Andrés Octavio ARAVENA DUARTE

Assistant Professor: (2014-Present). Molecular Biology and Genetics Department, Istanbul University

• Supervised the thesis of 3 Masters students. All of them defended successfully.
• Promoted the formation of a “Bioinformatics Laboratory” of the Molecular Biology and Genetics Department.
• Established an international scientific collaboration network focused on the identification of the taxonomical origin of archeological DNA using machine learning techniques. Preliminary results were presented on international conferences.
• Created the course “Computing in Molecular Biology” to teach Data Science and Computational Thinking to undergrad students.
• Created the course “Methodology of Scientific Research” to teach the mathematical and analytical tools essential for Scientific Thinking to Master level students.
• Created the course “Systems Biology” to teach reconstruction and analysis of biological networks at the molecular level to PhD students.
• Reformulated and updated the “Bioinformatics” course.
• Supervised short thesis preparation for three undergrad students each year.

Visiting Professor: (Aug 2022,
Jan 2023). Millennium Institute “Center for Genome Regulation”, Universidad de Chile.

Postdoctoral Researcher: (2013-2014). “Center for Genome Regulation”, Center of Mathematical Modeling, Universidad de Chile-CNRS.

PhD Thesist: (2011-2013). Team Dyliss, IRISA/Inria, Université de Rennes 1, France.

PhD Thesist: (2011-2013). “Center for Genome Regulation”, Center of Mathematical Modeling, Universidad de Chile-CNRS.

Bioinformatics Researcher on Salmon Nutriogenomics: (2009-2011). Project “Salmonid genomics: identification of genes related to protein and vegetal oil usage in Atlantic salmon and rainbow trout nutrition”.

• Provided reference genomic data and analized experimental results.
• Enabled the participation of Chile in CGRASP consortium project to sequence the genome of Salmo salar.

Bioinformatics Researcher on Grape Genomics: (2008-2012). INIA, Chilean National Agriculture Research Institute

• Provided reference genomic data and analized experimental results.

Statistical analyst in Breast Cancer Research: (2010). Project “Molecular profile of breast cancer at clinical stages II and III in Latin-American women receiving a standard reference treatment”.

Co-research in the modeling copper homeostasis in E.faecalis: (2007-2011). Funded by Fondecyt N17071083, National Fund for Science and Technology

• Project “Study of transcriptional changes induced by exposition to copper in Enterococcus faecalis: functional analysis and identification of regulatory networks.”

Project manager: (2007-2008). Project “Bioidentification system for industry-relevant microorganisms: application to avian and winery sectors”.

• Designed a PCR-based kit for detection of contaminant yeasts in exported chilean wine. Supervised the experimental validation

Chief Research Engineer: (2003-2010). Laboratory of Bioinformatics and Mathematics of Genome, Center for Mathematical Modeling, Universidad de Chile-CNRS

• Executive direction of a research contract for BioSigma S.A., subsidiary of Codelco, the biggest company on the country and one of the biggest mining companies worldwide.
• Copper is the main economical resource in Chile. The long term goal of this project is to make a significant contribution to the national economy via a science based technological breakthrough.
• This project focused on the biology of bioleaching bacteria, used in efficient and environmental friendly copper mining.
• Main results: assembly and annotation of 3 bacterial genomes, analysis of transcriptomic and metabolomic experiments, modeling of metabolism, development of bioidentification probe design and analysis tools used in environmental samples.
• Five patents have been granted based on these results.
• The bioidentification tools are currently used by BioSigma in everyday operation.

Chief Engineer: (2002). Network and Computing Services, Center for Mathematical Modeling, Universidad de Chile

Chief Engineer: (1996-2001). Network and Computing Services, Universidad Arturo Prat, Chile

Systems Biology. Istanbul University. Reconstruction of transcriptional regulatory networks using tools from probabilities.

Methodology of Scientific Research. Istanbul University. What is Science? Why it is important? Mathematical tools to help thinking.

Final project I and II. Istanbul University. Supervision and direction of students doing their graduation project.

Introduction to Computer Science. Istanbul University. Introduction to Scientific Computing. Unix command line.

Computing in Molecular Biology I. Istanbul University. Introduction to Data Science.

Computing in Molecular Biology II. Istanbul University. Introduction to Computational Thinking. Algorithms, simulation of deterministic and stochastic systems. Concepts of statistical inference.

Bioinformatics. Istanbul University. Introduction to genomics and transcriptomics.

Computational Statistics. Universidad de Chile.

Mathematical and Bioinformatic Methods in Biological Data Analysis. Medicine Faculty, Universidad de Chile.

Statistics. Universidad de Chile.

Computational Tools for Bioinformatics. Universidad de Chile.

Internship supervision. Universidad de Chile. Supervised more than 40 engineering students, from Chile, France, Germany and Netherlands that worked as interns in the bioinformatic laboratory.

Other Undergraduate courses. Universidad de Chile. Statistics, Applied Statistics, Computational Tools for Bioinformatics.

