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Bibliography (74 total) : Review Only   Up

• 2013


• Pawlowski PH, Kaczanowski S, Zielenkiewicz P (2013) A kinetic model of the evolution of a protein interaction network. BMC Genomics 14:172



• Lin CY, Chen YC, Lo YS, Yang JM (2013) Inferring homologous protein-protein interactions through pair position specific scoring matrix. BMC Bioinformatics 14 Suppl 2:S11



• Muley VY, Ranjan A (2013) Evaluation of physical and functional protein-protein interaction prediction methods for detecting biological pathways. PLoS One 8:e54325



• 2012


• Levy ED, De S, Teichmann SA (2012) Cellular crowding imposes global constraints on the chemistry and evolution of proteomes. Proc Natl Acad Sci U S A 109:20461-6



• Zheng N, Huang X, Yin B, Wang D, Xie Q (2012) An effective system for detecting protein-protein interaction based on in vivo cleavage by PPV NIa protease. Protein Cell 3:921-8



• Zhang QC, Petrey D, Deng L, Qiang L, Shi Y, Thu CA, Bisikirska B, Lefebvre C, Accili D, Hunter T, Maniatis T, Califano A, Honig B (2012) Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature 490:556-60



• Moreno-Hagelsieb G, Jokic P (2012) The evolutionary dynamics of functional modules and the extraordinary plasticity of regulons: the Escherichia coli perspective. Nucleic Acids Res 40:7104-12



• Battesti A, Bouveret E (2012) The bacterial two-hybrid system based on adenylate cyclase reconstitution in Escherichia coli. Methods :



• Rajagopala SV, Sikorski P, Caufield JH, Tovchigrechko A, Uetz P (2012) Studying protein complexes by the yeast two-hybrid system. Methods :



• Pache RA, Céol A, Aloy P (2012) NetAligner--a network alignment server to compare complexes, pathways and whole interactomes. Nucleic Acids Res 40:W157-61



• Gagarinova A, Emili A (2012) Genome-scale genetic manipulation methods for exploring bacterial molecular biology. Mol Biosyst 8:1626-38 Review



• Yapici E, Reddy DR, Miller LW (2012) An adaptable luminescence resonance energy transfer assay for measuring and screening protein-protein interactions and their inhibition. Chembiochem 13:553-8, 489



• Yang L, Zheng C, Weisbrod CR, Tang X, Munske GR, Hoopmann MR, Eng JK, Bruce JE (2012) In vivo application of photocleavable protein interaction reporter technology. J Proteome Res 11:1027-41



• Babu M, Kagan O, Guo H, Greenblatt J, Emili A (2012) Identification of protein complexes in Escherichia coli using sequential peptide affinity purification in combination with tandem mass spectrometry. J Vis Exp :



• de Vienne DM, Azé J (2012) Efficient prediction of co-complexed proteins based on coevolution. PLoS One 7:e48728



• Pellis M, Muyldermans S, Vincke C (2012) Bacterial two hybrid: a versatile one-step intracellular selection method. Methods Mol Biol 911:135-50



• Muley VY, Ranjan A (2012) Effect of reference genome selection on the performance of computational methods for genome-wide protein-protein interaction prediction. PLoS One 7:e42057



• Peng W, Wang J, Wang W, Liu Q, Wu FX, Pan Y (2012) Iteration method for predicting essential proteins based on orthology and protein-protein interaction networks. BMC Syst Biol 6:87



• Qin G, Gao L (2012) An algorithm for network motif discovery in biological networks. Int J Data Min Bioinform 6:1-16



• Zeng J, He ZG (2012) A new bacterial co-expression system for over-expressing soluble protein and validating protein-protein interaction. Methods Mol Biol 824:235-49



• Waraho D, DeLisa MP (2012) Identifying and optimizing intracellular protein-protein interactions using bacterial genetic selection. Methods Mol Biol 813:125-43



• 2011


• Slavoff SA, Liu DS, Cohen JD, Ting AY (2011) Imaging protein-protein interactions inside living cells via interaction-dependent fluorophore ligation. J Am Chem Soc 133:19769-76



• Shekhawat SS, Ghosh I (2011) Split-protein systems: beyond binary protein-protein interactions. Curr Opin Chem Biol 15:789-97 Review



• Pérez-Bercoff Å, McLysaght A, Conant GC (2011) Patterns of indirect protein interactions suggest a spatial organization to metabolism. Mol Biosyst 7:3056-64



• Zheng C, Yang L, Hoopmann MR, Eng JK, Tang X, Weisbrod CR, Bruce JE (2011) Cross-linking measurements of in vivo protein complex topologies. Mol Cell Proteomics 10:M110.006841



• Pan JY, Wu H, Liu X, Li PP, Li H, Wang SY, Peng XX (2011) Complexome of Escherichia coli cytosolic proteins under normal native conditions. Mol Biosyst 7:2651-63



