Publications using IGC Facilities

Animal House - Flies

  1. Koyama, Takashi and Mirth, Christen K.. Growth-Blocking Peptides As Nutrition-Sensitive Signals for Insulin Secretion and Body Size Regulation. PLOS Biology. 2016;14(2):e1002392. [doi]
  2. Mendes, C. C. and Mirth, C. K.. Stage-Specific Plasticity in Ovary Size Is Regulated by Insulin/Insulin-Like Growth Factor and Ecdysone Signaling in Drosophila. Genetics. 2016;202(2):703–719. [doi]
  3. Gutzwiller, F.; Carmo, C. R.; Miller, D. E.; Rice, D. W.; Newton, I. L. G.; Hawley, R. S.; Teixeira, L. and Bergman, C. M.. Dynamics of Wolbachia pipientis Gene Expression Across the Drosophila melanogaster Life Cycle. G3&\#58; Genes|Genomes|Genetics. 2015;5(12):2843–2856. [doi]
  4. Hatem, Nicole E.; Wang, Zhou; Nave, Keelin B.; Koyama, Takashi and Suzuki, Yuichiro. The role of juvenile hormone and insulin/TOR signaling in the growth of Manduca sexta. BMC Biology. 2015;13(1):44. [doi]
  5. Gutzwiller, F.; Carmo, C. R.; Miller, D. E.; Rice, D. W.; Newton, I. L. G.; Hawley, R. S.; Teixeira, L. and Bergman, C. M.. Dynamics of Wolbachia pipientis Gene Expression Across the Drosophila melanogaster Life Cycle. G3&\#58; Genes|Genomes|Genetics. 2015;5(12):2843–2856. [doi]
  6. Faria, Vítor G; Martins, Nelson E; Paulo, Tânia; Teixeira, Luís and Sucena, Élio. Evolution of Drosophila resistance against different pathogens and infection routes entails no detectable maintenance costs. Evolution; international journal of organic evolution. 2015;69(11):2799–809. [doi]
  7. Matavelli, Cristiane; Carvalho, Maria João A.; Martins, Nelson E. and Mirth, Christen K.. Differences in larval nutritional requirements and female oviposition preference reflect the order of fruit colonization of Zaprionus indianus and Drosophila simulans. Journal of Insect Physiology. 2015;82:66–74. [doi]
  8. Matavelli, Cristiane; Carvalho, Maria João A.; Martins, Nelson E. and Mirth, Christen K.. Differences in larval nutritional requirements and female oviposition preference reflect the order of fruit colonization of Zaprionus indianus and Drosophila simulans. Journal of Insect Physiology. 2015;82:66–74. [doi]
  9. Lopes, Carla A.M.; Jana, Swadhin Chandra; Cunha-Ferreira, Inês; Zitouni, Sihem; Bento, Inês; Duarte, Paulo; Gilberto, Samuel; Freixo, Francisco; Guerrero, Adán; Francia, Maria; Lince-Faria, Mariana and Carneiro, Jorge. PLK4 trans-Autoactivation Controls Centriole Biogenesis in Space. Developmental Cell. 2015;35(2):222–235. [doi]
  10. Rodrigues, Marisa A.; Martins, Nelson E.; Balancé, Lara F.; Broom, Lara N.; Dias, António J.S.; Fernandes, Ana Sofia D.; Rodrigues, Fábio; Sucena, Élio and Mirth, Christen K.. Drosophila melanogaster larvae make nutritional choices that minimize developmental time. Journal of Insect Physiology. 2015;81:69–80. [doi]
  11. Mirkovic, Mihailo; Hutter, Lukas H; Novák, Béla and Oliveira, Raquel A. Premature Sister Chromatid Separation Is Poorly Detected by the Spindle Assembly Checkpoint as a Result of System-Level Feedback. Cell reports. 2015;13(3):470–8. [doi]
  12. Chen, Jieyan V; Kao, Ling-Rong; Jana, Swadhin C; Sivan-Loukianova, Elena; Mendonça, Susana; Cabrera, Oscar A; Singh, Priyanka; Cabernard, Clemens; Eberl, Daniel F; Bettencourt-Dias, Monica and Megraw, Timothy L. Rootletin organizes the ciliary rootlet to achieve neuron sensory function in Drosophila. The Journal of cell biology. 2015;211(2):435–53. [doi]
  13. Herboso, Leire; Oliveira, Marisa M.; Talamillo, Ana; Pérez, Coralia; González, Monika; Martín, David; Sutherland, James D.; Shingleton, Alexander W.; Mirth, Christen K. and Barrio, Rosa. Ecdysone promotes growth of imaginal discs through the regulation of Thor in D. melanogaster. Scientific Reports. 2015;5:12383. [doi]
  14. Martinho, Rui G. and Guilgur, Leonardo G.. How gene expression in fast-proliferating cells keeps pace. BioEssays. 2015;37(5):514–524. [doi]
  15. Bras-Pereira, C.; Casares, F. and Janody, F.. The retinal determination gene dachshund restricts cell proliferation by limiting the activity of the Homothorax-Yorkie complex. Development. 2015;142(8):1470–1479. [doi]
  16. Bras-Pereira, C.; Casares, F. and Janody, F.. The retinal determination gene dachshund restricts cell proliferation by limiting the activity of the Homothorax-Yorkie complex. Development. 2015;142(8):1470–1479. [doi]
  17. Gaspar, Pedro; Holder, Maxine V.; Aerne, Birgit L.; Janody, Florence and Tapon, Nicolas. Zyxin Antagonizes the FERM Protein Expanded to Couple F-Actin and Yorkie-Dependent Organ Growth. Current Biology. 2015;25(6):679–689. [doi]
  18. Leitão, Alexandre B. Drosophila sessile hemocyte clusters are true hematopoietic tissues that regulate larval blood cell differentiation. eLife. 2015;4. [doi]
  19. Chrostek, Ewa and Teixeira, Luis. Mutualism Breakdown by Amplification of Wolbachia Genes. PLOS Biology. 2015;13(2):e1002065. [doi]
  20. Souto-Maior, Caetano; Lopes, Joao S.; Gjini, Erida; Struchiner, Claudio J. and Teixeira, Luis. Heterogeneity in symbiotic effects facilitates Wolbachia establishment in insect populations. Theoretical Ecology. Springer Netherlands; 2015;8(1):53–65. [doi]
  21. Ferreira, Álvaro Gil; Naylor, Huw; Esteves, Sara Santana; Pais, Inês Silva; Martins, Nelson Eduardo and Teixeira, Luis. The Toll-Dorsal Pathway Is Required for Resistance to Viral Oral Infection in Drosophila. PLoS Pathogens. 2014;10(12):e1004507. [doi]
  22. Koyama, Takashi; Rodrigues, Marisa A; Athanasiadis, Alekos; Shingleton, Alexander W and Mirth, Christen K. Nutritional control of body size through FoxO-Ultraspiracle mediated ecdysone biosynthesis. eLife. 2014;3. [doi]
  23. Oliveira, Raquel A.; Kotadia, Shaila; Tavares, Alexandra; Mirkovic, Mihailo; Bowlin, Katherine; Eichinger, Christian S.; Nasmyth, Kim and Sullivan, William. Centromere-Independent Accumulation of Cohesin at Ectopic Heterochromatin Sites Induces Chromosome Stretching during Anaphase. PLoS Biology. 2014;12(10):e1001962. [doi]
  24. Ferreira, Tânia and Prudêncio, Pedro. Drosophila protein kinase N (Pkn) is a negative regulator of actin–myosin activity during oogenesis. Developmental Biology. 2014;394(2):277–291. [doi]
  25. Chrostek, Ewa; Marialva, Marta S. P.; Yamada, Ryuichi; O'Neill, Scott L. and Teixeira, Luis. High Anti-Viral Protection without Immune Upregulation after Interspecies Wolbachia Transfer. PLoS ONE. 2014;9(6):e99025. [doi]
  26. Zitouni, Sihem; Nabais, Catarina; Jana, Swadhin Chandra and Guerrero, Adán. Polo-like kinases: structural variations lead to multiple functions. Nature Reviews Molecular Cell Biology. 2014;15(7):433–452. [doi]
  27. Cheng, CeCe; Ko, Amy; Chaieb, Leila; Koyama, Takashi; Sarwar, Prioty; Mirth, Christen K.; Smith, Wendy A. and Suzuki, Yuichiro. The POU Factor Ventral Veins Lacking/Drifter Directs the Timing of Metamorphosis through Ecdysteroid and Juvenile Hormone Signaling. PLoS Genetics. 2014;10(6):e1004425. [doi]
  28. Oliveira, Marisa M.; Shingleton, Alexander W. and Mirth, Christen K.. Coordination of Wing and Whole-Body Development at Developmental Milestones Ensures Robustness against Environmental and Physiological Perturbations. PLoS Genetics. 2014;10(6):e1004408. [doi]
  29. Mirth, C. K.; Tang, H. Y.; Makohon-Moore, S. C.; Salhadar, S.; Gokhale, R. H.; Warner, R. D.; Koyama, T.; Riddiford, L. M. and Shingleton, A. W.. Juvenile hormone regulates body size and perturbs insulin signaling in Drosophila. Proceedings of the National Academy of Sciences. 2014;111(19):7018–7023. [doi]
  30. Amândio, Ana Rita; Gaspar, Pedro; Whited, Jessica L. and Janody, Florence. Subunits of the Drosophila Actin-Capping Protein Heterodimer Regulate Each Other at Multiple Levels. PLoS ONE. 2014;9(5):e96326. [doi]
  31. Martins, N. E.; Faria, V. G.; Nolte, V.; Schlotterer, C.; Teixeira, L.; Sucena, E. and Magalhaes, S.. Host adaptation to viruses relies on few genes with different cross-resistance properties. Proceedings of the National Academy of Sciences. 2014;111(16):5938–5943. [doi]
  32. Pereira, Patrícia A.; Navarro-Costa, Paulo and Martinho, Rui Gonçalo. Evolutionarily conserved mechanisms of male germline development in flowering plants and animals: Figure 1. Biochemical Society Transactions. 2014;42(2):377–382. [doi]
  33. Martins, N. E.; Faria, V. G.; Nolte, V.; Schlotterer, C.; Teixeira, L.; Sucena, E. and Magalhaes, S.. Host adaptation to viruses relies on few genes with different cross-resistance properties. Proceedings of the National Academy of Sciences. 2014;111(16):5938–5943. [doi]
  34. Fernández, B G; Jezowska, B and Janody, F. Drosophila actin-Capping Protein limits JNK activation by the Src proto-oncogene. Oncogene. 2014;33(16):2027–2039. [doi]
  35. Guilgur, Leonardo Gastón; Prudêncio, Pedro; Sobral, Daniel; Liszekova, Denisa; Rosa, André and Martinho, Rui Goncalo. Requirement for highly efficient pre-mRNA splicing during Drosophila early embryonic development. eLife. 2014;3:e02181. [doi]
  36. Fauré, Adrien; Vreede, Barbara M. I.; Sucena, Élio and Chaouiya, Claudine. A Discrete Model of Drosophila Eggshell Patterning Reveals Cell-Autonomous and Juxtacrine Effects. PLoS Computational Biology. 2014;10(3):e1003527. [doi]
  37. Jana, Swadhin Chandra and Marteil, Gaëlle. Mapping molecules to structure: unveiling secrets of centriole and cilia assembly with near-atomic resolution. Current Opinion in Cell Biology. 2014;26:96–106. [doi]
  38. Chrostek, Ewa; Marialva, Marta S. P.; Esteves, Sara S.; Weinert, Lucy A.; Martinez, Julien; Jiggins, Francis M. and Teixeira, Luis. Wolbachia Variants Induce Differential Protection to Viruses in Drosophila melanogaster: A Phenotypic and Phylogenomic Analysis. PLoS Genetics. 2013;9(12):e1003896. [doi]
  39. Cunha-Ferreira, Inês; Bento, Inês; Pimenta-Marques, Ana; Jana, Swadhin Chandra; Lince-Faria, Mariana; Duarte, Paulo; Borrego-Pinto, Joana; Gilberto, Samuel; Amado, Tiago; Brito, Daniela; Rodrigues-Martins, Ana; Debski, Janusz and Dzhindzhev, Nikola. Regulation of Autophosphorylation Controls PLK4 Self-Destruction and Centriole Number. Current Biology. 2013;23(22):2245–2254. [doi]
  40. Martins, Nelson E.; Faria, Vitor G.; Teixeira, Luis and Magalhães, Sara. Host Adaptation Is Contingent upon the Infection Route Taken by Pathogens. PLoS Pathogens. 2013;9(9):e1003601. [doi]
  41. Faria, Vítor G and Sucena, Elio. Wolbachia in the Malpighian tubules: evolutionary dead-end or adaptation? Journal of experimental zoology. Part B, Molecular and developmental evolution. 2013;320(4):195–9. [doi]
  42. Marques-Pita, Manuel and Rocha, Luis M.. Canalization and Control in Automata Networks: Body Segmentation in Drosophila melanogaster. PLoS ONE. 2013;8(3):e55946. [doi]
  43. Vreede, Barbara MI; Lynch, Jeremy A and Roth, Siegfried. Co-option of a coordinate system defined by the EGFr and Dpp pathways in the evolution of a morphological novelty. EvoDevo. 2013;4(1):7. [doi]
  44. Koyama, Takashi; Mendes, Cláudia C. and Mirth, Christen K.. Mechanisms regulating nutrition-dependent developmental plasticity through organ-specific effects in insects. Frontiers in Physiology. 2013;4. [doi]
  45. Navarro-Costa, Paulo. Sex, rebellion and decadence: The scandalous evolutionary history of the human Y chromosome. Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease. 2012;1822(12):1851–1863. [doi]
  46. Jana, Swadhin Chandra and Bazan, J. Fernando. Polo Boxes Come out of the Crypt: A New View of PLK Function and Evolution. Structure. 2012;20(11):1801–1804. [doi]
  47. Teixeira, L.. Whole-genome expression profile analysis of Drosophila melanogaster immune responses. Briefings in Functional Genomics. 2012;11(5):375–386. [doi]
  48. Alves, Ema; Henriques, Bárbara J.; Rodrigues, João V.; Prudêncio, Pedro; Rocha, Hugo; Vilarinho, Laura and Martinho, Rui G.. Mutations at the flavin binding site of ETF:QO yield a MADD-like severe phenotype in Drosophila. Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease. 2012;1822(8):1284–1292. [doi]
  49. Florindo, C.; Perdigao, J.; Fesquet, D.; Schiebel, E.; Pines, J. and Tavares, A. A.. Human Mob1 proteins are required for cytokinesis by controlling microtubule stability. Journal of Cell Science. 2012;125(13):3085–3090. [doi]
  50. Guilgur, L. G.; Prudencio, P.; Ferreira, T.; Pimenta-Marques, A. R. and Martinho, R. G.. Drosophila aPKC is required for mitotic spindle orientation during symmetric division of epithelial cells. Development. 2012;139(3):503–513. [doi]
  51. Jana, Swadhin C and Machado, Pedro. A structural road map to unveil basal body composition and assembly. The EMBO Journal. 2012;31(3):519–521. [doi]
  52. Tavares, A.; Goncalves, J.; Florindo, C.; Tavares, A. A. and Soares, H.. Mob1: defining cell polarity for proper cell division. Journal of Cell Science. 2012;125(2):516–527. [doi]

