2016

Jaeger S, Igea A, Arroyo R, Alcalde V, Canovas B, Orozco M, Nebreda A and Aloy P,
Quantification of pathway crosstalk reveals novel synergistic drug combinations for breast cancer,
Cancer Research, 2016, Pubmed: 27879272, DOI: 10.1158/0008-5472.CAN-16-0097

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van Leeuwen J, Pons C, Mellor JC, Yamaguchi TN, Friesen H, Koschwanez J, Ušaj MM, Pechlaner M, Takar M, Ušaj M, VanderSluis B, Andrusiak K, Bansal P, Baryshnikova A, Boone CE, Cao J, Cote A, Gebbia M, Horecka G, Horecka I, Kuzmin E, Legro N, Liang W, van Lieshout N, McNee M, San Luis BJ, Shaeri F, Shuteriqi E, Sun S, Yang L, Youn JY, Yuen M, Costanzo M, Gingras AC, Aloy P, Oostenbrink C, Murray A, Graham TR, Myers CL, Andrews BJ, Roth FP, Boone C,
Exploring genetic suppression interactions on a global scale,
Science, 2016, 354, Pubmed: 27811238, DOI: 10.1126/science.aag0839

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Serra-Musach J, Mateo F, Capdevila-Busquets E, de Garibay GR, Zhang X, Guha R, Thomas CJ, Grueso J, Villanueva A, Jaeger S, Heyn H, Vizoso M, Pérez H, Cordero A, Gonzalez-Suarez E, Esteller M, Moreno-Bueno G, Tjärnberg A, Lázaro C, Serra V, Arribas J, Benson M, Gustafsson M, Ferrer M, Aloy P, Pujana MÀ,
Cancer network activity associated with therapeutic response and synergism,
Genome Medicine, 2016, 8:88, Pubmed: 27553366, DOI: 10.1186/s13073-016-0340-x, Supplementary material

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Zhong Q, Pevzner SJ, Hao T, Wang Y, Mosca R, Menche J, Taipale M, Taşan M, Fan C, Yang X, Haley P, Murray RR, Mer F, Gebreab F, Tam S, MacWilliams A, Dricot A, Reichert P, Santhanam B, Ghamsari L, Calderwood MA, Rolland T, Charloteaux B, Lindquist S, Barabási AL, Hill DE, Aloy P, Cusick ME, Xia Y, Roth FP, Vidal M,
An inter‐species protein–protein interaction network across vast evolutionary distance,
Molecular Systems Biology, 2016, 12:865, Pubmed: 27107014, DOI: 10.15252/msb.20156484

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Yachie N, Petsalaki E, Mellor JC, Weile J, Jacob Y, Verby M, Ozturk SB, Li S, Cote AG, Mosca R, Knapp JJ, Ko M, Yu A, Gebbia M, Sahni N, Yi S, Tyagi T, Sheykhkarimli D, Roth JF, Wong C, Musa L, Snider J, Liu YC, Yu H, Braun P, Stagljar I, Hao T, Calderwood MA, Pelletier L, Aloy P, Hill DE, Vidal M, Roth FP,
Pooled‐matrix protein interaction screens using Barcode Fusion Genetics,
Molecular Systems Biology, 2016, 12:863, Pubmed: 27107012, DOI: 10.15252/msb.20156660

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Gomez-Verjan JC, Estrella-Parra E, Vazquez-Martinez ER, Gonzalez-Sanchez I, Guerrero-Magos G, Mendoza-Villanueva D, Isus L, Alfaro A, Cerbón-Cervantes M, Aloy P, Reyes-Chilpa R,
Risk assessment of Soulatrolide and Mammea (A/BA+A/BB) coumarins from Calophyllum brasiliense by a toxicogenomic and toxicological approach,
Food and Chemical Toxicology, 2016, 91:117-129, Pubmed: 26995226, DOI: 10.1016/j.fct.2016.03.010

