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Items: 49

1.

Evolution, dynamics and dysregulation of kinase signalling.

Ochoa D, Bradley D, Beltrao P.

Curr Opin Struct Biol. 2018 Feb;48:133-140. doi: 10.1016/j.sbi.2017.12.008. Epub 2018 Jan 6. Review.

PMID:
29316484
2.

Phenotype inference in an Escherichia coli strain panel.

Galardini M, Koumoutsi A, Herrera-Dominguez L, Cordero Varela JA, Telzerow A, Wagih O, Wartel M, Clermont O, Denamur E, Typas A, Beltrao P.

Elife. 2017 Dec 27;6. pii: e31035. doi: 10.7554/eLife.31035.

3.

Sub-minute Phosphoregulation of Cell Cycle Systems during Plasmodium Gamete Formation.

Invergo BM, Brochet M, Yu L, Choudhary J, Beltrao P, Billker O.

Cell Rep. 2017 Nov 14;21(7):2017-2029. doi: 10.1016/j.celrep.2017.10.071.

4.

Widespread Post-transcriptional Attenuation of Genomic Copy-Number Variation in Cancer.

Gonçalves E, Fragoulis A, Garcia-Alonso L, Cramer T, Saez-Rodriguez J, Beltrao P.

Cell Syst. 2017 Oct 25;5(4):386-398.e4. doi: 10.1016/j.cels.2017.08.013. Epub 2017 Oct 11.

5.

Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells.

Roumeliotis TI, Williams SP, Gonçalves E, Alsinet C, Del Castillo Velasco-Herrera M, Aben N, Ghavidel FZ, Michaut M, Schubert M, Price S, Wright JC, Yu L, Yang M, Dienstmann R, Guinney J, Beltrao P, Brazma A, Pardo M, Stegle O, Adams DJ, Wessels L, Saez-Rodriguez J, McDermott U, Choudhary JS.

Cell Rep. 2017 Aug 29;20(9):2201-2214. doi: 10.1016/j.celrep.2017.08.010.

6.

Identifications of Putative PKA Substrates with Quantitative Phosphoproteomics and Primary-Sequence-Based Scoring.

Imamura H, Wagih O, Niinae T, Sugiyama N, Beltrao P, Ishihama Y.

J Proteome Res. 2017 Apr 7;16(4):1825-1830. doi: 10.1021/acs.jproteome.7b00087. Epub 2017 Mar 15.

PMID:
28287266
7.

Benchmarking substrate-based kinase activity inference using phosphoproteomic data.

Hernandez-Armenta C, Ochoa D, Gonçalves E, Saez-Rodriguez J, Beltrao P.

Bioinformatics. 2017 Jun 15;33(12):1845-1851. doi: 10.1093/bioinformatics/btx082.

8.

Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast.

Gonçalves E, Raguz Nakic Z, Zampieri M, Wagih O, Ochoa D, Sauer U, Beltrao P, Saez-Rodriguez J.

PLoS Comput Biol. 2017 Jan 10;13(1):e1005297. doi: 10.1371/journal.pcbi.1005297. eCollection 2017 Jan.

9.

An atlas of human kinase regulation.

Ochoa D, Jonikas M, Lawrence RT, El Debs B, Selkrig J, Typas A, Villén J, Santos SD, Beltrao P.

Mol Syst Biol. 2016 Dec 1;12(12):888. doi: 10.15252/msb.20167295.

10.

Evolution of protein phosphorylation across 18 fungal species.

Studer RA, Rodriguez-Mias RA, Haas KM, Hsu JI, Viéitez C, Solé C, Swaney DL, Stanford LB, Liachko I, Böttcher R, Dunham MJ, de Nadal E, Posas F, Beltrao P, Villén J.

Science. 2016 Oct 14;354(6309):229-232.

PMID:
27738172
11.

Uncovering Phosphorylation-Based Specificities through Functional Interaction Networks.

Wagih O, Sugiyama N, Ishihama Y, Beltrao P.

Mol Cell Proteomics. 2016 Jan;15(1):236-45. doi: 10.1074/mcp.M115.052357. Epub 2015 Nov 16.

12.

Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes.

Johnson JR, Santos SD, Johnson T, Pieper U, Strumillo M, Wagih O, Sali A, Krogan NJ, Beltrao P.

