Garrigues JM, Tsu BV, Daugherty MD, & Pasquinelli AE (2019). Diversification of the Caenorhabditis heat shock response by Helitron transposable elements. eLife [Link]

Schreiner WP, Pagliuso DC, Garrigues JM, Chen JS, Aalto AP, & Pasquinelli AE (2019). Remodeling of the Caenorhabditis elegans non-coding RNA transcriptome by heat shock. Nucleic Acids Research [Link]

De-Souza EA, Camara H, Salgueiro WG, Moro RP, Knittel TL, Tonon G, Pinto S, Pinca APF, Antebi A, Pasquinelli AE, Massirer KB, & Mori MA. (2019). RNA interference may result in unexpected phenotypes in Caenorhabditis elegans. Nucleic Acids Research [Link]

Chipman LB, & Pasquinelli AE. (2019). miRNA Targeting: Growing beyond the Seed. Trends Genet. [Link]

Nicholson AL, & Pasquinelli AE. (2019). Tales of Detailed Poly(A) Tails. Trends in Cell Biology [Link]


Aalto AP, Nicastro IA, Broughton JP, Chipman LB, Schreiner WP, Chen JS, & Pasquinelli AE. (2018). Opposing roles of microRNA Argonautes during Caenorhabditis elegans aging PLOS Genetics [Link]

Broughton JP, Pasquinelli AE. (2018). Detection of microRNA-Target Interactions by Chimera PCR (ChimP). Methods Mol Bio [Link]


Azoubel Lima S, Chipman LB, Nicholson AL, Chen YH, Yee BA, Yeo GW, Coller J & Pasquinelli AE. (2017). Short polyA tails are a conserved feature of highly expressed genes. Nature Structural and Molecular Biology [Link]

Schreiner WP & Pasquinelli AE. (2017). Making and Maintaining microRNAs in Animals. Essentials of Non-coding RNA in Neuroscience. [Link]


Broughton, J. P., & Pasquinelli, A. E. (2016). A tale of two sequences: microRNA-target chimeric reads. Genetics Selection Evolution [Link]

Broughton, J. P., Lovci, M., Huang, J., Yeo, G.W., Pasquinelli A.E. (2016). Pairing Beyond the Seed Supports MicroRNA Targeting Specificity. Molecular Cell [Link]

Pasquinelli A.E. (2016). A sense-able microRNA. Genes Dev [Link]


Mondol V, Ahn BC, Pasquinelli AE. (2015). Splicing remodels the let-7 primary microRNA to facilitate Drosha processing in Caenorhabditis elegans. RNA. [Link]

Pasquinelli AE. (2015). MicroRNAs: heralds of the noncoding RNA revolution. RNA. [Link]


Fonslow BR, Moresco JJ, Tu PG, Aalto AP, Pasquinelli AE, Dillin AG, Yates Iii JR. Mass spectrometry-based shotgun proteomic analysis of C. elegans protein complexes. WormBook. 2014 Jun 24:1-18. [Link]

Lima, S. A., Pasquinelli, A. E. (2014). Identification of miRNAs and Their Targets in C. elegans. Advances in Experimental Medicine and Biology. [Link]

Van Wynsberghe, P. M., Finnegan, E. F., Stark, T., Angelus, E. P., Homan, K. E., Yeo, G. W., & Pasquinelli, A. E. (2014). The Period protein homolog LIN-42 negatively regulates microRNA biogenesis in C. elegans. Developmental Biology. [Link]


Pasquinelli, A. E. (2013). The primary target of let-7 microRNA. Biochemical Society Transactions, 41, 821–824. [Link]

Broughton, J. P., & Pasquinelli, A. E. (2013). Identifying argonaute binding sites in Caenorhabditis elegans using iCLIP. Methods, 63, 119–125. [Link]

Hunter, S. E., Finnegan, E. F., Zisoulis, D. G., Lovci, M. T., Melnik-Martinez, K. V., Yeo, G. W., & Pasquinelli, A. E. (2013). Functional Genomic Analysis of the let-7 Regulatory Network in Caenorhabditis elegans. PLoS Genetics, 9. [Link]

Massirer, K. B., & Pasquinelli, A. E. (2013). MicroRNAs that interfere with RNAi. Worm, 2, e21835. [Link]

Kai, Z. S., Finnegan, E. F., Huang, S., & Pasquinelli, A. E. (2013). Multiple cis-elements and trans-acting factors regulate dynamic spatio-temporal transcription of let-7 in Caenorhabditis elegans. Developmental Biology, 374, 223–233. [Link]

Finnegan, E. F., & Pasquinelli, A. E. (2013). MicroRNA biogenesis: regulating the regulators. Critical Reviews in Biochemistry and Molecular Biology, 48, 51–68. [Link]


Pasquinelli, A. E. (2012). Birthing histone mRNAs by CSR-1 section. The EMBO Journal, 31(19), 3790–1. [Link]

