Inference of developmental gene regulatory networks beyond classical model systems: new approaches in the post-genomic era

Fernandez-Valverde SL+, Aguilera F+, and Ramos-Diaz RA. Integrative and Comparative Biology. In press +corresponding authors

Diverse RNA interference strategies in early-branching metazoans

Calcino AD, Fernandez-Valverde SL, Taft RJ and Degnan BM. bioRxiv. 284349, 2018

Landscape of histone modifications in a sponge reveals the origin of animal cis-regulatory complexity

Gaiti F, Jindrich K, Fernandez-Valverde SL, Roper KE, Degnan BM, Tanurdzic M. eLife. 10.7554/eLife.22194, 2017

The crown-of-thorns starfish genome as a guide for biocontrol of this coral reef pest

Hall MR*, Kocot KM*, Baughman KW*, Fernandez-Valverde SL, Gauthier ME, Hatleberg WL, Krishnan A, McDougall C, Motti CA, Shoguchi E, Wang T, Xiang X, Zhao M, Bose U, Shinzato C, Hisata K, Fujie M, Kanda M, Cummins SF, Satoh N, Degnan SM and Degnan BM. Nature. 544:231–234, 2017 *joint first authors

Bilaterian-like promoters in the highly compact Amphimedon queenslandica genome.

Fernandez-Valverde SL, and Degnan BM. Scientific reports. 6:22496, 2016

The mid-developmental transition and the evolution of animal body plans.

Levin M, Anavy L, Cole AG, Winter E, Mostov N, Khair S, Senderovich N, Kovalev E, Silver DH, Feder M, Fernandez-Valverde SL, Nakanishi N, Simmons D, Simakov O, Larsson T, Liu S-Y, Jerafi-Vider A, Yaniv K, Ryan JF, Martindale MQ, Rink JC, Arendt D, Degnan SM, Degnan BM, Hashimshony T, and Yanai I. Nature. 531:637-641, 2016

Dynamic and widespread lncRNA expression in the sponge and the origin of animal complexity.

Gaiti F, Fernandez-Valverde SL, Nakanishi N, Yanai I, Calcino AD, Tanurdzic M, Degnan BM Molecular Biology and Evolution. 32:2367-2382, 2015

Deep developmental transcriptome sequencing uncovers numerous new genes and enhances gene annotation in the sponge Amphimedon queenslandica.

Fernandez-Valverde SL, Calcino AD, Degnan BM BMC Genomics. 16:387, 2015

BLIND ordering of large-scale transcriptomic developmental timecourses.

Anavy L, Levin M, Khair S, Nakanishi N, Fernandez-Valverde SL, Degnan BM, Yanai I Development. 141(5):1161- 1166, 2014

SOX9 Regulates MicroRNA miR-202-5p/3p Expression During Mouse Testis Differentiation.

Wainwright EN, Jorgensen JS, Kim Y, Truong V, Bagheri-Fam S, Davidson T, Svingen T, Fernandez-Valverde SL, McClelland KS, Taft RJ, Harley VR, Koopman P, Wilhelm D Biology of Reproduction. 89(2):34, 2013

MicroRNAs-140-5p/140-3p modulate Leydig cell numbers in the developing mouse testis.

Rakoczy J*, Fernandez-Valverde SL*, Glazov EA, Wainwright EN, Sato T, Takada S, Combes AN, Korbie DJ, Miller D, Grimmond SM, Little MH, Asahara H, Mattick JS, Taft RJ, Wilhelm D Biology of Reproduction. 88(6):143, 2013 *joint first authors

Review: miRNAs in beta cell biology, insulin resistance, diabetes and its complications.

Fernandez-Valverde SL, Taft RJ, Mattick JS Diabetes. 60(7):1825-1831, 2011

Dynamic isomiR regulation in Drosophila development.

Fernandez-Valverde SL, Taft RJ, Mattick JS RNA. 16(10):1881-1888, 2010