Construction, comparison and evolution of networks in life sciences and other disciplines

Network approaches have become pervasive in many research fields. They allow for a more comprehensive understanding of complex relationships between entities as well as their group-level properties and dynamics. Many networks change over time, be it within seconds or millions of years, depending on the nature of the network. Our focus will be on comparative network analyses in life sciences, where deciphering temporal network changes is a core interest of molecular, ecological, neuropsychological and evolutionary biologists. Further, we will take a journey through different disciplines, such as social sciences, finance and computational gastronomy, to present commonalities and differences in how networks change and can be analysed. Finally, we envision how borrowing ideas from these disciplines could enrich the future of life science research.

[1]  R. Sharan,et al.  Metabolic-network-driven analysis of bacterial ecological strategies , 2009, Genome Biology.

[2]  Miguel Romance,et al.  Eigenvector centrality of nodes in multiplex networks , 2013, Chaos.

[3]  Alessandro Ingrosso,et al.  The patient-zero problem with noisy observations , 2014, 1408.0907.

[4]  Paul J. Laurienti,et al.  A permutation testing framework to compare groups of brain networks , 2013, Front. Comput. Neurosci..

[5]  Tom A. B. Snijders,et al.  Social Network Analysis , 2011, International Encyclopedia of Statistical Science.

[6]  Y. Gilad,et al.  Comparative studies of gene expression and the evolution of gene regulation , 2012, Nature Reviews Genetics.

[7]  A. Burgard,et al.  Minimal Reaction Sets for Escherichia coli Metabolism under Different Growth Requirements and Uptake Environments , 2001, Biotechnology progress.

[8]  D. Sade,et al.  Sociometrics of Macaca mulatta. I. Linkages and cliques in grooming matrices. , 1972, Folia primatologica; international journal of primatology.

[9]  Frédéric Baribaud,et al.  Integrating personalized gene expression profiles into predictive disease-associated gene pools , 2017, npj Systems Biology and Applications.

[10]  C Kooperberg,et al.  The use of phenome‐wide association studies (PheWAS) for exploration of novel genotype‐phenotype relationships and pleiotropy discovery , 2011, Genetic epidemiology.

[11]  Leng Han,et al.  Gene co-expression network analysis reveals common system-level properties of prognostic genes across cancer types , 2014, Nature Communications.

[12]  C. Sims MACROECONOMICS AND REALITY , 1977 .

[13]  S. Lee,et al.  Systems metabolic engineering of Escherichia coli for L-threonine production , 2007, Molecular systems biology.

[14]  G. Polis,et al.  Food webs, trophic cascades and community structure , 2006 .

[15]  Conrado J. Pérez Vicente,et al.  Diffusion dynamics on multiplex networks , 2012, Physical review letters.

[16]  Simon M Lin,et al.  Opportunities for drug repositioning from phenome-wide association studies , 2015, Nature Biotechnology.

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

[18]  Jane Memmott,et al.  Food webs: a ladder for picking strawberries or a practical tool for practical problems? , 2009, Philosophical Transactions of the Royal Society B: Biological Sciences.

[19]  Peixin Yang,et al.  Vascular and Metabolic Actions of the Green Tea Polyphenol Epigallocatechin Gallate , 2014, Current medicinal chemistry.

[20]  A. Wagner,et al.  Evolution of gene networks by gene duplications: a mathematical model and its implications on genome organization. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[21]  J. Davies,et al.  Molecular Biology of the Cell , 1983, Bristol Medico-Chirurgical Journal.

[22]  Hadley Wickham,et al.  Stringr: Modern, Consistent String Processing , 2010, R J..

[23]  Benno Schwikowski,et al.  Graph-based methods for analysing networks in cell biology , 2006, Briefings Bioinform..

[24]  Kush R. Varshney,et al.  Flavor Pairing in Medieval European Cuisine: A Study in Cooking with Dirty Data , 2013, ArXiv.

[25]  Jens Nielsen,et al.  Drug Repositioning for Effective Prostate Cancer Treatment , 2018, Front. Physiol..

[26]  Gerhard Weikum,et al.  KnowLife: A knowledge graph for health and life sciences , 2014, 2014 IEEE 30th International Conference on Data Engineering.

[27]  Carl T. Bergstrom,et al.  The Science of Science , 2018, Science.

[28]  Francis S Collins,et al.  A HapMap harvest of insights into the genetics of common disease. , 2008, The Journal of clinical investigation.

[29]  Bruce Hannon,et al.  Ecological network analysis : network construction , 2007 .

[30]  A. Neveu,et al.  A survey of network-based analysis and systemic risk measurement , 2018 .

[31]  A. Vespignani,et al.  The architecture of complex weighted networks. , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[32]  A. Barabasi,et al.  Tissue Specificity of Human Disease Module , 2016, Scientific Reports.

[33]  Maurits de Klepper,et al.  Food Pairing Theory: A European Fad , 2011 .

[34]  D. di Bernardo,et al.  How to infer gene networks from expression profiles , 2007, Molecular systems biology.

[35]  René S. Kahn,et al.  A Gene Co-Expression Network in Whole Blood of Schizophrenia Patients Is Independent of Antipsychotic-Use and Enriched for Brain-Expressed Genes , 2012, PloS one.

[36]  Eivind Almaas,et al.  Predicting Strain Engineering Strategies Using iKS1317: A Genome-Scale Metabolic Model of Streptomyces coelicolor. , 2019, Biotechnology journal.

[37]  Johan van de Koppel,et al.  Reconciling complexity with stability in naturally assembling food webs , 2009, Nature.

[38]  M. Pigliucci Is evolvability evolvable? , 2008, Nature Reviews Genetics.

[39]  R. Kuttan,et al.  Beneficial effects of green tea: A literature review , 2010, Chinese medicine.

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

[41]  Curtis Huttenhower,et al.  Microbial Co-occurrence Relationships in the Human Microbiome , 2012, PLoS Comput. Biol..

[42]  Brian Campbell,et al.  Rivers and the Power of Ancient Rome , 2012 .

[43]  Nikolaus Hautsch,et al.  Financial Network Systemic Risk Contributions , 2013 .

[44]  Ola Engkvist,et al.  On the Integration of In Silico Drug Design Methods for Drug Repurposing , 2017, Front. Pharmacol..

[45]  Marc-Thorsten Hütt,et al.  The interdependent network of gene regulation and metabolism is robust where it needs to be , 2017, Nature Communications.

[46]  Miguel Lurgi,et al.  Modularity and predicted functions of the global sponge-microbiome network , 2019, Nature Communications.

[47]  Albert Díaz-Guilera,et al.  Food-Bridging: A New Network Construction to Unveil the Principles of Cooking , 2017, Front. ICT.