Zisoulis, D. G., Kai, Z. S., Chang, R. K., & Pasquinelli, A. E. (2012). Autoregulation of microRNA biogenesis by let-7 and Argonaute. Nature. [Link]

Aalto, A. P., & Pasquinelli, A. E. (2012). Small non-coding RNAs mount a silent revolution in gene expression. Current Opinion in Cell Biology. [Link]

Pasquinelli, A. E. (2012). MicroRNAs and their targets: recognition, regulation and an emerging reciprocal relationship. Nature Reviews Genetics. [Link]

Massirer, K. B., Perez, S. G., Mondol, V., & Pasquinelli, A. E. (2012). The miR-35-41 family of microRNAs regulates RNAi sensitivity in caenorhabditis elegans. PLoS Genetics, 8. [Link]

Mondol, V., & Pasquinelli, A. E. (2012). Let’s Make It Happen. The Role of let-7 MicroRNA in Development. Current Topics in Developmental Biology, 99, 1–30. [Link]

Pasquinelli, A. E. (2012). A team effort blocks the ribosome in its tracks. Nature Structural & Molecular Biology, 19(2), 133–4. [Link]


Van Wynsberghe, P. M., Chan, S.-P., Slack, F. J., & Pasquinelli, A. E. (2011). Analysis of microRNA expression and function. Methods in Cell Biology, 106, 219–52. [Link]

Zisoulis, D. G., Yeo, G. W., & Pasquinelli, A. E. (2011). Comprehensive identification of miRNA target sites in live animals. Methods in Molecular Biology (Clifton, N.J.), 732, 169–185. [Link]

Van Wynsberghe, P. M., Kai, Z. S., Massirer, K. B., Burton, V. H., Yeo, G. W., & Pasquinelli, A. E. (2011). LIN-28 co-transcriptionally binds primary let-7 to regulate miRNA maturation in Caenorhabditis elegans. Nature Structural & Molecular Biology, 18, 302–308. [Link]


Bracht, J. R., Van Wynsberghe, P. M., Mondol, V., & Pasquinelli, A. E. (2010). Regulation of lin-4 miRNA expression, organismal growth and development by a conserved RNA binding protein in C. elegans. Developmental Biology, 348, 210–221. [Link]

Pasquinelli, A. E. (2010). Molecular biology. Paring miRNAs through pairing. Science (New York, N.Y.), 328(5985), 1494–5. [Link]

Godshalk, S. E., Melnik-Martinez, K. V, Pasquinelli, A. E., & Slack, F. J. (2010). MicroRNAs and cancer: a meeting summary of the eponymous Keystone Conference. Epigenetics : Official Journal of the DNA Methylation Society. [Link]

Kai, Z. S., & Pasquinelli, A. E. (2010). A genome wide view of hunchback-like-1 targets. Cell Cycle, 9(2), 230-1. [Link]

Kai, Z. S., & Pasquinelli, A. E. (2010). MicroRNA assassins: factors that regulate the disappearance of miRNAs. Nature Structural & Molecular Biology, 17, 5–10. [Link]

Zisoulis, D. G., Lovci, M. T., Wilbert, M. L., Hutt, K. R., Liang, T. Y., Pasquinelli, A. E., & Yeo, G. W. (2010). Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans. Nature Structural & Molecular Biology, 17, 173–179. [Link]

Hinton, A., Afrikanova, I., Wilson, M., King, C. C., Maurer, B., Yeo, G. W., … Pasquinelli, A. E. (2010). A distinct microRNA signature for definitive endoderm derived from human embryonic stem cells. Stem Cells and Development, 19, 797–807. [Link]


Holtz, J., & Pasquinelli, A. E. (2009). Uncoupling of lin-14 mRNA and protein repression by nutrient deprivation in Caenorhabditis elegans. RNA (New York, N.Y.), 15, 400–405. [Link]


Norden-Krichmar, T. M., Holtz, J., Pasquinelli, A. E., & Gaasterland, T. (2007). Computational prediction and experimental validation of Ciona intestinalis microRNA genes. BMC Genomics, 8, 445. [Link]

Chendrimada, T. P., Finn, K. J., Ji, X., Baillat, D., Gregory, R. I., Liebhaber, S. A., Pasquinell, A.E., & Shiekhattar, R. (2007). MicroRNA silencing through RISC recruitment of eIF6. Nature, 447, 823–828. [Link]


Pasquinelli, A. E. (2006). Demystifying small RNA pathways. In Developmental Cell (Vol. 10, pp. 419–424). [Link]

Massirer, K. B., & Pasquinelli, A. E. (2006). The evolving role of microRNAs in animal gene expression. BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology, 28, 449–452. [Link]

Bagga S., & Pasquinelli A.E. (2006). Identification and analysis of microRNAs. Genet Eng (N Y), 27, 1-20.


