AIMC Topic: Transcription Factors

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Cell death-associated genes as novel diagnostic biomarkers for autism spectrum disorder.

Apoptosis : an international journal on programmed cell death
Autism spectrum disorder (ASD) involves neuroinflammation and dysregulated neuronal death but lacks objective diagnostic biomarkers. This study investigated whether cell death could serve as a molecular basis for ASD diagnosis. We identified cell dea...

Investigating cis-regulatory elements and gene expression in multiple tomato varieties using interpretable deep learning.

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
Cis-regulatory elements (CREs) govern gene expression, and the relationship between non-coding regulatory elements and gene expression is inherently complex. To further elucidate how these elements influence gene expression, we refined previous model...

Unveiling the landscape of prokaryotic global regulators through deep protein language models.

mSystems
Global regulators (GRs) are key transcription factors that orchestrate the expression of multiple genes, playing essential roles in stress responses, virulence, secondary metabolism, and antibiotic resistance-traits that make them powerful tools for ...

A SWI/SNF complex-related genes signature predicts prognosis and immune infiltration in ccRCC with KCNK5 as a novel biomarker.

Scientific reports
Clear cell renal cell carcinoma (ccRCC) is the most common subtype of renal cell carcinoma (RCC). Although we have made many achievements in the therapy of RCC with the progress of medicine, the clinical management of metastatic RCC remains a dauntin...

Black pepper knowledge base (BlackPepKB): a centralized web resource for functional genomics of black pepper (Piper nigrum L.).

BMC genomics
BACKGROUND: Black pepper (Piper nigrum L.) is a highly valued spice crop with significant economic, medicinal, and cultural importance. While genomic and transcriptomic data for black pepper have rapidly accumulated in recent years, there is currentl...

Genetic regulations of citrus flowering: insights towards climatic factors and modern biotechnological approaches.

Planta
The review highlights the intricate relationship between genetic and molecular mechanisms that regulate floral development and responses in citrus under diverse climatic conditions. Citrus, the world's top traded and third most produced fruit crop, h...

AI cancer driver mutation predictions are valid in real-world data.

Nature communications
Characterizing and validating which mutations influence development of cancer is challenging. Artificial intelligence (AI) has delivered significant advances in protein structure prediction, but its utility for identifying cancer drivers is less expl...

Multiview Deep Learning Framework for Precise Prediction of Transcription Factor Binding Sites.

Journal of chemical information and modeling
Transcription factors (TFs) are essential proteins that regulate gene expression by specifically binding to transcription factor binding sites (TFBSs) within DNA sequences. Their ability to precisely control the transcription process is crucial for u...

Non-coding genetic elements of lung cancer identified using whole genome sequencing in 13,722 Chinese.

Nature communications
A substantial portion of lung cancer-associated genetic elements in East Asian populations remains unidentified, underscoring the need for large-scale genome-wide studies, particularly on non-coding regulation. We conducted a whole genome sequencing ...

Deep learning-based high-resolution time inference for deciphering dynamic gene regulation from fixed embryos.

Nature communications
Embryo development is driven by the spatiotemporal dynamics of complex gene regulatory networks. Uncovering these dynamics requires simultaneous tracking of multiple fluctuating molecular species over time, which exceeds the capabilities of tradition...