[48]  Devika Subramanian,et al.  Interface Network Models for Complex Urban Infrastructure Systems , 2011 .

[49]  Wolfgang Glänzel,et al.  Inflationary bibliometric values: The role of scientific collaboration and the need for relative indicators in evaluative studies , 2004, Scientometrics.

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

[51]  K. Vandepoele,et al.  Comparative co-expression analysis in plant biology. , 2012, Plant, cell & environment.

[52]  J. Stelling,et al.  Genome‐scale metabolic networks , 2009, Wiley interdisciplinary reviews. Systems biology and medicine.

[53]  Albert-László Barabási,et al.  A DIseAse MOdule Detection (DIAMOnD) Algorithm Derived from a Systematic Analysis of Connectivity Patterns of Disease Proteins in the Human Interactome , 2015, PLoS Comput. Biol..

[54]  Eric Smith,et al.  The compositional and evolutionary logic of metabolism , 2012, Physical biology.

[55]  R. Krueger,et al.  Toward scientifically useful quantitative models of psychopathology: The importance of a comparative approach , 2010, Behavioral and Brain Sciences.

[56]  Noah Fierer,et al.  Using network analysis to explore co-occurrence patterns in soil microbial communities , 2011, The ISME Journal.

[57]  Patrick C Phillips,et al.  Network thinking in ecology and evolution. , 2005, Trends in ecology & evolution.

[58]  Alexandre Arenas,et al.  Quantifying the diaspora of knowledge in the last century , 2016, Applied Network Science.

[59]  G. Burdock,et al.  Fenaroli's Handbook of Flavor Ingredients , 1997 .

[60]  A. Crespi,et al.  Tracking Individuals Shows Spatial Fidelity Is a Key Regulator of Ant Social Organization , 2013, Science.

[61]  Vangelis Sakkalis,et al.  Review of advanced techniques for the estimation of brain connectivity measured with EEG/MEG , 2011, Comput. Biol. Medicine.

[62]  Steve Horvath,et al.  Network module detection: Affinity search technique with the multi-node topological overlap measure , 2009, BMC Research Notes.

[63]  Robert E. Ulanowicz,et al.  Role of network analysis in comparative ecosystem ecology of estuaries , 2005 .

[64]  Barry Horwitz,et al.  The elusive concept of brain connectivity , 2003, NeuroImage.

[65]  Hesham H. Ali,et al.  On Mining Biological Signals Using Correlation Networks , 2013, 2013 IEEE 13th International Conference on Data Mining Workshops.

[66]  John F. Padgett,et al.  Robust Action and the Rise of the Medici, 1400-1434 , 1993, American Journal of Sociology.

[67]  M. V. D. Heuvel,et al.  Exploring the brain network: A review on resting-state fMRI functional connectivity , 2010, European Neuropsychopharmacology.

[68]  F. Kondrashov,et al.  The evolution of gene duplications: classifying and distinguishing between models , 2010, Nature Reviews Genetics.

[69]  A. Barabasi,et al.  A disease module in the interactome explains disease heterogeneity, drug response and captures novel pathways and genes in asthma. , 2015, Human molecular genetics.

[70]  Werner Baumgarten,et al.  Plasmodial vein networks of the slime mold Physarum polycephalum form regular graphs. , 2010, Physical review. E, Statistical, nonlinear, and soft matter physics.

[71]  Anthony M. Bolger,et al.  Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato , 2013, Proceedings of the National Academy of Sciences.

[72]  LAIRE,et al.  Taking time seriously How do we deal with change in historical networks ? , 2014 .

[73]  Yu Xia,et al.  Estimating dispensable content in the human interactome , 2019, Nature Communications.

[74]  Jure Leskovec,et al.  Predicting multicellular function through multi-layer tissue networks , 2017, Bioinform..

[75]  Martin Middendorf,et al.  Automated monitoring of behavior reveals bursty interaction patterns and rapid spreading dynamics in honeybee social networks , 2018, Proceedings of the National Academy of Sciences.

[76]  Kazuhiko Ohe,et al.  Identity Tracking of a Disease as a Causal Chain , 2012, ICBO.

[77]  A. Burgard,et al.  Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol. , 2011, Nature chemical biology.

[78]  F. Baker The basics of item response theory , 1985 .

[79]  Muna S. Al-Razgan,et al.  Exploring the Food Pairing Hypothesis in Arab Cuisine: A Study in Computational Gastronomy , 2016 .

[80]  Neo D. Martinez,et al.  Two degrees of separation in complex food webs , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[81]  B. Palsson,et al.  A protocol for generating a high-quality genome-scale metabolic reconstruction , 2010 .

[82]  A. Burgard,et al.  Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization , 2003, Biotechnology and bioengineering.

[83]  Mile Šikić,et al.  Identification of Patient Zero in Static and Temporal Networks: Robustness and Limitations. , 2015, Physical review letters.

[84]  Johannes Jaeger,et al.  Modularity, criticality, and evolvability of a developmental gene regulatory network , 2018, bioRxiv.

[85]  Yoshio Tateno,et al.  HGT-Gen: a tool for generating a phylogenetic tree with horizontal gene transfer , 2011, Bioinformation.

[86]  O. Hobert Gene Regulation by Transcription Factors and MicroRNAs , 2008, Science.

[87]  K. Sneppen,et al.  Specificity and Stability in Topology of Protein Networks , 2002, Science.

[88]  Marcus W Feldman,et al.  Evolution of Hierarchy in Bacterial Metabolic Networks , 2017, bioRxiv.

[89]  Sonia Kéfi,et al.  How Structured Is the Entangled Bank? The Surprisingly Simple Organization of Multiplex Ecological Networks Leads to Increased Persistence and Resilience , 2016, PLoS biology.

[90]  Loet Leydesdorff,et al.  Betweenness centrality as a driver of preferential attachment in the evolution of research collaboration networks , 2011, J. Informetrics.

[91]  Johanna J. Heymans,et al.  Network analysis of the South Florida Everglades graminoid marshes and comparison with nearby cypress ecosystems , 2002 .

[92]  F. Iorio,et al.  Transcriptional data: a new gateway to drug repositioning? , 2013, Drug discovery today.

[93]  Robert R. Christian,et al.  Organizing and understanding a winter's seagrass foodweb network through effective trophic levels , 1999 .

[94]  Joseph A. Veech,et al.  A probabilistic model for analysing species co-occurrence , 2013 .

[95]  Olaf Sporns,et al.  The small world of the cerebral cortex , 2007, Neuroinformatics.

[96]  Hyunjung Shin,et al.  Drug repurposing with network reinforcement , 2019, BMC Bioinformatics.

