My Peer-Reviewed Scientific Publications

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de Sousa AGG; Tomasino MP; Duarte P; Fernández-Méndez M; Assmy P; Ribeiro H; Surkont J; Leite RB; Pereira-Leal JB; Torgo L; Magalhães C, 2019. Diversity and Composition of Pelagic Prokaryotic and Protist Communities in a Thin Arctic Sea-Ice Regime.  Microb Ecol.

Hamblin KA; Flick-Smith H; Barnes KB; Pereira-Leal JB; Surkont J; Hampson R; Atkins HS; Harding SV, 2019. Disulfiram, an alcohol dependence therapy, can inhibit the in vitro growth of Francisella tularensis.  Int J Antimicrob Agents.

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, 2018. Centrosome amplification arises before neoplasia and increases upon p53 loss in tumorigenesis.  J Cell Biol 217(7):2353-2363

Semedo-Aguiar AP; Pereira-Leal JB; Leite RB, 2018. Microbial Diversity and Toxin Risk in Tropical Freshwater Reservoirs of Cape Verde.  Toxins (Basel) 10.

Rocha PRF; Silva AD; Godinho L; Dane W; Estrela P; Vandamme LKJ; Pereira-Leal JB; de Leeuw DM; Leite RB, 2018. Collective electrical oscillations of a diatom population induced by dark stress.  Sci Rep 8(1):5484

Brito PH; Chevreux B; Serra CR; Schyns G; Henriques AO; Pereira-Leal JB, 2018. Genetic Competence Drives Genome Diversity in Bacillus subtilis.  Genome Biol Evol 10(1):108-124

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, 2017. Actin stress fiber organization promotes cell stiffening and proliferation of pre-invasive breast cancer cells.  Nat Commun 8:15237

Surkont J; Diekmann Y; Pereira-Leal JB, 2017. Rabifier2: an improved bioinformatic classifier of Rab GTPases.  Bioinformatics 33(4):568-570

Braga S; Cardoso J; Andre S; Brito M; Sanchez P; Orvalho L; Salgado L; Dias S; Pereira-Leal JB; Passos-Coelho JL, 2017. Does Hypoxic Response Mediate Primary Resistance to Sunitinib in Untreated Locally Advanced Breast Cancer?  Curr Cancer Drug Targets 17(1):62-73

Passagem-Santos D; Bonnet M; Sobral D; Trancoso I; Silva JG; Barreto VM; Athanasiadis A; Demengeot J; Pereira-Leal JB, 2016. RAG Recombinase as a Selective Pressure for Genome Evolution.  Genome Biol Evol 8(11):3364-3376

Cardoso J; Mesquita M; Dias Pereira A; Bettencourt-Dias M; Chaves P; Pereira-Leal JB, 2016. CYR61 and TAZ Upregulation and Focal Epithelial to Mesenchymal Transition May Be Early Predictors of Barrett's Esophagus Malignant Progression.  PLoS One 11(9):e0161967

Surkont J; Pereira-Leal JB, 2016. Are There Rab GTPases in Archaea?  Mol Biol Evol 33(7):1833-42

Diekmann Y; Pereira-Leal JB, 2015. Bioinformatic approaches to identifying and classifying Rab proteins.  Methods Mol Biol 1298:17-28

Surkont J; Pereira-Leal JB, 2015. Evolutionary patterns in coiled-coils.  Genome Biol Evol 7(2):545-56

Ramos-Silva P; Brito PH; Serrano M; Henriques AO; Pereira-Leal JB, 2015. Rethinking the Niche of Upper-Atmosphere Bacteria: Draft Genome Sequences of Bacillus aryabhattai C765 and Bacillus aerophilus C772, Isolated from Rice Fields.  Genome Announc 3.

