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Title: Bipartite graphs in systems biology and medicine: a survey of methods and applications

Abstract

The latest advances in high-throughput techniques during the past decade allowed the systems biology field to expand significantly. Today, the focus of biologists has shifted from the study of individual biological components to the study of complex biological systems and their dynamics at a larger scale. Through the discovery of novel bioentity relationships, researchers reveal new information about biological functions and processes. Graphs are widely used to represent bioentities such as proteins, genes, small molecules, ligands, and others such as nodes and their connections as edges within a network. In this review, special focus is given to the usability of bipartite graphs and their impact on the field of network biology and medicine. Furthermore, their topological properties and how these can be applied to certain biological case studies are discussed. Finally, available methodologies and software are presented, and useful insights on how bipartite graphs can shape the path toward the solution of challenging biological problems are provided.

Authors:
 [1];  [2];  [3];  [4];  [2];  [2]
  1. Lawrence Berkeley Labs, DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
  2. University of Thessaly, Department of Computer Science and Biomedical Informatics, Papasiopoulou 2–4, Lamia, 35100, Greece
  3. Izmir International Biomedicine and Genome Institute (iBG-Izmir), Dokuz Eylül University, 35340, Turkey
  4. Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR7216, CNRS, France
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Univ. of California, Oakland, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1432564
Alternate Identifier(s):
OSTI ID: 1543958
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Published Article
Journal Name:
GigaScience
Additional Journal Information:
Journal Name: GigaScience Journal Volume: 7 Journal Issue: 4; Journal ID: ISSN 2047-217X
Publisher:
BioMed Central
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Life Sciences & Biomedicine - Other Topics; Science & Technology - Other Topics

Citation Formats

Pavlopoulos, Georgios A., Kontou, Panagiota I., Pavlopoulou, Athanasia, Bouyioukos, Costas, Markou, Evripides, and Bagos, Pantelis G. Bipartite graphs in systems biology and medicine: a survey of methods and applications. United Kingdom: N. p., 2018. Web. doi:10.1093/gigascience/giy014.
Pavlopoulos, Georgios A., Kontou, Panagiota I., Pavlopoulou, Athanasia, Bouyioukos, Costas, Markou, Evripides, & Bagos, Pantelis G. Bipartite graphs in systems biology and medicine: a survey of methods and applications. United Kingdom. doi:10.1093/gigascience/giy014.
Pavlopoulos, Georgios A., Kontou, Panagiota I., Pavlopoulou, Athanasia, Bouyioukos, Costas, Markou, Evripides, and Bagos, Pantelis G. Mon . "Bipartite graphs in systems biology and medicine: a survey of methods and applications". United Kingdom. doi:10.1093/gigascience/giy014.
@article{osti_1432564,
title = {Bipartite graphs in systems biology and medicine: a survey of methods and applications},
author = {Pavlopoulos, Georgios A. and Kontou, Panagiota I. and Pavlopoulou, Athanasia and Bouyioukos, Costas and Markou, Evripides and Bagos, Pantelis G.},
abstractNote = {The latest advances in high-throughput techniques during the past decade allowed the systems biology field to expand significantly. Today, the focus of biologists has shifted from the study of individual biological components to the study of complex biological systems and their dynamics at a larger scale. Through the discovery of novel bioentity relationships, researchers reveal new information about biological functions and processes. Graphs are widely used to represent bioentities such as proteins, genes, small molecules, ligands, and others such as nodes and their connections as edges within a network. In this review, special focus is given to the usability of bipartite graphs and their impact on the field of network biology and medicine. Furthermore, their topological properties and how these can be applied to certain biological case studies are discussed. Finally, available methodologies and software are presented, and useful insights on how bipartite graphs can shape the path toward the solution of challenging biological problems are provided.},
doi = {10.1093/gigascience/giy014},
journal = {GigaScience},
number = 4,
volume = 7,
place = {United Kingdom},
year = {2018},
month = {2}
}

Journal Article:
Free Publicly Available Full Text
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DOI: 10.1093/gigascience/giy014

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Works referenced in this record:

Community structure in social and biological networks
journal, June 2002

  • Girvan, M.; Newman, M. E. J.
  • Proceedings of the National Academy of Sciences, Vol. 99, Issue 12
  • DOI: 10.1073/pnas.122653799

Compression-based fixed-parameter algorithms for feedback vertex set and edge bipartization
journal, December 2006

  • Guo, Jiong; Gramm, Jens; Hüffner, Falk
  • Journal of Computer and System Sciences, Vol. 72, Issue 8
  • DOI: 10.1016/j.jcss.2006.02.001

Scientific collaboration networks. II. Shortest paths, weighted networks, and centrality
journal, June 2001


SCPS: a fast implementation of a spectral method for detecting protein families on a genome-wide scale
journal, March 2010

  • Nepusz, Tamás; Sasidharan, Rajkumar; Paccanaro, Alberto
  • BMC Bioinformatics, Vol. 11, Issue 1
  • DOI: 10.1186/1471-2105-11-120

Scientific collaboration networks.  I. Network construction and fundamental results
journal, June 2001


networksis : A Package to Simulate Bipartite Graphs with Fixed Marginals Through Sequential Importance Sampling
journal, January 2008

  • Admiraal, Ryan; Handcock, Mark S.
  • Journal of Statistical Software, Vol. 24, Issue 8
  • DOI: 10.18637/jss.v024.i08

