Interactome Networks and Human Disease

Emergence of Scaling in Random Networks

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Initial sequencing and analysis of the human genome

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Statistical mechanics of complex networks

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The sequence of the human genome

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Construction of a genetic linkage map in man using restriction fragment length polymorphisms.

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Network biology: understanding the cell's functional organization

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Network motifs: simple building blocks of complex networks.

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Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy AssessmentPreprint

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KEGG for linking genomes to life and the environment

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A novel genetic system to detect protein–protein interactions

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Stochastic Gene Expression in a Single Cell

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Lethality and centrality in protein networks

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Network medicine: a network-based approach to human disease

Barabási, A.-L., Gulbahce, N., & Loscalzo, J. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2918 · Cited by 5,034 · see citing works

The Large-Scale Organization of Metabolic Networks

Jeong, H., Tombor, B., Albert, R., Oltvai, Z. N., & Barabási, A.-L. (2000) · Nature · doi:10.1038/35036627 · Cited by 4,972 · see citing works

Functional organization of the yeast proteome by systematic analysis of protein complexes

Gavin, A., Böesche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J. M., Michon, A., Cruciat, C., et al. (2002) · Nature · doi:10.1038/415141a · Cited by 4,729 · see citing works

A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae

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Functional profiling of the Saccharomyces cerevisiae genome

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Hierarchical Organization of Modularity in Metabolic Networks

Ravasz, E., Somera, A. L., Mongru, D. A., Oltvai, Z. N., & Barabási, A.-L. (2002) · Science · doi:10.1126/science.1073374 · Cited by 4,224 · see citing works

Mammalian microRNAs predominantly act to decrease target mRNA levels

Guo, H., Ingolia, N. T., Weissman, J. S., & Bartel, D. P. (2010) · Nature · doi:10.1038/nature09267 · Cited by 3,886 · see citing works

Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry

Ho, Y., Gruhler, A., Heilbut, A. M., Bader, G. D., Moore, L., Adams, S., Millar, A., Taylor, P. P., Bennett, K. L., Boutilier, K., et al. (2002) · Nature · doi:10.1038/415180a · Cited by 3,573 · see citing works

A comprehensive two-hybrid analysis to explore the yeast protein interactome

Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M., & Sakaki, Y. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.061034498 · Cited by 3,566 · see citing works

The cancer genome

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Network motifs: theory and experimental approaches

Alon, U. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2102 · Cited by 3,279 · see citing works

The human disease network

Goh, K.-I., Cusick, M. E., Valle, D., Childs, B., Vidal, M., & Barabási, A.-L. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0701361104 · Cited by 3,242 · see citing works

Network motifs in the transcriptional regulation network of Escherichia coli

Shen-Orr, S. S., Milo, R., Mangan, S., & Alon, U. S. (2002) · Nature Genetics · doi:10.1038/ng881 · Cited by 2,970 · see citing works

Transcriptional Regulatory Networks in <i>Saccharomyces cerevisiae</i>

Lee, T. I., Rinaldi, N. J., Robert, F., Odom, D. T., Bar-Joseph, Z., Gerber, G. K., Hannett, N. M., Harbison, C. T., Thompson, C. M., Simon, I., et al. (2002) · Science · doi:10.1126/science.1075090 · Cited by 2,956 · see citing works

Towards a proteome-scale map of the human protein–protein interaction network

Rual, J.-F. M., Venkatesan, K., Hao, T., Hirozane-Kishikawa, T., Dricot, A., Li, N., Berriz, G. F., Gibbons, F. D., Dreze, M., Ayivi-Guedehoussou, N., et al. (2005) · Nature · doi:10.1038/nature04209 · Cited by 2,937 · see citing works

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

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Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

Hafner, M., Landthaler, M., Burger, L., Khorshid, M., Hausser, J., Berninger, P., Rothballer, A., Ascano, M., Jungkamp, A.-C., Munschauer, M., et al. (2010) · Cell · doi:10.1016/j.cell.2010.03.009 · Cited by 2,873 · see citing works

A generic protein purification method for protein complex characterization and proteome exploration

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Proteome survey reveals modularity of the yeast cell machinery

