Our Publications

Preprints

  • Medhi, Ragini & Price, Jonathan & Furlan, Giulia & Gorges, Beronia & Sapetschnig, Alexandra & Miska, Eric. (2021). RNA uridyl transferases TUT4/7 differentially regulate miRNA variants depending on the cancer cell-type. 10.1101/2021.07.12.451846.
  • Riehl, K., Riccio, C., Miska, E. A. & Hemberg, M. (2021). TransposonUltimate: software for transposon classification, annotation and detection. 10.1101/2021.04.30.442214.
  • Pirenne, L., Jakobs, M. A., Jordan, D., Franze, K., & Miska, E. A. (2021). The Orsay Virus as a model for population-wide viral infection dynamics. bioRxiv, 2021.03.02.43357.
  • Vernaz, G., Malinsky, M., Svardal, H., Du, M., Tyers, A. M., Santos, M. E., Durbin, R., Genner, M. J., Turner, G. F., & Miska, E. A. (2020). The methylomes of Lake Malawi cichlids reveal epigenetic variation associated with phenotypic diversification. bioRxiv, 2020.11.24.383034.
  • Protasio, A. V., Rawlinson, K. A., Miska, E. A., Berriman, M., & Rinaldi, G. (2020). Evidence for transposable element control by Argonautes in a parasitic flatworm lacking the piRNA pathway. bioRxiv, 670372.
  • Venkataraman, G. G., Miska, E. A., & Jordan, D. J. (n.d.). Geometric Requirements for Nonequilibrium Discrimination. Retrieved from http://arxiv.org/abs/2001.11918v2

2021

  • Gapp K, Parada G E, Gross F, Corcoba A, Kaur J, Grau E, Hemberg M, Bohacek J, Miska EA. Single paternal dexamethasone challenge programs offspring metabolism and reveals multiple candidates in RNA-mediated inheritance. iScience, 2021,
    doi:10.1016/j.isci.2021.102870.
  • Kranse O, Beasley H, Adams S, Pires-daSilva A, Bell C, Lilley CJ, Urwin PE, Bird D, Miska E, Smant G, Gheysen G, Jones J, Viney M, Abad P, Maier TR, Baum TJ, Siddique S, Williamson V, Akay A, Eves-van den Akker S. Toward genetic modification of plant-parasitic nematodes: delivery of macromolecules to adults and expression of exogenous mRNA in second stage juveniles. G3 (Bethesda). 2021 Feb 9;11(2):jkaa058. doi: 10.1093/g3journal/jkaa058. PMID: 33585878.
  • Berkyurek AC, Furlan G, Lampersberger L, Beltran T, Weick EM, Nischwitz E, Cunha Navarro I, Braukmann F, Akay A, Price J, Butter F, Sarkies P, Miska EA. The RNA polymerase II subunit RPB-9 recruits the integrator complex to terminate Caenorhabditis elegans piRNA transcription. EMBO J. 2021 Mar 1;40(5):e105565. doi: 10.15252/embj.2020105565. Epub 2021 Feb 3. PMID: 33533030; PMCID: PMC7917558.
  • Parada GE, Munita R, Georgakopoulos-Soares I, Fernandes HJR, Kedlian VR, Metzakopian E, Andres ME, Miska EA, Hemberg M. MicroExonator enables systematic discovery and quantification of microexons across mouse embryonic development. Genome Biol. 2021 Jan 22;22(1):43. doi: 10.1186/s13059-020-02246-2. PMID: 33482885; PMCID: PMC7821500.

