Publications

 

2021

Cnidarian hair cell development illuminates an ancient role for the class IV POU transcription factor in defining mechanoreceptor identity

Ozment E, Tamvacakis AN, Zhou J, Rosiles-Loeza PY, Escobar-Hernandez EE, Fernandez-Valverde SL, Nakanishi N. bioRxiv. 5464036, 2021

Ten Simple Rules for Organising a Bioinformatics Training Course in a Low-Middle Income Country

Moore B, Carvajal-Lopez P, Chauke PA, Cristancho M, Domiguez del Angel V, Fernandez-Valverde SL, Ghouila A, Gopalasingam P, Guerfali FZ, Matimba A, Morgan SL, Oliveira G, Ras V, Reyes A, De Las Rivas J, Mulder N PLoS Computational Biology. 17: e1009218, 2021

 

2020

Evolution of Genome-Organizing Long Non-coding RNAs in Metazoans

Ramirez Colmenero A, Oktaba K and Fernandez-Valverde SL+. Frontiers in Genetics. 11:1512, 2020 +corresponding authors

Voices of the new generation: being a junior PI in a developing country

Fernandez-Valverde SL. Nature Reviews Molecular Cell Biology . 11:1, 2020

Splicing conservation signals in plant long non-coding RNAs

Corona-Gomez JA, Garcia-Lopez IJ, Stadler PF+ and Fernandez-Valverde SL+. RNA. 26:784-793, 2020 +corresponding authors

Active and repressed biosynthetic gene clusters have spatially distinct chromosome states.

Nutzmann H-W*, Ramirez Colmenero A, Sotelo JE, Wegel E, di Stefano M, Wingett S, Fraser P, Hurst L, Fernandez-Valverde SL and Osbourn A . Proceedings of the National Academy of Science. 117:13800-1380, 2020

 

2019

Pluripotency and the origin of animal multicellularity

Sogabe S*, Hatleberg WL*, Kocot KM, Say TE, Stoupin D, Roper KE, Fernandez-Valverde SL, Degnan SM and Degnan BM. Nature. 570:519-522, 2019

Metatranscriptomics and nitrogen fixation from the rhizoplane of maize plantlets inoculated with a group of PGPRs

Gomez-Godinez LJ, Fernandez-Valverde SL, Martinez Romero JC and Martinez-Romero E. Systematic and Applied Microbiology. 42:517-525, 2019

 

2018

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. 58:640-653, 2018 +corresponding authors

Diverse RNA interference strategies in early-branching metazoans

Calcino AD, Fernandez-Valverde SL, Taft RJ and Degnan BM. BMC Evolutionary Biology. 18:160, 2018

 

2017

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

 

2016

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

 

2015

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

 

2014

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

 

2013

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

 

2011

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

 

2010

Dynamic isomiR regulation in Drosophila development.

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