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Cei Abreu-Goodger (CV)

Assistant Professor (3-A, SNI 1)
 

Cei Abreu-Goodger (CV)

Position

Assistant Professor (3-A, SNI 1)
 

Group

RNA Computational Genomics
 

E-mail

cei.abreu [at] cinvestav mx
 

Phone

52 462 1663006
 

Research

2008-2010: Postdoc at the EMBL-EBI (Anton Enright)
2006-2008: Postdoc at the Wellcome Trust Sanger Institute (Anton Enright)
2005-2006: Postdoc at the CCG-UNAM (Julio Collado)

Education

2000-2005: Ph.D. Biochemical Sciences (Bioinformatics) at the IBT-UNAM (Enrique Merino)
1995-2000: B.Sc. Basic Biomedical Research at the IBB-UNAM (Fernando Bastarrachea, Carmen Gómez-Eichelmann, Marco José-Valenzuela)

Publications
Google Scholar Citations

Publications in PubMed


2013

1. Davis MP, van Dongen S, Abreu-Goodger C, Bartonicek N, Enright AJ. 2013. Kraken: A set of tools for quality control and analysis of high-throughput sequence data. Methods. 63(1):41-9.

2. Carreras-Villaseñor N, Esquivel-Naranjo EU, Villalobos-Escobedo JM, Abreu-Goodger C, Herrera-Estrella A. 2013. The RNAi machinery regulates growth and development in the filamentous fungus Trichoderma atroviride. Mol Microbiol. 89(1):96-112.

3. 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. 2013. Enhanced susceptibility to Citrobacter rodentium infection in miR-155-deficient mice. Infect Immun. 81(3):723-32.


2012

4. Lehrbach NJ, Castro C, Murfitt KJ, Abreu-Goodger C, Griffin JL, Miska EA. 2012. Post-developmental microRNA expression is required for normal physiology, and regulates aging in parallel to insulin/IGF-1 signaling in C. elegans. RNA. 18(12):2220-35.

5. Davis MP, Abreu-Goodger C, van Dongen S, Lu D, Tate PH, Bartonicek N, Kutter C, Liu P, Skarnes WC, Enright AJ, Dunham I. 2012. Large-Scale Identification of MicroRNA Targets in Murine Dgcr8-Deficient Embryonic Stem Cell Lines. PLoS One. 7(8):e41762

6. Lu D, Davis MP, Abreu-Goodger C, Wang W, Campos LS, Siede J, Vigorito E, Skarnes WC, Dunham I, Enright AJ, Liu P. 2012. MiR-25 Regulates Wwp2 and Fbxw7 and Promotes Reprogramming of Mouse Fibroblast Cells to iPSCs. PLoS One. 7(8):e40938

7. 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. 2012. Extent, causes, and consequences of small RNA expression variation in human adipose tissue. PLoS Genet. 8(5):e1002704

8. 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. 2012. Targeted Deletion of MicroRNA-22 Promotes Stress-Induced Cardiac Dilation and Contractile Dysfunction. Circulation. 125(22):2751-61.

9. van Dongen S, Abreu-Goodger C. 2012. Using MCL to Extract Clusters from Networks. Methods Mol Biol. 804:281-95.


2011

10. Baudet ML, Zivraj KH, Abreu-Goodger C, Muldal A, Armisen J, Blenkiron C, Goldstein LD, Miska EA, Holt CE. 2011. miR-124 acts through CoREST to control onset of Sema3A sensitivity in navigating retinal growth cones. Nat Neurosci. 15(1):29-38.

11. De Fazio S, Bartonicek N, Di Giacomo M, Abreu-Goodger C, Sankar A, Funaya C, Antony C, Moreira PN, Enright AJ, O\\\\\\'Carroll D. 2011. The endonuclease activity of Mili fuels piRNA amplification that silences LINE1 elements. Nature. 480(7376):259-63.

12. Tripathi R, Saini HK, Rad R, Abreu-Goodger C, van Dongen S, Enright AJ. 2011. Messenger RNA and microRNA profiling during early mouse EB formation. Gene Expr Patterns. 11(5-6):334-344.

