Abul-Husn, N.S.; Bushlin, I.; Morón, J.A.; Jenkins, S.L.; Dolios, G.; Wang, R.; Iyengar, R.; Ma'ayan, A.; Devi, L.A.; Proteomics2009, 9(12), 3303-3315. Systems approach to explore components and interactions in the presynapse. [PubMed]
Allen, J.G.; Bourbeau, M.P.; Wohlhieter, G.E.; Bartberger, M.D.; Michelsen, K.; Hungate, R.; Gadwood, R.C.; Gaston, R.D.; Evans, B.; Mann, L.W.; Matison, M.E.; Schneider, S.; Huang, X.; Yu, D.; Andrews, P.S.; Reichelt, A.; Long, A.M.; Yakowec, P.; Yang, E.Y.; Lee, T.A.; Oliner, J.D.; J. Med. Chem. 2009, 52(22), 7044-7053. Discovery and optimization of chromenotriazolopyrimidines as potent inhibitors of the mouse double minute 2-tumor protein 53 protein-protein interaction. [PubMed]
Anamika, K.; Abhinandan, K.R.; Deshmukh, K.; Srinivasan, N.; Comp. Funct. Genomics2009, 365637. Classification of nonenzymatic homologues of protein kinases. [PubMed]
Andreopoulos, B.; Winter, C.; Labudde, D.; Schroeder, M.; BMC Bioinformatics2009, 10(1), 196. Triangle network motifs predict complexes by complementing high-error interactomes with structural information. [PubMed]
Andres Leon, E.; Ezkurdia, I.; García, B.; Valencia, A.; Juan, D.; Nucleic Acids Res. 2009, 37, D629-D635. EcID. A database for the inference of functional interactions in E. coli. [PubMed]
Antonov, A.V.; Dietmann, S.; Rodchenkov, I.; Mewes, H.W.; Proteomics2009, 9(10), 2740-2749. PPI spider: a tool for the interpretation of proteomics data in the context of protein-protein interaction networks. [PubMed]
Arafat, Y.; Kamruzzaman, J.; Karmakar, G.C.; Fernandez-Recio, J.; Int. J. Data Min. Bioinform.2009, 3(1), 55-67. Predicting protein-protein interfaces as clusters of optimal docking area points. [PubMed]
Audie, J.; Biophys. Chem. 2009, 143(3), 139-144. Continued development of an empirical function for predicting and rationalizing protein-protein binding affinities. [PubMed]
Ay, F.; Kahveci, T.; DE Crécy-Lagard, V.; J. Bioinform. Comput. Biol. 2009, 7(3), 389-428. A fast and accurate algorithm for comparative analysis of metabolic pathways. [PubMed]
Babu, M.; Krogan, N.J.; Awrey, D.E.; Emili, A.; Greenblatt, J.F.; Methods Mol. Biol.2009, 548, 187-207. Systematic characterization of the protein interaction network and protein complexes in Saccharomyces cerevisiae using tandem affinity purification and mass spectrometry. [PubMed]
Bachman, P.; Liu, Y.; Bioinformatics2009, 25(14), 1814-1821. Structure discovery in PPI networks using pattern-based network decomposition. [PubMed]
Baker, C.L.; Kettenbach, A.N.; Loros, J.J.; Gerber, S.A.; Dunlap, J.C.; Mol. Cell. 2009, 34(3), 354-363. Quantitative proteomics reveals a dynamic interactome and phase-specific phosphorylation in the Neurospora circadian clock. [PubMed]
Banky, D.; Ordog, R.; Grolmusz, V.; Bioinformation2009, 3(8), 361-363. NASCENT: An automatic protein interaction network generation tool for non-model organisms. [PubMed]
Bao, L.; Redondo, C.; Findlay, J.B.; Walker, J.H.; Ponnambalam, S.; Mol. Membr. Biol. 2009, 26(3), 127-135. Deciphering soluble and membrane protein function using yeast systems. [PubMed]
Barrenas, F.; Chavali, S.; Holme, P.; Mobini, R.; Benson, M.; PLoS One2009, 4(11), e8090. Network properties of complex human disease genes identified through genome-wide association studies. [PubMed]
Bavec, A.; Mol. Biol. Rep. 2009, [epub ahead of print]. Constructing glucagon like peptide-1 receptor fused with derivatives of GFP for visualizing protein-protein interaction in living cells. [PubMed]
Brehme, M.; Hantschel, O.; Colinge, J.; Kaupe, I.; Planyavsky, M.; Köcher, T.; Mechtler, K.; Bennett, K.L.; Superti-Furga, G.; Proc. Natl. Acad. Sci. USA2009, 106(18), 7414-7419. Charting the molecular network of the drug target Bcr-Abl. [PubMed]
Bröms, J.E.; Lavander, M.; Sjöstedt, A.; J. Bacteriol. 2009, 191(8), 2431-2446. A conserved alpha-helix essential for a type VI secretion-like system of Francisella tularensis. [PubMed]
Brückner, A.; Polge, C.; Lentze, N.; Auerbach, D.; Schlattner, U.; Int. J. Mol. Sci.2009, 10(6), 2763-2788. Yeast two-hybrid, a powerful tool for systems biology. [PubMed]
Brzostowski, J.A.; Meckel, T.; Hong, J.; Chen, A.; Jin, T.; Curr. Protoc. Protein Sci. 2009, Chapter 19, Unit19.5. Imaging protein-protein interactions by Förster resonance energy transfer (FRET) microscopy in live cells. [PubMed]
Camargo, A.; Kim, J.T.; Conf. Proc. IEEE Eng. Med. Biol. Soc.2009, 1, 6963-6968. Identification of markers of cardiovascular disease in women and the reconstruction of its corresponding protein interaction network. [PubMed]
Chakicherla, A.; Ecale Zhou, C.L.; Dang, M.L.; Rodriguez, V.; Hansen, J.N.; Zemla, A.; PLoS Comput. Biol. 2009, 5(6), e1000401. SpaK/SpaR two-component system characterized by a structure-driven domain-fusion method and in vitro phosphorylation studies. [PubMed]
Chatr-aryamontri, A.; Ceol, A.; Peluso, D.; Nardozza, A.; Panni, S.; Sacco, F.; Tinti, M.; Smolyar, A.; Castagnoli, L.; Vidal, M.; Cusick, M.E.; Cesareni, G.; Nucleic Acids Res. 2009, 37, D669-D673.
VirusMINT: a viral protein interaction database. [PubMed]
Chaurasia, G.; Malhotra, S.; Russ, J.; Schnoegl, S.; Hänig, C.; Wanker, E.E.; Futschik, M.E.; Nucleic Acids Res. 2009, 37, D657-D660.