Animal House - Mouse

  1. Casaca, A.; Novoa, A. and Mallo, M.. Hoxb6 can interfere with somitogenesis in the posterior embryo through a mechanism independent of its rib-promoting activity. Development. 2016;143(3):437–448. [doi]
  2. Azevedo, M.; Sousa, A.; Moura de Sousa, J.; Thompson, J. A.; Proença, J. T. and Gordo, I.. Trade-Offs of Escherichia coli Adaptation to an Intracellular Lifestyle in Macrophages. PLOS ONE. 2016;11(1):e0146123. [doi]
  3. Barroso-Batista, João; Demengeot, Jocelyne and Gordo, Isabel. Adaptive immunity increases the pace and predictability of evolutionary change in commensal gut bacteria. Nature Communications. 2015;6:8945. [doi]
  4. Monteiro, Marta; Agua-Doce, Ana; Almeida, Catarina F.; Fonseca-Pereira, Diogo; Veiga-Fernandes, Henrique and Graca, Luis. IL-9 Expression by Invariant NKT Cells Is Not Imprinted during Thymic Development. The Journal of Immunology. 2015;195(7):3463–3471. [doi]
  5. Zeng, Wenwen; Pirzgalska, Roksana M.; Pereira, Mafalda M.A.; Kubasova, Nadiya; Barateiro, Andreia; Seixas, Elsa; Lu, Yi-Hsueh; Kozlova, Albina; Voss, Henning; Martins, Gabriel G.; Friedman, Jeffrey M. and Domingos, Ana I.. Sympathetic Neuro-adipose Connections Mediate Leptin-Driven Lipolysis. Cell. 2015;163(1):84–94. [doi]
  6. Zeng, Wenwen; Pirzgalska, Roksana M.; Pereira, Mafalda M.A.; Kubasova, Nadiya; Barateiro, Andreia; Seixas, Elsa; Lu, Yi-Hsueh; Kozlova, Albina; Voss, Henning; Martins, Gabriel G.; Friedman, Jeffrey M. and Domingos, Ana I.. Sympathetic Neuro-adipose Connections Mediate Leptin-Driven Lipolysis. Cell. 2015;163(1):84–94. [doi]
  7. de Paiva e Almeida, Sílvia Cristina; de Oliveira, Vivian Leite and Parkhouse, Robert Michael Evans. Impact on antibody responses of B-cell-restricted transgenic expression of a viral gene inhibiting activation of NF-$\kappa$B and NFAT. Archives of Virology. 2015;160(6):1477–1488. [doi]
  8. Thompson, Jessica Ann; Oliveira, Rita Almeida; Djukovic, Ana; Ubeda, Carles and Xavier, Karina Bivar. Manipulation of the Quorum Sensing Signal AI-2 Affects the Antibiotic-Treated Gut Microbiota. Cell Reports. 2015;10(11):1861–1871. [doi]
  9. Alves-Pereira, Clara F.; de Freitas, Raquel; Lopes, Telma; Gardner, Rui; Marta, Filipa; Vieira, Paulo and Barreto, Vasco M.. Independent recruitment of Igh alleles in V(D)J recombination. Nature Communications. 2014;5:5623. [doi]
  10. Yilmaz, Bahtiyar; Portugal, Silvia; Tran, Tuan M.; Gozzelino, Raffaella; Ramos, Susana; Gomes, Joana; Regalado, Ana; Cowan, Peter J.; D'Apice, Anthony J.F.; Chong, Anita S.; Doumbo, Ogobara K.; Traore, Boubacar; Crompton, Peter D.; Silveira, Henrique and Soares, Miguel P.. Gut Microbiota Elicits a Protective Immune Response against Malaria Transmission. Cell. 2014;159(6):1277–1289. [doi]
  11. Jurberg, Arnon Dias; Aires, Rita; Nóvoa, Ana and Rowland, Jennifer Elizabeth. Compartment-dependent activities of Wnt3a/$\beta$-catenin signaling during vertebrate axial extension. Developmental Biology. 2014;394(2):253–263. [doi]
  12. Jeney, Viktória; Ramos, Susana; Bergman, Marie-Louise; Bechmann, Ingo; Tischer, Jasmin; Ferreira, Ana; Oliveira-Marques, Virginia; Janse, Chris J.; Rebelo, Sofia; Cardoso, Silvia and Soares, Miguel P.. Control of Disease Tolerance to Malaria by Nitric Oxide and Carbon Monoxide. Cell Reports. 2014;8(1):126–136. [doi]
  13. Barroso-Batista, João; Sousa, Ana; Lourenço, Marta; Bergman, Marie-Louise; Sobral, Daniel; Demengeot, Jocelyne; Xavier, Karina B. and Gordo, Isabel. The First Steps of Adaptation of Escherichia coli to the Gut Are Dominated by Soft Sweeps. PLoS Genetics. 2014;10(3):e1004182. [doi]
  14. Barroso-Batista, João; Sousa, Ana; Lourenço, Marta; Bergman, Marie-Louise; Sobral, Daniel; Demengeot, Jocelyne; Xavier, Karina B. and Gordo, Isabel. The First Steps of Adaptation of Escherichia coli to the Gut Are Dominated by Soft Sweeps. PLoS Genetics. 2014;10(3):e1004182. [doi]
  15. Miskinyte, Migla; Sousa, Ana; Ramiro, Ricardo S.; de Sousa, Jorge A. Moura; Kotlinowski, Jerzy; Caramalho, Iris; Magalhães, Sara; Soares, Miguel P. and Gordo, Isabel. The Genetic Basis of Escherichia coli Pathoadaptation to Macrophages. PLoS Pathogens. 2013;9(12):e1003802. [doi]
  16. Goncalves, L. A.; Rodrigues-Duarte, L.; Rodo, J.; Vieira de Moraes, L.; Marques, I. and Penha-Goncalves, C.. TREM2 governs Kupffer cell activation and explains belr1 genetic resistance to malaria liver stage infection. Proceedings of the National Academy of Sciences. 2013;110(48):19531–19536. [doi]
  17. Medeiros, Márcia M.; da Silva, Henrique B.; Reis, Aramys S.; Barboza, Renato; Thompson, Joanne; Lima, Maria Regina D'Império; Marinho, Cláudio R. F. and Tadokoro, Carlos E.. Liver Accumulation of Plasmodium chabaudi-Infected Red Blood Cells and Modulation of Regulatory T Cell and Dendritic Cell Responses. PLoS ONE. 2013;8(11):e81409. [doi]
  18. Lino, A. C.; Mohr, E. and Demengeot, J.. Naturally secreted immunoglobulins limit B1 and MZ B-cell numbers through a microbiota-independent mechanism. Blood. 2013;122(2):209–218. [doi]
  19. Silva-Gomes, S.; Appelberg, R.; Larsen, R.; Soares, M. P. and Gomes, M. S.. Heme Catabolism by Heme Oxygenase-1 Confers Host Resistance to Mycobacterium Infection. Infection and Immunity. 2013;81(7):2536–2545. [doi]
  20. Jurberg, Arnon Dias; Aires, Rita; Varela-Lasheras, Irma and Nóvoa, Ana. Switching Axial Progenitors from Producing Trunk to Tail Tissues in Vertebrate Embryos. Developmental Cell. 2013;25(5):451–462. [doi]
  21. Ball, E. A.; Sambo, M. R.; Martins, M.; Trovoada, M. J.; Benchimol, C.; Costa, J.; Antunes Goncalves, L.; Coutinho, A. and Penha-Goncalves, C.. IFNAR1 Controls Progression to Cerebral Malaria in Children and CD8+ T Cell Brain Pathology in Plasmodium berghei-Infected Mice. The Journal of Immunology. 2013;190(10):5118–5127. [doi]
  22. Paiva, R. S.; Lino, A. C.; Bergman, M.-L.; Caramalho, I.; Sousa, A. E.; Zelenay, S. and Demengeot, J.. Recent thymic emigrants are the preferential precursors of regulatory T cells differentiated in the periphery. Proceedings of the National Academy of Sciences. 2013;110(16):6494–6499. [doi]
  23. Cortesao, Catarina S; Freitas, Raquel F and Barreto, Vasco M. Activation-Induced Cytidine Deaminase Does Not Impact on Murine Meiotic Recombination. G3 (Bethesda, Md.). 2013. [doi]
  24. Monteiro, M.; Almeida, C. F.; Agua-Doce, A. and Graca, L.. Induced IL-17-Producing Invariant NKT Cells Require Activation in Presence of TGF-  and IL-1. The Journal of Immunology. 2013;190(2):805–811. [doi]
  25. de Moraes, Luciana Vieira; Tadokoro, Carlos Eduardo; Gómez-Conde, Iván and Olivieri, David N.. Intravital Placenta Imaging Reveals Microcirculatory Dynamics Impact on Sequestration and Phagocytosis of Plasmodium-Infected Erythrocytes. PLoS Pathogens. 2013;9(1):e1003154. [doi]
  26. Trancoso, Inês; Bonnet, Marie; Gardner, Rui; Carneiro, Jorge; Barreto, Vasco M.; Demengeot, Jocelyne and Sarmento, Leonor M.. A Novel Quantitative Fluorescent Reporter Assay for RAG Targets and RAG Activity. Frontiers in Immunology. 2013;4. [doi]
  27. Gozzelino, Raffaella; Andrade, Bruno Bezerril; Larsen, Rasmus; Luz, Nivea F.; Vanoaica, Liviu; Seixas, Elsa; Coutinho, Antonio; Cardoso, Sílvia; Rebelo, Sofia; Poli, Maura; Barral-Netto, Manoel; Darshan, Deepak; Kühn, Lukas C. and Soares, Miguel P.. Metabolic Adaptation to Tissue Iron Overload Confers Tolerance to Malaria. Cell Host & Microbe. 2012;12(5):693–704. [doi]
  28. Zenclussen, Ana C.; Olivieri, David N.; Dustin, Michael L. and Tadokoro, Carlos E.. In vivo Multiphoton Microscopy Technique to Reveal the Physiology of the Mouse Placenta. American Journal of Reproductive Immunology. 2012;68(3):271–278. [doi]
  29. Côrte-Real, J.; Duarte, N. and Tavares, L.. Innate stimulation of B1a cells enhances the autoreactive IgM repertoire in the NOD mouse: implications for type 1 diabetes. Diabetologia. 2012;55(6):1761–1772. [doi]
  30. da Silva, Henrique Borges; Caetano, Susana S.; Monteiro, Isadora; Gómez-Conde, Iván; Hanson, Kirsten; Penha-Gonçalves, Carlos; Olivieri, David N.; Mota, Maria M.; Marinho, Cláudio R.; D'Imperio Lima, Maria R. and Tadokoro, Carlos E.. Early skin immunological disturbance after Plasmodium-infected mosquito bites. Cellular Immunology. 2012;277(1-2):22–32. [doi]
  31. Rodrigues-Duarte, Lurdes; de Moraes, Luciana; Barboza, Renato; Marinho, Claudio RF; Franke-Fayard, Blandine and Janse, Chris J. Distinct placental malaria pathology caused by different Plasmodium berghei lines that fail to induce cerebral malaria in the C57BL/6 mouse. Malaria Journal. 2012;11(1):231. [doi]

