Bipartite graphs in systems biology and medicine: a survey of methods and applications
出版年份 2018 全文链接
标题
Bipartite graphs in systems biology and medicine: a survey of methods and applications
作者
关键词
-
出版物
GigaScience
Volume 7, Issue 4, Pages -
出版商
Oxford University Press (OUP)
发表日期
2018-02-19
DOI
10.1093/gigascience/giy014
参考文献
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注意:仅列出部分参考文献,下载原文获取全部文献信息。- BiRank: Towards Ranking on Bipartite Graphs
- (2017) Xiangnan He et al. IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING
- DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq experiments
- (2016) Aristidis G. Vrahatis et al. BIOINFORMATICS
- Network analysis of genes and their association with diseases
- (2016) Panagiota I. Kontou et al. GENE
- Network biology concepts in complex disease comorbidities
- (2016) Jessica Xin Hu et al. NATURE REVIEWS GENETICS
- Coming of age: ten years of next-generation sequencing technologies
- (2016) Sara Goodwin et al. NATURE REVIEWS GENETICS
- DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants
- (2016) Janet Piñero et al. NUCLEIC ACIDS RESEARCH
- IMG/M: integrated genome and metagenome comparative data analysis system
- (2016) I-Min A. Chen et al. NUCLEIC ACIDS RESEARCH
- Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution
- (2016) Eduardo Corel et al. TRENDS IN MICROBIOLOGY
- Bipartite Community Structure of eQTLs
- (2016) John Platig et al. PLoS Computational Biology
- SNAP
- (2016) Jure Leskovec et al. ACM Transactions on Intelligent Systems and Technology
- A Bipartite Network-based Method for Prediction of Long Non-coding RNA–protein Interactions
- (2016) Mengqu Ge et al. GENOMICS PROTEOMICS & BIOINFORMATICS
- Tissue Specificity of Human Disease Module
- (2016) Maksim Kitsak et al. Scientific Reports
- The Pfam protein families database: towards a more sustainable future
- (2015) Robert D. Finn et al. NUCLEIC ACIDS RESEARCH
- Network reliability analysis based on percolation theory
- (2015) Daqing Li et al. RELIABILITY ENGINEERING & SYSTEM SAFETY
- What do molecular methods bring to host–parasitoid food webs?
- (2015) Jan Hrček et al. TRENDS IN PARASITOLOGY
- Nationwide Population Science
- (2015) Ann W. Hsing et al. JAMA Internal Medicine
- Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future
- (2015) Georgios A. Pavlopoulos et al. GigaScience
- networksis: A Package to Simulate Bipartite Graphs with Fixed Marginals Through Sequential Importance Sampling
- (2015) Ryan Admiraal et al. Journal of Statistical Software
- Online collaboration: Scientists and the social network
- (2014) Richard Van Noorden NATURE
- Genenames.org: the HGNC resources in 2015
- (2014) Kristian A. Gray et al. NUCLEIC ACIDS RESEARCH
- DiseaseConnect: a comprehensive web server for mechanism-based disease–disease connections
- (2014) Chun-Chi Liu et al. NUCLEIC ACIDS RESEARCH
- OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders
- (2014) Joanna S. Amberger et al. NUCLEIC ACIDS RESEARCH
- Human cancer databases (Review)
- (2014) ATHANASIA PAVLOPOULOU et al. ONCOLOGY REPORTS
- Efficiently inferring community structure in bipartite networks
- (2014) Daniel B. Larremore et al. PHYSICAL REVIEW E
- An Online Database for Informing Ecological Network Models: http://kelpforest.ucsc.edu
- (2014) Rodrigo Beas-Luna et al. PLoS One
- Human symptoms–disease network
- (2014) XueZhong Zhou et al. Nature Communications
- enaR: Anrpackage for Ecosystem Network Analysis
- (2014) Stuart R. Borrett et al. Methods in Ecology and Evolution
- Generalised power graph compression reveals dominant relationship patterns in complex networks
- (2014) Sebastian E. Ahnert Scientific Reports
