Network-based methods for predicting essential genes or proteins: a survey
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Title
Network-based methods for predicting essential genes or proteins: a survey
Authors
Keywords
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Journal
BRIEFINGS IN BIOINFORMATICS
Volume -, Issue -, Pages -
Publisher
Oxford University Press (OUP)
Online
2019-01-24
DOI
10.1093/bib/bbz017
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Note: Only part of the references are listed.- Identifying essential proteins based on sub-network partition and prioritization by integrating subcellular localization information
- (2018) Min Li et al. JOURNAL OF THEORETICAL BIOLOGY
- Predicting essential proteins based on RNA-Seq, subcellular localization and GO annotation datasets
- (2018) Xiujuan Lei et al. KNOWLEDGE-BASED SYSTEMS
- Structure-oriented prediction in complex networks
- (2018) Zhuo-Ming Ren et al. PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS
- BiXGBoost: a scalable, flexible boosting-based method for reconstructing gene regulatory networks
- (2018) Ruiqing Zheng et al. BIOINFORMATICS
- Single-cell proteomics
- (2018) Allison Doerr NATURE METHODS
- United Complex Centrality for Identification of Essential Proteins from PPI Networks
- (2017) Min Li et al. IEEE-ACM Transactions on Computational Biology and Bioinformatics
- The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces
- (2017) Adrian M Altenhoff et al. NUCLEIC ACIDS RESEARCH
- Metabolic network analysis reveals microbial community interactions in anammox granules
- (2017) Christopher E. Lawson et al. Nature Communications
- A Comprehensive Overview of Online Resources to Identify and Predict Bacterial Essential Genes
- (2017) Chong Peng et al. Frontiers in Microbiology
- Predicting essential proteins based on subcellular localization, orthology and PPI networks
- (2016) Gaoshi Li et al. BMC BIOINFORMATICS
- An ensemble framework for identifying essential proteins
- (2016) Xue Zhang et al. BMC BIOINFORMATICS
- Characterize the relationship between essential and TATA-containing genes for S. cerevisiae by network topologies in the perturbation sensitivity network
- (2016) Lei Yang et al. GENOMICS
- Essential protein discovery based on a combination of modularity and conservatism
- (2016) Bihai Zhao et al. METHODS
- OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines
- (2016) Wei-Hua Chen et al. NUCLEIC ACIDS RESEARCH
- OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs
- (2016) Evgeny M. Zdobnov et al. NUCLEIC ACIDS RESEARCH
- Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center
- (2016) Alice R. Wattam et al. NUCLEIC ACIDS RESEARCH
- The BioGRID interaction database: 2017 update
- (2016) Andrew Chatr-aryamontri et al. NUCLEIC ACIDS RESEARCH
- Vital nodes identification in complex networks
- (2016) Linyuan Lü et al. PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS
- Identifying essential proteins based on dynamic protein-protein interaction networks and RNA-Seq datasets
- (2016) Xuequn Shang et al. Science China-Information Sciences
- A reliable neighbor-based method for identifying essential proteins by integrating gene expressions, orthology, and subcellular localization information
- (2016) Min Li et al. TSINGHUA SCIENCE AND TECHNOLOGY
- Mining Temporal Protein Complex Based on the Dynamic PIN Weighted with Connected Affinity and Gene Co-Expression
- (2016) Xianjun Shen et al. PLoS One
- CytoNCA: A cytoscape plugin for centrality analysis and evaluation of protein interaction networks
- (2015) Yu Tang et al. BIOSYSTEMS
- Identifying essential proteins from active PPI networks constructed with dynamic gene expression
- (2015) Qianghua Xiao et al. BMC GENOMICS
- UDoNC: An Algorithm for Identifying Essential Proteins Based on Protein Domains and Protein-Protein Interaction Networks
- (2015) Wei Peng et al. IEEE-ACM Transactions on Computational Biology and Bioinformatics
- A Topology Potential-Based Method for Identifying Essential Proteins from PPI Networks
- (2015) Min Li et al. IEEE-ACM Transactions on Computational Biology and Bioinformatics
- Discovering essential proteins based on PPI network and protein complex
- (2015) Jun Ren et al. International Journal of Data Mining and Bioinformatics
- eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences
- (2015) Jaime Huerta-Cepas et al. NUCLEIC ACIDS RESEARCH
- MetazSecKB: the human and animal secretome and subcellular proteome knowledgebase
- (2015) John Meinken et al. Database-The Journal of Biological Databases and Curation
- A feature selection method for prediction essential protein
- (2015) Jiancheng Zhong et al. TSINGHUA SCIENCE AND TECHNOLOGY
- Identification of Essential Proteins Based on a New Combination of Local Interaction Density and Protein Complexes
- (2015) Jiawei Luo et al. PLoS One
- Rechecking the Centrality-Lethality Rule in the Scope of Protein Subcellular Localization Interaction Networks
- (2015) Xiaoqing Peng et al. PLoS One
- Predicting Essential Proteins Based on Weighted Degree Centrality
- (2014) Xiwei Tang et al. IEEE-ACM Transactions on Computational Biology and Bioinformatics
- Effective identification of essential proteins based on priori knowledge, network topology and gene expressions
- (2014) Min Li et al. METHODS
- Identifying influential spreaders by weighted LeaderRank
- (2014) Qian Li et al. PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
- Localization and centrality in networks
- (2014) Travis Martin et al. PHYSICAL REVIEW E
