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Items: 46

1.

Analyses of mRNA structure dynamics identify embryonic gene regulatory programs.

Beaudoin JD, Novoa EM, Vejnar CE, Yartseva V, Takacs CM, Kellis M, Giraldez AJ.

Nat Struct Mol Biol. 2018 Aug;25(8):677-686. doi: 10.1038/s41594-018-0091-z. Epub 2018 Jul 30.

PMID:
30061596
2.

RES complex is associated with intron definition and required for zebrafish early embryogenesis.

Fernandez JP, Moreno-Mateos MA, Gohr A, Miao L, Chan SH, Irimia M, Giraldez AJ.

PLoS Genet. 2018 Jul 3;14(7):e1007473. doi: 10.1371/journal.pgen.1007473. eCollection 2018 Jul.

3.

Optimized CRISPR-Cpf1 system for genome editing in zebrafish.

Fernandez JP, Vejnar CE, Giraldez AJ, Rouet R, Moreno-Mateos MA.

Methods. 2018 Nov 1;150:11-18. doi: 10.1016/j.ymeth.2018.06.014. Epub 2018 Jun 28.

PMID:
29964176
4.

Corrigendum: Cloche is a bHLH-PAS transcription factor that drives haemato-vascular specification.

Reischauer S, Stone OA, Villasenor A, Chi N, Jin SW, Martin M, Lee MT, Fukuda N, Marass M, Witty A, Fiddes I, Kuo T, Chung WS, Salek S, Lerrigo R, Alsiö J, Luo S, Tworus D, Augustine SM, Mucenieks S, Nystedt B, Giraldez AJ, Schroth GP, Andersson O, Stainier DYR.

Nature. 2018 Mar 21;555(7697):543. doi: 10.1038/nature25991.

PMID:
29565360
5.

Erratum: Author Correction: Successful amplification of DNA aboard the International Space Station.

Boguraev AS, Christensen HC, Bonneau AR, Pezza JA, Nichols NM, Giraldez AJ, Gray MM, Wagner BM, Aken JT, Foley KD, Copeland DS, Kraves S, Saavedra EA.

NPJ Microgravity. 2018 Jan 10;4:2. doi: 10.1038/s41526-017-0035-7. eCollection 2018.

6.

CRISPR-Cpf1 mediates efficient homology-directed repair and temperature-controlled genome editing.

Moreno-Mateos MA, Fernandez JP, Rouet R, Vejnar CE, Lane MA, Mis E, Khokha MK, Doudna JA, Giraldez AJ.

Nat Commun. 2017 Dec 8;8(1):2024. doi: 10.1038/s41467-017-01836-2.

7.

Successful amplification of DNA aboard the International Space Station.

Boguraev AS, Christensen HC, Bonneau AR, Pezza JA, Nichols NM, Giraldez AJ, Gray MM, Wagner BM, Aken JT, Foley KD, Copeland DS, Kraves S, Alvarez Saavedra E.

NPJ Microgravity. 2017 Nov 16;3:26. doi: 10.1038/s41526-017-0033-9. eCollection 2017. Erratum in: NPJ Microgravity. 2018 Jan 10;4:2.

8.

RESA identifies mRNA-regulatory sequences at high resolution.

Yartseva V, Takacs CM, Vejnar CE, Lee MT, Giraldez AJ.

Nat Methods. 2017 Feb;14(2):201-207. doi: 10.1038/nmeth.4121. Epub 2016 Dec 26.

9.

Optimization Strategies for the CRISPR-Cas9 Genome-Editing System.

Vejnar CE, Moreno-Mateos MA, Cifuentes D, Bazzini AA, Giraldez AJ.

Cold Spring Harb Protoc. 2016 Oct 3;2016(10). doi: 10.1101/pdb.top090894. Review.

PMID:
27698246
10.

Optimized CRISPR-Cas9 System for Genome Editing in Zebrafish.

Vejnar CE, Moreno-Mateos MA, Cifuentes D, Bazzini AA, Giraldez AJ.

Cold Spring Harb Protoc. 2016 Oct 3;2016(10). doi: 10.1101/pdb.prot086850.

PMID:
27698232
11.

Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition.

Bazzini AA, Del Viso F, Moreno-Mateos MA, Johnstone TG, Vejnar CE, Qin Y, Yao J, Khokha MK, Giraldez AJ.

EMBO J. 2016 Oct 4;35(19):2087-2103. Epub 2016 Jul 19.

12.

Cloche is a bHLH-PAS transcription factor that drives haemato-vascular specification.

Reischauer S, Stone OA, Villasenor A, Chi N, Jin SW, Martin M, Lee MT, Fukuda N, Marass M, Witty A, Fiddes I, Kuo T, Chung WS, Salek S, Lerrigo R, Alsiö J, Luo S, Tworus D, Augustine SM, Mucenieks S, Nystedt B, Giraldez AJ, Schroth GP, Andersson O, Stainier DY.