- The role of a water bug,Sigara striata, in freshwater food webs
- (2014) Jan Klecka PeerJ
- AMBIENT: Active Modules for Bipartite Networks - using high-throughput transcriptomic data to dissect metabolic response
- (2013) William A Bryant et al. BMC Systems Biology
- Behavior Analysis of Internet Traffic via Bipartite Graphs and One-Mode Projections
- (2013) Kuai Xu et al. IEEE-ACM TRANSACTIONS ON NETWORKING
- The NHGRI GWAS Catalog, a curated resource of SNP-trait associations
- (2013) Danielle Welter et al. NUCLEIC ACIDS RESEARCH
- Spatial structure of ant-plant mutualistic networks
- (2013) Wesley Dáttilo et al. OIKOS
- Epidemic thresholds for bipartite networks
- (2013) D. G. Hernández et al. PHYSICAL REVIEW E
- Hidden Information Revealed by Optimal Community Structure from a Protein-Complex Bipartite Network Improves Protein Function Prediction
- (2013) Juyong Lee et al. PLoS One
- A Network-Based Method to Assess the Statistical Significance of Mild Co-Regulation Effects
- (2013) Emőke-Ágnes Horvát et al. PLoS One
- Integrating domain similarity to improve protein complexes identification in TAP-MS data
- (2013) Bingjing Cai et al. Proteome Science
- The ghost of nestedness in ecological networks
- (2013) Phillip P. A. Staniczenko et al. Nature Communications
- A method for detecting modules in quantitative bipartite networks
- (2013) Carsten F. Dormann et al. Methods in Ecology and Evolution
- Structural controllability of unidirectional bipartite networks
- (2013) Jose C. Nacher et al. Scientific Reports
- Unraveling genomic variation from next generation sequencing data
- (2013) Georgios A Pavlopoulos et al. BioData Mining
- Network-based analysis of vaccine-related associations reveals consistent knowledge with the vaccine ontology
- (2013) Yuji Zhang et al. Journal of Biomedical Semantics
- clusterMaker: a multi-algorithm clustering plugin for Cytoscape
- (2012) John H Morris et al. BMC BIOINFORMATICS
- Multiple graph regularized protein domain ranking
- (2012) Jim Wang et al. BMC BIOINFORMATICS
- Arena3D: visualizing time-driven phenotypic differences in biological systems
- (2012) Maria Secrier et al. BMC BIOINFORMATICS
- Network biology methods integrating biological data for translational science
- (2012) G. Bebek et al. BRIEFINGS IN BIOINFORMATICS
- SNP Web Resources and Their Potential Applications in Personalized Medicine
- (2012) Jingbo Wang et al. CURRENT DRUG METABOLISM
- Deciphering the molecular basis of human cardiovascular disease through network biology
- (2012) Stephen Y. Chan et al. CURRENT OPINION IN CARDIOLOGY
- Recommendation as link prediction in bipartite graphs: A graph kernel-based machine learning approach
- (2012) Xin Li et al. DECISION SUPPORT SYSTEMS
- Disentangling nestedness from models of ecological complexity
- (2012) Alex James et al. NATURE
- A travel guide to Cytoscape plugins
- (2012) Rintaro Saito et al. NATURE METHODS
- Topological analysis and interactive visualization of biological networks and protein structures
- (2012) Nadezhda T Doncheva et al. Nature Protocols
- Mining electronic health records: towards better research applications and clinical care
- (2012) Peter B. Jensen et al. NATURE REVIEWS GENETICS
- The Dynamics of Nestedness Predicts the Evolution of Industrial Ecosystems
- (2012) Sebastián Bustos et al. PLoS One
- The dynamics of sexual contact networks: Effects on disease spread and control
- (2012) Katy Robinson et al. THEORETICAL POPULATION BIOLOGY
- Sex differences in intimate relationships
- (2012) Vasyl Palchykov et al. Scientific Reports
- Prediction of Drug-Target Interactions and Drug Repositioning via Network-Based Inference