2020

  • Puntambekar S, Newhouse R, Navas JSM, Chauhan R, Vernaz G, Willis T, Wayland MT, Umrania Y, Miska EA, Prabakaran S. Evolutionary divergence of novel open reading frames in cichlids speciation. Sci Rep. 2020 Dec 9;10(1):21570. doi: 10.1038/s41598-020-78555-0. PMID: 33299045
  • Navarro IC, Tuorto F, Jordan D, Legrand C, Price J, Braukmann F, Hendrick AG, Akay A, Kotter A, Helm M, Lyko F, Miska EA. Translational adaptation to heat stress is mediated by RNA 5-methylcytosine in Caenorhabditis elegans. EMBO J. 2020 Dec 7:e105496. doi: 10.15252/embj.2020105496. Epub ahead of print. PMID: 33283887
  • Ziv O, Price J, Shalamova L, Kamenova T, Goodfellow I, Weber F, Miska EA. The Short- and Long-Range RNA-RNA Interactome of SARS-CoV-2. Mol Cell. 2020 Nov 5:S1097-2765(20)30782-6. doi: 10.1016/j.molcel.2020.11.004. Epub ahead of print. PMID: 33259809
  • Braukmann F, Jordan D, Jenkins B, Koulman A, Miska EA. SID-2 negatively regulates development likely independent of nutritional dsRNA uptake. RNA Biol. 2020 Oct 12:1-12. doi: 10.1080/15476286.2020.1827619. Epub ahead of print. PMID: 33044912
  • van Steenwyk G, Gapp K, Jawaid A, Germain PL, Manuella F, Tanwar DK, Zamboni N, Gaur N, Efimova A, Thumfart KM, Miska EA, Mansuy IM. Involvement of circulating factors in the transmission of paternal experiences through the germline. EMBO J. 2020 Oct 9:e104579. doi: 10.15252/embj.2020104579. Epub ahead of print. PMID: 33034389.
  • Suen KM, Braukmann F, Butler R, Bensaddek D, Akay A, Lin CC, Milonaitytė D, Doshi N, Sapetschnig A, Lamond A, Ladbury JE, Miska EA. DEPS-1 is required for piRNA-dependent silencing and PIWI condensate organisation in Caenorhabditis elegans. Nat Commun. 2020 Aug 25;11(1):4242. doi: 10.1038/s41467-020-18089-1. PMID: 32843637
  • Lewis SH, Ross L, Bain SA, Pahita E, Smith SA, Cordaux R, Miska EA, Lenhard B, Jiggins FM, Sarkies P. ——Widespread conservation and lineage-specific diversification of genome-wide DNA methylation patterns across arthropods. PLoS Genet. 2020 Jun 25;16(6):e1008864. doi: 10.1371/journal.pgen.1008864. PMID: 32584820
  • Chauve L, Le Pen J, Hodge F, Todtenhaupt P, Biggins L, Miska EA, Andrews S, Casanueva O. High-Throughput Quantitative RT-PCR in Single and Bulk C. elegans Samples Using Nanofluidic Technology. J Vis Exp. 2020 May 28;(159). doi: 10.3791/61132. PMID: 32538915
  • Lewis A, Berkyurek AC, Greiner A, Sawh AN, Vashisht A, Merrett S, Flamand MN, Wohlschlegel J, Sarov M, Miska EA, Duchaine TF. (2020) A Family of Argonaute-Interacting Proteins Gates Nuclear RNAi. Mol Cell. Online ahead of print. PMID: 32348780
  • Bista I, McCarthy SA, Wood J, Ning Z, Detrich Iii HW, Desvignes T, Postlethwait J, Chow W, Howe K, Torrance J, Smith M, Oliver K; Vertebrate Genomes Project Consortium, Miska EA, Durbin R. The genome sequence of the channel bull blenny, Cottoperca gobio (Günther, 1861). Wellcome Open Res. 2020 Jun 24;5:148. doi: 10.12688/wellcomeopenres.16012.1. PMID: 33195818
  • Burton NO, Riccio C, Dallaire A, Price J, Jenkins B, Koulman A, Miska EA. (2020) Cysteine synthases CYSL-1 and CYSL-2 mediate C. elegans heritable adaptation to P. vranovensis infection. Nat Commun. PMID: 32269224

2019

  • Svardal, H., Quah, F. X., Malinsky, M., Ngatunga, B. P., Miska, E. A., Salzburger, W., Genner, M. J., Turner, G. F., & Durbin, R. (2019). Ancestral hybridisation facilitated species diversification in the Lake Malawi cichlid fish adaptive radiation. Molecular biology and evolution, msz294. Advance online publication. PMID 31821500
  • Aloia L, McKie MA, Vernaz G, Cordero-Espinoza L, Aleksieva N, van den Ameele J, Antonica F, Font-Cunill B, Raven A, Aiese Cigliano R, Belenguer G, Mort RL, Brand AH, Zernicka-Goetz M, Forbes SJ, Miska EA, Huch M (2019) Epigenetic remodelling licences adult cholangiocytes for organoid formation and liver regeneration. Nat Cell Biol. PMID 31685987
  • Van Haute L, Lee SY, McCann BJ, Powell CA, Bansal D, Vasiliauskaitė L, Garone C, Shin S, Kim JS, Frye M, Gleeson JG, Miska EA, Rhee HW, Minczuk M (2019) NSUN2 introduces 5-methylcytosines in mammalian mitochondrial tRNAs. Nucleic Acids Res. PMID 31276587
  • LeBoeuf AC, Waridel P, Brent CS, Gonçalves AN, Menin L, Ortiz D, Riba-Grognuz O, Koto A, Soares ZG, Privman E, Miska EA, Benton R, Keller L (2019) Oral transfer of chemical cues, growth proteins and hormones in social insects. Elife. PMID 31424387
  • Matsushima W, Herzog VA, Neumann T, Gapp K, Zuber J, Ameres SL, Miska EA (2019) Sequencing cell-type-specific transcriptomes with SLAM-ITseq. Nat Protoc. PMID 31243395
  • Matsushima W, Brink K, Schroeder J, Miska EA, Gapp K (2019) Mature sperm small-RNA profile in the sparrow: implications for transgenerational effects of age on fitness. Environ Epigenet. PMID 31139435
  • Maori E, Navarro IC, Boncristiani H, Seilly DJ, Rudolph KLM, Sapetschnig A, Lin CC, Ladbury JE, Evans JD, Heeney JL, Miska EA (2019) A Secreted RNA Binding Protein Forms RNA-Stabilizing Granules in the Honeybee Royal Jelly. Mol Cell. PMID 31051140
  • Akay A, Jordan D, Navarro IC, Wrzesinski T, Ponting CP, Miska EA, Haerty W. (2019) Identification of functional long non-coding RNAs in C. elegans. BMC Biol. PMID 30777050
  • Bezler A, Braukmann F, West SM, Duplan A, Conconi R, Schütz F, Gönczy P, Piano F, Gunsalus K, Miska EA, Keller L. (2019) Tissue- and sex-specific small RNAomes reveal sex differences in response to the environment. PLoS Genet. PMID 30735500
  • Weng C, Kosalka J, Berkyurek AC, Stempor P, Feng X, Mao H, Zeng C, Li WJ, Yan YH, Dong MQ, Morero NR, Zuliani C, Barabas O, Ahringer J, Guang S, Miska EA (2019) The USTC co-opts an ancient machinery to drive piRNA transcription in C. elegans. Genes Dev. PMID 30567997

