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The poly(A) polymerase PAPS1 interacts with the RNA-directed DNA-methylation pathway in sporophyte and pollen development.

Zhang Y, Ramming A, Heinke L, Altschmied L, Slotkin RK, Becker JD, Kappel C, Lenhard M.

Plant J. 2019 Aug;99(4):655-672. doi: 10.1111/tpj.14348. Epub 2019 May 30.


Transcriptomics of Arabidopsis sperm cells at single-cell resolution.

Misra CS, Santos MR, Rafael-Fernandes M, Martins NP, Monteiro M, Becker JD.

Plant Reprod. 2019 Mar;32(1):29-38. doi: 10.1007/s00497-018-00355-4. Epub 2019 Jan 24.


The Trithorax group protein dMLL3/4 instructs the assembly of the zygotic genome at fertilization.

Prudêncio P, Guilgur LG, Sobral J, Becker JD, Martinho RG, Navarro-Costa P.

EMBO Rep. 2018 Aug;19(8). pii: e45728. doi: 10.15252/embr.201845728. Epub 2018 Jul 23.


The OmpR Regulator of Burkholderia multivorans Controls Mucoid-to-Nonmucoid Transition and Other Cell Envelope Properties Associated with Persistence in the Cystic Fibrosis Lung.

Silva IN, Pessoa FD, Ramires MJ, Santos MR, Becker JD, Cooper VS, Moreira LM.

J Bacteriol. 2018 Aug 10;200(17). pii: e00216-18. doi: 10.1128/JB.00216-18. Print 2018 Sep 1.


Comparative analysis of transcriptomic responses to sub-lethal levels of six environmentally relevant pesticides in Saccharomyces cerevisiae.

Gil FN, Gonçalves AC, Becker JD, Viegas CA.

Ecotoxicology. 2018 Sep;27(7):871-889. doi: 10.1007/s10646-018-1929-1. Epub 2018 Apr 2.


Blood-brain barrier transport and neuroprotective potential of blackberry-digested polyphenols: an in vitro study.

Figueira I, Tavares L, Jardim C, Costa I, Terrasso AP, Almeida AF, Govers C, Mes JJ, Gardner R, Becker JD, McDougall GJ, Stewart D, Filipe A, Kim KS, Brites D, Brito C, Brito MA, Santos CN.

Eur J Nutr. 2019 Feb;58(1):113-130. doi: 10.1007/s00394-017-1576-y. Epub 2017 Nov 18.


Isolation of Arabidopsis Pollen, Sperm Cells, and Vegetative Nuclei by Fluorescence-Activated Cell Sorting (FACS).

Santos MR, Bispo C, Becker JD.

Methods Mol Biol. 2017;1669:193-210. doi: 10.1007/978-1-4939-7286-9_16.


GLUTAMATE RECEPTOR-LIKE channels are essential for chemotaxis and reproduction in mosses.

Ortiz-Ramírez C, Michard E, Simon AA, Damineli DSC, Hernández-Coronado M, Becker JD, Feijó JA.

Nature. 2017 Sep 7;549(7670):91-95. doi: 10.1038/nature23478. Epub 2017 Jul 24.


Regulator LdhR and d-Lactate Dehydrogenase LdhA of Burkholderia multivorans Play Roles in Carbon Overflow and in Planktonic Cellular Aggregate Formation.

Silva IN, Ramires MJ, Azevedo LA, Guerreiro AR, Tavares AC, Becker JD, Moreira LM.

Appl Environ Microbiol. 2017 Sep 15;83(19). pii: e01343-17. doi: 10.1128/AEM.01343-17. Print 2017 Oct 1.


Low-dose ionizing radiation induces therapeutic neovascularization in a pre-clinical model of hindlimb ischemia.

Ministro A, de Oliveira P, Nunes RJ, Dos Santos Rocha A, Correia A, Carvalho T, Rino J, Faísca P, Becker JD, Goyri-O'Neill J, Pina F, Poli E, Silva-Santos B, Pinto F, Mareel M, Serre K, Constantino Rosa Santos S.

Cardiovasc Res. 2017 Jun 1;113(7):783-794. doi: 10.1093/cvr/cvx065.


Phylogenomic analysis of gene co-expression networks reveals the evolution of functional modules.

Ruprecht C, Proost S, Hernandez-Coronado M, Ortiz-Ramirez C, Lang D, Rensing SA, Becker JD, Vandepoele K, Mutwil M.

Plant J. 2017 May;90(3):447-465. doi: 10.1111/tpj.13502. Epub 2017 Mar 23.


