Biological network analysis: insights into structure and functions.

In the past two decades, great efforts have been devoted to extract the dependence and interplay between structure and functions in biological networks because they have strong relevance to biological processes. In this article, we reviewed the recent development in the biological network analysis. In detail, we first reviewed the interactome topological properties of biological networks, the methods for structure and functional patterns.

[1]  M. DePamphilis,et al.  HUMAN DISEASE , 1957, The Ulster Medical Journal.

[2]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[3]  Duncan J. Watts,et al.  Collective dynamics of ‘small-world’ networks , 1998, Nature.

[4]  Albert,et al.  Emergence of scaling in random networks , 1999, Science.

[5]  J. Hopfield,et al.  From molecular to modular cell biology , 1999, Nature.

[6]  R. Albert,et al.  The large-scale organization of metabolic networks , 2000, Nature.

[7]  D. Botstein,et al.  Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF , 2001, Nature.

[8]  Gary D Bader,et al.  Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants , 2001, Science.

[9]  Gary D Bader,et al.  Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry , 2002, Nature.

[10]  M E J Newman,et al.  Community structure in social and biological networks , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[11]  S. Shen-Orr,et al.  Network motifs in the transcriptional regulation network of Escherichia coli , 2002, Nature Genetics.

[12]  P. Bork,et al.  Functional organization of the yeast proteome by systematic analysis of protein complexes , 2002, Nature.

[13]  S. Shen-Orr,et al.  Network motifs: simple building blocks of complex networks. , 2002, Science.

[14]  B. Snel,et al.  Comparative assessment of large-scale data sets of protein–protein interactions , 2002, Nature.

[15]  A. Barabasi,et al.  Hierarchical Organization of Modularity in Metabolic Networks , 2002, Science.

[16]  Gary D. Bader,et al.  An automated method for finding molecular complexes in large protein interaction networks , 2003, BMC Bioinformatics.

[17]  Alessandro Vespignani,et al.  Evolution thinks modular , 2003, Nature Genetics.

[18]  R. Karp,et al.  Conserved pathways within bacteria and yeast as revealed by global protein network alignment , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[19]  Z N Oltvai,et al.  Evolutionary conservation of motif constituents in the yeast protein interaction network , 2003, Nature Genetics.

[20]  Sergei Egorov,et al.  Pathway studio - the analysis and navigation of molecular networks , 2003, Bioinform..

[21]  L. Mirny,et al.  Protein complexes and functional modules in molecular networks , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[22]  D. Bu,et al.  Topological structure analysis of the protein-protein interaction network in budding yeast. , 2003, Nucleic acids research.

[23]  Alexander Rives,et al.  Modular organization of cellular networks , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[24]  David J. Porteous,et al.  Speeding disease gene discovery by sequence based candidate prioritization , 2005, BMC Bioinformatics.

[25]  R. Milo,et al.  Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[26]  Anton J. Enright,et al.  Detection of functional modules from protein interaction networks , 2003, Proteins.

[27]  Igor Jurisica,et al.  Protein complex prediction via cost-based clustering , 2004, Bioinform..

[28]  Roded Sharan,et al.  PathBLAST: a tool for alignment of protein interaction networks , 2004, Nucleic Acids Res..

[29]  Peter Donnelly,et al.  Superfamilies of Evolved and Designed Networks , 2004 .

[30]  A. Barabasi,et al.  Network biology: understanding the cell's functional organization , 2004, Nature Reviews Genetics.

[31]  Michael Lässig,et al.  Local graph alignment and motif search in biological networks. , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[32]  Ravinder Singh,et al.  Fast-Find: A novel computational approach to analyzing combinatorial motifs , 2006, BMC Bioinformatics.

[33]  S. Salzberg,et al.  The Transcriptional Landscape of the Mammalian Genome , 2005, Science.

[34]  Hamid Bolouri,et al.  A data integration methodology for systems biology. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[35]  H. Lehrach,et al.  A Human Protein-Protein Interaction Network: A Resource for Annotating the Proteome , 2005, Cell.