2018

  • Malinsky M, Svardal H, Tyers AM, Miska EA, Genner MJ, Turner GF, Durbin R. (2018) Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow. Nat Ecol Evol. PMID 30455444
  • Gapp K, van Steenwyk G, Germain PL, Matsushima W, Rudolph KLM, Manuella F, Roszkowski M, Vernaz G, Ghosh T, Pelczar P, Mansuy IM, Miska EA (2018) Alterations in sperm long RNA contribute to the epigenetic inheritance of the effects of postnatal trauma. Mol Psychiatry. PMID 30374190
  • Ziv O, Gabryelska MM, Lun ATL, Gebert LFR, Sheu-Gruttadauria J, Meredith LW, Liu ZY, Kwok CK, Qin CF, MacRae IJ, Goodfellow I, Marioni JC, Kudla G, Miska EA (2018) COMRADES determines in vivo RNA structures and interactions. Nat Methods. PMID 30202058
  • Le Pen J, Jiang H, Di Domenico T, Kneuss E, Kosałka J, Leung C, Morgan M, Much C, Rudolph KLM, Enright AJ, O’Carroll D, Wang D, Miska EA (2018) Terminal uridylyltransferases target RNA viruses as part of the innate immune system. Nat Struct Mol Biol. PMID 30104661
  • Matsushima W, Herzog VA, Neumann T, Gapp K, Zuber J, Ameres SL, Miska EA (2018) SLAM-ITseq: sequencing cell type-specific transcriptomes without cell sorting. Development. PMID 29945865
  • Lewis SH, Quarles KA, Yang Y, Tanguy M, Frézal L, Smith SA, Sharma PP, Cordaux R, Gilbert C, Giraud I, Collins DH, Zamore PD, Miska EA, Sarkies P, Jiggins FM. (2018) Pan-arthropod analysis reveals somatic piRNAs as an ancestral defence against transposable elements. Nat Ecol Evol. PMID 29203920

2017

  • Tanguy M, Véron L, Stempor P, Ahringer J, Sarkies P, Miska EA, (2017) An Alternative STAT Signaling Pathway Acts in Viral Immunity in Caenorhabditis elegans. MBio. PMID 28874466
  • Akay A, Di Domenico T, Suen KM, Nabih A, Parada GE, Larance M, Medhi R, Berkyurek AC, Zhang X, Wedeles CJ, Rudolph KLM, Engelhardt J, Hemberg M, Ma P, Lamond AI, Claycomb JM, Miska EA, (2017) The Helicase Aquarius/EMB-4 Is Required to Overcome Intronic Barriers to Allow Nuclear RNAi Pathways to Heritably Silence Transcription. Dev Cell. PMID 28787591
  • Braukmann F, Jordan D, Miska E, (2017) Artificial and natural RNA interactions between bacteria and c.elegans. RNA Biology. PMID 28332918
  • van Delft P, Akay A, Huber SM, Bueschl C, Rudolph KLM, Di Domenico T, Schuhmacher R, Miska EA, Balasubramanian S (2017). The profile and dynamics of RNA modifications in animals. Chem Bio Chem. PMID 28449301

2016

  • Rainey SM, Martinez J, McFarlane M, Juneja P, Sarkies P, Lulia A, Schnettler E, Varjak M, Merits A, Miska EA, Jiggins FM, Kohl A (2016) Wolbachia Blocks Viral Genome Replication Early in Infection without a Transcriptonal Response by the Endosymbiont or Host Small RNA Pathways.  PLOS Pathog. PMID 27089431
  • Lightfoot HL, Miska EA, Balasubramanian S. (2016) Identification of small molecules inhibitors of the Lin28-mediated blockage of pre-let-7g processing. Org Biomol Chem. PMID 27731469
  • Cording, A, Gormally M, Bond PJ, Carrington M, Balasubramanian S, Miska EA, Thomas B (2016) Selective inhibitors of trypanosomal uridylyl transferase RET1 establish druggability of RNA post-transcriptional modifications.  RNA Biol. PMID 26786754
  • Gapp K, Miska EA (2016) tRNA fragments: novel players in intergenerational inheritance.  Cell Res. Apr;26(4):395-6. doi: 10.1038/cr.2016.24. Epub 2016 Feb 23. PMID: 26902286

