Genetically encoded affinity reagents (GEARs): A toolkit for visualizing and manipulating endogenous protein function in vivo. Boswell CW*, Hoppe C*, Sherrard A, Miao L, Kojima ML, Krishna S, Musaev D, Zhao N, Stasevich TJ, Giraldez AJ. biorxiv November 17, 2023. doi: 10.1101/2023.11.15.567075.
NaP-TRAP, a novel massively parallel reporter assay to quantify translation control. Strayer EC, Krishna S, Lee H, Vejnar C, Beaudoin JD, Giraldez AJ. biorxiv November 9, 2023. doi: 10.1101/2023.11.09.566434.
The scientific director: A complimentary model for academic leadership Hendry C, Giraldez AJ. Cell July 6, 2023. doi: 10.1016/j.cell.2023.05.036. PDF
Chromatin expansion microscopy reveals nanoscale organization of transcription and chromatin. Pownall ME, Miao L, Vejnar CE, M’Saad O, Sherrard A, Frederick MA, Benitez MDJ, Boswell CW, Zaret KS, Bewersdorf J, Giraldez AJ. Science July 5, 2023. doi: 10.1126/science.ade5308. [PDF] [Perspective] [Yale Feature]
linc-mipep and linc-wrb encode micropeptides that regulate chromatin accessibility in vertebrate-specific neural cells. Tornini VA, Miao L, Lee H, Gerson T, Dube SE, Schmidt VJ, Kroll F, Tang Y, Du K, Kuchroo M, Vejnar CE, Bazzini AA, Krishnaswamy S, Rihel J, Giraldez AJ. eLife May 16, 2023. doi: 10.7554/eLife.82249. PDF
Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing Begik O, Diensthuber G, Liu H, Delgado-Tejedor A, Kontur C, Niazi AM, Valen E, Giraldez AJ, Beaudoin JD, Mattick JS, Novoa EM Nature Methods Jan 2023. doi: 10.1038/s41592-022-01714-w. PDF
Stage Specific Transcriptomic Analysis and Database for Zebrafish Oogenesis Bogoch Y, Jamieson-Lucy A, Vejnar CE, Levy K, Giraldez AJ, Mullins MC, Elkouby YM. Frontiers in Cell and Developmental Biology June 6, 2022. doi: 10.3389/fcell.2022.826892. PDF
A group approach to growing as a principal investigator Greco V, Politi K, Eisenbarth S, Colón-Ramos D, Giraldez AJ, Bewersdorf J, Berg DN Current Biology June 6, 2022. doi: 10.1016/j.cub.2022.04.082. PDF
A proteomics approach identifies novel resident zebrafish Balbiani body proteins Cirbpa and Cirbpb Jamieson-Lucy AH, Kobayashi M, Aykit YJ, Elkouby YM, Escobar-Aguirre M, Vejnar CE, Giraldez AJ, Mullins MC Developmental Biology April 2022. doi: 10.1016/j.ydbio.2022.01.006. PDF
The landscape of pioneer factor activity reveals the mechanisms of chromatin reprogramming and genome activation. Miao L*, Tang Y*, Bonneau AR, Chan SH, Kojima ML, Pownall ME, Vejnar CE, Gao F, Krishnaswamy S, Hendry CE, Giraldez AJ. Molecular Cell Feb 18, 2022. doi: 10.1016/j.molcel.2022.01.024. PDF
Giving translation a hand. Strayer EC, Tornini VA, Giraldez AJ. Developmental Cell Nov 8, 2021. doi: 10.1016/j.devcel.2021.10.016. PDF
Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis Pradhan SJ, Reddy PC, Smutny M, Sharma A, Sako K, Oak MS, Shah R, Pal M, Deshpande O, Dsilva G, Tang Y, Mishra R, Deshpande G, Giraldez AJ, Sonawane M, Heisenberg C, Galande S Nature Communications Oct 19, 2021. doi: 10.1038/s41467-021-26234-7. PDF
Bicc1 and Dicer regulate left-right patterning through post-transcriptional control of the Nodal inhibitor Dand5 Maerker M, Getwan M, Dowdle ME , McSheene JC, Gonzalez V, Pelliccia JL, Hamilton DS, Yartseva V, Vejnar C, Tingler M, Minegishi K, Vick P, Giraldez AJ, Hamada H, Burdine RD, Sheets MD, Blum M, Schweickert A. Nature Communications Sept 16, 2021. doi: 10.1038/s41467-021-25464-z. PDF
