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Items: 1 to 50 of 53

1.

Centrosome amplification arises before neoplasia and increases upon p53 loss in tumorigenesis.

Lopes CAM, Mesquita M, Cunha AI, Cardoso J, Carapeta S, Laranjeira C, Pinto AE, Pereira-Leal JB, Dias-Pereira A, Bettencourt-Dias M, Chaves P.

J Cell Biol. 2018 Jul 2;217(7):2353-2363. doi: 10.1083/jcb.201711191. Epub 2018 May 8.

2.

Microbial Diversity and Toxin Risk in Tropical Freshwater Reservoirs of Cape Verde.

Semedo-Aguiar AP, Pereira-Leal JB, Leite RB.

Toxins (Basel). 2018 May 5;10(5). pii: E186. doi: 10.3390/toxins10050186.

3.

Collective electrical oscillations of a diatom population induced by dark stress.

Rocha PRF, Silva AD, Godinho L, Dane W, Estrela P, Vandamme LKJ, Pereira-Leal JB, de Leeuw DM, Leite RB.

Sci Rep. 2018 Apr 3;8(1):5484. doi: 10.1038/s41598-018-23928-9.

4.

Genetic Competence Drives Genome Diversity in Bacillus subtilis.

Brito PH, Chevreux B, Serra CR, Schyns G, Henriques AO, Pereira-Leal JB.

Genome Biol Evol. 2018 Jan 1;10(1):108-124. doi: 10.1093/gbe/evx270.

5.

Actin stress fiber organization promotes cell stiffening and proliferation of pre-invasive breast cancer cells.

Tavares S, Vieira AF, Taubenberger AV, Araújo M, Martins NP, Brás-Pereira C, Polónia A, Herbig M, Barreto C, Otto O, Cardoso J, Pereira-Leal JB, Guck J, Paredes J, Janody F.

Nat Commun. 2017 May 16;8:15237. doi: 10.1038/ncomms15237.

6.

RAG Recombinase as a Selective Pressure for Genome Evolution.

Passagem-Santos D, Bonnet M, Sobral D, Trancoso I, Silva JG, Barreto VM, Athanasiadis A, Demengeot J, Pereira-Leal JB.

Genome Biol Evol. 2016 Dec 14;8(11):3364-3376.

7.

Rabifier2: an improved bioinformatic classifier of Rab GTPases.

Surkont J, Diekmann Y, Pereira-Leal JB.

Bioinformatics. 2017 Feb 15;33(4):568-570. doi: 10.1093/bioinformatics/btw654.

PMID:
27797763
8.

Does Hypoxic Response Mediate Primary Resistance to Sunitinib in Untreated Locally Advanced Breast Cancer?

Braga S, Cardoso J, Andre S, Brito M, Sanchez P, Orvalho L, Salgado L, Dias S, Pereira-Leal JB, Passos-Coelho JL.

Curr Cancer Drug Targets. 2017;17(1):62-73.

PMID:
27784207
9.

CYR61 and TAZ Upregulation and Focal Epithelial to Mesenchymal Transition May Be Early Predictors of Barrett's Esophagus Malignant Progression.

Cardoso J, Mesquita M, Dias Pereira A, Bettencourt-Dias M, Chaves P, Pereira-Leal JB.

PLoS One. 2016 Sep 1;11(9):e0161967. doi: 10.1371/journal.pone.0161967. eCollection 2016.

10.

Are There Rab GTPases in Archaea?

Surkont J, Pereira-Leal JB.

Mol Biol Evol. 2016 Jul;33(7):1833-42. doi: 10.1093/molbev/msw061. Epub 2016 Mar 31.

11.

Gene Tree Affects Inference of Sites Under Selection by the Branch-Site Test of Positive Selection.

Diekmann Y, Pereira-Leal JB.

Evol Bioinform Online. 2016 Jan 18;11(Suppl 2):11-7. doi: 10.4137/EBO.S30902. eCollection 2015.

12.

Coiled-coil length: Size does matter.

Surkont J, Diekmann Y, Ryder PV, Pereira-Leal JB.

Proteins. 2015 Dec;83(12):2162-9. doi: 10.1002/prot.24932. Epub 2015 Oct 10.

PMID:
26387794
13.