- COMPARTMENTS: unification and visualization of protein subcellular localization evidence
- (2014) J. X. Binder et al. Database-The Journal of Biological Databases and Curation
- Prediction of essential proteins using topological properties in GO-pruned PPI network based on machine learning methods
- (2014) Wooyoung Kim TSINGHUA SCIENCE AND TECHNOLOGY
- SBEToolbox: A Matlab Toolbox for Biological Network Analysis
- (2013) Kranti Konganti et al. Evolutionary Bioinformatics
- Yin and Yang of disease genes and death genes between reciprocally scale-free biological networks
- (2013) Hyun Wook Han et al. NUCLEIC ACIDS RESEARCH
- Pfam: the protein families database
- (2013) Robert D. Finn et al. NUCLEIC ACIDS RESEARCH
- CentiLib: comprehensive analysis and exploration of network centralities
- (2012) J. Grassler et al. BIOINFORMATICS
- Iteration method for predicting essential proteins based on orthology and protein-protein interaction networks
- (2012) Wei Peng et al. BMC Systems Biology
- A new essential protein discovery method based on the integration of protein-protein interaction and gene expression data
- (2012) Min Li et al. BMC Systems Biology
- Reprint of: The anatomy of a large-scale hypertextual web search engine
- (2012) Sergey Brin et al. Computer Networks
- Dynamic Protein-Protein Interaction Wiring of the Human Spliceosome
- (2012) Anna Hegele et al. MOLECULAR CELL
- Computational approaches to predicting essential proteins: A survey
- (2012) Jianxin Wang et al. Proteomics Clinical Applications
- IDENTIFICATION OF ESSENTIAL PROTEINS FROM WEIGHTED PROTEIN–PROTEIN INTERACTION NETWORKS
- (2012) MIN LI et al. Journal of Bioinformatics and Computational Biology
- A comparison of the functional modules identified from time course and static PPI network data
- (2011) Xiwei Tang et al. BMC BIOINFORMATICS
- Integration of breast cancer gene signatures based on graph centrality
- (2011) Jianxin Wang et al. BMC Systems Biology
- A local average connectivity-based method for identifying essential proteins from the network level
- (2011) Min Li et al. COMPUTATIONAL BIOLOGY AND CHEMISTRY
- Identification of Essential Proteins Based on Edge Clustering Coefficient
- (2011) Jianxin Wang et al. IEEE-ACM Transactions on Computational Biology and Bioinformatics
- MINT, the molecular interaction database: 2012 update
- (2011) Luana Licata et al. NUCLEIC ACIDS RESEARCH
- The IntAct molecular interaction database in 2012
- (2011) S. Kerrien et al. NUCLEIC ACIDS RESEARCH
- Leaders in Social Networks, the Delicious Case
- (2011) Linyuan Lü et al. PLoS One
- Putative essential and core-essential genes in Mycoplasma genomes
- (2011) Yan Lin et al. Scientific Reports
- Toward the dynamic interactome: it's about time
- (2010) T. M. Przytycka et al. BRIEFINGS IN BIOINFORMATICS
- Identification of influential spreaders in complex networks
- (2010) Maksim Kitsak et al. Nature Physics
- LocDB: experimental annotations of localization for Homo sapiens and Arabidopsis thaliana
- (2010) Shruti Rastogi et al. NUCLEIC ACIDS RESEARCH
- IsoBase: a database of functionally related proteins across PPI networks
- (2010) D. Park et al. NUCLEIC ACIDS RESEARCH
- Investigating the predictability of essential genes across distantly related organisms using an integrative approach
- (2010) Jingyuan Deng et al. NUCLEIC ACIDS RESEARCH
- The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
- (2010) D. Szklarczyk et al. NUCLEIC ACIDS RESEARCH
- Analyzing biological network parameters with CentiScaPe
- (2009) Giovanni Scardoni et al. BIOINFORMATICS
- Towards the prediction of essential genes by integration of network topology, cellular localization and biological process information
- (2009) Marcio L Acencio et al. BMC BIOINFORMATICS
- How to identify essential genes from molecular networks?
- (2009) Gabriel del Rio et al. BMC Systems Biology
- Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants
- (2009) G. C. Langridge et al. GENOME RESEARCH
- A systems biology tour de force for a near-minimal bacterium
- (2009) John I Glass et al. Molecular Systems Biology
- InParanoid 7: new algorithms and tools for eukaryotic orthology analysis
- (2009) G. Ostlund et al. NUCLEIC ACIDS RESEARCH
- CORUM: the comprehensive resource of mammalian protein complexes—2009
- (2009) Andreas Ruepp et al. NUCLEIC ACIDS RESEARCH
- Modifying the DPClus algorithm for identifying protein complexes based on new topological structures
- (2008) Min Li et al. BMC BIOINFORMATICS
- Analysis of human disease genes in the context of gene essentiality
- (2008) Donghyun Park et al. GENOMICS
- Hubba: hub objects analyzer—a framework of interactome hubs identification for network biology
- (2008) Chung-Yen Lin et al. NUCLEIC ACIDS RESEARCH
- Up-to-date catalogues of yeast protein complexes
- (2008) Shuye Pu et al. NUCLEIC ACIDS RESEARCH
- Human Protein Reference Database--2009 update
- (2008) T. S. Keshava Prasad et al. NUCLEIC ACIDS RESEARCH
- DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes
- (2008) R. Zhang et al. NUCLEIC ACIDS RESEARCH
- Dynamic Proteomics of Individual Cancer Cells in Response to a Drug
- (2008) A. A. Cohen et al. SCIENCE
- Dynamic Changes in Protein Functional Linkage Networks Revealed by Integration with Gene Expression Data
- (2008) Shubhada R. Hegde et al. PLoS Computational Biology
- Why Do Hubs in the Yeast Protein Interaction Network Tend To Be Essential: Reexamining the Connection between the Network Topology and Essentiality
- (2008) Elena Zotenko et al. PLoS Computational Biology
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