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Items: 1 to 50 of 51

1.

Danger signals activate a putative innate immune system during regeneration in a filamentous fungus.

Medina-Castellanos E, Villalobos-Escobedo JM, Riquelme M, Read ND, Abreu-Goodger C, Herrera-Estrella A.

PLoS Genet. 2018 Nov 30;14(11):e1007390. doi: 10.1371/journal.pgen.1007390. eCollection 2018 Nov.

2.

Identification of miR-708-5p in peripheral blood monocytes: Potential marker for postmenopausal osteoporosis in Mexican-Mestizo population.

De-La-Cruz-Montoya AH, Ramírez-Salazar EG, Martínez-Aguilar MM, González-de-la-Rosa PM, Quiterio M, Abreu-Goodger C, Salmerón J, Velázquez-Cruz R.

Exp Biol Med (Maywood). 2018 Sep;243(13):1027-1036. doi: 10.1177/1535370218806828. Epub 2018 Oct 15.

PMID:
30322266
3.

Sex determination and differentiation genes in a functional hermaphrodite scallop, Nodipecten subnodosus.

Galindo-Torres P, García-Gasca A, Llera-Herrera R, Escobedo-Fregoso C, Abreu-Goodger C, Ibarra AM.

Mar Genomics. 2018 Feb;37:161-175. doi: 10.1016/j.margen.2017.11.004. Epub 2017 Nov 24.

PMID:
29239804
4.

Annotating and quantifying pri-miRNA transcripts using RNA-Seq data of wild type and serrate-1 globular stage embryos of Arabidopsis thaliana.

Lepe-Soltero D, Armenta-Medina A, Xiang D, Datla R, Gillmor CS, Abreu-Goodger C.

Data Brief. 2017 Oct 12;15:642-647. doi: 10.1016/j.dib.2017.10.019. eCollection 2017 Dec.

5.

Arabidopsis thaliana miRNAs promote embryo pattern formation beginning in the zygote.

Armenta-Medina A, Lepe-Soltero D, Xiang D, Datla R, Abreu-Goodger C, Gillmor CS.

Dev Biol. 2017 Nov 15;431(2):145-151. doi: 10.1016/j.ydbio.2017.09.009. Epub 2017 Sep 12.

6.

Transcriptional responses of ecologically diverse Drosophila species to larval diets differing in relative sugar and protein ratios.

Nazario-Yepiz NO, Loustalot-Laclette MR, Carpinteyro-Ponce J, Abreu-Goodger C, Markow TA.

PLoS One. 2017 Aug 23;12(8):e0183007. doi: 10.1371/journal.pone.0183007. eCollection 2017.

7.

miR-182 Regulates Slit2-Mediated Axon Guidance by Modulating the Local Translation of a Specific mRNA.

Bellon A, Iyer A, Bridi S, Lee FCY, Ovando-Vázquez C, Corradi E, Longhi S, Roccuzzo M, Strohbuecker S, Naik S, Sarkies P, Miska E, Abreu-Goodger C, Holt CE, Baudet ML.

Cell Rep. 2017 Jan 31;18(5):1171-1186. doi: 10.1016/j.celrep.2016.12.093.

8.

RNA-mediated communication between helminths and their hosts: The missing links.

Claycomb J, Abreu-Goodger C, Buck AH.

RNA Biol. 2017 Apr 3;14(4):436-441. doi: 10.1080/15476286.2016.1274852. Epub 2017 Jan 26. Review.

9.

The genome, transcriptome, and proteome of the nematode Steinernema carpocapsae: evolutionary signatures of a pathogenic lifestyle.

Rougon-Cardoso A, Flores-Ponce M, Ramos-Aboites HE, Martínez-Guerrero CE, Hao YJ, Cunha L, Rodríguez-Martínez JA, Ovando-Vázquez C, Bermúdez-Barrientos JR, Abreu-Goodger C, Chavarría-Hernández N, Simões N, Montiel R.

Sci Rep. 2016 Nov 23;6:37536. doi: 10.1038/srep37536.

10.

Genome Evolution in Three Species of Cactophilic Drosophila.

