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:
-
- Lawrence Berkeley Labs, DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
- University of Thessaly, Department of Computer Science and Biomedical Informatics, Papasiopoulou 2–4, Lamia, 35100, Greece
- Izmir International Biomedicine and Genome Institute (iBG-Izmir), Dokuz Eylül University, 35340, Turkey
- Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR7216, CNRS, France
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (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. https://doi.org/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. https://doi.org/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 = {Mon Feb 19 00:00:00 EST 2018},
month = {Mon Feb 19 00:00:00 EST 2018}
}
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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
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
Scientific collaboration networks. II. Shortest paths, weighted networks, and centrality
journal, June 2001
- Newman, M. E. J.
- Physical Review E, Vol. 64, Issue 1
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
Scientific collaboration networks. I. Network construction and fundamental results
journal, June 2001
- Newman, M. E. J.
- Physical Review E, Vol. 64, Issue 1
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
KONECT: the Koblenz network collection
conference, January 2013
- Kunegis, Jérôme
- Proceedings of the 22nd International Conference on World Wide Web - WWW '13 Companion
The Small World of Corporate Boards
journal, November 2006
- Conyon, Martin J.; Muldoon, Mark R.
- Journal of Business Finance & Accounting, Vol. 33, Issue 9-10
Link prediction in complex networks: A survey
journal, March 2011
- Lü, Linyuan; Zhou, Tao
- Physica A: Statistical Mechanics and its Applications, Vol. 390, Issue 6
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
FALCON: a software package for analysis of nestedness in bipartite networks
journal, January 2014
- Beckett, Stephen J.; Boulton, Chris A.; Williams, Hywel T. P.
- F1000Research, Vol. 3
Identifying statistically significant edges in one-mode projections
journal, March 2013
- Neal, Zachary
- Social Network Analysis and Mining, Vol. 3, Issue 4
Graph-based analysis and visualization of experimental results with ONDEX
journal, March 2006
- Kohler, J.; Baumbach, J.; Taubert, J.
- Bioinformatics, Vol. 22, Issue 11
A consumer's guide to nestedness analysis
journal, January 2009
- Ulrich, Werner; Almeida-Neto, Mário; Gotelli, Nicholas J.
- Oikos, Vol. 118, Issue 1
Network Analysis in Public Health: History, Methods, and Applications
journal, April 2007
- Luke, Douglas A.; Harris, Jenine K.
- Annual Review of Public Health, Vol. 28, Issue 1
The New Bioinformatics: Integrating Ecological Data from the Gene to the Biosphere
journal, December 2006
- Jones, Matthew B.; Schildhauer, Mark P.; Reichman, O. J.
- Annual Review of Ecology, Evolution, and Systematics, Vol. 37, Issue 1
The modular nature of genetic diseases
journal, October 2006
- Oti, M.; Brunner, Hg
- Clinical Genetics, Vol. 71, Issue 1
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
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
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
Finding odd cycle transversals
journal, July 2004
- Reed, Bruce; Smith, Kaleigh; Vetta, Adrian
- Operations Research Letters, Vol. 32, Issue 4
SNP Web Resources and Their Potential Applications in Personalized Medicine
journal, July 2012
- Wang, Jingbo; S. Y. Pang, Grace; S. Chong, Samuel
- Current Drug Metabolism, Vol. 13, Issue 7
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
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
Comparative analysis of the transcription-factor gene regulatory networks of E. coli and S. cerevisiae
journal, January 2008
- Guzmán-Vargas, Lev; Santillán, Moisés
- BMC Systems Biology, Vol. 2, Issue 1
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
The Dynamics of Nestedness Predicts the Evolution of Industrial Ecosystems
journal, November 2012
- Bustos, Sebastián; Gomez, Charles; Hausmann, Ricardo
- PLoS ONE, Vol. 7, Issue 11
Bipartite Community Structure of eQTLs
journal, September 2016
- Platig, John; Castaldi, Peter J.; DeMeo, Dawn
- PLOS Computational Biology, Vol. 12, Issue 9
AutoSOME: a clustering method for identifying gene expression modules without prior knowledge of cluster number
journal, March 2010
- Newman, Aaron M.; Cooper, James B.
