Andrés Octavio ARAVENA DUARTE

Applied Mathematician, Engineer, University Teacher, Researcher in Bioinformatics and Machine Learning
Assistant Professor, Molecular Biology and Genetics Department, Istanbul University

Nationality: Chilean
Contact Email: andres.aravena@gmail.com
Contact Phone: +90 (507) 013 31 84
Homepage: http://dry-lab.org/

Bachelor in Engineering Sciences, Major in Mathematics, University of Chile, 1992
Mathematical Engineer, University of Chile, Chile, 2002
PhD on Informatics, Inria-University Rennes I, France, 2013
PhD on Mathematical Modelling, University of Chile, 2013

Experience

2014-Present: Assistant Professor. Molecular Biology and Genetics Department, Istanbul University
Aug 2022, Jan 2023: Visiting Professor. Millennium Institute “Center for Genome Regulation”, Universidad de Chile.
2013-2014: Postdoctoral Researcher. “Center for Genome Regulation”, Center of Mathematical Modeling, Universidad de Chile-CNRS.
2011-2013: PhD Thesist. Team Dyliss, IRISA/Inria, Université de Rennes 1, France.
2011-2013: PhD Thesist. “Center for Genome Regulation”, Center of Mathematical Modeling, Universidad de Chile-CNRS.
2009-2011: Bioinformatics Researcher on Salmon Nutriogenomics. Project “Salmonid genomics: identification of genes related to protein and vegetal oil usage in Atlantic salmon and rainbow trout nutrition”.
2008-2012: Bioinformatics Researcher on Grape Genomics. INIA, Chilean National Agriculture Research Institute
2010: Statistical analyst in Breast Cancer Research. Project “Molecular profile of breast cancer at clinical stages II and III in Latin-American women receiving a standard reference treatment”.
2007-2011: Co-research in the modeling copper homeostasis in E.faecalis. Funded by Fondecyt N17071083, National Fund for Science and Technology
2007-2008: Project manager. Project “Bioidentification system for industry-relevant microorganisms: application to avian and winery sectors”.
2003-2010: Chief Research Engineer. Laboratory of Bioinformatics and Mathematics of Genome, Center for Mathematical Modeling, Universidad de Chile-CNRS
2002: Chief Engineer. Network and Computing Services, Center for Mathematical Modeling, Universidad de Chile
1996-2001: Chief Engineer. Network and Computing Services, Universidad Arturo Prat, Chile

Publications

Acuña, V., Aravena, A., Guziolowski, C., et al. (2016). Deciphering transcriptional regulations coordinating the response to environmental changes. BMC Bioinformatics 17, 35.

Alvarez, C., Aravena, A., Tapia, T., et al. (2016). Different Array CGH profiles within hereditary breast cancer tumors associated to BRCA1 expression and overall survival. BMC Cancer 16, 1–14.

Cordero, N., Maza, F., Navea-Perez, H., et al. (2016). Different Transcriptional Responses from Slow and Fast Growth Rate Strains of Listeria monocytogenes Adapted to Low Temperature. Frontiers in Microbiology 7, 1–9.

Latorre, M., Ehrenfeld, N., Cortés, M.P., et al. (2016). Global transcriptional responses of Acidithiobacillus ferrooxidans Wenelen under different sulfide minerals. Bioresource Technology 200, 29–34.

Uçarlı, C., McGuffin, L.J., Çaputlu, S., et al. (2016). Genetic diversity at the Dhn3 locus in Turkish Hordeum spontaneum populations with comparative structural analyses. Scientific Reports 6, 20966.

Çelik, Haluk, Andres Aravena, and Neslihan Turgut Kara. 2023. “Bioinformatics and Gene Expression Analysis of the Legume F-Box/WD40 Proteins in NaCl and High Temperature Stress.” Genetic Resources and Crop Evolution, May. https://doi.org/10.1007/s10722-023-01592-x.

Patents

“Array of DNA fragments from biomining microorganisms and method for detection of them”. Argentina: AR057612, granted Dec 5, 2007, Australia: AU2006241345, granted Oct 10, 2013, Chile: CL200503033, presented Nov 21, 2005, China: CN101275168, granted Jun 5, 2013, Mexico: MX 307357 B, granted Feb 13, 2013, Peru: PE1432-2010/DIN, granted Oct 28, 2010, South Africa: ZA2006/09650, granted Dec 27, 2007, USA: US7915031B2, granted Mar 29, 2011.
“Method for the design of oligonucleotides for molecular biology techniques”. Argentina: AR054923B1, granted Jul 25, 2007, Australia: AU2006203551B2, granted Jun 2, 2011, Mexico: MX 305872 B, granted Dec 4, 2012, South Africa: ZA200606828B, granted Mar 26, 2008, USA: US7853408B2, granted Dec 14, 2010.
“Array of nucleotidic sequences for the detection and identification of genes that codify proteins with activities relevant in biotechnology present in a microbiological sample, and method for using this array”. Australia: AU2008201183, granted Jan 9, 2014, Chile: CL201349170, granted Jun 13, 2013, Mexico: MX 298861 B, granted May 3, 2012, Peru: PE1602-2012/DIN, granted Nov 23, 2012, South Africa: ZA2008/02344, granted Nov 26, 2008, USA: US8207324, granted Jun 26, 2012.
“Microarray of nucleotide sequences for the detection and identification of transcripts related to resistance or susceptibility of salmo salar to infection by Piscirickettsia salmonis with; method of identifying fish families susceptible and resistant to infection with P. salmonis”. Chile: CL201202773, presented Oct 3, 2012.
“Method for the identification and quantification of microorganisms useful in biomining processes”. Australia: AU2006204629, granted Oct 11, 2012, Mexico: MX 307267 B, granted Feb 8, 2013, South Africa: ZA2006/07131, granted May 30, 2007, USA: US8492093, granted Jul 23, 2013.
“Method and array for detection and identification of microorganisms present in a sample by using genomic regions coding for different tRNA-synthetases”. Argentina: AR056179, granted Sep 20, 2008, Australia: AU2006241289, granted May 14, 2009, Mexico: MX 313904 B, granted Oct 2, 2013, South Africa: ZA2006/09649, presented Dec 27, 2007.

Further References

Dr. Alejandro Maass, Director of Center of Mathematical Modeling at the University of Chile, amaass@dim.uchile.cl.
Dr. Anne Siegel, Research director of Dyliss team, University of Rennes 1, Inria, CNRS, IRISA, anne.siegel@irisa.fr.
Dr. Nazlı Arda, Former Director of Molecular Biology and Genetics Department, Istanbul University, narda@istanbul.edu.tr.
Mr. Gustavo Soto, Former President, Universidad Arturo Prat, Chile, gustavo.soto@unap.cl.
Dr. Pilar Parada, Director, Systems Biotechnology Center at Universidad Andres Bello. Former Executive Director of Center for Systems Biotechnology at Fraunhofer-Chile. Former CEO of BioSigma S.A., pilar.parada@fraunhofer.cl.

Languages

Spanish (native), English (spoken, written), French (spoken, written), Italian (basic), Portuguese (basic), Turkish (basic).