UniHI 4: new tools for query, analysis and visualization of the human protein-protein interactome. [PubMed]
Chen, C.C.; Lin, C.Y.; Lo, Y.S.; Yang, J.M.; Nucleic Acids Res.2009, 37, W369-W375. PPISearch: a web server for searching homologous protein-protein interactions across multiple species. [PubMed]
Chen, J.; Aronow, B.J.; Jegga, A.G.; BMC Bioinformatics2009, 10(1), 406. Correction: Disease candidate gene identification and prioritization using protein interaction networks. [PubMed]
Chen, J.Y.; Youn, E.; Mooney, S.D.; Methods Mol. Biol.2009, 541, 449-461. Connecting protein interaction data, mutations, and disease using bioinformatics. [PubMed]
Chen, X.W.; Jeong, J.C.; Bioinformatics2009, 25(5), 585-591. Sequence-based prediction of protein interaction sites with an integrative method. [PubMed]
Chen, Y.R.; Chen, T.Y.; Zhang, S.L.; Lin, S.M.; Zhao, Y.R.; Ye, F.; Zhang, X.; Shi, L.; Dang, S.S.; Liu, M.; J. Gastroenterol. Hepatol. 2009, 24(7), 1300-1304. Identification of a novel protein binding to hepatitis C virus core protein. [PubMed]
Choi, Y.S.; Yang, J.S.; Choi, Y.; Ryu, S.H.; Kim, S.; Proteins2009, 77(1), 14-25. Evolutionary conservation in multiple faces of protein interaction. [PubMed]
Christensen, D.E.; Klevit, R.E.; FEBS J.2009, 276(19), 5381-5389. Dynamic interactions of proteins in complex networks: identifying the complete set of interacting E2s for functional investigation of E3-dependent protein ubiquitination. [PubMed]
Chu, J.; Zhang, Z.; Zheng, Y.; Yang, J.; Qin, L.; Lu, J.; Huang, Z.L.; Zeng, S.; Luo, Q.; Biosens. Bioelectron.2009, 25(1), 234-239.
A novel far-red bimolecular fluorescence complementation system that allows for efficient visualization of protein interactions under physiological conditions. [PubMed]
Cloutier, P.; Al-Khoury, R.; Lavallée-Adam, M.; Faubert, D.; Jiang, H.; Poitras, C.; Bouchard, A.; Forget, D.; Blanchette, M.; Coulombe, B.; Methods2009, 48(4), 381-386. High-resolution mapping of the protein interaction network for the human transcription machinery and affinity purification of RNA polymerase II-associated complexes. [PubMed]
Crisóstomo, F.R.; Feng, Y.; Zhu, X.; Welsh, K.; An, J.; Reed, J.C.; Huang, Z.; Bioorg. Med. Chem. Lett. 2009, 19(22), 6413-6418. Design and synthesis of a simplified inhibitor for XIAP-BIR3 domain. [PubMed]
Das, M.; Basu, G.; J. Mol. Graph. Model.2009, 27(7), 846-851. Coulomb energies of protein-protein complexes with monopole-free charge distributions. [PubMed]
De Luca, L.; Barreca, M.L.; Ferro, S.; Christ, F.; Iraci, N.; Gitto, R.; Monforte, A.M.; Debyser, Z.; Chimirri, A.; ChemMedChem. 2009, 4(8), 1311-1316. Pharmacophore-based discovery of small-molecule inhibitors of protein-protein interactions between HIV-1 integrase and cellular cofactor LEDGF/p75. [PubMed]
Dell'Orco, D.; Mol. Biosyst.2009, 5(4), 323-334. Fast predictions of thermodynamics and kinetics of protein-protein recognition from structures: from molecular design to systems biology. [PubMed]
Déliot, N.; Chavent, M.; Nourry, C.; Lécine, P.; Arnaud, C.; Hermant, A.; Maigret, B.; Borg, J.P.; Biochem. Biophys. Res. Commun. 2009, 378(3), 360-365.
Biochemical studies and molecular dynamics simulations of Smad3-Erbin interaction identify a non-classical Erbin PDZ binding. [PubMed]
Deng, L.; Guan, J.; Dong, Q.; Zhou, S.; BMC Bioinformatics2009, 10(1), 426. Prediction of protein-protein interaction sites using an ensemble method. [PubMed]
Ding, X.; Richter, T.; Chen, M.; Fujii, H.; Seo, Y.S.; Xie, M.; Zheng, X.; Kanrar, S.; Stevenson, R.A.; Dardick, C.; Li, Y.; Jiang, H.; Zhang, Y.; Yu, F.; Bartley, L.E.; Chern, M.; Bart, R.; Chen, X.; Zhu, L.; Farmerie, W.G.; Gribskov, M.; Zhu, J.K.; Fromm, M.E.; Ronald, P.C.; Song, W.Y.; Plant Physiol.2009, 149(3), 1478-1492. A rice kinase-protein interaction map. [PubMed]
Du, X.; Cheng, J.; Song, J.; Protein J. 2009, 28(6), 273-280.
Improved prediction of protein binding sites from sequences using genetic algorithm. [PubMed]
Edwards, A.N.; Fowlkes, J.D.; Owens, E.T.; Standaert, R.F.; Pelletier, D.A.; Hurst, G.B.; Doktycz, M.J.; Morrell-Falvey, J.L.; Anal. Biochem. 2009, 395(2), 166-177. An in vivo imaging-based assay for detecting protein interactions over a wide range of binding affinities. [PubMed]
Ernst, A.; Sazinsky, S.L.; Hui, S.; Currell, B.; Dharsee, M.; Seshagiri, S.; Bader, G.D.; Sidhu, S.S.; Sci. Signal2009, 2(87), ra50. Rapid evolution of functional complexity in a domain family. [PubMed]
Evans, P.; Dampier, W.; Ungar, L.; Tozeren, A.; BMC Med. Genomics 2009, 2(1), 27. Prediction of HIV-1 virus-host protein interactions using virus and host sequence motifs. [PubMed]
Fayruzov, T.; De Cock, M.; Cornelis, C.; Hoste, V.; BMC Bioinformatics2009, 10, 374.
Linguistic feature analysis for protein interaction extraction. [PubMed]
Fionda, V.; Palopoli, L.; Panni, S.; Rombo, S.E.; Int. J. Data Min. Bioinform. 2009, 3(4), 431-453. A technique to search for functional similarities in protein-protein interaction networks. [PubMed]
Fong, J.H.; Shoemaker, B.A.; Garbuzynskiy, S.O.; Lobanov, M.Y.; Galzitskaya, O.V.; Panchenko, A.R.; PLoS Comput. Biol. 2009, 5(3), e1000316. Intrinsic disorder in protein interactions: insights from a comprehensive structural analysis. [PubMed]
Frato, K.E.; Schleif, R.F.; J. Mol. Biol. 2009, 394(5), 805-814. A DNA-assisted binding assay for weak protein-protein interactions. [PubMed]
Frech, C.; Kommenda, M.; Dorfer, V.; Kern, T.; Hintner, H.; Bauer, J.W.; Oender, K.; BMC Bioinformatics 2009, 10(1), 21. Improved homology-driven computational validation of protein-protein interactions motivated by the evolutionary gene duplication and divergence hypothesis. [PubMed]
Free, R.B.; Hazelwood, L.A.; Sibley, D.R.; Curr. Protoc. Neurosci. 2009, Chapter 5, Unit 5.28. Identifying novel protein-protein interactions using co-immunoprecipitation and mass spectroscopy. [PubMed]
Fu, C.; Wu, C.; Liu, T.; Ago, T.; Zhai, P.; Sadoshima, J.; Li, H.; Mol Cell Proteomics2009, 8(7), 1674-1687. Elucidation of thioredoxin target protein networks in mouse. [PubMed]
Fuentes, G.; Oyarzabal, J.; Rojas, A.M.; Curr. Opin. Drug Discov. Devel. 2009, 12(3), 358-366. Databases of protein-protein interactions and their use in drug discovery. [PubMed]
Gao, S.; Wang, X.; J. Comput. Sci. Syst. Biol. 2009, 2, 133.