The Small World of Corporate Boards
journal, November 2006


Link prediction in complex networks: A survey
journal, March 2011


Network biology concepts in complex disease comorbidities
journal, August 2016

  • Hu, Jessica Xin; Thomas, Cecilia Engel; Brunak, Søren
  • Nature Reviews Genetics, Vol. 17, Issue 10
  • DOI: 10.1038/nrg.2016.87

FALCON: a software package for analysis of nestedness in bipartite networks
journal, January 2014


Identifying statistically significant edges in one-mode projections
journal, March 2013


Graph-based analysis and visualization of experimental results with ONDEX
journal, March 2006


A consumer's guide to nestedness analysis
journal, January 2009


Network Analysis in Public Health: History, Methods, and Applications
journal, April 2007


The New Bioinformatics: Integrating Ecological Data from the Gene to the Biosphere
journal, December 2006


The modular nature of genetic diseases
journal, October 2006


Extracting the multiscale backbone of complex weighted networks
journal, April 2009

  • Serrano, M. A.; Boguna, M.; Vespignani, A.
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 16
  • DOI: 10.1073/pnas.0808904106

An $n^{5/2} $ Algorithm for Maximum Matchings in Bipartite Graphs
journal, December 1973

  • Hopcroft, John E.; Karp, Richard M.
  • SIAM Journal on Computing, Vol. 2, Issue 4
  • DOI: 10.1137/0202019

Resources for integrative systems biology: from data through databases to networks and dynamic system models
journal, October 2006

  • Ng, Aylwin; Bursteinas, Borisas; Gao, Qiong
  • Briefings in Bioinformatics, Vol. 7, Issue 4
  • DOI: 10.1093/bib/bbl036

Finding odd cycle transversals
journal, July 2004


SNP Web Resources and Their Potential Applications in Personalized Medicine
journal, July 2012


Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution
journal, March 2016

  • Corel, Eduardo; Lopez, Philippe; Méheust, Raphaël
  • Trends in Microbiology, Vol. 24, Issue 3
  • DOI: 10.1016/j.tim.2015.12.003

Internal links and pairs as a new tool for the analysis of bipartite complex networks
journal, February 2012

  • Allali, Oussama; Tabourier, Lionel; Magnien, Clémence
  • Social Network Analysis and Mining, Vol. 3, Issue 1
  • DOI: 10.1007/s13278-012-0053-0

Comparative analysis of the transcription-factor gene regulatory networks of E. coli and S. cerevisiae
journal, January 2008


AMBIENT: Active Modules for Bipartite Networks - using high-throughput transcriptomic data to dissect metabolic response
journal, January 2013

  • Bryant, William A.; Sternberg, Michael JE; Pinney, John W.
  • BMC Systems Biology, Vol. 7, Issue 1
  • DOI: 10.1186/1752-0509-7-26

The Dynamics of Nestedness Predicts the Evolution of Industrial Ecosystems
journal, November 2012


Bipartite Community Structure of eQTLs
journal, September 2016


AutoSOME: a clustering method for identifying gene expression modules without prior knowledge of cluster number
journal, March 2010


Multiple graph regularized protein domain ranking
journal, January 2012


BicAT: a biclustering analysis toolbox
journal, March 2006


Edge crossings in drawings of bipartite graphs
journal, April 1994

  • Eades, Peter; Wormald, Nicholas C.
  • Algorithmica, Vol. 11, Issue 4
  • DOI: 10.1007/BF01187020

On the degree distribution of projected networks mapped from bipartite networks
journal, November 2011

  • Nacher, J. C.; Akutsu, T.
  • Physica A: Statistical Mechanics and its Applications, Vol. 390, Issue 23-24
  • DOI: 10.1016/j.physa.2011.06.073

Visualization of omics data for systems biology
journal, March 2010

  • Gehlenborg, Nils; O'Donoghue, Seán I.; Baliga, Nitin S.
  • Nature Methods, Vol. 7, Issue S3
  • DOI: 10.1038/nmeth.1436

Structural controllability of unidirectional bipartite networks
journal, April 2013

  • Nacher, Jose C.; Akutsu, Tatsuya
  • Scientific Reports, Vol. 3, Issue 1
  • DOI: 10.1038/srep01647

Drug—target network
journal, October 2007

  • Yıldırım, Muhammed A.; Goh, Kwang-Il; Cusick, Michael E.
  • Nature Biotechnology, Vol. 25, Issue 10
  • DOI: 10.1038/nbt1338

The protein–protein interaction map of Helicobacter pylori
journal, January 2001

  • Rain, Jean-Christophe; Selig, Luc; De Reuse, Hilde
  • Nature, Vol. 409, Issue 6817
  • DOI: 10.1038/35051615

Systems biological approach on neurological disorders: a novel molecular connectivity to aging and psychiatric diseases
journal, January 2011

  • Ahmed, Shiek SSJ; Ahameethunisa, Abdul R.; Santosh, Winkins
  • BMC Systems Biology, Vol. 5, Issue 1
  • DOI: 10.1186/1752-0509-5-6

The measure of order and disorder in the distribution of species in fragmented habitat
journal, December 1993


Finding and evaluating community structure in networks
journal, February 2004


The genetics of autoimmune diseases: a networked perspective
journal, December 2009


