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Items: 1 to 50 of 113

1.

Truncating variant burden in high-functioning autism and pleiotropic effects of LRP1 across psychiatric phenotypes

Torrico B, Shaw AD, Mosca R, Vivó-Luque N, Hervás A, Fernàndez-Castillo N, Aloy P, Bayés M, Fullerton JM, Cormand B, Toma C.

J Psychiatry Neurosci. 2019 Sep 1;44(5):350-359.

2.

In silico Characterization of Human Prion-Like Proteins: Beyond Neurological Diseases.

Iglesias V, Paladin L, Juan-Blanco T, Pallarès I, Aloy P, Tosatto SCE, Ventura S.

Front Physiol. 2019 Mar 27;10:314. doi: 10.3389/fphys.2019.00314. eCollection 2019.

3.

Encircling the regions of the pharmacogenomic landscape that determine drug response.

Fernández-Torras A, Duran-Frigola M, Aloy P.

Genome Med. 2019 Mar 26;11(1):17. doi: 10.1186/s13073-019-0626-x.

4.

Cell-specific proteome analyses of human bone marrow reveal molecular features of age-dependent functional decline.

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.

Nat Commun. 2018 Oct 1;9(1):4004. doi: 10.1038/s41467-018-06353-4.

5.

DynBench3D, a Web-Resource to Dynamically Generate Benchmark Sets of Large Heteromeric Protein Complexes.

Bertoni M, Aloy P.

J Mol Biol. 2018 Oct 19;430(21):4431-4438. doi: 10.1016/j.jmb.2018.09.011. Epub 2018 Sep 22.

PMID:
30274705
6.

Exploring the OncoGenomic Landscape of cancer.

Mateo L, Guitart-Pla O, Duran-Frigola M, Aloy P.

Genome Med. 2018 Aug 3;10(1):61. doi: 10.1186/s13073-018-0571-0.

7.

Systems analysis of intracellular pH vulnerabilities for cancer therapy.

Persi E, Duran-Frigola M, Damaghi M, Roush WR, Aloy P, Cleveland JL, Gillies RJ, Ruppin E.

Nat Commun. 2018 Jul 31;9(1):2997. doi: 10.1038/s41467-018-05261-x.

8.

The transcriptomic and epigenetic map of vascular quiescence in the continuous lung endothelium.

Schlereth K, Weichenhan D, Bauer T, Heumann T, Giannakouri E, Lipka D, Jaeger S, Schlesner M, Aloy P, Eils R, Plass C, Augustin HG.

Elife. 2018 May 11;7. pii: e34423. doi: 10.7554/eLife.34423.

9.

Rationalizing Drug Response in Cancer Cell Lines.

Juan-Blanco T, Duran-Frigola M, Aloy P.

J Mol Biol. 2018 Sep 14;430(18 Pt A):3016-3027. doi: 10.1016/j.jmb.2018.03.021. Epub 2018 Apr 4.

PMID:
29626539
10.

Proteome Data Improves Protein Function Prediction in the Interactome of Helicobacter pylori.

Wuchty S, Müller SA, Caufield JH, Häuser R, Aloy P, Kalkhof S, Uetz P.

Mol Cell Proteomics. 2018 May;17(5):961-973. doi: 10.1074/mcp.RA117.000474. Epub 2018 Feb 1.

11.

A framework for exhaustively mapping functional missense variants.

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.

Mol Syst Biol. 2017 Dec 21;13(12):957. doi: 10.15252/msb.20177908.

12.

Detecting similar binding pockets to enable systems polypharmacology.

Duran-Frigola M, Siragusa L, Ruppin E, Barril X, Cruciani G, Aloy P.

PLoS Comput Biol. 2017 Jun 29;13(6):e1005522. doi: 10.1371/journal.pcbi.1005522. eCollection 2017 Jun.

13.

A PanorOmic view of personal cancer genomes.

Mateo L, Guitart-Pla O, Pons C, Duran-Frigola M, Mosca R, Aloy P.

Nucleic Acids Res. 2017 Jul 3;45(W1):W195-W200. doi: 10.1093/nar/gkx311.