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Yang X, Coulombe-Huntington J, Kang S, Sheynkman GM, Hao T, Richardson A, Sun S, Yang F, Shen YA, Murray RR, Spirohn K, Begg BE, Duran-Frigola M, MacWilliams A, Pevzner SJ, Zhong Q, Trigg SA, Tam S, Ghamsari L, Sahni N, Yi S, Rodriguez MD, Balcha D, Tan G, Costanzo M, Andrews B, Boone C, Zhou XJ, Salehi-Ashtiani K, Charloteaux B, Chen AA, Calderwood MA, Aloy P, Roth FP, Hill DE, Iakoucheva LM, Xia Y, Vidal M,
Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing,
Cell, 2016, 164(4):805-817, Pubmed: 26871637, DOI: 10.1016/j.cell.2016.01.029

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Oberhardt MA, Zarecki R, Reshef L, Xia F, Duran-Frigola M, Schreiber R, Henry CS, Ben-Tal N, Dwyer DJ, Gophna U, Ruppin E,
Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5’-Phosphate Production in E. coli,
PLOS Computational Biology, 2016, 12(1):1-19, Pubmed: 26821166, DOI: 10.1371/journal.pcbi.1004705

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Herrando-Grabulosa M, Mulet R, Pujol A, Mas JM, Navarro X, Aloy P, Coma M, Casas C,
Novel Neuroprotective Multicomponent Therapy for Amyotrophic Lateral Sclerosis Designed by Networked Systems,
PLoS One, 2016, 11(1):1-17, Pubmed: 26807587, DOI: 10.1371/journal.pone.0147626

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Kumar A, Beloglazova N, Bundalovic-Torma C, Phanse S, Deineko V, Gagarinova A, Musso G, Vlasblom J, Lemak S, Hooshyar M, Minic Z, Wagih O, Mosca R, Aloy P, Golshani A, Parkinson J, Emili A, F. Yakunin A, Babu M,
Conditional Epistatic Interaction Maps Reveal Global Functional Rewiring of Genome Integrity Pathways in Escherichia coli,
Cell Reports, 2016, 14:648-661, Pubmed: 26774489, DOI: 10.1016/j.celrep.2015.12.060

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Sfriso P, Duran-Frigola M, Mosca R, Emperador A, Aloy P, Orozco M,
Residues Coevolution Guides the Systematic Identification of Alternative Functional Conformations in Proteins,
Structure, 2016, 24:1-11, Pubmed: 26688214, DOI: 10.1016/j.str.2015.10.025

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2015

Jung P, Sommer C, Barriga FM, Buczacki SJ, Hernando-Momblona X, Sevillano M, Duran-Frigola M, Aloy P, Selbach M, Winton DJ, Batlle E,
Isolation of Human Colon Stem Cells Using Surface Expression of PTK7,
Stem Cell Reports, 2015, 5:1-9, Pubmed: 26549850, DOI: 10.1016/j.stemcr.2015.10.003

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Jaeger S, Duran-Frigola M, Aloy P,
Drug sensitivity in cancer cell lines is not tissue-specific,
Molecular Cancer, 2015, 14:40:1-4, Pubmed: 25881072, DOI: 10.1186/s12943-015-0312-6

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Segura J, Sorzano COS, Cuenca-Alba J, Aloy P, Carazo JM,
Using neighborhood cohesiveness to infer interactions between protein domains,
Bioinformatics, 2015:1-8, Pubmed: 25838464, DOI: 10.1093/bioinformatics/btv188

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Casas C, Isús L, Herrando-Grabulosa M, Mancuso FM, Borrás E, Sabidó E, Forés J, Aloy P,
Network-based proteomic approaches reveal the neurodegenerative, neuroprotective and pain-related mechanisms involved after retrograde axonal damage,
Scientific Reports, 2015, 5: 9185:1-13, Pubmed: 25784190, DOI: 10.1038/srep09185

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Mosca R, Tenorio-Laranga J, Olivella R, Alcalde V, Ceol A, Soler-López M, Aloy P,
dSysMap: Exploring the edgetic role of disease mutations,
Nature Methods, 2015, 12:167–168, Pubmed: 25719824, DOI: 10.1038/nmeth.3289