Sanchez-Flores A, Peñaloza F, Carpinteyro-Ponce J, Nazario-Yepiz N, Abreu-Goodger C, Machado CA, Markow TA.

G3 (Bethesda). 2016 Oct 13;6(10):3097-3105. doi: 10.1534/g3.116.033779.

11.

The IL-4/STAT6 signaling axis establishes a conserved microRNA signature in human and mouse macrophages regulating cell survival via miR-342-3p.

Czimmerer Z, Varga T, Kiss M, Vázquez CO, Doan-Xuan QM, Rückerl D, Tattikota SG, Yan X, Nagy ZS, Daniel B, Poliska S, Horvath A, Nagy G, Varallyay E, Poy MN, Allen JE, Bacso Z, Abreu-Goodger C, Nagy L.

Genome Med. 2016 May 31;8(1):63. doi: 10.1186/s13073-016-0315-y.

12.

Improving microRNA target prediction with gene expression profiles.

Ovando-Vázquez C, Lepe-Soltero D, Abreu-Goodger C.

BMC Genomics. 2016 May 17;17:364. doi: 10.1186/s12864-016-2695-1.

13.

High-Throughput Profiling of Caenorhabditis elegans Starvation-Responsive microRNAs.

Garcia-Segura L, Abreu-Goodger C, Hernandez-Mendoza A, Dimitrova Dinkova TD, Padilla-Noriega L, Perez-Andrade ME, Miranda-Rios J.

PLoS One. 2015 Nov 10;10(11):e0142262. doi: 10.1371/journal.pone.0142262. eCollection 2015.

14.

Erratum: Exosomes secreted by nematode parasites transfer small RNAs to mammalian cells and modulate innate immunity.

Buck AH, Coakley G, Simbari F, McSorley HJ, Quintana JF, Le Bihan T, Kumar S, Abreu-Goodger C, Lear M, Harcus Y, Ceroni A, Babayan SA, Blaxter M, Ivens A, Maizels RM.

Nat Commun. 2015 Oct 22;6:8772. doi: 10.1038/ncomms9772. No abstract available.

15.

The maize (Zea mays ssp. mays var. B73) genome encodes 33 members of the purple acid phosphatase family.

González-Muñoz E, Avendaño-Vázquez AO, Montes RA, de Folter S, Andrés-Hernández L, Abreu-Goodger C, Sawers RJ.

Front Plant Sci. 2015 May 19;6:341. doi: 10.3389/fpls.2015.00341. eCollection 2015.

16.

Transcriptome diversity among rice root types during asymbiosis and interaction with arbuscular mycorrhizal fungi.

Gutjahr C, Sawers RJ, Marti G, Andrés-Hernández L, Yang SY, Casieri L, Angliker H, Oakeley EJ, Wolfender JL, Abreu-Goodger C, Paszkowski U.

Proc Natl Acad Sci U S A. 2015 May 26;112(21):6754-9. doi: 10.1073/pnas.1504142112. Epub 2015 May 6.

17.

Exosomes secreted by nematode parasites transfer small RNAs to mammalian cells and modulate innate immunity.

Buck AH, Coakley G, Simbari F, McSorley HJ, Quintana JF, Le Bihan T, Kumar S, Abreu-Goodger C, Lear M, Harcus Y, Ceroni A, Babayan SA, Blaxter M, Ivens A, Maizels RM.

Nat Commun. 2014 Nov 25;5:5488. doi: 10.1038/ncomms6488. Erratum in: Nat Commun. 2015;6:8772.

18.

The miR-155-PU.1 axis acts on Pax5 to enable efficient terminal B cell differentiation.

Lu D, Nakagawa R, Lazzaro S, Staudacher P, Abreu-Goodger C, Henley T, Boiani S, Leyland R, Galloway A, Andrews S, Butcher G, Nutt SL, Turner M, Vigorito E.

J Exp Med. 2014 Oct 20;211(11):2183-98. doi: 10.1084/jem.20140338. Epub 2014 Oct 6.

19.

Global analyses of the effect of different cellular contexts on microRNA targeting.

Nam JW, Rissland OS, Koppstein D, Abreu-Goodger C, Jan CH, Agarwal V, Yildirim MA, Rodriguez A, Bartel DP.

