Dr Selene Fernandez Valverde
Senior Lecturer

Dr Selene Fernandez Valverde

Science
School of Biotech & Biomolecular Science

Check out the lab website here ---> https://regrnalab.github.io/

Dr Fernandez is a genomic scientist & bioinformatician interested in understanding the role non-coding RNAs play in the evolution of gene regulatory landscapes within and across eukaryotes.

She is a Senior Lecturer RNA New Research Talent Program (Level C) funded by the UNSW RNA Institute. Her laboratory focuses on studying the evolution of long non-coding RNAs in various plants and animals to predict their functions better using bioinformatic tools and genomic approaches. She is particularly interested in how these could be leveraged to impact food production and disease in crops and humans. 

Dr Fernandez holds a BSc in Genomic Sciences from the National Autonomous University of Mexico (2007). She completed her doctorate at the University of Queensland (UQ), studying new classes of small RNAs with Prof. John Mattick in 2013. As a postdoc, she used comparative genomics to identify regulatory changes that facilitated the evolution of multicellular organisms and morphological diversity in the animal kingdom in the laboratory of Prof. Bernie Degnan, UQ (2012-2015). She then returned to her native Mexico as a Principal Investigator at the Advanced Genomics Unit of Cinvestav (2016-2023) before joining UNSW as a Senior Lecturer in mid-2023.  

Dr Fernandez was awarded the Mexico national scholarship L’Oreal-UNESCO-AMC-CONACYT for Women in Science in 2016, the International Rising Talents Fellowship of L’Oreal-UNESCO in 2018 and the Gender Equality Award by the International Union of Immunological Societies in 2019. She is a founding member of Mas Ciencia por Mexico (More Science for Mexico), the Mexican Network of Bioinformatics (Red Mexicana de Bioinformática), and a volunteer instructor of Software Carpentry and previously Clubes de Ciencia Mexico.

She has served as a volunteer mentor at foundations such as Ekpapalek and the “Mujeres en STEM: Futuras Líderes” program of the US-Mexico Foundation. Forbes Mexico magazine selected her as one of the 100 most powerful women in Mexico in 2018. She was recently elected in the competitive female climate leadership program 'Homeward Bound' and is part of #TeamHB8. 

Location
School of Biotechnology and Biomolecular Sciences Room 301D, Level 2, Biological Science North Building (D26) UNSW Sydney NSW 2052 Australia
  • Book Chapters | 2022
    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 | 2023
    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
    Journal articles | 2023
    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
    Journal articles | 2023
    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
    Journal articles | 2023
    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
    Journal articles | 2022
    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', Scientific Reports, 12, http://dx.doi.org/10.1038/s41598-022-18254-0
    Journal articles | 2022
    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
    Journal articles | 2022
    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
    Journal articles | 2021
    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
    Journal articles | 2021
    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
    Journal articles | 2020
    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
    Journal articles | 2020
    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
    Journal articles | 2020
    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
    Journal articles | 2020
    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
    Journal articles | 2019
    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
    Journal articles | 2019
    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
    Journal articles | 2018
    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
    Journal articles | 2018
    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
    Journal articles | 2017
    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
    Journal articles | 2017
    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
    Journal articles | 2016
    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
    Journal articles | 2016
    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
    Journal articles | 2015
    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
    Journal articles | 2015
    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
    Journal articles | 2014
    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
    Journal articles | 2013
    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
    Journal articles | 2013
    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
    Journal articles | 2011
    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
    Journal articles | 2010
    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
  • Preprints | 2023
    Corona-Gomez JA; Stadler PF; Fernandez-Valverde SL, 2023, Evolutionary conservation of secondary structures in the lncRNAs of plants, , http://dx.doi.org/10.1101/2023.08.13.553158
    Preprints | 2022
    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
    Preprints | 2022
    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
    Preprints | 2022
    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
    Preprints | 2021
    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
    Preprints | 2019
    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
    Preprints | 2019
    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
    Preprints | 2018
    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

  • 2021: Bioinformatics training room infrastructure upgrade: increasing bioinformatics training accessibility in Mexico CABANA Training Infrastructure Award, CABANA Innovation Fund, EMBL-EBI, UK (7,925.38 GBP)
  • 2020: Patrones de expresión alelo específicos en lupus eritematoso sistémico durante la inducción de tolerancia (Allele-specific expression patterns in systemic lupus erythematosus during tolerance induction) Convocatoria 2019 de Proyectos de Ciencia de Frontera, Modalidad de Grupo, CONACYT, Mexico ($3,149,880.30 MXN ~285,750 AUD)
  • 2018: Co-expresión tejido específica de dominios estructurales conservados en ARNs largos no codificantes (Tissue-specific co-expression of conserved structural domains in long non-coding RNAs) Convocatoria 2017-2018 de Proyectos de Investigación Científica Básica, Investigador Joven, CONACYT, Mexico ($1,418,200.00 MXN ~128,656 AUD)
  • 2018: The evolutionary dynamics of long non-coding RNAs and chromatin structure in plants. Newton Advanced Fellowship Research Fellow, The Royal Society, UK (105,500.00 GBP)