13. Medina-Rivera A, Abreu-Goodger C, Thomas-Chollier M, Salgado H, Collado-Vides J, van Helden J. 2011. Theoretical and empirical quality assessment of transcription factor-binding motifs. Nucleic Acids Res. 39(3):808-824.


2010

14. 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. 2010. Combined agonist-antagonist genome-wide functional screening identifies broadly active antiviral microRNAs. Proc Natl Acad Sci USA. 107(31):13830-13835.

15. 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. 2010. The miR-144/451 locus is required for erythroid homeostasis. J Exp Med. 207(7):1351-1358.

16. 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. 2010. Malignant germ cell tumors display common microRNA profiles resulting in global changes in expression of messenger RNA targets. Cancer Res. 70(7):2911-2923.

17. Fabani M, Abreu-Goodger C, Williams D, Lyons P, Torres A, Smith K, Enright A, Gait M, Vigorito E. 2010. Efficient inhibition of miR-155 function in vivo by Peptide Nucleic Acids. Nucleic Acids Res. 38(13):4466-4475.



2009

18. 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. 2009. An ENU-induced mutation of miR-96 associated with progressive hearing loss in mice. Nature Genetics. 41(5):614-618.

19. Mishima Y, Abreu-Goodger C, Staton AA, Stahlhut C, Shou C, Cheng C, Gerstein M, Enright AJ, Giraldez AJ. 2009. Zebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organization. Genes & Development. 23(5):619-632.



2008

20. van Dongen S*, Abreu-Goodger C*, Enright AJ. 2008. Detecting microRNA binding and siRNA off-target effects from expression data. Nature Methods. 5(12):1023-1025. (*co-first authors)

21. Martinez-Guerrero CE, Ciria R, Abreu-Goodger C, Moreno-Hagelsieb G, Merino E. 2008. GeConT 2: gene context analysis for orthologous proteins, conserved domains and metabolic pathways. Nucleic Acids Res. 36(Web Server issue):W176-W180.

22. Gama-Castro S, Jiménez-Jacinto V, Peralta-Gil M, Santos-Zavaleta A, Peñaloza-Spinola M, 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 A, Treviño-Quintanilla L, Collado-Vides J. 2008. RegulonDB (version 6.0): Gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res. 36(Database issue):D210-D124.


2007

23. Vigorito E, Perks KL, Abreu-Goodger C, Bunting S, Xiang Z, Kohlhaas S, Das PP, Miska EA, Rodriguez AR, Bradley A, Smith KGC, Rada C, Enright AJ, Toellner K, MacLennan CM, Turner M. 2007. bic/miR-155 regulates the generation of Ig class switched plasma cells. Immunity. 27(6):847-859.

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

25. Poggio S, Abreu-Goodger C, Fabela S, Osorio A, Dreyfus G, Vinuesa P, Camarena L. 2007. A complete set of flagellar genes acquired by horizontal transfer coexists with the endogenous flagellar system in Rhodobacter sphaeroides. J Bacteriol. 189(8): 3208-3216.


2003 - 2006

26. Abreu-Goodger C, Merino E. 2006. Identificacion de riboswitches bacterianos mediante genomica comparativa. Rev. Latinoam Microbiol 48:143-145. (Artículo en español)

27. Abreu­Goodger C, Merino E. 2005. RibEx: a web server for locating riboswitches and other conserved bacterial regulatory elements. Nucleic Acids Res. 33(Web Server issue): W690­W692.

28. Abreu­Goodger C, Ontiveros­Palacios N, Ciria R, Merino E. 2004. Conserved regulatory motifs in bacteria: riboswitches and beyond. Trends in Genetics. 20(10): 475­479.

29. Ciria R, Abreu­Goodger C, Morett E, Merino E. 2004. GeConT: gene context analysis. Bioinformatics. 20(14): 2307­2308.

30. Jauregui R, Abreu­Goodger C, Moreno­Hagelsieb G, Collado­Vides J, Merino E. 2003. Conservation of DNA curvature signals in regulatory regions of prokaryotic genes. Nucleic Acids Res. 31(23): 6770­6777.

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