- BMC Bioinformatics, Vol. 11, Issue 1
Multiple graph regularized protein domain ranking
journal, January 2012
- Wang, Jim; Bensmail, Halima; Gao, Xin
- BMC Bioinformatics, Vol. 13, Issue 1
BicAT: a biclustering analysis toolbox
journal, March 2006
- Barkow, S.; Bleuler, S.; Prelic, A.
- Bioinformatics, Vol. 22, Issue 10
Edge crossings in drawings of bipartite graphs
journal, April 1994
- Eades, Peter; Wormald, Nicholas C.
- Algorithmica, Vol. 11, Issue 4
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
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
Structural controllability of unidirectional bipartite networks
journal, April 2013
- Nacher, Jose C.; Akutsu, Tatsuya
- Scientific Reports, Vol. 3, Issue 1
Drug—target network
journal, October 2007
- Yıldırım, Muhammed A.; Goh, Kwang-Il; Cusick, Michael E.
- Nature Biotechnology, Vol. 25, Issue 10
The protein–protein interaction map of Helicobacter pylori
journal, January 2001
- Rain, Jean-Christophe; Selig, Luc; De Reuse, Hilde
- Nature, Vol. 409, Issue 6817
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
The measure of order and disorder in the distribution of species in fragmented habitat
journal, December 1993
- Atmar, Wirt; Patterson, Bruce D.
- Oecologia, Vol. 96, Issue 3
Finding and evaluating community structure in networks
journal, February 2004
- Newman, M. E. J.; Girvan, M.
- Physical Review E, Vol. 69, Issue 2
The genetics of autoimmune diseases: a networked perspective
journal, December 2009
- Baranzini, Sergio E.
- Current Opinion in Immunology, Vol. 21, Issue 6
A systematic comparison and evaluation of biclustering methods for gene expression data
journal, February 2006
- Prelić, Amela; Bleuler, Stefan; Zimmermann, Philip
- Bioinformatics, Vol. 22, Issue 9
Simulated Epidemics in an Empirical Spatiotemporal Network of 50,185 Sexual Contacts
journal, March 2011
- Rocha, Luis E. C.; Liljeros, Fredrik; Holme, Petter
- PLoS Computational Biology, Vol. 7, Issue 3
Spatial structure of ant-plant mutualistic networks
journal, May 2013
- Dáttilo, Wesley; Guimarães, Paulo R.; Izzo, Thiago J.
- Oikos, Vol. 122, Issue 11
Using graph theory to analyze biological networks
journal, April 2011
- Pavlopoulos, Georgios A.; Secrier, Maria; Moschopoulos, Charalampos N.
- BioData Mining, Vol. 4, Issue 1
An Overview of NCA-Based Algorithms for Transcriptional Regulatory Network Inference
journal, November 2015
- Wang, Xu; Alshawaqfeh, Mustafa; Dang, Xuan
- Microarrays, Vol. 4, Issue 4
Food webs are built up with nested subwebs
journal, November 2010
- Kondoh, Michio; Kato, Satoshi; Sakato, Yoshikuni
- Ecology, Vol. 91, Issue 11
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
An efficient algorithm for large-scale detection of protein families
journal, April 2002
- Enright, A. J.
- Nucleic Acids Research, Vol. 30, Issue 7
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
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
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
Epidemic thresholds for bipartite networks
journal, November 2013
- Hernández, D. G.; Risau-Gusman, S.
- Physical Review E, Vol. 88, Issue 5
Modularity and community detection in bipartite networks
journal, December 2007
- Barber, Michael J.
- Physical Review E, Vol. 76, Issue 6
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
Invariant properties in coevolutionary networks of plant-animal interactions: Invariant properties in coevolutionary networks
journal, December 2002
- Jordano, Pedro; Bascompte, Jordi; Olesen, Jens M.
- Ecology Letters, Vol. 6, Issue 1
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
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
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
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
Biclustering in data mining
journal, September 2008
- Busygin, Stanislav; Prokopyev, Oleg; Pardalos, Panos M.