Animal House - Zebra Fish

  1. Teles, Magda C. and Oliveira, Rui F.. Androgen response to social competition in a shoaling fish. Hormones and Behavior. 2016;78:8–12. [doi]
  2. Koyama, Takashi and Mirth, Christen K.. Growth-Blocking Peptides As Nutrition-Sensitive Signals for Insulin Secretion and Body Size Regulation. PLOS Biology. 2016;14(2):e1002392. [doi]
  3. Teles, Magda C.; Cardoso, Sara D. and Oliveira, Rui F.. Social Plasticity Relies on Different Neuroplasticity Mechanisms across the Brain Social Decision-Making Network in Zebrafish. Frontiers in Behavioral Neuroscience. 2016;10. [doi]
  4. Teles, Magda C. and Oliveira, Rui F.. Androgen response to social competition in a shoaling fish. Hormones and Behavior. 2016;78:8–12. [doi]
  5. Teles, Magda C. and Oliveira, Rui F.. Androgen response to social competition in a shoaling fish. Hormones and Behavior. 2016;78:8–12. [doi]
  6. Rathore, Om Singh; Faustino, Alexandra; Prudêncio, Pedro; Van Damme, Petra and Cox, Cymon J.. Absence of N-terminal acetyltransferase diversification during evolution of eukaryotic organisms. Scientific Reports. 2016;6:21304. [doi]
  7. Oliveira, Rui F.; Simões, José M.; Teles, Magda C.; Oliveira, Catarina R. and Becker, Jorg D.. Assessment of fight outcome is needed to activate socially driven transcriptional changes in the zebrafish brain. Proceedings of the National Academy of Sciences. 2016;113(5):E654–E661. [doi]
  8. Carneiro, Madalena C.; Henriques, Catarina M.; Nabais, Joana; Ferreira, Tânia; Carvalho, Tânia and Ferreira, Miguel Godinho. Short Telomeres in Key Tissues Initiate Local and Systemic Aging in Zebrafish. PLOS Genetics. 2016;12(1):e1005798. [doi]
  9. Teles, Magda C; Cardoso, Sara D and Oliveira, Rui F. Social Plasticity Relies on Different Neuroplasticity Mechanisms across the Brain Social Decision-Making Network in Zebrafish. Frontiers in behavioral neuroscience. 2016;10:16. [doi]
  10. Lopes, João Sollari; Abril-de-Abreu, Rodrigo and Oliveira, Rui F.. Brain Transcriptomic Response to Social Eavesdropping in Zebrafish (Danio rerio). PLOS ONE. 2015;10(12):e0145801. [doi]
  11. Gualda, Emilio J; Pereira, Hugo; Vale, Tiago; Estrada, Marta Falcão; Brito, Catarina and Moreno, Nuno. SPIM-fluid: open source light-sheet based platform for high-throughput imaging. Biomedical optics express. 2015;6(11):4447–56. [doi]
  12. Roxo-Rosa, M.; Jacinto, R.; Sampaio, P. and Lopes, S. S.. The zebrafish Kupffer's vesicle as a model system for the molecular mechanisms by which the lack of Polycystin-2 leads to stimulation of CFTR. Biology Open. 2015;4(11):1356–1366. [doi]
  13. Teles, Magda C.; Almeida, Olinda; Lopes, João S. and Oliveira, Rui F.. Social interactions elicit rapid shifts in functional connectivity in the social decision-making network of zebrafish. Proceedings of the Royal Society B: Biological Sciences. 2015;282(1816):20151099. [doi]
  14. Abril-de-Abreu, Rodrigo; Cruz, José and Oliveira, Rui F.. Social Eavesdropping in Zebrafish: Tuning of Attention to Social Interactions. Scientific Reports. 2015;5:12678. [doi]
  15. Abril-de-Abreu, Rodrigo; Cruz, Ana S. and Oliveira, Rui F.. Social dominance modulates eavesdropping in zebrafish. Royal Society Open Science. 2015;2(8):150220. [doi]
  16. Mateus, R.; Lourenco, R.; Fang, Y.; Brito, G.; Farinho, A.; Valerio, F. and Jacinto, A.. Control of tissue growth by Yap relies on cell density and F-actin in zebrafish fin regeneration. Development. 2015;142(16):2752–2763. [doi]
  17. Cruz, Ana S. and Oliveira, Rui F.. Audience effects and aggressive priming in agonistic behaviour of male zebrafish, Danio rerio. Animal Behaviour. 2015;107:269–276. [doi]
  18. Sampaio, Pedro; Ferreira, Rita R.; Guerrero, Adán; Pintado, Petra; Tavares, Bárbara; Amaro, Joana; Smith, Andrew A.; Montenegro-Johnson, Thomas; Smith, David J. and Lopes, Susana S.. Left-Right Organizer Flow Dynamics: How Much Cilia Activity Reliably Yields Laterality? Developmental Cell. 2014;29(6):716–728. [doi]
  19. Teles, Magda C.; Dahlbom, S. Josefin; Winberg, Svante and Oliveira, Rui F.. Social modulation of brain monoamine levels in zebrafish. Behavioural Brain Research. 2013;253:17–24. [doi]
  20. Henriques, Catarina M.; Carneiro, Madalena C.; Tenente, Inês M.; Jacinto, António and Ferreira, Miguel Godinho. Telomerase Is Required for Zebrafish Lifespan. PLoS Genetics. 2013;9(1):e1003214. [doi]

Antibodies

  1. Yilmaz, B; Portugal, S; Tran, T M; Gozzelino, R; Ramos, S; Gomes, J; Regalado, A; Cowan, P J; D'Apice, A J; Chong, A S; Doumbo, O K; Traore, B; Crompton, P D; Silveira, H and Soares, M P. Gut microbiota elicits a protective immune response against malaria transmission. Cell. 2014;159(6):1277–1289.