14.

Quantification of Pathway Cross-talk Reveals Novel Synergistic Drug Combinations for Breast Cancer.

Jaeger S, Igea A, Arroyo R, Alcalde V, Canovas B, Orozco M, Nebreda AR, Aloy P.

Cancer Res. 2017 Jan 15;77(2):459-469. doi: 10.1158/0008-5472.CAN-16-0097. Epub 2016 Nov 22.

15.

Exploring genetic suppression interactions on a global scale.

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.

Science. 2016 Nov 4;354(6312). pii: aag0839.

16.

Cancer network activity associated with therapeutic response and synergism.

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.

Genome Med. 2016 Aug 24;8(1):88. doi: 10.1186/s13073-016-0340-x.

17.

An inter-species protein-protein interaction network across vast evolutionary distance.

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.

Mol Syst Biol. 2016 Apr 22;12(4):865. doi: 10.15252/msb.20156484.

18.

Pooled-matrix protein interaction screens using Barcode Fusion Genetics.

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.

Mol Syst Biol. 2016 Apr 22;12(4):863. doi: 10.15252/msb.20156660.

19.

Risk assessment of Soulatrolide and Mammea (A/BA+A/BB) coumarins from Calophyllum brasiliense by a toxicogenomic and toxicological approach.

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.

Food Chem Toxicol. 2016 May;91:117-29. doi: 10.1016/j.fct.2016.03.010. Epub 2016 Mar 16.

PMID:
26995226
20.

Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing.

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.

Cell. 2016 Feb 11;164(4):805-17. doi: 10.1016/j.cell.2016.01.029.

21.

Novel Neuroprotective Multicomponent Therapy for Amyotrophic Lateral Sclerosis Designed by Networked Systems.

Herrando-Grabulosa M, Mulet R, Pujol A, Mas JM, Navarro X, Aloy P, Coma M, Casas C.

PLoS One. 2016 Jan 25;11(1):e0147626. doi: 10.1371/journal.pone.0147626. eCollection 2016.

22.

Conditional Epistatic Interaction Maps Reveal Global Functional Rewiring of Genome Integrity Pathways in Escherichia coli.

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, Yakunin AF, Babu M.

Cell Rep. 2016 Jan 26;14(3):648-661. doi: 10.1016/j.celrep.2015.12.060. Epub 2016 Jan 8.

23.

Residues Coevolution Guides the Systematic Identification of Alternative Functional Conformations in Proteins.

Sfriso P, Duran-Frigola M, Mosca R, Emperador A, Aloy P, Orozco M.

Structure. 2016 Jan 5;24(1):116-126. doi: 10.1016/j.str.2015.10.025. Epub 2015 Dec 10.

24.

Isolation of Human Colon Stem Cells Using Surface Expression of PTK7.

Jung P, Sommer C, Barriga FM, Buczacki SJ, Hernando-Momblona X, Sevillano M, Duran-Frigola M, Aloy P, Selbach M, Winton DJ, Batlle E.

Stem Cell Reports. 2015 Dec 8;5(6):979-987. doi: 10.1016/j.stemcr.2015.10.003. Epub 2015 Nov 5.

25.

Drug sensitivity in cancer cell lines is not tissue-specific.

Jaeger S, Duran-Frigola M, Aloy P.

Mol Cancer. 2015 Feb 15;14:40. doi: 10.1186/s12943-015-0312-6.

26.

Using neighborhood cohesiveness to infer interactions between protein domains.

Segura J, Sorzano CO, Cuenca-Alba J, Aloy P, Carazo JM.

Bioinformatics. 2015 Aug 1;31(15):2545-52. doi: 10.1093/bioinformatics/btv188. Epub 2015 Apr 2.

PMID:
25838464
27.

Network-based proteomic approaches reveal the neurodegenerative, neuroprotective and pain-related mechanisms involved after retrograde axonal damage.

Casas C, Isus L, Herrando-Grabulosa M, Mancuso FM, Borrás E, Sabidó E, Forés J, Aloy P.