Predicting type 1 diabetes candidate genes using human protein-protein interaction networks. [PubMed]
Garg, S.K.; Alam, M.S.; Bajpai, R.; Kishan, K.R.; Agrawal, P.; BMC Biochem. 2009, 10(1), 1. Redox biology of Mycobacterium tuberculosis H37Rv: protein-protein interaction between GlgB and WhiB1 involves exchange of thiol-disulfide. [PubMed]
Garzon, J.I.; Lopéz-Blanco, J.R.; Pons, C.; Kovacs, J.; Abagyan, R.; Fernandez-Recio, J.; Chacon, P.; Bioinformatics2009, 25(19), 2544-2551.
FRODOCK: a new approach for fast rotational protein-protein docking. [PubMed]
Gehl, C.; Waadt, R.; Kudla, J.; Mendel, R.R.; Hänsch, R.; Mol. Plant2009, 2(5), 1051-1058. New GATEWAY vectors for high throughput analyses of protein-protein interactions by bimolecular fluorescence complementation. [PubMed]
Gerek, Z.N.; Keskin, O.; Ozkan, S.B.; Proteins2009, 77(4), 796-811. Identification of specificity and promiscuity of PDZ domain interactions through their dynamic behavior. [PubMed]
Gibson, T.A.; Goldberg, D.S.; PLoS Comput. Biol. 2009, 5(1), e1000252. Questioning the ubiquity of neofunctionalization. [PubMed]
Gong, Y.; Kakihara, Y.; Krogan, N.; Greenblatt, J.; Emili, A.; Zhang, Z.; Houry, W.A.; Mol. Syst. Biol. 2009, 5, 275. An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell. [PubMed]
Gsponer, J.; Madan Babu, M.; Prog. Biophys. Mol. Biol.2009, 99(2-3), 94-103. The rules of disorder or why disorder rules. [PubMed]
Guharoy, M.; Chakrabarti, P.; J. Comput. Aided Mol. Des. 2009, 23(9), 645-654.
Empirical estimation of the energetic contribution of individual interface residues in structures of protein-protein complexes. [PubMed]
Han, G.W.; Rife, C.; Sawaya, M.R.; Methods Mol. Biol.2009, 569, 157-172. Applications of bioinformatics to protein structures: how protein structure and bioinformatics overlap. [PubMed]
Harauz, G.; Libich, D.S.; Curr. Protein Pept. Sci.2009, 10(3),196-215. The classic basic protein of myelin - conserved structural motifs and the dynamic molecular barcode involved in membrane adhesion and protein-protein interactions. [PubMed]
Hase, T.; Tanaka, H.; Suzuki, Y.; Nakagawa, S.; Kitano, H.; PLoS Comput. Biol. 2009, 5(10), e1000550. Structure of protein interaction networks and their implications on drug design. [PubMed]
Hawkins, T.; Chitale, M.; Luban, S.; Kihara, D.; Proteins2009, 74(3), 566-582. PFP: automated prediction of gene ontology functional annotations with confidence scores using protein sequence data. [PubMed]
He, J.; Sun, J.; Deem, M.W.; Phys. Rev. E Stat. Nonlin. Soft Matter Phys.2009, 79(3, Pt. 1), 031907. Spontaneous emergence of modularity in a model of evolving individuals and in real networks. [PubMed]
He, X.; Zhang, J.; PLoS Comput. Biol. 2009, 5(3), e1000320. On the growth of scientific knowledge: yeast biology as a case study. [PubMed]
He, Y.F.; Bao, H.M.; Xiao, X.F.; Zuo, S.; Du, R.Y.; Tang, S.W.; Yang, P.Y.; Chen, X.; Proteomics2009, 9(24), 5414-5424.
Biotin tagging coupled with amino acid-coded mass tagging for efficient and precise screening of interaction proteome in mammalian cells. [PubMed]
Heide, H.; Nordhues, A.; Drepper, F.; Nick, S.; Schulz-Raffelt, M.; Haehnel, W.; Schroda, M.; Proteomics2009, 9(11), 3079-3089. Application of quantitative immunoprecipitation combined with knockdown and cross-linking to Chlamydomonas reveals the presence of vesicle-inducing protein in plastids 1 in a common complex with chloroplast HSP90C. [PubMed]
Hendrickx, A.; Beullens, M.; Ceulemans, H.; Den Abt, T.; Van Eynde, A.; Nicolaescu, E.; Lesage, B.; Bollen, M.; Chem. Biol.2009, 16(4), 365-371. Docking motif-guided mapping of the interactome of protein phosphatase-1. [PubMed]
Herron, L.R.; Hill, M.; Davey, F.; Gunn-Moore, F.J.; Biochem. J. 2009, 419(3), 519-531. The intracellular interactions of the L1 family of cell adhesion molecules. [PubMed]
Hida, N.; Awais, M.; Takeuchi, M.; Ueno, N.; Tashiro, M.; Takagi, C.; Singh, T.; Hayashi, M.; Ohmiya, Y.; Ozawa, T.; PLoS One2009, 4(6), e5868.
High-sensitivity real-time imaging of dual protein-protein interactions in living subjects using multicolor luciferases. [PubMed]
Higurashi, M.; Ishida, T.; Kinoshita, K.; Nucleic Acids Res. 2009, 37, D360-D364. PiSite: a database of protein interaction sites using multiple binding states in the PDB. [PubMed]
Hongsthong, A.; Sirijuntarut, M.; Yutthanasirikul, R.; Senachak, J.; Kurdrid, P.; Cheevadhanarak, S.; Tanticharoen, M.; Proteome Sci.2009, 7, 33. Subcellular proteomic characterization of the high-temperature stress response of the cyanobacterium Spirulina platensis. [PubMed]
Huang, B.; OMICS2009, 13(4), 325-330.
MetaPocket: a meta approach to improve protein ligand binding site prediction. [PubMed]
Huang, H.; Li, J.; Chen, J.Y.; Conf. Proc. IEEE Eng. Med. Biol. Soc. 2009, 1, 6416-6419. Disease gene-fishing in molecular interaction networks: a case study in colorectal cancer. [PubMed]
Huang, S.S.; Fraenkel, E.; Sci. Signal.2009, 2(81), ra40. Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks. [PubMed]
Huang, S.Y.; Bolser, D.; Liu, H.Y.; Hwang, T.C.; Zou, X.; J. Mol. Graph Model.2009, 27(7), 822-828. Molecular modeling of the heterodimer of human CFTR's nucleotide-binding domains using a protein-protein docking approach. [PubMed]
Hwang, T.; Park, T.; BMC Bioinformatics2009, 10(1), 128. Identification of differentially expressed sub-networks based on multivariate ANOVA scoring method. [PubMed]
Hwang, Y.C.; Lin, C.C.; Chang, J.Y.; Mori, H.; Juan, H.F.; Huang, H.C.; Mol. Biosyst.2009, 5(12), 1672-1678. Predicting essential genes based on network and sequence analysis. [PubMed]
Ihekwaba, A.E.; Nguyen, P.T.; Priami, C.; BMC Bioinformatics2009, 10, 370. Elucidation of functional consequences of signalling pathway interactions. [PubMed]
Jang, Y.H.; Park, H.Y.; Kim, S.K.; Lee, J.H.; Suh, M.C.; Chung, Y.S.; Paek, K.H.; Kim, J.K.; Plant Cell Physiol.2009, 50(8), 1479-1492. Survey of rice proteins interacting with OsFCA and OsFY proteins which are homologous to the Arabidopsis flowering time proteins, FCA and FY. [PubMed]
Janga, S.C.; Babu, M.M.; Mol. Biosyst. 2009, 5(2), 154-162. Transcript stability in the protein interaction network of Escherichia coli. [PubMed]
Jochim, A.L.; Arora, P.S.; Mol. Biosyst.2009, 5(9), 924-926. Assessment of helical interfaces in protein-protein interactions. [PubMed]
Kahali, B.; Ahmad, S.; Ghosh, T.C.; Gene2009, 429(1-2), 18-22.
