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Computational Biology

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Identification of mitophagy-related genes and analysis of immune infiltration in the astrocytes based on machine learning in the pathogenesis of major depressive disorder.

Journal of affective disorders
BACKGROUNDS: Major depressive disorder (MDD) is a pervasive mental and mood disorder with complicated and heterogeneous etiology. Mitophagy, a selective autophagy of cells, specifically eliminates dysfunctional mitochondria. The mitochondria dysfunct...

RNAfcg: RNA Flexibility Prediction Based on Topological Centrality and Global Features.

Journal of chemical information and modeling
The dynamics of RNAs are related intimately to their functions. Molecular flexibility, as a starting point for understanding their dynamics, has been utilized to predict many characteristics associated with their functions. Since the experimental mea...

Systems Biology and Machine Learning Identify Genetic Overlaps Between Lung Cancer and Gastroesophageal Reflux Disease.

Omics : a journal of integrative biology
One Health and planetary health place emphasis on the common molecular mechanisms that connect several complex human diseases as well as human and planetary ecosystem health. For example, not only lung cancer (LC) and gastroesophageal reflux disease ...

Impact of Multi-Factor Features on Protein Secondary Structure Prediction.

Biomolecules
Protein secondary structure prediction (PSSP) plays a crucial role in resolving protein functions and properties. Significant progress has been made in this field in recent years, and the use of a variety of protein-related features, including amino ...

Integrating multi-omics and machine learning survival frameworks to build a prognostic model based on immune function and cell death patterns in a lung adenocarcinoma cohort.

Frontiers in immunology
INTRODUCTION: The programmed cell death (PCD) plays a key role in the development and progression of lung adenocarcinoma. In addition, immune-related genes also play a crucial role in cancer progression and patient prognosis. However, further studies...

Bioinformatics challenges for profiling the microbiome in cancer: pitfalls and opportunities.

Trends in microbiology
Increasing evidence suggests that the human microbiome plays an important role in cancer risk and treatment. Untargeted 'omics' techniques have accelerated research into microbiome-cancer interactions, supporting the discovery of novel associations a...

Comparison and benchmark of deep learning methods for non-coding RNA classification.

PLoS computational biology
The involvement of non-coding RNAs in biological processes and diseases has made the exploration of their functions crucial. Most non-coding RNAs have yet to be studied, creating the need for methods that can rapidly classify large sets of non-coding...

Accurately identifying positive and negative regulation of apoptosis using fusion features and machine learning methods.

Computational biology and chemistry
Apoptotic proteins play a crucial role in the apoptosis process, ensuring a balance between cell proliferation and death. Thus, further elucidating the regulatory mechanisms of apoptosis will enhance our understanding of their functions. However, the...

DeepDBS: Identification of DNA-binding sites in protein sequences by using deep representations and random forest.

Methods (San Diego, Calif.)
Interactions of biological molecules in organisms are considered to be primary factors for the lifecycle of that organism. Various important biological functions are dependent on such interactions and among different kinds of interactions, the protei...