- (2012) Feixiong Cheng et al. PLoS Computational Biology
- The data paper: a mechanism to incentivize data publishing in biodiversity science
- (2011) Vishwas Chavan et al. BMC BIOINFORMATICS
- Systems biological approach on neurological disorders: a novel molecular connectivity to aging and psychiatric diseases
- (2011) Shiek SSJ Ahmed et al. BMC Systems Biology
- Hive plots--rational approach to visualizing networks
- (2011) M. Krzywinski et al. BRIEFINGS IN BIOINFORMATICS
- Small Molecule Databases and Chemical Descriptors Useful in Chemoinformatics: An Overview
- (2011) Rafael Gozalbes et al. COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING
- Discovery of Protein Complexes with Core-Attachment Structures from Tandem Affinity Purification (TAP) Data
- (2011) Min Wu et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- Controllability of complex networks
- (2011) Yang-Yu Liu et al. NATURE
- A note on a generalization of eigenvector centrality for bipartite graphs and applications
- (2011) Peteris Daugulis NETWORKS
- GeneWeaver: a web-based system for integrative functional genomics
- (2011) Erich J. Baker et al. NUCLEIC ACIDS RESEARCH
- On the degree distribution of projected networks mapped from bipartite networks
- (2011) J.C. Nacher et al. PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
- Understanding how both the partitions of a bipartite network affect its one-mode projection
- (2011) Animesh Mukherjee et al. PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
- Statistically Validated Networks in Bipartite Complex Systems
- (2011) Michele Tumminello et al. PLoS One
- Biology, Methodology or Chance? The Degree Distributions of Bipartite Ecological Networks
- (2011) Richard J. Williams PLoS One
- A Network of Genes, Genetic Disorders, and Brain Areas
- (2011) Satoru Hayasaka et al. PLoS One
- Simulated Epidemics in an Empirical Spatiotemporal Network of 50,185 Sexual Contacts
- (2011) Luis E. C. Rocha et al. PLoS Computational Biology
- Using graph theory to analyze biological networks
- (2011) Georgios A Pavlopoulos et al. BioData Mining
- SCPS: a fast implementation of a spectral method for detecting protein families on a genome-wide scale
- (2010) Tamás Nepusz et al. BMC BIOINFORMATICS
- Uncovering packaging features of co-regulated modules based on human protein interaction and transcriptional regulatory networks
- (2010) Lina Chen et al. BMC BIOINFORMATICS
- AutoSOME: a clustering method for identifying gene expression modules without prior knowledge of cluster number
- (2010) Aaron M Newman et al. BMC BIOINFORMATICS
- Use of the Szeged index and the revised Szeged index for measuring network bipartivity
- (2010) Tomaž Pisanski et al. DISCRETE APPLIED MATHEMATICS
- Food webs are built up with nested subwebs
- (2010) Michio Kondoh et al. ECOLOGY
- A straightforward computational approach for measuring nestedness using quantitative matrices
- (2010) Mário Almeida-Neto et al. ENVIRONMENTAL MODELLING & SOFTWARE
- Challenges in Computational Analysis of Mass Spectrometry Data for Proteomics
- (2010) Bin Ma JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY
- Learning to rank on graphs
- (2010) Shivani Agarwal MACHINE LEARNING
- Partitioning biological data with transitivity clustering
- (2010) Tobias Wittkop et al. NATURE METHODS
- Visualization of omics data for systems biology
- (2010) Nils Gehlenborg et al. NATURE METHODS
- Network medicine: a network-based approach to human disease
- (2010) Albert-László Barabási et al. NATURE REVIEWS GENETICS
- Percolation on bipartite scale-free networks
- (2010) H. Hooyberghs et al. PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