2015

  • Malinsky M, Challis RJ, Tyers AM, Schiffels S, Terai Y, Ngatunga BP, Miska EA, Durbin R, Genner MJ, Turner GF (2016) Genomic Islands of speciation separate cichlid ecomorphs in an East African crater lake. Science. Dec 18;350(6267):1493-8. doi: 10.1126/science.aac9927 PMID: 2668019
  • Sapetschnig A, Sarkies P, Lehrbach NJ, Miska EA. (2015) Tertiary siRNAs Mediate Paramutation in C. elegans. PLoS Genet. 2015 Mar 26;11(3):e1005078. doi: 10.1371/journal.pgen.1005078. eCollection 2015 Feb. PMID: 25811365
  • Huber SM, van Delft P, Mendil L, Bachman M, Smollett K, Werner F, Miska EA, Balasubramanian S (2015) Formation and abundance of 5-hydroxymethylcytosine in RNA. Chembiochem. 2015 Mar 23;16(5):752-5. doi: 10.1002/cbic.201500013. Epub 2015 Feb 12. PMID: 25676849
  • Sarkies P, Selkirk ME, Jones JT, Blok V, Boothby T, Goldstein B, Hanelt B, Ardila-Garcia A, Fast NM, Schiffer PM, Kraus C, Taylor MJ, Koutsovoulos G, Blaxter ML, Miska EA (2015) Ancient and novel small RNA pathways compensate for the loss of piRNAs in multiple independent nematode lineages. PLoS Biol. 2015 Feb 10;13(2):e1002061. doi: 10.1371/journal.pbio.1002061. eCollection 2015 Feb. PMID: 25668728
  • Sakaguchi A, Sarkies P, Simon M, Doebley AL, Goldstein LD, Hedges A, Ikegami K, Alvares SM, Yang L, LaRocque JR, Hall J, Miska EA, Ahmed S (2015) Caenorhabditis elegans RSD-2 and RSD-6 promote germ cell immortality by maintaining small interfering RNA populations. Proc Natl Acad Sci 2014 Oct 14;111(41):E4323-31. doi: 10.1073/pnas.1406131111. Epub 2014 Sep 25. PMID: 25258416

2014

  • Brawand D, Wagner CE, Li YI, Malinsky M … et al … Miska EA, Lander ES, Venkatesh B, Fernald RD, Meyer A, Ponting CP, Streelman JT, Lindblad-Toh K, Seehausen O, Di Palma F. (2014) The Genomic Substrate for adaptive radiation in African cichlid fish. Nature. 2014, Sept 18. 515, 374-381, doi: 10.1038/nature13726. PMID:25186727
  • Weick EM, Miska EA. (2014) piRNAs: from biogenesis to function. Development. 2014. Sept 14. 141(18); 3458-71. do: 10.1242/dev.094037. PMID 25183868. Free Article.
  • Sakaguchi A, Sarkies P, Simon M, Doebley AL, Goldstein LD, Hedges A, Ikegami K, Alvares SM, Yang L, LaRocque JR, Hall J, Miska EA, Ahmed, S (2014). Caenorhabditis elegans RSD-2 and RSD-6 promote germ cell immortality by maintaining small interfering RNA populations. PNAS. 2014, Sept 3. 111(41):E4323-31.doi: 10.1073/pnas.1406131111.  PMID: 25258416
  • Peden AS, Mac P, Fei YJ, Castro C, Jiang G, Murfitt KJ, Miska EA, Griffin JL, Ganapathy V, Jorgensen EM (2014) Erratum: Betaine acts on a ligand-gated ion channel in the nervous system of the nematode C. elegans. Nature Neuroscience. 2014 Nov 21, 17, 1840 (2014). doi:10.1038/nn1214-1840f. PMID:25413096
  • Bassett AR, Akhtar A, Barlow DP, Bird AP, Brockdorff N, Duboule D, Ephrussi A, Ferguson-Smith AC, Gingeras TR, Haerty W, Higgs DR, Miska EA, Ponting CP (2014). Considerations when investigating IncRNA function in vivo. Elife. 2014 Aug 14;3:e03058. doi: 10.7554/eLife.03058. PMID 25124674. PMCID: PMC4132285. Free Article.
  • Sarkies P, Miska EA. (2014) Small RNAs break out: the molecular cell biology of mobile small RNAs. Nature Rev Mol Cell Biol. 2014 Aug 15(8):525-35. do: 10.1038/nrm3840. Review. PMID 25053358.
  • Sapetschnig A, Miska EA. (2014). Getting a grip on piRNA cluster transcription. Cell. 2014 June 5;157(6):1253-4, doi: 10.1016/j.cell.2014.05.022. PMID 24906143. PMCID: PMC4053829
  • Simon M, Sarkies P, Ikegami K, Doebley AL, Goldstein LD, Mitchell J, Sakaguchi A, Miska EA, Ahmed S. (2014). Reduced insulin/GF-1 signaling restores germ cell immortality to caenorhabditis elegans Piwi mutans.
  • Weick EM, Sarkies, P, Silva N, Chen RA, Moss SM, Cording AC, Ahringer J, Martinez-Perez, Miska EA. (2014). PRDE-1 is a nuclear factor essential for the biogenesis of Ruby motif-dependent piRNAs in C. elegans. Genes Dev. 2014 Apr 1;28(7):783-96. doi: 10.1101/gad.238105.114.  PMID: 24696457 [PubMed – in process] Free Article
  • Gapp K, Jawaid A, Sarkies P, Bohacek J, Pelczar P, Prados J, Farinelli L, Miska EA, Mansuy IM. (2014). Implication of sperm RNAs in transgenerational inheritance of the effects of early trauma in mice. Nat Neurosci. 2014 Apr 13. doi: 10.1038/nn.3695. [Epub ahead of print] PMID: 24728267 [PubMed – as supplied by publisher]