Mol Cell. 2014 Mar 20;53(6):1031-1043. doi: 10.1016/j.molcel.2014.02.013. Epub 2014 Mar 13.

20.

A practical guide to sequencing genomes and transcriptomes.

Sanchez-Flores A, Abreu-Goodger C.

Curr Top Med Chem. 2014;14(3):398-406. Review.

PMID:
24304310
21.

microRNA-22 promotes heart failure through coordinate suppression of PPAR/ERR-nuclear hormone receptor transcription.

Gurha P, Wang T, Larimore AH, Sassi Y, Abreu-Goodger C, Ramirez MO, Reddy AK, Engelhardt S, Taffet GE, Wehrens XH, Entman ML, Rodriguez A.

PLoS One. 2013 Sep 27;8(9):e75882. doi: 10.1371/journal.pone.0075882. eCollection 2013.

22.

Identification of male gametogenesis expressed genes from the scallop Nodipecten subnodosus by suppressive subtraction hybridization and pyrosequencing.

Llera-Herrera R, García-Gasca A, Abreu-Goodger C, Huvet A, Ibarra AM.

PLoS One. 2013 Sep 16;8(9):e73176. doi: 10.1371/journal.pone.0073176. eCollection 2013.

23.

Kraken: a set of tools for quality control and analysis of high-throughput sequence data.

Davis MP, van Dongen S, Abreu-Goodger C, Bartonicek N, Enright AJ.

Methods. 2013 Sep 1;63(1):41-9. doi: 10.1016/j.ymeth.2013.06.027. Epub 2013 Jun 29.

24.

The RNAi machinery regulates growth and development in the filamentous fungus Trichoderma atroviride.

Carreras-Villaseñor N, Esquivel-Naranjo EU, Villalobos-Escobedo JM, Abreu-Goodger C, Herrera-Estrella A.

Mol Microbiol. 2013 Jul;89(1):96-112. doi: 10.1111/mmi.12261. Epub 2013 Jun 7.

25.

Enhanced susceptibility to Citrobacter rodentium infection in microRNA-155-deficient mice.

Clare S, John V, Walker AW, Hill JL, Abreu-Goodger C, Hale C, Goulding D, Lawley TD, Mastroeni P, Frankel G, Enright AJ, Vigorito E, Dougan G.

Infect Immun. 2013 Mar;81(3):723-32. doi: 10.1128/IAI.00969-12. Epub 2012 Dec 21.

26.

Post-developmental microRNA expression is required for normal physiology, and regulates aging in parallel to insulin/IGF-1 signaling in C. elegans.

Lehrbach NJ, Castro C, Murfitt KJ, Abreu-Goodger C, Griffin JL, Miska EA.

RNA. 2012 Dec;18(12):2220-35. doi: 10.1261/rna.035402.112. Epub 2012 Oct 24.

27.

Large-scale identification of microRNA targets in murine Dgcr8-deficient embryonic stem cell lines.

Davis MP, Abreu-Goodger C, van Dongen S, Lu D, Tate PH, Bartonicek N, Kutter C, Liu P, Skarnes WC, Enright AJ, Dunham I.

PLoS One. 2012;7(8):e41762. doi: 10.1371/journal.pone.0041762. Epub 2012 Aug 17.

28.

MiR-25 regulates Wwp2 and Fbxw7 and promotes reprogramming of mouse fibroblast cells to iPSCs.

Lu D, Davis MP, Abreu-Goodger C, Wang W, Campos LS, Siede J, Vigorito E, Skarnes WC, Dunham I, Enright AJ, Liu P.

PLoS One. 2012;7(8):e40938. doi: 10.1371/journal.pone.0040938. Epub 2012 Aug 17.

29.

Extent, causes, and consequences of small RNA expression variation in human adipose tissue.

Parts L, Hedman ÅK, Keildson S, Knights AJ, Abreu-Goodger C, van de Bunt M, Guerra-Assunção JA, Bartonicek N, van Dongen S, Mägi R, Nisbet J, Barrett A, Rantalainen M, Nica AC, Quail MA, Small KS, Glass D, Enright AJ, Winn J; MuTHER Consortium, Deloukas P, Dermitzakis ET, McCarthy MI, Spector TD, Durbin R, Lindgren CM.

