We are a research group at the UNSW RNA Institute and School of Biotechnology and Biomolecular Sciences in Sydney, Australia. We study how RNA controls gene expression and changes using genomics and bionformatics.
Research
The recent advent of high-throughput or "next generation" sequencing (NGS) of nucleic acids has unveiled a plethora of novel regulatory molecules, in particular non-coding RNAs - RNA molecules that presumably do not encode proteins. Even though some RNAs have long been known to have gene regulatory and catalytic capabilities, only in recent years has the sheer scale of regulatory capabilities of non-coding RNAs been truly envisioned.
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.
People
Selene Fernandez-Valverde
Senior Lecturer/Group Leader
I’m a bioinformatician and genomic data scientist studying the evolution of gene regulatory mechanisms underlying the phenotypic diversity and cell differentiation in multicellular eukaryotes. I’m particularly interested in the regulatory roles of non-coding RNAs in these processes.
I have a BSc in Genomic Sciences from the National Autonomous University of Mexico (LCG-UNAM) and a PhD in Bioinformatics from the Institute for Molecular Biosciences (IMB) at the University of Queensland, Australia. I did my postdoc at the School of Biological Sciences, also at UQ.
In addition to my academic roles, I actively participate in initiatives that link scientists and the general public (such as Mas Ciencia por Mexico, Clubes de Ciencia Mexico), programs to introduce researchers to computing (Software/Data Carpentry, Red Mexicana de Bioinformatica) as well as mentoring programs (Ekpapalek and Mujeres en STEM: Futuras Líderes, from the US-Mexico Foundation).
I’ve been honoured with one of five recipients of the L’Oreal-UNESCO research fellowship For Women in Science - Mexico chapter - in 2016 and one of 15 worldwide L’Oreal-UNESCO For Women In Science International Rising Talents fellowship in 2018. I was also named one of 100 most powerful women in Mexico by Forbes Mexico magazine in 2018. I’m an ARC Future Fellow since January 2025.
When not behing a computer, you can find me hiking, scuba diving or spending time with my F1.
Gabriela Santos Rodriguez
Postdoctoral Researcher, UNSW
She holds a BSc in Biology from the Faculty of Science, UNAM, Mexico, and an MSc in Integrative Biology from Cinvestav, Mexico. She recently submitted her PhD thesis from the University of New South Wales. She is interested in Evolution and RNA Biology; her research expands from microRNA evolution in Metazoa and circular RNAs in Primates to mRNA isoform evolution in Vertebrates. She has recently joined the Regulatory RNA lab to study the evolution of lncRNAs in Brassicaceae. In her free time, she enjoys training Muay Thai and BJJ and spending time with her cat.
Xingyu Yan
PhD Candidate, UNSW
Xingyu holds a BSc in Plant Protection from the Faculty of Plant Health & Medicine, QAU, China, and an MSc in Plant Sciences from the Faculty of Mathematics and Natural Sciences, University of Bonn, Germany. She later spent a year as a research assistant in the School of Life Sciences, CUHK, Hong Kong SAR. Her main interest is Plant RNA Biology, she joined the Regulatory RNA lab in 2024 to dive deep into the world of RNA-protein interactions in plants. While she’s currently making her mark in the wet lab, she’s also an enthusiastic beginner in bioinformatics, eager to expand her skills!
Putri Adiela Agson Gani
PhD Candidate, UNSW
She holds a Bachelor of Engineering and a master’s degree in biotechnology from Institut Teknologi Bandung, Indonesia, where she focused on post-harvest handling and technology of crops. Before commencing her PhD at UNSW, she worked as a business consultant, with a growing interest in integrating plant science and technology into industry applications. Her current research focuses on analysing RNA structure and its interaction with proteins, particularly in the context of gene regulation in plants. She is also expanding her budding skills in bioinformatics. Outside of research, she enjoys hiking and crocheting.
Irving García
PhD Plant Biotechnology Candidate, Cinvestav
Billi Ilkovski
RA/Laboratory Manager (Part-time)
Billi completed a Bachelor of Biotechnology degree (1st Class Honours) at The University of Wollongong in 1997. She worked as a Research Assistant at the Royal North Shore Hospital and at The Children’s Hospital at Westmead. She completed her PhD in 2004 at The University of Sydney and continued as a Post-doc for the next decade working on genetic neuromuscular disorders. In 2019, Billi joined UNSW as a lab manager and has continued in this role with the Regulatory RNA lab in February 2025.
Alumni
Sergio Nigenda-Morales, Postdoctoral Researcher, Cinvestav
Victor Flores Lopez, Postdoctoral Researcher, Cinvestav
Jose Cetz-Chel, Postdoctoral Researcher, Cinvestav
Gabriel Martinez Medina - MSc Plant Biotechnology, 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
Rafael Rincon Ramirez, Internship, Cinvestav
Lorena Gomez Godinez, Internship, Cinvestav
Christopher Klapproth, Internship, Cinvestav
Leyda Cortez Maldonado, Internship, Cinvestav
Jose Luis Garcia Corona, Internship, Cinvestav
Ramon Valdez Melchor, Internship, Cinvestav
Dharam Arora, Undergrad Internship, Computer Science, UNSW
Rotation students not listed
Publications
Want to read our latest research? Check out our preprints on bioRxiv
2024
MAYEX is an old long noncoding RNA recruited for X chromosome dosage compensation in a reptile.
