Functional and Evolutionary Genomics of Regulatory RNA

GRUPOS DE TRABAJO

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Dr. Selene L. Fernández Valverde

Principal Investigator

The recent advent of genomic information fostered by the invention of high-throughput sequencing has unveiled a plethora of regulatory molecules, including a large number of non-coding RNAs – RNA molecules little or no protein-coding potential. Many of these RNAs have important functions as modulators of gene expression.
In our group, we study the evolutionary dynamics of non-coding RNA molecules using a variety of plant and animal species with diverse evolutionary scales. We use bioinformatics and genomic data to understand the evolution of these molecules and the regulatory mechanisms in which they participate.

Research lines:

  • Comparative genomics of syntenic regions that generate long non-coding RNAs (lncRNAs) to characterize their evolutionary dynamics.
  • lncRNAs evolution in regeneration processes and embryonic development in plants and animals.
  • Identification of functionally homologous structural modules in lncRNAs.
  • Identification of lncRNAs associated to cardio-metabolic syndromes in Mexican human populations.

Recent projects:

  • “International Rising Talents”. L’Oréal-UNESCO 2018.
  • "The evolutionary dynamics of long non-coding RNAs and chromatin structure in plants". The Royal Society, Newton Advanced Fellowship 2017.
  • “Validation of the existence of protein-binding domains in a long non-coding RNA.” L’Oréal-UNESCO-CONACYT-AMC Fellowships for Women in Science, Mexico (2016).

Most relevant publications:

Recent publications:

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work team


Dr. Selene L. Fernández Valverde

Principal Investigator

"My research focuses on genomics and bioinformatics. My core academic interest is contributing to the understanding of the mechanisms involved in the wide phenotypical diversity present in the animal and plant kingdom. I’m particularly interested in the role of non-coding RNAs in the evolution of regulatory landscapes within and between species"

selene.fernandez@cinvestav.mx

Ing. Mayra Imelda Flores Barraza

Administrative Assistant

Dr. Francisco Javier Pérez de los Santos

Postdoc

“Experimental Characterisation of Conserved structures in long non coding RNAs. Mi project aims at experimentally studying secondary structures and protein-RNA interactions in long non coding RNAs (lncRNAs) predicted to be conserved by computational methods”

M. Sc. José Antonio Corona Gómez

PhD student in Plant Biotechnology

"My project is focused on the identification of evolutionary conservation of the lncRNA structure in Brasiliaceae using bioinformatic tools and comparative genomics”

M.Sc. Evelia Lorena Coss Navarrete

PhD student in Plant Biotechnology

“The main objective of my project is to identify the orthologous lncRNAs present in the aerial part and roots in seedlings of various Brasicáseas, through the use of bioinformatic tools and experimental validation”

Francisco J. Falcón Hernández

Master’s student in Integrative Biology

"My project focuses on the study of two species of axolotl using comparative genomics to better understand the regeneration process. I’m particularly interested in non-coding RNAs and their role in the maintenance of pluripotency (in codirection with Dr. Alfredo Cruz)”

Luis Jordan Perez Medina

Master’s student in Plant Biotechnology

"My project is focused in identifying co-expressed RNAs in specific human tissues that can share functions, with the purpose of identifying conserved structural domains"

Irving Jair García López

Master’s student in Plant Biotechnology

“Using bioinformatics, we’re looking for long non-coding RNAs (lncRNAs) that are regulating the elongation of specific plant organs (hypocotyls and cotyledons), in response to low light availability during a very common phenomenon among plants called neighbor proximity, using Arabidopsis thaliana as a model"

Rene Alexander Ramos Díaz

Master’s student in Integrative Biology

“Application of machine learning methods for data analysis and simulation of biological processes, EvoDevo and evolution of multicellularity”

Jesús Emiliano Sotelo Fonseca

Master’s student in Plant Biotechnology

“Studies how the spatial conformation changes in the genome during development and under different experimental conditions. He evaluates bioinformatic tools that identify changes in the tridimensional structure of the genome from capture data of chromosomal conformation (Hi-C)”

Jaime Alejandro Pérez Patiño

Master’s student in Plant Biotechnology

“Works on the analysis of pipelines for the detection of structural conservation in long non-coding RNAs to determine which bioinformatic strategy produces the best results when compared with experimental data”

América Ramírez Colmenero

Master’s student in Integrative Biology

“Works the characterization and comparison of the genomic architecture and chromatin- associated lncRNAs on organs of different Brassica species, using chromosome conformation capture methods (Hi-C and ChAR-seq)”

Esteban Elías Escobar Hernández

Master's Student in Plant Biotechnology

“Works on the identification and characterization of m6A methylated transcripts during the development of outbreaks in Physcomitrella patens using epitranscriptomic bioinformatics tools”

Stephanie Mata Bonilla

Master's Student in Plant Biotechnology

“Works with Botryococcus braunii Race B (Showa), a microalga producer of hydrocarbons called botryococcenos, and my interest is to study at a transcriptomic level that mRNAs and lncRNAs are differentially expressed under different culture conditions of the microalga and characterize the processes in which they participate”