Quantifying the effect of experimental perturbations at single-cell resolution. Burkhardt DB, Stanley JS 3rd, Tong A, Perdigoto AL, Gigante SA, Herold KC, Wolf G, Giraldez AJ, van Dijk D, Krishnaswamy S. Nature Biotechnology May 2021. doi: 10.1038/s41587-020-00803-5. PDF
Ythdf m6A Readers Function Redundantly during Zebrafish Development. Kontur C, Jeong M, Cifuentes D, Giraldez AJ. Cell Reports. Dec 29, 2020. doi: 10.1016/j.celrep.2020.108598. PDF
A Functional Non-coding RNA Is Produced from xbp-1 mRNA Liu X, Beaudoin JD, Davison CA, Kosmaczewski SG, Meyer BI, Giraldez AJ, Hammarlund M. Neuron Sept 9, 2020. doi: 10.1016/j.neuron.2020.06.015. PDF
LabxDB: versatile databases for genomic sequencing and lab management. Vejnar CE, Giraldez AJ. Bioinformatics. Aug 15, 2020. doi: 10.1093/bioinformatics/btaa557. PDF
Genome wide analysis of 3’ UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish. Vejnar CE*, Abdel Messih M*, Takacs CM*, Yartseva V*, Oikonomou P*, Christiano R, Stoeckius M, Lau S, Lee MT, Beaudoin JD, Musaev D, Darwich-Codore H, Walther TC, Tavazoie S, Cifuentes D, Giraldez AJ. Genome Research. ePub June 21, 2019. doi: 10.1101/gr.245159.118. PDF
Brd4 and P300 confer transcriptional competency during zygotic genome activation. Chan SH, Tang Y, Miao L, Darwich-Codore H, Vejnar CE, Beaudoin JD, Musaev D, Fernandez JP, Benitez MDJ, Bazzini AA, Moreno-Mateos MA, Giraldez AJ. Developmental Cell. June 17, 2019. doi: 10.1016/j.devcel.2019.05.037. PDF
Genetic compensation triggered by mutant mRNA degradation. El-Brolosy MA, Kontarakis Z, Rossi A, Kuenne C, Günther S, Fukuda N, Kikhi K, Boezio GLM, Takacs CM, Lai SL, Fukuda R, Gerri C, Giraldez AJ, Stainier DYR. Nature. April 3, 2019. doi: 10.1038/s41586-019-1064-z. PDF
Analyses of mRNA structure dynamics identify embryonic gene regulatory programs. Jean-Denis Beaudoin, Eva Maria Novoa, Charles E Vejnar, Valeria Yartseva, Carter Takacs, Manolis Kellis, Antonio J Giraldez. Nat Struct Mol Biol. August 25, 2018. doi: 10.1038/s41594-018-0091-z. PDF
RES complex is associated with intron definition and required for zebrafish early embryogenesis. Juan Fernandez*, Miguel Moreno-Mateos*, Andre Gohr, Liyun Miao, Shun Hang Chan, Manuel Irimia, Antonio Giraldez. PLoS Genet. 2018 Jul 3;14(7):e1007473. doi: 10.1371/journal.pgen.1007473. PDF
Optimized CRISPR-Cpf1 system for genome editing in zebrafish. Juan P. Fernandez*, Charles E. Vejnar*, Antonio J. Giraldez, Romain Rouet, Miguel A. Moreno-Mateos. Methods. June 2018. doi:10.1016/j.ymeth.2018.06.014. PDF
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 Communications. 2017 Dec 8;8(1):2024. doi: 10.1038/s41467-017-01836-2. PDF
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. PDF
RNA Methylation Clears the Way. Kontur C, Giraldez A. Dev Cell. 2017 Mar 13;40(5):427-428. doi: 10.1016/j.devcel.2017.02.024. PDF
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. PDF
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. PDF
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. PDF
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. PDF
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. PDF
miR-430 regulates oriented cell division during neural tube development in zebrafish. Takacs C and Giraldez. AJ. Developmental Biology, 2016 Jan 15;409(2):442-50. PDF