A systematic comparison and evaluation of biclustering methods for gene expression data
journal, February 2006


Simulated Epidemics in an Empirical Spatiotemporal Network of 50,185 Sexual Contacts
journal, March 2011


Spatial structure of ant-plant mutualistic networks
journal, May 2013


Using graph theory to analyze biological networks
journal, April 2011

  • Pavlopoulos, Georgios A.; Secrier, Maria; Moschopoulos, Charalampos N.
  • BioData Mining, Vol. 4, Issue 1
  • DOI: 10.1186/1756-0381-4-10

An Overview of NCA-Based Algorithms for Transcriptional Regulatory Network Inference
journal, November 2015


Food webs are built up with nested subwebs
journal, November 2010

  • Kondoh, Michio; Kato, Satoshi; Sakato, Yoshikuni
  • Ecology, Vol. 91, Issue 11
  • DOI: 10.1890/09-2219.1

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations
journal, December 2013

  • Welter, Danielle; MacArthur, Jacqueline; Morales, Joannella
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1229

An efficient algorithm for large-scale detection of protein families
journal, April 2002


Medusa: A tool for exploring and clustering biological networks
journal, October 2011

  • Pavlopoulos, Georgios A.; Hooper, Sean D.; Sifrim, Alejandro
  • BMC Research Notes, Vol. 4, Issue 1
  • DOI: 10.1186/1756-0500-4-384

The dynamics of sexual contact networks: Effects on disease spread and control
journal, March 2012

  • Robinson, Katy; Cohen, Ted; Colijn, Caroline
  • Theoretical Population Biology, Vol. 81, Issue 2
  • DOI: 10.1016/j.tpb.2011.12.009

Percolation on bipartite scale-free networks
journal, August 2010

  • Hooyberghs, H.; Van Schaeybroeck, B.; Indekeu, J. O.
  • Physica A: Statistical Mechanics and its Applications, Vol. 389, Issue 15
  • DOI: 10.1016/j.physa.2009.12.068

Epidemic thresholds for bipartite networks
journal, November 2013


Modularity and community detection in bipartite networks
journal, December 2007


Replication validity of genetic association studies
journal, October 2001

  • Ioannidis, John P. A.; Ntzani, Evangelia E.; Trikalinos, Thomas A.
  • Nature Genetics, Vol. 29, Issue 3
  • DOI: 10.1038/ng749

Invariant properties in coevolutionary networks of plant-animal interactions: Invariant properties in coevolutionary networks
journal, December 2002


An analytic approach to the measurement of nestedness in bipartite networks
journal, April 2010

  • Araujo, Aderaldo I. L.; Corso, Gilberto; Almeida, Adriana M.
  • Physica A: Statistical Mechanics and its Applications, Vol. 389, Issue 7
  • DOI: 10.1016/j.physa.2009.11.030

Network-based analysis of vaccine-related associations reveals consistent knowledge with the vaccine ontology
journal, January 2013

  • Zhang, Yuji; Tao, Cui; He, Yongqun
  • Journal of Biomedical Semantics, Vol. 4, Issue 1
  • DOI: 10.1186/2041-1480-4-33

A Dynamic Network Approach for the Study of Human Phenotypes
journal, April 2009

  • Hidalgo, César A.; Blumm, Nicholas; Barabási, Albert-László
  • PLoS Computational Biology, Vol. 5, Issue 4
  • DOI: 10.1371/journal.pcbi.1000353

Network component analysis: Reconstruction of regulatory signals in biological systems
journal, December 2003

  • Liao, J. C.; Boscolo, R.; Yang, Y. -L.
  • Proceedings of the National Academy of Sciences, Vol. 100, Issue 26
  • DOI: 10.1073/pnas.2136632100

Biclustering in data mining
journal, September 2008

  • Busygin, Stanislav; Prokopyev, Oleg; Pardalos, Panos M.
  • Computers & Operations Research, Vol. 35, Issue 9
  • DOI: 10.1016/j.cor.2007.01.005

SNAP: A General-Purpose Network Analysis and Graph-Mining Library
journal, July 2016

  • Leskovec, Jure; Sosič, Rok
  • ACM Transactions on Intelligent Systems and Technology, Vol. 8, Issue 1
  • DOI: 10.1145/2898361

Controllability of complex networks
journal, May 2011

  • Liu, Yang-Yu; Slotine, Jean-Jacques; Barabási, Albert-László
  • Nature, Vol. 473, Issue 7346
  • DOI: 10.1038/nature10011

Clustering coefficient and community structure of bipartite networks
journal, December 2008

  • Zhang, Peng; Wang, Jinliang; Li, Xiaojia
  • Physica A: Statistical Mechanics and its Applications, Vol. 387, Issue 27
  • DOI: 10.1016/j.physa.2008.09.006

Generalised power graph compression reveals dominant relationship patterns in complex networks
journal, March 2014


Community Detection in Large-Scale Bipartite Networks
conference, September 2009

  • Liu, Xin; Murata, Tsuyoshi
  • 2009 IEEE/WIC/ACM International Joint Conference on Web Intelligence and Intelligent Agent Technology
  • DOI: 10.1109/WI-IAT.2009.15

Collective dynamics of ‘small-world’ networks
journal, June 1998

  • Watts, Duncan J.; Strogatz, Steven H.
  • Nature, Vol. 393, Issue 6684
  • DOI: 10.1038/30918