Staphylococcus aureus Survives with a Minimal Peptidoglycan Synthesis Machine but Sacrifices Virulence and Antibiotic Resistance.

Reed P, Atilano ML, Alves R, Hoiczyk E, Sher X, Reichmann NT, Pereira PM, Roemer T, Filipe SR, Pereira-Leal JB, Ligoxygakis P, Pinho MG.

PLoS Pathog. 2015 May 7;11(5):e1004891. doi: 10.1371/journal.ppat.1004891. eCollection 2015 May.

14.

Rethinking the Niche of Upper-Atmosphere Bacteria: Draft Genome Sequences of Bacillus aryabhattai C765 and Bacillus aerophilus C772, Isolated from Rice Fields.

Ramos-Silva P, Brito PH, Serrano M, Henriques AO, Pereira-Leal JB.

Genome Announc. 2015 Apr 9;3(2). pii: e00094-15. doi: 10.1128/genomeA.00094-15.

15.

Bioinformatic approaches to identifying and classifying Rab proteins.

Diekmann Y, Pereira-Leal JB.

Methods Mol Biol. 2015;1298:17-28. doi: 10.1007/978-1-4939-2569-8_2.

PMID:
25800829
16.

Evolutionary patterns in coiled-coils.

Surkont J, Pereira-Leal JB.

Genome Biol Evol. 2015 Jan 10;7(2):545-56. doi: 10.1093/gbe/evv007.

17.

Evolutionary cell biology: two origins, one objective.

Lynch M, Field MC, Goodson HV, Malik HS, Pereira-Leal JB, Roos DS, Turkewitz AP, Sazer S.

Proc Natl Acad Sci U S A. 2014 Dec 2;111(48):16990-4. doi: 10.1073/pnas.1415861111. Epub 2014 Nov 17.

18.

Hope for GWAS: relevant risk genes uncovered from GWAS statistical noise.

Correia C, Diekmann Y, Vicente AM, Pereira-Leal JB.

Int J Mol Sci. 2014 Sep 29;15(10):17601-21. doi: 10.3390/ijms151017601.

19.

A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing.

Pereira-Leal JB, Abreu IA, Alabaça CS, Almeida MH, Almeida P, Almeida T, Amorim MI, Araújo S, Azevedo H, Badia A, Batista D, Bohn A, Capote T, Carrasquinho I, Chaves I, Coelho AC, Costa MM, Costa R, Cravador A, Egas C, Faro C, Fortes AM, Fortunato AS, Gaspar MJ, Gonçalves S, Graça J, Horta M, Inácio V, Leitão JM, Lino-Neto T, Marum L, Matos J, Mendonça D, Miguel A, Miguel CM, Morais-Cecílio L, Neves I, Nóbrega F, Oliveira MM, Oliveira R, Pais MS, Paiva JA, Paulo OS, Pinheiro M, Raimundo JA, Ramalho JC, Ribeiro AI, Ribeiro T, Rocheta M, Rodrigues AI, Rodrigues JC, Saibo NJ, Santo TE, Santos AM, Sá-Pereira P, Sebastiana M, Simões F, Sobral RS, Tavares R, Teixeira R, Varela C, Veloso MM, Ricardo CP.

BMC Genomics. 2014 May 15;15:371. doi: 10.1186/1471-2164-15-371.

20.

Bioinformatics projects supporting life-sciences learning in high schools.

Marques I, Almeida P, Alves R, Dias MJ, Godinho A, Pereira-Leal JB.

PLoS Comput Biol. 2014 Jan;10(1):e1003404. doi: 10.1371/journal.pcbi.1003404. Epub 2014 Jan 23.

21.

inTB - a data integration platform for molecular and clinical epidemiological analysis of tuberculosis.

Soares P, Alves RJ, Abecasis AB, Penha-Gonçalves C, Gomes MG, Pereira-Leal JB.

BMC Bioinformatics. 2013 Aug 30;14:264. doi: 10.1186/1471-2105-14-264.

22.

Aurora at the pole and equator: overlapping functions of Aurora kinases in the mitotic spindle.

Hochegger H, Hégarat N, Pereira-Leal JB.

Open Biol. 2013 Mar 20;3(3):120185. doi: 10.1098/rsob.120185. Review.

23.

Genome of a Gut Strain of Bacillus subtilis.