The Maternal-to-Zygotic Transition During Vertebrate Development: A Model for Reprogramming. Yartseva V, Giraldez AJ. Curr Top Dev Biol. 2015;113:191-232. PDF
CRISPRscan: designing highly efficient sgRNAs for CRISPR/Cas9 targeting in vivo. Moreno-Mateos MA*, Vejnar CE*, Beaudoin JD, Fernandez JP, Mis EK, Khokha MK and Giraldez AJ. Nature Methods. 2015 Oct;12(10):982-8. PDF
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. PDF
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. PDF
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 Sep 22. doi: 10.1038/nature12632. PDF
PARN mediates 3′-end trimming of Argonaute-cleaved precursor microRNAs Yoda M*, Cifuentes D*, Izumi N, Sakaguchi Y, Suzuki T, Giraldez AJ and Tomari Y. Cell Reports, Nov 14;5(3):715-26. doi: 10.1016/j.celrep.2013.09.029. Epub 2013 Oct 24. PDF
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. PDF
Ribosome Profiling Shows That miR-430 Reduces Translation Before Causing mRNA Decay in Zebrafish. Bazzini AA, Lee MT, Giraldez AJ. Science. 13 April 2012: 233-237. PDF
Use of target protector morpholinos to analyze the physiological roles of specific miRNA-mRNA pairs in vivo Alison A Staton & Antonio J Giraldez. 2011. 423 Nature Protocols. December 2011, Volume 6 No 12 - pp2035 - 2049 PDF
miRNA regulation of Sdf1 chemokine signaling provides genetic robustness to germ cell migration Staton AA, Knaut H and Giraldez AJ. Nature Genetics. 2011. Published online 23 January 2011. PDF
MicroRNAs Sculpt Gene Expression in Embryonic Development: New Insights from Plants. Bazzini AA, Giraldez AJ. Dev Cell. 2011 Jan 18;20(1):3-4. PDF
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. 2010 Dec 12. PDF
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. Epub 2010 May 6. PDF
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. Epub 2010 May 6. Review. PDF
MicroRNAs as genetic sculptors: fishing for clues. Takacs CM, Giraldez AJ. Semin Cell Dev Biol. 2010 Sep;21(7):760-7. Epub 2010 Feb 10. Review. PDF
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 & Development. 2009 Mar 1;23(5):619-32. [PDF](/docs/Genes Dev.-2009-Mishima-619-32.pdf)
MicroRNAs in Development and Disease Alison A Staton, Antonio J Giraldez. Encyclopedia of Life Sciences. Review. Published online: 15 July, 2008 PDF
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 RH, Schier AF, Dulac C. Neuron. 2008 Jan 10;57(1):41-55. PDF
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. ‡Corresponding authors.PDF
miR-1-2 gets to the heart of the matter. Mishima Y, Stahlhut C, Giraldez AJ‡. Cell. 2007 Apr 20;129(2):247-9. Review. PDF
MicroRNA function and mechanism: insights from zebra fish Schier AF, Giraldez AJ. Cold Spring Harb Symp Quant Biol. 2006. 71:195-203. Review. PDF
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. (2006) Curr Biol, 2006. Nov 7;16(21):2135-42 PDF
Zebrafish miR-430 promotes deadenylation and clearance of maternal mRNAs. Giraldez AJ, Mishima Y, Rihel J, Grocock R, van Dongen S, Inoue, K, Enright A, and Schier AF‡. Science. 2006.Apr 7;312(5770):75-9. PDF
MicroRNAs regulate brain morphogenesis in zebrafish. Giraldez AJ, Cinalli RM, Glasner ME, Enright A, Thomson JM, Baskerville S, Hammond SM, Bartel D, and Schier AF. Science. 2005 May 6;308(5723):833-8. PDF