By Dr Selene Fernandez Valverde

Book Chapters

Pérez-de los Santos FJ; Sotelo-Fonseca JE; Ramírez-Colmenero A; Nützmann HW; Fernandez-Valverde SL; Oktaba K, 2022, 'Plant In Situ Hi-C Experimental Protocol and Bioinformatic Analysis', in Methods in Molecular Biology, pp. 217 - 247, http://dx.doi.org/10.1007/978-1-0716-2429-6_13

Journal articles

Tenorio M; Serwatowska J; Fernandez-Valverde SL; Oktaba K; Cortez D, 2023, 'Genome-wide analysis of RNA-chromatin interactions in lizards as a mean for functional lncRNA identification', BMC Genomics, 24, http://dx.doi.org/10.1186/s12864-023-09545-5

Sohail M; Palma-Martínez MJ; Chong AY; Quinto-Cortés CD; Barberena-Jonas C; Medina-Muñoz SG; Ragsdale A; Delgado-Sánchez G; Cruz-Hervert LP; Ferreyra-Reyes L; Ferreira-Guerrero E; Mongua-Rodríguez N; Canizales-Quintero S; Jimenez-Kaufmann A; Moreno-Macías H; Aguilar-Salinas CA; Auckland K; Cortés A; Acuña-Alonzo V; Gignoux CR; Wojcik GL; Ioannidis AG; Fernández-Valverde SL; Hill AVS; Tusié-Luna MT; Mentzer AJ; Novembre J; García-García L; Moreno-Estrada A, 2023, 'Mexican Biobank advances population and medical genomics of diverse ancestries', Nature, 622, pp. 775 - 783, http://dx.doi.org/10.1038/s41586-023-06560-0

Fernandez-Valverde SL, 2023, 'Down memory lane — unravelling the puzzle of gene regulation', Nature Reviews Genetics, 24, pp. 275, http://dx.doi.org/10.1038/s41576-023-00575-z

Domínguez-Rosas E; Hernández-Oñate MÁ; Fernandez-Valverde SL; Tiznado-Hernández ME, 2023, 'Plant long non-coding RNAs: identification and analysis to unveil their physiological functions', Frontiers in Plant Science, 14, http://dx.doi.org/10.3389/fpls.2023.1275399

Corona-Gomez JA; Coss-Navarrete EL; Garcia-Lopez IJ; Klapproth C; Pérez-Patiño JA; Fernandez-Valverde SL; Fernandez Valverde S, 2022, 'Transcriptome-guided annotation and functional classification of long non-coding RNAs in Arabidopsis thaliana', Scientific Reports, 12, pp. 14063, http://dx.doi.org/10.1038/s41598-022-18254-0

, 2022, 'Plants & Python: A series of lessons in coding, plant biology, computation, and bioinformatics.', Plant Cell, 34, pp. e1, http://dx.doi.org/10.1093/plcell/koac187

Jiménez-Kaufmann A; Chong AY; Cortés A; Quinto-Cortés CD; Fernandez-Valverde SL; Ferreyra-Reyes L; Cruz-Hervert LP; Medina-Muñoz SG; Sohail M; Palma-Martinez MJ; Delgado-Sánchez G; Mongua-Rodríguez N; Mentzer AJ; Hill AVS; Moreno-Macías H; Huerta-Chagoya A; Aguilar-Salinas CA; Torres M; Kim HL; Kalsi N; Schuster SC; Tusié-Luna T; Del-Vecchyo DO; García-García L; Moreno-Estrada A, 2022, 'Imputation Performance in Latin American Populations: Improving Rare Variants Representation With the Inclusion of Native American Genomes', Frontiers in Genetics, 12, http://dx.doi.org/10.3389/fgene.2021.719791

Ozment E; Tamvacakis AN; Zhou J; Rosiles-Loeza PY; Escobar-Hernandez EE; Fernandez-Valverde SL; Nakanishi N, 2021, 'Cnidarian hair cell development illuminates an ancient role for the class IV POU transcription factor in defining mechanoreceptor identity', eLife, 10, http://dx.doi.org/10.7554/eLife.74336

Moore B; Carvajal-Lopez P; Chauke PA; Cristancho M; Del Angel VD; 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, 2021, 'Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries', PLoS Computational Biology, 17, http://dx.doi.org/10.1371/journal.pcbi.1009218

