Abreu RNAlab @ Edinburgh

Publications

For an updated list of publications, see PubMed or Google Scholar.

  1. Gene Expression Differentiation In The Reproductive Tissues Of Drosophila willistoni Subspecies And Their Hybrids. Ranz JM, Go AC, González PM, Clifton BD, Gomes S, Jaberyzadeh A, Woodbury A, Chan C, Gandasetiawan KA, Jayasekera S, Gaudreau C, Ma HC, Salceda VM, Abreu-Goodger C, Civetta A. Mol Ecol. 2023 Mar 31. doi: 10.1111/mec.16941.
  2. Translation Comes First: Ancient and Convergent Selection of Codon Usage Bias Across Prokaryotic Genomes. González-Serrano F, Abreu-Goodger C, Delaye L. J Mol Evol. 2022 Dec;90(6):438-451. doi: 10.1007/s00239-022-10074-0.
  3. Hybridization alters maternal and paternal genome contributions to early plant embryogenesis. Alaniz-Fabián J, Orozco-Nieto A, Abreu-Goodger C, Gillmor CS. Development. 2022 Nov 15;149(22):dev201025. doi: 10.1242/dev.201025.
  4. Trichoderma atroviride hyphal regeneration and conidiation depend on cell-signaling processes regulated by a microRNA-like RNA. Villalobos-Escobedo JM, Martínez-Hernández JP, Pelagio-Flores R, González-De la Rosa PM, Carreras-Villaseñor N, Abreu-Goodger C, Herrera-Estrella AH. Microb Genom. 2022 Oct;8(10):mgen000869. doi: 10.1099/mgen.0.000869.
  5. Multiscale analysis of the randomization limits of the chromosomal gene organization between Lepidoptera and Diptera. Ranz JM, González PM, Su RN, Bedford SJ, Abreu-Goodger C, Markow T. Proc Biol Sci. 2022 Jan 26;289(1967):20212183. doi: 10.1098/rspb.2021.2183.
  6. A de novo transcriptional atlas in Danaus plexippus reveals variability in dosage compensation across tissues. Ranz JM, González PM, Clifton BD, Nazario-Yepiz NO, Hernández-Cervantes PL, Palma-Martínez MJ, Valdivia DI, Jiménez-Kaufman A, Lu MM, Markow TA, Abreu-Goodger C. Commun Biol. 2021 Jun 25;4(1):791. doi: 10.1038/s42003-021-02335-3.
  7. Narnaviruses: novel players in fungal-bacterial symbioses. Espino-Vázquez AN, Bermúdez-Barrientos JR, Cabrera-Rangel JF, Córdova-López G, Cardoso-Martínez F, Martínez-Vázquez A, Camarena-Pozos DA, Mondo SJ, Pawlowska TE, Abreu-Goodger C, Partida-Martínez LP. ISME J. 2020 Jul;14(7):1743-1754. doi: 10.1038/s41396-020-0638-y.
  8. Axonal precursor miRNAs hitchhike on endosomes and locally regulate the development of neural circuits. Corradi E, Dalla Costa I, Gavoci A, Iyer A, Roccuzzo M, Otto TA, Oliani E, Bridi S, Strohbuecker S, Santos-Rodriguez G, Valdembri D, Serini G, Abreu-Goodger C, Baudet ML. EMBO J. 2020 Mar 16;39(6):e102513. doi: 10.15252/embj.2019102513.
  9. Disentangling sRNA-Seq data to study RNA communication between species. Bermúdez-Barrientos JR, Ramírez-Sánchez O, Chow FW, Buck AH, Abreu-Goodger C. Nucleic Acids Res. 2020 Feb 28;48(4):e21. doi: 10.1093/nar/gkz1198.
  10. Secretion of an Argonaute protein by a parasitic nematode and the evolution of its siRNA guides. Chow FW, Koutsovoulos G, Ovando-Vázquez C, Neophytou K, Bermúdez-Barrientos JR, Laetsch DR, Robertson E, Kumar S, Claycomb JM, Blaxter M, Abreu-Goodger C, Buck AH. Nucleic Acids Res. 2019 Apr 23;47(7):3594-3606. doi: 10.1093/nar/gkz142.
  11. Highlights of the mini-symposium on extracellular vesicles in inter-organismal communication, held in Munich, Germany, August 2018. Bielska E, Birch PRJ, Buck AH, Abreu-Goodger C, Innes RW, Jin H, Pfaffl MW, Robatzek S, Regev-Rudzki N, Tisserant C, Wang S, Weiberg A. J Extracell Vesicles. 2019 Mar 18;8(1):1590116. doi: 10.1080/20013078.2019.1590116.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. 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.
  22. 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.
  23. 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.
  24. 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.
  25. 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.
  26. 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.
  27. 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.
  28. 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.
  29. 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.
  30. A practical guide to sequencing genomes and transcriptomes. Sanchez-Flores A, Abreu-Goodger C. Curr Top Med Chem. 2014;14(3):398-406. doi: 10.2174/1568026613666131204142353.
  31. 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.
  32. 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. 
  33. 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.
  34. 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.
  35. 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.
  36. 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.
  37. 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.
  38. 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.
  39. 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.
  40. 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.
  41. 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.
  42. 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.
  43. 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.
  44. 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.
  45. 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.
  46. 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.
  47. 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.
  48. 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.
  49. 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.
  50. 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.
  51. 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.
  52. 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.
  53. 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.
  54. 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. doi: 10.1093/nar/gkm994.
  55. 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. doi: 10.1016/j.immuni.2007.10.009.
  56. 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. doi: 10.1128/JB.01681-06.
  57. 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. doi: 10.1159/000103594.
  58. 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. doi: 10.1093/nar/gki445.
  59. 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. doi: 10.1016/j.tig.2004.08.003.
  60. GeConT: gene context analysis. Ciria R, Abreu-Goodger C, Morett E, Merino E. Bioinformatics. 2004 Sep 22;20(14):2307-8. doi: 10.1093/bioinformatics/bth216.
  61. Conservation of DNA curvature signals in regulatory regions of prokaryotic genes. Jáuregui R, Abreu-Goodger C, Moreno-Hagelsieb G, Collado-Vides J, Merino E. Nucleic Acids Res. 2003 Dec 1;31(23):6770-7. doi: 10.1093/nar/gkg882.