Nature. 2016 Jul 14;535(7611):294-8. doi: 10.1038/nature18614. Erratum in: Nature. 2018 Mar 21;555(7697):543.

PMID:
27411634
13.

Upstream ORFs are prevalent translational repressors in vertebrates.

Johnstone TG, Bazzini AA, Giraldez AJ.

EMBO J. 2016 Apr 1;35(7):706-23. doi: 10.15252/embj.201592759. Epub 2016 Feb 19.

14.

Estrogens Suppress a Behavioral Phenotype in Zebrafish Mutants of the Autism Risk Gene, CNTNAP2.

Hoffman EJ, Turner KJ, Fernandez JM, Cifuentes D, Ghosh M, Ijaz S, Jain RA, Kubo F, Bill BR, Baier H, Granato M, Barresi MJ, Wilson SW, Rihel J, State MW, Giraldez AJ.

Neuron. 2016 Feb 17;89(4):725-33. doi: 10.1016/j.neuron.2015.12.039. Epub 2016 Jan 28.

15.

miR-430 regulates oriented cell division during neural tube development in zebrafish.

Takacs CM, Giraldez AJ.

Dev Biol. 2016 Jan 15;409(2):442-50. doi: 10.1016/j.ydbio.2015.11.016. Epub 2015 Nov 30.

16.

The Maternal-to-Zygotic Transition During Vertebrate Development: A Model for Reprogramming.

Yartseva V, Giraldez AJ.

Curr Top Dev Biol. 2015;113:191-232. doi: 10.1016/bs.ctdb.2015.07.020. Epub 2015 Aug 13. Review.

17.

CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo.

Moreno-Mateos MA, Vejnar CE, Beaudoin JD, Fernandez JP, Mis EK, Khokha MK, Giraldez AJ.

Nat Methods. 2015 Oct;12(10):982-8. doi: 10.1038/nmeth.3543. Epub 2015 Aug 31.

18.

Adenylation of maternally inherited microRNAs by Wispy.

Lee M, Choi Y, Kim K, Jin H, Lim J, Nguyen TA, Yang J, Jeong M, Giraldez AJ, Yang H, Patel DJ, Kim VN.

Mol Cell. 2014 Dec 4;56(5):696-707. doi: 10.1016/j.molcel.2014.10.011. Epub 2014 Nov 13.

19.

Zygotic genome activation during the maternal-to-zygotic transition.

Lee MT, Bonneau AR, Giraldez AJ.

Annu Rev Cell Dev Biol. 2014;30:581-613. doi: 10.1146/annurev-cellbio-100913-013027. Epub 2014 Aug 11. Review.

20.

Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation.

Bazzini AA, Johnstone TG, Christiano R, Mackowiak SD, Obermayer B, Fleming ES, Vejnar CE, Lee MT, Rajewsky N, Walther TC, Giraldez AJ.

EMBO J. 2014 May 2;33(9):981-93. doi: 10.1002/embj.201488411. Epub 2014 Apr 4.

21.

Poly(A)-specific ribonuclease mediates 3'-end trimming of Argonaute2-cleaved precursor microRNAs.

Yoda M, Cifuentes D, Izumi N, Sakaguchi Y, Suzuki T, Giraldez AJ, Tomari Y.

Cell Rep. 2013 Nov 14;5(3):715-26. doi: 10.1016/j.celrep.2013.09.029. Epub 2013 Oct 24.

22.

Reply to: "On the robustness of germ cell migration and microRNA-mediated regulation of chemokine signaling".

Staton AA, Knaut H, Giraldez AJ.

Nat Genet. 2013 Nov;45(11):1266-7. doi: 10.1038/ng.2812. No abstract available.

PMID:
24165725
23.

Nanog, Pou5f1 and SoxB1 activate zygotic gene expression during the maternal-to-zygotic transition.

Lee MT, Bonneau AR, Takacs CM, Bazzini AA, DiVito KR, Fleming ES, Giraldez AJ.

Nature. 2013 Nov 21;503(7476):360-4. doi: 10.1038/nature12632. Epub 2013 Sep 22.

24.

miR-1 and miR-206 regulate angiogenesis by modulating VegfA expression in zebrafish.

Stahlhut C, Suárez Y, Lu J, Mishima Y, Giraldez AJ.

Development. 2012 Dec 1;139(23):4356-64. doi: 10.1242/dev.083774.

25.

Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish.

Bazzini AA, Lee MT, Giraldez AJ.

Science. 2012 Apr 13;336(6078):233-7. doi: 10.1126/science.1215704. Epub 2012 Mar 15.

26.

Use of target protector morpholinos to analyze the physiological roles of specific miRNA-mRNA pairs in vivo.

Staton AA, Giraldez AJ.

Nat Protoc. 2011 Dec 1;6(12):2035-49. doi: 10.1038/nprot.2011.423.

27.

Evaluation and application of modularly assembled zinc-finger nucleases in zebrafish.