Ramírez-Colmenero A; Oktaba K; Fernandez-Valverde SL, 2020, 'Evolution of Genome-Organizing Long Non-coding RNAs in Metazoans', Frontiers in Genetics, 11, http://dx.doi.org/10.3389/fgene.2020.589697

Fernandez-Valverde SL, 2020, 'Voices of the new generation: being a junior PI in a developing country', Nature Reviews Molecular Cell Biology, 21, pp. 561, http://dx.doi.org/10.1038/s41580-020-0263-7

Corona-Gomez JA; Garcia-Lopez IJ; Stadler PF; Fernandez-Valverde SL, 2020, 'Splicing conservation signals in plant long noncoding RNAs', RNA, 26, pp. 784 - 793, http://dx.doi.org/10.1261/rna.074393.119

Nützmann HW; Doerr D; Ramírez-Colmenero A; Sotelo-Fonseca JE; Wegel E; Di Stefano M; Wingett SW; Fraser P; Hurst L; Fernandez-Valverde SL; Osbourn A, 2020, 'Active and repressed biosynthetic gene clusters have spatially distinct chromosome states', Proceedings of the National Academy of Sciences of the United States of America, 117, pp. 13800 - 13809, http://dx.doi.org/10.1073/pnas.1920474117

Gómez-Godínez LJ; Fernandez-Valverde SL; Martinez Romero JC; Martínez-Romero E, 2019, 'Metatranscriptomics and nitrogen fixation from the rhizoplane of maize plantlets inoculated with a group of PGPRs', Systematic and Applied Microbiology, 42, pp. 517 - 525, http://dx.doi.org/10.1016/j.syapm.2019.05.003

Sogabe S; Hatleberg WL; Kocot KM; Say TE; Stoupin D; Roper KE; Fernandez-Valverde SL; Degnan SM; Degnan BM, 2019, 'Pluripotency and the origin of animal multicellularity', Nature, 570, pp. 519 - 522, http://dx.doi.org/10.1038/s41586-019-1290-4

Calcino AD; Fernandez-Valverde SL; Taft RJ; Degnan BM, 2018, 'Diverse RNA interference strategies in early-branching metazoans', BMC Evolutionary Biology, 18, http://dx.doi.org/10.1186/s12862-018-1274-2

Fernandez-Valverde SL; Aguilera F; Ramos-Dıaz RA, 2018, 'Inference of developmental gene regulatory networks beyond classical model systems: New approaches in the post-genomic era', Integrative and Comparative Biology, 58, pp. 640 - 653, http://dx.doi.org/10.1093/icb/icy061

Gaiti F; Jindrich K; Fernandez-Valverde SL; Roper KE; Degnan BM; Tanurdžić M, 2017, 'Landscape of histone modifications in a sponge reveals the origin of animal cis-regulatory complexity', eLife, 6, http://dx.doi.org/10.7554/eLife.22194

Hall MR; Kocot KM; Baughman KW; Fernandez-Valverde SL; Gauthier MEA; 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; Degnan BM, 2017, 'The crown-of-thorns starfish genome as a guide for biocontrol of this coral reef pest', Nature, 544, pp. 231 - 234, http://dx.doi.org/10.1038/nature22033

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 SY; Jerafi-Vider A; Yaniv K; Ryan JF; Martindale MQ; Rink JC; Arendt D; Degnan SM; Degnan BM; Hashimshony T; Yanai I, 2016, 'The mid-developmental transition and the evolution of animal body plans', Nature, 531, pp. 637 - 641, http://dx.doi.org/10.1038/nature16994

Fernandez-Valverde SL; Degnan BM, 2016, 'Bilaterian-like promoters in the highly compact Amphimedon queenslandica genome', Scientific Reports, 6, http://dx.doi.org/10.1038/srep22496

Gaiti F; Fernandez-Valverde SL; Nakanishi N; Calcino AD; Yanai I; Tanurdzic M; Degnan BM, 2015, 'Dynamic and widespread lncRNA expression in a sponge and the origin of animal complexity', Molecular Biology and Evolution, 32, pp. 2367 - 2382, http://dx.doi.org/10.1093/molbev/msv117

Fernandez-Valverde SL; Calcino AD; Degnan BM, 2015, 'Deep developmental transcriptome sequencing uncovers numerous new genes and enhances gene annotation in the sponge Amphimedon queenslandica', BMC Genomics, 16, http://dx.doi.org/10.1186/s12864-015-1588-z