Schyns G, Serra CR, Lapointe T, Pereira-Leal JB, Potot S, Fickers P, Perkins JB, Wyss M, Henriques AO.

Genome Announc. 2013 Jan;1(1). pii: e00184-12. doi: 10.1128/genomeA.00184-12. Epub 2013 Feb 14.

24.

A genomic signature and the identification of new sporulation genes.

Abecasis AB, Serrano M, Alves R, Quintais L, Pereira-Leal JB, Henriques AO.

J Bacteriol. 2013 May;195(9):2101-15. doi: 10.1128/JB.02110-12. Epub 2013 Feb 8.

25.

Evolution of intracellular compartmentalization.

Diekmann Y, Pereira-Leal JB.

Biochem J. 2013 Jan 15;449(2):319-31. doi: 10.1042/BJ20120957. Review.

PMID:
23240612
26.

Thousands of rab GTPases for the cell biologist.

Diekmann Y, Seixas E, Gouw M, Tavares-Cadete F, Seabra MC, Pereira-Leal JB.

PLoS Comput Biol. 2011 Oct;7(10):e1002217. doi: 10.1371/journal.pcbi.1002217. Epub 2011 Oct 13.

27.

The superfamily of heme-copper oxygen reductases: types and evolutionary considerations.

Sousa FL, Alves RJ, Ribeiro MA, Pereira-Leal JB, Teixeira M, Pereira MM.

Biochim Biophys Acta. 2012 Apr;1817(4):629-37. doi: 10.1016/j.bbabio.2011.09.020. Epub 2011 Oct 6.

28.

Mechanisms underlying the dual-mode regulation of microtubule dynamics by Kip3/kinesin-8.

Su X, Qiu W, Gupta ML Jr, Pereira-Leal JB, Reck-Peterson SL, Pellman D.

Mol Cell. 2011 Sep 2;43(5):751-63. doi: 10.1016/j.molcel.2011.06.027.

29.

Evolution: Tracing the origins of centrioles, cilia, and flagella.

Carvalho-Santos Z, Azimzadeh J, Pereira-Leal JB, Bettencourt-Dias M.

J Cell Biol. 2011 Jul 25;194(2):165-75. doi: 10.1083/jcb.201011152. Review. Erratum in: J Cell Biol. 2011 Oct 17;195(2):341.

30.

A bioinformatics classifier and database for heme-copper oxygen reductases.

Sousa FL, Alves RJ, Pereira-Leal JB, Teixeira M, Pereira MM.

PLoS One. 2011 Apr 29;6(4):e19117. doi: 10.1371/journal.pone.0019117.

31.

Loss of genetic redundancy in reductive genome evolution.

Mendonça AG, Alves RJ, Pereira-Leal JB.

PLoS Comput Biol. 2011 Feb;7(2):e1001082. doi: 10.1371/journal.pcbi.1001082. Epub 2011 Feb 17.

32.

Stepwise evolution of the centriole-assembly pathway.

Carvalho-Santos Z, Machado P, Branco P, Tavares-Cadete F, Rodrigues-Martins A, Pereira-Leal JB, Bettencourt-Dias M.

J Cell Sci. 2010 May 1;123(Pt 9):1414-26. doi: 10.1242/jcs.064931. Epub 2010 Apr 14.

33.

Single choroideremia gene in nonmammalian vertebrates explains early embryonic lethality of the zebrafish model of choroideremia.

Moosajee M, Tulloch M, Baron RA, Gregory-Evans CY, Pereira-Leal JB, Seabra MC.

Invest Ophthalmol Vis Sci. 2009 Jun;50(6):3009-16. doi: 10.1167/iovs.08-2755. Epub 2008 Dec 30.

PMID:
19117920
34.

Evolution and dynamics of protein interactions and networks.

Levy ED, Pereira-Leal JB.

Curr Opin Struct Biol. 2008 Jun;18(3):349-57. doi: 10.1016/j.sbi.2008.03.003. Epub 2008 Apr 28. Review.

PMID:
18448325
35.

The Ypt/Rab family and the evolution of trafficking in fungi.

Pereira-Leal JB.

Traffic. 2008 Jan;9(1):27-38. Epub 2007 Nov 27.

36.
37.

Evolution of protein complexes by duplication of homomeric interactions.

Pereira-Leal JB, Levy ED, Kamp C, Teichmann SA.