Zhu C, Smith T, McNulty J, Rayla AL, Lakshmanan A, Siekmann AF, Buffardi M, Meng X, Shin J, Padmanabhan A, Cifuentes D, Giraldez AJ, Look AT, Epstein JA, Lawson ND, Wolfe SA.

Development. 2011 Oct;138(20):4555-64. doi: 10.1242/dev.066779.

28.

miRNA regulation of Sdf1 chemokine signaling provides genetic robustness to germ cell migration.

Staton AA, Knaut H, Giraldez AJ.

Nat Genet. 2011 Mar;43(3):204-11. doi: 10.1038/ng.758. Epub 2011 Jan 23.

29.

MicroRNAs sculpt gene expression in embryonic development: new insights from plants.

Bazzini AA, Giraldez AJ.

Dev Cell. 2011 Jan 18;20(1):3-4. doi: 10.1016/j.devcel.2010.12.013.

30.

Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA).

Sander JD, Dahlborg EJ, Goodwin MJ, Cade L, Zhang F, Cifuentes D, Curtin SJ, Blackburn JS, Thibodeau-Beganny S, Qi Y, Pierick CJ, Hoffman E, Maeder ML, Khayter C, Reyon D, Dobbs D, Langenau DM, Stupar RM, Giraldez AJ, Voytas DF, Peterson RT, Yeh JR, Joung JK.

Nat Methods. 2011 Jan;8(1):67-9. doi: 10.1038/nmeth.1542. Epub 2010 Dec 12.

31.

microRNAs, the cell's Nepenthe: clearing the past during the maternal-to-zygotic transition and cellular reprogramming.

Giraldez AJ.

Curr Opin Genet Dev. 2010 Aug;20(4):369-75. doi: 10.1016/j.gde.2010.04.003. Epub 2010 May 6. Review.

32.

A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity.

Cifuentes D, Xue H, Taylor DW, Patnode H, Mishima Y, Cheloufi S, Ma E, Mane S, Hannon GJ, Lawson ND, Wolfe SA, Giraldez AJ.

Science. 2010 Jun 25;328(5986):1694-8. doi: 10.1126/science.1190809. Epub 2010 May 6.

33.

MicroRNAs as genetic sculptors: fishing for clues.

Takacs CM, Giraldez AJ.

Semin Cell Dev Biol. 2010 Sep;21(7):760-7. doi: 10.1016/j.semcdb.2010.02.003. Epub 2010 Feb 10. Review.

34.

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.

35.

Members of the miRNA-200 family regulate olfactory neurogenesis.

Choi PS, Zakhary L, Choi WY, Caron S, Alvarez-Saavedra E, Miska EA, McManus M, Harfe B, Giraldez AJ, Horvitz HR, Schier AF, Dulac C.

Neuron. 2008 Jan 10;57(1):41-55. doi: 10.1016/j.neuron.2007.11.018.

36.

Target protectors reveal dampening and balancing of Nodal agonist and antagonist by miR-430.

Choi WY, Giraldez AJ, Schier AF.

Science. 2007 Oct 12;318(5848):271-4. Epub 2007 Aug 30.

37.

miR-1-2 gets to the heart of the matter.

Mishima Y, Stahlhut C, Giraldez AJ.

Cell. 2007 Apr 20;129(2):247-9.

38.

MicroRNA function and mechanism: insights from zebra fish.

Schier AF, Giraldez AJ.

Cold Spring Harb Symp Quant Biol. 2006;71:195-203. Review.

PMID:
17381297
39.

Differential regulation of germline mRNAs in soma and germ cells by zebrafish miR-430.

Mishima Y, Giraldez AJ, Takeda Y, Fujiwara T, Sakamoto H, Schier AF, Inoue K.

Curr Biol. 2006 Nov 7;16(21):2135-42.

40.

Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs.

Giraldez AJ, Mishima Y, Rihel J, Grocock RJ, Van Dongen S, Inoue K, Enright AJ, Schier AF.

Science. 2006 Apr 7;312(5770):75-9. Epub 2006 Feb 16.

41.

MicroRNAs regulate brain morphogenesis in zebrafish.

Giraldez AJ, Cinalli RM, Glasner ME, Enright AJ, Thomson JM, Baskerville S, Hammond SM, Bartel DP, Schier AF.

Science. 2005 May 6;308(5723):833-8. Epub 2005 Mar 17.

42.

Nodal stability determines signaling range.

Le Good JA, Joubin K, Giraldez AJ, Ben-Haim N, Beck S, Chen Y, Schier AF, Constam DB.

Curr Biol. 2005 Jan 11;15(1):31-6.

43.

Opposing activities of Dally-like glypican at high and low levels of Wingless morphogen activity.

Kreuger J, Perez L, Giraldez AJ, Cohen SM.

Dev Cell. 2004 Oct;7(4):503-12.

44.
45.
46.

HSPG modification by the secreted enzyme Notum shapes the Wingless morphogen gradient.

Giráldez AJ, Copley RR, Cohen SM.

Dev Cell. 2002 May;2(5):667-76.

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