Gavin, A., Aloy, P., Grandi, P., Krause, R., Böesche, M., Marzioch, M., Rau, C., Jensen, L. J., Bastuck, S., Dümpelfeld, B., et al. (2006) · Nature · doi:10.1038/nature04532 · Cited by 2,544 · see citing works

A Human Protein-Protein Interaction Network: A Resource for Annotating the Proteome

Stelzl, U., Worm, U., Lalowski, M. M., Haenig, C., Brembeck, F. H., Goehler, H., Strödicke, M., Zenkner, M., Schoenherr, A., Koeppen, S., et al. (2005) · Cell · doi:10.1016/j.cell.2005.08.029 · Cited by 2,389 · see citing works

Comparative assessment of large-scale data sets of protein–protein interactions

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A Protein Interaction Map of Drosophila melanogaster

Giot, L., Bader, J. S., Brouwer, C., Chaudhuri, A., Kuang, B., Li, Y., Hao, Y. L., Ooi, C., Godwin, B., Vitols, E., et al. (2003) · Science · doi:10.1126/science.1090289 · Cited by 2,266 · see citing works

A Gene-Coexpression Network for Global Discovery of Conserved Genetic Modules

Stuart, J. M., Segal, E., Koller, D., & Kim, S. K. (2003) · Science · doi:10.1126/science.1087447 · Cited by 2,235 · see citing works

The Genetic Landscape of a Cell

Costanzo, M., Baryshnikova, A., Bellay, J., Kim, Y., Spear, E. D., Sevier, C. S., Ding, H., Koh, J. L. Y., Toufighi, K., Mostafavi, S., et al. (2010) · Science · doi:10.1126/science.1180823 · Cited by 2,162 · see citing works

Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants

Tong, A. H. Y., Evangelista, M., Parsons, A. B., Xu, H., Bader, G. D., Pagé, N., Robinson, M., Raghibizadeh, S., Hogue, C. W. V., Bussey, H., et al. (2001) · Science · doi:10.1126/science.1065810 · Cited by 2,138 · see citing works

Quantifying <i>E. coli</i> Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

Taniguchi, Y., Choi, P. J., Li, G.-W., Chen, H., Babu, M., Hearn, J., Emili, A., & Xie, X. S. (2010) · Science · doi:10.1126/science.1188308 · Cited by 1,982 · see citing works

Link communities reveal multiscale complexity in networks

Ahn, Y., Bagrow, J. P., & Lehmann, S. (2010) · Nature · doi:10.1038/nature09182 · Cited by 1,964 · see citing works

Evidence for dynamically organized modularity in the yeast protein–protein interaction network

Han, J. J., Bertin, N., Hao, T., Goldberg, D. S., Berriz, G. F., Zhang, L. V., Dupuy, D., Walhout, A. J. M., Cusick, M. E., Roth, F. P., et al. (2004) · Nature · doi:10.1038/nature02555 · Cited by 1,789 · see citing works

Noise in Gene Expression: Origins, Consequences, and Control

Raser, J. M., & O’Shea, E. K. (2005) · Science · doi:10.1126/science.1105891 · Cited by 1,719 · see citing works

Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data

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Noise in eukaryotic gene expression

Blake, W. J., Kærn, M., Cantor, C. R., & Collins, J. J. (2003) · Nature · doi:10.1038/nature01546 · Cited by 1,636 · see citing works

A Map of the Interactome Network of the Metazoan C. elegans

Li, S., Armstrong, C. M., Bertin, N., Ge, H., Milstein, S., Boxem, M., Vidalain, P., Han, J.-D. J., Chesneau, A., Hao, T., et al. (2004) · Science · doi:10.1126/science.1091403 · Cited by 1,628 · see citing works

A census of human transcription factors: function, expression and evolution

Vaquerizas, J. M., Kummerfeld, S. K., Teichmann, S. A., & Luscombe, N. M. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2538 · Cited by 1,573 · see citing works

Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease

Botstein, D., & Risch, N. (2003) · Nature Genetics · doi:10.1038/ng1090 · Cited by 1,503 · see citing works

Genetic Mapping in Human Disease

Altshuler, D., Daly, M. J., & Lander, E. S. (2008) · Science · doi:10.1126/science.1156409 · Cited by 1,452 · see citing works

