2022

Fernandez-Torras A, Duran-Frigola M, Bertoni M, Locatelli M, Aloy P,
Integrating and formatting biomedical data as pre-calculated knowledge graph embeddings in the Bioteque,
Nature Communications, 2022, DOI: https://doi.org/10.1038/s41467-022-33026-0

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Kim DK, Weller B, Lin CW, Sheykhkarimli D, Knapp JJ, Dugied G, Zanzoni A, Pons C, Tofaute MJ, Maseko SB, Spirohn K, Laval F, Lambourne L, Kishore N, Rayhan A, Sauer M, Young V, Halder H, la Rosa NM, Pogoutse O, Strobel A, Schwehn P, Li R, Rothballer ST, Altmann M, Cassonnet P, Coté AG, Vergara LE, Hazelwood I, Liu BB, Nguyen M, Pandiarajan R, Dohai B, Coloma PAR, Poirson J, Giuliana P, Willems L, Taipale M, Jacob Y, Hao T, Hill DE, Brun C, Twizere JC, Krappmann D, Heinig M, Falter C, Aloy P, Demeret C, Vidal M, Calderwood MA, Roth FP, Falter-Braun P,
A proteome-scale map of the SARS-CoV-2-human contactome,
Nature Biotechnology, 2022, Pubmed: 36217029, DOI: https://doi.org/10.1038/s41587-022-01475-z

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Douglass Jr. EF, Allaway RJ, Szalai B, Wang W, Allaway RJ, Szalai B, Wang W, Tian T, Fernández-Torras A, Realubit R, Karan C, Zheng S, Pessia A, Tanoli Z, Jafari M, Wan F, Li S, Xiong Y, Duran-Frigola M, Bertoni M, Badia-i-Mompel P, Mateo L, Guitart-Pla O, Chung V, DREAM CTD-squared Pancancer Drug Activity Challenge Consortium, Tang J, Zeng J, Aloy P, Saez-Rodriguez J, Guinney J, Gerhard DS, Califano A,
A community challenge for a pancancer drug mechanism of action inference from perturbational profile data,
Cell Reports Medicine, 2022, 3, Pubmed: 35106508, DOI: 10.1016/j.xcrm.2021.100492

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Pons C, Almacellas E, Tauler A, Mauvezin C,
Detection of Nuclear Biomarkers for Chromosomal Instability,
Methods in Molecular Biology, 2022, 2445:117-125, Pubmed: 34972989, DOI: 10.1007/978-1-0716-2071-7_8

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Fernández-Torras A, Comajuncosa-Creus A, Duran-Frigola M, Aloy P,
Connecting chemistry and biology through molecular descriptors,
Current Opinion in Chemical Biology, 2022, 66:10290, Pubmed: 34626922, DOI: 10.1016/j.cbpa.2021.09.001

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2021

Lambourne L, Yadav A, Wang Y, Desbuleux A, Kim DK, Cafarelli T, Pons C, Kovács IA, Jailkhani N, Schlabach S, De Ridder D, Luck K, Bian W, Shen Y, Mee M, Jacob Y, Lemmens I, Rolland T, Tavernier J, Spirohn K, Zhong Q, Aloy P, Hao T, Charloteaux B, Roth FP, Hill DE, Calderwood MA, Twizere JC, Vidal M,
Binary Interactome Models of Inner-Versus Outer-Complexome Organization,
bioRxiv, 2021, DOI: 10.1101/2021.03.16.435663

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Pauls E, Bayod S, Mateo L, Alcalde L, Juan-Blanco T, Saido TC, Saito T, Berenguer-Llergo A, Attolini CSO, Gay M, de Oliveira E, Duran-Frigola M , Aloy P ,
Identification and drug-induced reversion of molecular signatures of Alzheimers disease onset and progression in AppNL-GF, AppNL-F and 3xTg-AD mouse models,
Genome Medicine , 2021, 13, Pubmed: 34702310, DOI: https://doi.org/10.1186/s13073-021-00983-y