Exploring the evolutionary rate differences of party hub and date hub proteins in Saccharomyces cerevisiae protein-protein interaction network. [PubMed]
Kann, M.G.; Shoemaker, B.A.; Panchenko, A.R.; Przytycka, T.M.; J. Mol. Biol. 2009, 385(1), 91-98. Correlated evolution of interacting proteins: looking behind the mirrortree. [PubMed]
Kar, G.; Gursoy, A.; Keskin, O.; PLoS Comput. Biol. 2009, 5(12), e1000601. Human cancer protein-protein interaction network: a structural perspective. [PubMed]
Kathiresan, T.; Harvey, M.C.; Sokolowski, B.H.; Methods Mol. Biol.2009, 493, 269-286. The use of 2-D gels to identify novel protein-protein interactions in the cochlea. [PubMed]
Kerppola, T.K.; Chem. Soc. Rev. 2009, 38(10), 2876-2886.
Visualization of molecular interactions using bimolecular fluorescence complementation analysis: characteristics of protein fragment complementation. [PubMed]
Kim, J.; Cantor, A.B.; Orkin, S.H.; Wang, J.; Nat. Protoc. 2009, 4(4), 506-517. Use of in vivo biotinylation to study protein-protein and protein-DNA interactions in mouse embryonic stem cells. [PubMed]
Kim, Y.P.; Jin, Z.; Kim, E.; Park, S.; Oh, Y.H.; Kim, H.S.; Biochem. Biophys. Res. Commun. 2009, 382(3), 530-534. Analysis of in vitro SUMOylation using bioluminescence resonance energy transfer (BRET). [PubMed]
Knight, C.G.; Pinney, J.W.; Bioessays2009, 31(10), 1080-1090. Making the right connections: biological networks in the light of evolution. [PubMed]
Ko, S.; Lee, H.; BMC Bioinformatics 2009, 10, 455. Integrative approaches to the prediction of protein functions based on the feature selection. [PubMed]
Komurov, K.; Gunes, M.H.; White, M.A.; PLoS One2009, 4(6), e6017. Fine-scale dissection of functional protein network organization by statistical network analysis. [PubMed]
Konietzny, R.; König, A.; Wotzlaw, C.; Bernadini, A.; Berchner-Pfannschmidt, U.; Fandrey, J.; Ann. N Y Acad. Sci.2009, 1177, 74-81. Molecular imaging: into in vivo interaction of HIF-1alpha and HIF-2alpha with ARNT. [PubMed]
Krishnamoorthy, G.; Carlen, E.T.; Kohlheyer, D.; Schasfoort, R.B.; van den Berg, A.; Anal. Chem. 2009, 81(5), 1957-1963.
Integrated electrokinetic sample focusing and surface plasmon resonance imaging system for measuring biomolecular interactions. [PubMed]
Krüger, B.; Dandekar, T.; Methods Mol. Biol. 2009, 564, 401-431. Bioinformatical approaches to detect and analyze protein interactions. [PubMed]
Kuang, Z.; Yao, S.; Xu, Y.; Lewis, R.S.; Low, A.; Masters, S.L.; Willson, T.A.; Kolesnik, T.B.; Nicholson, S.E.; Garrett, T.J.; Norton, R.S.; J. Mol. Biol.2009, 386(3), 662-674. SPRY domain-containing SOCS box protein 2: crystal structure and residues critical for protein binding. [PubMed]
Kumaran, S.; Yi, H.; Krishnan, H.B.; Jez, J.M.; J. Biol. Chem. 2009, 284(15), 10268-10275. Assembly of the cysteine synthase complex and the regulatory role of protein-protein interactions. [PubMed]
Kushwaha, S.K.; Shakya, M.; Bioinformation2009, 3(10), 419-421. PINAT1.0: Protein interaction network analysis tool. [PubMed]
Lacomble, S.; Portman, N.; Gull, K.; PLoS One2009, 4(11), e7685. A protein-protein interaction map of the Trypanosoma brucei paraflagellar rod. [PubMed]
Lehne, B.; Schlitt, T.; Hum. Genomics2009, 3(3), 291-297. Protein-protein interaction databases: keeping up with growing interactomes. [PubMed]
Li, J.; Zimmerman, L.J.; Park, B.H.; Tabb, D.L.; Liebler, D.C.; Zhang, B.; Mol. Syst. Biol.2009, 5, 303. Network-assisted protein identification and data interpretation in shotgun proteomics. [PubMed]
Li, Y.; Zhou, Z.; Alimandi, M.; Chen, C.; Oncogene2009, 28(33), 2948-2958. WW domain containing E3 ubiquitin protein ligase 1 targets the full-length ErbB4 for ubiquitin-mediated degradation in breast cancer. [PubMed]
Liang, S.; Li, L.; Hsu, W.L.; Pilcher, M.N.; Uversky, V.; Zhou, Y.; Dunker, A.K.; Meroueh, S.O.; Biochemistry2009, 48(2), 399-414. Exploring the molecular design of protein interaction sites with molecular dynamics simulations and free energy calculations. [PubMed]
Liang, S.; Yu, Y.; Yang, P.; Gu, S.; Xue, Y.; Chen, X.; J. Chromatogr. B Analyt. Technol. Biomed. Life Sci.2009, 877(7), 627-634. Analysis of the protein complex associated with 14-3-3 epsilon by a deuterated-leucine labeling quantitative proteomics strategy. [PubMed]
Lievens, S.; Lemmens, I.; Tavernier, J.; Trends Biochem. Sci.2009, 34(11), 579-588. Mammalian two-hybrids come of age. [PubMed]
Lievens, S.; Vanderroost, N.; Van der Heyden, J.; Gesellchen, V.; Vidal, M.; Tavernier, J.; J. Proteome Res. 2009, 8(2), 877-886. Array MAPPIT: high-throughput interactome analysis in mammalian cells. [PubMed]
Lin, X.; Liu, M.; Chen, X.W.; BMC Bioinformatics2009, 10(Suppl. 4), S5. Assessing reliability of protein-protein interactions by integrative analysis of data in model organisms. [PubMed]
Lise, S.; Archambeau, C.; Pontil, M.; Jones, D.T.; BMC Bioinformatics2009, 10, 365. Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methods. [PubMed]
Liu, G.; Wong, L.; Chua, H.N.; Bioinformatics2009, 25(15), 1891-1897. Complex discovery from weighted PPI networks. [PubMed]
Loganantharaj, R.; Chung, J.; J. Biomed. Biotechnol.2009, 2009, 648987. Integrating diverse information to gain more insight into microarray analysis. [PubMed]
Lubovac, Z.; J. Biomed. Biotechnol. 2009, 2009, 472415. Investigating topological and functional features of multimodular proteins. [PubMed]
Luo, F.; Li, B.; Wan, X.F.; Scheuermann, R.H.; BMC Bioinformatics 2009, 10(Suppl. 4), S8. Core and periphery structures in protein interaction networks. [PubMed]
Luo, Y.; Blex, C.; Baessler, O.; Glinski, M.; Dreger, M.; Sefkow, M.; Köster, H.; Mol. Cell Proteomics2009, 8(12), 2843-2856. The cAMP-capture compound mass spectrometry as a novel tool for targeting cAMP binding proteins: from protein kinase a to potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channels. [PubMed]
Lybarger, S.R.; Johnson, T.L.; Gray, M.D.; Sikora, A.E.; Sandkvist, M.; J. Bacteriol.2009, 191(9), 3149-3161. Docking and assembly of the type II secretion complex of Vibrio cholerae. [PubMed]
Lysenko, A.; Hindle, M.M.; Taubert, J.; Saqi, M.; Rawlings, C.J.; Brief Bioinform.2009, 10(6), 676-693. Data integration for plant genomics - exemplars from the integration of Arabidopsis thaliana databases. [PubMed]
Ma, L.S.; Lin, J.S.; Lai, E.M.; J. Bacteriol. 2009, 191(13), 4316-4329. An IcmF-family protein ImpLM is an integral inner membrane protein interacting with ImpKL and its Walker A motif is required for type VI secretion system-mediated Hcp secretion in Agrobacterium tumefaciens. [PubMed]
Machida, K.; Mayer, B.J.; Methods Mol. Biol.2009, 536, 313-329. Detection of protein-protein interactions by far-western blotting. [PubMed]
Macropol, K.; Can, T.; Singh, A.K.; BMC Bioinformatics2009, 10, 283.