  • 2019: Gender Equality Award. International Union of Immunological Societies (IUIS)
  • 2018: L’Oréal-UNESCO For Women In Science, International Rising Talents Fellow (15,000 euros)
  • 2016: L’Oréal-UNESCO-CONACYT-AMC Fellowship for Women in Science (Becas Para las Mujeres en la Ciencia) - Mexico ($100,000 MXN)
  • 2008-2011: UQ International Research Tuition Award (UQIRTA)
  • 2008-2011: Research Scholar scholarship from the Institute for Molecular Bioscience
  • 2006: ICE-EM International Travel Scholarship to attend the BioInfoSummer symposium at the Australian National University in Canberra ($2,500 AUD)

In the RegRNALab, we leverage bioinformatic and genomic data analysis to understand how gene regulatory mechanisms change through time, while mantaining the intricate development and diversity of cells we find in multicellular plants and animals.

We are particularly interested in understanding the evolutionary dynamics of non coding RNA molecules. For this, we study a number of biological models that span different evolutionary scales, including humans, plants and animals.

We aim to identify and characterise gene control mechanisms to unveil new medical and biotechnological applications of transitory gene control using RNA.

Comparative genomics of synthenic regions that generate long non-coding RNAs (lncRNAs) to model their evolutionary dynamics.

We are currently comparing the evolution of lncRNAs in synthenic regions in plants to measure how quickly they are lost gain across plant evolution. We also aim to understand what fraction of lncRNAs are under splicing, positional and structural selection in this kingdom.

Identification of functionally homologous lncRNA structural modules.

One of the greatest limiting factors in the identification of lncRNA function is the lack of functional information at the modular level that could potentially be extrapolated to other lncRNAs. We are working in the identification of “structural domains” in lncRNAs that allow us to infer the function of such molecules de novo using bioinformatic methods for their identification join with experimental methods for functional validation.

Identification of lncRNAs under recent selection in human populations.

In collaboration with the group of Dr. Andres Moreno-Estrada we recently characterized the genetic variation of modern Mexicans across Mexico.
We are leveraging this and other Biobanks to identify lncRNAs under selection as well as associated to cardio-metabolic syndromes in admixed populations. We are very interested in how genetic diversity and admixture in humans impacts disease.

My Research Supervision

 

  • Irving Jair García (PhD candidate, based at the Advanced Genomics Unit, Cinvestav, Mexico - jointly advised with Dr. Stewart Gillmor)
  • Gabriel Martinez (MSc student, based at the Unidad Irapuato, Cinvestav, Mexico - jointly advised with Dr. Katarzyna Oktaba)

Lab Alumni

  • Sergio Nigenda-Morales, Postdoctoral Researcher, Cinvestav 
  • Victor Flores Lopez, Postdoctoral Researcher, Cinvestav
  • Jose Cetz-Chel, Postdoctoral Researcher, Cinvestav
  • Adrián Díaz Chávez - MSc Integrative Biology, Cinvestav
  • Evelia Coss Navarrete - PhD Plant Biotechnology, Cinvestav
  • Jaime Pérez Patiño - BSc & MSc Plant Biotechnology, Cinvestav
  • Pablo Rosiles Loeza - MSc Plant Biotechnology, Cinvestav
Judith Ballesteros Villascan - MSc Integrative Biology, Cinvestav
  • América Ramírez Colmenero - MSc Integrative Biology, Cinvestav
  • Stephanie Mata Bonilla - MSc Plant Biotechnology, Cinvestav
  • José Antonio Corona Gómez - Postdoctoral Researcher & PhD Plant Biotechnology, Cinvestav
  • Jordan Pérez Medina - MSc Plant Biotechnology, Cinvestav
  • Emiliano Sotelo Fonseca - BSc & MSc Plant Biotechnology, Cinvestav
  • Alexander Ramos Díaz - MSc Integrative Biology, Cinvestav
  • Francisco Falcón Chávez - MSc Integrative Biology, Cinvestav
  • Federico Gaiti - PhD, School of Biological Sciences, The University of Queensland
  • Andrew Calcino - PhD, School of Biological Sciences, The University of Queensland