Overlapping Community Detection in Bipartite Networks
conference, December 2008

  • Du, Nan; Wang, Bai; Wu, Bin
  • 2008 IEEE/WIC/ACM International Conference on Web Intelligence and Intelligent Agent Technology
  • DOI: 10.1109/WIIAT.2008.98

Circos: An information aesthetic for comparative genomics
journal, June 2009


Food-web structure and network theory: The role of connectance and size
journal, September 2002

  • Dunne, J. A.; Williams, R. J.; Martinez, N. D.
  • Proceedings of the National Academy of Sciences, Vol. 99, Issue 20
  • DOI: 10.1073/pnas.192407699

Coming of age: ten years of next-generation sequencing technologies
journal, May 2016

  • Goodwin, Sara; McPherson, John D.; McCombie, W. Richard
  • Nature Reviews Genetics, Vol. 17, Issue 6
  • DOI: 10.1038/nrg.2016.49

Two-mode network modeling and analysis of dengue epidemic behavior in Gombak, Malaysia
journal, March 2017

  • Malik, Hafiz Abid Mahmood; Mahesar, Abdul Waheed; Abid, Faiza
  • Applied Mathematical Modelling, Vol. 43
  • DOI: 10.1016/j.apm.2016.10.060

Why Most Published Research Findings Are False
journal, August 2005


Online collaboration: Scientists and the social network
journal, August 2014


Genenames.org: the HGNC resources in 2015
journal, October 2014

  • Gray, Kristian A.; Yates, Bethan; Seal, Ruth L.
  • Nucleic Acids Research, Vol. 43, Issue D1
  • DOI: 10.1093/nar/gku1071

Network bipartivity
journal, November 2003


Arena3D: visualizing time-driven phenotypic differences in biological systems
journal, March 2012

  • Secrier, Maria; Pavlopoulos, Georgios A.; Aerts, Jan
  • BMC Bioinformatics, Vol. 13, Issue 1
  • DOI: 10.1186/1471-2105-13-45

The maximum edge biclique problem is NP-complete
journal, September 2003


ProViz: protein interaction visualization and exploration
journal, September 2004


Network reliability analysis based on percolation theory
journal, October 2015


A systematic approach to the one-mode projection of bipartite graphs
journal, April 2011

  • Zweig, Katharina Anna; Kaufmann, Michael
  • Social Network Analysis and Mining, Vol. 1, Issue 3
  • DOI: 10.1007/s13278-011-0021-0

Unraveling Protein Networks with Power Graph Analysis
journal, July 2008


A Bipartite Network-based Method for Prediction of Long Non-coding RNA–protein Interactions
journal, February 2016


Algorithms for drawing graphs: an annotated bibliography
journal, October 1994


Network Robustness and Fragility: Percolation on Random Graphs
journal, December 2000

  • Callaway, Duncan S.; Newman, M. E. J.; Strogatz, Steven H.
  • Physical Review Letters, Vol. 85, Issue 25
  • DOI: 10.1103/PhysRevLett.85.5468

Network Properties of Complex Human Disease Genes Identified through Genome-Wide Association Studies
journal, November 2009


What do molecular methods bring to host–parasitoid food webs?
journal, January 2015


Scalable multipartite subgraph enumeration for integrative analysis of heterogeneous experimental functional genomics data
conference, January 2015

  • Phillips, Charles A.; Wang, Kai; Bubier, Jason
  • Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics - BCB '15
  • DOI: 10.1145/2808719.2812595

Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future
journal, August 2015

  • Pavlopoulos, Georgios A.; Malliarakis, Dimitris; Papanikolaou, Nikolas
  • GigaScience, Vol. 4, Issue 1
  • DOI: 10.1186/s13742-015-0077-2

A straightforward computational approach for measuring nestedness using quantitative matrices
journal, February 2011


Stable marriage and indifference
journal, February 1994


Modeling the Spread of Vector-Borne Diseases on Bipartite Networks
journal, November 2010


NAP: The Network Analysis Profiler, a web tool for easier topological analysis and comparison of medium-scale biological networks
journal, July 2017

  • Theodosiou, Theodosios; Efstathiou, Georgios; Papanikolaou, Nikolas
  • BMC Research Notes, Vol. 10, Issue 1
  • DOI: 10.1186/s13104-017-2607-8

The nested assembly of plant-animal mutualistic networks
journal, July 2003

  • Bascompte, J.; Jordano, P.; Melian, C. J.
  • Proceedings of the National Academy of Sciences, Vol. 100, Issue 16
  • DOI: 10.1073/pnas.1633576100

Disentangling nestedness from models of ecological complexity
journal, June 2012

  • James, Alex; Pitchford, Jonathan W.; Plank, Michael J.
  • Nature, Vol. 487, Issue 7406
  • DOI: 10.1038/nature11214

Small Molecule Databases and Chemical Descriptors Useful in Chemoinformatics: An Overview
journal, July 2011

  • Gozalbes, Rafael; Pineda-Lucena, Antonio
  • Combinatorial Chemistry & High Throughput Screening, Vol. 14, Issue 6
  • DOI: 10.2174/138620711795767857

A protein-protein interaction map of the Caenorhabditis elegans 26S proteasome
journal, September 2001