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Macip G, Garcia-Segura P, Mestres-Truyol J, Saldivar-Espinoza B, Ojeda-Montes MJ, Gimeno A, Cereto-Massagué A, Garcia-Vallvé S, Pujadas G,
Haste makes waste: A critical review of docking-based virtual screening in drug repurposing for SARS-CoV-2 main protease (M-pro) inhibition,
Medicinal research reviews, 2021, Pubmed: 34697818, DOI: 10.1002/med.21862

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Gimeno A, Cuffaro D, Nuti E, Ojeda-Montes MJ, Beltrán-Debón R, Mulero M, Rossello A, Pujadas G, Garcia-Vallvé S,
Identification of Broad-Spectrum MMP Inhibitors by Virtual Screening,
Molecules, 2021, 26:4553, Pubmed: 34361703, DOI: 10.3390/molecules26154553

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Fehér C, Pastor-Lbáñez R, Leal L, Plana M, Arnedo M, Van den Ham HJ, Andeweg AC, Gruters RA, Díez-Fuertes F, Alcamí J, Aloy P, García F,
Association of Transcriptomic Signatures of Inflammatory Response with Viral Control after Dendritic Cell-Based Therapeutic Vaccination in HIV-1 Infected Individuals,
Vaccines, 2021, 9:799, Pubmed: 34358215, DOI: 10.3390/vaccines9070799

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Bertoni M, Duran-Frigola M, Badia-i-Mompel P, Orozco-Ruiz M, Guitart-Pla O, Aloy P,
Bioactivity descriptors for uncharacterized compounds,
Nature Communications, 2021, 12:1-13, Pubmed: 34168145, DOI: 10.1038/s41467-021-24150-4

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Tomas-Hernandez S, Blanco J, Garcia-Vallvé S, Pujadas G, Ojeda-Montes MJ, Gimeno A, Arola L, Minghetti L, Beltrán-Debón R, Mulero M,
Anti-Inflammatory and Immunomodulatory Effects of the Grifola frondosa Natural Compound o-Orsellinaldehyde on LPS-Challenged Murine Primary Glial Cells. Roles of NF-κβ and MAPK,
Pharmaceutics, 2021, 13:806, Pubmed: 34071571, DOI: 10.3390/pharmaceutics13060806

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Parts L, Batté A, Lopes M, Yuen MW, Laver M, San Luis BJ, Yue JX, Pons C, Eray E, Aloy P, Liti G, van Leeuwen J,
Natural variants suppress mutations in hundreds of essential genes,
Molecular systems biology, 2021, 17:e10138, Pubmed: 34042294, DOI: 10.15252/msb.202010138

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Costanzo M, Hou J, Messier V, Nelson J, Rahman M, VanderSluis B, Wang W, Pons C, Ross C, Ušaj M, San Luis BJ, Shuteriqi E, Koch EN, Aloy P, Myers CL, Boone C, Andrews B,
Environmental robustness of the global yeast genetic interaction network,
Science, 2021, 372:6542, Pubmed: 33958448, DOI: 10.1126/science.abf8424

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Meldal BHM, Pons C, Perfetto L, Del-Toro N, Wong E, Aloy P, Hermjakob H, Orchard S, Porras P,
Analysing the yeast complexome—the Complex Portal rising to the challenge,
Nucleic acids research, 2021, 49:3156-3167, Pubmed: 33677561, DOI: /10.1093/nar/gkab077

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2020

van Leeuwen J, Pons C, Tan G, Wang JZ, Hou J, Weile J, Gebbia M, Liang W, Shuteriqi E, Li Z, Lopes M, Ušaj M, Dos Santos Lopes A, van Lieshout N, Myers CL, Roth FP, Aloy P, Andrews BJ, Boone C,
Systematic analysis of bypass suppression of essential genes,
Molecular Systems Biology, 2020, 16(9):e9828, Pubmed: 32939983, DOI: 10.15252/msb.20209828