- Computers & Operations Research, Vol. 35, Issue 9
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
Controllability of complex networks
journal, May 2011
- Liu, Yang-Yu; Slotine, Jean-Jacques; Barabási, Albert-László
- Nature, Vol. 473, Issue 7346
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
Generalised power graph compression reveals dominant relationship patterns in complex networks
journal, March 2014
- Ahnert, Sebastian E.
- Scientific Reports, Vol. 4, Issue 1
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
Collective dynamics of ‘small-world’ networks
journal, June 1998
- Watts, Duncan J.; Strogatz, Steven H.
- Nature, Vol. 393, Issue 6684
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
Circos: An information aesthetic for comparative genomics
journal, June 2009
- Krzywinski, M.; Schein, J.; Birol, I.
- Genome Research, Vol. 19, Issue 9
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
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
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
Why Most Published Research Findings Are False
journal, August 2005
- Ioannidis, John P. A.
- PLoS Medicine, Vol. 2, Issue 8
Online collaboration: Scientists and the social network
journal, August 2014
- Van Noorden, Richard
- Nature, Vol. 512, Issue 7513
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
Network bipartivity
journal, November 2003
- Holme, Petter; Liljeros, Fredrik; Edling, Christofer R.
- Physical Review E, Vol. 68, Issue 5
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
The maximum edge biclique problem is NP-complete
journal, September 2003
- Peeters, René
- Discrete Applied Mathematics, Vol. 131, Issue 3
ProViz: protein interaction visualization and exploration
journal, September 2004
- Iragne, F.; Nikolski, M.; Mathieu, B.
- Bioinformatics, Vol. 21, Issue 2
Network reliability analysis based on percolation theory
journal, October 2015
- Li, Daqing; Zhang, Qiong; Zio, Enrico
- Reliability Engineering & System Safety, Vol. 142
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
Unraveling Protein Networks with Power Graph Analysis
journal, July 2008
- Royer, Loïc; Reimann, Matthias; Andreopoulos, Bill
- PLoS Computational Biology, Vol. 4, Issue 7
A Bipartite Network-based Method for Prediction of Long Non-coding RNA–protein Interactions
journal, February 2016
- Ge, Mengqu; Li, Ao; Wang, Minghui
- Genomics, Proteomics & Bioinformatics, Vol. 14, Issue 1
Algorithms for drawing graphs: an annotated bibliography
journal, October 1994
- Battista, Giuseppe Di; Eades, Peter; Tamassia, Roberto
- Computational Geometry, Vol. 4, Issue 5
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
Network Properties of Complex Human Disease Genes Identified through Genome-Wide Association Studies
journal, November 2009
- Barrenas, Fredrik; Chavali, Sreenivas; Holme, Petter
- PLoS ONE, Vol. 4, Issue 11
What do molecular methods bring to host–parasitoid food webs?
journal, January 2015
- Hrček, Jan; Godfray, H. Charles J.
- Trends in Parasitology, Vol. 31, Issue 1
Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances: MICROBIAL ECOLOGICAL GENOMICS
journal, March 2006
- Xu, Jianping
- Molecular Ecology, Vol. 15, Issue 7
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
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
A straightforward computational approach for measuring nestedness using quantitative matrices
journal, February 2011
- Almeida-Neto, Mário; Ulrich, Werner
- Environmental Modelling & Software, Vol. 26, Issue 2
Stable marriage and indifference
journal, February 1994
- Irving, Robert W.
- Discrete Applied Mathematics, Vol. 48, Issue 3
Modeling the Spread of Vector-Borne Diseases on Bipartite Networks
journal, November 2010
- Bisanzio, Donal; Bertolotti, Luigi; Tomassone, Laura
- PLoS ONE, Vol. 5, Issue 11
Epidemiologic and Genetic Approaches in the Study of Gene-Environment Interaction: an Overview of Available Methods
journal, January 1998
- Andrieu, N.; Goldstein, A. M.
- Epidemiologic Reviews, Vol. 20, Issue 2
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
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
Disentangling nestedness from models of ecological complexity
journal, June 2012
- James, Alex; Pitchford, Jonathan W.; Plank, Michael J.