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, 2015. Staphylococcus aureus Survives with a Minimal Peptidoglycan Synthesis Machine but Sacrifices Virulence and Antibiotic Resistance.  PLoS Pathog 11(5):e1004891

Surkont J; Diekmann Y; Ryder PV; Pereira-Leal JB, 2015. Coiled-coil length: Size does matter.  Proteins 83(12):2162-9

Diekmann Y; Pereira-Leal JB, 2015. Gene Tree Affects Inference of Sites Under Selection by the Branch-Site Test of Positive Selection.  Evol Bioinform Online 11(Suppl 2):11-7

Lynch M; Field MC; Goodson HV; Malik HS; Pereira-Leal JB; Roos DS; Turkewitz AP; Sazer S, 2014. Evolutionary cell biology: two origins, one objective.  Proc Natl Acad Sci U S A 111(48):16990-4

Correia C; Diekmann Y; Vicente AM; Pereira-Leal JB, 2014. Hope for GWAS: relevant risk genes uncovered from GWAS statistical noise.  Int J Mol Sci 15(10):17601-21

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, 2014. A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing.  BMC Genomics 15:371

Marques I; Almeida P; Alves R; Dias MJ; Godinho A; Pereira-Leal JB, 2014. Bioinformatics projects supporting life-sciences learning in high schools.  PLoS Comput Biol 10(1):e1003404

Soares P; Alves RJ; Abecasis AB; Penha-Gonçalves C; Gomes MG; Pereira-Leal JB, 2013. inTB - a data integration platform for molecular and clinical epidemiological analysis of tuberculosis.  BMC Bioinformatics 14:264

Lopes JS; Marques I; Soares P; Nebenzahl-Guimaraes H; Costa J; Miranda A; Duarte R; Alves A; Macedo R; Duarte TA; Barbosa T; Oliveira M; Nery JS; Boechat N; Pereira SM; Barreto ML; Pereira-Leal J; Gomes MG; Penha-Goncalves C, 2013. SNP typing reveals similarity in Mycobacterium tuberculosis genetic diversity between Portugal and Northeast Brazil.  Infect Genet Evol 18:238-46

Hochegger H; Hégarat N; Pereira-Leal JB, 2013. Aurora at the pole and equator: overlapping functions of Aurora kinases in the mitotic spindle.  Open Biol 3(3):120185

Schyns G; Serra CR; Lapointe T; Pereira-Leal JB; Potot S; Fickers P; Perkins JB; Wyss M; Henriques AO, 2013. Genome of a Gut Strain of Bacillus subtilis.  Genome Announc 1.

Abecasis AB; Serrano M; Alves R; Quintais L; Pereira-Leal JB; Henriques AO, 2013. A genomic signature and the identification of new sporulation genes.  J Bacteriol 195(9):2101-15

Diekmann Y; Pereira-Leal JB, 2013. Evolution of intracellular compartmentalization.  Biochem J 449(2):319-31

Sousa FL; Alves RJ; Ribeiro MA; Pereira-Leal JB; Teixeira M; Pereira MM, 2012. The superfamily of heme-copper oxygen reductases: types and evolutionary considerations.  Biochim Biophys Acta 1817(4):629-37

Sousa FL; Alves RJ; Pereira-Leal JB; Teixeira M; Pereira MM, 2011. A bioinformatics classifier and database for heme-copper oxygen reductases.  PLoS One 6(4):e19117

Mendonça AG; Alves RJ; Pereira-Leal JB, 2011. Loss of genetic redundancy in reductive genome evolution.  PLoS Comput Biol 7(2):e1001082

Diekmann Y; Seixas E; Gouw M; Tavares-Cadete F; Seabra MC; Pereira-Leal JB, 2011. Thousands of rab GTPases for the cell biologist.  PLoS Comput Biol 7(10):e1002217

Carvalho-Santos Z; Azimzadeh J; Pereira-Leal JB; Bettencourt-Dias M, 2011. Evolution: Tracing the origins of centrioles, cilia, and flagella.  J Cell Biol 194(2):165-75

Su X; Qiu W; Gupta ML Jr; Pereira-Leal JB; Reck-Peterson SL; Pellman D, 2011. Mechanisms underlying the dual-mode regulation of microtubule dynamics by Kip3/kinesin-8.  Mol Cell 43(5):751-63

Carvalho-Santos Z; Machado P; Branco P; Tavares-Cadete F; Rodrigues-Martins A; Pereira-Leal JB; Bettencourt-Dias M, 2010. Stepwise evolution of the centriole-assembly pathway.  J Cell Sci 123(Pt 9):1414-26