Transcriptomic comparison between two Vitis vinifera L. varieties (Trincadeira and Touriga Nacional) in abiotic stress conditions.

Rocheta M, Coito JL, Ramos MJ, Carvalho L, Becker JD, Carbonell-Bejerano P, Amâncio S.

BMC Plant Biol. 2016 Oct 12;16(1):224.


Early programming of the oocyte epigenome temporally controls late prophase I transcription and chromatin remodelling.

Navarro-Costa P, McCarthy A, Prudêncio P, Greer C, Guilgur LG, Becker JD, Secombe J, Rangan P, Martinho RG.

Nat Commun. 2016 Aug 10;7:12331. doi: 10.1038/ncomms12331.


Plant Evolution: What Does It Take To Be an Egg?

Boavida LC, Becker JD.

Curr Biol. 2016 Jul 11;26(13):R527-R530. doi: 10.1016/j.cub.2016.05.044.


Transcriptomic and metabolomic profiling of ionic liquid stimuli unveils enhanced secondary metabolism in Aspergillus nidulans.

Alves PC, Hartmann DO, Núñez O, Martins I, Gomes TL, Garcia H, Galceran MT, Hampson R, Becker JD, Silva Pereira C.

BMC Genomics. 2016 Apr 12;17:284. doi: 10.1186/s12864-016-2577-6.


Assessment of fight outcome is needed to activate socially driven transcriptional changes in the zebrafish brain.

Oliveira RF, Simões JM, Teles MC, Oliveira CR, Becker JD, Lopes JS.

Proc Natl Acad Sci U S A. 2016 Feb 2;113(5):E654-61. doi: 10.1073/pnas.1514292113. Epub 2016 Jan 19.


A Transcriptome Atlas of Physcomitrella patens Provides Insights into the Evolution and Development of Land Plants.

Ortiz-Ramírez C, Hernandez-Coronado M, Thamm A, Catarino B, Wang M, Dolan L, Feijó JA, Becker JD.

Mol Plant. 2016 Feb 1;9(2):205-220. doi: 10.1016/j.molp.2015.12.002. Epub 2015 Dec 11.


Hydroxyproline O-arabinosyltransferase mutants oppositely alter tip growth in Arabidopsis thaliana and Physcomitrella patens.

MacAlister CA, Ortiz-Ramírez C, Becker JD, Feijó JA, Lippman ZB.

Plant J. 2016 Jan;85(2):193-208. doi: 10.1111/tpj.13079. Epub 2015 Dec 27.


Intercellular communication in Arabidopsis thaliana pollen discovered via AHG3 transcript movement from the vegetative cell to sperm.

Jiang H, Yi J, Boavida LC, Chen Y, Becker JD, Köhler C, McCormick S.

Proc Natl Acad Sci U S A. 2015 Oct 27;112(43):13378-83. doi: 10.1073/pnas.1510854112. Epub 2015 Oct 14.


Genome-Wide Analysis of PAPS1-Dependent Polyadenylation Identifies Novel Roles for Functionally Specialized Poly(A) Polymerases in Arabidopsis thaliana.

Kappel C, Trost G, Czesnick H, Ramming A, Kolbe B, Vi SL, Bispo C, Becker JD, de Moor C, Lenhard M.

PLoS Genet. 2015 Aug 25;11(8):e1005474. doi: 10.1371/journal.pgen.1005474. eCollection 2015 Aug.


Transcriptional profiling of Arabidopsis root hairs and pollen defines an apical cell growth signature.

Becker JD, Takeda S, Borges F, Dolan L, Feijó JA.

BMC Plant Biol. 2014 Aug 1;14:197. doi: 10.1186/s12870-014-0197-3.


Elucidating how the saprophytic fungus Aspergillus nidulans uses the plant polyester suberin as carbon source.

Martins I, Hartmann DO, Alves PC, Martins C, Garcia H, Leclercq CC, Ferreira R, He J, Renaut J, Becker JD, Silva Pereira C.

BMC Genomics. 2014 Jul 21;15:613. doi: 10.1186/1471-2164-15-613.


Potential mechanisms underlying response to effects of the fungicide pyrimethanil from gene expression profiling in Saccharomyces cerevisiae.

Gil FN, Becker JD, Viegas CA.

J Agric Food Chem. 2014 Jun 11;62(23):5237-47. doi: 10.1021/jf5007775. Epub 2014 May 28.


V-ATPase proton pumping activity is required for adult zebrafish appendage regeneration.

Monteiro J, Aires R, Becker JD, Jacinto A, Certal AC, Rodríguez-León J.