Sci Rep. 2015 Mar 18;5:9185. doi: 10.1038/srep09185.

28.

dSysMap: exploring the edgetic role of disease mutations.

Mosca R, Tenorio-Laranga J, Olivella R, Alcalde V, Céol A, Soler-López M, Aloy P.

Nat Methods. 2015 Mar;12(3):167-8. doi: 10.1038/nmeth.3289. No abstract available.

PMID:
25719824
29.

Systematic identification of molecular links between core and candidate genes in breast cancer.

Arroyo R, Suñé G, Zanzoni A, Duran-Frigola M, Alcalde V, Stracker TH, Soler-López M, Aloy P.

J Mol Biol. 2015 Mar 27;427(6 Pt B):1436-1450. doi: 10.1016/j.jmb.2015.01.014. Epub 2015 Jan 29.

PMID:
25640309
30.

Breast cancer genes PSMC3IP and EPSTI1 play a role in apoptosis regulation.

Capdevila-Busquets E, Badiola N, Arroyo R, Alcalde V, Soler-López M, Aloy P.

PLoS One. 2015 Jan 15;10(1):e0115352. doi: 10.1371/journal.pone.0115352. eCollection 2015.

31.

Yeast mitochondrial protein-protein interactions reveal diverse complexes and disease-relevant functional relationships.

Jin K, Musso G, Vlasblom J, Jessulat M, Deineko V, Negroni J, Mosca R, Malty R, Nguyen-Tran DH, Aoki H, Minic Z, Freywald T, Phanse S, Xiang Q, Freywald A, Aloy P, Zhang Z, Babu M.

J Proteome Res. 2015 Feb 6;14(2):1220-37. doi: 10.1021/pr501148q. Epub 2015 Jan 20.

PMID:
25546499
32.

The EHEC-host interactome reveals novel targets for the translocated intimin receptor.

Blasche S, Arens S, Ceol A, Siszler G, Schmidt MA, Häuser R, Schwarz F, Wuchty S, Aloy P, Uetz P, Stradal T, Koegl M.

Sci Rep. 2014 Dec 18;4:7531. doi: 10.1038/srep07531.

33.

A chemo-centric view of human health and disease.

Duran-Frigola M, Rossell D, Aloy P.

Nat Commun. 2014 Dec 1;5:5676. doi: 10.1038/ncomms6676.

34.

A proteome-scale map of the human interactome network.

Rolland T, Taşan M, Charloteaux B, Pevzner SJ, Zhong Q, Sahni N, Yi S, Lemmens I, Fontanillo C, Mosca R, Kamburov A, Ghiassian SD, Yang X, Ghamsari L, Balcha D, Begg BE, Braun P, Brehme M, Broly MP, Carvunis AR, Convery-Zupan D, Corominas R, Coulombe-Huntington J, Dann E, Dreze M, Dricot A, Fan C, Franzosa E, Gebreab F, Gutierrez BJ, Hardy MF, Jin M, Kang S, Kiros R, Lin GN, Luck K, MacWilliams A, Menche J, Murray RR, Palagi A, Poulin MM, Rambout X, Rasla J, Reichert P, Romero V, Ruyssinck E, Sahalie JM, Scholz A, Shah AA, Sharma A, Shen Y, Spirohn K, Tam S, Tejeda AO, Trigg SA, Twizere JC, Vega K, Walsh J, Cusick ME, Xia Y, Barabási AL, Iakoucheva LM, Aloy P, De Las Rivas J, Tavernier J, Calderwood MA, Hill DE, Hao T, Roth FP, Vidal M.

Cell. 2014 Nov 20;159(5):1212-1226. doi: 10.1016/j.cell.2014.10.050.

35.

IntSide: a web server for the chemical and biological examination of drug side effects.

Juan-Blanco T, Duran-Frigola M, Aloy P.

Bioinformatics. 2015 Feb 15;31(4):612-3. doi: 10.1093/bioinformatics/btu688. Epub 2014 Oct 17.

PMID:
25380960
36.

Assessing the applicability of template-based protein docking in the twilight zone.

