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1. Protein interaction networks
: computational analysis
by Zhang, Aidong, 1961
2009, ISBN 0521888956, Volume 9780521888950, xiv, 278 p., [8] p. of plates
The analysis of protein-protein interactions is fundamental to the understanding of cellular organization, processes, and functions. Proteins seldom act as... 
methods | Computational Biology | Protein Binding | physiology | Data processing | Mathematical models | Protein-protein interactions | Protein Interaction Mapping | Protein Interaction Mapping - methods
Book
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2. Full Text Biological data mining in protein interaction networks
by Li, Xiao-Li, 1969 and Ng, See-Kiong
2009, ISBN 9781605663982, 450
"The goal of this book is to disseminate research results and best practices from cross-disciplinary researchers and practitioners interested in, and working... 
Databases, Protein | methods | Computational Biology | Proteomics | Data processing | Data mining | Protein-protein interactions | Protein Interaction Mapping | Biology, life sciences
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3. Full Text Controllability in protein interaction networks
by Stefan Wuchty
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 5/2014, Volume 111, Issue 19, pp. 7156 - 7160
Recently, the focus of network research shifted to network controllability, prompting us to determine proteins that are important for the control of the... 
Yeasts | Transcription factors | Phosphorylation | Essential genes | Databases | Social interaction | Genes | Humans | Viruses | Human genetics | INTERACTION MAP | EVOLUTIONARY | PHOSPHORYLATION | MULTIDISCIPLINARY SCIENCES | RESOURCE | Transcription Factors - metabolism | Saccharomyces cerevisiae - physiology | Saccharomyces cerevisiae - genetics | Databases, Protein | Databases, Genetic | Saccharomyces cerevisiae Proteins - physiology | Software | Saccharomyces cerevisiae Proteins - genetics | Transcription Factors - genetics | Protein Interaction Mapping | Proteins | Physiological aspects | Research | Health aspects | Protein kinases | Biological Sciences
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4. Full Text Fundamentals of protein interaction network mapping
by Snider, Jamie and Kotlyar, Max and Saraon, Punit and Yao, Zhong and Jurisica, Igor and Stagljar, Igor
Molecular Systems Biology, ISSN 1744-4292, 12/2015, Volume 11, Issue 12, pp. 848 - n/a
Studying protein interaction networks of all proteins in an organism (“interactomes”) remains one of the major challenges in modern biomedicine. Such... 
interactome mapping | PPI technologies | protein‐protein interactions (PPIs) | proteomics | bioinformatics | protein-protein interactions (PPIs) | COMPLEX PREDICTION | COMPLEMENTATION BIFC ANALYSIS | BIOCHEMISTRY & MOLECULAR BIOLOGY | YEAST 2-HYBRID | RESONANCE ENERGY-TRANSFER | MOLECULAR INTERACTION DATABASE | MEMBRANE 2-HYBRID ASSAY | ATTACHMENT BASED METHOD | FUNCTIONAL MODULES | INTERACTION LANDSCAPE | AFFINITY-PURIFICATION | Mammals - metabolism | Protein Interaction Mapping - methods | Computational Biology - methods | Animals | Proteins - metabolism | Humans | Protein Interaction Maps | Proteins | Biochemistry | Cellular biology | Molecular biology | Laboratories | Medical treatment | Mapping | Genetic diversity | Research | Gene expression | Peptide mapping | Studies | Researchers | Computer applications | Proteomics | Gene mapping | Bioinformatics | Methods
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5. Full Text A Global Protein Kinase and Phosphatase Interaction Network in Yeast
by Ashton Breitkreutz and Hyungwon Choi and Jeffrey R. Sharom and Lorrie Boucher and Victor Neduva and Brett Larsen and Zhen-Yuan Lin and Bobby-Joe Breitkreutz and Chris Stark and Guomin Liu and Jessica Ahn and Danielle Dewar-Darch and Teresa Reguly and Xiaojing Tang and Ricardo Almeida and Zhaohui Steve Qin and Tony Pawson and Anne-Claude Gingras and Alexey I. Nesvizhskii and Mike Tyers
Science, ISSN 0036-8075, 5/2010, Volume 328, Issue 5981, pp. 1043 - 1046
The interactions of protein kinases and phosphatases with their regulatory subunits and substrates underpin cellular regulation. We identified a kinase and... 