PLoS One. 2014 Mar 26;9(3):e92594. doi: 10.1371/journal.pone.0092594. eCollection 2014.


Evolutionarily conserved mechanisms of male germline development in flowering plants and animals.

Pereira PA, Navarro-Costa P, Martinho RG, Becker JD.

Biochem Soc Trans. 2014 Apr;42(2):377-82. doi: 10.1042/BST20130261. Review.


The Sinorhizobium meliloti EmrR regulator is required for efficient colonization of Medicago sativa root nodules.

Santos MR, Marques AT, Becker JD, Moreira LM.

Mol Plant Microbe Interact. 2014 Apr;27(4):388-99. doi: 10.1094/MPMI-09-13-0284-R.


Heat and water stress induce unique transcriptional signatures of heat-shock proteins and transcription factors in grapevine.

Rocheta M, Becker JD, Coito JL, Carvalho L, Amâncio S.

Funct Integr Genomics. 2014 Mar;14(1):135-48.


Transthyretin proteins regulate angiogenesis by conferring different molecular identities to endothelial cells.

Nunes RJ, de Oliveira P, Lages A, Becker JD, Marcelino P, Barroso E, Perdigoto R, Kelly JW, Quintas A, Santos SC.

J Biol Chem. 2013 Nov 1;288(44):31752-60. doi: 10.1074/jbc.M113.469858. Epub 2013 Sep 12.


Arabidopsis tetraspanins are confined to discrete expression domains and cell types in reproductive tissues and form homo- and heterodimers when expressed in yeast.

Boavida LC, Qin P, Broz M, Becker JD, McCormick S.

Plant Physiol. 2013 Oct;163(2):696-712. doi: 10.1104/pp.113.216598. Epub 2013 Aug 14.


LegumeGRN: a gene regulatory network prediction server for functional and comparative studies.

Wang M, Verdier J, Benedito VA, Tang Y, Murray JD, Ge Y, Becker JD, Carvalho H, Rogers C, Udvardi M, He J.

PLoS One. 2013 Jul 3;8(7):e67434. doi: 10.1371/journal.pone.0067434. Print 2013.


cell- and tissue-specific transcriptome analyses of Medicago truncatula root nodules.

Limpens E, Moling S, Hooiveld G, Pereira PA, Bisseling T, Becker JD, Küster H.

PLoS One. 2013 May 29;8(5):e64377. doi: 10.1371/journal.pone.0064377. Print 2013. Erratum in: PLoS One. 2014;9(1). doi:10.1371/annotation/d8bce646-4127-410a-b4dd-d2d2779a4745.


Comparative transcriptomic analysis of the Burkholderia cepacia tyrosine kinase bceF mutant reveals a role in tolerance to stress, biofilm formation, and virulence.

Ferreira AS, Silva IN, Oliveira VH, Becker JD, Givskov M, Ryan RP, Fernandes F, Moreira LM.

Appl Environ Microbiol. 2013 May;79(9):3009-20. doi: 10.1128/AEM.00222-13. Epub 2013 Feb 22.


Expression-based and co-localization detection of arabinogalactan protein 6 and arabinogalactan protein 11 interactors in Arabidopsis pollen and pollen tubes.

Costa M, Nobre MS, Becker JD, Masiero S, Amorim MI, Pereira LG, Coimbra S.

BMC Plant Biol. 2013 Jan 8;13:7. doi: 10.1186/1471-2229-13-7.


FACS-based purification of Arabidopsis microspores, sperm cells and vegetative nuclei.

Borges F, Gardner R, Lopes T, Calarco JP, Boavida LC, Slotkin RK, Martienssen RA, Becker JD.

Plant Methods. 2012 Oct 17;8(1):44. doi: 10.1186/1746-4811-8-44.


Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA.

Calarco JP, Borges F, Donoghue MT, Van Ex F, Jullien PE, Lopes T, Gardner R, Berger F, Feijó JA, Becker JD, Martienssen RA.

Cell. 2012 Sep 28;151(1):194-205. doi: 10.1016/j.cell.2012.09.001. Epub 2012 Sep 20.


Plant genes related to gibberellin biosynthesis and signaling are differentially regulated during the early stages of AM fungal interactions.

Ortu G, Balestrini R, Pereira PA, Becker JD, Küster H, Bonfante P.

Mol Plant. 2012 Jul;5(4):951-4. doi: 10.1093/mp/sss027. Epub 2012 Mar 26. No abstract available.


Inhibition of glutamine synthetase by phosphinothricin leads to transcriptome reprograming in root nodules of Medicago truncatula.

Seabra AR, Pereira PA, Becker JD, Carvalho HG.

