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

Hernández-Ledesma AL; Coss-Navarrete EL; Salazar-Magaña S; Ramírez-Espinosa D; Tinajero-Nieto L; Torres-Valdez E; Peña-Ayala AH; Félix-Rodriguez G; Frontana-Vázquez G; García Sotelo JS; Thomas-Chollier M; Trynka G; Rosetti F; Fernandez-Valverde SL; Gutiérrez-Arcelus M; Alpízar-Rodríguez D; Medina-Rivera A, 2026, 'Gene expression profiling of dendritic cell tolerance dysfunction in women with systemic lupus erythematosus', Frontiers in Immunology, 17, http://dx.doi.org/10.3389/fimmu.2026.1771959

García-López IJ; Vélez-Ramírez AI; Gillmor CS; Fernandez-Valverde SL, 2024, 'lncRNAs involved in the Shade Avoidance Syndrome (SAS) in Arabidopsis thaliana', BMC Genomics, 25, pp. 802, http://dx.doi.org/10.1186/s12864-024-10718-z

Tenorio M; Cruz-Ruiz S; Encarnación-Guevara S; Hernández M; Corona-Gomez JA; Sheccid-Santiago F; Serwatowska J; López-Perdomo S; Flores-Aguirre CD; Arenas-Moreno DM; Ossiboff RJ; Méndez-De-la-Cruz F; Fernandez-Valverde SL; Zurita M; Oktaba K; Cortez D, 2024, 'MAYEX is an old long noncoding RNA recruited for X chromosome dosage compensation in a reptile', Science, 385, pp. 1347 - 1354, http://dx.doi.org/10.1126/science.adp1932

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

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, pp. 444, http://dx.doi.org/10.1186/s12864-023-09545-5

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, 2022, 'Transcriptome-guided annotation and functional classification of long non-coding RNAs in Arabidopsis thaliana.', Sci Rep, 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', The Plant Cell, 34, pp. e1 - 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-López P; Chauke PA; Cristancho M; Dominguez 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, 2021, 'Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries.', PLoS Comput Biol, 17, pp. e1009218, http://dx.doi.org/10.1371/journal.pcbi.1009218

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 H-W; 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.', Proc Natl Acad Sci U S A, 117, pp. 13800 - 13809, http://dx.doi.org/10.1073/pnas.1920474117

Ramírez-Colmenero A; Oktaba K; Fernandez-Valverde SL, 2020, 'Evolution of Genome-Organizing Long Non-coding RNAs in Metazoans.', Front Genet, 11, pp. 589697, http://dx.doi.org/10.3389/fgene.2020.589697

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

Conference Papers

Hernandez-Ledesma AL; Salazar-Magana S; Coss-Navarrete EL; Nunez-Reza KJ; Nieto LT; Pena-Ayala A; Torres-Valdez E; Rodriguez GF; Frontana-Vazquez G; Rosetti F; Fernandez-Valverde SL; Arcelus MG; Alpizar-Rodrigue D; Medina-Rivera A, 2024, 'ALLELE SPECIFIC GENE EXPRESSION DURING TOLERANCE INDUCTION ON DENDRITIC CELLS FROM MEXICAN WOMEN WITH SYSTEMIC LUPUS ERYTHEMATOSUS', in ANNALS OF THE RHEUMATIC DISEASES, ELSEVIER, AUSTRIA, Vienna, presented at Meeting of the European-Alliance-of-Associations-for-Rheumatology (EULAR), AUSTRIA, Vienna, 12 June 2024 - 15 June 2024, http://dx.doi.org/10.1136/annrheumdis-2024-eular.2067

Sohail M; Chong AY; Palma MJ; Quinto-Cortes CD; Ragsdale A; Medina SG; Delgado-Sanchez G; Cruz-Hervert LP; Ferreyra-Reyes L; Moreno-Macias H; Aguilar-Salinas CA; Cortes A; Fernandez-Valverde SL; Acuia-Alonzo V; Wojcik G; Gignoux CR; Bustamante CD; Hill A; Tusie MT; Mentzer AJ; Novembre J; Garcia-Garcia L; Moreno-Estrada A, 2022, 'Unraveling demographic history and complex trait architecture from 6,000 Mexican genomes', in AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY, WILEY, pp. 172 - 172

Fernandez-Valverde SL; Degnan BM, 2018, 'Early evolution of gene regulatory networks in metazoan development', in INTEGRATIVE AND COMPARATIVE BIOLOGY, OXFORD UNIV PRESS INC, CA, San Francisco, pp. E63 - E63, presented at Symposium on Science in the Public Eye - Leveraging Partnerships at the Annual Meeting of the Society-for-Integrative-and-Comparative-Biology (SICB), CA, San Francisco, 03 January 2018 - 07 January 2018

Preprints

Vargas-Mejía P; Olguín-Lamas A; Fernandez-Valverde SL; Lund G; Vielle-Calzada J-P; Silva-Rosales L, 2026, Plasmodesmatal callose deposition is associated with tissue-specific restriction of Tobacco etch virus during recovery in transgenic tobacco, http://dx.doi.org/10.2139/ssrn.7391737

Hernández-Ledesma AL; Coss-Navarrete EL; Salazar-Magaña S; Ramírez-Espinosa D; Tinajero-Nieto L; Torres-Valdez E; Peña-Ayala A; Félix-Rodriguez G; Frontana-Vázquez G; García Sotelo JS; Trynka G; Rosetti F; Fernandez-Valverde SL; Gutiérrez-Arcelus M; Alpízar-Rodríguez D; Medina-Rivera A, 2025, Gene expression profiling of dendritic cell tolerance dysfunction in women with Systemic lupus erythematosus, http://dx.doi.org/10.64898/2025.12.21.695630

Vargas-Mejía P; Olguín-Lamas A; Fernandez-Valverde SL; Flores-García CM; Lund G; Vielle-Calzada J-P; Silva-Rosales L, Callose deposition at plasmodesmata suggests a role in viral movement restriction in transgenic tobacco plants during recovery from Tobacco etch virus infection, http://dx.doi.org/10.1101/2022.11.08.515744

Ozment E; Tamvacakis AN; Zhou J; Rosiles-Loeza PY; Escobar-Hernandez EE; Fernandez-Valverde SL; Nakanishi N, 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

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

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

Sohail M; Chong AY; Quinto-Cortes CD; Palma-Martínez MJ; Ragsdale A; Medina-Muñoz SG; 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 CA; Auckland K; Cortés A; Acuña-Alonzo V; Ioannidis AG; Gignoux CR; Wojcik GL; Fernández-Valverde SL; Hill AVS; Tusié-Luna MT; Mentzer AJ; Novembre J; García-García L; Moreno-Estrada A, 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

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

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

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

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