Genome Biol. 2007;8(4):R51.

38.

3D complex: a structural classification of protein complexes.

Levy ED, Pereira-Leal JB, Chothia C, Teichmann SA.

PLoS Comput Biol. 2006 Nov 17;2(11):e155. Epub 2006 Oct 5.

39.

The origins and evolution of functional modules: lessons from protein complexes.

Pereira-Leal JB, Levy ED, Teichmann SA.

Philos Trans R Soc Lond B Biol Sci. 2006 Mar 29;361(1467):507-17. Review.

40.

The vertebrate Hef ortholog is a component of the Fanconi anemia tumor-suppressor pathway.

Mosedale G, Niedzwiedz W, Alpi A, Perrina F, Pereira-Leal JB, Johnson M, Langevin F, Pace P, Patel KJ.

Nat Struct Mol Biol. 2005 Sep;12(9):763-71. Epub 2005 Aug 21.

PMID:
16116434
41.

Comparative genomics of trypanosomatid parasitic protozoa.

El-Sayed NM, Myler PJ, Blandin G, Berriman M, Crabtree J, Aggarwal G, Caler E, Renauld H, Worthey EA, Hertz-Fowler C, Ghedin E, Peacock C, Bartholomeu DC, Haas BJ, Tran AN, Wortman JR, Alsmark UC, Angiuoli S, Anupama A, Badger J, Bringaud F, Cadag E, Carlton JM, Cerqueira GC, Creasy T, Delcher AL, Djikeng A, Embley TM, Hauser C, Ivens AC, Kummerfeld SK, Pereira-Leal JB, Nilsson D, Peterson J, Salzberg SL, Shallom J, Silva JC, Sundaram J, Westenberger S, White O, Melville SE, Donelson JE, Andersson B, Stuart KD, Hall N.

Science. 2005 Jul 15;309(5733):404-9.

42.

Novel specificities emerge by stepwise duplication of functional modules.

Pereira-Leal JB, Teichmann SA.

Genome Res. 2005 Apr;15(4):552-9.

43.

An exponential core in the heart of the yeast protein interaction network.

Pereira-Leal JB, Audit B, Peregrin-Alvarez JM, Ouzounis CA.

Mol Biol Evol. 2005 Mar;22(3):421-5. Epub 2004 Oct 20. Erratum in: Mol Biol Evol. 2005 Apr;22(4):1157.

PMID:
15496552
44.

Functional evolution of the yeast protein interaction network.

Kunin V, Pereira-Leal JB, Ouzounis CA.

Mol Biol Evol. 2004 Jul;21(7):1171-6. Epub 2004 Apr 7.

PMID:
15071090
45.

Detection of functional modules from protein interaction networks.

Pereira-Leal JB, Enright AJ, Ouzounis CA.

Proteins. 2004 Jan 1;54(1):49-57.

PMID:
14705023
46.

Genome evolution reveals biochemical networks and functional modules.

von Mering C, Zdobnov EM, Tsoka S, Ciccarelli FD, Pereira-Leal JB, Ouzounis CA, Bork P.

Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15428-33. Epub 2003 Dec 12.

47.

Classification schemes for protein structure and function.

Ouzounis CA, Coulson RM, Enright AJ, Kunin V, Pereira-Leal JB.

Nat Rev Genet. 2003 Jul;4(7):508-19. Review.

PMID:
12838343
48.

Beyond 100 genomes.

Janssen P, Audit B, Cases I, Darzentas N, Goldovsky L, Kunin V, Lopez-Bigas N, Peregrin-Alvarez JM, Pereira-Leal JB, Tsoka S, Ouzounis CA.

Genome Biol. 2003;4(5):402. Epub 2003 Apr 28.

49.

Structural determinants of Rab and Rab Escort Protein interaction: Rab family motifs define a conserved binding surface.

Pereira-Leal JB, Strom M, Godfrey RF, Seabra MC.

Biochem Biophys Res Commun. 2003 Jan 31;301(1):92-7.

PMID:
12535645
50.

Analysis and preparation of stable complexes between Rab GTPases, Rab escort protein, and Rab geranylgeranyl transferase.

Pereira-Leal JB, Gomes AQ, Seabra MC.

Methods Mol Biol. 2002;189:157-65. No abstract available.

PMID:
12094584

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