Machine learning for integrating data in biology and medicine: Principles, practice, and opportunities

M Zitnik, F Nguyen, B Wang, J Leskovec… - Information …, 2019 - Elsevier
New technologies have enabled the investigation of biology and human health at an
unprecedented scale and in multiple dimensions. These dimensions include a myriad of …

Reuse of public genome-wide gene expression data

J Rung, A Brazma - Nature Reviews Genetics, 2013 - nature.com
Our understanding of gene expression has changed dramatically over the past decade,
largely catalysed by technological developments. High-throughput experiments …

Network-based methods for predicting essential genes or proteins: a survey

X Li, W Li, M Zeng, R Zheng, M Li - Briefings in bioinformatics, 2020 - academic.oup.com
Genes that are thought to be critical for the survival of organisms or cells are called essential
genes. The prediction of essential genes and their products (essential proteins) is of great …

XGBFEMF: an XGBoost-based framework for essential protein prediction

J Zhong, Y Sun, W Peng, M Xie… - IEEE transactions on …, 2018 - ieeexplore.ieee.org
Essential proteins as a vital part of maintaining the cells' life play an important role in the
study of biology and drug design. With the generation of large amounts of biological data …

Machine learning approach to gene essentiality prediction: a review

O Aromolaran, D Aromolaran, I Isewon… - Briefings in …, 2021 - academic.oup.com
Essential genes are critical for the growth and survival of any organism. The machine
learning approach complements the experimental methods to minimize the resources …

A deep learning framework for identifying essential proteins by integrating multiple types of biological information

M Zeng, M Li, Z Fei, FX Wu, Y Li… - … /ACM transactions on …, 2019 - ieeexplore.ieee.org
Computational methods including centrality and machine learning-based methods have
been proposed to identify essential proteins for understanding the minimum requirements of …

A computational framework based on ensemble deep neural networks for essential genes identification

NQK Le, DT Do, TNK Hung, LHT Lam… - International journal of …, 2020 - mdpi.com
Essential genes contain key information of genomes that could be the key to a
comprehensive understanding of life and evolution. Because of their importance, studies of …

Iteration method for predicting essential proteins based on orthology and protein-protein interaction networks

W Peng, J Wang, W Wang, Q Liu, FX Wu, Y Pan - BMC systems biology, 2012 - Springer
Background Identification of essential proteins plays a significant role in understanding
minimal requirements for the cellular survival and development. Many computational …

Genome-wide essential gene identification in Streptococcus sanguinis

P Xu, X Ge, L Chen, X Wang, Y Dou, JZ Xu, JR Patel… - Scientific reports, 2011 - nature.com
A clear perception of gene essentiality in bacterial pathogens is pivotal for identifying drug
targets to combat emergence of new pathogens and antibiotic-resistant bacteria, for …

Bacterial genome reductions: Tools, applications, and challenges

N LeBlanc, TC Charles - Frontiers in Genome Editing, 2022 - frontiersin.org
Bacterial cells are widely used to produce value-added products due to their versatility, ease
of manipulation, and the abundance of genome engineering tools. However, the efficiency of …