Publications

A full publication profile can be seen here and here.



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. PubMed PMID: 27876851; PubMed Central PMCID: PMC5120318.

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. PubMed PMID: 27489210; PubMed Central PMCID: PMC5068933.

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. PubMed PMID: 27245778; PubMed Central PMCID:PMC4886428.

Improving microRNA target prediction with gene expression profiles. Ovando-Vázquez C, Lepe-Soltero D and Abreu-Goodger C. BMC Genomics. 2016 May 17;17:364. doi: 10.1186/s12864-016-2695-1.

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. PubMed PMID: 26042133; PubMed Central PMCID: PMC4436580.

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 USA. 2015 May 26;112(21):6754-9. doi: 10.1073/pnas.1504142112. Epub 2015 May 6. PubMed PMID: 25947154; PubMed Central PMCID: PMC4450400.

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. PubMed PMID: 25421927; PubMed Central PMCID: PMC4263141.

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. PubMed PMID: 25288398; PubMed Central PMCID: PMC4203942.

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):1031-43. doi:10.1016/j.molcel.2014.02.013. Epub 2014 Mar 13. PubMed PMID: 24631284; PubMed Central PMCID: PMC4062300.

A practical guide to sequencing genomes and transcriptomes. Sanchez-Flores A, Abreu-Goodger C. Curr Top Med Chem. 2014;14(3):398-406. Review. PubMed PMID:24304310.


Older publications

7: 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. microRNA-22 promotes
heart failure through coordinate suppression of PPAR/ERR-nuclear hormone receptor
transcription. PLoS One. 2013 Sep 27;8(9):e75882. doi:
10.1371/journal.pone.0075882. eCollection 2013. PubMed PMID: 24086656; PubMed
Central PMCID: PMC3785418.


8: Llera-Herrera R, García-Gasca A, Abreu-Goodger C, Huvet A, Ibarra AM.
Identification of male gametogenesis expressed genes from the scallop Nodipecten 
subnodosus by suppressive subtraction hybridization and pyrosequencing. PLoS One.
2013 Sep 16;8(9):e73176. doi: 10.1371/journal.pone.0073176. eCollection 2013.
PubMed PMID: 24066034; PubMed Central PMCID: PMC3774672.


9: Davis MP, van Dongen S, Abreu-Goodger C, Bartonicek N, Enright AJ. Kraken: a
set of tools for quality control and analysis of high-throughput sequence data.
Methods. 2013 Sep 1;63(1):41-9. doi: 10.1016/j.ymeth.2013.06.027. Epub 2013 Jun
29. PubMed PMID: 23816787; PubMed Central PMCID: PMC3991327.


10: Carreras-Villaseñor N, Esquivel-Naranjo EU, Villalobos-Escobedo JM,
Abreu-Goodger C, Herrera-Estrella A. The RNAi machinery regulates growth and
development in the filamentous fungus Trichoderma atroviride. Mol Microbiol. 2013
Jul;89(1):96-112. doi: 10.1111/mmi.12261. Epub 2013 Jun 7. PubMed PMID: 23672609.


11: 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. Enhanced
susceptibility to Citrobacter rodentium infection in microRNA-155-deficient mice.
Infect Immun. 2013 Mar;81(3):723-32. doi: 10.1128/IAI.00969-12. Epub 2012 Dec 21.
PubMed PMID: 23264052; PubMed Central PMCID: PMC3584869.


12: Lehrbach NJ, Castro C, Murfitt KJ, Abreu-Goodger C, Griffin JL, Miska EA.
Post-developmental microRNA expression is required for normal physiology, and
regulates aging in parallel to insulin/IGF-1 signaling in C. elegans. RNA. 2012
Dec;18(12):2220-35. doi: 10.1261/rna.035402.112. Epub 2012 Oct 24. PubMed PMID:
23097426; PubMed Central PMCID: PMC3504673.


13: Davis MP, Abreu-Goodger C, van Dongen S, Lu D, Tate PH, Bartonicek N, Kutter 
C, Liu P, Skarnes WC, Enright AJ, Dunham I. Large-scale identification of
microRNA targets in murine Dgcr8-deficient embryonic stem cell lines. PLoS One.
2012;7(8):e41762. doi: 10.1371/journal.pone.0041762. Epub 2012 Aug 17. PubMed
PMID: 22912678; PubMed Central PMCID: PMC3422281.