[36]  R. Karp,et al.  From the Cover : Conserved patterns of protein interaction in multiple species , 2005 .

[37]  Ron Shamir,et al.  Integrative analysis of genome-wide experiments in the context of a large high-throughput data compendium , 2005, Molecular systems biology.

[38]  Ignacio Marín,et al.  Iterative Cluster Analysis of Protein Interaction Data , 2005, Bioinform..

[39]  Tomoyuki Higuchi,et al.  Estimating time-dependent gene networks from time series microarray data by dynamic linear models with Markov switching , 2005, 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05).

[40]  Susumu Goto,et al.  Extraction of phylogenetic network modules from the metabolic network , 2006, BMC Bioinformatics.

[41]  R. Guimerà,et al.  Functional cartography of complex metabolic networks , 2005, Nature.

[42]  S. L. Wong,et al.  Towards a proteome-scale map of the human protein–protein interaction network , 2005, Nature.

[43]  Meng Xu,et al.  Comparison of protein interaction networks reveals species conservation and divergence , 2006, BMC Bioinformatics.

[44]  Sebastian Wernicke,et al.  Efficient Detection of Network Motifs , 2006, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[45]  Wojciech Szpankowski,et al.  Pairwise Alignment of Protein Interaction Networks , 2006, J. Comput. Biol..

[46]  T. Ideker,et al.  Modeling cellular machinery through biological network comparison , 2006, Nature Biotechnology.

[47]  Yongjin Li,et al.  Discovering disease-genes by topological features in human protein-protein interaction network , 2006, Bioinform..

[48]  G. Vriend,et al.  A text-mining analysis of the human phenome , 2006, European Journal of Human Genetics.

[49]  Ting Chen,et al.  Network motif identification in stochastic networks. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[50]  B. Snel,et al.  Predicting disease genes using protein–protein interactions , 2006, Journal of Medical Genetics.

[51]  Antal F. Novak,et al.  networks Græmlin : General and robust alignment of multiple large interaction data , 2006 .

[52]  Jacques van Helden,et al.  Evaluation of clustering algorithms for protein-protein interaction networks , 2006, BMC Bioinformatics.

[53]  Kyongbum Lee,et al.  An algorithm for modularity analysis of directed and weighted biological networks based on edge-betweenness centrality , 2006, Bioinform..

[54]  Shi-Hua Zhang,et al.  Alignment of molecular networks by integer quadratic programming , 2007, Bioinform..

[55]  U. Alon.  Network motifs: theory and experimental approaches , 2007, Nature Reviews Genetics.

[56]  K. Komurov,et al.  Revealing static and dynamic modular architecture of the eukaryotic protein interaction network , 2007, Molecular Systems Biology.

[57]  M. Oti,et al.  The modular nature of genetic diseases , 2006, Clinical genetics.

[58]  Pall I. Olason,et al.  A human phenome-interactome network of protein complexes implicated in genetic disorders , 2007, Nature Biotechnology.

[59]  A. Barabasi,et al.  The human disease network , 2007, Proceedings of the National Academy of Sciences.

[60]  M. Gerstein,et al.  Getting connected: analysis and principles of biological networks. , 2007, Genes & development.

[61]  Kok-Leong Ong,et al.  Dynamical Systems for Discovering Protein Complexes and Functional Modules from Biological Networks , 2007, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[62]  Monica L. Mo,et al.  Global reconstruction of the human metabolic network based on genomic and bibliomic data , 2007, Proceedings of the National Academy of Sciences.

[63]  Yoonsuck Choe,et al.  Dynamical pathway analysis , 2008, BMC Systems Biology.

[64]  Srinivasan Parthasarathy,et al.  An ensemble framework for clustering protein-protein interaction networks , 2007, ISMB/ECCB.

[65]  Adam S. Kibel,et al.  Integrative molecular concept modeling of prostate cancer progression , 2007 .

[66]  Mark Gerstein,et al.  The Importance of Bottlenecks in Protein Networks: Correlation with Gene Essentiality and Expression Dynamics , 2007, PLoS Comput. Biol..