- Link prediction in complex networks: A survey
- (2010) Linyuan Lü et al. PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
- Modeling the Spread of Vector-Borne Diseases on Bipartite Networks
- (2010) Donal Bisanzio et al. PLoS One
- The genetics of autoimmune diseases: a networked perspective
- (2009) Sergio E Baranzini CURRENT OPINION IN IMMUNOLOGY
- Weighted-Interaction Nestedness Estimator (WINE): A new estimator to calculate over frequency matrices
- (2009) Javier Galeano et al. ENVIRONMENTAL MODELLING & SOFTWARE
- Comparison of methods for the detection of node group membership in bipartite networks
- (2009) E. N. Sawardecker et al. EUROPEAN PHYSICAL JOURNAL B
- Circos: An information aesthetic for comparative genomics
- (2009) M. Krzywinski et al. GENOME RESEARCH
- Network visualization and analysis of gene expression data using BioLayout Express3D
- (2009) Athanasios Theocharidis et al. Nature Protocols
- VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology
- (2009) Zhenjun Hu et al. NUCLEIC ACIDS RESEARCH
- An analytic approach to the measurement of nestedness in bipartite networks
- (2009) Aderaldo I.L. Araujo et al. PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
- Community detection in graphs
- (2009) Santo Fortunato PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS
- Network Properties of Complex Human Disease Genes Identified through Genome-Wide Association Studies
- (2009) Fredrik Barrenas et al. PLoS One
- Extracting the multiscale backbone of complex weighted networks
- (2009) M. A. Serrano et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Using Network Component Analysis to Dissect Regulatory Networks Mediated by Transcription Factors in Yeast
- (2009) Chun Ye et al. PLoS Computational Biology
- A Dynamic Network Approach for the Study of Human Phenotypes
- (2009) César A. Hidalgo et al. PLoS Computational Biology
- Comparative analysis of the complex transcription-factor gene regulatory networks of E. coli and S. cerevisiae
- (2008) Lev Guzman-Vargas et al. BMC Systems Biology
- Arena3D: visualization of biological networks in 3D
- (2008) Georgios A Pavlopoulos et al. BMC Systems Biology
- Drug-Binding Databases
- (2008) Luis Fernando Macedo Timmers et al. CURRENT DRUG TARGETS
- WHAT DO INTERACTION NETWORK METRICS TELL US ABOUT SPECIALIZATION AND BIOLOGICAL TRAITS
- (2008) Nico Blüthgen et al. ECOLOGY
- Systems biology model databases and resources
- (2008) Carel van Gend et al. Essays in Biochemistry
- Network medicine
- (2008) Tony Pawson et al. FEBS LETTERS
- Separating the Wheat from the Chaff: Unbiased Filtering of Background Tandem Mass Spectra Improves Protein Identification
- (2008) Magno Junqueira et al. JOURNAL OF PROTEOME RESEARCH
- RNA-Seq: a revolutionary tool for transcriptomics
- (2008) Zhong Wang et al. NATURE REVIEWS GENETICS
- A consumer's guide to nestedness analysis
- (2008) Werner Ulrich et al. OIKOS
- Clustering coefficient and community structure of bipartite networks
- (2008) Peng Zhang et al. PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
- Two classes of bipartite networks: Nested biological and social systems
- (2008) Enrique Burgos et al. PHYSICAL REVIEW E
- Drug Target Identification Using Side-Effect Similarity
- (2008) M. Campillos et al. SCIENCE
- Unraveling Protein Networks with Power Graph Analysis
- (2008) Loïc Royer et al. PLoS Computational Biology
- A survey of visualization tools for biological network analysis
- (2008) Georgios A Pavlopoulos et al. BioData Mining
- Biclustering in data mining
- (2007) Stanislav Busygin et al. COMPUTERS & OPERATIONS RESEARCH
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