Negroni J, Mosca R, Aloy P.

Structure. 2014 Sep 2;22(9):1356-1362. doi: 10.1016/j.str.2014.07.009. Epub 2014 Aug 21.

37.

Increasing the precision of orthology-based complex prediction through network alignment.

Pache RA, Aloy P.

PeerJ. 2014 May 29;2:e413. doi: 10.7717/peerj.413. eCollection 2014.

38.

A second-generation protein-protein interaction network of Helicobacter pylori.

Häuser R, Ceol A, Rajagopala SV, Mosca R, Siszler G, Wermke N, Sikorski P, Schwarz F, Schick M, Wuchty S, Aloy P, Uetz P.

Mol Cell Proteomics. 2014 May;13(5):1318-29. doi: 10.1074/mcp.O113.033571. Epub 2014 Mar 13.

39.

The binary protein-protein interaction landscape of Escherichia coli.

Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Häuser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P.

Nat Biotechnol. 2014 Mar;32(3):285-290. doi: 10.1038/nbt.2831. Epub 2014 Feb 23.

40.

Charting the molecular links between driver and susceptibility genes in colorectal cancer.

Arroyo R, Duran-Frigola M, Berenguer C, Soler-López M, Aloy P.

Biochem Biophys Res Commun. 2014 Mar 21;445(4):734-8. doi: 10.1016/j.bbrc.2013.12.012. Epub 2014 Jan 9.

PMID:
24412244
41.

3did: a catalog of domain-based interactions of known three-dimensional structure.

Mosca R, Céol A, Stein A, Olivella R, Aloy P.

Nucleic Acids Res. 2014 Jan;42(Database issue):D374-9. doi: 10.1093/nar/gkt887. Epub 2013 Sep 29.

42.

Towards a detailed atlas of protein-protein interactions.

Mosca R, Pons T, Céol A, Valencia A, Aloy P.

Curr Opin Struct Biol. 2013 Dec;23(6):929-40. doi: 10.1016/j.sbi.2013.07.005. Epub 2013 Jul 26. Review.

PMID:
23896349
43.

Structural systems pharmacology: the role of 3D structures in next-generation drug development.

Duran-Frigola M, Mosca R, Aloy P.

Chem Biol. 2013 May 23;20(5):674-84. doi: 10.1016/j.chembiol.2013.03.004. Review.

44.

Functional and structural analysis of C-terminal BRCA1 missense variants.

Quiles F, Fernández-Rodríguez J, Mosca R, Feliubadaló L, Tornero E, Brunet J, Blanco I, Capellá G, Pujana MÀ, Aloy P, Monteiro A, Lázaro C.

PLoS One. 2013 Apr 17;8(4):e61302. doi: 10.1371/journal.pone.0061302. Print 2013.

45.

Analysis of chemical and biological features yields mechanistic insights into drug side effects.

Duran-Frigola M, Aloy P.

Chem Biol. 2013 Apr 18;20(4):594-603. doi: 10.1016/j.chembiol.2013.03.017.

46.

The proton-pump inhibitor lansoprazole enhances amyloid beta production.

Badiola N, Alcalde V, Pujol A, Münter LM, Multhaup G, Lleó A, Coma M, Soler-López M, Aloy P.

PLoS One. 2013;8(3):e58837. doi: 10.1371/journal.pone.0058837. Epub 2013 Mar 8.

47.

Interactome3D: adding structural details to protein networks.

Mosca R, Céol A, Aloy P.

Nat Methods. 2013 Jan;10(1):47-53. doi: 10.1038/nmeth.2289. Epub 2012 Dec 16.

PMID:
23399932
48.

NetAligner--a network alignment server to compare complexes, pathways and whole interactomes.

Pache RA, Céol A, Aloy P.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W157-61. doi: 10.1093/nar/gks446. Epub 2012 May 22.

49.

From protein interaction networks to novel therapeutic strategies.

Jaeger S, Aloy P.

IUBMB Life. 2012 Jun;64(6):529-37. doi: 10.1002/iub.1040. Epub 2012 May 9. Review.

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