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Mateo L, Duran-Frigola M, Gris-Oliver A, Palafox M, Scaltriti M, Razavi P, Chandarlapaty S, Arribas J, Bellet M, Serra V, Aloy P,
Personalized Cancer Therapy Prioritization Based on Driver Alteration Co-occurrence Patterns,
Genome Medicine, 2020, 12, Pubmed: 32907621, DOI: https://doi.org/10.1186/s13073-020-00774-x

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Mateo L, Duran-Frigola M, Gris-Oliver A, Palafox M, Scaltriti M, Razavi P, Chandarlapaty S, Arribas J, Bellet M, Serra V, Aloy P,
Personalized cancer therapy prioritization based on driver alteration co-occurrence patterns,
Genome Medicine, 2020, 12(1):78, Pubmed: 32907621, DOI: 10.1186/s13073-020-00774-x

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Duran-Frigola M, Bertoni M, Blanco R, Martínez V, Pauls E, Alcalde V, Turon G, Villegas N, Fernández-Torras A, Pons C, Mateo L, Guitart-Pla O, Badia-i-Mompel P, Gimeno A, Soler N, Brun-Heath I, Zaragoza H, Aloy P,
Bioactivity Profile Similarities to Expand the Repertoire of COVID-19 Drugs,
Journal of Chemical Information and Modeling, 2020, Pubmed: 32672454, DOI: https://doi.org/10.1021/acs.jcim.0c00420

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Duran-Frigola M, Pauls E, Guitart-Pla O, Bertoni M, Alcalde V, Amat D, Juan-Blanco T, Aloy P,
Publisher Correction: Extending the small-molecule similarity principle to all levels of biology with the Chemical Checker ,
10.1038/s41587-020-0564-6 , 2020, 38(9):1098, Pubmed: 32440008, DOI: 10.1038/s41587-020-0564-6

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Duran-Frigola M, Pauls E, Guitart-Pla O, Bertoni M, Alcalde V, Amat D, Juan-Blanco T, Aloy P,
Extending the small-molecule similarity principle to all levels of biology with the Chemical Checker,
Nature Biotechnology, 2020, 38(9):1087-1096, Pubmed: 32440005, DOI: https://doi.org/10.1038/s41587-020-0502-7, Supplementary material

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Moncunill G , Scholzen A, Mpina M, Nhabomba A, Bouyoukou Hounkpatin A, Osaba L, Valls R, Campo JJ, Sanz H, Jairoce C, Williams NA, Pasini EM, Arteta D, Maynou J, Palacios L, Duran-Frigola M, Aponte JJ, Kocken CHM, Todagbe Agnandji S, Mas J, Mordmüller B, Daubenberger C, Sauerwein R, Carlota Dobaño C,
Antigen-stimulated PBMC transcriptional protective signatures for malaria immunization,
Science Translational Medicine, 2020, 12, Pubmed: 32404508, DOI: 10.1126/scitranslmed.aay8924

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Luck K, Kim D, Lambourne L, Spirohn K, Begg BE, Bian W, Brignall R, Cafarelli T, Campos-Laborie FJ, Charloteaux B, Choi D, Coté AG, Daley M, Deimling S, Desbuleux A, Dricot A, Gebbia M, Hardy MF, Kishore N, Knapp JJ, Kovács IA, Lemmens I, Mee MW, Mellor JC, Pollis C, Pons C, Richardson AD, Schlabach S, Teeking B, Yadav A, Babor M, Balcha D, Basha O, Bowman-Colin C, Chin S, Gang Choi S, Colabella C, Coppin G, D’Amata C, De Ridder D, De Rouck S, Duran-Frigola M, Ennajdaoui H, Goebels F, Goehring L, Gopal A, Haddad G, Hatchi E, Helmy M, Jacob Y, Kassa Y, Landini S, Li R, van Lieshout N, MacWilliams A, Markey D, Paulson JN, Rangarajan S, Rasla J, Rayhan A, Rolland T, San-Miguel A, Shen Y, Sheykhkarimli D, Sheynkman GM, Simonovsky E, Taşan M, Tejeda A, Tropepe V, Twizere J, Wang Y, Weatheritt RJ, Weile J, Xia Y, Yang X, Yeger-Lotem E, Zhong Q, Aloy P, Bader GD, Rivas J, Gaudet S, Hao T, Rak J, Tavernier J, Hill DE, Vidal M, Calderwood F,
A reference map of the human binary protein interactome,
Nature , 2020, 580:402-408, Pubmed: 32296183, DOI: 10.1038/s41586-020-2188-x, Supplementary material