PLoS Comput Biol. 2015 Aug 27;11(8):e1004362. doi: 10.1371/journal.pcbi.1004362. eCollection 2015 Aug.

13.

Towards the computational design of protein post-translational regulation.

Strumillo M, Beltrao P.

Bioorg Med Chem. 2015 Jun 15;23(12):2877-82. doi: 10.1016/j.bmc.2015.04.056. Epub 2015 Apr 25. Review.

14.

Differential genetic interactions of yeast stress response MAPK pathways.

Martin H, Shales M, Fernandez-Piñar P, Wei P, Molina M, Fiedler D, Shokat KM, Beltrao P, Lim W, Krogan NJ.

Mol Syst Biol. 2015 Apr 17;11(4):800. doi: 10.15252/msb.20145606.

15.

Kinase-two-hybrid: towards the conditional interactome.

Ochoa D, Beltrao P.

Mol Syst Biol. 2015 Mar 26;11(3):798. doi: 10.15252/msb.20156107.

16.

Nanometer scale titanium surface texturing are detected by signaling pathways involving transient FAK and Src activations.

Zambuzzi WF, Bonfante EA, Jimbo R, Hayashi M, Andersson M, Alves G, Takamori ER, Beltrão PJ, Coelho PG, Granjeiro JM.

PLoS One. 2014 Jul 7;9(7):e95662. doi: 10.1371/journal.pone.0095662. eCollection 2014.

17.

Phosphoproteomic analysis reveals regulatory mechanisms at the kidney filtration barrier.

Rinschen MM, Wu X, König T, Pisitkun T, Hagmann H, Pahmeyer C, Lamkemeyer T, Kohli P, Schnell N, Schermer B, Dryer S, Brooks BR, Beltrao P, Krueger M, Brinkkoetter PT, Benzing T.

J Am Soc Nephrol. 2014 Jul;25(7):1509-22. doi: 10.1681/ASN.2013070760. Epub 2014 Feb 7.

18.

Evolution and functional cross-talk of protein post-translational modifications.

Beltrao P, Bork P, Krogan NJ, van Noort V.

Mol Syst Biol. 2013 Dec 22;9:714. doi: 10.1002/msb.201304521. Print 2013. Review.

19.

Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.

Swaney DL, Beltrao P, Starita L, Guo A, Rush J, Fields S, Krogan NJ, Villén J.

Nat Methods. 2013 Jul;10(7):676-82. doi: 10.1038/nmeth.2519. Epub 2013 Jun 9.

20.

Metagenomic analysis of the microbiota from the crop of an invasive snail reveals a rich reservoir of novel genes.

Cardoso AM, Cavalcante JJ, Cantão ME, Thompson CE, Flatschart RB, Glogauer A, Scapin SM, Sade YB, Beltrão PJ, Gerber AL, Martins OB, Garcia ES, de Souza W, Vasconcelos AT.

PLoS One. 2012;7(11):e48505. doi: 10.1371/journal.pone.0048505. Epub 2012 Nov 1.

21.

Comparative interaction networks: bridging genotype to phenotype.

Beltrao P, Ryan C, Krogan NJ.

Adv Exp Med Biol. 2012;751:139-56. doi: 10.1007/978-1-4614-3567-9_7. Review.

22.

Systematic functional prioritization of protein posttranslational modifications.

Beltrao P, Albanèse V, Kenner LR, Swaney DL, Burlingame A, Villén J, Lim WA, Fraser JS, Frydman J, Krogan NJ.

Cell. 2012 Jul 20;150(2):413-25. doi: 10.1016/j.cell.2012.05.036.

23.

Hierarchical modularity and the evolution of genetic interactomes across species.

Ryan CJ, Roguev A, Patrick K, Xu J, Jahari H, Tong Z, Beltrao P, Shales M, Qu H, Collins SR, Kliegman JI, Jiang L, Kuo D, Tosti E, Kim HS, Edelmann W, Keogh MC, Greene D, Tang C, Cunningham P, Shokat KM, Cagney G, Svensson JP, Guthrie C, Espenshade PJ, Ideker T, Krogan NJ.

Mol Cell. 2012 Jun 8;46(5):691-704. doi: 10.1016/j.molcel.2012.05.028.