Superfamilies of Evolved and Designed Networks

Milo, R., Itzkovitz, S., Kashtan, N., Levitt, R., Shen-Orr, S. S., Ayzenshtat, I., Sheffer, M., & Alon, U. S. (2004) · Science · doi:10.1126/science.1089167 · Cited by 1,427 · see citing works

High-Quality Binary Protein Interaction Map of the Yeast Interactome Network

Yu, H., Braun, P., Yıldırım, M. A., Lemmens, I., Venkatesan, K., Sahalie, J., Hirozane-Kishikawa, T., Gebreab, F., Li, N., Simonis, N., et al. (2008) · Science · doi:10.1126/science.1158684 · Cited by 1,392 · see citing works

Genetic Control of Biochemical Reactions in Neurospora

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DNA Cloning Using In Vitro Site-Specific RecombinationPreprint

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Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs

Cawley, S., Bekiranov, S., Ng, H. H., Kapranov, P., Sekinger, E. A., Kampa, D., Piccolboni, A., Sementchenko, V., Cheng, J., Williams, A. J., et al. (2004) · Cell · doi:10.1016/s0092-8674(04)00127-8 · Cited by 1,095 · see citing works

A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks

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In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data

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Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens

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An empirical framework for binary interactome mapping

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Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans

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Evolutionary Rate in the Protein Interaction Network

Fraser, H. B., Hirsh, A. E., Steinmetz, L. M., Scharfe, C., & Feldman, M. W. (2002) · Science · doi:10.1126/science.1068696 · Cited by 869 · see citing works

Elemente der exakten Erblichkeitslehre

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Applications of genome‐scale metabolic reconstructions

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Toward a protein–protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins

Ito, T., Tashiro, K., Muta, S., Ozawa, R., Chiba, T., Nishizawa, M., Yamamoto, K., Kuhara, S., & Sakaki, Y. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.3.1143 · Cited by 814 · see citing works

Toward a Comprehensive Atlas of the Physical Interactome of Saccharomyces cerevisiae

Collins, S. R., Kemmeren, P., Zhao, X.-C., Greenblatt, J. F., Spencer, F., Holstege, F. C. P., Weissman, J. S., & Krogan, N. J. (2007) · Molecular &amp; Cellular Proteomics · doi:10.1074/mcp.m600381-mcp200 · Cited by 795 · see citing works

A Protein–Protein Interaction Network for Human Inherited Ataxias and Disorders of Purkinje Cell Degeneration

Lim, J., Hao, T., Shaw, C., Patel, A. J., Szabó, G., Rual, J.-F., Fisk, C. J., Li, N., Smolyar, A., Hill, D. E., et al. (2006) · Cell · doi:10.1016/j.cell.2006.03.032 · Cited by 789 · see citing works

Protein Interaction Mapping in C. elegans Using Proteins Involved in Vulval Development

Walhout, A. J. M., Sordella, R., Lu, X., Hartley, J. L., Temple, G. F., Brasch, M. A., Thierry‐Mieg, N., & Vidal, M. (2000) · Science · doi:10.1126/science.287.5450.116 · Cited by 757 · see citing works

McKusick's Online Mendelian Inheritance in Man (OMIM(R))

Amberger, J., Bocchini, C. A., Scott, A. F., & Hamosh, A. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn665 · Cited by 717 · see citing works

Dynamic modularity in protein interaction networks predicts breast cancer outcome

Taylor, I. W., Linding, R., Warde-Farley, D., Liu, Y., Pesquita, C., Faria, D., Bull, S. B., Pawson, T. J., Morris, Q., & Wrana, J. L. (2009) · Nature Biotechnology · doi:10.1038/nbt.1522 · Cited by 690 · see citing works

A Dynamic Network Approach for the Study of Human Phenotypes

Hidalgo, C. A., Blumm, N., Barabási, A.-Ĺ., & Christakis, N. A. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000353 · Cited by 670 · see citing works

Exploring genetic interactions and networks with yeast

Boone, C., Bussey, H., & Andrews, B. J. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2085 · Cited by 661 · see citing works

A Gene Expression Map for Caenorhabditis elegans

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Relating Whole-Genome Expression Data with Protein-Protein InteractionsPreprint