Bagga, S., Bracht, J., Hunter, S., Massirer, K., Holtz, J., Eachus, R., & Pasquinelli, A. E. (2005). Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell, 122, 553–563. [Link]

Kim, J. K., Gabel, H. W., Kamath, R. S., Tewari, M., Pasquinelli, A., Rual, J.-F., … Ruvkun, G. (2005). Functional genomic analysis of RNA interference in C. elegans. Science (New York, N.Y.), 308, 1164–1167. [Link]

Pasquinelli, A. E., Hunter, S., & Bracht, J. (2005). MicroRNAs: A developing story. Current Opinion in Genetics and Development. [Link]

Pasquinelli, A.E. (2005). MicroRNAs: a Small Contribution from Worms. In RNA Interference Technology: From Basic Science to Drug Development, ed. K Appasani. Cambridge, UK: Cambridge University Press. p69-83.


Mansfield, J. H., Harfe, B. D., Nissen, R., Obenauer, J., Srineel, J., Chaudhuri, A., Farzan-Kashani, R., Zuker, M., Pasuqinelli, A. E., Ruvkun, G., SHarp, P. A., Tabin, C. J., & McManus, M. T. (2004). MicroRNA-responsive “sensor” transgenes uncover Hox-like and other developmentally regulated patterns of vertebrate microRNA expression. Nature Genetics, 36, 1079–1083. [Link]

Bracht, J., Hunter, S., Eachus, R., Weeks, P., & Pasquinelli, A. E. (2004). Trans-splicing and polyadenylation of let-7 microRNA primary transcripts. RNA (New York, N.Y.), 10, 1586–1594. [Link]


Pasquinelli, A. E., McCoy, A., Jimenez, E., Salo, E., Ruvkun, G., Martindale, M. Q., & Baguna, J. (2003). Expression of the 22 nucleotide let-7 heterochronic RNA throughout the Metazoa: a role in life history evolution? Evolution and Development, 5(4), 372–378. [Link]

Bashirullah, A., Pasquinelli, A. E., Kiger, A. A., Perrimon, N., Ruvkun, G., & Thummel, C. S. (2003). Coordinate regulation of small temporal RNAs at the onset of Drosophila metamorphosis. Developmental Biology, 259, 1–8. [Link]

Lin, S. Y., Johnson, S. M., Abraham, M., Vella, M. C., Pasquinelli, A., Gamberi, C., … Slack, F. J. (2003). The C. elegans hunchback homolog, hbl-1, controls temporal patterning and is a probable MicroRNA target. Developmental Cell. [Link]

Pasquinelli, A. E. (2002). MicroRNAs: Deviants no longer. Trends in Genetics. [Link]

Pasquinelli, A. E., & Ruvkun, G. (2002). Control of developmental timing by microRNAs and their targets. Annual Review of Cell and Developmental Biology, 18, 495–513. [Link]

Hutvágner, G., McLachlan, J., Pasquinelli, A. E., Bálint, E., Tuschl, T., & Zamore, P. D. (2001). A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science (New York, N.Y.), 293, 834–838. [Link]

Grishok, A., Pasquinelli, A. E., Conte, D., Li, N., Parrish, S., Ha, I., … Mello, C. C. (2001). Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell, 106, 23–34. [Link]

Pierce, S. B., Costa, M., Wisotzkey, R., Devadhar, S., Homburger, S. A., Buchman, A. R., Pasquinelli, A. E., … Ruvkun, G. (2001). Regulation of DAF-2 receptor signaling by human insulin and ins-1, a member of the unusually large and diverse C. elegans insulin gene family. Genes & Development, 15(6), 672–86. [Link]

Pasquinelli, A. E., Reinhart, B. J., Slack, F., Martindale, M. Q., Kuroda, M. I., Maller, B., … Ruvkun, G. (2000). Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature, 408, 86–89. [Link]

Reinhart, B. J., Slack, F. J., Basson, M., Pasquinelli, A. E., Bettinger, J. C., Rougvie, A. E., … Ruvkun, G. (2000). The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature, 403, 901–906. [Link]

Pasquinelli, A. E., Ernst, R. K., Lund, E., Grimm, C., Zapp, M. L., Rekosh, D., … Dahlberg, J. E. (1997). The constitutive transport element (CTE) of Mason-Pfizer monkey virus (MPMV) accesses a cellular mRNA export pathway. The EMBO Journal, 16, 7500–7510. [Link]

Pasquinelli, A. E., Powers, M. A., Lund, E., Forbes, D., & Dahlberg, J. E. (1997). Inhibition of mRNA export in vertebrate cells by nuclear export signal conjugates. Proceedings of the National Academy of Sciences of the United States of America, 94, 14394–14399. [Link]

Pasquinelli, A. E., Dahlberg, J. E., & Lund, E. (1995). Reverse 5’ caps in RNAs made in vitro by phage RNA polymerases. RNA (New York, N.Y.), 1, 957–967.