urgent need for novel, …
Read PDFErratum: Integrative bioinformatics approach for identifying key genes and potential therapeutic targets in the concurrent manifestation of hypertrophic cardiomyopathy and pulmonary hypertension
[This corrects the article DOI: 10.21037/jtd-23-1822.].
Read PDFDockingDB: An online reverse-docking database for plant hormone research
No abstract available.
Read PDFEthnopharmacological evaluation and metabolic mechanism of Sanjie Xiaoliu Granule in breast cancer with depression
<h4>Background</h4>Sanjie Xiaoliu Granule (SJXLG), a traditional multi-herbal prescription widely used in Chinese medicine, has been historically applied to "disperse nodules, soothe the liver, and relieve depression." It is clinically prescribed for patients with breast lumps, …
Read PDFScreening and comprehensive analysis of endoplasmic reticulum stress-related biomarkers in atherosclerosis
Atherosclerosis (AS) is a chronic inflammatory vascular disorder in which endoplasmic reticulum stress (ERS) plays a crucial regulatory role. However, the biological and translational relevance of ERS-related gene networks in AS remains largely unexplored. This …
Read PDFIntegrating curation into scientific publishing to train AI models
<h4>Motivation</h4>High-throughput extraction and structured labeling of data from academic articles are crucial for enabling downstream machine learning applications and secondary analyses. Current approaches lack integration with the publishing process and comprehensive annotation of experimental roles …
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