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Arroyo R, Suñé G, Zanzoni A, Duran-Frigola M, Alcalde V, Stracker TH, Soler-López M, Aloy P,
Systematic identification of molecular links between core and candidate genes in breast cancer,
Journal of Molecular Biology, 2015, 427:1436-1450, Pubmed: 25640309, DOI: 10.1016/j.jmb.2015.01.014

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Capdevila-Busquets E, Badiola N, Arroyo R, Alcalde V, Soler-López M, Aloy P,
Breast Cancer Genes PSMC3IP and EPSTI1 Play a Role in Apoptosis Regulation,
PLoS ONE, 2015, 10(1): e0115352, Pubmed: 25590583, DOI: 10.1371/journal.pone.0115352

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Jin K, Musso G, Vlasblom J, Jessulat M, Deineko V, Negroni J, Mosca R ... Aloy P, Zhang Z, Babu M,
Yeast Mitochondrial Protein-Protein Interactions Reveal Diverse Complexes and Disease-Relevant Functional Relationships,
Journal of Proteome Research, Advanced Online Publication, 2015, 14:1220−1237, Pubmed: 25546499, DOI: 10.1021/pr501148q

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Juan-Blanco T, Duran-Frigola M, Aloy P,
IntSide: a web server for the chemical and biological examination of drug side effects,
Bioinformatics, 2015, 31 (4):612-613, Pubmed: 25380960, DOI: 10.1093/bioinformatics/btu688

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2014

Blasche S, Arens S, Ceol A, Siszler G, Schmidt MA, Häuser R, Schwarz F, Wuchty S, Aloy P, Uetz P, Stradal T, Kögl M,
The EHEC-host interactome reveals novel targets for the translocated intimin receptor,
Scientific Reports, 2014, 4: 7531, Pubmed: 25519916, DOI: 10.1038/srep07531

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Duran-Frigola M, Rossell D, Aloy P,
A chemo-centric view of human health and disease,
Nature Communications, 2014, 5:5676, Pubmed: 25435099, DOI: 10.1038/ncomms6676

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Rolland T et al. (including Mosca R and Aloy P),
A Proteome-Scale Map of the Human Interactome Network,
Cell, 2014, 159(5):1212–1226, Pubmed: 25416956, DOI: 10.1016/j.cell.2014.10.050

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Negroni J, Mosca R, Aloy P,
Assessing the applicability of template-based protein docking in the twilight zone,
Structure, 2014, 22(9):1356–1362, Pubmed: 25156427, DOI: 10.1016/j.str.2014.07.009

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Pache R, Aloy P,
Increasing the precision of orthology-based complex prediction through network alignment,
PeerJ, 2014, 2:e413, Pubmed: 24918034, DOI: 10.7717/peerj.413

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Häuser R, Ceol A, Rajagopala S, Mosca R, Siszler G, Wemke N, Sikorski P, Schwarz F, Schick M, Wuchty S, Aloy P, Uetz P,
An Second-generation Protein-Protein Interaction Network of Helicobacter pylori,
Molecular & Cellular Proteomics, 2014, 13:1318-1329, Pubmed: 24627523, DOI: 10.1074/mcp.O113.033571

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Rajagopala S, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala S, Phanse S, Ceol A, Häuser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P,
The binary protein-protein interaction landscape of Escherichia coli,
Nature Biotechnology, 2014, 32:285–290, Pubmed: 24561554, DOI: doi:10.1038/nbt.2831

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Arroyo R, Duran-Frigola, Berenguer C, Soler-López M, Aloy P,
Charting the molecular links between driver and susceptibility genes in colorectal cancer,
Biochem. Biophys. Res. Commun, 2014, 445(4):734–738, Pubmed: 24412244, DOI: 10.1016/j.bbrc.2013.12.012