Bioinformatics

  1. Passagem-Santos, D.; Bonnet, M.; Sobral, D.; Trancoso, I.; Silva, J. G.; Barreto, V. M.; Athanasiadis, A.; Demengeot, J. and Pereira-Leal, J. B.. RAG Recombinase as a Selective Pressure for Genome Evolution. Genome Biol Evol. 2016;8(11):3364–3376.
  2. Vasconcelos, F. F.; Sessa, A.; Laranjeira, C.; Raposo, A. A.; Teixeira, V.; Hagey, D. W.; Tomaz, D. M.; Muhr, J.; Broccoli, V. and Castro, D. S.. MyT1 Counteracts the Neural Progenitor Program to Promote Vertebrate Neurogenesis. Cell Rep. 2016;17(2):469–483.
  3. Zerbino, D. R.; Johnson, N.; Juetteman, T.; Sheppard, D.; Wilder, S. P.; Lavidas, I.; Nuhn, M.; Perry, E.; Raffaillac-Desfosses, Q.; Sobral, D.; Keefe, D.; Graf, S.; Ahmed, I.; Kinsella, R.; Pritchard, B.; Brent, S.; Amode, R.; Parker, A.; Trevanion, S.; Birney, E.; Dunham, I. and Flicek, P.. Ensembl regulation resources. Database (Oxford). 2016;2016.
  4. Duarte, M.; Carvalho, C.; Bernardo, S.; Barros, S. V.; Benevides, S.; Flor, L.; Monteiro, M.; Marques, I.; Henriques, M.; Barros, S. C.; Fagulha, T.; Ramos, F.; Luis, T. and Fevereiro, M.. Rabbit haemorrhagic disease virus 2 (RHDV2) outbreak in Azores: Disclosure of common genetic markers and phylogenetic segregation within the European strains. Infect. Genet. Evol.. 2015;35:163–171.
  5. Gilchrist, M. J.; Sobral, D.; Khoueiry, P.; Daian, F.; Laporte, B.; Patrushev, I.; Matsumoto, J.; Dewar, K.; Hastings, K. E.; Satou, Y.; Lemaire, P. and Rothbacher, U.. A pipeline for the systematic identification of non-redundant full-ORF cDNAs for polymorphic and evolutionary divergent genomes: Application to the ascidian Ciona intestinalis. Dev. Biol.. 2015;404(2):149–163.
  6. Raposo, A. A.; Vasconcelos, F. F.; Drechsel, D.; Marie, C.; Johnston, C.; Dolle, D.; Bithell, A.; Gillotin, S.; van den Berg, D. L.; Ettwiller, L.; Flicek, P.; Crawford, G. E.; Parras, C. M.; Berninger, B.; Buckley, N. J.; Guillemot, F. and Castro, D. S.. Ascl1 Coordinately Regulates Gene Expression and the Chromatin Landscape during Neurogenesis. Cell Rep. 2015.
  7. Bouzid, D.; Fourati, H.; Amouri, A.; Marques, I.; Abida, O.; Tahri, N.; Penha-Goncalves, C. and Masmoudi, H.. Autoimmune diseases association study with the KIAA1109-IL2-IL21 region in a Tunisian population. Mol. Biol. Rep.. 2014;41(11):7133–7139.
  8. Correia, C.; Diekmann, Y.; Vicente, A. M. and Pereira-Leal, J. B.. Hope for GWAS: relevant risk genes uncovered from GWAS statistical noise. Int J Mol Sci. 2014;15(10):17601–17621.
  9. Guilgur, L. G.; Prudencio, P.; Sobral, D.; Liszekova, D.; Rosa, A. and Martinho, R. G.. Requirement for highly efficient pre-mRNA splicing during Drosophila early embryonic development. Elife. 2014;3:e02181.
  10. Trovoada, M. d. e. J.; Martins, M.; Ben Mansour, R.; Sambo, M. d. o. R.; Fernandes, A. B.; Antunes Goncalves, L.; Borja, A.; Moya, R.; Almeida, P.; Costa, J.; Marques, I.; Macedo, M. P.; Coutinho, A.; Narum, D. L. and Penha-Goncalves, C.. NOS2 variants reveal a dual genetic control of nitric oxide levels, susceptibility to Plasmodium infection, and cerebral malaria. Infect. Immun.. 2014;82(3):1287–1295.
  11. Barroso-Batista, J.; Sousa, A.; Lourenco, M.; Bergman, M. L.; Sobral, D.; Demengeot, J.; Xavier, K. B. and Gordo, I.. The first steps of adaptation of Escherichia coli to the gut are dominated by soft sweeps. PLoS Genet.. 2014;10(3):e1004182.
  12. Marques, I.; Almeida, P.; Alves, R.; Dias, M. J.; Godinho, A. and Pereira-Leal, J. B.. Bioinformatics projects supporting life-sciences learning in high schools. PLoS Comput. Biol.. 2014;10(1):e1003404.
  13. Goncalves, L. A.; Rodrigues-Duarte, L.; Rodo, J.; Vieira de Moraes, L.; Marques, I. and Penha-Goncalves, C.. TREM2 governs Kupffer cell activation and explains belr1 genetic resistance to malaria liver stage infection. Proc. Natl. Acad. Sci. U.S.A.. 2013;110(48):19531–19536.
  14. Soares, P.; Alves, R. J.; Abecasis, A. B.; Penha-Goncalves, C.; Gomes, M. G. and Pereira-Leal, J. B.. inTB - a data integration platform for molecular and clinical epidemiological analysis of tuberculosis. BMC Bioinformatics. 2013;14:264.
  15. Lopes, J. S.; Marques, I.; Soares, P.; Nebenzahl-Guimaraes, H.; Costa, J.; Miranda, A.; Duarte, R.; Alves, A.; Macedo, R.; Duarte, T. A.; Barbosa, T.; Oliveira, M.; Nery, J. S.; Boechat, N.; Pereira, S. M.; Barreto, M. L.; Pereira-Leal, J.; Gomes, M. G. and Penha-Goncalves, C.. SNP typing reveals similarity in Mycobacterium tuberculosis genetic diversity between Portugal and Northeast Brazil. Infect. Genet. Evol.. 2013;18:238–246.
  16. Bouzid, D.; Fourati, H.; Amouri, A.; Marques, I.; Abida, O.; Haddouk, S.; Ben Ayed, M.; Tahri, N.; Penha-Goncalves, C. and Masmoudi, H.. Association of ZAP70 and PTPN6, but Not BANK1 or CLEC2D, with inflammatory bowel disease in the Tunisian population. Genet Test Mol Biomarkers. 2013;17(4):321–326.
  17. Sousa, F. L.; Alves, R. J.; Ribeiro, M. A.; Pereira-Leal, J. B.; Teixeira, M. and Pereira, M. M.. The superfamily of heme-copper oxygen reductases: types and evolutionary considerations. Biochim. Biophys. Acta. 2012;1817(4):629–637.
  18. Sharma, R.; Goossens, B.; Kun-Rodrigues, C.; Teixeira, T.; Othman, N.; Boone, J. Q.; Jue, N. K.; Obergfell, C.; O'Neill, R. J. and Chikhi, L.. Two different high throughput sequencing approaches identify thousands of de novo genomic markers for the genetically depleted Bornean elephant. PLoS ONE. 2012;7(11):e49533.
  19. Ribeiro, T.; Santos, S.; Marques, M. I.; Gilmore, M. and de Fatima Silva Lopes, M.. Identification of a new gene, vanV, in vanB operons of Enterococcus faecalis. Int. J. Antimicrob. Agents. 2011;37(6):554–557.
  20. Sambo, M. R.; Trovoada, M. J.; Benchimol, C.; Quinhentos, V.; Goncalves, L.; Velosa, R.; Marques, M. I.; Sepulveda, N.; Clark, T. G.; Mustafa, S.; Wagner, O.; Coutinho, A. and Penha-Goncalves, C.. Transforming growth factor beta 2 and heme oxygenase 1 genes are risk factors for the cerebral malaria syndrome in Angolan children. PLoS ONE. 2010;5(6):e11141.

Electron Microscopy

  1. Vale-Costa, Sílvia; Alenquer, Marta; Sousa, Ana Laura; Kellen, Bárbara; Ramalho, José and Tranfield, Erin M.. Influenza A virus ribonucleoproteins modulate host recycling by competing with Rab11 effectors. Journal of Cell Science. 2016;129(8):1697–1710. [doi]
  2. Escrevente, Cristina; Grammel, Nicolas; Kandzia, Sebastian; Zeiser, Johannes; Tranfield, Erin M. and Conradt, Harald S.. Sialoglycoproteins and N-Glycans from Secreted Exosomes of Ovarian Carcinoma Cells. PLoS ONE. 2013;8(10):e78631. [doi]

Flow Cytometry

  1. Cardoso, M Margarida; Peça, Inês N; Raposo, Cláudia D; Petrova, Krasimira T; Barros, M Teresa; Gardner, Rui and Bicho, A. Doxorubicin-loaded galactose-conjugated poly(d,l-lactide-co-glycolide) nanoparticles as hepatocyte-targeting drug carrier. Journal of Microencapsulation. 2016;33(4):315–322. [doi]
  2. Carqueijeiro, Ines Teto; Guimarães, Ana Luísa; Bettencourt, Sara; Martínez-Cortés, Teresa; Guedes, Joana; Gardner, Rui; Lopes, Telma; Andrade, Cláudia; Bispo, Cláudia; Martins, Nuno Pimpão; Andrade, Paula; Valentão, Patrícia; Valente, Inês Maria; Rodrigues, José António; Duarte, Patrícia and Sottomayor, Mariana. Isolation of cells specialized in anticancer alkaloid metabolism by fluorescence activated cell sorting. Plant Physiology. 2016:pp.00588.2016. [doi]
  3. Calisto, Filipa; Refojo, Patrícia N.; Bispo, Cláudia; Andrade, Cláudia; Gardner, Rui; Madl, Tobias; López de Lacey, Antonio; Teixeira, Miguel and Pereira, Manuela M.. Characterization and activity of Alternative Complex III from Rhodothermus marinus. Biochimica et Biophysica Acta (BBA) - Bioenergetics. 2016;1857(Supplement):e36. [doi]
  4. Barsky, Lora W.; Black, Michele; Cochran, Matthew; Daniel, Benjamin J.; Davies, Derek; DeLay, Monica; Gardner, Rui; Gregory, Michael; Kunkel, Desiree; Lannigan, Joanne; Marvin, James; Salomon, Robert; Torres, Carina and Walker, Rachael. International Society for Advancement of Cytometry (ISAC) flow cytometry shared resource laboratory (SRL) best practices. Cytometry Part A. 2016:1–14. [doi]
  5. Traunecker, Emmanuel; Gardner, Rui; Fonseca, Jo??o Eurico; Polido-Pereira, Joaquim; Seitz, Michael; Villiger, Peter M.; Iezzi, Giandomenica and Padovan, Elisabetta. Blocking of LFA-1 enhances expansion of Th17 cells induced by human CD14+CD16++ nonclassical monocytes. European Journal of Immunology. 2015;45(5):1414–1425. [doi]
  6. Riddell, Andrew; Gardner, Rui; Perez-Gonzalez, Alexis; Lopes, Telma and Martinez, Lola. Rmax: A systematic approach to evaluate instrument sort performance using center stream catch. Methods. Elsevier Inc.; 2015;82:64–73. [doi]
  7. Rebelo, Maria; Tempera, Carolina; Bispo, Claudia; Andrade, Claudia; Gardner, Rui; Shapiro, Howard M. and H??nscheid, Thomas. Light depolarization measurements in malaria: A new job for an old friend. Cytometry Part A. 2015;87(5):437–445. [doi]
  8. Peça, Inês N.; Bicho, A.; Gardner, Rui and Cardoso, M. Margarida. Control of doxorubicin release from magnetic Poly(dl-lactide-co-glycolide) nanoparticles by application of a non-permanent magnetic field. Journal of Nanoparticle Research. 2015;17(11):427. [doi]
  9. Kappel, Christian; Trost, Gerda; Czesnick, Hjördis; Ramming, Anna; Kolbe, Benjamin; Vi, Son Lang; Bispo, Cláudia; Becker, Jörg D.; de Moor, Cornelia and Lenhard, Michael. Genome-Wide Analysis of PAPS1-Dependent Polyadenylation Identifies Novel Roles for Functionally Specialized Poly(A) Polymerases in Arabidopsis thaliana. PLoS Genetics. 2015;11(8):1–30. [doi]
  10. Alves-Pereira, Clara F; de Freitas, Raquel; Lopes, Telma; Gardner, Rui; Marta, Filipa; Vieira, Paulo and Barreto, Vasco M. Independent recruitment of Igh alleles in V(D)J recombination. Nature communications. Nature Publishing Group; 2014;5(D):5623. [doi]
  11. Vidigal, João; Dias, Mafalda M.; Fernandes, Fabiana; Patrone, Marco; Bispo, Cláudia; Andrade, Cláudia; Gardner, Rui; Carrondo, Manuel J T; Alves, Paula M. and Teixeira, Ana P.. A cell sorting protocol for selecting high-producing sub-populations of Sf9 and High Five™ cells. Journal of Biotechnology. Elsevier B.V.; 2013;168(4):436–439. [doi]
  12. Trancoso, Inês; Bonnet, Marie; Gardner, Rui; Carneiro, Jorge; Barreto, Vasco M.; Demengeot, Jocelyne and Sarmento, Leonor M.. A novel quantitative fluorescent reporter assay for RAG targets and RAG activity. Frontiers in Immunology. 2013;4(MAY):1–17. [doi]
  13. Moran, Barry; Blanco-Fern??ndez, Alfonso; Gardner, Rui; Tigges, John; Toxavidis, Vasilis and Daley, John F.. Remote access technology offers tremendous possibilities to the cytometry community. Cytometry Part A. 2013;83(12):1062–1065. [doi]
  14. Brás-Rosário, Luis; Matsuda, Alex; Pinheiro, Ana Isabel; Gardner, Rui; Lopes, Telma; Amaral, Andreia and Gama-Carvalho, Margarida. Expression Profile of microRNAs Regulating Proliferation and Differentiation in Mouse Adult Cardiac Stem Cells. PLoS ONE. 2013;8(5). [doi]
  15. Mata, João F.; Lopes, Telma; Gardner, Rui and Jansen, Lars E T. A rapid FACS-based strategy to isolate human gene knockin and knockout clones. PLoS ONE. 2012;7(2). [doi]
  16. Gomes-Santos, Carina S S; Itoe, Maurice A.; Afonso, Cristina; Henriques, Ricardo; Gardner, Rui; Sepúlveda, Nuno; Simões, Pedro D.; Raquel, Helena; Almeida, António Paulo; Moita, Luis F.; Frischknecht, Friedrich and Mota, Maria M.. Highly dynamic host actin reorganization around developing Plasmodium inside hepatocytes. PLoS ONE. 2012;7(1). [doi]
  17. Calarco, Joseph P.; Borges, Filipe; Donoghue, Mark T A; Van Ex, Frédéric; Jullien, Pauline E.; Lopes, Telma; Gardner, Rui; Berger, Frédéric; Feijó, José A.; Becker, Jörg D. and Martienssen, Robert A.. Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA. Cell. 2012;151(1):194–205. [doi]
  18. Borges, Filipe; Gardner, Rui; Lopes, Telma; Calarco, Joseph P; Boavida, Leonor C; Keith Slotkin, R and Martienssen, Robert A. FACS-based purification of Arabidopsis microspores, sperm cells and vegetative nuclei. Plant Methods. 2012;8:1. [doi]
  19. Teixeira, Vera; Arede, Natacha; Gardner, Rui; Rodríguez-León, Joaquín and Tavares, Ana T. Targeting the hemangioblast with a novel cell type-specific enhancer. BMC Developmental Biology. 2011;11(1):76. [doi]
  20. Matos, Isa; Sucena, Élio; Machado, Miguel P; Gardner, Rui; Inácio, Ângela; Schartl, Manfred and Coelho, Maria M. Ploidy mosaicism and allele-specific gene expression differences in the allopolyploid Squalius alburnoides. BMC Genetics. 2011;12(1):101. [doi]
  21. Fernandes, Andreia S.; Pedro Gonçalves, A.; Castro, Ana; Lopes, Telma A.; Gardner, Rui; Louise Glass, N. and Videira, Arnaldo. Modulation of fungal sensitivity to staurosporine by targeting proteins identified by transcriptional profiling. Fungal Genetics and Biology. Elsevier Inc.; 2011;48(12):1130–1138. [doi]
  22. Borges, Filipe; Gomes, Gabriela; Gardner, Rui; Moreno, Nuno; McCormick, Sheila and Feijó, José a. Comparative transcriptomics of Arabidopsis sperm cells. Plant physiology. 2008;148(2):1168–1181. [doi]