Tenorio M, Cruz-Ruiz S, Encarnacion-Guevara S, Hernandez M, Corona-Gomez JA, Sheccid-Santiago F, Serwatowska J, Lopez-Perdomo S, Flores-Aguirre CD, Arenas-Moreno DM, Ossiboff RJ, Mendez-de-la-Cruz F, Fernandez-Valverde SL, Zurita M, Oktaba K, Cortez D. Science | Journal
lncRNAs involved in the Shade Avoidance Syndrome (SAS) in Arabidopsis thaliana.
Garcia-Lopez IJ, Velez-Ramirez AI, Gillmor CS, Fernandez-Valverde SL.
BMC Genomics
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2023
Plant long non-coding RNAs: identification and analysis to unveil their physiological functions.
Domínguez-Rosas E, Hernández-Oñate MÁ, Fernandez-Valverde SL, Tiznado-Hernández ME. Frontiers in Plant Science | PDF | Journal
Mexican Biobank advances population and medical genomics of diverse ancestries
Sohail M, Palma-Martinez MJ, Chong AY, Quinto-Cortes CD, Ragsdale A, Medina-Munoz SG, Barberena- Jonas C, Delgado-Sanchez G, Cruz-Hervert LP, Ferreyra-Reyes L, Ferreira-Guerrero E, Mongua-Rodriguez N, Jimenez-Kaufmann A, Moreno-Macias H, Aguilar-Salinas CA, Auckland K, Cortes A, Acuna-Alonzo V, Ioannidis AG, Gignoux CR, Wojcik GL, Fernandez-Valverde SL, Hill AVS, Tusie-Luna MT, Mentzer AJ, Novembre J, Garcia-Garcia L, Moreno-Estrada Nature | ReadCube | Journal | bioRxiv
Genome-wide analysis of RNA-chromatin interactions in lizards as a mean for functional lncRNA identification.
Tenorio M, Serwatowska J, Fernandez-Valverde SL, Oktaba K, Cortez D. BMC Genomics | PDF | Journal
Down memory lane - unravelling the puzzle of gene regulation.
Fernandez-Valverde SL Nature Reviews Genetics | PDF | Journal
2022
Plant in-situ Hi-C experimental protocol and bioinformatic analysis
Perez-de los Santos FJ, Sotelo-Fonseca JE, Ramirez-Colmenero A, Nutzmann H-W, Fernandez-Valverde SL*
Oktaba K
Book chapter. Plant Comparative Genomics. Methods in Molecular Biology
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| Journal
* Corresponding author
Transcriptome-guided annotation and functional classification of long non-coding RNAs in Arabidopsis thaliana
Corona-Gomez JA, Coss-Navarrete EL, Garcia-Lopez IJ, Klapproth C, Perez-Patino JA, Fernandez-Valverde
SL*
Scientific Reports
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| Journal
| bioRxiv
* Corresponding author
Plants & Python: A series of lessons in coding, plant biology, computation, and bioinformatics.
VanBuren R, Rougon-Cardoso A, Amezquita EJ, Coss-Navarrete E, Espinosa-Jaime A, Gonzalez-Iturbe O, Luckie-Duque A, Mendoza-Galindo E, Pardo J, Rodriguez-Guerrero G, Rosiles-Loeza P, Vasquez-Cruz M, Fernandez-Valverde SL, Hernandez-Hernandez T, Palande S, Chitwood DH The Plant Cell - Teaching tools in plant biology | PDF | Journal
Imputation performance in Latin American populations: improving rare variants representation with the inclusion of Native American genomes
Jimenez-Kaufmann A, Chong AY, Cortes A, Fernandez-Valverde SL, Ferreyra-Reyes L, Cruz-Hervert P, Quinto-Cortes CD, Sohail M, Palma-Martinez MJ, Delgado-Sanchez G, Mentzer AJ, Hill AV, Moreno- Macias H, Huerta-Chagoya A, Aguilar-Salinas CA, Torres M, Kim HL, Kalsi N, Schuster SC, Tusie-Luna T, Ortega-Del Vecchyo D, Garcia-Garcia L and Moreno-Estrada A Frontiers in Genetics | PDF | Journal
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 eLife | PDF | Journal | bioRxiv
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 | PDF | Journal
2020
Evolution of Genome-Organizing Long Non-coding RNAs in Metazoans
Ramirez Colmenero A, Oktaba K and Fernandez-Valverde SL*. Frontiers in Genetics | PDF | Journal * Corresponding author
Voices of the new generation: being a junior PI in a developing country
Fernandez-Valverde SL Nature Reviews Molecular Cell Biology | PDF | Journal
Splicing conservation signals in plant long non-coding RNAs
Corona-Gomez JA, Garcia-Lopez IJ, Stadler PF* and Fernandez-Valverde SL*.
RNA
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| bioRxiv
* Corresponding author
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
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* Corresponding author
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 | ReadCube | Journal | bioRxiv * Equal contribution
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 | PDF | Journal
2018-2010
Find earlier publications on Pubmed and Google Scholar
Opportunities
If you are interested in joining the lab please email Selene at:
s [ d o t ] fernandez [ _ ] valverde [ A T ] unsw [ d o t ] edu [ d o t ] au
Please write a brief description of your background and research interests as well as the project that you are most interested in.
Acknowledgement of country
We acknowledge the Bedegal people, the Traditional Owners of Country where the lab is currently located. We pay our respect to Aboriginal and Torres Strait Islander, Indigenous peoples of the Americas and First Nations people and cultures across the world.