Jansen, R., Greenbaum, D. S., & Gerstein, M. (2002) · Genome Research · doi:10.1101/gr.205602 · Cited by 657 · see citing works

Network‐based global inference of human disease genes

Wu, X., Jiang, R., Zhang, M. Q., & Li, S. (2008) · Molecular Systems Biology · doi:10.1038/msb.2008.27 · Cited by 654 · see citing works

[34] GATEWAY recombinational cloning: Application to the cloning of large numbers of open reading frames or ORFeomes

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A Physical and Regulatory Map of Host-Influenza Interactions Reveals Pathways in H1N1 Infection

Shapira, S. D., Gat‐Viks, I., Shum, B. O. V., Dricot, A., DeGrace, M. M., Wu, L., Gupta, P. B., Hao, T., Silver, S. J., Root, D. E., et al. (2009) · Cell · doi:10.1016/j.cell.2009.12.018 · Cited by 630 · see citing works

Network modeling links breast cancer susceptibility and centrosome dysfunction

Pujana, M. Á., Han, J.-D. J., Starita, L. M., Purrington, K. S., Tewari, M., Ahn, J. S., Rennert, G., Moreno, V. R., Kirchhoff, T., Gold, B., et al. (2007) · Nature Genetics · doi:10.1038/ng.2007.2 · Cited by 611 · see citing works

Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae

Ge, H., Liu, Z., Church, G. M., & Vidal, M. (2001) · Nature Genetics · doi:10.1038/ng776 · Cited by 575 · see citing works

Predicting disease genes using protein–protein interactions

Oti, M., Snel, ‎., Huynen, M. A., & Brunner, H. G. (2006) · Journal of Medical Genetics · doi:10.1136/jmg.2006.041376 · Cited by 574 · see citing works

Network motifs in integrated cellular networks of transcription–regulation and protein–protein interaction

Yeger‐Lotem, E., Sattath, S., Kashtan, N., Itzkovitz, S., Milo, R., Pinter, R. Y., Alon, U. S., & Margalit, H. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0306752101 · Cited by 536 · see citing works

The molecular sociology of the cell

Robinson, C. V., Šali, A., & Baumeister, W. P. (2007) · Nature · doi:10.1038/nature06523 · Cited by 533 · see citing works

Global topological features of cancer proteins in the human interactome

Jonsson, P. F., & Bates, P. A. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl390 · Cited by 490 · see citing works

The implications of human metabolic network topology for disease comorbidity

Lee, D., Park, J., Kay, K. A., Christakis, N. A., Oltvai, Z. N., & Barabási, A.-Ĺ. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0802208105 · Cited by 489 · see citing works

Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses

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Modeling of Protein Interaction Networks

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Proteome organization in a genome-reduced bacterium

Kühner, S., van Noort, V., Betts, M. J., Leo-Macias, A., Batisse, C., Rode, M., Yamada, T., Maier, T., Bader, S., Beltran-Alvarez, P., et al. (2009) · Science · doi:10.1126/science.1176343 · Cited by 471 · see citing works

Defining genetic interaction

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Evolutionary conservation of motif constituents in the yeast protein interaction network

Wuchty, S., Oltvai, Z. N., & Barabási, A.-Ĺ. (2003) · Nature Genetics · doi:10.1038/ng1242 · Cited by 445 · see citing works

The Edinburgh human metabolic network reconstruction and its functional analysis

Ma, H., Sorokin, A., Mazein, A., Selkov, A., Selkov, E., Demin, O., & Goryanin, I. (2007) · Molecular Systems Biology · doi:10.1038/msb4100177 · Cited by 435 · see citing works

Integrating ‘omic’ information: a bridge between genomics and systems biology

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MAP Kinases with Distinct Inhibitory Functions Impart Signaling Specificity during Yeast Differentiation

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Evolving protein interaction networks through gene duplication

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Herpesviral Protein Networks and Their Interaction with the Human Proteome

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Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues

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High-resolution DNA-binding specificity analysis of yeast transcription factorsPreprint

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Epstein–Barr virus and virus human protein interaction maps

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Role of Shankhpushpi (Convolvulus pluricaulis) in neurological disorders: An umbrella review covering evidence from ethnopharmacology to clinical studies