Gene Expression - Arrays

  1. Muñoz-Ruiz, Miguel; Ribot, Julie C; Grosso, Ana R; Gonçalves-Sousa, Natacha; Pamplona, Ana and Pennington Daniel J; Regueiro, José R and Fernández-Malavé Edgar and Silva-Santos, Bruno. TCR signal strength controls thymic differentiation of discrete proinflammatory $\gamma$$\delta$ T cell subsets. Nat. Immunol.. 2016;17(6):721–727. [doi]
  2. MacAlister, Cora A; Ortiz-Ramírez, Carlos; Becker, Jörg D; Feijó, José A and Lippman, Zachary B. Hydroxyproline O-arabinosyltransferase mutants oppositely alter tip growth in Arabidopsis thaliana and Physcomitrella patens. Plant J.. 2016;85(2):193–208. [doi]
  3. Vasconcelos, Francisca F; Sessa, Alessandro; Laranjeira, Cátia; Raposo, Alexandre A S F; Teixeira, Vera and Hagey Daniel W; Tomaz, Diogo M; Muhr, Jonas and Broccoli Vania and Castro, Diogo S. MyT1 Counteracts the Neural Progenitor Program to Promote Vertebrate Neurogenesis. Cell Rep.. Cell Press; 2016;17(2):469–483. [doi]
  4. Sousa, Inês; Abrantes, Patrícia; Francisco, Vânia; Teixeira, Gilberto; Monteiro, Marta and Neves João; Norte, Ana; Robalo Cordeiro, Carlos and Moura E Sá João; Reis, Ernestina; Santos, Patrícia; Oliveira, Manuela; Sousa, Susana and Fradinho Marta; Malheiro, Filipa; Negrão, Luís; Feijó, Salvato and Oliveira, Sofia A. Multicentric Genome-Wide Association Study for Primary Spontaneous Pneumothorax. PLoS One. 2016;11(5):e0156103. [doi]
  5. Oliveira, Rui F; Simões, José M; Teles, Magda C; Oliveira, Catarina R; Becker, Jorg D and Lopes, João S. Assessment of fight outcome is needed to activate socially driven transcriptional changes in the zebrafish brain. Proc. Natl. Acad. Sci. U. S. A.. 2016;113(5):E654–61. [doi]
  6. Ortiz-Ramírez, Carlos; Hernandez-Coronado, Marcela and Thamm Anna; Catarino, Bruno; Wang, Mingyi; Dolan, Liam and Feijó, José A. A Transcriptome Atlas of Physcomitrella patens Provides Insights into the Evolution and Development of Land Plants. Mol. Plant. Elsevier; 2016;9(2):205–220. [doi]
  7. Costa, Aida and Henrique, Domingos. Transcriptome profiling of induced hair cells (iHCs) generated by combined expression of Gfi1, Pou4f3 and Atoh1 during embryonic stem cell differentiation. Genom Data. 2015;6:77–80. [doi]
  8. Xavier, Joana M; Shahram, Farhad; Sousa, Inês and Davatchi Fereydoun; Matos, Mafalda; Abdollahi, Bahar Sadeghi; Sobral, João; Nadji, Abdolhadi and Oliveira Manuela; Ghaderibarim, Fahmida; Shafiee, Niloofar Mojarad and Oliveira, Sofia A. FUT2: filling the gap between genes and environment in Behçet's disease? Ann. Rheum. Dis.. 2015;74(3):618–624. [doi]
  9. Lopes, João Sollari and Abril-de-Abreu, Rodrigo and Oliveira Rui F. Brain Transcriptomic Response to Social Eavesdropping in Zebrafish (Danio rerio). PLoS One. 2015;10(12):e0145801. [doi]
  10. Costa, Aida; Sanchez-Guardado, Luis; Juniat, Stephanie; Gale, Jonathan E; Daudet, Nicolas and Henrique, Domingos. Generation of sensory hair cells by genetic programming with a combination of transcription factors. Development. Oxford University Press for The Company of Biologists Limited; 2015;142(11):1948–1959. [doi]
  11. Abrantes, Patrícia; Santos, Maria M; Sousa, Inês; Xavier, Joana M; Francisco, Vânia and Krug Tiago; Sobral, João; Matos, Mafalda and Martins Madalena; Jacinto, António; Coiteiro, Domingos and Oliveira, Sofia A. Genetic Variants Underlying Risk of Intracranial Aneurysms: Insights from a GWAS in Portugal. PLoS One. 2015;10(7):e0133422. [doi]
  12. Santos, Mário R; Marques, Andreia T; Becker, Jörg D and Moreira, Leonilde M. The Sinorhizobium meliloti EmrR regulator is required for efficient colonization of Medicago sativa root nodules. Mol. Plant. Microbe. Interact.. 2014;27(4):388–399. [doi]
  13. Liehl, Peter; Zuzarte-Luís, Vanessa; Chan, Jennie; Zillinger, Thomas; Baptista, Fernanda; Carapau, Daniel; Konert, Madlen; Hanson, Kirsten K; Carret, Céline; Lassnig, Caroline; Müller, Mathias and Kalinke Ulrich; Saeed, Mohsan; Chora, Angelo Ferreira; Golenbock, Douglas T; Strobl, Birgit; Prudêncio, Miguel; Coelho, Luis P; Kappe, Stefan H and Superti-Furga Giulio; Pichlmair, Andreas; Vigário, Ana M; Rice, Charles M; Fitzgerald, Katherine A and Barchet Winfried and Mota, Maria M. Host-cell sensors for Plasmodium activate innate immunity against liver-stage infection. Nat. Med.. 2014;20(1):47–53. [doi]
  14. dos Santos, Catarina Rodrigues; Domingues, Germana and Matias Inês; Matos, João; Fonseca, Isabel and de Almeida José Mendes and Dias, Sérgio. LDL-cholesterol signaling induces breast cancer proliferation and invasion. Lipids Health Dis.. 2014;13:16. [doi]
  15. Martins, Isabel; Hartmann, Diego O; Alves, Paula C and Martins Celso; Garcia, Helga; Leclercq, Céline C; Ferreira, Rui; He, Ji; Renaut, Jenny; Becker, Jörg D and Silva Pereira, Cristina. Elucidating how the saprophytic fungus Aspergillus nidulans uses the plant polyester suberin as carbon source. BMC Genomics. 2014;15:613. [doi]
  16. Becker, Jörg D; Takeda, Seiji; Borges, Filipe and Dolan Liam and Feijó, José A. Transcriptional profiling of Arabidopsis root hairs and pollen defines an apical cell growth signature. BMC Plant Biol.. 2014;14:197. [doi]
  17. Rodrigues, Joana L; Sousa, Marta; Prather, Kristala L J; Kluskens, Leon D and Rodrigues, Ligia R. Selection of Escherichia coli heat shock promoters toward their application as stress probes. J. Biotechnol.. 2014;188:61–71. [doi]
  18. Carvalho, Ana S; Ribeiro, Helena; Voabil, Paula; Penque, Deborah; Jensen, Ole N; Molina, Henrik and Matthiesen, Rune. Global mass spectrometry and transcriptomics array based drug profiling provides novel insight into glucosamine induced ER stress. Mol. Cell. Proteomics. 2014. [doi]
  19. Monteiro, Joana; Aires, Rita; Becker, Jörg D and Jacinto António and Certal, Ana C and Rodríguez-León Joaquín. V-ATPase proton pumping activity is required for adult zebrafish appendage regeneration. PLoS One. 2014;9(3):e92594. [doi]
  20. Gil, Fátima N; Becker, Jörg D and Viegas, Cristina A. Potential mechanisms underlying response to effects of the fungicide pyrimethanil from gene expression profiling in Saccharomyces cerevisiae. J. Agric. Food Chem.. 2014;62(23):5237–5247. [doi]
  21. Regan, Jennifer C; Brandão, Ana S; Leitão, Alexandre B; Mantas Dias, Angela Raquel; Sucena, Elio; Jacinto, António and Zaidman-Rémy, Anna. Steroid hormone signaling is essential to regulate innate immune cells and fight bacterial infection in Drosophila. PLoS Pathog.. 2013;9(10):e1003720. [doi]
  22. Ciolfi, Andrea; Sessa, Giovanna; Sassi, Massimiliano and Possenti Marco; Salvucci, Samanta; Carabelli, Monica; Morelli, Giorgio and Ruberti, Ida. Dynamics of the shade-avoidance response in Arabidopsis. Plant Physiol.. 2013;163(1):331–353. [doi]
  23. Xavier, Joana M; Krug, Tiago; Davatchi, Fereydoun and Shahram Farhad; Fonseca, Benedita V; Jesus, Gorete and Barcelos Filipe; Vedes, Joana; Salgado, Manuel and Abdollahi Bahar Sadeghi; Nadji, Abdolhadi and Moraes-Fontes Maria Francisca; Shafiee, Niloofar Mojarad; Ghaderibarmi, Fahmida; Vaz Patto, José; Crespo, Jorge and Oliveira, Sofia A. Gene expression profiling and association studies implicate the neuregulin signaling pathway in Behçet's disease susceptibility. J. Mol. Med.. 2013;91(8):1013–1023. [doi]
  24. Ferreira, Ana S; Silva, Inês N; Oliveira, Vítor H; Becker, Jörg D; Givskov, Michael; Ryan, Robert P; Fernandes, Fábio and Moreira, Leonilde M. Comparative transcriptomic analysis of the Burkholderia cepacia tyrosine kinase bceF mutant reveals a role in tolerance to stress, biofilm formation, and virulence. Appl. Environ. Microbiol.. 2013;79(9):3009–3020. [doi]
  25. Wang, Mingyi; Verdier, Jerome; Benedito, Vagner A and Tang Yuhong; Murray, Jeremy D; Ge, Yinbing; Becker, Jörg D; Carvalho, Helena; Rogers, Christian and Udvardi Michael and He, Ji. LegumeGRN: a gene regulatory network prediction server for functional and comparative studies. PLoS One. 2013;8(7):e67434. [doi]
  26. Limpens, Erik; Moling, Sjef; Hooiveld, Guido and Pereira Patrícia A; Bisseling, Ton and Becker, Jörg D. cell- and tissue-specific transcriptome analyses of Medicago truncatula root nodules. PLoS One. 2013;8(5):e64377. [doi]
  27. Confraria, Ana; Martinho, Cláudia; Elias, Alexandre; Rubio-Somoza, Ignacio and Baena-González, Elena. miRNAs mediate SnRK1-dependent energy signaling in Arabidopsis. Front. Plant Sci.. 2013;4:197. [doi]
  28. Malecki, Michal; Viegas, Sandra C; Carneiro, Tiago and Golik Pawel; Dressaire, Clémentine; Ferreira, Miguel G and Arraiano, Cecília M. The exoribonuclease Dis3L2 defines a novel eukaryotic RNA degradation pathway. EMBO J.. 2013;32(13):1842–1854. [doi]
  29. Clarke, Luka A; Sousa, Lisete and Barreto, Celeste and Amaral Margarida D. Changes in transcriptome of native nasal epithelium expressing F508del-CFTR and intersecting data from comparable studies. Respir. Res.. 2013;14:38. [doi]
  30. Costa, Mário; Nobre, Margarida Sofia; Becker, Jörg D; Masiero, Simona; Amorim, Maria Isabel and Pereira Luís Gustavo and Coimbra, Sílvia. Expression-based and co-localization detection of arabinogalactan protein 6 and arabinogalactan protein 11 interactors in Arabidopsis pollen and pollen tubes. BMC Plant Biol.. 2013;13:7. [doi]
  31. Hogekamp, Claudia. A roadmap of cell-type specific gene expression during sequential stages of the arbuscular mycorrhiza symbiosis. BMC Genomics. 2013;14:306. [doi]
  32. Costa, Ana; Afonso, Joana; Osório, Catarina and Gomes Ana L; Caiado, Francisco; Valente, Joana and Aguiar Sandra I; Pinto, Francisco; Ramirez, Mário and Dias, Sérgio. miR-363-5p regulates endothelial cell properties and their communication with hematopoietic precursor cells. J. Hematol. Oncol.. 2013;6(1):87. [doi]
  33. Nunes, Raquel J; de Oliveira, Paula; Lages, Ana and Becker Jörg D; Marcelino, Paulo; Barroso, Eduardo; Perdigoto, Rui; Kelly, Jeffery W; Quintas, Alexandre and Santos, Susana Constantino Rosa. Transthyretin proteins regulate angiogenesis by conferring different molecular identities to endothelial cells. J. Biol. Chem.. 2013;288(44):31752–31760. [doi]
  34. Silveira, Henrique; Gabriel, Ana; Ramos, Susana and Palma Joel; Felix, Rute; Custódio, Ana and Collins, L Vincent. CpG-containing oligodeoxynucleotides increases resistance of Anopheles mosquitoes to Plasmodium infection. Insect Biochem. Mol. Biol.. 2012;42(10):758–765. [doi]
  35. Czaja, Lisa F; Hogekamp, Claudia; Lamm, Patrick and Maillet Fabienne; Martinez, Eduardo Andres; Samain, Eric and Dénarié, Jean. Transcriptional responses toward diffusible signals from symbiotic microbes reveal MtNFP- and MtDMI3-dependent reprogramming of host gene expression by arbuscular mycorrhizal fungal lipochitooligosaccharides. Plant Physiol.. 2012;159(4):1671–1685. [doi]
  36. Seabra, Ana R; Pereira, Patrícia A; Becker, Jörg D and Carvalho, Helena G. Inhibition of glutamine synthetase by phosphinothricin leads to transcriptome reprograming in root nodules of Medicago truncatula. Mol. Plant. Microbe. Interact.. 2012;25(7):976–992. [doi]
  37. Ortu, Giuseppe; Balestrini, Raffaella; Pereira, Patrícia A; Becker, Jörg D; Küster, Helge and Bonfante, Paola. Plant genes related to gibberellin biosynthesis and signaling are differentially regulated during the early stages of AM fungal interactions. Mol. Plant. 2012;5(4):951–954. [doi]