[97]  Noa Pinter-Wollman,et al.  Underlying mechanisms and ecological consequences of variation in exploratory behavior of the Argentine ant, Linepithema humile , 2018, bioRxiv.

[98]  Aarash Bordbar,et al.  A Systems Approach to Predict Oncometabolites via Context-Specific Genome-Scale Metabolic Networks , 2014, PLoS Comput. Biol..

[99]  H. Kitano Systems Biology: A Brief Overview , 2002, Science.

[100]  Karthik Raman,et al.  MINREACT: an efficient algorithm for identifying minimal metabolic networks , 2020, bioRxiv.

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

[102]  R. Tsien,et al.  Specificity and Stability in Topology of Protein Networks , 2022 .

[103]  Ilya R. Fischhoff,et al.  Network metrics reveal differences in social organization between two fission–fusion species, Grevy’s zebra and onager , 2007, Oecologia.

[104]  Stephen G. Oliver,et al.  Yeast Systems Biology: Towards a Systems Understanding of Regulation of Eukaryotic Networks in Complex Diseases and Biotechnology , 2011 .

[105]  Joaquín Goñi,et al.  On the origins of hierarchy in complex networks , 2013, Proceedings of the National Academy of Sciences.

[106]  W. Wong,et al.  Modeling gene regulation from paired expression and chromatin accessibility data , 2017, Proceedings of the National Academy of Sciences.

[107]  Giulia Menichetti,et al.  Network integration of multi-tumour omics data suggests novel targeting strategies , 2017, bioRxiv.

[108]  Stuart R. Borrett,et al.  Six general ecosystem properties are more intense in biogeochemical cycling networks than food webs , 2015, J. Complex Networks.

[109]  Matteo Marsili,et al.  Reconstruction of financial networks for robust estimation of systemic risk , 2011 .

[110]  Walter E. Beyeler,et al.  The topology of interbank payment flows , 2007 .

[111]  Natasa Przulj,et al.  Biological network comparison using graphlet degree distribution , 2007, Bioinform..

[112]  A. Howe,et al.  Ecology, Evolution and Organismal Biology Publications Ecology, Evolution and Organismal Biology Demonstrating Microbial Co-occurrence Pattern Analyses within and between Ecosystems Demonstrating Microbial Co-occurrence Pattern Analyses within and between Ecosystems , 2022 .

[113]  Silvio Waschina,et al.  LESS IS MORE: SELECTIVE ADVANTAGES CAN EXPLAIN THE PREVALENT LOSS OF BIOSYNTHETIC GENES IN BACTERIA , 2014, Evolution; international journal of organic evolution.

[114]  Alessandro Vespignani,et al.  Measurability of the epidemic reproduction number in data-driven contact networks , 2018, Proceedings of the National Academy of Sciences.

[115]  Insuk Lee,et al.  Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics , 2009, PLoS biology.

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

[117]  U. Alon,et al.  Environmental variability and modularity of bacterial metabolic networks , 2007, BMC Evolutionary Biology.

[118]  Albert-László Barabási,et al.  Flavor network and the principles of food pairing , 2011, Scientific reports.

[119]  Chris Rorden,et al.  Assessing the Clinical Effect of Residual Cortical Disconnection After Ischemic Strokes , 2014, Stroke.

[120]  G Katriel,et al.  Mathematical modelling and prediction in infectious disease epidemiology. , 2013, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[121]  M. Newman,et al.  Network theory and SARS: predicting outbreak diversity , 2004, Journal of Theoretical Biology.

[122]  Yan Yu,et al.  Knockdown of EWSR1/FLI1 expression alters the transcriptome of Ewing sarcoma cells in vitro , 2016, Journal of bone oncology.

[123]  David Lusseau,et al.  The emergent properties of a dolphin social network , 2003, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[124]  S. Horvath,et al.  Variations in DNA elucidate molecular networks that cause disease , 2008, Nature.

[125]  Min Chen,et al.  Comparing Statistical Methods for Constructing Large Scale Gene Networks , 2012, PloS one.

[126]  D. Geschwind,et al.  Human-Specific Transcriptional Networks in the Brain , 2012, Neuron.

[127]  R. Cotter,et al.  Mass Spectrometry , 1992, Bio/Technology.

[128]  R. Sharan,et al.  Protein networks in disease. , 2008, Genome research.

[129]  Enys Mones,et al.  Hierarchy Measure for Complex Networks , 2012, PloS one.

[130]  Chao Chen,et al.  csuWGCNA: a combination of signed and unsigned WGCNA to capture negative correlations , 2018, bioRxiv.

[131]  F Alex Feltus,et al.  The Association of Multiple Interacting Genes with Specific Phenotypes in Rice Using Gene Coexpression Networks1[C][W][OA] , 2010, Plant Physiology.

[132]  C. Myers,et al.  Using networks to measure similarity between genes: association index selection , 2013, Nature Methods.

[133]  Albert-László Barabási,et al.  Nature’s reach: narrow work has broad impact , 2019, Nature.

[134]  B. Palsson Systems Biology: Constraint-based Reconstruction and Analysis , 2015 .

[135]  A. Wagner The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. , 2001, Molecular biology and evolution.

[136]  Eva Ceulemans,et al.  Assessing Temporal Emotion Dynamics Using Networks , 2016, Assessment.

[137]  Petter Holme,et al.  Simulated Epidemics in an Empirical Spatiotemporal Network of 50,185 Sexual Contacts , 2010, PLoS Comput. Biol..

[138]  M. Newman Analysis of weighted networks. , 2004, Physical review. E, Statistical, nonlinear, and soft matter physics.

[139]  Jie Li,et al.  Review of Drug Repositioning Approaches and Resources , 2018, International journal of biological sciences.

[140]  Mahsa Alikhani,et al.  Reviewing the Issues and Challenges of Electronic Banking Regime in Iran , 2018 .

[141]  Joshua L. Payne,et al.  RNA-mediated gene regulation is less evolvable than transcriptional regulation , 2018, Proceedings of the National Academy of Sciences.

[142]  Ken Albala Pleyn Delit: Medieval Cookery for Modern Cooks , 1976 .

[143]  W. Hoppitt,et al.  Social Network Analysis Shows Direct Evidence for Social Transmission of Tool Use in Wild Chimpanzees , 2014, PLoS biology.

[144]  S. Lee,et al.  Metabolic engineering of Escherichia coli for the production of l-valine based on transcriptome analysis and in silico gene knockout simulation , 2007, Proceedings of the National Academy of Sciences.

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

[146]  S. Berto,et al.  Species-Specific Changes in a Primate Transcription Factor Network Provide Insights into the Molecular Evolution of the Primate Prefrontal Cortex , 2018, Genome biology and evolution.