Prediction of Drug-Target Interactions and Drug Repositioning via Network-Based Inference
journal, May 2012


PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways
journal, July 2002


Two classes of bipartite networks: Nested biological and social systems
journal, October 2008


A note on a generalization of eigenvector centrality for bipartite graphs and applications
journal, May 2011


Network thinking in ecology and evolution
journal, June 2005


Sex differences in intimate relationships
journal, April 2012

  • Palchykov, Vasyl; Kaski, Kimmo; Kertész, Janos
  • Scientific Reports, Vol. 2, Issue 1
  • DOI: 10.1038/srep00370

Topological analysis and interactive visualization of biological networks and protein structures
journal, March 2012

  • Doncheva, Nadezhda T.; Assenov, Yassen; Domingues, Francisco S.
  • Nature Protocols, Vol. 7, Issue 4
  • DOI: 10.1038/nprot.2012.004

Using Network Component Analysis to Dissect Regulatory Networks Mediated by Transcription Factors in Yeast
journal, March 2009


Plant-Animal Mutualistic Networks: The Architecture of Biodiversity
journal, December 2007


Integrating domain similarity to improve protein complexes identification in TAP-MS data
journal, January 2013


Tissue Specificity of Human Disease Module
journal, October 2016

  • Kitsak, Maksim; Sharma, Amitabh; Menche, Jörg
  • Scientific Reports, Vol. 6, Issue 1
  • DOI: 10.1038/srep35241

Arena3D: visualization of biological networks in 3D
journal, January 2008

  • Pavlopoulos, Georgios A.; O'Donoghue, Seán I.; Satagopam, Venkata P.
  • BMC Systems Biology, Vol. 2, Issue 1
  • DOI: 10.1186/1752-0509-2-104

The structure of scientific collaboration networks
journal, January 2001

  • Newman, M. E. J.
  • Proceedings of the National Academy of Sciences, Vol. 98, Issue 2
  • DOI: 10.1073/pnas.98.2.404

Social network analysis: developments, advances, and prospects
journal, October 2010


Small Worlds Among Interlocking Directors: Network Structure and Distance in Bipartite Graphs
journal, May 2004


The ghost of nestedness in ecological networks
journal, January 2013

  • Staniczenko, Phillip P. A.; Kopp, Jason C.; Allesina, Stefano
  • Nature Communications, Vol. 4, Issue 1
  • DOI: 10.1038/ncomms2422

Nationwide Population Science: Lessons From the Taiwan National Health Insurance Research Database
journal, September 2015


Clustering by Passing Messages Between Data Points
journal, February 2007


OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders
journal, November 2014

  • Amberger, Joanna S.; Bocchini, Carol A.; Schiettecatte, François
  • Nucleic Acids Research, Vol. 43, Issue D1
  • DOI: 10.1093/nar/gku1205

Partitioning biological data with transitivity clustering
journal, June 2010

  • Wittkop, Tobias; Emig, Dorothea; Lange, Sita
  • Nature Methods, Vol. 7, Issue 6
  • DOI: 10.1038/nmeth0610-419

From molecular to modular cell biology
journal, December 1999

  • Hartwell, Leland H.; Hopfield, John J.; Leibler, Stanislas
  • Nature, Vol. 402, Issue S6761
  • DOI: 10.1038/35011540

Network visualization and analysis of gene expression data using BioLayout Express3D
journal, October 2009

  • Theocharidis, Athanasios; van Dongen, Stjin; Enright, Anton J.
  • Nature Protocols, Vol. 4, Issue 10
  • DOI: 10.1038/nprot.2009.177

Host-Parasitoid Population Interactions
journal, January 1984


Separating the Wheat from the Chaff: Unbiased Filtering of Background Tandem Mass Spectra Improves Protein Identification
journal, August 2008

  • Junqueira, Magno; Spirin, Victor; Santana Balbuena, Tiago
  • Journal of Proteome Research, Vol. 7, Issue 8
  • DOI: 10.1021/pr800140v

An algorithm for counting short cycles in bipartite graphs
journal, January 2006

  • Halford, T. R.; Chugg, K. M.
  • IEEE Transactions on Information Theory, Vol. 52, Issue 1
  • DOI: 10.1109/TIT.2005.860472

On the k-path partition of graphs
journal, January 2003


Bipartite graphs as models of complex networks
journal, November 2006

  • Guillaume, Jean-Loup; Latapy, Matthieu
  • Physica A: Statistical Mechanics and its Applications, Vol. 371, Issue 2
  • DOI: 10.1016/j.physa.2006.04.047

Data and programs in support of network analysis of genes and their association with diseases
journal, September 2016


A branch and bound algorithm for minimizing the number of crossing arcs in bipartite graphs
journal, April 1996


Network analysis of genes and their association with diseases
journal, September 2016


Challenges in Computational Analysis of Mass Spectrometry Data for Proteomics
journal, January 2010


Integrated Assessment and Prediction of Transcription Factor Binding
journal, January 2006


A novel genetic system to detect protein–protein interactions
journal, July 1989

  • Fields, Stanley; Song, Ok-kyu
  • Nature, Vol. 340, Issue 6230, p. 245-246
  • DOI: 10.1038/340245a0

The Genetic Association Database
journal, May 2004

  • Becker, Kevin G.; Barnes, Kathleen C.; Bright, Tiffani J.
  • Nature Genetics, Vol. 36, Issue 5
  • DOI: 10.1038/ng0504-431