[67]  Bonnie Berger,et al.  Pairwise Global Alignment of Protein Interaction Networks by Matching Neighborhood Topology , 2007, RECOMB.

[68]  T. Ideker,et al.  Network-based classification of breast cancer metastasis , 2007, Molecular systems biology.

[69]  Serafim Batzoglou,et al.  Automatic Parameter Learning for Multiple Network Alignment , 2008, RECOMB.

[70]  Yanjun Qi,et al.  Protein complex identification by supervised graph local clustering , 2008, ISMB.

[71]  P. Robinson,et al.  Walking the interactome for prioritization of candidate disease genes. , 2008, American journal of human genetics.

[72]  Michael W. Mahoney,et al.  Algorithmic and statistical challenges in modern largescale data analysis are the focus of MMDS 2008 , 2008, SKDD.

[73]  Laura Bonetta.  Getting Up Close and Personal with Your Genome , 2008, Cell.

[74]  Michael Q. Zhang,et al.  Network-based global inference of human disease genes , 2008, Molecular systems biology.

[75]  Sayan Mukherjee,et al.  Modeling Cancer Progression via Pathway Dependencies , 2008, PLoS Comput. Biol..

[76]  Concettina Guerra,et al.  A review on models and algorithms for motif discovery in protein-protein interaction networks. , 2008, Briefings in functional genomics & proteomics.

[77]  D. Koller,et al.  Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network , 2008, Nature Biotechnology.

[78]  Ming Wu,et al.  Gene module level analysis: identification to networks and dynamics. , 2008, Current opinion in biotechnology.

[79]  Ichigaku Takigawa,et al.  Probabilistic path ranking based on adjacent pairwise coexpression for metabolic transcripts analysis , 2007, Bioinform..

[80]  A. Barabasi,et al.  Cancer metastasis networks and the prediction of progression patterns , 2009, British Journal of Cancer.

[81]  S. Friend,et al.  A network view of disease and compound screening , 2009, Nature Reviews Drug Discovery.

[82]  Bonnie Berger,et al.  IsoRankN: spectral methods for global alignment of multiple protein networks , 2009, Bioinform..

[83]  Thierry Emonet,et al.  Understanding Modularity in Molecular Networks Requires Dynamics , 2009, Science Signaling.

[84]  Serafim Batzoglou,et al.  Automatic Parameter Learning for Multiple Local Network Alignment , 2009, J. Comput. Biol..

[85]  Albert-László Barabási,et al.  A Dynamic Network Approach for the Study of Human Phenotypes , 2009, PLoS Comput. Biol..

[86]  O. Kuchaiev,et al.  Simulating trait evolution for cross-cultural comparison , 2010, Philosophical Transactions of the Royal Society B: Biological Sciences.

[87]  Francis Bach,et al.  Global alignment of protein–protein interaction networks by graph matching methods , 2009, Bioinform..

[88]  Qifang Liu,et al.  Align human interactome with phenome to identify causative genes and networks underlying disease families , 2009, Bioinform..

[89]  David Warde-Farley,et al.  Dynamic modularity in protein interaction networks predicts breast cancer outcome , 2009, Nature Biotechnology.

[90]  Susmita Datta,et al.  A statistical framework for differential network analysis from microarray data , 2010, BMC Bioinformatics.

[91]  David Baker,et al.  Structure similarity measure with penalty for close non-equivalent residues , 2009, Bioinform..

[92]  Sophie Lèbre,et al.  Statistical Applications in Genetics and Molecular Biology Inferring Dynamic Genetic Networks with Low Order Independencies Inferring Dynamic Genetic Networks with Low Order Independencies ∗ , 2009 .

[93]  Michael P. H. Stumpf,et al.  Statistical inference of the time-varying structure of gene-regulation networks , 2010, BMC Systems Biology.

[94]  J. Bader,et al.  Dynamic Networks from Hierarchical Bayesian Graph Clustering , 2010, PloS one.

