Zhenfeng Deng
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View article: Cross-platform motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors
Cross-platform motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors Open
A sequence motif representing the DNA-binding specificity of a transcription factor (TF) is commonly modelled with a positional weight matrix (PWM). Focusing on understudied human TFs, we processed results of 4,237 experiments for 394 TFs,…
View article: Development of siRNA therapeutics to combat microbial infections: a bibliometric analysis
Development of siRNA therapeutics to combat microbial infections: a bibliometric analysis Open
Background The rise of antimicrobial resistance and the COVID-19 pandemic highlight the limitations of traditional therapies. Small interfering RNA (siRNA) therapeutics, which utilize RNA interference for targeted gene silencing, present a…
View article: Evaluation of hybrid capture-based targeted and metagenomic next-generation sequencing for pathogenic microorganism detection in infectious keratitis
Evaluation of hybrid capture-based targeted and metagenomic next-generation sequencing for pathogenic microorganism detection in infectious keratitis Open
Objective This study aimed to compare the performance of hybrid capture-based targeted next-generation sequencing (hc-tNGS) and metagenomic next-generation sequencing (mNGS) in detecting the causative pathogens of infectious keratitis. Met…
View article: Discovery of RNA‐Targeting Small Molecules: Challenges and Future Directions
Discovery of RNA‐Targeting Small Molecules: Challenges and Future Directions Open
RNA‐targeting small molecules represent a transformative frontier in drug discovery, offering novel therapeutic avenues for diseases traditionally deemed undruggable. This review explores the latest advancements in the development of RNA‐b…
View article: Targeted next-generation sequencing characterization of respiratory pathogens in children with acute respiratory infection
Targeted next-generation sequencing characterization of respiratory pathogens in children with acute respiratory infection Open
This study represents the first investigation utilizing oropharyngeal swabs for tNGS in diagnosing and treating ARIs. By analyzing surveillance data from a local hospital's patients with ARIs, we have identified the spectrum of bacterial a…
View article: Targeted next-generation sequencing for pulmonary infection diagnosis in patients unsuitable for bronchoalveolar lavage
Targeted next-generation sequencing for pulmonary infection diagnosis in patients unsuitable for bronchoalveolar lavage Open
Background Targeted next-generation sequencing (tNGS) has emerged as a rapid diagnostic technology for identifying a wide spectrum of pathogens responsible for pulmonary infections. Methods Sputum samples were collected from patients unabl…
View article: CD4<sup>+</sup>CD25<sup>+</sup> regulatory T cells decreased future liver remnant after associating liver partition and portal vein ligation for staged hepatectomy
CD4<sup>+</sup>CD25<sup>+</sup> regulatory T cells decreased future liver remnant after associating liver partition and portal vein ligation for staged hepatectomy Open
CD4+CD25+ Tregs in the peripheral blood of patients with massive HCC at stage 1 ALPPS were negatively correlated with indicators of FLR regeneration after stage 1 ALPPS and may influence the degree of fibrosis in patients' livers. Treg per…
View article: Pulmonary nocardiosis with bloodstream infection diagnosed by metagenomic next-generation sequencing in a kidney transplant recipient: A case report
Pulmonary nocardiosis with bloodstream infection diagnosed by metagenomic next-generation sequencing in a kidney transplant recipient: A case report Open
A case of pulmonary nocardiosis with an accompanying bloodstream infection was diagnosed and promptly treated before the dissemination of the infection. This report emphasizes the value of mNGS in the diagnosis of nocardiosis. mNGS may be …
View article: A retrospective cohort study of geographic differences in the semen of 1,012 sperm donors in China
A retrospective cohort study of geographic differences in the semen of 1,012 sperm donors in China Open
We hypothesize environmental pollution and mental stress due to the increased population size may be the main factors underlying differences in the sperm quality of men in northern and southern China.
View article: Construction of a 3-mRNA hypoxia prognostic model to evaluate immune microenvironment in hepatocellular carcinoma
Construction of a 3-mRNA hypoxia prognostic model to evaluate immune microenvironment in hepatocellular carcinoma Open
Background: Hypoxia is a key factor in the development of hepatocellular carcinoma (HCC), which is the most common primary liver cancer with poor prognosis. The current study aimed to identify the potential prognostic biomarkers of the hyp…
View article: Change of tumor-infiltrating lymphocyte of associating liver partition and portal vein ligation for staged hepatectomy for hepatocellular carcinoma
Change of tumor-infiltrating lymphocyte of associating liver partition and portal vein ligation for staged hepatectomy for hepatocellular carcinoma Open
TIL infiltration level maintained a dynamic balance during the preoperative period of ALPPS. Compared with right hemi-hepatectomy, the ALPPS procedure does not cause severe immunosuppression with the decrease in TIL infiltration and pathol…
View article: Bioinformatics analysis and experimental verification of five metabolism-related lncRNAs as prognostic models for hepatocellular carcinoma
Bioinformatics analysis and experimental verification of five metabolism-related lncRNAs as prognostic models for hepatocellular carcinoma Open
Background: The number of patients with hepatocellular carcinoma (HCC) is showing a growing trend all over the world. The metabolic microenvironment has been shown to play a key role in the pathogenesis of HCC in recent studies. The expres…
View article: Analysis of Screening Results of 1012 Sperm Donors in China: A Retrospective Cohort Study of Geographic Differences in Semen Quality
Analysis of Screening Results of 1012 Sperm Donors in China: A Retrospective Cohort Study of Geographic Differences in Semen Quality Open
Male reproductive health has become a concern in public health, and semen quality is essential to male reproduction. To investigate the geographical differences in semen quality of sperm donors from the north and south of China, a total of…
View article: Identification of Prognostic Immune‐Related Genes in Pancreatic Adenocarcinoma and Establishment of a Prognostic Nomogram: A Bioinformatic Study
Identification of Prognostic Immune‐Related Genes in Pancreatic Adenocarcinoma and Establishment of a Prognostic Nomogram: A Bioinformatic Study Open
Background . The prognosis of pancreatic adenocarcinoma (PAAD) is extremely poor and has not been improved. Thus, an effective method to assess the prognosis of patients must be established to improve their survival rate. Method . This stu…
View article: Mining TCGA Database for Tumor Microenvironment-Related Genes of Prognostic Value in Hepatocellular Carcinoma
Mining TCGA Database for Tumor Microenvironment-Related Genes of Prognostic Value in Hepatocellular Carcinoma Open
Hepatocellular carcinoma (HCC) is one of the most common and lethal malignancies. Recent studies reveal that tumor microenvironment (TME) components significantly affect HCC growth and progression, particularly the infiltrating stromal and…