DeepEnhancerPPO: An Interpretable Deep Learning Approach for Enhancer Classification.

Enhancers are short genomic segments located in non-coding regions of the genome that play a critical role in regulating the expression of target genes. Despite their importance in transcriptional regulation, effective methods for classifying enhancer categories and regulatory strengths remain limited. To address this challenge, we propose a novel end-to-end deep learning architecture named DeepEnhancerPPO.

Spike-In Proteome Enhances Data-Independent Acquisition for Thermal Proteome Profiling.

Target deconvolution is essential for elucidating the molecular mechanisms, therapeutic efficacy, and off-target toxicity of small-molecule drugs. Thermal proteome profiling (TPP) is a robust and popular method for identifying drug-protein interactions. Nevertheless, classical implementation of TPP using isobaric labeling of peptides is tedious, time-consuming, and costly.

Elucidating the Functional Roles of Long Non-Coding RNAs in Alzheimer's Disease.

Alzheimer's disease (AD) is a multifaceted neurodegenerative disorder characterized by cognitive decline and neuronal loss, representing a most challenging health issue. We present a computational analysis of transcriptomic data of AD tissues vs. healthy controls, focused on the elucidation of functional roles played by long non-coding RNAs (lncRNAs) throughout the AD progression.

Analysis and prediction of interactions between transmembrane and non-transmembrane proteins.

Background: Most of the important biological mechanisms and functions of transmembrane proteins (TMPs) are realized through their interactions with non-transmembrane proteins(nonTMPs). The interactions between TMPs and nonTMPs in cells play vital roles in intracellular signaling, energy metabolism, investigating membrane-crossing mechanisms, correlations between disease and drugs.

Results: Despite the importance of TMP-nonTMP interactions, the study of them remains in the wet experimental stage, lacking specific and comprehensive studies in the field of bioinformatics.