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Mattiazzi Usaj M, Sahin N, Friesen H, Pons C, Usaj M, Masinas MPD, Shuteriqi E, Shkurin A, Aloy P, Morris Q, Boone C, Andrews BJ,
Systematic genetics and single-cell imaging reveal widespread morphological pleiotropy and cell-to-cell variability,
Molecular Systems Biology, 2020, Pubmed: 32064787, DOI: 10.15252/msb.20199243

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Feher C, Plana M, Guardo AC, Climent N, Leal L, Ugarte A, fernandez I, Florencia Etcheverry M, María Gatell J, Sanchez-Palomino S, GarcÍa F, Aloy P,
A classifier to predict viral control after antiretroviral treatment interruption in chronic HIV-1 infected patients,
Journal of Acquire Immune Deficiency Syndrome, 2020, Pubmed: 31904703, DOI: 10.1097/QAI.0000000000002281

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2019

Iglesias V , Paladin L , Juan-Blanco T , Pallarès I , Aloy P , Tosatto S , Ventura S,
In silico Characterization of Human Prion-Like Proteins: Beyond Neurological Diseases,
Frontiers in Physiology, 2019, DOI: https://doi.org/10.3389/fphys.2019.00314

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De Toma I, Ortega M, Aloy P, Sabidó E, Dierssen M,
DYRK1A Overexpression Alters Cognition and Neural-Related Proteomic Pathways in the Hippocampus That Are Rescued by Green Tea Extract and/or Environmental Enrichment,
Frontiers in molecular Neuroscience, 2019, Pubmed: 31803016, DOI: 10.3389/fnmol.2019.00272

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Torrico B, Shaw AD, Mosca R, Vivó-Luque N, Hervás A, Fernàndez-Castillo N, Aloy P, Bayés M, Fullerton JM, Cormand B, Toma C,
Truncating variant burden in high-functioning autism and pleiotropic effects of LRP1 across psychiatric phenotypes,
Journal of Psychiatry & Neuroscience, 2019, 44(5):350-359, Pubmed: 31094488, DOI: https://doi.org/10.1503/jpn.180184

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Fernández-Torras A, Duran-Frigola M, Aloy P,
Encircling the regions of the pharmacogenomic landscape that determine drug response,
Genome Medicine, 2019, 11:17, Pubmed: 30914058, DOI: https://doi.org/10.1186/s13073-019-0626-x

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2018

Duran‐Frigola M, Fernández‐Torras A, Bertoni M, Aloy P,
Formatting biological big data for modern machine learning in drug discovery,
WIREs Computational Molecular Science, 2018, DOI: 10.1002/wcms.1408

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Hennrich ML, Romanov N, Horn P, Jaeger S, Eckstein V, Steeples V, Ye F, Ding X, Poisa-Beiro L, Lai MC, Lang B, Boultwood J, Luft T, Zaugg JB, Pellagatti A, Bork P, Aloy P, Gavin AC, Ho AD,
Cell-specific proteome analyses of human bone marrow reveal molecular features of age-dependent functional decline,
Nature Communications, 2018, 9(1):4004, Pubmed: 30275468, DOI: 10.1038/s41467-018-06353-4

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Bertoni M, Aloy P,
DynBench3D, a Web-Resource to Dynamically Generate Benchmark Sets of Large Heteromeric Protein Complexes,
Journal of Molecular Biology, 2018, 18:30769, Pubmed: 30274705, DOI: https://doi.org/10.1016/j.jmb.2018.09.011