What do Interaction Network Metrics tell us About Specialization and Biological Traits
journal, December 2008

  • Blüthgen, Nico; Fründ, Jochen; Vázquez, Diego P.
  • Ecology, Vol. 89, Issue 12
  • DOI: 10.1890/07-2121.1

Network medicine: a network-based approach to human disease
journal, December 2010

  • Barabási, Albert-László; Gulbahce, Natali; Loscalzo, Joseph
  • Nature Reviews Genetics, Vol. 12, Issue 1
  • DOI: 10.1038/nrg2918

Versatility and Connectivity Efficiency of Bipartite Transcription Networks
journal, October 2006


Genome-wide analysis of vaccinia virus protein-protein interactions
journal, April 2000

  • McCraith, S.; Holtzman, T.; Moss, B.
  • Proceedings of the National Academy of Sciences, Vol. 97, Issue 9
  • DOI: 10.1073/pnas.080078197

Link prediction in bipartite graphs using internal links and weighted projection
conference, April 2011

  • Allali, Oussama; Magnien, Clemence; Latapy, Matthieu
  • IEEE INFOCOM 2011 - IEEE Conference on Computer Communications Workshops, 2011 IEEE Conference on Computer Communications Workshops (INFOCOM WKSHPS)
  • DOI: 10.1109/INFCOMW.2011.5928947

mapman: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes
journal, March 2004


Mining electronic health records: towards better research applications and clinical care
journal, May 2012

  • Jensen, Peter B.; Jensen, Lars J.; Brunak, Søren
  • Nature Reviews Genetics, Vol. 13, Issue 6
  • DOI: 10.1038/nrg3208

The Pfam protein families database: towards a more sustainable future
journal, December 2015

  • Finn, Robert D.; Coggill, Penelope; Eberhardt, Ruth Y.
  • Nucleic Acids Research, Vol. 44, Issue D1
  • DOI: 10.1093/nar/gkv1344

Self-organization of collaboration networks
journal, September 2004

  • Ramasco, José J.; Dorogovtsev, S. N.; Pastor-Satorras, Romualdo
  • Physical Review E, Vol. 70, Issue 3
  • DOI: 10.1103/PhysRevE.70.036106

On the meaning and measurement of nestedness of species assemblages
journal, December 1992


Drug Target Identification Using Side-Effect Similarity
journal, July 2008


Basic notions for the analysis of large two-mode networks
journal, January 2008


Legislative cosponsorship networks in the US House and Senate
journal, October 2006


Cluster analysis and display of genome-wide expression patterns
journal, December 1998

  • Eisen, M. B.; Spellman, P. T.; Brown, P. O.
  • Proceedings of the National Academy of Sciences, Vol. 95, Issue 25
  • DOI: 10.1073/pnas.95.25.14863

RNA-Seq: a revolutionary tool for transcriptomics
journal, January 2009

  • Wang, Zhong; Gerstein, Mark; Snyder, Michael
  • Nature Reviews Genetics, Vol. 10, Issue 1
  • DOI: 10.1038/nrg2484

Learning to rank on graphs
journal, May 2010


The new geography of global civil society: NGOs in the world city network
journal, December 2004


Human cancer databases (Review)
journal, October 2014

  • Pavlopoulou, Athanasia; Spandidos, Demetrios A.; Michalopoulos, Ioannis
  • Oncology Reports, Vol. 33, Issue 1
  • DOI: 10.3892/or.2014.3579

Small World Patterns in Food Webs
journal, February 2002

  • Montoya, Jose M.; SolÉ, Ricard V.
  • Journal of Theoretical Biology, Vol. 214, Issue 3
  • DOI: 10.1006/jtbi.2001.2460

GUESS: a language and interface for graph exploration
conference, January 2006

  • Adar, Eytan
  • Proceedings of the SIGCHI conference on Human Factors in computing systems - CHI '06
  • DOI: 10.1145/1124772.1124889

Network medicine
journal, February 2008


clusterMaker: a multi-algorithm clustering plugin for Cytoscape
journal, November 2011

  • Morris, John H.; Apeltsin, Leonard; Newman, Aaron M.
  • BMC Bioinformatics, Vol. 12, Issue 1
  • DOI: 10.1186/1471-2105-12-436

Spectral measures of bipartivity in complex networks
journal, October 2005


Drug-Binding Databases
journal, December 2008

  • Macedo Timmers, Luis Fernando; Pauli, Ivani; Caceres, Rafael
  • Current Drug Targets, Vol. 9, Issue 12
  • DOI: 10.2174/138945008786949379

Generalized blockmodeling of two-mode network data
journal, January 2004


Review of Biological Network Data and Its Applications
journal, January 2013


Network analysis of 2-mode data
journal, August 1997


Supervised Machine Learning Applied to Link Prediction in Bipartite Social Networks
conference, August 2010

  • Benchettara, Nesserine; Kanawati, Rushed; Rouveirol, Céline
  • 2010 International Conference on Advances in Social Networks Analysis and Mining (ASONAM 2010)
  • DOI: 10.1109/ASONAM.2010.87

Bipartite network projection and personal recommendation
journal, October 2007


An Online Database for Informing Ecological Network Models: http://kelpforest.ucsc.edu
journal, October 2014


