AIMC Topic: Promoter Regions, Genetic

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Silencing of optogenetic and chemogenetic transgenes in human iPSCs involves promoter methylation and methylation-independent mechanisms.

Epigenetics
The transplantation of neural progenitor cells derived from induced pluripotent stem cells (iPSCs) has therapeutic potential for the treatment of neurological diseases. However, the functional integration of transplanted iPSC-derived neurons into hos...

Prompt-CBP: A Novel Prompt Learning-Based Model for Predicting Cross-Species Promoters.

Journal of chemical information and modeling
Promoter sequences across species exhibit both specificity and conservation. The specificity of promoter sequences typically leads to lower cross-species prediction performance compared to within-species prediction. However, conserved promoter motifs...

The - 216G/T polymorphism in the EGFR gene: A review focusing on Non-Small lung cancer.

Molecular biology reports
The epidermal growth factor receptor (EGFR) is a key regulator of cell proliferation and a well-established therapeutic target in non-small-cell lung cancer (NSCLC). Somatic mutations in the EGFR gene have been widely studied in the context of tyrosi...

iPro-MP: a BERT-based model to predict multiple prokaryotic promoters.

Genome biology
BACKGROUND: Promoters, as essential cis-regulatory elements in prokaryotes, govern gene expression by mediating RNA polymerase binding through core motifs and long-range regulatory interactions, playing a pivotal role in cell metabolism and environme...

Identification of methylation-related genes and the potential regulatory mechanism of SLAMF6 in CMS4 colorectal cancer.

Clinical epigenetics
BACKGROUNDS: Consensus molecular subtype 4 (CMS4) of colorectal cancer (CRC) is characterized by TGF-β activation, and generally accompanied with metastasis and recurrence. Nevertheless, molecular biomarkers and regulatory mechanisms underlying CMS4 ...

Computational Pipeline for Targeted Integration and Variable Payload Expression in Bacteriophage Engineering.

ACS synthetic biology
Bacteriophages offer a promising alternative to conventional antimicrobials, especially when such treatments fail. While natural phages are viable for therapy, advances in synthetic biology allow precise genome modifications to enhance their therapeu...

Deciphering the sequence basis and application of transcriptional initiation regulation in plant genomes through deep learning.

Genome biology
BACKGROUND: Transcription initiation is a key checkpoint in plant gene regulation, yet the DNA features that determine where and the frequency of the genes start transcription remain unclear.

YTK Display-and-Secrete: Screening for Optimal Protein Secretion Elements in .

ACS synthetic biology
Engineering yeast to secrete target proteins requires searching for optimal combinations of promoters and signal peptides so that genes can be composed that give a high expression and efficient secretion. Most methods for this involve laborious, one-...

Prediction of MGMT methylation status in glioblastoma patients based on radiomics feature extracted from intratumoral and peritumoral MRI imaging.

Scientific reports
Assessing MGMT promoter methylation is crucial for determining appropriate glioblastoma therapy. Previous studies have focused on intratumoral regions, overlooking the peritumoral area. This study aimed to develop a radiomic model using MRI-derived f...

Learning the sequence code of protein expression in human immune cells.

Science advances
Accurate protein expression in human immune cells is essential for appropriate cellular function. The mechanisms that define protein abundance are complex and are executed on transcriptional, posttranscriptional, and posttranslational levels. Here, w...