2013

  • Akay, A., Craig, A., Lehrbach, N., Larance, M., Pourkarimi, E., Wright, J. E., et al. (2013). RNA-binding protein GLD-1/quaking genetically interacts with the mir-35 and the let-7 miRNA pathways in Caenorhabditis elegans. Open Biology, 3(11), 130151–130151. doi:10.1098/rsob.130151 PDF
  • Peden, A. S., Mac, P., Fei, Y.-J., Castro, C., Jiang, G., Murfitt, K. J., et al. (2013). Betaine acts on a ligand-gated ion channel in the nervous system of the nematode C. elegans. Nat Neurosci doi:10.1038/nn.3575 PDF
  • Tanguy, M., & Miska, E. A. (2013). Antiviral RNA interference in animals: piecing together the evidence. Nature Structural & Molecular Biology, 20(11), 1239–1241. doi:10.1038/nsmb.2708 PDF
  • Ashe A., Bélicard T., Le Pen J., Sarkies P., Frézal L., Lehrbach N. J., Félix M.-A., Miska E. A., 2013   A deletion polymorphism in the Caenorhabditis elegans RIG-I homolog disables viral RNA dicing and antiviral immunity. eLife 2: e00994. PDF
  • Harding J.L., Horswell S., Heliot C., Armisen J., Luscombe N.M., Zimmerman L., Miska E.A., and Hill C.S. 2013  Small RNA profiling of Xenopus embryos reveals novel miRNAs and a new class of small RNAs derived from intronic transposable elements. Genome Res published ahead of print online. PDF 
  • Mok Y., Schwierzeck V., Thomas D. C., Vigorito E., Rayner T. F., Jarvis L. B., Prosser H. M., Bradley A., Withers D. R., Mårtensson I.-L., Corcoran L. M., Blenkiron C., Miska E. A., Lyons P. A., Smith K. G. C., 2013   MiR-210 Is Induced by Oct-2, Regulates B Cells, and Inhibits Autoantibody Production. J Immunol.  PDF
  • Sarkies P., Miska E. A., 2013   Molecular biology. Is there social RNA? Science 341: 467–468. PDF
  • Sarkies P., Miska E. A., 2013   RNAi pathways in the recognition of foreign RNA: antiviral responses and host-parasite interactions in nematodes. Biochem. Soc. Trans. 41: 876–880. PDF
  • Sarkies P., Ashe A., Le Pen J., McKie M. A., Miska E. A., 2013   Competition between virus-derived and endogenous small RNAs regulates gene expression in Caenorhabditis elegans. Genome Res 23: 1258–1270. PDF
  • Dvinge H., Git A., Gräf S., Salmon-Divon M., Curtis C., Sottoriva A., Zhao Y., Hirst M., Armisen J., Miska E. A., Chin S.-F., Provenzano E., Turashvili G., Green A., Ellis I., Aparicio S., Caldas C., 2013   The shaping and functional consequences of the microRNA landscape in breast cancer. Nature 497: 378–382. PDF
  • Castro C., Krumsiek J., Lehrbach N. J., Murfitt S. A., Miska E. A., Griffin J. L., 2013   A study of Caenorhabditis elegans DAF-2 mutants by metabolomics and differential correlation networks. Mol Biosyst 9: 1632–1642. PDF