[147]  Z. Neda,et al.  Measuring preferential attachment in evolving networks , 2001, cond-mat/0104131.

[148]  Raymond L. Lindeman The trophic-dynamic aspect of ecology , 1942 .

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

[150]  Khader Shameer,et al.  In silico methods for drug repurposing and pharmacology , 2016, Wiley interdisciplinary reviews. Systems biology and medicine.

[151]  Albert-László Barabási,et al.  The unmapped chemical complexity of our diet , 2019, Nature Food.

[152]  A. Arenas,et al.  Abrupt transition in the structural formation of interconnected networks , 2013, Nature Physics.

[153]  Olaf Sporns,et al.  THE HUMAN CONNECTOME: A COMPLEX NETWORK , 2011, Schizophrenia Research.

[154]  L. Altenberg,et al.  PERSPECTIVE: COMPLEX ADAPTATIONS AND THE EVOLUTION OF EVOLVABILITY , 1996, Evolution; international journal of organic evolution.

[155]  E. Almaas Biological impacts and context of network theory , 2007, Journal of Experimental Biology.

[156]  C. Huttenhower,et al.  Cross-biome comparison of microbial association networks , 2015, Front. Microbiol..

[157]  N. Price,et al.  Genome-scale modeling for metabolic engineering , 2015, Journal of Industrial Microbiology & Biotechnology.

[158]  Constantinos Dovrolis,et al.  The hourglass effect in hierarchical dependency networks , 2016, Network Science.

[159]  Judith L. Bronstein,et al.  Duality of interaction outcomes in a plant–frugivore multilayer network , 2017 .

[160]  Alessandro Gozzi,et al.  MultiLink Analysis: Brain Network Comparison via Sparse Connectivity Analysis , 2018, Scientific Reports.

[161]  A. Barabasi,et al.  Global organization of metabolic fluxes in the bacterium Escherichia coli , 2004, Nature.

[162]  Yizhen Yan,et al.  Accurate Drug Repositioning through Non-tissue-Specific Core Signatures from Cancer Transcriptomes. , 2018, Cell reports.

[163]  M E J Newman Assortative mixing in networks. , 2002, Physical review letters.

[164]  J. Mattick,et al.  Non-coding RNA. , 2006, Human molecular genetics.

[165]  Jason A. Papin,et al.  Whole-genome metabolic network reconstruction and constraint-based modeling. , 2011, Methods in enzymology.

[166]  D. Borsboom,et al.  Network analysis: an integrative approach to the structure of psychopathology. , 2013, Annual review of clinical psychology.

[167]  Luis E C Rocha,et al.  Information dynamics shape the sexual networks of Internet-mediated prostitution , 2010, Proceedings of the National Academy of Sciences.

[168]  Fred Russell Kramer,et al.  Oligonucleotide Arrays: New Concepts and Possibilities , 1994, Bio/Technology.

[169]  P. Park ChIP–seq: advantages and challenges of a maturing technology , 2009, Nature Reviews Genetics.

[170]  Olaf Sporns,et al.  The Human Connectome: A Structural Description of the Human Brain , 2005, PLoS Comput. Biol..

[171]  Pedro Zambianchi,et al.  The non-equilibrium nature of culinary evolution , 2008, 0802.4393.

[172]  Deisy Morselli Gysi,et al.  Comparing multiple networks using the Co-expression Differential Network Analysis (CoDiNA) , 2018, 1802.00828.

[173]  Robert E. Ulanowicz,et al.  Quantitative methods for ecological network analysi , 2004, Comput. Biol. Chem..

[174]  Verena D. Schmittmann,et al.  The Small World of Psychopathology , 2011, PloS one.

[175]  E. Lanza,et al.  Tell me who your friends are and I might be able to tell you what language(s) you speak: Social network analysis, multilingualism, and identity , 2007 .

[176]  Allen Holder,et al.  Robust Analysis of Fluxes in Genome-Scale Metabolic Pathways , 2017, Scientific Reports.

[177]  R. K. De,et al.  Comparing methods for metabolic network analysis and an application to metabolic engineering. , 2013, Gene.

[178]  Kevin Murphy,et al.  Psilocybin for treatment-resistant depression: fMRI-measured brain mechanisms , 2017, Scientific Reports.

[179]  Roded Sharan,et al.  QNet: A Tool for Querying Protein Interaction Networks , 2007, RECOMB.

[180]  E. Koonin,et al.  Scale-free networks in biology: new insights into the fundamentals of evolution? , 2002, BioEssays : news and reviews in molecular, cellular and developmental biology.

[181]  Albert,et al.  Topology of evolving networks: local events and universality , 2000, Physical review letters.

[182]  Andrew Zalesky,et al.  Disruption of structure–function coupling in the schizophrenia connectome , 2014, NeuroImage: Clinical.

[183]  Tanya Y. Berger-Wolf,et al.  A framework for community identification in dynamic social networks , 2007, KDD '07.

[184]  Sara Ballouz,et al.  Guidance for RNA-seq co-expression network construction and analysis: safety in numbers , 2015, Bioinform..

[185]  Chris Wiggins,et al.  ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context , 2004, BMC Bioinformatics.

[186]  Marco Rosa,et al.  Four degrees of separation , 2011, WebSci '12.

[187]  P. Marquet,et al.  Species co-occurrence networks: Can they reveal trophic and non-trophic interactions in ecological communities? , 2018, Ecology.

[188]  A. Barabasi,et al.  Uncovering disease-disease relationships through the incomplete interactome , 2015, Science.

[189]  E. Ravussin,et al.  Insulin resistance and insulin secretory dysfunction as precursors of non-insulin-dependent diabetes mellitus. Prospective studies of Pima Indians. , 1993, The New England journal of medicine.

[190]  Jeffrey D Orth,et al.  What is flux balance analysis? , 2010, Nature Biotechnology.

[191]  Brian D. Fath,et al.  Network mutualism: Positive community-level relations in ecosystems , 2007 .

[192]  A. Fukushima DiffCorr: an R package to analyze and visualize differential correlations in biological networks. , 2013, Gene.

[193]  Santanu Ray,et al.  Comparative study of virgin and reclaimed islands of Sundarban mangrove ecosystem through network analysis , 2008 .

[194]  Taro Takaguchi,et al.  Social dynamics of financial networks , 2017, EPJ Data Science.

[195]  M. Newman,et al.  Why social networks are different from other types of networks. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

[196]  Jinling Huang,et al.  Horizontal gene transfer: building the web of life , 2015, Nature Reviews Genetics.

[197]  Dimitri Van De Ville,et al.  Decoding brain states from fMRI connectivity graphs , 2011, NeuroImage.

[198]  Ilias Tagkopoulos,et al.  Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli , 2016, Nature Communications.