Moosajee M; Tulloch M; Baron RA; Gregory-Evans CY; Pereira-Leal JB; Seabra MC, 2009. Single choroideremia gene in nonmammalian vertebrates explains early embryonic lethality of the zebrafish model of choroideremia.  Invest Ophthalmol Vis Sci 50(6):3009-16

Levy ED; Pereira-Leal JB, 2008. Evolution and dynamics of protein interactions and networks.  Curr Opin Struct Biol 18(3):349-57

Pereira-Leal JB, 2008. The Ypt/Rab family and the evolution of trafficking in fungi.  Traffic 9(1):27-38

Rasteiro R; Pereira-Leal JB, 2007. Multiple domain insertions and losses in the evolution of the Rab prenylation complex.  BMC Evol Biol 7:140

Pereira-Leal JB; Levy ED; Kamp C; Teichmann SA, 2007. Evolution of protein complexes by duplication of homomeric interactions.  Genome Biol 8(4):R51

Levy ED; Pereira-Leal JB; Chothia C; Teichmann SA, 2006. 3D complex: a structural classification of protein complexes.  PLoS Comput Biol 2(11):e155

Pereira-Leal JB; Levy ED; Teichmann SA, 2006. The origins and evolution of functional modules: lessons from protein complexes.  Philos Trans R Soc Lond B Biol Sci 361(1467):507-17

Pereira-Leal JB; Audit B; Peregrin-Alvarez JM; Ouzounis CA, 2005. An exponential core in the heart of the yeast protein interaction network.  Mol Biol Evol 22(3):421-5

Vogel C; Teichmann SA; Pereira-Leal J, 2005. The relationship between domain duplication and recombination.  J Mol Biol 346(1):355-65

Pereira-Leal JB; Teichmann SA, 2005. Novel specificities emerge by stepwise duplication of functional modules.  Genome Res 15(4):552-9

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, 2005. Comparative genomics of trypanosomatid parasitic protozoa.  Science 309(5733):404-9

Mosedale G; Niedzwiedz W; Alpi A; Perrina F; Pereira-Leal JB; Johnson M; Langevin F; Pace P; Patel KJ, 2005. The vertebrate Hef ortholog is a component of the Fanconi anemia tumor-suppressor pathway.  Nat Struct Mol Biol 12(9):763-71

Kunin V; Pereira-Leal JB; Ouzounis CA, 2004. Functional evolution of the yeast protein interaction network.  Mol Biol Evol 21(7):1171-6

Pereira-Leal JB; Enright AJ; Ouzounis CA, 2004. Detection of functional modules from protein interaction networks.  Proteins 54(1):49-57

von Mering C; Zdobnov EM; Tsoka S; Ciccarelli FD; Pereira-Leal JB; Ouzounis CA; Bork P, 2003. Genome evolution reveals biochemical networks and functional modules.  Proc Natl Acad Sci U S A 100(26):15428-33

Ouzounis CA; Coulson RM; Enright AJ; Kunin V; Pereira-Leal JB, 2003. Classification schemes for protein structure and function.  Nat Rev Genet 4(7):508-19

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, 2003. Beyond 100 genomes.  Genome Biol 4(5):402

Pereira-Leal JB; Strom M; Godfrey RF; Seabra MC, 2003. Structural determinants of Rab and Rab Escort Protein interaction: Rab family motifs define a conserved binding surface.  Biochem Biophys Res Commun 301(1):92-7

Pereira-Leal JB; Gomes AQ; Seabra MC, 2002. Analysis and preparation of stable complexes between Rab GTPases, Rab escort protein, and Rab geranylgeranyl transferase.  Methods Mol Biol 189:157-65

Pereira-Leal JB; Seabra MC, 2001. Evolution of the Rab family of small GTP-binding proteins.  J Mol Biol 313(4):889-901

Pereira-Leal JB; Hume AN; Seabra MC, 2001. Prenylation of Rab GTPases: molecular mechanisms and involvement in genetic disease.  FEBS Lett 498(2-3):197-200

Pereira-Leal JB; Seabra MC, 2000. The mammalian Rab family of small GTPases: definition of family and subfamily sequence motifs suggests a mechanism for functional specificity in the Ras superfamily.  J Mol Biol 301(4):1077-87

Publication list retrieved from NCBI using ImpactPubs

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