• Clark MB, Amaral PP, Schlesinger FJ, Dinger ME, Taft RJ, Rinn JL, Ponting CP, Stadler PF, Morris KV, Morillon A, Rozowsky JS, Gerstein MB, Wahlestedt C, Hayashizaki Y, Carninci P, Gingeras TR, Mattick JS (2011) The reality of pervasive transcription. PLoS Biol 9:e1000625; discussion e1001102



• D'Antonio M, Ciccarelli FD (2011) Modification of gene duplicability during the evolution of protein interaction network. PLoS Comput Biol 7:e1002029



• Gophna U, Ofran Y (2011) Lateral acquisition of genes is affected by the friendliness of their products. Proc Natl Acad Sci U S A 108:343-8



• Latha AB, Nair AS, Sivasankaran A, Dhar PK (2011) Identification of hub proteins from sequence. Bioinformation 7:163-8



• Yosef N, Zalckvar E, Rubinstein AD, Homilius M, Atias N, Vardi L, Berman I, Zur H, Kimchi A, Ruppin E, Sharan R (2011) ANAT: a tool for constructing and analyzing functional protein networks. Sci Signal 4:pl1



• Ren X, Wang YC, Wang Y, Zhang XS, Deng NY (2011) Improving accuracy of protein-protein interaction prediction by considering the converse problem for sequence representation. BMC Bioinformatics 12:409



• Joce C, Wiener A, Yin H (2011) Transmembrane domain oligomerization propensity determined by ToxR assay. J Vis Exp :



• Sitaraman K, Chatterjee DK (2011) Protein-protein interactions: an application of Tus-Ter mediated protein microarray system. Methods Mol Biol 723:185-200



• Kanno A, Ozawa T, Umezawa Y (2011) Detection of protein-protein interactions in bacteria by GFP-fragment reconstitution. Methods Mol Biol 705:251-8 Review



• 2010


• Rashid M, Ramasamy S, Raghava GP (2010) A simple approach for predicting protein-protein interactions. Curr Protein Pept Sci 11:589-600



• Prischi F, Pastore C, Carroni M, Iannuzzi C, Adinolfi S, Temussi P, Pastore A (2010) Of the vulnerability of orphan complex proteins: the case study of the E. coli IscU and IscS proteins. Protein Expr Purif 73:161-6



• Yang L, Xia JF, Gui J (2010) Prediction of protein-protein interactions from protein sequence using local descriptors. Protein Pept Lett 17:1085-90



• Pan JY, Li H, Ma Y, Chen P, Zhao P, Wang SY, Peng XX (2010) Complexome of Escherichia coli envelope proteins under normal physiological conditions. J Proteome Res 9:3730-40



• Hormozdiari F, Salari R, Bafna V, Sahinalp SC (2010) Protein-protein interaction network evaluation for identifying potential drug targets. J Comput Biol 17:669-84



• Grünberg R, Ferrar TS, van der Sloot AM, Constante M, Serrano L (2010) Building blocks for protein interaction devices. Nucleic Acids Res 38:2645-62



• Yang Z, Lin H, Li Y (2010) BioPPISVMExtractor: a protein-protein interaction extractor for biomedical literature using SVM and rich feature sets. J Biomed Inform 43:88-96



• Gupta S, Wallqvist A, Bondugula R, Ivanic J, Reifman J (2010) Unraveling the conundrum of seemingly discordant protein-protein interaction datasets. Conf Proc IEEE Eng Med Biol Soc 2010:783-6



• Guo Y, Li M, Pu X, Li G, Guang X, Xiong W, Li J (2010) PRED_PPI: a server for predicting protein-protein interactions based on sequence data with probability assignment. BMC Res Notes 3:145



• Jessulat M, Buist T, Alamgir M, Hooshyar M, Xu J, Aoki H, Ganoza MC, Butland G, Golshani A (2010) In vivo investigation of protein-protein interactions for helicases using tandem affinity purification. Methods Mol Biol 587:99-111



• Hu P, Jiang H, Emili A (2010) Predicting protein functions by relaxation labelling protein interaction network. BMC Bioinformatics 11 Suppl 1:S64



• 2009


• Peregrín-Alvarez JM, Xiong X, Su C, Parkinson J (2009) The Modular Organization of Protein Interactions in Escherichia coli. PLoS Comput Biol 5:e1000523



• Hu P, Janga SC, Babu M, Díaz-Mejía JJ, Butland G, Yang W, Pogoutse O, Guo X, Phanse S, Wong P, Chandran S, Christopoulos C, Nazarians-Armavil A, Nasseri NK, Musso G, Ali M, Nazemof N, Eroukova V, Golshani A, Paccanaro A, Greenblatt JF, Moreno-Hagelsieb G, Emili A (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol 7:e96



