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Genomics02:02

Genomics

37.5K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
37.5K
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

19.3K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
19.3K
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

4.3K
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
4.3K
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

6.2K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
6.2K
Human Genetics01:28

Human Genetics

730
Human genetics provides a profound framework for understanding the interplay between genetic predispositions and human psychology. At the heart of this discipline lies the study of how genes influence physical traits, behaviors, and susceptibility to diseases. Each person carries a unique genetic code that subtly or significantly shapes their psychological and behavioral landscape.
The complex relationship between genetics and psychology is observable through common biological components such...
730
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

14.3K
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
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Related Experiment Video

Updated: Sep 14, 2025

Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons
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Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons

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A deep ensemble framework for human essential gene prediction by integrating multi-omics data.

Xue Zhang1, Weijia Xiao2, Brent Cochran3

  • 1College of Information Science and Engineering, Provincial Key Laboratory of Informational Service for Rural Area of Southwestern Hunan, Shaoyang University, Shaoyang, 422000, China. lindajia03@gmail.com.

Scientific Reports
|July 21, 2025
PubMed
Summary

We developed DeEPsnap, a deep learning method to predict essential genes in humans. This approach accurately identifies genes critical for life, aiding disease research and drug development.

Keywords:
Deep learningEssential gene predictionMulti-omics data integrationSnapshot ensemble

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Essential genes are crucial for organism survival and reproduction.
  • Understanding gene essentiality advances basic life science, human disease research, and drug discovery.

Purpose of the Study:

  • To propose DeEPsnap, a novel deep neural network method for predicting human essential genes.
  • To integrate diverse biological data for enhanced prediction accuracy.

Main Methods:

  • DeEPsnap utilizes a snapshot ensemble deep neural network.
  • It integrates features from DNA/protein sequences and functional data (gene ontology, protein complexes, domains, interaction networks).
  • Cost-sensitive deep neural networks are trained with over 200 integrated features.

Main Results:

  • DeEPsnap achieved high predictive performance: 96.16% AUROC, 93.83% AUPRC, and 92.36% accuracy via 10-fold cross-validation.
  • Comparative experiments demonstrated DeEPsnap's superiority over traditional and other deep learning models.
  • The method effectively predicts human gene essentiality.

Conclusions:

  • DeEPsnap is an effective and accurate method for predicting human essential genes.
  • The integration of multiple feature types significantly improves prediction.
  • This tool has potential applications in understanding fundamental biology and developing therapeutics.