RRW: repeated random walks on genome-scale protein networks for local cluster discovery. [PubMed]
Maeda, M.H.; Kinoshita, K.; J. Mol. Graph. Model2009, 27(6), 706-711. Development of new indices to evaluate protein-protein interfaces: assembling space volume, assembling space distance, and global shape descriptor. [PubMed]
Makhnevych, T.; Sydorskyy, Y.; Xin, X.; Srikumar, T.; Vizeacoumar, F.J.; Jeram, S.M.; Li, Z.; Bahr, S.; Andrews, B.J.; Boone, C.; Raught, B.; Mol Cell.2009, 33(1), 124-135. Global map of SUMO function revealed by protein-protein interaction and genetic networks. [PubMed]
Malik, S.S.; Luthra, A.; Ramachandran, R.; Biochim. Biophys. Acta2009, 1794(3), 541-553. Interactions of the M. tuberculosis UsfX with the cognate sigma factor SigF and the anti-anti sigma factor RsfA. [PubMed]
Malik, S.; Shukla, A.; Sen, P.; Bhaumik, S.R.; J. Biol. Chem. 2009, 284(51), 35714-35724. The 19 s proteasome subcomplex establishes a specific protein interaction network at the promoter for stimulated transcriptional initiation in vivo. [PubMed]
Markson, G.; Kiel, C.; Hyde, A.R.; Brown, S.; Charalabous, P.; Bremm, A.; Semple, J.; Woodsmith, J.; Duley, S.; Salehi-Ashtiani, K.; Vidal, M.; Komander, D.; Serrano, L.; Lehner, P.; Sanderson, C.; Genome Res.2009, 19(10), 1905-1911. Analysis of the human E2 ubiquitin conjugating enzyme protein interaction network. [PubMed]
Massanet, R.; Gallardo-Chacon, J.J.; Caminal, P.; Perera, A.; Conf. Proc. IEEE Eng. Med. Biol. Soc.2009, 1, 7079-7082. Search of phenotype related candidate genes using gene ontology-based semantic similarity and protein interaction information: application to Brugada syndrome. [PubMed]
Matsuzaki, Y.; Matsuzaki, Y.; Sato, T.; Akiyama, Y.; J. Bioinform. Comput. Biol.2009, 7(6), 991-1012.
In silico screening of protein-protein interactions with all-to-all rigid docking and clustering: an application to pathway analysis. [PubMed]
McGinty, J.; Soloviev, V.Y.; Tahir, K.B.; Laine, R.; Stuckey, D.W.; Hajnal, J.V.; Sardini, A.; French, P.M.; Arridge, S.R.; Opt. Lett. 2009, 34(18), 2772-2774. Three-dimensional imaging of Förster resonance energy transfer in heterogeneous turbid media by tomographic fluorescent lifetime imaging. [PubMed]
McKee, C.J.; Kessl, J.J.; Norris, J.O.; Shkriabai, N.; Kvaratskhelia, M.; Methods2009, 47(4), 304-307. Mass spectrometry-based footprinting of protein-protein interactions. [PubMed]
Mehta, K.; Hoppe, A.D.; Kainkaryam, R.; Woolf, P.J.; Linderman, J.J.; Proteomics2009, 9(23), 5371-5383. A computational approach to inferring cellular protein-binding affinities from quantitative fluorescence resonance energy transfer imaging. [PubMed]
Miller, B.W.; Lau, G.; Grouios, C.; Mollica, E.; Barrios-Rodiles, M.; Liu, Y.; Datti, A.; Morris, Q.; Wrana, J.L.; Attisano, L.; Mol. Syst. Biol.2009, 5, 315. Application of an integrated physical and functional screening approach to identify inhibitors of the Wnt pathway. [PubMed]
Minguez, P.; Götz, S.; Montaner, D.; Al-Shahrour, F.; Dopazo, J.; Nucleic Acids Res. 2009, 37, W109-W114. SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks. [PubMed]
Mohamed, M.R.; Rahman, M.M.; Lanchbury, J.S.; Shattuck, D.; Neff, C.; Dufford, M.; van Buuren, N.; Fagan, K.; Barry, M.; Smith, S.; Damon, I.; McFadden, G.; Proc. Natl. Acad. Sci. USA 2009, 106(22), 9045-9050. Proteomic screening of variola virus reveals a unique NF-{kappa}B inhibitor that is highly conserved among pathogenic orthopoxviruses. [PubMed]
Monie, T.P.; Moncrieffe, M.C.; Gay, N.J.; Immunol. Rev.2009, 227(1), 161-175. Structure and regulation of cytoplasmic adapter proteins involved in innate immune signaling. [PubMed]
Monti, M.; Cozzolino, M.; Cozzolino, F.; Vitiello, G.; Tedesco, R.; Flagiello, A.; Pucci, P.; Expert. Rev. Proteomics 2009, 6(2), 159-169. Puzzle of protein complexes in vivo: a present and future challenge for functional proteomics. [PubMed]
Mosca, E.; Bertoli, G.; Piscitelli, E.; Vilardo, L.; Reinbold, R.A.; Zucchi, I.; Milanesi, L.; BMC Bioinformatics2009, 10(Suppl. 12), S8. Identification of functionally related genes using data mining and data integration: a breast cancer case study. [PubMed]
Mosca, R.; Pons, C.; Fernández-Recio, J.; Aloy, P.; PLoS Comput. Biol.2009, 5(8), e1000490.
