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Marcos J. Araúzo-Bravo is a scientist and project leader at the MPI. As it emerges from his published work, his main research has been devoted to the development and application of computer tools for analyzing and solving biological problems. He received his doctoral degrees in industrial technologies from the University of Cartagena, Spain (2001), and in information technology and biotechnology from the Kyushu Institute of Technology, Fukuoka, Japan (2003). As a postdoctoral fellow he was granted by the Japan Society for the Promotion of Science (JSPS) to study the synergetic control of genetic networks through transcriptional regulators at the Kyushu Institute of Technology (2004-2006).
Development of computer tools for understanding the mechanism underlying genetic regulatory networks of the toti-, pluripotential stem cells and reprogrammed cells. To elucidate the cross talk of the main pluripotency players at the molecular level and to provide answers to the remaining questions concerning the reprogramming mechanisms, we are implementing an integrative approach collecting measurements of different nature (gene expression, microRNA expression, epigenetic profiles, protein abundance, metabolic measurements) performed in a holistic way thanks to the use of high throughput techniques, combining the measurements obtaining in our lab with data compiled from databases and gluing all these data by recycling computational biological tools and developing our own new ones.
Characterization of the properties of the genetic regulatory networks of the toti-, pluripotential stem cells
Embryonic stem cells (ESCs) have the capability for self-renewal and the potential to form all the cell types of the body. This brings the possibility to exploit ESC populations as a cellular source for therapies in medical situations with irreversible tissue damage. To make this potential a reality, we need a better understanding of the interplay of the transcription factors (TFs) and their binding sites involved in the regulation of the transcription network that determine the ability of ESCs to maintain their self-renewal and pluripotency.
In the last years, a trio of transcription factors (OCT4, SOX2, and NANOG) has been identified that plays a key role in determining the fate of ES cells. Strong efforts have been done on discovering these main players, generating large quantities of data with high throughput techniques. But the transcription regulatory network that rules the self-renewal and pluripotency states remains to be elusive.
Computational programming of biological reprogramming
A cocktail of transcription factors (OCT4, SOX2, C-MYC and KLF4) has been successfully applied to rewind the clock of unipotent cells, reverting them to a state resembling the ESC, thus acquiring self-renewal and pluripotential capabilities. Generating the so-called reprogrammed induced pluripotent (iPS) stem cells. iPS help to overcome some of the ethical concerns due to the use of human ESCs. But reprogramming does not normally occur in vivo and its mechanism is intriguing.
The four ingredients of the reprogramming cocktail have been reduced by researchers from our lab to two (Kim et al, 2008), one (Kim et al, 2009; Kim et al, 2009), and even zero (Ko et al, 2008), for some specific cell types. We expect to take advantage of this progressive complexity reduction to disentangle the reprogramming mechanisms.
Master and doctoral positions available
Currently we are recruiting doctoral students and postdocs in computational biology and bioinformatics at the department of Cell and Developmental Biology at the Max Planck Institute for Molecular Biomedicine in Münster (Germany).
If you are interested in doing your PhD in Systems Biology and Bioinformatics or to do a postdoc in computer science applied to biology in an exciting environment at the Max Planck Institute in Münster (Germany), please contact me at email@example.com
Some representative publications
Kim JB, Greber B, Araúzo-Bravo MJ, Meyer J, Park KI, Zaehres H and Schöler HR
Kim JB, Zaehres H, Araúzo-Bravo MJ and Schöler HR
Ko K, Tapia N, Wu G, Kim JB, Araúzo-Bravo MJ, Sasse, P, Glaser T, Ruau D, Han DW, Greber B, Hausdörfer K, Sebastiano V, Stehling M, Fleischmann BK,
Brüstle O, Zenke M and Schöler HR
Kim JB, Sebastiano V, Wu G, Araúzo-Bravo MJ, Sasse P, Gentile L, Ko K, Ruau D, Ehrich M, van den Boom D, Meyer J,
Hübner K, Bernemann C, Ortmeier C, Zenke M, Fleischmann BK, Zaehres H and Schöler HR (2009).
Kim JB, Zaehres H, Wu G, Gentile L, Ko K, Sebastiano V, Araúzo-Bravo MJ, Ruau D, Han DW, Zenke M and Schöler HR
Struckmann S, Araúzo-Bravo MJ, Schöler HR, Reinbold RA and Fuellen G
Araúzo-Bravo MJ and Sarai A.
del Sol A, Araúzo-Bravo MJ, Amoros D and Nussinov R
Ahmad S, Kono H, Araúzo-Bravo MJ and Sarai A
Araúzo-Bravo MJ, Fujii S, Kono H, Ahmad S, Sarai A
Peng L, Araúzo-Bravo MJ, Shimizu K
Zaid KS, Araúzo-Bravo MJ, Shimizu K
Zaid KS, Araúzo-Bravo MJ, Shimizu K
Araúzo-Bravo MJ, Cano-Izquierdo JM, Gómez-Sánchez E, López-Nieto MJ, Dimitriadis YA, López-Coronado J
Araúzo-Bravo MJ, Shimizu K
For a complete list of publications please see.
Some microarrays uploaded in the Gene Expression Omnibus (GEO) database
Zero-factor reprogramming. Heat-map of expression of pluripotent and germ cell marker genes extracted from gene expression microarrays, showing differential expression patterns between mouse Germ Stem Cells (GSCs), and ESCs and germ-line-derived pluripotent stem cells (gPS). (see).
One-factor reprogramming. Tri-dimensional scatter plot of the 1 factor (OCT4) reprogrammed human neural stem cells (1F hNiPS) versus H9 and H1 human embryonic stem cells (ESC). (see).
Two-factors reprogramming. Scatter plot of the 2 factor (Oct4, Klf4) reprogrammed mouse neural stem cells (2F iPS) versus embryonic stem cells (ESC). (see).
DNA recognition by drugs. Worm graph of the DNA imidazole-pyrrole-hydroxypyrrole polyamide binding complex. (see).
Metabolic engineering based on labeling techniques. Metabolic Flux Analysis of Escherichia coli pykF mutant. (see).
Allosteric communication in proteins. Modular decomposition and interconnectivity determinants identify key residues for allosteric communications in rhodopsin. (see).