How do cells reprogram their phenotypes? Embryonic cells dividing into specialized tissues or microorganisms adapting to industrial culture conditions are striking examples of cells’ capacity to re-purpose their biochemical machinery. We address this question by studying how metabolic and genetic regulatory mechanisms interplay to deliver spot-on cellular adaptations.


González-Arrué, N., Inostroza, I., Conejeros, R. and Rivas-Astroza, M., 2023. Phenotype-specific estimation of metabolic fluxes using gene expression data. iScience, p.106201.

Rivas-Astroza, M., Paredes, I., Guerrero, K., Mau, S., Quintero, J., Gentina, J.C., Conejeros, R. and Aroca, G., 2021. Kinetic model of Clostridium beijerinckii's Acetone-Butanol-Ethanol fermentation considering metabolically diverse cell types. Journal of Biotechnology, 342, pp.1-12.

Rivas-Astroza, M. and Conejeros, R., 2020. Metabolic flux configuration determination using information entropy. Plos one, 15(12), p.e0243067.

Biase, F.H., Wu, Q., Calandrelli, R., Rivas-Astroza, M., Zhou, S., Chen, Z. and Zhong, S., 2018. Rainbow-Seq: combining cell lineage tracing with single-cell RNA sequencing in preimplantation embryos. Iscience, 7, pp.16-29.

Maier, J.A., Rivas-Astroza, M., Deng, J., Dowling, A., Oboikovitz, P., Cao, X., Behringer, R.R., Cretekos, C.J., Rasweiler, J.J., Zhong, S. and Sears, K.E., 2017. Transcriptomic insights into the genetic basis of mammalian limb diversity. BMC evolutionary biology, 17(1), p.86.

Xiao, S., Lu, J., Sridhar, B., Cao, X., Yu, P., Zhao, T., Chen, C.C., McDee, D., Sloofman, L., Wang, Y. and Rivas-Astroza, M., 2017. SMARCAD1 contributes to the regulation of naive pluripotency by interacting with histone citrullination. Cell reports, 18(13), pp.3117-3128.

Sridhar, B., Rivas-Astroza, M., Nguyen, T.C., Chen, W., Yan, Z., Cao, X., Hebert, L. and Zhong, S., 2017. Systematic mapping of RNA-chromatin interactions in vivo. Current Biology, 27(4), pp.602-609.

Sears, K.E., Maier, J.A., Rivas-Astroza, M., Poe, R., Zhong, S., Kosog, K., Marcot, J.D., Behringer, R.R., Cretekos, C.J., Rasweiler IV, J.J. and Rapti, Z., 2015. The relationship between gene network structure and expression variation among individuals and species. PLoS Genet, 11(8), p.e1005398.

Lee, J., Seok, S., Yu, P., Kim, K., Smith, Z., Rivas‐Astroza, M., Zhong, S. and Kemper, J.K., 2012. Genomic analysis of hepatic farnesoid X receptor binding sites reveals altered binding in obesity and direct gene repression by farnesoid X receptor in mice. Hepatology, 56(1), pp.108-117.

Rivas-Astroza, M., Xie, D., Cao, X. and Zhong, S., 2011. Mapping personal functional data to personal genomes. Bioinformatics, 27(24), pp.3427-3429.