Undergraduate courses. Universidad Arturo Prat, Chile. Numerical calculus, Data structures, Analysis of Algorithms, Operating systems theory, Video over IP workshop.

Outreach talks. Universidad de Chile. “Mathematics of Genome”. Targeted to high school students in four cities across the country.

Vicente Acuña, Andres Aravena, Carito Guziolowski, Damien Eveillard, Anne Siegel, Alejandro Maass, “Deciphering transcriptional regulations coordinating the response to environmental changes”. 2016 10.1186/s12859-016-0885-0

Carolina Alvarez, Andrés Aravena, Teresa Tapia, Ester Rozenblum, Luisa Solís, Alejandro Corvalán, Mauricio Camus, Manuel Alvarez, David Munroe, Alejandro Maass, Pilar Carvallo, “Different array CGH profiles within hereditary breast cancer tumors associated to BRCA1 expression and overall survival”. 2016 10.1186/s12885-016-2261-x

Ninoska Cordero, Felipe Maza, Helen Navea-Perez, Andres Aravena, Bárbara Marquez-Fontt, Paola Navarrete, Guillermo Figueroa, Mauricio González, Mauricio Latorre, Angélica Reyes-Jara, “Different transcriptional responses from slow and fast growth rate strains of listeria monocytogenes adapted to low temperature”. 2016 10.3389/fmicb.2016.00229

Vicente Acuña, Andres Aravena, Alejandro Maass, Anne Siegel, “Modeling parsimonious putative regulatory networks: Complexity and heuristic approach”. Springer. 2014 10.1007/978-3-642-54013-4_18

Claudia Muñoz, Alex Di Genova, Alejandro Maass, Ariel Orellana, Patricio Hinrichsen, Andres Aravena, “Vitis vinifera genome annotation improvement using next-generation sequencing technologies and NCBI public data”. 2014

Alex Di Génova, Andres Aravena, Luis Zapata, Mauricio González, Alejandro Maass, Patricia Iturra, “SalmonDB: A bioinformatics resource for salmo salar and oncorhynchus mykiss”. 2011

Christian Hödar, Rodrigo Assar, Marcela Colombres, Andres Aravena, Leonardo Pavez, Mauricio González, Servet Martínez, Nibaldo C. Inestrosa, Alejandro Maass, “Genome-wide identification of new wnt/beta-catenin target genes in the human genome using CART method.”. 2010 10.1186/1471-2164-11-348

Macarena S Arrázola, Lorena Varela-Nallar, Marcela Colombres, Enrique M Toledo, Fernando Cruzat, Leonardo Pavez, Rodrigo Assar, Andres Aravena, Mauricio González, Martín Montecino, Alejandro Maass, Servet Martínez, Nibaldo C Inestrosa, “Calcium/calmodulin-dependent protein kinase type IV is a target gene of the wnt/beta-catenin signaling pathway.”. 2009 10.1002/jcp.21902

Alicia Colombo, Marina Mione, Iskra Signore, Felipe Olivares, Ramón Pérez, Mauricio Gonzalez, Andres Aravena, Stephen Wilson, Miguel Concha, “11-p008 identification of genes with asymmetric expression in the zebrafish brain”. 2009 10.1016/j.mod.2009.06.445

Nicole Ehrenfeld, Andres Aravena, Angelica Reyes-Jara, Marlene Barreto, Rodrigo Assar, Alejandro Maass, Pilar Parada, “Design and use of oligonucleotide microarrays for identification of biomining microorganisms”. 2009

Haluk Çelik, Andres Aravena, Neslihan Turgut Kara, “Bioinformatics and gene expression analysis of the legume f-box/WD40 proteins in NaCl and high temperature stress”. 2023 10.1007/s10722-023-01592-x

Emrah Kırdök, Natalija Kashuba, Hege Damlien, Mikael A. Manninen, Bengt Nordqvist, Anna Kjellström, Mattias Jakobsson, A. Michael Lindberg, Jan Storå, Per Persson, Björn Andersson, Andrés Aravena, Anders Götherström, “Metagenomic analysis of mesolithic chewed pitch reveals poor oral health among stone age individuals”. 2024 10.1038/s41598-023-48762-6

Mauricio Latorre, Nicole Ehrenfeld, María Paz Cortés, Dante Travisany, Marko Budinich, Andrés Aravena, Mauricio González, Roberto A. Bobadilla-Fazzini, Pilar Parada, Alejandro Maass, “Global transcriptional responses of acidithiobacillus ferrooxidans wenelen under different sulfide minerals”. 2016 10.1016/j.biortech.2015.09.110

Cüneyt Uçarlı, Liam J. McGuffin, Süleyman Çaputlu, Andres Aravena, Filiz Gürel, “Genetic diversity at the dhn3 locus in turkish hordeum spontaneum populations with comparative structural analyses”. 2016 10.1038/srep20966