24.

Secreted human amyloid precursor protein binds semaphorin 3a and prevents semaphorin-induced growth cone collapse.

Magdesian MH, Gralle M, Guerreiro LH, Beltrão PJ, Carvalho MM, Santos LE, de Mello FG, Reis RA, Ferreira ST.

PLoS One. 2011;6(7):e22857. doi: 10.1371/journal.pone.0022857. Epub 2011 Jul 29.

25.

Site-specific acetylation mark on an essential chromatin-remodeling complex promotes resistance to replication stress.

Charles GM, Chen C, Shih SC, Collins SR, Beltrao P, Zhang X, Sharma T, Tan S, Burlingame AL, Krogan NJ, Madhani HD, Narlikar GJ.

Proc Natl Acad Sci U S A. 2011 Jun 28;108(26):10620-5. doi: 10.1073/pnas.1019735108. Epub 2011 Jun 14.

26.

Phenotypic landscape of a bacterial cell.

Nichols RJ, Sen S, Choo YJ, Beltrao P, Zietek M, Chaba R, Lee S, Kazmierczak KM, Lee KJ, Wong A, Shales M, Lovett S, Winkler ME, Krogan NJ, Typas A, Gross CA.

Cell. 2011 Jan 7;144(1):143-56. doi: 10.1016/j.cell.2010.11.052. Epub 2010 Dec 23.

27.

Cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action.

Kapitzky L, Beltrao P, Berens TJ, Gassner N, Zhou C, Wüster A, Wu J, Babu MM, Elledge SJ, Toczyski D, Lokey RS, Krogan NJ.

Mol Syst Biol. 2010 Dec 21;6:451. doi: 10.1038/msb.2010.107.

28.

A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers.

Lefebvre C, Rajbhandari P, Alvarez MJ, Bandaru P, Lim WK, Sato M, Wang K, Sumazin P, Kustagi M, Bisikirska BC, Basso K, Beltrao P, Krogan N, Gautier J, Dalla-Favera R, Califano A.

Mol Syst Biol. 2010 Jun 8;6:377. doi: 10.1038/msb.2010.31.

29.

Quantitative genetic interactions reveal biological modularity.

Beltrao P, Cagney G, Krogan NJ.

Cell. 2010 May 28;141(5):739-45. doi: 10.1016/j.cell.2010.05.019.

30.

ADAN: a database for prediction of protein-protein interaction of modular domains mediated by linear motifs.

Encinar JA, Fernandez-Ballester G, Sánchez IE, Hurtado-Gomez E, Stricher F, Beltrao P, Serrano L.

Bioinformatics. 2009 Sep 15;25(18):2418-24. doi: 10.1093/bioinformatics/btp424. Epub 2009 Jul 14.

PMID:
19602529
31.

Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species.

Beltrao P, Trinidad JC, Fiedler D, Roguev A, Lim WA, Shokat KM, Burlingame AL, Krogan NJ.

PLoS Biol. 2009 Jun 16;7(6):e1000134. doi: 10.1371/journal.pbio.1000134. Epub 2009 Jun 23. Erratum in: PLoS Biol. 2009 Nov;7(11). doi: 10.1371/annotation/66479889-5e57-4213-bf25-c4e8cf3d933b.

32.

Structure-based prediction of the Saccharomyces cerevisiae SH3-ligand interactions.

Fernandez-Ballester G, Beltrao P, Gonzalez JM, Song YH, Wilmanns M, Valencia A, Serrano L.

J Mol Biol. 2009 May 15;388(4):902-16. doi: 10.1016/j.jmb.2009.03.038. Epub 2009 Mar 24.

PMID:
19324052
33.

Microblogging the ISMB: a new approach to conference reporting.

Saunders N, Beltrão P, Jensen L, Jurczak D, Krause R, Kuhn M, Wu S.

PLoS Comput Biol. 2009 Jan;5(1):e1000263. doi: 10.1371/journal.pcbi.1000263. Epub 2009 Jan 30. No abstract available.

34.

Evolvability and hierarchy in rewired bacterial gene networks.

Isalan M, Lemerle C, Michalodimitrakis K, Horn C, Beltrao P, Raineri E, Garriga-Canut M, Serrano L.