Datasets | Research fellowships | Yeasts | Protein metabolism | Phosphatases | Cellular metabolism | REPORTS | Cell cycle | Research grants | Proteomes | Nitrogen | MITOSIS | SIGNAL | PHOSPHORYLATION | MULTIDISCIPLINARY SCIENCES | TRANSDUCTION | CELL-CYCLE | SACCHAROMYCES-CEREVISIAE | FEEDBACK | PROTEOMICS | Protein Kinases - metabolism | Carbon - metabolism | Nitrogen - metabolism | Phosphorylation | Signal Transduction | Phosphoprotein Phosphatases - metabolism | Cell Cycle Proteins - metabolism | Protein Tyrosine Phosphatases - metabolism | Proteome | Protein Subunits - metabolism | MAP Kinase Signaling System | Protein Interaction Mapping | Saccharomyces cerevisiae - metabolism | Metabolic Networks and Pathways | Models, Biological | Mass Spectrometry | Saccharomyces cerevisiae Proteins - metabolism | Saccharomyces cerevisiae - enzymology | DNA Damage | Binding Sites | Protein-Serine-Threonine Kinases - metabolism | Physiological aspects | Genetic aspects | Research | Yeast fungi | Protein kinases | Proteins | Enzymes | Yeast | Microbiology | Kinases
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6. Full Text An Oct4-Centered Protein Interaction Network in Embryonic Stem Cells
by van den Berg, Debbie L.C and Snoek, Tim and Mullin, Nick P and Yates, Adam and Bezstarosti, Karel and Demmers, Jeroen and Chambers, Ian and Poot, Raymond A
Cell Stem Cell, ISSN 1934-5909, 04/2010, Volume 6, Issue 4, pp. 369 - 381
Transcription factors, such as Oct4, are critical for establishing and maintaining pluripotent cell identity. Whereas the genomic locations of several... 
STEMCELL | OCT4 | SOX2 | COMPLEX | COACTIVATOR | REGULATES SELF-RENEWAL | MOUSE | RECEPTOR-BETA | PLURIPOTENCY | NANOG | TRANSCRIPTIONAL REGULATION | CELL & TISSUE ENGINEERING | CELL BIOLOGY | Cell Line | Embryonic Stem Cells - metabolism | Cell Proliferation | Embryonic Stem Cells - cytology | Gene Regulatory Networks - genetics | Transcription Factors - chemistry | Protein Transport | Transcription Factors - metabolism | Phenotype | Animals | Gene Expression Regulation, Developmental | Mass Spectrometry | Octamer Transcription Factor-3 - metabolism | Protein Binding | Transcription Factors - isolation & purification | Mice | Resource
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7. Full Text Dynamic protein interaction network construction and applications
by Wang, Jianxin and Peng, Xiaoqing and Peng, Wei and Wu, Fang‐Xiang
PROTEOMICS, ISSN 1615-9853, 03/2014, Volume 14, Issue 4-5, pp. 338 - 352
With more dynamic information available, researchers’ attention has recently shifted from static properties to dynamic properties of protein–protein... 
