RNA Computational genomics



More about us:

Dr. Cei Abreu Goodger

Principal Investigator

Our interests lie within the realm of gene regulation, with a focus on RNA-based regulatory mechanisms.
We develop computational approaches to study the functional and evolutionary effects that microRNAs have on gene expression. Highly conserved miRNAs are particularly interesting in this regard, since they tend to affect larger numbers of transcripts, even though the majority of individual target sites are not highly conserved. By comparing experiments performed in different species or reconstructing ancestral sequences, we can study the evolution of miRNA-target networks across various evolutionary distances.
We are also interested in studying small RNAs that can be transferred between cells and even between species. Recently many extra-cellular small RNAs, including microRNAs, have been discovered, usually within exosomes. A few cases of RNA-based communication between species have been documented, but many questions remain.

Research lines:

  • Prediction of microRNA function.
  • Evolution of microRNA regulatory networks.
  • Function and evolution of methylation systems in bacteria.
  • RNA-based communication between species.

Recent projects:

  • "Estudio de la función de RNAs pequeños en simbiontes". SEP-CONACYT Basic Research grant (2018-2021).
  • "Generation of a de novo genome assembly and gene annotation for the Monarch butterfly Danaus plexippus". UC-MEXUS-CONACYT (2017-2018).
  • "An extracellular RNAi pathway as a mechanism of parasite-host communication". Human Frontiers Science Program (2014-2018).
  • "Evolución de la regulación por microRNAs en animales: análisis sistemático de su plasticidad funcional". SEP/CONACYT - Basic Research grant (2011-2015).

Most relevant publications:

work team

Dr. Cei Abreu Goodger

Principal Investigator

"I’m interested in the world of non-coding RNA, especially the so-called small RNAs. In addition to being important regulators in almost all multicellular organisms, we now realize that they can be transmitted between different organisms, with effects that we are just beginning to glimpse"


Eng. Mayra Imelda Flores Barraza

Research assistant


Dr. Sergio Nigenda Morales


"My research interests are focused on ecological and evolutionary genomics, phylogeography, phenotypic diversity associated to patterns of gene expression and adaptation to different environments in non-model mammals (i.e. whales, marsupials and coatis) (in codirection with Dr. Andrés Moreno)"


Dr. Obed Ramírez Sánchez


“I am evaluating and developing strategies for de novo small RNA assembly and their effect on gene expression and phylogenetic analyses"


Dr. José Manuel Villalobos Escobedo


“Transcriptional analysis of plant-fungus communication. I am currently studying the molecular dialogue between Trichoderma and plants, deciphering the transcriptomic changes that occur when these organisms interact. I am also initiating a research line focused on the fungal innate immune system during regeneration”


M. Sc. Daniel Lepe Soltero

PhD student in Plant Biotechnology

"I study the effect of different hybrid combinations on parent-of-origin gene expression in early embryogenesis in Arabidopsis thaliana (in codirection with Dr. Stewart Gillmor)"


M. Sc. José Roberto Bermúdez Barrientos

PhD student in Integrative Biology

"I study species interactions mediated by small RNAs (sRNAs) using the parasitic nematode Heligmosomoides bakeri as a model. I use bioinformatic tools to describe the sRNAs produced and secreted by H. bakeri and predict targets in its host"


Michelle Crisely

Master’s student in Integrative Biology

"I want to understand the genes and processes that extend the longevity effect of metformin in the budding yeast Saccharomyces cerevisiae (in codirection with Dr. Alexander de Luna)"


Carlos Luna

Master’s student in Integrative Biology

“I study the tissue-specific enhancers and their target genes that are involved in the development of Drosophila melanogaster (in codirection with Dra. Kasia Oktaba)”


Gonzalo Córdova López

Master's student in Integrative Biology

“I study the role of narnaviruses within the phytopathogenic fungus Rhizopus microsporus. I am interested in its involvement in the alliance established between the same fungus and its endosymbiont, a bacterium known as Burkholderia rhizoxinica (in codirection with Dr. Laila Pamela Partida)”


Isaac Martínez Ugalde

Master’s student in Integrative Biology

“I study the biogenesis of small interfering RNAs in nematodes and their function in parasitism, using Heligmosomoides bakeri as a model”