14: Lu D, Davis MP, Abreu-Goodger C, Wang W, Campos LS, Siede J, Vigorito E,
Skarnes WC, Dunham I, Enright AJ, Liu P. MiR-25 regulates Wwp2 and Fbxw7 and
promotes reprogramming of mouse fibroblast cells to iPSCs. PLoS One.
2012;7(8):e40938. doi: 10.1371/journal.pone.0040938. Epub 2012 Aug 17. PubMed
PMID: 22912667; PubMed Central PMCID: PMC3422229.


15: 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. Extent, causes, and consequences of small RNA expression variation
in human adipose tissue. PLoS Genet. 2012;8(5):e1002704. doi:
10.1371/journal.pgen.1002704. Epub 2012 May 10. PubMed PMID: 22589741; PubMed
Central PMCID: PMC3349731.


16: 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. Targeted deletion of microRNA-22 promotes
stress-induced cardiac dilation and contractile dysfunction. Circulation. 2012
Jun 5;125(22):2751-61. doi: 10.1161/CIRCULATIONAHA.111.044354. Epub 2012 May 8.
PubMed PMID: 22570371; PubMed Central PMCID: PMC3503489.


17: van Dongen S, Abreu-Goodger C. Using MCL to extract clusters from networks.
Methods Mol Biol. 2012;804:281-95. doi: 10.1007/978-1-61779-361-5_15. PubMed
PMID: 22144159.


18: Baudet ML, Zivraj KH, Abreu-Goodger C, Muldal A, Armisen J, Blenkiron C,
Goldstein LD, Miska EA, Holt CE. miR-124 acts through CoREST to control onset of 
Sema3A sensitivity in navigating retinal growth cones. Nat Neurosci. 2011 Dec
4;15(1):29-38. doi: 10.1038/nn.2979. PubMed PMID: 22138647; PubMed Central PMCID:
PMC3661270.


19: De Fazio S, Bartonicek N, Di Giacomo M, Abreu-Goodger C, Sankar A, Funaya C, 
Antony C, Moreira PN, Enright AJ, O'Carroll D. The endonuclease activity of Mili 
fuels piRNA amplification that silences LINE1 elements. Nature. 2011 Oct
23;480(7376):259-63. doi: 10.1038/nature10547. PubMed PMID: 22020280.


20: Tripathi R, Saini HK, Rad R, Abreu-Goodger C, van Dongen S, Enright AJ.
Messenger RNA and microRNA profiling during early mouse EB formation. Gene Expr
Patterns. 2011 Jun-Jul;11(5-6):334-44. doi: 10.1016/j.gep.2011.03.004. Epub 2011 
Apr 1. PubMed PMID: 21440681.


21: Medina-Rivera A, Abreu-Goodger C, Thomas-Chollier M, Salgado H, Collado-Vides
J, van Helden J. Theoretical and empirical quality assessment of transcription
factor-binding motifs. Nucleic Acids Res. 2011 Feb;39(3):808-24. doi:
10.1093/nar/gkq710. Epub 2010 Oct 4. PubMed PMID: 20923783; PubMed Central PMCID:
PMC3035439.


22: 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. Combined agonist-antagonist genome-wide functional
screening identifies broadly active antiviral microRNAs. Proc Natl Acad Sci U S
A. 2010 Aug 3;107(31):13830-5. doi: 10.1073/pnas.1008861107. Epub 2010 Jul 19.
PubMed PMID: 20643939; PubMed Central PMCID: PMC2922253.


23: 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. The miR-144/451
locus is required for erythroid homeostasis. J Exp Med. 2010 Jul 5;207(7):1351-8.
doi: 10.1084/jem.20100458. Epub 2010 May 31. PubMed PMID: 20513743; PubMed
Central PMCID: PMC2901075.


24: 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. Malignant germ cell tumors display common microRNA profiles
resulting in global changes in expression of messenger RNA targets. Cancer Res.
2010 Apr 1;70(7):2911-23. doi: 10.1158/0008-5472.CAN-09-3301. Epub 2010 Mar 23.
PubMed PMID: 20332240; PubMed Central PMCID: PMC3000593.


25: Fabani MM, Abreu-Goodger C, Williams D, Lyons PA, Torres AG, Smith KG,
Enright AJ, Gait MJ, Vigorito E. Efficient inhibition of miR-155 function in vivo
by peptide nucleic acids. Nucleic Acids Res. 2010 Jul;38(13):4466-75. doi:
10.1093/nar/gkq160. Epub 2010 Mar 11. PubMed PMID: 20223773; PubMed Central
PMCID: PMC2910044.