Protein complex | Biomarker | Network medicine | Dynamic protein interaction networks | Gene expression | Bioinformatics | LOCALIZATION | QUANTIFICATION | BIOCHEMISTRY & MOLECULAR BIOLOGY | BIOCHEMICAL RESEARCH METHODS | SPECTROMETRY-BASED PROTEOMICS | TIME-COURSE | IDENTIFICATION | SACCHAROMYCES-CEREVISIAE | YEAST | RNA-SEQ | GENE-EXPRESSION | CYCLE | Proteins - genetics | Protein Interaction Maps - genetics | Genomics | Humans | Computational Biology | Proteomics | Transcriptome | Biomarkers | Proteins | Binding sites
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8. Full Text FunRich: An open access standalone functional enrichment and interaction network analysis tool
by Pathan, Mohashin and Keerthikumar, Shivakumar and Ang, Ching‐Seng and Gangoda, Lahiru and Quek, Camelia Y.J and Williamson, Nicholas A and Mouradov, Dmitri and Sieber, Oliver M and Simpson, Richard J and Salim, Agus and Bacic, Antony and Hill, Andrew F and Stroud, David A and Ryan, Michael T and Agbinya, Johnson I and Mariadason, John M and Burgess, Antony W and Mathivanan, Suresh
PROTEOMICS, ISSN 1615-9853, 08/2015, Volume 15, Issue 15, pp. 2597 - 2601
As high‐throughput techniques including proteomics become more accessible to individual laboratories, there is an urgent need for a user‐friendly... 
Interaction networks | Enrichment analysis | Bioinformatics | Omics | OMICS DATA | BIOCHEMISTRY & MOLECULAR BIOLOGY | BIOCHEMICAL RESEARCH METHODS | LARGE GENE LISTS | User-Computer Interface | Computational Biology - methods | Data Interpretation, Statistical | Reproducibility of Results | Humans | Gene Expression Profiling - methods | Gene Regulatory Networks | Metabolomics - methods | Protein Interaction Maps | Software | Internet | Proteomics - methods | Genomics - methods | Gene Ontology | Genomics | Data bases | Open access | Proteomics
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9. Full Text A global genetic interaction network maps a wiring diagram of cellular function
by Costanzo, Michael and VanderSluis, Benjamin and Koch, Elizabeth N and Baryshnikova, Anastasia and Pons, Carles and Tan, Guihong and Wang, Wen and Usaj, Matej and Hanchard, Julia and Lee, Susan D and Pelechano, Vicent and Styles, Erin B and Billmann, Maximilian and Van Leeuwen, Jolanda and Van Dyk, Nydia and Lin, Zhen-Yuan and Kuzmin, Elena and Nelson, Justin and Piotrowski, Jeff S and Srikumar, Tharan and Bahr, Sondra and Chen, Yiqun and Deshpande, Raamesh and Kurat, Christoph F and Li, Sheena C and Li, Zhijian and Usaj, Mojca Mattiazzi and Okada, Hiroki and Pascoe, Natasha and Luis, Bryan-Joseph San and Sharifpoor, Sara and Shuteriqi, Emira and Simpkins, Scott W and Snider, Jamie and Suresh, Harsha Garadi and Tan, Yizhao and Zhu, Hongwei and Malod-Dognin, Noel and Janjic, Vuk and Przulj, Natasa and Troyanskaya, Olga G and Stagljar, Igor and Xia, Tian and Ohya, Yoshikazu and Gingras, Anne-Claude and Raught, Brian and Boutros, Michael and Steinmetz, Lars M and Moore, Claire L and Rosebrock, Adam P and Caudy, Amy A and Myers, Chad L and Andrews, Brenda and Boone, Charles
Science, ISSN 0036-8075, 09/2016, Volume 353, Issue 6306, pp. aaf1420 - aaf1420
We generated a global genetic interaction network for Saccharomyces cerevisiae, constructing more than 23 million double mutants, identifying about 550,000... 
SACCHAROMYCES-CEREVISIAE GENOME | SUPPRESSOR | COMPLEX | CONSERVATION | METABOLISM | BUDDING YEAST | MULTIDISCIPLINARY SCIENCES | EXPLORATION | EPISTASIS | CANCER | REVEALS | Epistasis, Genetic | Saccharomyces cerevisiae - genetics | Genetic Pleiotropy - physiology | Saccharomyces cerevisiae Proteins - genetics | Gene Regulatory Networks | Genes, Essential | Genes, Fungal - physiology | Genotype & phenotype | Genetics | Maps | Cellular biology | Diagrams | Wiring | Networks | Pathways | Genes | Modules | Mathematical models
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