Nature. 2008 Apr 17;452(7189):840-5. doi: 10.1038/nature06847.

35.

Genome-wide prediction of SH2 domain targets using structural information and the FoldX algorithm.

Sánchez IE, Beltrao P, Stricher F, Schymkowitz J, Ferkinghoff-Borg J, Rousseau F, Serrano L.

PLoS Comput Biol. 2008 Apr 4;4(4):e1000052. doi: 10.1371/journal.pcbi.1000052.

36.

Analyzing protein interaction networks using structural information.

Kiel C, Beltrao P, Serrano L.

Annu Rev Biochem. 2008;77:415-41. doi: 10.1146/annurev.biochem.77.062706.133317. Review.

PMID:
18304007
37.

Structures in systems biology.

Beltrao P, Kiel C, Serrano L.

Curr Opin Struct Biol. 2007 Jun;17(3):378-84. Epub 2007 Jun 15. Review.

PMID:
17574836
38.

A genome-wide Ras-effector interaction network.

Kiel C, Foglierini M, Kuemmerer N, Beltrao P, Serrano L.

J Mol Biol. 2007 Jul 27;370(5):1020-32. Epub 2007 May 22.

PMID:
17544445
39.

In-hospital and late outcomes after coronary stenting in patient with unstable angina and myelodysplastic syndrome.

Wercules O, Meireles GC, Longhi A, Beltrão P, Pimenta J.

Arq Bras Cardiol. 2006 Nov;87(5):e168-71. English, Portuguese.

40.

Specificity and evolvability in eukaryotic protein interaction networks.

Beltrao P, Serrano L.

PLoS Comput Biol. 2007 Feb 16;3(2):e25. Epub 2006 Dec 28. Erratum in: PLoS Comput Biol. 2007 Mar;3(3):e70.

41.

SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: analysis of simple networks.

Ander M, Beltrao P, Di Ventura B, Ferkinghoff-Borg J, Foglierini M, Kaplan A, Lemerle C, Tomás-Oliveira I, Serrano L.

Syst Biol (Stevenage). 2004 Jun;1(1):129-38.

PMID:
17052123
42.

Comparative genomics and disorder prediction identify biologically relevant SH3 protein interactions.

Beltrao P, Serrano L.

PLoS Comput Biol. 2005 Aug;1(3):e26. Epub 2005 Aug 12.

43.

Comparative evolutionary genomics unveils the molecular mechanism of reassignment of the CTG codon in Candida spp.

Massey SE, Moura G, Beltrão P, Almeida R, Garey JR, Tuite MF, Santos MA.

Genome Res. 2003 Apr;13(4):544-57.

44.

[Treatment of subclavian artery stenosis with stents in patients previously treated with internal mammary left anterior descending artery bypass surgery].

Salvadori Júnior D, Ferreira BM, Gebara OC, Beltrão PE, Mangione JA.

Arq Bras Cardiol. 1997 May;68(5):363-5. Portuguese.

PMID:
9497526
45.

[Single coronary artery and acute myocardial infarction].

Moreira AE, Meireles GC, Silva MV, Peter V, Beltrão PE, Pimenta J.

Arq Bras Cardiol. 1996 Apr;66(4):225-8. Portuguese.

PMID:
8935689
46.

[Anomalous origin of the circumflex artery and coronary spasm].

Moreira AE, Meireles GC, Ladeira RM, Beltrão PE, Pimenta J.

Arq Bras Cardiol. 1995 Apr;64(4):341-3. Portuguese.

PMID:
7495393
47.

[World population at a new turning point].

Beltrao PC.

Rev Cult Vozes. 1981 Jan-Feb;74(1):25-38. Portuguese.

PMID:
12265160
48.

[A historic turning point in world population].

Beltrao PC.

Bol Inf Cent Doc Pesqui. 1978;7(1-2):3-21. Portuguese. No abstract available.

PMID:
12337721
49.

[Evaluation of pulmonary vascular resistance in surgical selection of patients with intracardial arteriovenous shunts].

Konstadinidis T, Beltrão P, Arakaki H, Gembrini P.

Arq Bras Cardiol. 1975 Dec;28(6):651-60. Portuguese. No abstract available.

PMID:
1218013

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