4.6 Article

A deep learning framework for identifying essential proteins based on multiple biological information

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemistry & Molecular Biology

OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines

Sanathoi Gurumayum et al.

Summary: OGEE is an online database focusing on gene essentiality, providing data for 91 species and expanding collection of human essential genes for cancer research. It includes experimentally tested gene essentiality data and associated gene properties, allowing researchers to study the complex interplays between gene functions and environmental/experimental perturbations.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemical Research Methods

DMFLDA: A Deep Learning Framework for Predicting lncRNA-Disease Associations

Min Zeng et al.

Summary: A deep matrix factorization model (DMFLDA) is proposed to predict lncRNA-disease associations, which uses a cascade of non-linear hidden layers to learn latent representations and achieves more accurate representation learning, outperforming existing methods.

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2021)

Article Computer Science, Artificial Intelligence

Content-aware convolutional neural networks

Yong Guo et al.

Summary: The article introduces a Content-aware Convolution (CAC) method, which reduces convolution computation redundancy by automatically detecting smooth windows and applying smaller convolutional kernels to improve the performance of Convolutional Neural Networks (CNNs). Experiments demonstrate the significant advantages of this method in various computer vision tasks.

NEURAL NETWORKS (2021)

Article Biochemical Research Methods

A novel essential protein identification method based on PPI networks and gene expression data

Jiancheng Zhong et al.

Summary: The study introduces a new essential protein identification method, JDC, which outperforms existing prediction methods by combining PPI network data and gene expression data. JDC utilizes a dynamic threshold method to binarize gene expression data and calculates JDC scores for proteins in the PPI network based on degree centrality and Jaccard similarity index. Experimental results demonstrate that JDC method achieves higher accuracy in predicting essential proteins.

BMC BIOINFORMATICS (2021)

Article Genetics & Heredity

Method for Essential Protein Prediction Based on a Novel Weighted Protein-Domain Interaction Network

Zixuan Meng et al.

Summary: A prediction model called WPDINM is proposed in this study to detect key proteins based on a novel weighted protein-domain interaction network. Experimental results show that WPDINM achieves significantly higher predictive accuracy for key protein identification compared to traditional competing measures.

FRONTIERS IN GENETICS (2021)

Article Biochemical Research Methods

An iteration model for identifying essential proteins by combining comprehensive PPI network with biological information

Shiyuan Li et al.

Summary: This study proposed a new prediction model TGSO, which constructed a comprehensive interactive network based on multi-source data to improve the accuracy of essential protein prediction.

BMC BIOINFORMATICS (2021)

Review Biochemical Research Methods

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

Xingyi Li et al.

BRIEFINGS IN BIOINFORMATICS (2020)

Article Biochemical Research Methods

DeepHE: Accurately predicting human essential genes based on deep learning

Xue Zhang et al.

PLOS COMPUTATIONAL BIOLOGY (2020)

Article Biochemical Research Methods

XGBFEMF: An XGBoost-Based Framework for Essential Protein Prediction

Jiancheng Zhong et al.

IEEE TRANSACTIONS ON NANOBIOSCIENCE (2018)

Article Biochemical Research Methods

Prediction of Essential Proteins Based on Local Interaction Density

Yi Qi et al.

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2016)

Article Computer Science, Information Systems

A Feature Selection Method for Prediction Essential Protein

Jiancheng Zhong et al.

TSINGHUA SCIENCE AND TECHNOLOGY (2015)

Article Biochemical Research Methods

Predicting Essential Proteins Based on Weighted Degree Centrality

Xiwei Tang et al.

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2014)

Article Mathematical & Computational Biology

COMPARTMENTS: unification and visualization of protein subcellular localization evidence

Janos X. Binder et al.

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2014)

Article Mathematical & Computational Biology

Natural selection drives rapid evolution of mouse embryonic heart enhancers

Ben-Yang Liao et al.

BMC SYSTEMS BIOLOGY (2012)

Article Biochemistry & Molecular Biology

Hubba: hub objects analyzer - a framework of interactome hubs identification for network biology

Chung-Yen Lin et al.

NUCLEIC ACIDS RESEARCH (2008)

Article Biotechnology & Applied Microbiology

Differences in the evolutionary history of disease genes affected by dominant or recessive mutations

Simon J. Furney et al.

BMC GENOMICS (2006)

Article Biochemistry & Molecular Biology

BioGRID: a general repository for interaction datasets

Chris Stark et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Biotechnology & Applied Microbiology

High-betweenness proteins in the yeast protein interaction network

MP Joy et al.

JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY (2005)

Article Cell Biology

Genome-wide screening for gene function using RNAi in mammalian cells

LM Cullen et al.

IMMUNOLOGY AND CELL BIOLOGY (2005)

Article Physics, Fluids & Plasmas

Subgraph centrality in complex networks -: art. no. 056103

E Estrada et al.

PHYSICAL REVIEW E (2005)

Article Biochemistry & Molecular Biology

Large-scale essential gene identification in Candida albicans and applications to antifungal drug discovery

T Roemer et al.

MOLECULAR MICROBIOLOGY (2003)

Article Biology

Centers of complex networks

S Wuchty et al.

JOURNAL OF THEORETICAL BIOLOGY (2003)

Article Multidisciplinary Sciences

Functional profiling of the Saccharomyces cerevisiae genome

G Giaever et al.

NATURE (2002)

Article Multidisciplinary Sciences

Lethality and centrality in protein networks

H Jeong et al.

NATURE (2001)

Article Multidisciplinary Sciences

A comprehensive two-hybrid analysis to explore the yeast protein interactome

T Ito et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)