2012

  • Lehrbach N. J., Castro C., Murfitt K. J., Abreu-Goodger C., Griffin J. L., Miska E. A., 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: 2220–2235. PDF
  • Ashe A., Sapetschnig A., Weick E.-M., Mitchell J., Bagijn M. P., Cording A. C., Doebley A.-L., Goldstein L. D., Lehrbach N. J., Le Pen J., Pintacuda G., Sakaguchi A., Sarkies P., Ahmed S., Miska E. A., 2012   piRNAs Can Trigger a Multigenerational Epigenetic Memory in the Germline of C. elegans. Cell 150: 88–99. PDF
  • Kamminga L. M., van Wolfswinkel J. C., Luteijn M. J., Kaaij L. J. T., Bagijn M. P., Sapetschnig A., Miska E. A., Berezikov E., Ketting R. F., 2012   Differential Impact of the HEN1 Homolog HENN-1 on 21U and 26G RNAs in the Germline of Caenorhabditis elegans. PLoS Genet 8: e1002702. PDF
  • Bagijn M. P., Goldstein L. D., Sapetschnig A., Weick E.-M., Bouasker S., Lehrbach N. J., Simard M. J., Miska E. A., 2012   Function, targets, and evolution of Caenorhabditis elegans piRNAs. Science 337: 574–578. PDF
  • Jovanovic M., Reiter L., Clark A., Weiss M., Picotti P., Rehrauer H., Frei A., Neukomm L. J., Kaufman E., Wollscheid B., Simard M. J., Miska E. A., Aebersold R., Gerber A. P., Hengartner M. O., 2012   RIP-chip-SRM–a new combinatorial large-scale approach identifies a set of translationally regulated bantam/miR-58 targets in C. elegans. Genome Res 22: 1360–1371. PDF
  • Castro C., Sar F., Shaw W. R., Mishima M., Miska E. A., Griffin J. L., 2012   A metabolomic strategy defines the regulation of lipid content and global metabolism by Δ9 desaturases in Caenorhabditis elegans. BMC Genomics 13: 36. PDF
  • Vasquez-Rifo A., Jannot G., Armisen J., Labouesse M., Bukhari S. I. A., Rondeau E. L., Miska E. A., Simard M. J., 2012   Developmental characterization of the microRNA-specific C. elegans Argonautes alg-1 and alg-2. PLoS One 7: e33750. PDF
  • Baudet M.-L., Zivraj K. H., Abreu-Goodger C., Muldal A., Armisen J., Blenkiron C., Goldstein L. D., Miska E. A., Holt C. E., 2012   miR-124 acts through CoREST to control onset of Sema3A sensitivity in navigating retinal growth cones. Nat. Neurosci. 15: 29–38. PDF

2011

  • Lightfoot H. L., Bugaut A., Armisen J., Lehrbach N. J., Miska E. A., Balasubramanian S., 2011   A LIN28-dependent structural change in pre-let-7g directly inhibits dicer processing. Biochemistry 50: 7514–7521. PDF
  • Félix M.-A., Ashe A., Piffaretti J., Wu G., Nuez I., Bélicard T., Jiang Y., Zhao G., Franz C. J., Goldstein L. D., Sanroman M., Miska E. A., Wang D., 2011   Natural and experimental infection of nematodes by novel viruses related to nodaviruses. PLoS Biol. 9: e1000586. PDF

2010

  • Lehrbach N. J., Miska E. A., 2010   Regulation of pre-miRNA Processing. Adv Exp Med Biol 700: 67–75. BOOK
  • Hanina S. A., Mifsud W., Down T. A., Hayashi K., O’Carroll D., Lao K., Miska E. A., Surani M. A., 2010   Genome-wide identification of targets and function of individual MicroRNAs in mouse embryonic stem cells. PLoS Genet 6: e1001163. PDF
  • Jovanovic M., Reiter L., Picotti P., Lange V., Bogan E., Hurschler B. A., Blenkiron C., Lehrbach N. J., Ding X. C., Weiss M., Schrimpf S. P., Miska E. A., Grosshans H., Aebersold R., Hengartner M. O., 2010   A quantitative targeted proteomics approach to validate predicted microRNA targets in C. elegans. Nat. Methods 7: 837–842. PDF
  • Kaufman E. J., Miska E. A., 2010   The microRNAs of Caenorhabditis elegans. Semin Cell Dev Biol 21: 728–737. PDF
  • Shaw W. R., Armisen J., Lehrbach N. J., Miska E. A., 2010   The conserved miR-51 microRNA family is redundantly required for embryonic development and pharynx attachment in Caenorhabditis elegans. Genetics 185: 897–905. PDF
  • Clark A. M., Goldstein L. D., Tevlin M., Tavaré S., Shaham S., Miska E. A., 2010   The microRNA miR-124 controls gene expression in the sensory nervous system of Caenorhabditis elegans. Nucleic Acids Res. 38: 3780–3793. PDF

2009

  • Armisen J., Gilchrist M. J., Wilczynska A., Standart N., Miska E. A., 2009   Abundant and dynamically expressed miRNAs, piRNAs, and other small RNAs in the vertebrate Xenopus tropicalis. Genome Res 19: 1766–1775. PDF
  • Lehrbach N. J., Armisen J., Lightfoot H. L., Murfitt K. J., Bugaut A., Balasubramanian S., Miska E. A., 2009   LIN-28 and the poly(U) polymerase PUP-2 regulate let-7 microRNA processing in Caenorhabditis elegans. Nat Struct Mol Biol 16: 1016–1020. PDF
  • Wilczynska A., Minshall N., Armisen J., Miska E. A., Standart N., 2009   Two Piwi proteins, Xiwi and Xili, are expressed in the Xenopus female germline. RNA 15: 337–345. PDF
  • Avril-Sassen S., Goldstein L. D., Stingl J., Blenkiron C., Le Quesne J., Spiteri I., Karagavriilidou K., Watson C. J., Tavaré S., Miska E. A., Caldas C., 2009   Characterisation of microRNA expression in post-natal mouse mammary gland development. BMC Genomics 10: 548. PDF