  38. Krug, Tiago; Gabriel, João Paulo; Taipa, Ricardo and Fonseca Benedita V; Domingues-Montanari, Sophie and Fernandez-Cadenas Israel; Manso, Helena; Gouveia, Liliana O; Sobral, João; Albergaria, Isabel and Gaspar Gisela; Jiménez-Conde, Jordi; Rabionet, Raquel; Ferro, José M; Montaner, Joan; Vicente, Astrid M; Silva, Mário Rui; Matos, Ilda; Lopes, Gabriela and Oliveira, Sofia A. TTC7B emerges as a novel risk factor for ischemic stroke through the convergence of several genome-wide approaches. J. Cereb. Blood Flow Metab.. 2012;32(6):1061–1072. [doi]
  39. Gomes-Santos, Carina S S; Itoe, Maurice A; Afonso, Cristina; Henriques, Ricardo; Gardner, Rui and Sepúlveda Nuno; Simões, Pedro D; Raquel, Helena; Almeida, António Paulo; Moita, Luis F and Frischknecht Friedrich and Mota, Maria M. Highly dynamic host actin reorganization around developing Plasmodium inside hepatocytes. PLoS One. 2012;7(1):e29408. [doi]
  40. Almeida, Sílvia Cristina Paiva; de Oliveira, Vivian Leite; Ventura, Sónia and Bofill, Margarita and Parkhouse Robert Michael Evans. Neoplastic transformation of T lymphocytes through transgenic expression of a virus host modification protein. PLoS One. 2012;7(4):e34140. [doi]
  41. Hogekamp, Claudia; Arndt, Damaris; Pereira, Patrícia A; Becker, Jörg D and Hohnjec, Natalija. Laser microdissection unravels cell-type-specific transcription in arbuscular mycorrhizal roots, including CAAT-box transcription factor gene expression correlating with fungal contact and spread. Plant Physiol.. 2011;157(4):2023–2043. [doi]
  42. Silva, Inês N; Ferreira, Ana S; Becker, Jörg D; Zlosnik, James E A; Speert, David P; He, Ji and Mil-Homens Dalila and Moreira, Leonilde M. Mucoid morphotype variation of Burkholderia multivorans during chronic cystic fibrosis lung infection is correlated with changes in metabolism, motility, biofilm formation and virulence. Microbiology. 2011;157(Pt 11):3124–3137. [doi]
  43. Carvalho, Luísa C; Vilela, Belmiro J; Mullineaux, Phil M and Amâncio, Sara. Comparative transcriptomic profiling of Vitis vinifera under high light using a custom-made array and the Affymetrix GeneChip. Mol. Plant. 2011;4(6):1038–1051. [doi]
  44. Gil, Fátima N; Gonçalves, Alina C; Jacinto, Maria João; Becker, Jörg D and Viegas, Cristina A. Transcriptional profiling in Saccharomyces cerevisiae relevant for predicting alachlor mechanisms of toxicity. Environ. Toxicol. Chem.. 2011;30(11):2506–2518. [doi]
  45. Bento, Margaret; Correia, Elizabeth; Tavares, Ana T and Becker Jörg D and Belo, José A. Identification of differentially expressed genes in the heart precursor cells of the chick embryo. Gene Expr. Patterns. 2011;11(7):437–447. [doi]
  46. Portugal, Silvia; Carret, Céline; Recker, Mario and Armitage Andrew E; Gonçalves, Lígia A and Epiphanio Sabrina; Sullivan, David; Roy, Cindy and Newbold Chris I; Drakesmith, Hal and Mota, Maria M. Host-mediated regulation of superinfection in malaria. Nat. Med.. 2011;17(6):732–737. [doi]
  47. Boavida, Leonor C; Borges, Filipe; Becker, Jörg D and Feijó, José A. Whole genome analysis of gene expression reveals coordinated activation of signaling and metabolic pathways during pollen-pistil interactions in Arabidopsis. Plant Physiol.. 2011;155(4):2066–2080. [doi]
  48. Maillet, Fabienne; Poinsot, Véréna; André, Olivier; Puech-Pagès, Virginie; Haouy, Alexandra and Gueunier Monique; Cromer, Laurence; Giraudet, Delphine; Formey, Damien; Niebel, Andreas; Martinez, Eduardo Andres; Driguez, Hugues and Bécard, Guillaume and Dénarié Jean. Fungal lipochitooligosaccharide symbiotic signals in arbuscular mycorrhiza. Nature. 2011;469(7328):58–63. [doi]
  49. Teixeira, Vera; Arede, Natacha; Gardner, Rui and Rodríguez-León Joaquín and Tavares, Ana T. Targeting the hemangioblast with a novel cell type-specific enhancer. BMC Dev. Biol.. 2011;11:76. [doi]
  50. Lourenço, T; Saibo, N; Batista, R; Pinto Ricardo, C and Oliveira, M M. Inducible and constitutive expression of HvCBF4 in rice leads to differential gene expression and drought tolerance. Biol. Plant.. Springer Netherlands; 2011;55(4):653. [doi]
  51. Gonçalves, Lisa; Filipe, Mário; Marques, Sara; Salgueiro, Ana-Marisa; Becker, Jorg D and Belo, José António. Identification and functional analysis of novel genes expressed in the Anterior Visceral Endoderm. Int. J. Dev. Biol.. 2011;55(3):281–295. [doi]
  52. Mira, Nuno P; Becker, Jorg D and Sá-Correia, Isabel. Genomic expression program involving the Haa1p-regulon in Saccharomyces cerevisiae response to acetic acid. OMICS. 2010;14(5):587–601. [doi]
  53. Gomes, Anita Q; Correia, Daniel V; Grosso, Ana R and Lança Telma; Ferreira, Cristina; Lacerda, João F; Barata, João T and Silva, Maria Gomes da and Silva-Santos Bruno. Identification of a panel of ten cell surface protein antigens associated with immunotargeting of leukemias and lymphomas by peripheral blood gammadelta T cells. Haematologica. 2010;95(8):1397–1404. [doi]
  54. Santos, Mário R; Cosme, Ana M; Becker, Jörg D; Medeiros, João M C; Mata, Márcia F and Moreira, Leonilde M. Absence of functional TolC protein causes increased stress response gene expression in Sinorhizobium meliloti. BMC Microbiol.. 2010;10:180. [doi]
  55. Schlüter, Jan-Philip; Reinkensmeier, Jan and Daschkey Svenja; Evguenieva-Hackenberg, Elena; Janssen, Stefan; Jänicke, Sebastian; Becker, Jörg D; Giegerich, Robert and Becker, Anke. A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti. BMC Genomics. 2010;11:245. [doi]
  56. dos Santos, Sandra C; Tenreiro, Sandra; Palma, Margarida; Becker, Jorg and Sá-Correia, Isabel. Transcriptomic profiling of the Saccharomyces cerevisiae response to quinine reveals a glucose limitation response attributable to drug-induced inhibition of glucose uptake. Antimicrob. Agents Chemother.. 2009;53(12):5213–5223. [doi]
  57. Nobre, Lígia S; Al-Shahrour, Fátima; Dopazo, Joaquin and Saraiva, Lígia M. Exploring the antimicrobial action of a carbon monoxide-releasing compound through whole-genome transcription profiling of Escherichia coli. Microbiology. 2009;155(Pt 3):813–824. [doi]
  58. Mira, Nuno P; Lourenço, Artur B; Fernandes, Alexandra R; Becker, Jorg D and Sá-Correia, Isabel. The RIM101 pathway has a role in Saccharomyces cerevisiae adaptive response and resistance to propionic acid and other weak acids. FEMS Yeast Res.. 2009;9(2):202–216. [doi]
  59. Albuquerque, Sónia S; Carret, Céline; Grosso, Ana Rita; Tarun, Alice S; Peng, Xinxia; Kappe, Stefan H I; Prudêncio, Miguel and Mota, Maria M. Host cell transcriptional profiling during malaria liver stage infection reveals a coordinated and sequential set of biological events. BMC Genomics. 2009;10:270. [doi]
  60. Correia, Daniel V; d'Orey, Francisco; Cardoso, Bruno A; Lança, Telma; Grosso, Ana R; deBarros, Ana and Martins Leila R; Barata, João T and Silva-Santos, Bruno. Highly active microbial phosphoantigen induces rapid yet sustained MEK/Erk- and PI-3K/Akt-mediated signal transduction in anti-tumor human gammadelta T-cells. PLoS One. Public Library of Science; 2009;4(5):e5657. [doi]
  61. Pita, J M; Banito, A; Cavaco, B M and Leite, V. Gene expression profiling associated with the progression to poorly differentiated thyroid carcinomas. Br. J. Cancer. 2009;101(10):1782–1791. [doi]
  62. Correia, D V; d'Orey, F; Cardoso, B A; Lanca, T and Grosso A R; deBarros, A; Martins, L R and Barata, J T and Silva-Santos B. Highly Active Microbial Phosphoantigen Induces Rapid yet Sustained MEK/Erk- and PI-3K/Akt-Mediated Signal Transduction in Anti-Tumor Human gamma delta T-Cells. PLoS One. 2009;4(5).
  63. Borges, Filipe; Gomes, Gabriela; Gardner, Rui and Moreno Nuno; McCormick, Sheila and Feijó, José A. Comparative transcriptomics of Arabidopsis sperm cells. Plant Physiol.. 2008;148(2):1168–1181. [doi]
  64. Igreja, Cátia; Fragoso, Rita; Caiado, Francisco and Clode Nuno; Henriques, Alexandra; Camargo, Lauren and Reis Eduardo M and Dias, Sérgio. Detailed molecular characterization of cord blood-derived endothelial progenitors. Exp. Hematol.. 2008;36(2):193–203. [doi]
  65. Trindade, Alexandre; Kumar, S Ram; Scehnet, Jeffrey S; Lopes-da-Costa, Luis; Becker, Jorg; Jiang, Weidong; Liu, Ren; Gill, Parkash S and Duarte, Antonio. Overexpression of delta-like 4 induces arterialization and attenuates vessel formation in developing mouse embryos. Blood. 2008;112(5):1720–1729. [doi]
  66. Pina, Cristina; May, Gillian; Soneji, Shamit; Hong, Dengli and Enver, Tariq. MLLT3 regulates early human erythroid and megakaryocytic cell fate. Cell Stem Cell. 2008;2(3):264–273. [doi]
  67. Batista, Rita; Saibo, Nelson and Lourenço, Tiago and Oliveira Maria Margarida. Microarray analyses reveal that plant mutagenesis may induce more transcriptomic changes than transgene insertion. Proc. Natl. Acad. Sci. U. S. A.. 2008;105(9):3640–3645. [doi]
  68. Carapau, Daniel; Kruhofer, Mogens; Chatalbash, Allison; Orengo, Jamie Marie; Mota, Maria Manuel and Rodriguez, Ana. Transcriptome profile of dendritic cells during malaria: cAMP regulation of IL-6. Cell. Microbiol.. 2007;9(7):1738–1752. [doi]
  69. Igreja, Cátia; Courinha, Margarida; Cachaço, Ana Sofia; Pereira, Teresa; Cabeçadas, José; da Silva, Maria Gomes and Dias, Sérgio. Characterization and clinical relevance of circulating and biopsy-derived endothelial progenitor cells in lymphoma patients. Haematologica. 2007;92(4):469–477. [doi]
  70. Schiedlmeier, Bernhard; Santos, Ana Cristina; Ribeiro, Ana; Moncaut, Natalia; Lesinski, Dietrich; Auer, Herbert; Kornacker, Karl; Ostertag, Wolfram; Baum, Christopher; Mallo, Moises and Klump, Hannes. HOXB4's road map to stem cell expansion. Proc. Natl. Acad. Sci. U. S. A.. 2007;104(43):16952–16957. [doi]
  71. Rodrigues, R F; Roque, L; Krug, T and Leite, V. Poorly differentiated and anaplastic thyroid carcinomas: chromosomal and oligo-array profile of five new cell lines. Br. J. Cancer. 2007;96(8):1237–1245. [doi]
  72. Carabelli, Monica; Possenti, Marco; Sessa, Giovanna and Ciolfi Andrea; Sassi, Massimiliano; Morelli, Giorgio and Ruberti, Ida. Canopy shade causes a rapid and transient arrest in leaf development through auxin-induced cytokinin oxidase activity. Genes Dev.. 2007;21(15):1863–1868. [doi]
  73. Marsch-Martinez, Nayelli; Greco, Raffaella; Becker, Jörg D; Dixit, Shital; Bergervoet, Jan H W and Karaba Aarati; de Folter, Stefan and Pereira, Andy. BOLITA, an Arabidopsis AP2/ERF-like transcription factor that affects cell expansion and proliferation/differentiation pathways. Plant Mol. Biol.. 2006;62(6):825–843. [doi]
  74. Teixeira, Miguel Cacho and Fernandes, Alexandra Ramos and Mira Nuno Pereira. Early transcriptional response of Saccharomyces cerevisiae to stress imposed by the herbicide 2,4-dichlorophenoxyacetic acid. FEMS Yeast Res.. 2006;6(2):230–248. [doi]
  75. Pina, Cristina; Pinto, Francisco and Feijó, José A. Gene family analysis of the Arabidopsis pollen transcriptome reveals biological implications for cell growth, division control, and gene expression regulation. Plant Physiol.. 2005;138(2):744–756. [doi]
  76. Sessa, Giovanna; Carabelli, Monica; Sassi, Massimiliano; Ciolfi, Andrea; Possenti, Marco; Mittempergher, Francesca; Becker, Jorg; Morelli, Giorgio and Ruberti, Ida. A dynamic balance between gene activation and repression regulates the shade avoidance response in Arabidopsis. Genes Dev.. 2005;19(23):2811–2815. [doi]
  77. Becker, Jörg D; Boavida, Leonor C; Carneiro, Jorge; Haury, Matthias and Feijó, José A. Transcriptional profiling of Arabidopsis tissues reveals the unique characteristics of the pollen transcriptome. Plant Physiol.. 2003;133(2):713–725. [doi]