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Mateo L, Guitart-Pla O, Duran-Frigola M, Aloy P,
Exploring the OncoGenomic Landscape of cancer,
Genome Medicine, 2018, 10:61, Pubmed: 30071882, DOI: 10.1186/s13073-018-0571-0

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Persi E, Duran-Frigola M, Damaghi M, Roush WR, Aloy P, Cleveland JL, Gillies RJ, Ruppin E,
Systems analysis of intracellular pH vulnerabilities for cancer therapy,
Nature Communications, 2018, 9:2997, Pubmed: 30065243, DOI: 10.1038/s41467-018-05261-x

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Schlereth K, Weichenhan D, Bauer T, Heumann T, Giannakouri E, Lipka D, Jaeger S, Schlesner M, Aloy P, Eils R, Plass C Augustin HG,
The transcriptomic and epigenetic map of vascular quiescence in the continuous lung endothelium,
eLife, 2018, 7:e34423, Pubmed: 29749927, DOI: 10.7554/eLife.34423

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Juan-Blanco T, Duran-Frigola M, Aloy P,
Rationalizing Drug Response in Cancer Cell Lines,
Journal of Molecular Biology, 2018, 430(18 Pt A):3016-3027, Pubmed: 29626539, DOI: 10.1016/j.jmb.2018.03.021

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Wuchty S, Mueller S, Caufield H, Haeuser R, Aloy P, Kalkhof S, Uetz P,
Proteome data improves protein function prediction in the interactome of H. pylori,
Molecular & Cell Proteomics, 2018, 17(5):961-973, Pubmed: 29414760, DOI: 10.1074/mcp.RA117.000474

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2017

Duran-Frigola M , Mateo L and Aloy P,
Drug repositioning beyond the low-hanging fruits,
Current Opinion in Systems Biology, 2017, 3:95–102, DOI: 10.1016/j.coisb.2017.04.010

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Weile J, Sun S, Cote AG, Knapp J, Verby M, Mellor JC, Wu Y, Pons C, Wong C, van Lieshout N, Yang F, Tasan M, Tan G, Yang S, Fowler DM, Nussbaum R, Bloom JD, Vidal M, Hill DE, Aloy P, Roth FP,
A framework for exhaustively mapping functional missense variants,
Molecular Systems Biology, 2017, 13(12):957, Pubmed: 29269382, DOI: 10.15252/msb.20177908

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Rizzolo K, Huen J, Kumar A, Phanse S, Vlasblom J, Kakihara Y, Zeineddine HA, Minic Z, Snider J, Wang W, Pons C, Seraphim TV, Boczek EE, Alberti S, Costanzo M, Myers CL, Stagljar I, Boone C, Babu M, Houry WA,
Features of the Chaperone Cellular Network Revealed through Systematic Interaction Mapping,
Cell Reports, 2017, 20(11):2735-2748, Pubmed: 28903051, DOI: http://dx.doi.org/10.1016/j.celrep.2017.08.074

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Duran-Frigola M, Siragusa L, Ruppin E, Barril X, Cruciani G, Aloy P,
Detecting similar binding pockets to enable systems polypharmacology,
PLoS Computational Biology, 2017, 13(6):e1005522, Pubmed: 28662117, DOI: 10.1371/journal.pcbi.1005522

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van Leeuwen J, Pons C, Boone C, Andrews BJ,
Mechanisms of suppression: The wiring of genetic resilience,
BioEssays, 2017, 39(7), Pubmed: 28582599, DOI: 10.1002/bies.201700042

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Mateo L, Guitart-Pla O, Pons C, Duran-Frigola M, Mosca R, Aloy P ,
A PanorOmic view of personal cancer genomes,
Nucleic Acids Research, 2017, 45(W1):W195-W200, Pubmed: 28453651, DOI: 10.1093/nar/gkx311

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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, 2017, 77(2):459-469, Pubmed: 27879272, DOI: 10.1158/0008-5472.CAN-16-0097

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2016

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 R, 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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