Pushing structural information into the yeast interactome by high-throughput protein docking experiments.[PubMed]
Moschopoulos, C.N.; Pavlopoulos, G.A.; Schneider, R.; Likothanassis, S.D.; Kossida, S.; BMC Bioinformatics2009, 10(Suppl. 6), S11. GIBA: a clustering tool for detecting protein complexes. [PubMed]
Navaratnam, D.S.; Methods Mol. Biol. 2009, 493, 257-268. Yeast two-hybrid screening to test for protein-protein interactions in the auditory system. [PubMed]
Norris, J.D.; Joseph, J.D.; Sherk, A.B.; Juzumiene, D.; Turnbull, P.S.; Rafferty, S.W.; Cui, H.; Anderson, E.; Fan, D.; Dye, D.A.; Deng, X.; Kazmin, D.; Chang, C.Y.; Willson, T.M.; McDonnell, D.P.; Chem. Biol. 2009, 16(4), 452-460. Differential presentation of protein interaction surfaces on the androgen receptor defines the pharmacological actions of bound ligands. [PubMed]
Nowak, J.; Iovanna, J.L.; Autophagy2009, 5(3), 383-384. TP53INP2 is the new guest to the table of self-eating. [PubMed]
O'Connell, M.R.; Gamsjaeger, R.; Mackay, J.P.; Proteomics2009, 9(23), 5224-5232. The structural analysis of protein-protein interactions by NMR spectroscopy. [PubMed]
Omidi, S.; Schreiber, F.; Masoudi-Nejad, A.; Genes Genet. Syst.2009, 84(5), 385-395.
MODA: an efficient algorithm for network motif discovery in biological networks. [PubMed]
Pajunen, M.; Poussu, E.; Turakainen, H.; Savilahti, H.; Methods2009, 49(3), 255-262.
Application of Mu in vitro transposition for high-precision mapping of protein-protein interfaces on a yeast two-hybrid platform. [PubMed]
Parashar, A.; Colvin, K.R.; Bignell, D.R.; Leskiw, B.K.; J. Bacteriol.2009, 191(8), 2541-2550. BldG and SCO3548 interact antagonistically to control key developmental processes in Streptomyces coelicolor. [PubMed]
Park, S.J.; Choi, J.S.; Kim, B.C.; Jho, S.W.; Ryu, J.W.; Park, D.; Lee, K.A.; Bhak, J.; Kim, S.I.; BMC Genomics2009, 10(Suppl. 3), S18.
PutidaNET: interactome database service and network analysis of Pseudomonas putida KT2440. [PubMed]
Pattin, K.A.; Moore, J.H.; Expert. Rev. Proteomics2009, 6(6), 647-659. Role for protein-protein interaction databases in human genetics. [PubMed]
Pednekar, D.; Tendulkar, A.; Durani, S.; Proteins2009, 74(1), 155-163. Electrostatics-defying interaction between arginine termini as a thermodynamic driving force in protein-protein interaction. [PubMed]
Pellet, J.; Meyniel, L.; Vidalain, P.O.; de Chassey, B.; Tafforeau, L.; Lotteau, V.; Rabourdin-Combe, C.; Navratil, V.; BMC Res. Notes2009, 2(1), 220. pISTil: a pipeline for yeast two-hybrid interaction sequence tags identification and analysis. [PubMed]
Peregrín-Alvarez, J.M.; Xiong, X.; Su, C.; Parkinson, J.; PLoS Comput. Biol.2009, 5(10), e1000523.
The modular organization of protein interactions in Escherichia coli. [PubMed]
Pinto, M.G.; Villegas, J.M.; Peter, J.; Haase, R.; Haas, J.; Lotz, A.S.; Muntau, A.C.; Baiker, A.; Proteomics2009, 9(23), 5303-5308. LuMPIS - a modified luminescence-based mammalian interactome mapping pull-down assay for the investigation of protein-protein interactions encoded by GC-low ORFs. [PubMed]
Qian, X.; Yoon, B.J.; PLoS One2009, 4(12), e8070. Effective identification of conserved pathways in biological networks using hidden Markov models. [PubMed]
Qureshi, A.H.; Chaoji, V.; Maiguel, D.; Faridi, M.H.; Barth, C.J.; Salem, S.M.; Singhal, M.; Stoub, D.; Krastins, B.; Ogihara, M.; Zaki, M.J.; Gupta, V.; PLoS One2009, 4(10), e7627. Proteomic and phospho-proteomic profile of human platelets in basal, resting state: insights into integrin signaling. [PubMed]
Rao, A.; Yeleswarapu, S.J.; Raghavendra, G.; Srinivasan, R.; Bulusu, G.; In Silico Biol.2009, 9(4), 195-202. PlasmoID: A P. falciparum protein information discovery tool. [PubMed]
Rao, R.; Tun, K.; Lakshminarayanan, S.; Dhar, P.K.; In Silico Biol.2009, 9(4), 179-194. Amino-acid residue association models for large scale protein-protein interaction prediction. [PubMed]
Ratmann, O.; Andrieu, C.; Wiuf, C.; Richardson, S.; Proc. Natl. Acad. Sci. USA2009, 106(26), 10576-10581. Model criticism based on likelihood-free inference, with an application to protein network evolution. [PubMed]
Ratmann, O.; Wiuf, C.; Pinney, J.W.; HFSP J. 2009, 3(5), 290-306. From evidence to inference: probing the evolution of protein interaction networks. [PubMed]
Remmerie, N.; Roef, L.; Van De Slijke, E.; Van Leene, J.; Persiau, G.; Eeckhout, D.; Stals, H.; Laukens, K.; Lemière, F.; Esmans, E.; Van Onckelen, H.; Inzé, D.; De Jaeger, G.; Witters, E.; Proteomics2009, 9(3), 598-609. A bioanalytical method for the proteome wide display and analysis of protein complexes from whole plant cell lysates. [PubMed]
Renaut, L.; Bouayadi, K.; Kharrat, H.; Mondon, P.; Anal. Biochem. 2009, 384(2), 362-364.
A cytoplasmic protein-protein interaction detection method based on reporter translation. [PubMed]
Reja, R.; Venkatakrishnan, A.J.; Lee, J.; Kim, B.C.; Ryu, J.W.; Gong, S.; Bhak, J.; Park, D.; BMC Genomics 2009, 10(Suppl. 3), S20. MitoInteractome: mitochondrial protein interactome database, and its application in 'aging network' analysis. [PubMed]
Ribeiro, D.; Borst, J.W.; Goldbach, R.; Kormelink, R.; Virology2009, 383(1), 121-130. Tomato spotted wilt virus nucleocapsid protein interacts with both viral glycoproteins Gn and Gc in planta. [PubMed]
Robida, A.M.; Kerppola, T.K.; J. Mol. Biol. 2009, 394(3), 391-409.
