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