PLoS Genet. 2012;8(5):e1002704. doi: 10.1371/journal.pgen.1002704. Epub 2012 May 10.

30.

Targeted deletion of microRNA-22 promotes stress-induced cardiac dilation and contractile dysfunction.

Gurha P, Abreu-Goodger C, Wang T, Ramirez MO, Drumond AL, van Dongen S, Chen Y, Bartonicek N, Enright AJ, Lee B, Kelm RJ Jr, Reddy AK, Taffet GE, Bradley A, Wehrens XH, Entman ML, Rodriguez A.

Circulation. 2012 Jun 5;125(22):2751-61. doi: 10.1161/CIRCULATIONAHA.111.044354. Epub 2012 May 8.

31.

Using MCL to extract clusters from networks.

van Dongen S, Abreu-Goodger C.

Methods Mol Biol. 2012;804:281-95. doi: 10.1007/978-1-61779-361-5_15.

PMID:
22144159
32.

miR-124 acts through CoREST to control onset of Sema3A sensitivity in navigating retinal growth cones.

Baudet ML, Zivraj KH, Abreu-Goodger C, Muldal A, Armisen J, Blenkiron C, Goldstein LD, Miska EA, Holt CE.

Nat Neurosci. 2011 Dec 4;15(1):29-38. doi: 10.1038/nn.2979.

33.

The endonuclease activity of Mili fuels piRNA amplification that silences LINE1 elements.

De Fazio S, Bartonicek N, Di Giacomo M, Abreu-Goodger C, Sankar A, Funaya C, Antony C, Moreira PN, Enright AJ, O'Carroll D.

Nature. 2011 Oct 23;480(7376):259-63. doi: 10.1038/nature10547.

PMID:
22020280
34.

Messenger RNA and microRNA profiling during early mouse EB formation.

Tripathi R, Saini HK, Rad R, Abreu-Goodger C, van Dongen S, Enright AJ.

Gene Expr Patterns. 2011 Jun-Jul;11(5-6):334-44. doi: 10.1016/j.gep.2011.03.004. Epub 2011 Apr 1.

PMID:
21440681
35.

Theoretical and empirical quality assessment of transcription factor-binding motifs.

Medina-Rivera A, Abreu-Goodger C, Thomas-Chollier M, Salgado H, Collado-Vides J, van Helden J.

Nucleic Acids Res. 2011 Feb;39(3):808-24. doi: 10.1093/nar/gkq710. Epub 2010 Oct 4.

36.

Combined agonist-antagonist genome-wide functional screening identifies broadly active antiviral microRNAs.

Santhakumar D, Forster T, Laqtom NN, Fragkoudis R, Dickinson P, Abreu-Goodger C, Manakov SA, Choudhury NR, Griffiths SJ, Vermeulen A, Enright AJ, Dutia B, Kohl A, Ghazal P, Buck AH.

Proc Natl Acad Sci U S A. 2010 Aug 3;107(31):13830-5. doi: 10.1073/pnas.1008861107. Epub 2010 Jul 19.

37.

The miR-144/451 locus is required for erythroid homeostasis.

Rasmussen KD, Simmini S, Abreu-Goodger C, Bartonicek N, Di Giacomo M, Bilbao-Cortes D, Horos R, Von Lindern M, Enright AJ, O'Carroll D.

J Exp Med. 2010 Jul 5;207(7):1351-8. doi: 10.1084/jem.20100458. Epub 2010 May 31.

38.

Malignant germ cell tumors display common microRNA profiles resulting in global changes in expression of messenger RNA targets.

Palmer RD, Murray MJ, Saini HK, van Dongen S, Abreu-Goodger C, Muralidhar B, Pett MR, Thornton CM, Nicholson JC, Enright AJ, Coleman N; Children's Cancer and Leukaemia Group.

Cancer Res. 2010 Apr 1;70(7):2911-23. doi: 10.1158/0008-5472.CAN-09-3301. Epub 2010 Mar 23.

39.

Efficient inhibition of miR-155 function in vivo by peptide nucleic acids.