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Mosca R, Céol A, Stein A, Olivella R, Aloy P,
3did: a catalogue of domain-based interactions of known three-dimensional structure,
Nucleic Acids Research, 2014, 42 (D1):D374-D379, Pubmed: 24081580, DOI: 10.1093/nar/gkt887

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2013

Mosca R, Pons T, Céol A, Valencia A, Aloy P,
Towards a detailed atlas of protein-protein interactions,
Current Opinion in Structural Biology, 2013, 23(6):929–940, Pubmed: 23896349, DOI: 10.1016/j.sbi.2013.07.005

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Duran-Frigola M, Mosca R, Aloy P,
Structural Systems Pharmacology: the role of 3D structures in next generation drug development,
Chemistry & Biology, 2013, 20(5):674-684, Pubmed: 23706634, DOI: 10.1016/j.chembiol.2013.03.004

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Quiles F, Fernández-Rodríguez J, Mosca R, Feliubadaló L, Tornero E, Brunet J, Blanco I, Capellá G, Pujana MA, Aloy P, Monteiro A, Lázaro C,
Functional and Structural Analysis of C-Terminal BRCA1 Missense Variants,
PLoS ONE, 2013, 8(4):e61302, Pubmed: 23613828, DOI: 10.1371/journal.pone.0061302

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Duran-Frigola M, Aloy P,
Analysis of chemical and biological features yields mechanistic insights into drug side effects,
Chemistry & Biology, 2013, 20:594-603, Pubmed: 23601648, DOI: 10.1016/j.chembiol.2013.03.017

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Badiola N, Alcalde V, Pujol A, Münter LM, Multhaup G, Lleó A, Coma M, Soler-López M, Aloy P,
The proton-pump inhibitor lansoprazole enhances amyloid beta production,
PLoS ONE, 2013, 8(3):e58837, Pubmed: 23520537, DOI: 10.1371/journal.pone.0058837

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Mosca M, Céol A, Aloy P,
Interactome3D: adding structural details to protein networks,
Nature Methods, 2013, 10(1):47-53, Pubmed: 23399932, DOI: 10.1038/nmeth.2289, Supplementary material

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2012

Pache RA, Céol A, Aloy P,
NetAligner – A network alignment server to compare complexes, pathways and whole interactomes,
Nucleic Acids Res, 2012, Pubmed: 22618871, DOI: 10.1093/nar/gks446

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Jaeger S, Aloy P,
From protein interaction networks to novel therapeutic strategies,
IUBMB Life, 2012, Pubmed: 22573601, DOI: 10.1002/iub.1040

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Soler-López M, Badiola N, Zanzoni A, Aloy P,
Towards Alzheimer's root cause: ECSIT as an integrating hub between oxidative stress, inflammation and mitochondrial dysfunction,
BioEssays, 2012, Pubmed: 22513506, DOI: 10.1002/bies.201100193

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Mosca M, Pache RA, Aloy P,
The role of structural disorder in the rewiring of protein interactions through evolution,
Mol Cell Proteomics, 2012, Pubmed: 22389433, DOI: 10.1074/mcp.M111.014969

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Pache RA, Aloy P,
A Novel Framework for the Comparative Analysis of Biological Networks,
PLoS ONE, 2012, 7 (2), Pubmed: 22363585, DOI: 10.1371/journal.pone.0031220

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Duran-Frigola M, Aloy P,
Recycling side-effects into clinical markers for drug repositioning,
Genome Medicine, 2012, 4:3, Pubmed: 22283977, DOI: 10.1186/gm302

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2011

Aranda B, Blankenburg H, Kerrien S, Brinkman FS, Ceol A, Chautard E, Dana JM, De Las Rivas J, Dumousseau M, Galeota E, Gaulton A, Goll J, Hancock RE, Isserlin R, Jimenez RC, Kerssemakers J, Khadake J, Lynn DJ, Michaut M, O'Kelly G, Ono K, Orchard S, Prieto C, Razick S, Rigina O, Salwinski L, Simonovic M, Velankar S, Winter A, Wu G, Bader GD, Cesareni G, Donaldson IM, Eisenberg D, Kleywegt GJ, Overington J, Ricard-Blum S, Tyers M, Albrecht M, Hermjakob H,
PSICQUIC and PSISCORE: accessing and scoring molecular interactions,
Nature Methods, 2011, 8:528–529, Pubmed: 21716279, DOI: 10.1038/nmeth.1637