- Nature, Vol. 487, Issue 7406
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
A protein-protein interaction map of the Caenorhabditis elegans 26S proteasome
journal, September 2001
- Davy, Anne; Bello, Paul; Thierry-Mieg, Nicolas
- EMBO reports, Vol. 2, Issue 9
Prediction of Drug-Target Interactions and Drug Repositioning via Network-Based Inference
journal, May 2012
- Cheng, Feixiong; Liu, Chuang; Jiang, Jing
- PLoS Computational Biology, Vol. 8, Issue 5
PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways
journal, July 2002
- Demir, E.; Babur, O.; Dogrusoz, U.
- Bioinformatics, Vol. 18, Issue 7
Two classes of bipartite networks: Nested biological and social systems
journal, October 2008
- Burgos, Enrique; Ceva, Horacio; Hernández, Laura
- Physical Review E, Vol. 78, Issue 4
A note on a generalization of eigenvector centrality for bipartite graphs and applications
journal, May 2011
- Daugulis, Peteris
- Networks, Vol. 59, Issue 2
Network thinking in ecology and evolution
journal, June 2005
- Proulx, S.; Promislow, D.; Phillips, P.
- Trends in Ecology & Evolution, Vol. 20, Issue 6
Sex differences in intimate relationships
journal, April 2012
- Palchykov, Vasyl; Kaski, Kimmo; Kertész, Janos
- Scientific Reports, Vol. 2, Issue 1
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
Using Network Component Analysis to Dissect Regulatory Networks Mediated by Transcription Factors in Yeast
journal, March 2009
- Ye, Chun; Galbraith, Simon J.; Liao, James C.
- PLoS Computational Biology, Vol. 5, Issue 3
Plant-Animal Mutualistic Networks: The Architecture of Biodiversity
journal, December 2007
- Bascompte, Jordi; Jordano, Pedro
- Annual Review of Ecology, Evolution, and Systematics, Vol. 38, Issue 1
Integrating domain similarity to improve protein complexes identification in TAP-MS data
journal, January 2013
- Cai, Bingjing; Wang, Haiying; Zheng, Huiru
- Proteome Science, Vol. 11, Issue Suppl 1
Tissue Specificity of Human Disease Module
journal, October 2016
- Kitsak, Maksim; Sharma, Amitabh; Menche, Jörg
- Scientific Reports, Vol. 6, Issue 1
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
The structure of scientific collaboration networks
journal, January 2001
- Newman, M. E. J.
- Proceedings of the National Academy of Sciences, Vol. 98, Issue 2
Social network analysis: developments, advances, and prospects
journal, October 2010
- Scott, John
- Social Network Analysis and Mining, Vol. 1, Issue 1
Small Worlds Among Interlocking Directors: Network Structure and Distance in Bipartite Graphs
journal, May 2004
- Robins, Garry; Alexander, Malcolm
- Computational & Mathematical Organization Theory, Vol. 10, Issue 1
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
Nationwide Population Science: Lessons From the Taiwan National Health Insurance Research Database
journal, September 2015
- Hsing, Ann W.; Ioannidis, John P. A.
- JAMA Internal Medicine, Vol. 175, Issue 9
Clustering by Passing Messages Between Data Points
journal, February 2007
- Frey, B. J.; Dueck, D.
- Science, Vol. 315, Issue 5814
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
Partitioning biological data with transitivity clustering
journal, June 2010
- Wittkop, Tobias; Emig, Dorothea; Lange, Sita
- Nature Methods, Vol. 7, Issue 6
From molecular to modular cell biology
journal, December 1999
- Hartwell, Leland H.; Hopfield, John J.; Leibler, Stanislas
- Nature, Vol. 402, Issue S6761
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
Host-Parasitoid Population Interactions
journal, January 1984
- Hassell, M. P.; Waage, J. K.
- Annual Review of Entomology, Vol. 29, Issue 1
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
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
On the k-path partition of graphs
journal, January 2003
- Steiner, George
- Theoretical Computer Science, Vol. 290, Issue 3
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
Data and programs in support of network analysis of genes and their association with diseases
journal, September 2016
- Kontou, Panagiota I.; Pavlopoulou, Athanasia; Dimou, Niki L.