Fabani MM, Abreu-Goodger C, Williams D, Lyons PA, Torres AG, Smith KG, Enright AJ, Gait MJ, Vigorito E.

Nucleic Acids Res. 2010 Jul;38(13):4466-75. doi: 10.1093/nar/gkq160. Epub 2010 Mar 11.

40.

An ENU-induced mutation of miR-96 associated with progressive hearing loss in mice.

Lewis MA, Quint E, Glazier AM, Fuchs H, De Angelis MH, Langford C, van Dongen S, Abreu-Goodger C, Piipari M, Redshaw N, Dalmay T, Moreno-Pelayo MA, Enright AJ, Steel KP.

Nat Genet. 2009 May;41(5):614-8. doi: 10.1038/ng.369. Epub 2009 Apr 12.

41.

Zebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organization.

Mishima Y, Abreu-Goodger C, Staton AA, Stahlhut C, Shou C, Cheng C, Gerstein M, Enright AJ, Giraldez AJ.

Genes Dev. 2009 Mar 1;23(5):619-32. doi: 10.1101/gad.1760209. Epub 2009 Feb 24.

42.

Detecting microRNA binding and siRNA off-target effects from expression data.

van Dongen S, Abreu-Goodger C, Enright AJ.

Nat Methods. 2008 Dec;5(12):1023-5. doi: 10.1038/nmeth.1267. Epub 2008 Nov 2.

43.

GeConT 2: gene context analysis for orthologous proteins, conserved domains and metabolic pathways.

Martinez-Guerrero CE, Ciria R, Abreu-Goodger C, Moreno-Hagelsieb G, Merino E.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W176-80. doi: 10.1093/nar/gkn330. Epub 2008 May 29.

44.

RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation.

Gama-Castro S, Jiménez-Jacinto V, Peralta-Gil M, Santos-Zavaleta A, Peñaloza-Spinola MI, Contreras-Moreira B, Segura-Salazar J, Muñiz-Rascado L, Martínez-Flores I, Salgado H, Bonavides-Martínez C, Abreu-Goodger C, Rodríguez-Penagos C, Miranda-Ríos J, Morett E, Merino E, Huerta AM, Treviño-Quintanilla L, Collado-Vides J.

Nucleic Acids Res. 2008 Jan;36(Database issue):D120-4. Epub 2007 Dec 23.

45.

microRNA-155 regulates the generation of immunoglobulin class-switched plasma cells.

Vigorito E, Perks KL, Abreu-Goodger C, Bunting S, Xiang Z, Kohlhaas S, Das PP, Miska EA, Rodriguez A, Bradley A, Smith KG, Rada C, Enright AJ, Toellner KM, Maclennan IC, Turner M.

Immunity. 2007 Dec;27(6):847-59. Epub 2007 Dec 6.

46.

Diminished redundancy of outer membrane factor proteins in rhizobiales: a nodT homolog is essential for free-living Rhizobium etli.

Hernández-Mendoza A, Nava N, Santana O, Abreu-Goodger C, Tovar A, Quinto C.

J Mol Microbiol Biotechnol. 2007;13(1-3):22-34.

PMID:
17693710
47.

A complete set of flagellar genes acquired by horizontal transfer coexists with the endogenous flagellar system in Rhodobacter sphaeroides.

Poggio S, Abreu-Goodger C, Fabela S, Osorio A, Dreyfus G, Vinuesa P, Camarena L.

J Bacteriol. 2007 Apr;189(8):3208-16. Epub 2007 Feb 9.

48.

RibEx: a web server for locating riboswitches and other conserved bacterial regulatory elements.

Abreu-Goodger C, Merino E.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W690-2.

49.

Conserved regulatory motifs in bacteria: riboswitches and beyond.

Abreu-Goodger C, Ontiveros-Palacios N, Ciria R, Merino E.

Trends Genet. 2004 Oct;20(10):475-9.

PMID:
15363900
50.

GeConT: gene context analysis.

Ciria R, Abreu-Goodger C, Morett E, Merino E.

Bioinformatics. 2004 Sep 22;20(14):2307-8. Epub 2004 Apr 8.

PMID:
15073003

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