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Stein A, Rueda M, Panjkovich A, Orozco M, Aloy P,
A Systematic Study of the Energetics Involved in Structural Changes upon Association and Connectivity in Protein Interaction Networks,
Structure, 2011, 19(6):881-9, Pubmed: 21645858, DOI: 10.1016/j.str.2011.03.009, Supplementary material

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Feliu E, Aloy P, Oliva B,
On the analysis of protein-protein interactions via knowledge-based potentials for the prediction of protein-protein docking,
Protein Sci, 2011, 20(3):529–541, Pubmed: 21432933, DOI: 10.1002/pro.585

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Stein A, Mosca R, Aloy P,
Three-dimensional modeling of protein interactions and complexes is going 'omics,
Curr Opin Struct Biol, 2011, 21(2):200-8, Pubmed: 21320770, DOI: 10.1016/j.sbi.2011.01.005

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Soler-López M, Zanzoni A, Lluís R, Stelzl U, Aloy P,
Interactome mapping suggests new mechanistic details underlying Alzheimer's disease,
Genome Res, 2011, 21(3):364-76, Pubmed: 21163940, DOI: 10.1101/gr.114280.110, Supplementary material

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Zanzoni A, Carbajo D, Diella F, Gherardini PF, Tramontano A, Helmer-Citterich M, Via A,
Phospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites,
Nucleic Acids Res, 2011, 39(Database issue):D268-71, Pubmed: 20965970, DOI: 10.1093/nar/gkq936

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Stein A, Céol A, Aloy P,
3did: identification and classification of domain-based interactions of known three-dimensional structure,
Nucleic Acids Res, 2011, 39(Database issue):D718–D723, Pubmed: 20965963, DOI: 10.1093/nar/gkq962

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2010

Farrés J, Pujol A, Coma M, Ruiz JL, Naval J, Mas JM, Molins A, Fondevila J, Aloy P,
Revealing the molecular relationship between type 2 diabetes and the metabolic changes induced by a very-low-carbohydrate low-fat ketogenic diet,
Nutr Metab (Lond), 2010, 9(7):88, Pubmed: 21143928, DOI: 10.1186/1743-7075-7-88

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Sardon T, Pache RA, Stein A, Molina H, Vernos I, Aloy P,
Uncovering new substrates for Aurora A kinase,
EMBO Rep, 2010, 11:977-984, Pubmed: 21072059, DOI: 10.1038/embor.2010.171, Supplementary material

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Brooks MA, Gewartowski K, Mitsiki E, Létoquart J, Pache RA, Billier Y, Bertero M, Corréa M, Czarnocki-Cieciura M, Dadlez M, Henriot V, Lazar N, Delbos L, Lebert D, Piwowarski J, Rochaix P, Böttcher B, Serrano L, Séraphin B, van Tilbeurgh H, Aloy P, Perrakis A, Dziembowski A,
Systematic bioinformatics and experimental validation of yeast complexes reduces the rate of attrition during structural investigations,
Structure, 2010, 9(8):1075-1082, Pubmed: 20826334, DOI: 10.1016/j.str.2010.08.001, Supplementary material

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Stein A, Aloy P. ,
Novel peptide-mediated interactions derived from high-resolution 3-dimensional structures,
PLoS Comput Biol, 2010, 6(5):e1000789, Pubmed: 20502673, DOI: 10.1371/journal.pcbi.1000789

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Littler DR, Alvarez-Fernández M, Stein A, Hibbert RG, Heidebrecht T, Aloy P, Medema RH, Perrakis A,
Structure of the FoxM1 DNA-recognition domain bound to a promoter sequence,
Nucleic Acids Res, 2010, 38(13):4527-38, Pubmed: 20360045, DOI: 10.1093/nar/gkq194