• 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

• 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

• 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

• Chile: CL201202773, presented Oct 3, 2012

• 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

• 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

Machine learning analysis on transcriptomic data reveals novel target genes of the WNT/β-catenin pathway in colorectal cancer Cemre Kefeli, Andrés Aravena, Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM 2022). Rennes France, July 2022

Machine learning analysis on transcriptomic data reveals novel target genes of the WNT/β-catenin pathway in colorectal cancer Cemre Kefeli, Andrés Aravena, 8th International Congress of the Molecular Biology Association of Turkey (MolBiyoKon’22). Istanbul Turkey, June 2022

Novel targets of the WNT/β-catenin pathway discovered using gene expression data mining Cemre Kefeli, Andrés Aravena, 5th International Symposium on Bioinformatics (InSyB2021). Istanbul Turkey, December 2021

Predicting oral health using machine learning Emrah Kırdök, Andrés Aravena, 14th International Symposium on Health Informatics and Bioinformatics (HIBIT). Ankara Turkey, September 2021

Identification of autophagy-related miRNA–mRNA regulatory network in calorie-restricted mouse brain Atakan Ayden, Elif Yılmaz, Bilge G. Tuna, Ayşegul Kuskucu, Ömer F. Bayrak, Andrés Aravena and Soner Doǧan, 14th International Symposium on Health Informatics and Bioinformatics (HIBIT). Ankara Turkey, September 2021

Evolutionary perspective to untangle DNA sequence organization of a multi-drug resistant plasmid Faruk Üstünel, Terje Steinum, Andrés Aravena, 12th International Symposium on Health Informatics and Bioinformatics (HIBIT). Izmir Turkey, October 2019

Using metagenomics and machine-learning to understand the oral health Emrah Kırdök, Andrés Aravena, 12th International Symposium on Health Informatics and Bioinformatics (HIBIT). Izmir Turkey, October 2019

Authentication of ancient DNA sequences when there is no reference genome Emrah Kırdök, Andrés Aravena, Macha Nikolski, 5th Ecology and Evolutionary Biology Symposium. Izmir Turkey, July 2018

Assigning taxonomy without a reference sequence Emrah Kırdök, Andrés Aravena, 4th Ecology and Evolutionary Biology Symposium. Istanbul Turkey, July 2017

Assessment of taxonomic binning methods on ancient DNA metagenomic samples Emrah Kırdök, A. Aravena, 3rd Ecology and Evolutionary Biology Symposium. Ankara Turkey, August 2016

Mathematics, probabilities and statistics in ecology and evolution. Andrés Aravena, Computational Ecology and Evolution Workshop. Nesin Foundation Mathematics Village of Şirince Turkey, September 2016

Assessment of taxonomic binning methods on ancient DNA metagenomic samples Emrah Kırdök, Andrés Aravena, International Conference on Systems Biology. Barcelona Spain, September 2016

Modeling parsimonious putative regulatory networks: Complexity and heuristic approach. V. Acuña, A. Aravena, A. Maass, A. Siegel, Verification, Model Checking, and Abstract Interpretation. San Diego, California USA, January 2014

A logics-based integrative approach to decipher putative regulatory relationships inferred from genomic and transcriptomic data. A. Aravena, D. Eveillard, A. Maass, A. Siegel, STATSEQ meeting on Gene Network Inference with Systems genetic data and beyond. Paris France, March 2013

BRCA1 expression and genomic aberrations in triple negative breast tumors. T. Tapia, A. Aravena, C. Alvarez, V. Cornejo, W. Fernandez, M. Camus, A. Maass, P. Carvallo, American Association for Cancer Research (AACR), Annual Meeting 2013. Washington DC USA, April 2013

Using Mutual Information and Answer Set Programming to refine PWM based transcription regulation network. A. Aravena, C. Guziolowski, A. Siegel, A. Maass, Actes 13th Journées Ouvertes de Biologie, Informatique et Mathématiques (JOBIM) 2012. Rennes France, June 2012

Array CGH genomic profile of hereditary breast cancer tumors. Identification of suppressor genes in deleted regions, determination of promoter hypermethylation and their protein expression in tumor biopsies. C. Alvarez, T. Tapia, V. Cornejo, A. Aravena, W. Fernandez, M. Alvarez, M. Camus, A. Maass, P. Carvallo, Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research. Chicago, IL USA, April 2012

ProbeMaker: a Tool for Simple Description and Parallelization of Bioinformatics Pipelines. A. Aravena, A. Maass, , The 12th International Conference on Systems Biology. Heidelberg/Mannheim Germany, August 2011

Identification of genes with asymmetric expression in the zebrafish brain. A. Colombo, M. Mione, I. Signore, F. Olivares, R. Pérez, M. Gonzalez, A. Aravena, S. Wilson, M. Concha, Mechanisms of Development 126 (2009): S186. 11-P008. , 2009

Bioinformatics in Biomining. N. Loira, A. Aravena, Gelato ICE: Itanium Conference & Expo. San Jose, CA USA, April 2006

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.