[199]  Hod Lipson,et al.  The evolutionary origins of modularity , 2012, Proceedings of the Royal Society B: Biological Sciences.

[200]  O. Sporns,et al.  Organization, development and function of complex brain networks , 2004, Trends in Cognitive Sciences.

[201]  Loet Leydesdorff,et al.  Network Structure, Self-Organization and the Growth of International Collaboration in Science.Research Policy, 34(10), 2005, 1608-1618. , 2005, 0911.4299.

[202]  Jukka-Pekka Onnela,et al.  Community Structure in Time-Dependent, Multiscale, and Multiplex Networks , 2009, Science.

[203]  Katja Nowick,et al.  A Consensus Network of Gene Regulatory Factors in the Human Frontal Lobe , 2016, Front. Genet..

[204]  Naama Barkai,et al.  Comparative biology: beyond sequence analysis. , 2007, Current opinion in biotechnology.

[205]  Genevieve Konopka,et al.  Molecular networks and the evolution of human cognitive specializations. , 2014, Current opinion in genetics & development.

[206]  Laleh Soltan Ghoraie,et al.  A review of connectivity map and computational approaches in pharmacogenomics , 2017, Briefings Bioinform..

[207]  Atsushi Fukushima,et al.  1. Using the DiffCorr Package to Analyze and Visualize Differential Correlations in Biological Networks , 2016 .

[208]  Denny Borsboom,et al.  Repetitive Behaviors in Autism and Obsessive–Compulsive Disorder: New Perspectives from a Network Analysis , 2014, Journal of Autism and Developmental Disorders.

[209]  Bingshan Li,et al.  Learning Opportunities for Drug Repositioning via GWAS and PheWAS Findings , 2018, AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science.

[210]  Juan M Morales,et al.  Invasive Mutualists Erode Native Pollination Webs , 2008, PLoS biology.

[211]  A. Barabasi,et al.  Network-based in silico drug efficacy screening , 2016, Nature Communications.

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

[213]  João Pedro de Magalhães,et al.  Gene co-expression analysis for functional classification and gene–disease predictions , 2017, Briefings Bioinform..

[214]  Sébastien Lê,et al.  Applied Multivariate Statistics , 2018, Sensory Evaluation of Sound.

[215]  D. Fell,et al.  The small world inside large metabolic networks , 2000, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[216]  Fredrik Liljeros,et al.  Preferential attachment in sexual networks , 2007, Proceedings of the National Academy of Sciences.

[217]  J. Bascompte,et al.  Ecological networks : beyond food webs Ecological networks – beyond food webs , 2008 .

[218]  Michael Watson,et al.  CoXpress: differential co-expression in gene expression data , 2006, BMC Bioinformatics.

[219]  Marc Niethammer,et al.  Compressing Networks with Super Nodes , 2017, Scientific Reports.

[220]  Bernard C. Patten,et al.  Food network unfolding: An extension of trophic dynamics for application to natural ecosystems , 1989 .

[221]  L. Furlong Human diseases through the lens of network biology. , 2013, Trends in genetics : TIG.

[222]  David Gomez-Cabrero,et al.  Data integration in the era of omics: current and future challenges , 2014, BMC Systems Biology.

[223]  Henning Hermjakob,et al.  Analyzing protein-protein interaction networks. , 2012, Journal of proteome research.

[224]  Kenli Li,et al.  cooccurNet: an R package for co‐occurrence network construction and analysis , 2017, Bioinform..

[225]  J. Raes,et al.  Microbial interactions: from networks to models , 2012, Nature Reviews Microbiology.

[226]  A. Butte,et al.  The Integrative Human Microbiome Project: Dynamic Analysis of Microbiome-Host Omics Profiles during Periods of Human Health and Disease , 2014, Cell host & microbe.

[227]  M. Scheffer,et al.  Complexity theory and financial regulation , 2016, Science.

[228]  G. Sandini,et al.  Graph theoretical analysis of magnetoencephalographic functional connectivity in Alzheimer's disease. , 2009, Brain : a journal of neurology.

[229]  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.

[230]  Laura Sheble,et al.  Bibliometric review of ecological network analysis: 2010–2016 , 2018, Ecological Modelling.

[231]  P. Thiran,et al.  Error and attack tolerance of layered complex networks. , 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.

[232]  W. Zachary,et al.  An Information Flow Model for Conflict and Fission in Small Groups , 1977, Journal of Anthropological Research.

[233]  Thomas Schmickl,et al.  Trophallaxis within a robotic swarm: bio-inspired communication among robots in a swarm , 2008, Auton. Robots.

[234]  Mark Blaxter,et al.  Defining operational taxonomic units using DNA barcode data , 2005, Philosophical Transactions of the Royal Society B: Biological Sciences.

[235]  L. Mirny,et al.  Using orthologous and paralogous proteins to identify specificity determining residues , 2002, Genome Biology.

[236]  V. Calhoun,et al.  A Review of Challenges in the Use of fMRI for Disease Classification / Characterization and A Projection Pursuit Application from A Multi-site fMRI Schizophrenia Study , 2008, Brain Imaging and Behavior.

[237]  Arne Elofsson,et al.  Preferential attachment in the evolution of metabolic networks , 2005, BMC Genomics.

[238]  Juan F. Velasco-Muñoz,et al.  Mining Waste and Its Sustainable Management: Advances in Worldwide Research , 2018, Minerals.

[239]  Stefan Wuertz,et al.  Studying plasmid horizontal transfer in situ: a critical review , 2005, Nature Reviews Microbiology.

[240]  Werner Ulrich,et al.  Consumer-resource body-size relationships in natural food webs. , 2006, Ecology.

[241]  Bing Li,et al.  Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes , 2015, The ISME Journal.

[242]  Zechao Li,et al.  Tracking the evolution of overlapping communities in dynamic social networks , 2018, Knowl. Based Syst..

[243]  Danielle S Bassett,et al.  Brain graphs: graphical models of the human brain connectome. , 2011, Annual review of clinical psychology.

[244]  Grit Laudel,et al.  Collaboration, creativity and rewards: why and how scientists collaborate , 2001, Int. J. Technol. Manag..

[245]  D. Long Networks of the Brain , 2011 .

[246]  Judith A. Schwartzbaum,et al.  Bacterial 16S Sequence Analysis of Severe Caries in Young Permanent Teeth , 2010, Journal of Clinical Microbiology.

[247]  Yukiko Matsuoka,et al.  Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases , 2011, Bioinform..

[248]  Roded Sharan,et al.  The large-scale organization of the bacterial network of ecological co-occurrence interactions , 2010, Nucleic acids research.