26: 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. An ENU-induced mutation of miR-96 associated with progressive hearing
loss in mice. Nat Genet. 2009 May;41(5):614-8. doi: 10.1038/ng.369. Epub 2009 Apr
12. PubMed PMID: 19363478; PubMed Central PMCID: PMC2705913.


27: Mishima Y, Abreu-Goodger C, Staton AA, Stahlhut C, Shou C, Cheng C, Gerstein 
M, Enright AJ, Giraldez AJ. Zebrafish miR-1 and miR-133 shape muscle gene
expression and regulate sarcomeric actin organization. Genes Dev. 2009 Mar
1;23(5):619-32. doi: 10.1101/gad.1760209. Epub 2009 Feb 24. PubMed PMID:
19240126; PubMed Central PMCID: PMC2658521.


28: van Dongen S, Abreu-Goodger C, Enright AJ. Detecting microRNA binding and
siRNA off-target effects from expression data. Nat Methods. 2008
Dec;5(12):1023-5. doi: 10.1038/nmeth.1267. Epub 2008 Nov 2. PubMed PMID:
18978784; PubMed Central PMCID: PMC2635553.


29: Martinez-Guerrero CE, Ciria R, Abreu-Goodger C, Moreno-Hagelsieb G, Merino E.
GeConT 2: gene context analysis for orthologous proteins, conserved domains and
metabolic pathways. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W176-80.
doi: 10.1093/nar/gkn330. Epub 2008 May 29. PubMed PMID: 18511460; PubMed Central 
PMCID: PMC2447741.


30: 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. RegulonDB (version 6.0): gene regulation 
model of Escherichia coli K-12 beyond transcription, active (experimental)
annotated promoters and Textpresso navigation. Nucleic Acids Res. 2008
Jan;36(Database issue):D120-4. Epub 2007 Dec 23. PubMed PMID: 18158297; PubMed
Central PMCID: PMC2238961.


31: 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. microRNA-155 regulates the generation of immunoglobulin
class-switched plasma cells. Immunity. 2007 Dec;27(6):847-59. Epub 2007 Dec 6.
PubMed PMID: 18055230; PubMed Central PMCID: PMC4135426.


32: Hernández-Mendoza A, Nava N, Santana O, Abreu-Goodger C, Tovar A, Quinto C.
Diminished redundancy of outer membrane factor proteins in rhizobiales: a nodT
homolog is essential for free-living Rhizobium etli. J Mol Microbiol Biotechnol. 
2007;13(1-3):22-34. PubMed PMID: 17693710.


33: Poggio S, Abreu-Goodger C, Fabela S, Osorio A, Dreyfus G, Vinuesa P, Camarena
L. A complete set of flagellar genes acquired by horizontal transfer coexists
with the endogenous flagellar system in Rhodobacter sphaeroides. J Bacteriol.
2007 Apr;189(8):3208-16. Epub 2007 Feb 9. PubMed PMID: 17293429; PubMed Central
PMCID: PMC1855832.


34: Abreu-Goodger C, Merino E. RibEx: a web server for locating riboswitches and 
other conserved bacterial regulatory elements. Nucleic Acids Res. 2005 Jul
1;33(Web Server issue):W690-2. PubMed PMID: 15980564; PubMed Central PMCID:
PMC1160206.


35: Abreu-Goodger C, Ontiveros-Palacios N, Ciria R, Merino E. Conserved
regulatory motifs in bacteria: riboswitches and beyond. Trends Genet. 2004
Oct;20(10):475-9. PubMed PMID: 15363900.


36: Ciria R, Abreu-Goodger C, Morett E, Merino E. GeConT: gene context analysis. 
Bioinformatics. 2004 Sep 22;20(14):2307-8. Epub 2004 Apr 8. PubMed PMID:
15073003.


37: Jáuregui R, Abreu-Goodger C, Moreno-Hagelsieb G, Collado-Vides J, Merino E.
Conservation of DNA curvature signals in regulatory regions of prokaryotic genes.
Nucleic Acids Res. 2003 Dec 1;31(23):6770-7. PubMed PMID: 14627810; PubMed
Central PMCID: PMC290252.