RNA Computational genomics

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:

• 1. Secretion of an Argonaute protein by a parasitic nematode and the evolution of its siRNA guides. DNucleic Acids Res. 2019 Apr 23;47(7):3594-3606.
• 2. Danger signals activate a putative innate immune system during regeneration in a filamentous fungus. PLoS Genet. 2018 Nov 30;14(11):e1007390.
• 3. Annotating and quantifying pri-miRNA transcripts using RNA-Seq data of wild type and serrate-1 globular stage embryos of Arabidopsis thaliana. Data Brief. 2017 Oct 12;15:642-647.
• 4. Improving microRNA target prediction with gene expression profiles. BMC Genomics. 2016 May 17;17:364.
• 5. Exosomes secreted by nematode parasites transfer small RNAs to mammalian cells and modulate innate immunity. Nat Commun. 2014 Nov 25;5:5488.

Recent publications:

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