[95]  Robin Palotai,et al.  Community Landscapes: An Integrative Approach to Determine Overlapping Network Module Hierarchy, Identify Key Nodes and Predict Network Dynamics , 2009, PloS one.

[96]  D. Galas,et al.  Diseases as network perturbations. , 2010, Current opinion in biotechnology.

[97]  Lin Gao,et al.  Identification of core-attachment complexes based on maximal frequent patterns in protein-protein interaction networks , 2010, 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW).

[98]  Tamer Kahveci,et al.  Finding Dynamic Modules of Biological Regulatory Networks , 2010, 2010 IEEE International Conference on BioInformatics and BioEngineering.

[99]  Oren Shoval,et al.  SnapShot: Network Motifs , 2010, Cell.

[100]  Liang Yu,et al.  A hybrid clustering algorithm for identifying modules in Protein - Protein Interaction networks , 2010, Int. J. Data Min. Bioinform..

[101]  A. Barabasi,et al.  Network medicine : a network-based approach to human disease , 2010 .

[102]  Mehmet Koyutürk,et al.  An Integrative -omics Approach to Identify Functional Sub-Networks in Human Colorectal Cancer , 2010, PLoS Comput. Biol..

[103]  Roded Sharan,et al.  Associating Genes and Protein Complexes with Disease via Network Propagation , 2010, PLoS Comput. Biol..

[104]  G. Nolan,et al.  Computational solutions to large-scale data management and analysis , 2010, Nature Reviews Genetics.

[105]  Mona Singh,et al.  Toward the dynamic interactome: it's about time , 2010, Briefings Bioinform..

[106]  Yen-Jen Oyang,et al.  Dynamic functional modules in co-expressed protein interaction networks of dilated cardiomyopathy , 2010, BMC Systems Biology.

[107]  R. Linding,et al.  Network‐based drugs and biomarkers , 2010, The Journal of pathology.

[108]  Peter Bühlmann,et al.  Predicting causal effects in large-scale systems from observational data , 2010, Nature Methods.

[109]  Russell A. Poldrack,et al.  Large-scale automated synthesis of human functional neuroimaging data , 2011, Nature Methods.

[110]  Lin Gao,et al.  Global Network Alignment Based on Multiple Hub Seeds , 2011, 2011 IEEE International Conference on Bioinformatics and Biomedicine.

[111]  Xingli Guo,et al.  A Computational Method Based on the Integration of Heterogeneous Networks for Predicting Disease-Gene Associations , 2011, PloS one.

[112]  Lin Gao,et al.  International Journal of Biological Sciences , 2011 .

[113]  Natasa Przulj,et al.  Integrative network alignment reveals large regions of global network similarity in yeast and human , 2011, Bioinform..

[114]  E. Marcotte,et al.  Prioritizing candidate disease genes by network-based boosting of genome-wide association data. , 2011, Genome research.

[115]  Reinhard Guthke,et al.  Regulatory interactions for iron homeostasis in Aspergillus fumigatus inferred by a Systems Biology approach , 2012, BMC Systems Biology.

[116]  Mehmet Koyutürk,et al.  Disease Gene Prioritization Based on Topological Similarity in Protein-Protein Interaction Networks , 2011, RECOMB.

[117]  Robert Clarke,et al.  Dynamic modelling of oestrogen signalling and cell fate in breast cancer cells , 2011, Nature Reviews Cancer.

[118]  Lin Gao,et al.  Predicting protein complexes in protein interaction networks using a core-attachment algorithm based on graph communicability , 2012, Inf. Sci..

[119]  Lin Gao,et al.  Discovering protein complexes in protein interaction networks via exploring the weak ties effect , 2012, BMC Systems Biology.

[120]  Haiyuan Yu,et al.  Three-dimensional reconstruction of protein networks provides insight into human genetic disease , 2012, Nature Biotechnology.

[121]  Vesna Memisevic,et al.  Global G RAph A Lignment of Biological Networks , 2022 .

[122]  Chun-Hsi Huang,et al.  Biological network motif detection: principles and practice , 2012, Briefings Bioinform..