- Data in Brief, Vol. 8
A branch and bound algorithm for minimizing the number of crossing arcs in bipartite graphs
journal, April 1996
- Valls, Vicente; Martí, Rafael; Lino, Pilar
- European Journal of Operational Research, Vol. 90, Issue 2
Network analysis of genes and their association with diseases
journal, September 2016
- Kontou, Panagiota I.; Pavlopoulou, Athanasia; Dimou, Niki L.
- Gene, Vol. 590, Issue 1
Challenges in Computational Analysis of Mass Spectrometry Data for Proteomics
journal, January 2010
- Ma, Bin
- Journal of Computer Science and Technology, Vol. 25, Issue 1
Integrated Assessment and Prediction of Transcription Factor Binding
journal, January 2006
- Beyer, Andreas; Workman, Christopher; Hollunder, Jens
- PLoS Computational Biology, Vol. 2, Issue 6
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
The Genetic Association Database
journal, May 2004
- Becker, Kevin G.; Barnes, Kathleen C.; Bright, Tiffani J.
- Nature Genetics, Vol. 36, Issue 5
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
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
Versatility and Connectivity Efficiency of Bipartite Transcription Networks
journal, October 2006
- Brynildsen, Mark P.; Tran, Linh M.; Liao, James C.
- Biophysical Journal, Vol. 91, Issue 8
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
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)
mapman: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes
journal, March 2004
- Thimm, Oliver; Bläsing, Oliver; Gibon, Yves
- The Plant Journal, Vol. 37, Issue 6, p. 914-939
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
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
Self-organization of collaboration networks
journal, September 2004
- Ramasco, José J.; Dorogovtsev, S. N.; Pastor-Satorras, Romualdo
- Physical Review E, Vol. 70, Issue 3
On the meaning and measurement of nestedness of species assemblages
journal, December 1992
- Wright, David H.; Reeves, Jaxk H.
- Oecologia, Vol. 92, Issue 3
Drug Target Identification Using Side-Effect Similarity
journal, July 2008
- Campillos, M.; Kuhn, M.; Gavin, A. -C.
- Science, Vol. 321, Issue 5886
Basic notions for the analysis of large two-mode networks
journal, January 2008
- Latapy, Matthieu; Magnien, Clémence; Vecchio, Nathalie Del
- Social Networks, Vol. 30, Issue 1
Legislative cosponsorship networks in the US House and Senate
journal, October 2006
- Fowler, James H.
- Social Networks, Vol. 28, Issue 4
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
RNA-Seq: a revolutionary tool for transcriptomics
journal, January 2009
- Wang, Zhong; Gerstein, Mark; Snyder, Michael
- Nature Reviews Genetics, Vol. 10, Issue 1
The new geography of global civil society: NGOs in the world city network
journal, December 2004
- Taylor, Peter J.
- Globalizations, Vol. 1, Issue 2
Human cancer databases (Review)
journal, October 2014
- Pavlopoulou, Athanasia; Spandidos, Demetrios A.; Michalopoulos, Ioannis
- Oncology Reports, Vol. 33, Issue 1
Small World Patterns in Food Webs
journal, February 2002
- Montoya, Jose M.; SolÉ, Ricard V.
- Journal of Theoretical Biology, Vol. 214, Issue 3
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
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
Spectral measures of bipartivity in complex networks
journal, October 2005
- Estrada, Ernesto; Rodríguez-Velázquez, Juan A.
- Physical Review E, Vol. 72, Issue 4
Drug-Binding Databases
journal, December 2008
- Macedo Timmers, Luis Fernando; Pauli, Ivani; Caceres, Rafael
- Current Drug Targets, Vol. 9, Issue 12
Generalized blockmodeling of two-mode network data
journal, January 2004
- Doreian, Patrick; Batagelj, Vladimir; Ferligoj, Anuška
- Social Networks, Vol. 26, Issue 1
Review of Biological Network Data and Its Applications
journal, January 2013
- Yu, Donghyeon; Kim, MinSoo; Xiao, Guanghua
- Genomics & Informatics, Vol. 11, Issue 4
The backbone of bipartite projections: Inferring relationships from co-authorship, co-sponsorship, co-attendance and other co-behaviors
journal, October 2014
- Neal, Zachary
- Social Networks, Vol. 39
Network analysis of 2-mode data
journal, August 1997
- Borgatti, Stephen P.; Everett, Martin G.