2008

  • Das P. P., Bagijn M. P., Goldstein L. D., Woolford J. R., Lehrbach N. J., Sapetschnig A., Buhecha H. R., Gilchrist M. J., Howe K. L., Stark R., Matthews N., Berezikov E., Ketting R. F., Tavaré S., Miska E. A., 2008   Piwi and piRNAs act upstream of an endogenous siRNA pathway to suppress Tc3 transposon mobility in the Caenorhabditis elegans germline. Mol. Cell 31: 79–90. PDF
  • Hayashi K., Chuva de Sousa Lopes S. M., Kaneda M., Tang F., Hajkova P., Lao K., O’Carroll D., Das P. P., Tarakhovsky A., Miska E. A., Surani M. A., 2008   MicroRNA biogenesis is required for mouse primordial germ cell development and spermatogenesis. PLoS One 3: e1738. PDF
  • Lykke-Andersen K., Gilchrist M. J., Grabarek J. B., Das P., Miska E., Zernicka-Goetz M., 2008   Maternal Argonaute 2 is essential for early mouse development at the maternal-zygotic transition. Mol. Biol. Cell 19: 4383–4392. PDF
  • Sassen S., Miska E. A., Caldas C., 2008   MicroRNA: implications for cancer. Virchows Arch. 452: 1–10. PDF
  • Lehrbach N. J., Miska E. A., 2008   Functional genomic, computational and proteomic analysis of C. elegans microRNAs. Briefings in functional genomics & proteomics 7: 228–235. PDF
  • Choi P. S., Zakhary L., Choi W.-Y., Caron S., Alvarez-Saavedra E., Miska E. A., McManus M., Harfe B., Giraldez A. J., Horvitz H. R., Schier A. F., Dulac C., 2008   Members of the miRNA-200 family regulate olfactory neurogenesis. Neuron 57: 41–55. PDF
  • Atherton H. J., Jones O. A., Malik S., Miska E. A., Griffin J. L., 2008   A comparative metabolomic study of NHR-49 in Caenorhabditis elegans and PPAR-alpha in the mouse. FEBS Lett 582: 1661–1666. PDF
  • Miska E. A., 2008   MicroRNAs–keeping cells in formation. Nat Cell Biol 10: 501–502. PDF

2007

  • Blenkiron C., Goldstein L. D., Thorne N. P., Spiteri I., Chin S.-F., Dunning M. J., Barbosa-Morais N. L., Teschendorff A. E., Green A. R., Ellis I. O., Tavaré S., Caldas C., Miska E. A., 2007   MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype. Genome Biol 8: R214. PDF
  • Vigorito E., Perks K. L., Abreu-Goodger C., Bunting S., Xiang Z., Kohlhaas S., Das P. P., Miska E. A., Rodriguez A., Bradley A., Smith K. G., Rada C., Enright A. J., Toellner K. M., Maclennan I. C., Turner M., 2007   microRNA-155 regulates the generation of immunoglobulin class-switched plasma cells. Immunity 27: 847–859. PDF
  • Alvarez-Garcia I., Miska E. A., 2007  miRNA expression analysis in C. elegans and mammals by microarrays. In: microRNAs: from basic science to disease biology, Appasani K (ed.) Cambridge University Press, ISBN 978-0-521-86598-2 BOOK
  • Miska E. A., Alvarez-Saavedra E., Abbott A. L., Lau N. C., Hellman A. B., McGonagle S. M., Bartel D. P., Ambros V. R., Horvitz H. R., 2007   Most Caenorhabditis elegans microRNAs are individually not essential for development or viability. PLoS Genet 3: e215. PDF
  • O’Carroll D., Mecklenbrauker I., Das P. P., Santana A., Koenig U., Enright A. J., Miska E. A., Tarakhovsky A., 2007   A Slicer-independent role for Argonaute 2 in hematopoiesis and the microRNA pathway. Genes Dev. 21: 1999–2004. PDF
  • Miska E. A., 2007  The expanding world of small RNA: from germ cells to cancer. Pharmaceutical Review 5: 34-37
  • Rodriguez A., Vigorito E., Clare S., Warren M. V., Couttet P., Soond D. R., van Dongen S., Grocock R. J., Das P. P., Miska E. A., Vetrie D., Okkenhaug K., Enright A. J., Dougan G., Turner M., Bradley A., 2007   Requirement of bic/microRNA-155 for normal immune function. Science 316: 608–611. PDF
  • Blenkiron C., Miska E. A., 2007   miRNAs in cancer: approaches, aetiology, diagnostics and therapy. Hum. Mol. Genet. 16 Spec No 1: R106–13. PDF
  • Miska E. A., Ahringer J., 2007   RNA interference has second helpings. Nat. Biotechnol. 25: 302–303. PDF
  • Lujambio A., Ropero S., Ballestar E., Fraga M. F., Cerrato C., Setién F., Casado S., Suarez-Gauthier A., Sanchez-Cespedes M., Git A., Gitt A., Spiteri I., Das P. P., Caldas C., Miska E., Esteller M., 2007   Genetic unmasking of an epigenetically silenced microRNA in human cancer cells. Cancer Res 67: 1424–1429. PDF

2006

  • Miska E. A., 2006  Functional Roles of RNAi in C. elegans, in: RNA Interference: Principles and Applications. Henry Stewart Talks Series 