Gene Expression - NGS

  1. Ramiro, Ricardo S; Costa, Henrique and Gordo, Isabel. Macrophage adaptation leads to parallel evolution of genetically diverse Escherichia coli small-colony variants with increased fitness in vivo and antibiotic collateral sensitivity. Evol. Appl.. 2016;9(8):994–1004. [doi]
  2. Silva, Inês N; Santos, Pedro M; Santos, Mário R; Zlosnik, James E A; Speert, David P; Buskirk, Sean W; Bruger, Eric L; Waters, Christopher M; Cooper, Vaughn S and Moreira, Leonilde M. Long-Term Evolution of Burkholderia multivorans during a Chronic Cystic Fibrosis Infection Reveals Shifting Forces of Selection. mSystems. 2016;1(3):e00029–16. [doi]
  3. Godoy-Vitorino, Filipa; Rodriguez-Hilario, Arnold and Alves Ana Luísa; Gonçalves, Filipa and Cabrera-Colon Beatriz; Mesquita, Cristina Sousa and Soares-Castro Pedro; Ferreira, Marisa; Marçalo, Ana; Vingada, José; Eira, Catarina and Santos, Pedro Miguel. The microbiome of a striped dolphin (Stenella coeruleoalba) stranded in Portugal. Res. Microbiol.. 2016. [doi]
  4. Gonçalves, Margarida; Pontes, Ana; Almeida, Pedro; Barbosa, Raquel; Serra, Marta; Libkind, Diego and Hutzler Mathias; Gonçalves, Paula and Sampaio, José Paulo. Distinct Domestication Trajectories in Top-Fermenting Beer Yeasts and Wine Yeasts. Curr. Biol.. 2016;26(20):2750–2761. [doi]
  5. Barbosa, Raquel; Almeida, Pedro; Safar, Silvana V B and Santos Renata Oliveira; Morais, Paula B and Nielly-Thibault Lou; Leducq, Jean-Baptiste; Landry, Christian R; Gonçalves, Paula and Rosa, Carlos A and Sampaio José Paulo. Evidence of Natural Hybridization in Brazilian Wild Lineages of Saccharomyces cerevisiae. Genome Biol. Evol.. 2016;8(2):317–329. [doi]
  6. Azevedo, M; Sousa, A; Moura de Sousa, J; Thompson, J A; Proença, J T and Gordo, I. Trade-Offs of Escherichia coli Adaptation to an Intracellular Lifestyle in Macrophages. PLoS One. 2016;11(1):e0146123. [doi]
  7. Almeida, Pedro; Barbosa, Raquel; Zalar, Polona and Imanishi Yumi; Shimizu, Kiminori; Turchetti, Benedetta; Legras, Jean-Luc; Serra, Marta; Dequin, Sylvie and Couloux Arnaud; Guy, Julie; Bensasson, Douda and Gonçalves Paula and Sampaio, José Paulo. A population genomics insight into the Mediterranean origins of wine yeast domestication. Mol. Ecol.. 2015;24(21):5412–5427. [doi]
  8. Reed, Patricia; Atilano, Magda L; Alves, Renato and Hoiczyk Egbert; Sher, Xinwei; Reichmann, Nathalie T and Pereira Pedro M; Roemer, Terry; Filipe, Sérgio R; Pereira-Leal, José B and Ligoxygakis, Petros and Pinho Mariana G. Staphylococcus aureus Survives with a Minimal Peptidoglycan Synthesis Machine but Sacrifices Virulence and Antibiotic Resistance. PLoS Pathog.. 2015;11(5):e1004891. [doi]
  9. Ramos-Silva, Paula; Brito, Patrícia H; Serrano, Mónica; Henriques, Adriano O and Pereira-Leal, José B. Rethinking the Niche of Upper-Atmosphere Bacteria: Draft Genome Sequences of Bacillus aryabhattai C765 and Bacillus aerophilus C772, Isolated from Rice Fields. Genome Announc.. 2015;3(2). [doi]
  10. Barroso-Batista, João; Demengeot, Jocelyne and Gordo, Isabel. Adaptive immunity increases the pace and predictability of evolutionary change in commensal gut bacteria. Nat. Commun.. 2015;6:8945. [doi]
  11. de Sousa, Jorge Moura; Sousa, Ana and Bourgard, Catarina and Gordo Isabel. Potential for adaptation overrides cost of resistance. Future Microbiol.. 2015;10(9):1415–1431. [doi]
  12. Barroso-Batista, João; Sousa, Ana; Lourenço, Marta; Bergman, Marie-Louise; Sobral, Daniel and Demengeot Jocelyne; Xavier, Karina B and Gordo, Isabel. The first steps of adaptation of Escherichia coli to the gut are dominated by soft sweeps. PLoS Genet.. 2014;10(3):e1004182. [doi]
  13. Almeida, Pedro; Gonçalves, Carla; Teixeira, Sara and Libkind Diego; Bontrager, Martin; Masneuf-Pomarède, Isabelle; Albertin, Warren; Durrens, Pascal; Sherman, David James; Marullo, Philippe; Hittinger, Chris Todd; Gonçalves, Paula and Sampaio, José Paulo. A Gondwanan imprint on global diversity and domestication of wine and cider yeast Saccharomyces uvarum. Nat. Commun.. 2014;5(May):4044. [doi]