- Social Networks, Vol. 19, Issue 3
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)
Bipartite network projection and personal recommendation
journal, October 2007
- Zhou, Tao; Ren, Jie; Medo, Matúš
- Physical Review E, Vol. 76, Issue 4
An Online Database for Informing Ecological Network Models: http://kelpforest.ucsc.edu
journal, October 2014
- Beas-Luna, Rodrigo; Novak, Mark; Carr, Mark H.
- PLoS ONE, Vol. 9, Issue 10
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
Behavior Analysis of Internet Traffic via Bipartite Graphs and One-Mode Projections
journal, June 2014
- Xu, Kuai; Wang, Feng; Gu, Lin
- IEEE/ACM Transactions on Networking, Vol. 22, Issue 3
Efficiently inferring community structure in bipartite networks
journal, July 2014
- Larremore, Daniel B.; Clauset, Aaron; Jacobs, Abigail Z.
- Physical Review E, Vol. 90, Issue 1
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
Hidden Information Revealed by Optimal Community Structure from a Protein-Complex Bipartite Network Improves Protein Function Prediction
journal, April 2013
- Lee, Juyong; Lee, Jooyoung
- PLoS ONE, Vol. 8, Issue 4
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
Extracting Multi-facet Community Structure from Bipartite Networks
conference, August 2009
- Suzuki, Kenta; Wakita, Ken
- 2009 International Conference on Computational Science and Engineering
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
Recommendation as link prediction in bipartite graphs: A graph kernel-based machine learning approach
journal, January 2013
- Li, Xin; Chen, Hsinchun
- Decision Support Systems, Vol. 54, Issue 2
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
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
Human symptoms–disease network
journal, June 2014
- Zhou, XueZhong; Menche, Jörg; Barabási, Albert-László
- Nature Communications, Vol. 5, Issue 1
Hive plots--rational approach to visualizing networks
journal, December 2011
- Krzywinski, M.; Birol, I.; Jones, S. J.
- Briefings in Bioinformatics, Vol. 13, Issue 5
The role of a water bug, Sigara striata , in freshwater food webs
journal, January 2014
- Klecka, Jan
- PeerJ, Vol. 2
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
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
Unraveling genomic variation from next generation sequencing data
journal, July 2013
- Pavlopoulos, Georgios A.; Oulas, Anastasis; Iacucci, Ernesto
- BioData Mining, Vol. 6, Issue 1
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
Use of the Szeged index and the revised Szeged index for measuring network bipartivity
journal, October 2010
- Pisanski, Tomaž; Randić, Milan
- Discrete Applied Mathematics, Vol. 158, Issue 17
Protein-Protein Interaction Detection: Methods and Analysis
journal, January 2014
- Rao, V. Srinivasa; Srinivas, K.; Sujini, G. N.
- International Journal of Proteomics, Vol. 2014
A Network of Genes, Genetic Disorders, and Brain Areas
journal, June 2011
- Hayasaka, Satoru; Hugenschmidt, Christina E.; Laurienti, Paul J.
- PLoS ONE, Vol. 6, Issue 6
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
Cycles and clustering in bipartite networks
journal, November 2005
- Lind, Pedro G.; González, Marta C.; Herrmann, Hans J.
- Physical Review E, Vol. 72, Issue 5
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
Determination of argininosuccinate lyase and arginase activities with an amino acid analyzer
journal, December 1990
- Bastone, Antonio; Diomede, Luisa; Parini, Rossella
- Analytical Biochemistry, Vol. 191, Issue 2
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
Uncovering packaging features of co-regulated modules based on human protein interaction and transcriptional regulatory networks
journal, July 2010
- Chen, Lina; Wang, Hong; Zhang, Liangcai
- BMC Bioinformatics, Vol. 11, Issue 1
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
College Admissions and the Stability of Marriage
journal, January 1962
- Gale, D.; Shapley, L. S.
