Bipartite graphs in systems biology and medicine: a survey of methods and applications
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Title
Bipartite graphs in systems biology and medicine: a survey of methods and applications
Authors
Keywords
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Journal
GigaScience
Volume 7, Issue 4, Pages -
Publisher
Oxford University Press (OUP)
Online
2018-02-19
DOI
10.1093/gigascience/giy014
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Note: Only part of the references are listed.- BiRank: Towards Ranking on Bipartite Graphs
- (2017) Xiangnan He et al. IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING
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- (2016) Jessica Xin Hu et al. NATURE REVIEWS GENETICS
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- SNAP
- (2016) Jure Leskovec et al. ACM Transactions on Intelligent Systems and Technology
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- (2015) Robert D. Finn et al. NUCLEIC ACIDS RESEARCH
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- (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
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- (2014) ATHANASIA PAVLOPOULOU et al. ONCOLOGY REPORTS
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- (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
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- (2014) XueZhong Zhou et al. Nature Communications
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- (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
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- (2014) Jan Klecka PeerJ
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- (2013) William A Bryant et al. BMC Systems Biology
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- (2013) D. G. Hernández et al. PHYSICAL REVIEW E
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- (2013) Juyong Lee et al. PLoS One
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- (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
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- (2013) Carsten F. Dormann et al. Methods in Ecology and Evolution
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- (2013) Jose C. Nacher et al. Scientific Reports
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- (2013) Georgios A Pavlopoulos et al. BioData Mining
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- (2013) Yuji Zhang et al. Journal of Biomedical Semantics
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- (2012) John H Morris et al. BMC BIOINFORMATICS
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- (2012) Jim Wang et al. BMC BIOINFORMATICS
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- (2012) Maria Secrier et al. BMC BIOINFORMATICS
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- (2010) Aaron M Newman et al. BMC BIOINFORMATICS
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- (2010) Tomaž Pisanski et al. DISCRETE APPLIED MATHEMATICS
- Food webs are built up with nested subwebs
- (2010) Michio Kondoh et al. ECOLOGY
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- (2010) Mário Almeida-Neto et al. ENVIRONMENTAL MODELLING & SOFTWARE
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- (2010) Bin Ma JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY
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- (2010) Shivani Agarwal MACHINE LEARNING
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- (2010) Tobias Wittkop et al. NATURE METHODS
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- (2010) Nils Gehlenborg et al. NATURE METHODS
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- (2010) H. Hooyberghs et al. PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
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- (2010) Donal Bisanzio et al. PLoS One
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- Weighted-Interaction Nestedness Estimator (WINE): A new estimator to calculate over frequency matrices
- (2009) Javier Galeano et al. ENVIRONMENTAL MODELLING & SOFTWARE
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- (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
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- (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
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- (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
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- (2008) Carel van Gend et al. Essays in Biochemistry
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- (2008) Tony Pawson et al. FEBS LETTERS
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- RNA-Seq: a revolutionary tool for transcriptomics
- (2008) Zhong Wang et al. NATURE REVIEWS GENETICS
- A consumer's guide to nestedness analysis
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- Clustering coefficient and community structure of bipartite networks
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- Two classes of bipartite networks: Nested biological and social systems
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- (2007) Stanislav Busygin et al. COMPUTERS & OPERATIONS RESEARCH
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