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

[250]  Ilias Tagkopoulos,et al.  A network-based model for drug repurposing in Rheumatoid Arthritis , 2018, bioRxiv.

[251]  A. Barabasi,et al.  Network medicine--from obesity to the "diseasome". , 2007, The New England journal of medicine.

[252]  Daniel H. Geschwind,et al.  Human Brain Evolution: Harnessing the Genomics (R)evolution to Link Genes, Cognition, and Behavior , 2010, Neuron.

[253]  Eivind Almaas,et al.  wTO: an R package for computing weighted topological overlap and a consensus network with integrated visualization tool , 2017, BMC Bioinformatics.

[254]  Pietro Liò,et al.  The Genome Conformation As an Integrator of Multi-Omic Data: The Example of Damage Spreading in Cancer , 2016, Front. Genet..

[255]  Eléonore Toufektchan,et al.  The Guardian of the Genome Revisited: p53 Downregulates Genes Required for Telomere Maintenance, DNA Repair, and Centromere Structure , 2018, Cancers.

[256]  Enrique Castano,et al.  Transcriptomics and co-expression networks reveal tissue-specific responses and regulatory hubs under mild and severe drought in papaya (Carica papaya L.) , 2018, Scientific Reports.

[257]  Carsten F. Dormann,et al.  Ecological networks - foodwebs and beyond , 2009 .

[258]  Konstantinos Mavromatis,et al.  Microbial co-habitation and lateral gene transfer: what transposases can tell us , 2009, Genome Biology.

[259]  Albert-László Barabási,et al.  Network-based approach to prediction and population-based validation of in silico drug repurposing , 2018, Nature Communications.

[260]  Jong H. Yoon,et al.  General and Specific Functional Connectivity Disturbances in First-Episode Schizophrenia During Cognitive Control Performance , 2011, Biological Psychiatry.

[261]  Manlio De Domenico,et al.  Multilayer network modeling of integrated biological systems: Comment on "Network science of biological systems at different scales: A review" by Gosak et al. , 2017, Physics of life reviews.

[262]  Erich Bornberg-Bauer,et al.  The Evolution of Protein Interaction Networks in Regulatory Proteins , 2004, Comparative and functional genomics.

[263]  Albert-László Barabási,et al.  The Activity Reaction Core and Plasticity of Metabolic Networks , 2005, PLoS Comput. Biol..

[264]  Eleonora Patacchini,et al.  Organized Crime Networks: an Application of Network Analysis Techniques to the American Mafia , 2012 .

[265]  Tamás Vicsek,et al.  Hierarchical Self-Organization of Non-Cooperating Individuals , 2013, PloS one.

[266]  Vito Latora,et al.  Structural measures for multiplex networks. , 2013, Physical review. E, Statistical, nonlinear, and soft matter physics.

[267]  K. N. Chandrika,et al.  Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets , 2006, Nature Genetics.

[268]  Martin G. Everett,et al.  A Graph-theoretic perspective on centrality , 2006, Soc. Networks.

[269]  Allan R. Jones,et al.  Canonical Genetic Signatures of the Adult Human Brain , 2015, Nature Neuroscience.

[270]  Kevin Lee,et al.  A review of dynamic network models with latent variables. , 2017, Statistics surveys.

[271]  M. Metzker Sequencing technologies — the next generation , 2010, Nature Reviews Genetics.

[272]  M. Vidal,et al.  Integrating 'omic' information: a bridge between genomics and systems biology. , 2003, Trends in genetics : TIG.

[273]  Ulf Leser,et al.  Comparative assessment of differential network analysis methods , 2016, Briefings Bioinform..

[274]  J. Miro-Julia,et al.  Marvel Universe looks almost like a real social network , 2002 .

[275]  D. Lusseau,et al.  Quantifying the influence of sociality on population structure in bottlenose dolphins. , 2006, The Journal of animal ecology.

[276]  Emilio Ferrara,et al.  Bots increase exposure to negative and inflammatory content in online social systems , 2018, Proceedings of the National Academy of Sciences.

[277]  Yan Zhang,et al.  Ecological network analysis of an urban energy metabolic system: Model development, and a case study of four Chinese cities , 2010 .

[278]  S. Horvath,et al.  Statistical Applications in Genetics and Molecular Biology , 2011 .

[279]  R. Young,et al.  RNA polymerase II. , 1991, Annual review of biochemistry.

[280]  Sabina Kanton,et al.  The role of gene regulatory factors in the evolutionary history of humans. , 2014, Current opinion in genetics & development.

[281]  B. Nijssen,et al.  FOOD PAIRING FROM THE PERSPECTIVE OF THE ‘ VOLATILE COMPOUNDS IN FOOD ’ DATABASE , 2010 .

[282]  Stuart R. Borrett,et al.  Indirect effects and distributed control in ecosystems: Comparative network environ analysis of a seven-compartment model of nitrogen storage in the Neuse River Estuary, USA: Time series analysis , 2014 .

[283]  W. Fitch Homology a personal view on some of the problems. , 2000, Trends in genetics : TIG.

[284]  Jodi R Parrish,et al.  Yeast two-hybrid contributions to interactome mapping. , 2006, Current opinion in biotechnology.

[285]  Gang Wu,et al.  MIMO: an efficient tool for molecular interaction maps overlap , 2013, BMC Bioinformatics.

[286]  Cécile Viboud,et al.  The future of influenza forecasts , 2019, Proceedings of the National Academy of Sciences.

[287]  Daniel J. Brass,et al.  Network Analysis in the Social Sciences , 2009, Science.

[288]  Alexis Battle,et al.  Co-expression networks reveal the tissue-specific regulation of transcription and splicing , 2019 .

[289]  Teri A Manolio,et al.  Genomewide association studies and assessment of the risk of disease. , 2010, The New England journal of medicine.

[290]  John G. Field,et al.  The Need to Analyze Ecological Networks , 1989 .

[291]  S. Horvath,et al.  Conservation and evolution of gene coexpression networks in human and chimpanzee brains , 2006, Proceedings of the National Academy of Sciences.

[292]  James R. Knight,et al.  A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae , 2000, Nature.

[293]  Ginestra Bianconi,et al.  Multiplex PageRank , 2013, PloS one.

[294]  Sebastian E Ahnert,et al.  Network analysis and data mining in food science: the emergence of computational gastronomy , 2013, Flavour.

[295]  D. Garlaschelli,et al.  Early-warning signals of topological collapse in interbank networks , 2013, Scientific Reports.

[296]  D. Latchman Transcription factors: an overview. , 1997, The international journal of biochemistry & cell biology.

[297]  Wei Zhao,et al.  Weighted Gene Coexpression Network Analysis: State of the Art , 2010, Journal of biopharmaceutical statistics.