• Janga SC, Babu MM (2009) Transcript stability in the protein interaction network of Escherichia coli. Mol Biosyst 5:154-62



• Ivanic J, Yu X, Wallqvist A, Reifman J (2009) Influence of protein abundance on high-throughput protein-protein interaction detection. PLoS One 4:e5815



• Kentner D, Sourjik V (2009) Dynamic map of protein interactions in the Escherichia coli chemotaxis pathway. Mol Syst Biol 5:238



• 2008


• Vinogradov AE (2008) Modularity of cellular networks shows general center-periphery polarization. Bioinformatics 24:2814-7



• Maggi S, Massidda O, Luzi G, Fadda D, Paolozzi L, Ghelardini P (2008) Division protein interaction web: identification of a phylogenetically conserved common interactome between Streptococcus pneumoniae and Escherichia coli. Microbiology 154:3042-52



• Kazuta Y, Adachi J, Matsuura T, Ono N, Mori H, Yomo T (2008) Comprehensive analysis of the effects of Escherichia coli ORFs on protein translation reaction. Mol Cell Proteomics 7:1530-40



• Alon N, Dao P, Hajirasouliha I, Hormozdiari F, Sahinalp SC (2008) Biomolecular network motif counting and discovery by color coding. Bioinformatics 24:i241-9



• Huthmacher C, Gille C, Holzhütter HG (2008) A computational analysis of protein interactions in metabolic networks reveals novel enzyme pairs potentially involved in metabolic channeling. J Theor Biol 252:456-64



• Dong M, Yang LL, Williams K, Fisher SJ, Hall SC, Biggin MD, Jin J, Witkowska HE (2008) A "tagless" strategy for identification of stable protein complexes genome-wide by multidimensional orthogonal chromatographic separation and iTRAQ reagent tracking. J Proteome Res 7:1836-49



• Karimpour-Fard A, Leach SM, Gill RT, Hunter LE (2008) Predicting protein linkages in bacteria: which method is best depends on task. BMC Bioinformatics 9:397



• Konagurthu AS, Lesk AM (2008) On the origin of distribution patterns of motifs in biological networks. BMC Syst Biol 2:73



• Pazos F, Juan D, Izarzugaza JM, Leon E, Valencia A (2008) Prediction of protein interaction based on similarity of phylogenetic trees. Methods Mol Biol 484:523-35



• Karimpour-Fard A, Leach SM, Hunter LE, Gill RT (2008) The topology of the bacterial co-conserved protein network and its implications for predicting protein function. BMC Genomics 9:313



• Ivanic J, Wallqvist A, Reifman J (2008) Evidence of probabilistic behaviour in protein interaction networks. BMC Syst Biol 2:11



• Pandey J, Koyutürk M, Szpankowski W, Grama A (2008) Annotating pathways in interaction networks. Pac Symp Biocomput :153-65



• Guan H, Kiss-Toth E (2008) Advanced technologies for studies on protein interactomes. Adv Biochem Eng Biotechnol 110:1-24 Review



• Su C, Peregrin-Alvarez JM, Butland G, Phanse S, Fong V, Emili A, Parkinson J (2008) Bacteriome.org--an integrated protein interaction database for E. coli. Nucleic Acids Res 36:D632-6



• 2007


• Kim SM, Bowers PM, Pal D, Strong M, Terwilliger TC, Kaufmann M, Eisenberg D (2007) Functional linkages can reveal protein complexes for structure determination. Structure 15:1079-89



• Huthmacher C, Gille C, Holzhütter HG (2007) Computational analysis of protein-protein interactions in metabolic networks of Escherichia coli and yeast. Genome Inform 18:162-72



• Hegyi H, Schad E, Tompa P (2007) Structural disorder promotes assembly of protein complexes. BMC Struct Biol 7:65



• Karimpour-Fard A, Detweiler CS, Erickson KD, Hunter L, Gill RT (2007) Cross-species cluster co-conservation: a new method for generating protein interaction networks. Genome Biol 8:R185



• 2006


• Izarzugaza JM, Juan D, Pons C, Ranea JA, Valencia A, Pazos F (2006) TSEMA: interactive prediction of protein pairings between interacting families. Nucleic Acids Res 34:W315-9



• 2004


• Cordwell SJ (2004) Exploring and exploiting bacterial proteomes. Methods Mol Biol 266:115-35 Review



• 2002


• Valencia A, Pazos F (2002) Computational methods for the prediction of protein interactions. Curr Opin Struct Biol 12:368-73 Review



• Deane CM, SalwiÅ„ski Å�, Xenarios I, Eisenberg D (2002) Protein interactions: two methods for assessment of the reliability of high throughput observations. Mol Cell Proteomics 1:349-56



• 1996


• Harrison PT (1996) Protein:protein interactions in the lipid bilayer (review). Mol Membr Biol 13:67-79 Review