Anavy L; Levin M; Khair S; Nakanishi N; Fernandez-Valverde SL; Degnan BM; Yanai I, 2014, 'BLIND ordering of large-scale transcriptomic developmental timecourses', Development (Cambridge), 141, pp. 1161 - 1166, http://dx.doi.org/10.1242/dev.105288

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, 2013, 'SOX9 regulates microRNA miR-202-5p/3p expression during mouse testis differentiation', Biology of Reproduction, 89, http://dx.doi.org/10.1095/biolreprod.113.110155

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, 2013, 'Micrornas-140-5p/140-3p modulate leydig cell numbers in the developing mouse testis', Biology of Reproduction, 88, http://dx.doi.org/10.1095/biolreprod.113.107607

Fernandez-Valverde SL; Taft RJ; Mattick JS, 2011, 'MicroRNAs in β-cell biology, insulin resistance, diabetes and its complications', Diabetes, 60, pp. 1825 - 1831, http://dx.doi.org/10.2337/db11-0171

Fernandez-Valverde SL; Taft RJ; Mattick JS, 2010, 'Dynamic isomiR regulation in Drosophila development', RNA, 16, pp. 1881 - 1888, http://dx.doi.org/10.1261/rna.2379610

, 'Introduction to RNA-seq and functional interpretation: Course materials', , http://dx.doi.org/10.6019/tol.rnaseqmaterials-t.2022.00001.1

Preprints

Corona-Gomez JA; Stadler P; Fernandez-Valverde S, 2023, Evolutionary conservation of secondary structures in the lncRNAs of plants, , http://dx.doi.org/10.1101/2023.08.13.553158

Vargas-Mejía P; Olguín-Lamas A; Fernandez-Valverde S; Lund G; Vielle-Calzada J-P; Silva-Rosales L, 2022, Differential RNA-silencing and plasmodesmata callose deposition in leaves and stems of transgenic tobacco plants duringTobacco etch virusinfection recovery, , http://dx.doi.org/10.1101/2022.11.08.515744

Sohail M; Chong A; Quinto-Cortes C; Palma-Martínez M; Ragsdale A; Medina-Muñoz S; Barberena-Jonas C; Delgado-Sánchez G; Cruz-Hervert LP; Ferreyra-Reyes L; Ferreira-Guerrero E; Mongua-Rodríguez N; Jimenez-Kaufmann A; Moreno-Macías H; Aguilar-Salinas C; Auckland K; Cortés A; Acuña-Alonzo V; Ioannidis A; Gignoux C; Wojcik G; Fernández-Valverde S; Hill AVS; Tusié-Luna MT; Mentzer A; Novembre J; García-García L; Moreno-Estrada A, 2022, Nationwide genomic biobank in Mexico unravels demographic history and complex trait architecture from 6,057 individuals, , http://dx.doi.org/10.1101/2022.07.11.499652

Corona-Gomez JA; Coss-Navarrete EL; Garcia-Lopez IJ; Pérez-Patiño JA; Fernandez-Valverde S, 2022, Transcriptome-guided annotation and functional classification of long non-coding RNAs in Arabidopsis thaliana, , http://dx.doi.org/10.1101/2022.04.18.488676

Ozment E; Tamvacakis AN; Zhou J; Rosiles-Loeza PY; Escobar-Hernandez EE; Fernandez-Valverde SL; Nakanishi N, 2021, Cnidarian hair cell development illuminates an ancient role for the class IV POU transcription factor in defining mechanoreceptor identity, , http://dx.doi.org/10.1101/2021.10.12.464036

Sogabe S; Hatleberg WL; Kocot KM; Say TE; Stoupin D; Roper KE; Fernandez-Valverde SL; Degnan SM; Degnan BM, 2019, Pluripotency and the origin of animal multicellularity, , http://dx.doi.org/10.1101/564518

Corona-Gomez JA; Garcia-Lopez IJ; Stadler P; Fernandez-Valverde S, 2019, Splicing conservation signals in plant long non-coding RNAs, , http://dx.doi.org/10.1101/588954

Calcino AD; Fernandez-Valverde SL; Taft RJ; Degnan BM, 2018, Diverse RNA interference strategies in early-branching metazoans, , http://dx.doi.org/10.1101/284349

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