Mol Plant Microbe Interact. 2012 Jul;25(7):976-92. doi: 10.1094/MPMI-12-11-0322.


Laser microdissection unravels cell-type-specific transcription in arbuscular mycorrhizal roots, including CAAT-box transcription factor gene expression correlating with fungal contact and spread.

Hogekamp C, Arndt D, Pereira PA, Becker JD, Hohnjec N, Küster H.

Plant Physiol. 2011 Dec;157(4):2023-43. doi: 10.1104/pp.111.186635. Epub 2011 Oct 27.


Transcriptional profiling in Saccharomyces cerevisiae relevant for predicting alachlor mechanisms of toxicity.

Gil FN, Gonçalves AC, Jacinto MJ, Becker JD, Viegas CA.

Environ Toxicol Chem. 2011 Nov;30(11):2506-18. doi: 10.1002/etc.640. Epub 2011 Sep 19.


Mucoid morphotype variation of Burkholderia multivorans during chronic cystic fibrosis lung infection is correlated with changes in metabolism, motility, biofilm formation and virulence.

Silva IN, Ferreira AS, Becker JD, Zlosnik JE, Speert DP, He J, Mil-Homens D, Moreira LM.

Microbiology. 2011 Nov;157(Pt 11):3124-37. doi: 10.1099/mic.0.050989-0. Epub 2011 Aug 11.


Identification of differentially expressed genes in the heart precursor cells of the chick embryo.

Bento M, Correia E, Tavares AT, Becker JD, Belo JA.

Gene Expr Patterns. 2011 Oct;11(7):437-47. doi: 10.1016/j.gep.2011.07.002. Epub 2011 Jul 13.


Identification and functional analysis of novel genes expressed in the Anterior Visceral Endoderm.

Gonçalves L, Filipe M, Marques S, Salgueiro AM, Becker JD, Belo JA.

Int J Dev Biol. 2011;55(3):281-95. doi: 10.1387/ijdb.103273lg.


MicroRNA activity in the Arabidopsis male germline.

Borges F, Pereira PA, Slotkin RK, Martienssen RA, Becker JD.

J Exp Bot. 2011 Mar;62(5):1611-20. doi: 10.1093/jxb/erq452. Review. Erratum in: J Exp Bot. 2011 Jun;62(10):3699.


Whole genome analysis of gene expression reveals coordinated activation of signaling and metabolic pathways during pollen-pistil interactions in Arabidopsis.

Boavida LC, Borges F, Becker JD, Feijó JA.

Plant Physiol. 2011 Apr;155(4):2066-80. doi: 10.1104/pp.110.169813. Epub 2011 Feb 11.


Genomic expression program involving the Haa1p-regulon in Saccharomyces cerevisiae response to acetic acid.

Mira NP, Becker JD, Sá-Correia I.

OMICS. 2010 Oct;14(5):587-601. doi: 10.1089/omi.2010.0048.


Absence of functional TolC protein causes increased stress response gene expression in Sinorhizobium meliloti.

Santos MR, Cosme AM, Becker JD, Medeiros JM, Mata MF, Moreira LM.

BMC Microbiol. 2010 Jun 23;10:180. doi: 10.1186/1471-2180-10-180.


"I didn't know what was wrong:" how people with undiagnosed depression recognize, name and explain their distress.

Epstein RM, Duberstein PR, Feldman MD, Rochlen AB, Bell RA, Kravitz RL, Cipri C, Becker JD, Bamonti PM, Paterniti DA.

J Gen Intern Med. 2010 Sep;25(9):954-61. doi: 10.1007/s11606-010-1367-0. Epub 2010 May 15.


A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti.

Schlüter JP, Reinkensmeier J, Daschkey S, Evguenieva-Hackenberg E, Janssen S, Jänicke S, Becker JD, Giegerich R, Becker A.

BMC Genomics. 2010 Apr 17;11:245. doi: 10.1186/1471-2164-11-245.


The RIM101 pathway has a role in Saccharomyces cerevisiae adaptive response and resistance to propionic acid and other weak acids.

Mira NP, Lourenço AB, Fernandes AR, Becker JD, Sá-Correia I.

FEMS Yeast Res. 2009 Mar;9(2):202-16. doi: 10.1111/j.1567-1364.2008.00473.x.


Epigenetic reprogramming and small RNA silencing of transposable elements in pollen.

Slotkin RK, Vaughn M, Borges F, Tanurdzić M, Becker JD, Feijó JA, Martienssen RA.

Cell. 2009 Feb 6;136(3):461-72. doi: 10.1016/j.cell.2008.12.038.

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