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Panjkovich A, Aloy P,
Predicting protein-protein interaction specificity through the integration of three-dimensional structural information and the evolutionary record of protein domains,
Mol Biosyst, 2010, 6(4):741-9, Pubmed: 20237652, DOI: 10.1039/B918395G

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Pujol A, Mosca R, Farrés J, Aloy P,
Unveiling the role of network and systems biology in drug discovery,
Trends in Pharmacological Sciences, 2010, 31(3):115-123, Pubmed: 20117850, DOI: 10.1016/j.tips.2009.11.006

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2009

Aloy P, Oliva B,
Splitting statistical potentials into meaningful scoring functions: testing the prediction of near-native structures from decoy conformations,
BMC Struct Biol, 2009, 16(9):71, Pubmed: 19917096, DOI: 10.1186/1472-6807-9-71

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Mosca R, Pons C, Fernández-Recio J, Aloy P,
Pushing structural information into the yeast interactome by high-throughput protein docking experiments,
PLoS computational biology, 2009, 5(8):e1000490, Pubmed: 19714207, DOI: 10.1371/journal.pcbi.1000490, Supplementary material

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Stein A, Pache RA, Bernadó P, Pons M, Aloy P,
Dynamic interactions of proteins in complex networks: a more structured view,
FEBS J, 2009, 276(19):5390-405, Pubmed: 19712106, DOI: 10.1111/j.1742-4658.2009.07251.x

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Pache RA, Babu MM, Aloy P,
Exploiting gene deletion fitness effects in yeast to understand the modular architecture of protein complexes under different growth conditions,
BMC Systems Biology, 2009, 3:74, Pubmed: 19615085, DOI: 10.1186/1752-0509-3-74

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Zanzoni A, Soler-López M, Aloy P,
A network medicine approach to human disease,
FEBS Letters, 2009, 583(11):1759-65, Pubmed: 19269289, DOI: doi:10.1016/j.febslet.2009.03.001

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Stein A, Panjkovich A, Aloy P,
3did Update: domain-domain and peptide-mediated interactions of known 3D structure,
Nucleic Acids Res, 2009, 37(Database issue):D300-4, Pubmed: 18953040, DOI: 10.1093/nar/gkn690

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2008

Russell RB, Aloy P,
Targeting and tinkering with interaction networks,
Nat Chem Biol, 2008, 4(11):666-73, Pubmed: 18936751, DOI: 10.1038/nchembio.119

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Parthasarathi L, Casey F, Stein A, Aloy P, Shields DC,
Approved drug mimics of short peptide ligands from protein interaction motifs,
J Chem Inf Model, 2008, 48(10):1943-8, Pubmed: 18826301, DOI: 10.1021/ci800174c

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Stein A, Aloy P,
Contextual specificity in peptide-mediated protein interactions,
PLoS One, 2008, 3(7):e2524, Pubmed: 18596940, DOI: 10.1371/journal.pone.0002524

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Pache RA, Aloy P,
Incorporating high-throughput proteomics experiments into structural biology pipelines: Identification of the low-hanging fruits,
Proteomics, 2008, 8(10):1959–1964, Pubmed: 18491310, DOI: 10.1002/pmic.200700966

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Pache RA, Zanzoni A, Naval J, Mas JM, Aloy P,
Towards a molecular characterisation of pathological pathways,
FEBS Lett, 2008, 582(8):1259-65, Pubmed: 18282477, DOI: 10.1016/j.febslet.2008.02.014

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Stein A, Aloy P. ,
A molecular interpretation of genetic interactions in yeast,
FEBS Lett, 2008, 582(8):1245-50, Pubmed: 18282475, DOI: 10.1016/j.febslet.2008.02.020

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2007

Aloy P,
Shaping the future of interactome networks,
Genome Biol, 2007, 8(10):316, Pubmed: 17980052, DOI: 10.1186/gb-2007-8-10-316

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