Bimolecular fluorescence complementation analysis of inducible protein interactions: effects of factors affecting protein folding on fluorescent protein fragment association. [PubMed]
Rodrigues, F.A.; Costa Lda, F.; Mol. Biosyst.2009, 5(4), 385-390. Protein lethality investigated in terms of long range dynamical interactions. [PubMed]
Russo, A.L.; Jedlicka, K.; Wernick, M.; McNally, D.; Kirk, M.; Sproull, M.; Smith, S.; Shankavaram, U.; Kaushal, A.; Figg, W.D.; Dahut, W.; Citrin, D.; Bottaro, D.P.; Albert, P.S.; Tofilon, P.J.; Camphausen, K.; Clin. Cancer Res.2009, 15(13), 4292-4298. Urine analysis and protein networking identify met as a marker of metastatic prostate cancer. [PubMed]
Sardiu, M.E.; Florens, L.; Washburn, M.P.; J. Proteome Res. 2009, 8(6), 2944-2952. Evaluation of clustering algorithms for protein complex and protein interaction network assembly. [PubMed]
Sardiu, M.E.; Gilmore, J.M.; Carrozza, M.J.; Li, B.; Workman, J.L.; Florens, L.; Washburn, M.P.; PLoS One2009, 4(10), e7310. Determining protein complex connectivity using a probabilistic deletion network derived from quantitative proteomics. [PubMed]
Sato, R.; FEBS J. 2009, 276(3), 622-627. SREBPs: protein interaction and SREBPs. [PubMed]
Schauer, K.; Stingl, K.; Genome Dyn. 2009, 6, 48-61. 'Guilty by association' - protein-protein interactions (PPIs) in bacterial pathogens. [PubMed]
Schillinger, C.; Boisguerin, P.; Krause, G.; Bioinformatics2009, 25(13), 1632-1639. Domain Interaction Footprint: a multi-classification approach to predict domain-peptide interactions. [PubMed]
Schrum, A.G.; Curr. Protoc. Immunol.2009, Chapter 5, Unit5.9.
Visualization of multiprotein complexes by flow cytometry. [PubMed]
Selbach, M.; Paul, F.E.; Brandt, S.; Guye, P.; Daumke, O.; Backert, S.; Dehio, C.; Mann, M.; Cell Host Microbe2009, 5(4), 397-403. Host cell interactome of tyrosine-phosphorylated bacterial proteins. [PubMed]
Seo, P.S.; Quinn, B.J.; Khan, A.A.; Zeng, L.; Takoudis, C.G.; Hanada, T.; Bolis, A.; Bolino, A.; Chishti, A.H.; Exp. Biol. Med. (Maywood) 2009, 234(3), 255-262.
Identification of erythrocyte p55/MPP1 as a binding partner of NF2 tumor suppressor protein/Merlin. [PubMed]
Sharon, I.; Davis, J.V.; Yona, G.; Methods Mol. Biol.2009, 541, 61-88. Prediction of protein-protein interactions: a study of the co-evolution model. [PubMed]
Shin, C.J.; Davis, M.J.; Ragan, M.A.; Proteomics2009, 9(23), 5256-5266. Towards the mammalian interactome: Inference of a core mammalian interaction set in mouse. [PubMed]
Simkó, G.I.; Gyurkó, D.; Veres, D.V.; Nánási, T.; Csermely, P.; Genome Med.2009, 1(9), 90. Network strategies to understand the aging process and help age-related drug design. [PubMed]
Smart, S.K.; Mackintosh, S.G.; Edmondson, R.D.; Taverna, S.D.; Tackett, A.J.; Protein Sci.2009, 18(9), 1987-1997.
Mapping the local protein interactome of the NuA3 histone acetyltransferase. [PubMed]
Snyder, M.; Gallagher, J.E.; FEBS Lett.2009, 583(24), 3895-3899. Systems biology from a yeast omics perspective. [PubMed]
Srihari, S.; Ning, K.; Leong, H.W.; Genome Inform.2009, 23(1), 159-168.
Refining Markov Clustering for protein complex prediction by incorporating core-attachment structure. [PubMed]
Steen, J.A.; Bannam, T.L.; Teng, W.L.; Devenish, R.J.; Rood, J.I.; J. Bacteriol. 2009, 191(9), 2926-2933. The putative coupling protein TcpA interacts with other pCW3-encoded proteins to form an essential part of the conjugation complex. [PubMed]
Stojmirovic, A.; Yu, Y.K.; Bioinformatics2009, 25(18), 2447-2449. ITM Probe: analyzing information flow in protein networks. [PubMed]
Stollar, E.J.; Garcia, B.; Chong, P.A.; Rath, A.; Lin, H.; Forman-Kay, J.D.; Davidson, A.R.; J. Biol. Chem. 2009, 284(39), 26918-26927. Structural, functional, and bioinformatic studies demonstrate the crucial role of an extended peptide binding site for the SH3 domain of yeast Abp1p. [PubMed]
Sugaya, N.; Ikeda, K.; BMC Bioinformatics2009, 10, 263.
Assessing the druggability of protein-protein interactions by a supervised machine-learning method. [PubMed]
Tatonetti, N.P.; Liu, T.; Altman, R.B.; Genome Biol. 2009, 10(9), 238. Predicting drug side-effects by chemical systems biology. [PubMed]
Taylor, R.; Singhal, M.; Methods Mol. Biol. 2009, 541, 551-576. Biological network inference and analysis using SEBINI and CABIN. [PubMed]
Taylor, R.C.; Singhal, M.; Daly, D.S.; Gilmore, J.; Cannon, W.R.; Domico, K.; White, A.M.; Auberry, D.L.; Auberry, K.J.; Hooker, B.S.; Hurst, G.; McDermott, J.E.; McDonald, W.H.; Pelletier, D.A,; Schmoyer, D.; Wiley, H.S.; Int. J. Data Min. Bioinform.2009, 3(4), 409-430. An analysis pipeline for the inference of protein-protein interaction networks. [PubMed]
Terentiev, A.A.; Moldogazieva, N.T.; Shaitan, K.V.; Biochemistry (Mosc).2009, 74(13), 1586-1607.