- The American Mathematical Monthly, Vol. 69, Issue 1
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
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
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)
Human sexual contact network as a bipartite graph
journal, May 2002
- Ergün, Güler
- Physica A: Statistical Mechanics and its Applications, Vol. 308, Issue 1-4
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
Biology, Methodology or Chance? The Degree Distributions of Bipartite Ecological Networks
journal, March 2011
- Williams, Richard J.
- PLoS ONE, Vol. 6, Issue 3
Weighted-Interaction Nestedness Estimator (WINE): A new estimator to calculate over frequency matrices
journal, November 2009
- Galeano, Javier; Pastor, Juan M.; Iriondo, Jose M.
- Environmental Modelling & Software, Vol. 24, Issue 11
Triadic closure in two-mode networks: Redefining the global and local clustering coefficients
journal, May 2013
- Opsahl, Tore
- Social Networks, Vol. 35, Issue 2
The Complexity of Enumeration and Reliability Problems
journal, August 1979
- Valiant, Leslie G.
- SIAM Journal on Computing, Vol. 8, Issue 3
A travel guide to Cytoscape plugins
journal, November 2012
- Saito, Rintaro; Smoot, Michael E.; Ono, Keiichiro
- Nature Methods, Vol. 9, Issue 11
Technique for Analyzing Overlapping Memberships
journal, January 1972
- Bonacich, Phillip
- Sociological Methodology, Vol. 4
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
Spatial structures of network flows: A graph theoretical approach
journal, December 1987
- Gutiérrez Puebla, Javier
- Transportation Research Part B: Methodological, Vol. 21, Issue 6
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
Drawing graphs in two layers
journal, September 1994
- Eades, Peter; Whitesides, Sue
- Theoretical Computer Science, Vol. 131, Issue 2
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
journal, November 2003
- Shannon, P.
- Genome Research, Vol. 13, Issue 11
Deciphering the molecular basis of human cardiovascular disease through network biology
journal, January 2012
- Chan, Stephen Y.; White, Kevin; Loscalzo, Joseph
- Current Opinion in Cardiology, Vol. 27, Issue 3
Improving the analyses of nestedness for large sets of matrices
journal, October 2006
- Guimaraesjr, P.; Guimaraes, P.
- Environmental Modelling & Software, Vol. 21, Issue 10
Systems biology model databases and resources
journal, September 2008
- van Gend, Carel; Snoep, Jacky L.
- Essays in Biochemistry, Vol. 45
DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq experiments
journal, August 2016
- Vrahatis, Aristidis G.; Balomenos, Panos; Tsakalidis, Athanasios K.
- Bioinformatics, Vol. 32, Issue 24
The data paper: a mechanism to incentivize data publishing in biodiversity science
journal, December 2011
- Chavan, Vishwas; Penev, Lyubomir
- BMC Bioinformatics, Vol. 12, Issue S15
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
Global Analysis of Protein Activities Using Proteome Chips
journal, July 2001
- Zhu, H.
- Science, Vol. 293, Issue 5537
A Network-Based Method to Assess the Statistical Significance of Mild Co-Regulation Effects
journal, September 2013
- Horvát, Emőke-Ágnes; Zhang, Jitao David; Uhlmann, Stefan
- PLoS ONE, Vol. 8, Issue 9
Statistically Validated Networks in Bipartite Complex Systems
journal, March 2011
- Tumminello, Michele; Miccichè, Salvatore; Lillo, Fabrizio
- PLoS ONE, Vol. 6, Issue 3
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
Degree distribution in plant-animal mutualistic networks: forbidden links or random interactions?
journal, February 2005
- Vázquez, Diego P.
- Oikos, Vol. 108, Issue 2
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
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
Community detection in graphs
journal, February 2010
- Fortunato, Santo
- Physics Reports, Vol. 486, Issue 3-5
A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae
journal, February 2000
- Uetz, Peter; Giot, Loic; Cagney, Gerard
- Nature, Vol. 403, Issue 6770
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