IMG/M: integrated genome and metagenome comparative data analysis system
journal, October 2016

  • Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken
  • Nucleic Acids Research, Vol. 45, Issue D1
  • DOI: 10.1093/nar/gkw929

Behavior Analysis of Internet Traffic via Bipartite Graphs and One-Mode Projections
journal, June 2014


Efficiently inferring community structure in bipartite networks
journal, July 2014


Protein-protein interaction and group testing in bipartite graphs
journal, January 2005

  • Li, Yingshu; Thai, My T.; Liu, Zhen
  • International Journal of Bioinformatics Research and Applications, Vol. 1, Issue 4
  • DOI: 10.1504/IJBRA.2005.008444

A survey of visualization tools for biological network analysis
journal, November 2008

  • Pavlopoulos, Georgios A.; Wegener, Anna-Lynn; Schneider, Reinhard
  • BioData Mining, Vol. 1, Issue 1
  • DOI: 10.1186/1756-0381-1-12

Extracting Multi-facet Community Structure from Bipartite Networks
conference, August 2009

  • Suzuki, Kenta; Wakita, Ken
  • 2009 International Conference on Computational Science and Engineering
  • DOI: 10.1109/CSE.2009.451

DiseaseConnect: a comprehensive web server for mechanism-based disease–disease connections
journal, June 2014

  • Liu, Chun-Chi; Tseng, Yu-Ting; Li, Wenyuan
  • Nucleic Acids Research, Vol. 42, Issue W1
  • DOI: 10.1093/nar/gku412

Recommendation as link prediction in bipartite graphs: A graph kernel-based machine learning approach
journal, January 2013


A sexual affiliation network of swingers, heterosexuals practicing risk behaviours that potentiate the spread of sexually transmitted infections: A two-mode approach
journal, May 2013

  • Niekamp, Anne-Marie; Mercken, Liesbeth A. G.; Hoebe, Christian J. P. A.
  • Social Networks, Vol. 35, Issue 2
  • DOI: 10.1016/j.socnet.2013.02.006

Understanding how both the partitions of a bipartite network affect its one-mode projection
journal, October 2011

  • Mukherjee, Animesh; Choudhury, Monojit; Ganguly, Niloy
  • Physica A: Statistical Mechanics and its Applications, Vol. 390, Issue 20
  • DOI: 10.1016/j.physa.2011.05.007

Human symptoms–disease network
journal, June 2014

  • Zhou, XueZhong; Menche, Jörg; Barabási, Albert-László
  • Nature Communications, Vol. 5, Issue 1
  • DOI: 10.1038/ncomms5212

Hive plots--rational approach to visualizing networks
journal, December 2011

  • Krzywinski, M.; Birol, I.; Jones, S. J.
  • Briefings in Bioinformatics, Vol. 13, Issue 5
  • DOI: 10.1093/bib/bbr069

The role of a water bug, Sigara striata , in freshwater food webs
journal, January 2014


OpenOrd: an open-source toolbox for large graph layout
conference, January 2011

  • Martin, Shawn; Brown, W. Michael; Klavans, Richard
  • IS&T/SPIE Electronic Imaging, SPIE Proceedings
  • DOI: 10.1117/12.871402

VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology
journal, May 2009

  • Hu, Zhenjun; Hung, Jui-Hung; Wang, Yan
  • Nucleic Acids Research, Vol. 37, Issue suppl_2
  • DOI: 10.1093/nar/gkp406

Unraveling genomic variation from next generation sequencing data
journal, July 2013

  • Pavlopoulos, Georgios A.; Oulas, Anastasis; Iacucci, Ernesto
  • BioData Mining, Vol. 6, Issue 1
  • DOI: 10.1186/1756-0381-6-13

A comprehensive two-hybrid analysis to explore the yeast protein interactome
journal, March 2001

  • Ito, T.; Chiba, T.; Ozawa, R.
  • Proceedings of the National Academy of Sciences, Vol. 98, Issue 8
  • DOI: 10.1073/pnas.061034498

Use of the Szeged index and the revised Szeged index for measuring network bipartivity
journal, October 2010


Protein-Protein Interaction Detection: Methods and Analysis
journal, January 2014

  • Rao, V. Srinivasa; Srinivas, K.; Sujini, G. N.
  • International Journal of Proteomics, Vol. 2014
  • DOI: 10.1155/2014/147648

A Network of Genes, Genetic Disorders, and Brain Areas
journal, June 2011


DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants
journal, October 2016

  • Piñero, Janet; Bravo, Àlex; Queralt-Rosinach, Núria
  • Nucleic Acids Research, Vol. 45, Issue D1
  • DOI: 10.1093/nar/gkw943

Cycles and clustering in bipartite networks
journal, November 2005


Comparison of methods for the detection of node group membership in bipartite networks
journal, November 2009

  • Sawardecker, E. N.; Amundsen, C. A.; Sales-Pardo, M.
  • The European Physical Journal B, Vol. 72, Issue 4
  • DOI: 10.1140/epjb/e2009-00397-6

Determination of argininosuccinate lyase and arginase activities with an amino acid analyzer
journal, December 1990


Weighted networks of scientific communication: the measurement and topological role of weight
journal, May 2005

  • Li, Menghui; Fan, Ying; Chen, Jiawei
  • Physica A: Statistical Mechanics and its Applications, Vol. 350, Issue 2-4
  • DOI: 10.1016/j.physa.2004.11.039