[298]  M. Feldman,et al.  Large-scale reconstruction and phylogenetic analysis of metabolic environments , 2008, Proceedings of the National Academy of Sciences.

[299]  E. Levanon,et al.  Preferential attachment in the protein network evolution. , 2003, Physical review letters.

[300]  Vito Latora,et al.  Structural reducibility of multilayer networks , 2015, Nature Communications.

[301]  Anirban Dutta,et al.  CompNet: a GUI based tool for comparison of multiple biological interaction networks , 2016, BMC Bioinformatics.

[302]  Debby Van Dam,et al.  Handbook of Biologically Active Peptides, 1st ed., A.J. Kastin (Ed.). Academic Press (2006), 1640 pp., Hardback, Price: £ 135.00, $ 229.95, € 195, ISBN: 0-12-369442-6 , 2007 .

[303]  R. Albert Scale-free networks in cell biology , 2005, Journal of Cell Science.

[304]  Eivind Almaas,et al.  A composite network of conserved and tissue specific gene interactions reveals possible genetic interactions in glioma , 2017, PLoS Comput. Biol..

[305]  Meng Xu,et al.  NetAlign: a web-based tool for comparison of protein interaction networks , 2006, Bioinform..

[306]  Sergio Gómez,et al.  Ranking in interconnected multilayer networks reveals versatile nodes , 2015, Nature Communications.

[307]  M. Gallegati,et al.  Finding Communities in Credit Networks , 2013 .

[308]  D. Wayne Osgood,et al.  The Evolution of Youth Friendship Networks from 6th to 12th Grade: School Transitions, Popularity and Centrality , 2018 .

[309]  Shili Lin,et al.  Network construction and structure detection with metagenomic count data , 2015, BioData Mining.

[310]  R. Huerta,et al.  Task allocation and site fidelity jointly influence foraging regulation in honeybee colonies , 2017, Royal Society Open Science.

[311]  Dewen Hu,et al.  Unsupervised classification of major depression using functional connectivity MRI , 2014, Human brain mapping.

[312]  Joel E. Cohen,et al.  Bacterial traits, organism mass, and numerical abundance in the detrital soil food web of Dutch agricultural grasslands , 2004 .

[313]  M. Perc,et al.  Network science of biological systems at different scales: A review. , 2017, Physics of life reviews.

[314]  O. Sporns Small-world connectivity, motif composition, and complexity of fractal neuronal connections. , 2006, Bio Systems.

[315]  Karthik Raman,et al.  Understanding the evolution of functional redundancy in metabolic networks , 2018, Bioinform..

[316]  Steven J. M. Jones,et al.  Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. , 2011, The New England journal of medicine.

[317]  Tudor I. Oprea,et al.  Drug Repurposing from an Academic Perspective. , 2011, Drug discovery today. Therapeutic strategies.

[318]  Steve Horvath,et al.  WGCNA: an R package for weighted correlation network analysis , 2008, BMC Bioinformatics.

[319]  K. Worsley,et al.  Impaired small-world efficiency in structural cortical networks in multiple sclerosis associated with white matter lesion load. , 2009, Brain : a journal of neurology.

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

[321]  Guy Woodward,et al.  BODY SIZE DETERMINANTS OF THE STRUCTURE AND DYNAMICS OF ECOLOGICAL NETWORKS: SCALING FROM THE INDIVIDUAL TO THE ECOSYSTEM , 2005 .

[322]  Olaf Sporns,et al.  Complex network measures of brain connectivity: Uses and interpretations , 2010, NeuroImage.

[323]  Jie Wu,et al.  Small Worlds: The Dynamics of Networks between Order and Randomness , 2003 .

[324]  A. Singleton,et al.  Genomewide association studies and human disease. , 2009, The New England journal of medicine.

[325]  O. Sporns,et al.  Complex brain networks: graph theoretical analysis of structural and functional systems , 2009, Nature Reviews Neuroscience.

[326]  Juyong Park,et al.  Topology and evolution of the network of western classical music composers , 2015, EPJ Data Science.

[327]  Konstantin Avrachenkov,et al.  Cooperative Game Theory Approaches for Network Partitioning , 2017, COCOON.

[328]  Frederick S. Barrett,et al.  Classic psychedelics: An integrative review of epidemiology, therapeutics, mystical experience, and brain network function , 2019, Pharmacology & therapeutics.

[329]  P. Bork,et al.  Enterotypes of the human gut microbiome , 2011, Nature.

[330]  Christophe Dessimoz,et al.  Inferring Horizontal Gene Transfer , 2015, PLoS Comput. Biol..

[331]  Jessica H. Fong,et al.  Predicting specificity in bZIP coiled-coil protein interactions , 2004, Genome Biology.

[332]  Ginestra Bianconi,et al.  Weighted Multiplex Networks , 2013, PloS one.

[333]  Jason Hinds,et al.  Comparative transcriptomics reveals key gene expression differences between the human and bovine pathogens of the Mycobacterium tuberculosis complex. , 2007, Microbiology.

[334]  Katja Nowick,et al.  Lineage-specific transcription factors and the evolution of gene regulatory networks. , 2010, Briefings in functional genomics.

[335]  Dong-Gi Lee,et al.  Inference on chains of disease progression based on disease networks , 2019, PloS one.

[336]  Polina Mamoshina,et al.  Design of efficient computational workflows for in silico drug repurposing. , 2017, Drug discovery today.

[337]  A. Barabasi,et al.  Evolution of the social network of scientific collaborations , 2001, cond-mat/0104162.

[338]  Frank Harary,et al.  Graph Theory , 2016 .

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

[340]  Guoqing Wang,et al.  A parsimonious statistical method to detect groupwise differentially expressed functional connectivity networks , 2015, Human brain mapping.

[341]  Peter F. Stadler,et al.  Combined Experimental and System-Level Analyses Reveal the Complex Regulatory Network of miR-124 during Human Neurogenesis , 2018, Cell systems.

[342]  Anat Kreimer,et al.  The evolution of modularity in bacterial metabolic networks , 2008, Proceedings of the National Academy of Sciences.

[343]  Alessandro Vespignani Modelling dynamical processes in complex socio-technical systems , 2011, Nature Physics.

[344]  Steve Horvath,et al.  Network neighborhood analysis with the multi-node topological overlap measure , 2007, Bioinform..

[345]  U. Alon,et al.  Spontaneous evolution of modularity and network motifs. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[346]  Stephen S Fong,et al.  Metabolic gene–deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes , 2004, Nature Genetics.

[347]  Patricia C Babbitt,et al.  Can sequence determine function? , 2000, Genome Biology.

[348]  Jignesh M. Patel,et al.  SAGA: a subgraph matching tool for biological graphs , 2007, Bioinform..