Sharma, R., Singla, R. K., Banerjee, S., Sinha, B., Shen, B., & Sharma, R. (2022) · Neuroscience &amp; Biobehavioral Reviews · doi:10.1016/j.neubiorev.2022.104795 · Cited by 81 · see citing works

Multiplexed Screening of Thousands of Natural Products for Protein–Ligand Binding in Native Mass Spectrometry

Nguyen, G. T. H., Bennett, J. L., Liu, S., Hancock, S. E., Winter, D. L., Glover, D. J., & Donald, W. A. (2021) · Journal of the American Chemical Society · doi:10.1021/jacs.1c10408 · Cited by 66 · see citing works

Microglia recapitulate a hematopoietic master regulator network in the aging human frontal cortex

Wehrspaun, C. C., Haerty, W., & Ponting, C. P. (2015) · Neurobiology of Aging · doi:10.1016/j.neurobiolaging.2015.04.008 · Cited by 64 · see citing works

PINA 3.0: mining cancer interactome

Du, Y., Cai, M., Xing, X., Ji, J., Yang, E., & Wu, J. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa1075 · Cited by 60 · see citing works

Targeting protein–protein interactions in hematologic malignancies: still a challenge or a great opportunity for future therapies?

Cierpicki, T., & Grembecka, J. (2015) · Immunological Reviews · doi:10.1111/imr.12244 · Cited by 53 · see citing works

RNA-Seq Reveals Novel Transcriptional Reorganization in Human Alcoholic Brain

Farris, S. P., & Dayne Mayfield, R. (2014) · International Review of Neurobiology · doi:10.1016/b978-0-12-801105-8.00011-4 · Cited by 49 · see citing works

Transcriptional alterations related to neuropathology and clinical manifestation of Alzheimer’s disease

Silva, A. R. T., Grinberg, L. T., Farfel, J. M., Diniz, B. S., Lima, L. A., Silva, P. J. S., Ferretti, R. E. L., Rocha, R. M., Filho, W. J., Carraro, D. M., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0048751 · Cited by 40 · see citing works

The human proteome – a scientific opportunity for transforming diagnostics, therapeutics, and healthcare

Vidal, M., Chan, D. W., Gerstein, M., Mann, M., Omenn, G. S., Tagle, D., Sechi, S., & Participants, W. (2012) · Clinical Proteomics · doi:10.1186/1559-0275-9-6 · Cited by 41 · see citing works

Perspectives on the Genomics of HSP Beyond Mendelian Inheritance

Bis-Brewer, D. M., & Züchner, S. (2018) · Frontiers in Neurology · doi:10.3389/fneur.2018.00958 · Cited by 31 · see citing works

Towards perturbation prediction of biological networks using deep learning

Li, D., & Gao, J. (2019) · Scientific Reports · doi:10.1038/s41598-019-48391-y · Cited by 16 · see citing works

The 4E approach to the human microbiome: Nested interactions between the gut-brain/body system within natural and built environments

Palacios‐García, I., Mhuireach, G. A., Grasso‐Cladera, A., Cryan, J. F., & Parada, F. J. (2022) · BioEssays · doi:10.1002/bies.202100249 · Cited by 14 · see citing works

Biomolecular network querying: a promising approach in systems biology

Zhang, S., Zhang, X., & Chen, L. (2008) · BMC Systems Biology · doi:10.1186/1752-0509-2-5 · Cited by 33 · see citing works

An Overview of Systems Biology

Albert, R., & Assmann, S. M. (2017) · Annual Plant Reviews online · doi:10.1002/9781119312994.apr0373

Computational challenges in systems biology

Heath, A. P., & Kavraki, L. E. (2009) · Computer Science Review · doi:10.1016/j.cosrev.2009.01.002 · Cited by 53 · see citing works

Methods to study systems biology of signaling networks: A case study of NSCLC

Samarth, N. H., & Singh, S. (2022) · Elsevier eBooks · doi:10.1016/b978-0-323-90264-9.00037-4 · Cited by 1 · see citing works

Boolean factor graph model for biological systems: the yeast cell-cycle network

Kotiang, S., & Eslami, A. (2021) · BMC Bioinformatics · doi:10.1186/s12859-021-04361-8 · Cited by 4 · see citing works