Uncovering packaging features of co-regulated modules based on human protein interaction and transcriptional regulatory networks
journal, July 2010


enaR : An r package for Ecosystem Network Analysis
journal, October 2014

  • Borrett, Stuart R.; Lau, Matthew K.
  • Methods in Ecology and Evolution, Vol. 5, Issue 11
  • DOI: 10.1111/2041-210X.12282

College Admissions and the Stability of Marriage
journal, January 1962


The human disease network
journal, May 2007

  • Goh, K. -I.; Cusick, M. E.; Valle, D.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 21
  • DOI: 10.1073/pnas.0701361104

A method for detecting modules in quantitative bipartite networks
journal, December 2013

  • Dormann, Carsten F.; Strauss, Rouven
  • Methods in Ecology and Evolution, Vol. 5, Issue 1
  • DOI: 10.1111/2041-210X.12139

graphVizdb: A scalable platform for interactive large graph visualization
conference, May 2016

  • Bikakis, Nikos; Liagouris, John; Krommyda, Maria
  • 2016 IEEE 32nd International Conference on Data Engineering (ICDE)
  • DOI: 10.1109/ICDE.2016.7498340

Human sexual contact network as a bipartite graph
journal, May 2002


Fibonacci heaps and their uses in improved network optimization algorithms
journal, July 1987

  • Fredman, Michael L.; Tarjan, Robert Endre
  • Journal of the ACM, Vol. 34, Issue 3
  • DOI: 10.1145/28869.28874

Weighted-Interaction Nestedness Estimator (WINE): A new estimator to calculate over frequency matrices
journal, November 2009


The Complexity of Enumeration and Reliability Problems
journal, August 1979

  • Valiant, Leslie G.
  • SIAM Journal on Computing, Vol. 8, Issue 3
  • DOI: 10.1137/0208032

A travel guide to Cytoscape plugins
journal, November 2012

  • Saito, Rintaro; Smoot, Michael E.; Ono, Keiichiro
  • Nature Methods, Vol. 9, Issue 11
  • DOI: 10.1038/nmeth.2212

Technique for Analyzing Overlapping Memberships
journal, January 1972

  • Bonacich, Phillip
  • Sociological Methodology, Vol. 4
  • DOI: 10.2307/270732

Empirical Comparison of Visualization Tools for Larger-Scale Network Analysis
journal, January 2017

  • Pavlopoulos, Georgios A.; Paez-Espino, David; Kyrpides, Nikos C.
  • Advances in Bioinformatics, Vol. 2017
  • DOI: 10.1155/2017/1278932

Spatial structures of network flows: A graph theoretical approach
journal, December 1987


BiRank: Towards Ranking on Bipartite Graphs
journal, January 2017

  • He, Xiangnan; Gao, Ming; Kan, Min-Yen
  • IEEE Transactions on Knowledge and Data Engineering, Vol. 29, Issue 1
  • DOI: 10.1109/TKDE.2016.2611584

Drawing graphs in two layers
journal, September 1994


Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
journal, November 2003


Deciphering the molecular basis of human cardiovascular disease through network biology
journal, January 2012


Improving the analyses of nestedness for large sets of matrices
journal, October 2006


Systems biology model databases and resources
journal, September 2008

  • van Gend, Carel; Snoep, Jacky L.
  • Essays in Biochemistry, Vol. 45
  • DOI: 10.1042/bse0450223

DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq experiments
journal, August 2016


The data paper: a mechanism to incentivize data publishing in biodiversity science
journal, December 2011


GeneWeaver: a web-based system for integrative functional genomics
journal, November 2011

  • Baker, Erich J.; Jay, Jeremy J.; Bubier, Jason A.
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr968

Global Analysis of Protein Activities Using Proteome Chips
journal, July 2001


A Network-Based Method to Assess the Statistical Significance of Mild Co-Regulation Effects
journal, September 2013


Statistically Validated Networks in Bipartite Complex Systems
journal, March 2011


The modularity of pollination networks
journal, December 2007

  • Olesen, J. M.; Bascompte, J.; Dupont, Y. L.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 50
  • DOI: 10.1073/pnas.0706375104

Discovery of Protein Complexes with Core-Attachment Structures from Tandem Affinity Purification (TAP) Data
journal, September 2012

  • Wu, Min; Li, Xiao-li; Kwoh, Chee-Keong
  • Journal of Computational Biology, Vol. 19, Issue 9
  • DOI: 10.1089/cmb.2010.0293

On Bipartite Drawings and the Linear Arrangement Problem
journal, January 2001

  • Shahrokhi, Farhad; Sýkora, Ondrej; Székely, László A.
  • SIAM Journal on Computing, Vol. 30, Issue 6
  • DOI: 10.1137/S0097539797331671

Community detection in graphs
journal, February 2010


A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae
journal, February 2000

  • Uetz, Peter; Giot, Loic; Cagney, Gerard
  • Nature, Vol. 403, Issue 6770
  • DOI: 10.1038/35001009

Network biology methods integrating biological data for translational science
journal, March 2012

  • Bebek, G.; Koyuturk, M.; Price, N. D.
  • Briefings in Bioinformatics, Vol. 13, Issue 4
  • DOI: 10.1093/bib/bbr075