[349]  D. Caetano-Anollés,et al.  Emergence of Hierarchical Modularity in Evolving Networks Uncovered by Phylogenomic Analysis , 2019, Evolutionary bioinformatics online.

[350]  J. A. Aas,et al.  Defining the Normal Bacterial Flora of the Oral Cavity , 2005, Journal of Clinical Microbiology.

[351]  J. Moody The Structure of a Social Science Collaboration Network: Disciplinary Cohesion from 1963 to 1999 , 2004 .

[352]  Nagiza F. Samatova,et al.  From pull-down data to protein interaction networks and complexes with biological relevance. , 2008, Bioinformatics.

[353]  Kelly R. Finn,et al.  Novel insights into animal sociality from multilayer networks , 2017 .

[354]  Sergio Gómez,et al.  Centrality rankings in multiplex networks , 2014, WebSci '14.

[355]  Eytan Ruppin,et al.  Modeling cancer metabolism on a genome scale , 2015, Molecular systems biology.

[356]  Yan Zhang Urban metabolism: a review of research methodologies. , 2013, Environmental pollution.

[357]  C. Maranas,et al.  Succinate Overproduction: A Case Study of Computational Strain Design Using a Comprehensive Escherichia coli Kinetic Model , 2015, Front. Bioeng. Biotechnol..

[358]  M. Newman,et al.  Mixing patterns in networks. , 2002, Physical review. E, Statistical, nonlinear, and soft matter physics.

[359]  Robert E. Ulanowicz,et al.  The Comparative Ecology of Six Marine Ecosystems , 1991 .

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

[361]  G. Robinson Regulation of division of labor in insect societies. , 1992, Annual review of entomology.

[362]  E. Bullmore,et al.  Disrupted Axonal Fiber Connectivity in Schizophrenia , 2011, Biological Psychiatry.

[363]  Joong-Hwan Oh,et al.  Changing patterns of social network structure in composer-singer relationships: A case study of the Korean popular music industry, 1927–1997 , 2002 .

[364]  Hernan G. Garcia,et al.  Principles of Systems Biology, No. 30. , 2018, Cell systems.

[365]  Patrick Thiran,et al.  Layered complex networks. , 2006, Physical review letters.

[366]  神田 信彦 Beck Depression Inventory-IIについての一考察 , 2004 .

[367]  Mingkun Jiao,et al.  Computational drug repositioning for cancer therapeutics. , 2015, Current topics in medicinal chemistry.

[368]  Jens Nielsen,et al.  Systems biology based drug repositioning for development of cancer therapy. , 2019, Seminars in cancer biology.

[369]  A. Vázquez Growing network with local rules: preferential attachment, clustering hierarchy, and degree correlations. , 2002, Physical review. E, Statistical, nonlinear, and soft matter physics.

[370]  Erik Kristiansson,et al.  Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential , 2015, BMC Genomics.

[371]  S. Borrett,et al.  Environ centrality reveals the tendency of indirect effects to homogenize the functional importance of species in ecosystems. , 2011, Journal of theoretical biology.

[372]  Judith L Bronstein,et al.  Few Ant Species Play a Central Role Linking Different Plant Resources in a Network in Rupestrian Grasslands , 2016, PloS one.

[373]  E. Borenstein,et al.  Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules , 2013, Proceedings of the National Academy of Sciences.

[374]  M. Newman,et al.  Scientific collaboration networks. II. Shortest paths, weighted networks, and centrality. , 2001, Physical review. E, Statistical, nonlinear, and soft matter physics.

[375]  V. Isaeva Self-organization in biological systems , 2012, Biology Bulletin.

[376]  M. Vidal,et al.  A genome-wide positioning systems network algorithm for in silico drug repurposing , 2019, Nature Communications.

[377]  Mason A. Porter,et al.  Multilayer networks , 2013, J. Complex Networks.

[378]  Katherine A. Hollywood,et al.  High throughput screening of complex biological samples with mass spectrometry - from bulk measurements to single cell analysis. , 2019, The Analyst.

[379]  Günter P. Wagner,et al.  Complex Adaptations and the Evolution of Evolvability , 2005 .

[380]  A. Newton,et al.  Second Messengers. , 2016, Cold Spring Harbor perspectives in biology.

[381]  L. Stubbs,et al.  Differences in human and chimpanzee gene expression patterns define an evolving network of transcription factors in brain , 2009, Proceedings of the National Academy of Sciences.

[382]  D. Mason,et al.  Compartments revealed in food-web structure , 2003, Nature.

[383]  Qi Qiao,et al.  Unified network analysis on the organization of an industrial metabolic system , 2017 .

[384]  Eugene V Koonin,et al.  An apology for orthologs - or brave new memes , 2001, Genome Biology.

[385]  A. Wagner DOES EVOLUTIONARY PLASTICITY EVOLVE? , 1996, Evolution; international journal of organic evolution.

[386]  Ganesh Bagler,et al.  Analysis of Food Pairing in Regional Cuisines of India , 2015, PloS one.

[387]  D. Caron,et al.  Marine bacterial, archaeal and protistan association networks reveal ecological linkages , 2011, The ISME Journal.

[388]  Bernhard Voelkl,et al.  A social network analysis of primate groups , 2009, Primates.

[389]  Daniel M. Griffith,et al.  cooccur: Probabilistic Species Co-Occurrence Analysis in R , 2016 .

[390]  Denny Borsboom,et al.  Mental Disorders as Causal Systems , 2015 .

[391]  Thomas Oatley,et al.  The Political Economy of Global Finance: A Network Model , 2013, Perspectives on Politics.

[392]  Christopher L. Magee,et al.  ESD Working Paper Series ESD-WP-2010-01 , 2010 .

[393]  M. Newman,et al.  The structure of scientific collaboration networks. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[394]  A. G. de la Fuente From 'differential expression' to 'differential networking' - identification of dysfunctional regulatory networks in diseases. , 2010, Trends in genetics : TIG.

[395]  A. Takamatsu,et al.  Characterization of Adaptation by Morphology in a Planar Biological Network of Plasmodial Slime Mold , 2011 .

[396]  V. Christensen Ecosystem maturity - towards quantification , 1995 .

[397]  E. Marcotte,et al.  An Improved, Bias-Reduced Probabilistic Functional Gene Network of Baker's Yeast, Saccharomyces cerevisiae , 2007, PloS one.

[398]  Joshua L. Payne,et al.  The Robustness and Evolvability of Transcription Factor Binding Sites , 2014, Science.

[399]  E. Winzeler,et al.  Genomics, gene expression and DNA arrays , 2000, Nature.

[400]  S. L. Wong,et al.  A Map of the Interactome Network of the Metazoan C. elegans , 2004, Science.