Dynamic proteomics in modeling of the living cell. Protein-protein interactions. [PubMed]
Tillier, E.R.; Charlebois, R.L.; Genome Res.2009, 19(10), 1861-1871. The human protein coevolution network. [PubMed]
Tran, N.; Qu, P.P.; Simpson, D.A.; Lindsey-Boltz, L.; Guan, X.; Schmitt, C.P.; Ibrahim, J.G.; Kaufmann, W.K.; Cell Biochem. Biophys. 2009, 53(2), 101-114. In silico construction of a protein interaction landscape for nucleotide excision repair. [PubMed]
Tripathi, A.; Ren, Y.; Jeffrey, P.D.; Hughson, F.M.; Nat. Struct. Mol. Biol.2009, 16(2), 114-123. Structural characterization of Tip20p and Dsl1p, subunits of the Dsl1p vesicle tethering complex. [PubMed]
Tsai, C.J.; Ma, B.; Nussinov, R.; Trends Biochem. Sci. 2009, 34(12), 594-600. Protein-protein interaction networks: how can a hub protein bind so many different partners? [PubMed]
Tuncbag, N.; Kar, G.; Gursoy, A.; Keskin, O.; Nussinov, R.; Mol. Biosyst. 2009, 5(12), 1770-1778. Towards inferring time dimensionality in protein-protein interaction networks by integrating structures: the p53 example. [PubMed]
Tyagi, N.; Krishnadev, O.; Srinivasan, N.; Mol. Biosyst.2009, 5(12), 1630-1635. Prediction of protein-protein interactions between Helicobacter pylori and a human host. [PubMed]
Vallabhaneni, H.; Farabaugh, P.J.; RNA2009,15(6), 1100-1109. Accuracy modulating mutations of the ribosomal protein S4-S5 interface do not necessarily destabilize the rps4-rps5 protein-protein interaction. [PubMed]
van Haagen, H.H.; 't Hoen, P.A.; Botelho Bovo, A.; de Morrée, A.; van Mulligen, E.M.; Chichester, C.; Kors, J.A.; den Dunnen, J.T.; van Ommen, G.J.; van der Maarel, S.M.; Kern, V.M.; Mons, B.; Schuemie, M.J.; PLoS One2009, 4(11), e7894. Novel protein-protein interactions inferred from literature context. [PubMed]
van Wijk, S.J.; de Vries, S.J.; Kemmeren, P.; Huang, A.; Boelens, R.; Bonvin, A.M.; Timmers, H.T.; Mol. Syst. Biol.2009, 5, 295. A comprehensive framework of E2-RING E3 interactions of the human ubiquitin-proteasome system. [PubMed]
Vidi, P.A.; Watts, V.J.; Mol. Pharmacol.2009, 75(4),733-739. Fluorescent and bioluminescent protein-fragment complementation assays in the study of G protein-coupled receptor oligomerization and signaling. [PubMed]
Vinogradov, A.E.; J. Mol. Evol.2009,68(2), 192-196. Global versus local centrality in evolution of yeast protein network. [PubMed]
Visvanathan, M.; Pfeifer, B.; Baumgartner, C.; Tilg, B.; Lushington, G.H.; Lect. Notes Comput. Sci.2009, 5542, 63-74. Integrative approach for combining TNFalpha-NFkappaB mathematical model to a protein interaction connectivity map. [PubMed]
Voevodski, K.; Teng, S.H.; Xia, Y.; BMC Syst. Biol.2009, 3, 112. Spectral affinity in protein networks. [PubMed]
Vu, T.Q.; Liu, H.Y.; Methods Mol. Biol.2009, 544, 381-391. Quantum dot hybrid gel blotting: a technique for identifying quantum dot-protein/protein-protein interactions. [PubMed]
Wang, C.; Cheng, J.; Su, S.; Protein J. 2009, 28(2), 111-115. Prediction of interacting protein pairs from sequence using a Bayesian method. [PubMed]
Wang, H.; Huang, M.; Zhu, X.; BMC Bioinformatics2009, 10(Suppl. 1), S55. Extract interaction detection methods from the biological literature. [PubMed]
Wang, W.; Nunez-Iglesias, J.; Luan, Y.; Sun, F.; BMC Bioinformatics2009, 10(1), 277. Usefulness and limitations of dK random graph models to predict interactions and functional homogeneity in biological networks under a pseudo-likelihood parameter estimation approach. [PubMed]
Weigt, M.; White, R.A.; Szurmant, H.; Hoch, J.A.; Hwa, T.; Proc. Natl. Acad. Sci. USA2009, 106(1), 67-72. Identification of direct residue contacts in protein-protein interaction by message passing. [PubMed]
Wu, X.; Pandey, R.; Chen, J.Y.; Conf. Proc. IEEE Eng. Med. Biol. Soc. 2009, 1, 6954-6957. Network topological reordering revealing systemic patterns in yeast protein interaction networks. [PubMed]
Wu, Z.; Elgart, V.; Qian, H.; Xing, J.; J. Phys. Chem. B 2009, 113(36), 12375-12381. Amplification and detection of single-molecule conformational fluctuation through a protein interaction network with bimodal distributions. [PubMed]
Xin, X.; Rual, J.F.; Hirozane-Kishikawa, T.; Hill, D.E.; Vidal, M.; Boone, C.; Thierry-Mieg, N.; Genome Res. 2009, 19(7), 1262-1269. Shifted transversal design smart-pooling for high coverage interactome mapping. [PubMed]
Yamada, T.; Bork, P.; Nat. Rev. Mol. Cell. Biol.2009, 10(11), 791-803. Evolution of biomolecular networks: lessons from metabolic and protein interactions. [PubMed]
Yan, P.; Wang, T.; Newton, G.J.; Knyushko, T.V.; Xiong, Y.; Bigelow, D.J.; Squier, T.C.; Mayer, M.U.; Chembiochem. 2009, 10(9), 1507-1518. A targeted releasable affinity probe (TRAP) for in vivo photocrosslinking. [PubMed]
Yin, S.; Proctor, E.A.; Lugovskoy, A.A.; Dokholyan, N.V.; Proc. Natl. Acad. Sci. USA2009, 106(39), 16622-16626. Fast screening of protein surfaces using geometric invariant fingerprints. [PubMed]
Yoneya, T.; Nishida, R.; BMC Bioinformatics2009, 10(1), 9. TCP: a tool for designing chimera proteins based on the tertiary structure information. [PubMed]
Yura, K.; Hayward, S.; Bioinformatics2009, 25(23), 3108-3113. The interwinding nature of protein-protein interfaces and its implication for protein complex formation. [PubMed]
Zaki, N.; Lazarova-Molnar, S.; El-Hajj, W.; Campbell, P.; BMC Bioinformatics 2009, 10(1), 150. Protein-protein interaction based on pairwise similarity. [PubMed]
Zhang, H.; Tang, X.; Munske, G.R.; Tolic, N.; Anderson, G.A.; Bruce, J.E.; Mol. Cell Proteomics2009, 8(3), 409-420. Identification of protein-protein interactions and topologies in living cells with chemical cross-linking and mass spectrometry. [PubMed]
Zhang, K.X.; Ouellette, B.F.; BMC Bioinformatics2009, 10(Suppl. 1), S60. GAIA: a gram-based interaction analysis tool - an approach for identifying interacting domains in yeast. [PubMed]
Zhang, L.; Villa, N.Y.; Rahman, M.M.; Smallwood, S.; Shattuck, D.; Neff, C.; Dufford, M.; Lanchbury, J.S.; Labaer, J.; McFadden, G.; J. Proteome Res.2009, 8(9), 4311-4318. Analysis of vaccinia virus-host protein-protein interactions: validations of yeast two-hybrid screenings. [PubMed]
Zhang, S.; Chen, H.; Liu, K.; Sun, Z.; BMC Bioinformatics2009, 10, 395. Inferring protein function by domain context similarities in protein-protein interaction networks. [PubMed]
Zhou, L.; Ma, X.; Arbeitman, M.N.; Sun, F.; PLoS One2009, 4(11), e8086. Chromatin regulation and gene centrality are essential for controlling fitness pleiotropy in yeast. [PubMed]
Zhu, M.; Gao, L.; Li, X.; Liu, Z.; Sci. China C Life Sci. 2009, 52(4), 398-404. Identifying drug-target proteins based on network features. [PubMed]
Zhuang, M.; Calabrese, M.F.; Liu, J.; Waddell, M.B.; Nourse, A.; Hammel, M.; Miller, D.J.; Walden, H.; Duda, D.M.; Seyedin, S.N.; Hoggard, T.; Harper, J.W.; White, K.P.; Schulman, B.A.; Mol. Cell. 2009, 36(1), 39-50. Structures of SPOP-substrate complexes: insights into molecular architectures of BTB-Cul3 ubiquitin ligases. [PubMed]