2005

  • Alvarez-Saavedra E. A., Miska E. A., 2005   Caenorhabditis elegans and friends in Los Angeles. Genome Biol 6: 358. PDF
  • Alvarez-Garcia I., Miska E. A., 2005   MicroRNA functions in animal development and human disease. Development 132: 4653–4662. PDF
  • Miska E. A., 2005   How microRNAs control cell division, differentiation and death. Curr. Opin. Genet. Dev. 15: 563–568. PDF
  • Abbott A. L., Alvarez-Saavedra E., Miska E. A., Lau N. C., Bartel D. P., Horvitz H. R., Ambros V., 2005   The let-7 MicroRNA family members mir-48, mir-84, and mir-241 function together to regulate developmental timing in Caenorhabditis elegans. Dev Cell 9: 403–414. PDF
  • Wienholds E., Kloosterman W. P., Miska E., Alvarez-Saavedra E., Berezikov E., de Bruijn E., Horvitz H. R., Kauppinen S., Plasterk R. H. A., 2005   MicroRNA expression in zebrafish embryonic development. Science 309: 310–311. PDF
  • Lu J., Getz G., Miska E. A., Alvarez-Saavedra E., Lamb J., Peck D., Sweet-Cordero A., Ebert B. L., Mak R. H., Ferrando A. A., Downing J. R., Jacks T., Horvitz H. R., Golub T. R., 2005   MicroRNA expression profiles classify human cancers. Nature 435: 834–838. PDF

2004

  • Miska E. A., Alvarez-Saavedra E., Townsend M., Yoshii A., Sestan N., Rakic P., Constantine-Paton M., Horvitz H. R., 2004   Microarray analysis of microRNA expression in the developing mammalian brain. Genome Biol 5: R68. PDF 

2002

  • Wolf D., Rodova M., Miska E. A., Calvet J. P., Kouzarides T., 2002   Acetylation of beta-catenin by CREB-binding protein (CBP). J Biol Chem 277: 25562–25567. PDF
  • Kirsh O., Seeler J.-S., Pichler A., Gast A., Müller S., Miska E., Mathieu M., Harel-Bellan A., Kouzarides T., Melchior F., Dejean A., 2002   The SUMO E3 ligase RanBP2 promotes modification of the HDAC4 deacetylase. Embo J 21: 2682–2691. PDF

2001

  • Miska E. A., Langley E., Wolf D., Karlsson C., Pines J., Kouzarides T., 2001   Differential localization of HDAC4 orchestrates muscle differentiation. Nucleic Acids Res. 29: 3439–3447. PDF
  • Bannister A. J., Zegerman P., Partridge J. F., Miska E. A., Thomas J. O., Allshire R. C., Kouzarides T., 2001   Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410: 120–124. PDF
  • Miska E. A., Brehm A.. 2001  Remodelling chromatin in worms. ELSO Gazette 5 PDF

2000

  • Huang E. Y., Zhang J., Miska E. A., Guenther M. G., Kouzarides T., Lazar M. A., 2000   Nuclear receptor corepressors partner with class II histone deacetylases in a Sin3-independent repression pathway. Genes Dev. 14: 45–54. PDF
  • Bannister A. J., Miska E. A., 2000   Regulation of gene expression by transcription factor acetylation. Cell. Mol. Life Sci. 57: 1184–1192. PDF
  • Bannister A. J., Miska E. A., Görlich D., Kouzarides T., 2000   Acetylation of importin-alpha nuclear import factors by CBP/p300. Curr. Biol. 10: 467–470. PDF
  • Grimes J. A., Nielsen S. J., Battaglioli E., Miska E. A., Speh J. C., Berry D. L., Atouf F., Holdener B. C., Mandel G., Kouzarides T., 2000   The co-repressor mSin3A is a functional component of the REST-CoREST repressor complex. J Biol Chem 275: 9461–9467. PDF

1999

  • Miska E. A., Karlsson C., Langley E., Nielsen S. J., Pines J., Kouzarides T., 1999   HDAC4 deacetylase associates with and represses the MEF2 transcription factor. Embo J 18: 5099–5107. PDF
  • Sparrow D. B., Miska E. A., Langley E., Reynaud-Deonauth S., Kotecha S., Towers N., Spohr G., Kouzarides T., Mohun T. J., 1999   MEF-2 function is modified by a novel co-repressor, MITR. Embo J 18: 5085–5098. PDF
  • Brehm A., Miska E., Reid J., Bannister A., Kouzarides T., 1999   The cell cycle-regulating transcription factors E2F-RB. Br J Cancer 80 Suppl 1: 38–41.
  • Brehm A., Nielsen S. J., Miska E. A., McCance D. J., Reid J. L., Bannister A. J., Kouzarides T., 1999   The E7 oncoprotein associates with Mi2 and histone deacetylase activity to promote cell growth. Embo J 18: 2449–2458. PDF

1998

  • Brehm A., Miska E. A., McCance D. J., Reid J. L., Bannister A. J., Kouzarides T., 1998   Retinoblastoma protein recruits histone deacetylase to repress transcription. Nature 391: 597–601. PDF