Genomics

  1. do Sambo, Maria Rosário; Penha-Gonçalves, Carlos; Trovoada, Maria Jesus; Costa, João and Lardoeyt, Roberto. Quantitative trait locus analysis of parasite density reveals that HbS gene carriage protects severe malaria patients against Plasmodium falciparum hyperparasitaemia. Malaria Journal. 2015;14(1):393. [doi]
  2. Alves, Joao M; Lima, Ana C; Pais, Isa A; Amir, Nadir; Celestino, Ricardo; Piras, Giovanna; Monne, Maria; Comas, David; Heutink, Peter; Chikhi, Lounès; Amorim, António and Lopes, Alexandra M. Reassessing the Evolutionary History of the 17q21 Inversion Polymorphism. Genome biology and evolution. 2015;7(12):3239–48. [doi]
  3. Santos, Marlene; Carvalho, Serafim; Lima, Luís; Mota-Pereira, Jorge; Pimentel, Paulo; Maia, Dulce; Correia, Diana; Gomes, Sofia; Cruz, Agostinho and Medeiros, Rui. FAS -670A\textgreaterG genetic polymorphism Is associated with Treatment Resistant Depression. Journal of Affective Disorders. 2015;185:164–169. [doi]
  4. Theologidis, Ioannis; Chelo, Ivo M and Goy, Christine. Reproductive assurance drives transitions to self-fertilization in experimental Caenorhabditis elegans. BMC Biology. 2014;12(1):93. [doi]
  5. Lima, A.; Bernardes, M.; Azevedo, R.; Monteiro, J.; Sousa, H.; Medeiros, R. and Seabra, V.. SLC19A1, SLC46A1 and SLCO1B1 Polymorphisms as Predictors of Methotrexate-Related Toxicity in Portuguese Rheumatoid Arthritis Patients. Toxicological Sciences. 2014;142(1):196–209. [doi]
  6. Bouzid, Dorra; Fourati, Hajer; Amouri, Ali; Marques, Isabel; Abida, Olfa; Tahri, Nabil; Penha-Gonçalves, Carlos and Masmoudi, Hatem. Autoimmune diseases association study with the KIAA1109–IL2–IL21 region in a Tunisian population. Molecular Biology Reports. 2014;41(11):7133–7139. [doi]
  7. Matos, Mafalda; Xavier, Joana M; Abrantes, Patrícia; Sousa, Inês; Rei, Nádia; Davatchi, Fereydoun; Shahram, Farhad; Jesus, Gorete; Barcelos, Filipe; Vedes, Joana; Salgado, Manuel; Abdollahi, Bahar Sadeghi; Nadji, Abdolhadi; Moraes-Fontes, Maria Francisca; Shafiee, Niloofar Mojarad; Ghaderibarmi, Fahmida; Vaz Patto, José; Crespo, Jorge and Oliveira, Sofia A. IL10 low-frequency variants in Behçet's disease patients. International journal of rheumatic diseases. 2014. [doi]
  8. Chelo, I M; Carvalho, S; Roque, M and Proulx, S R. The genetic basis and experimental evolution of inbreeding depression in Caenorhabditis elegans. Heredity. 2014;112(3):248–254. [doi]
  9. Trovoada, M. d. J.; Martins, M.; Ben Mansour, R.; Sambo, M. d. R.; Fernandes, A. B.; Antunes Goncalves, L.; Borja, A.; Moya, R.; Almeida, P.; Costa, J.; Marques, I.; Macedo, M. P.; Coutinho, A.; Narum, D. L. and Penha-Goncalves, C.. NOS2 Variants Reveal a Dual Genetic Control of Nitric Oxide Levels, Susceptibility to Plasmodium Infection, and Cerebral Malaria. Infection and Immunity. 2014;82(3):1287–1295. [doi]
  10. Zouidi, Ferjani; Stayoussef, Mouna; Bouzid, Dorra; Fourati, Hajer; Abida, Olfa; João, Costa; Ayed, Mourad Ben; Fakhfakh, Raouia; Thouraya, Kammoun; Monjia, Hachicha; Carlos, Penha-Gonçalves and Masmoudi, Hatem. Association of BANK1 and cytokine gene polymorphisms with type 1 diabetes in Tunisia. Gene. 2014;536(2):296–301. [doi]
  11. Zouidi, Ferjeni; Stayoussef, Mouna; Bouzid, Dorra; Fourati, Hajer; Abida, Olfa; Ayed, M Ben; Kammoun, Thouraya; Hachicha, Monjia; Penha-Gonçalves, Carlos and Masmoudi, Hatem. Contribution of PTPN22, CD28, CTLA-4 and ZAP-70 variants to the risk of type 1 diabetes in Tunisians. Gene. 2014;533(1):420–6. [doi]
  12. Carvalho, Sara; Chelo, Ivo M and Goy, Christine. The role of hermaphrodites in the experimental evolution of increased outcrossing rates in Caenorhabditis elegans. BMC Evolutionary Biology. 2014;14(1):116. [doi]
  13. Goncalves, L. A.; Rodrigues-Duarte, L.; Rodo, J.; Vieira de Moraes, L.; Marques, I. and Penha-Goncalves, C.. TREM2 governs Kupffer cell activation and explains belr1 genetic resistance to malaria liver stage infection. Proceedings of the National Academy of Sciences. 2013;110(48):19531–19536. [doi]
  14. Bouzid, Dorra; Amouri, Ali; Fourati, Hajer; Marques, Isabel; Abida, Olfa; Tahri, Nabil; Goncalves, Carlos Penha and Masmoudi, Hatem. Polymorphisms in the IL2RA and IL2RB genes in inflammatory bowel disease risk. Genetic testing and molecular biomarkers. 2013;17(11):833–9. [doi]
  15. Chelo, Ivo M.; Nédli, Judit and Gordo, Isabel. An experimental test on the probability of extinction of new genetic variants. Nature Communications. 2013;4. [doi]
  16. Caratão, Nadine; Cortesão, Catarina S.; Reis, Pedro H.; Freitas, Raquel F.; Jacob, Cristina M.A.; Pastorino, Antonio C.; Carneiro-Sampaio, Magda and Barreto, Vasco M.. A novel activation-induced cytidine deaminase (AID) mutation in Brazilian patients with hyper-IgM type 2 syndrome. Clinical Immunology. 2013;148(2):279–286. [doi]
  17. Xavier, Joana M.; Krug, Tiago; Davatchi, Fereydoun; Shahram, Farhad; Fonseca, Benedita V.; Jesus, Gorete; Barcelos, Filipe; Vedes, Joana; Salgado, Manuel; Abdollahi, Bahar Sadeghi; Nadji, Abdolhadi; Moraes-Fontes, Maria Francisca; Shafiee, Niloofar Mojarad; Ghaderibarmi, Fahmida; Vaz Patto, José; Crespo, Jorge and Oliveira, Sofia A.. Gene expression profiling and association studies implicate the neuregulin signaling pathway in Behçet's disease susceptibility. Journal of Molecular Medicine. 2013;91(8):1013–1023. [doi]
  18. Lopes, Joao S.; Marques, Isabel; Soares, Patricia; Nebenzahl-Guimaraes, Hanna; Costa, Joao; Miranda, Anabela; Duarte, Raquel; Alves, Adriana; Macedo, Rita; Duarte, Tonya A.; Barbosa, Theolis; Oliveira, Martha; Nery, Joilda S.; Boechat, Neio; Pereira, Susan M.; Barreto, Mauricio L.; Pereira-Leal, Jose; Gomes, Maria Gabriela Miranda and Penha-Goncalves, Carlos. SNP typing reveals similarity in Mycobacterium tuberculosis genetic diversity between Portugal and Northeast Brazil. Infection, Genetics and Evolution. 2013;18:238–246. [doi]
  19. Ball, E. A.; Sambo, M. R.; Martins, M.; Trovoada, M. J.; Benchimol, C.; Costa, J.; Antunes Goncalves, L.; Coutinho, A. and Penha-Goncalves, C.. IFNAR1 Controls Progression to Cerebral Malaria in Children and CD8+ T Cell Brain Pathology in Plasmodium berghei-Infected Mice. The Journal of Immunology. 2013;190(10):5118–5127. [doi]
  20. Bouzid, Dorra; Fourati, Hajer; Amouri, Ali; Marques, Isabel; Abida, Olfa; Haddouk, Samy; Ben Ayed, Mourad; Tahri, Nabil; Penha-Gonçalves, Carlos and Masmoudi, Hatem. Association of ZAP70 and PTPN6, but Not BANK1 or CLEC2D, with inflammatory bowel disease in the Tunisian population. Genetic testing and molecular biomarkers. 2013;17(4):321–6. [doi]
  21. Cortesao, Catarina S; Freitas, Raquel F and Barreto, Vasco M. Activation-Induced Cytidine Deaminase Does Not Impact on Murine Meiotic Recombination. G3 (Bethesda, Md.). 2013. [doi]
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Histopathology

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Optical Microscopy

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Transgenics

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