Ergodic Theory, Dynamical Systems, Systems Biology and Bioinformatics

Direction of Ph.d. Theses
1. Pierre-Paul Romagnoli: (co-direction Francois Blanchard)
Ph.d. in Mathematics University of Chile and Aix-Marseille University, 2002. Actual job: Dean Faculty of Sciences Universidad Andrés Bello, Chile.
2. María Isabel Cortez: (co-direction Jean Marc Gambaudo)
Ph.d. in Mathematics University of Chile and University of Burgundy, 2005. Actual job: Associate Professor Pontificia Universidad Católica de Chile, Chile.
3. Camilo Jadur:
Ph.d. in Mathematics University of Chile, 2005. Actual job: Associate Professor Universidad Nacional de Salta, Argentina.
4. Jorge Yazlle:
Ph.d. in Mathematics University of Chile, 2005. Actual job: Dean Faculty of Sciences Universidad Nacional de Salta, Argentina.
5. Mathieu Sablik: (co-direction Francois Blanchard)
Ph.d. in Mathematics University of Chile and Aix-Marseille University, 2006. Actual job: Professeur Université de Toulouse III-Paul Sabatier, France.
6. José Aliste: (co-direction Jean Marc Gambaudo)
Ph.d. in Mathematics University of Chile and University of Nice, June 2009. Actual job: Associate Professor Universidad Andrés Bello, Chile.
7. Alvaro Coronel: (co-direction Jean Marc Gambaudo)
Ph.d. in Mathematics University of Chile and University of Nice, June 2009. Actual job: Associate Professor Pontificia Universidad Católica de Chile, Chile.
8. Guillermo Espinoza: (co-direction Elisabeth Pécou)
Ph.d. in Mathematics University of Chile and University of Nice, December 2010. Actual job: private sector, Chile.
9. Andrés Aravena: (co-direction Anne Siegel)
Ph.d. in Mathematics University of Chile and University Rennes I, December 2013. Actual job: Assistant Professor Istanbul University, Turkey.
10. Alexander Frank:
Ph.d. in Mathematics University of Chile, May 2014. Actual job: Fondecyt Postdoctoral position, Universidad Andrés Bello, Chile.
11. Sebastián Donoso: (co-direction Bernard Host)
Ph.d. in Mathematics University of Chile and University Paris-Est, May 2015. Actual job: Assistant Professor Universidad de Chile, Chile.
12. Karina Castillo: (co-direction Frédérique Aberlenc-Bertossi)
Ph.d. in Bioinformatics University of Montpelier I, December 2015. Actual job: private sector, France.
13. Alex Di Genova: (co-direction Gonzalo Ruz)
Ph.d. in Complex Systems University Adolfo Ibáñez, November 2017. Actual job: Postdoctoral position International Agency for Research on Cancer, Lyon, France.
14. María Paz Cortés: (co-direction Eric Goles)
Ph.d. in Complex Systems University Adolfo Ibáñez, December 2017. Actual job: Scientist BUPA, Chile.
15. Dante Travisany: (co-direction Eric Goles)
Ph.d. in Complex Systems University Adolfo Ibáñez, May 2019. Actual job: Scientist Center for Mathematical Modeling and INRIA-Chile, Chile.
16. Martín Ríos: (co-direction Eric Goles)
Ph.d. in Mathematics University of Chile, May 2021. Actual Job: Assistant Professor University Adolfo Ibá˜nez, Chile.
17. Bastián Espinoza: (co-direction Fabien Durand)
Ph.d. in Mathematics University of Chile and PhD in Mathematics University of Picardie, June 2023.
Actual Job: Postdoc University of Liège, Belgium.
18. Hugo Maturana: (co-direction Michael Schraudner)
Ph.d. in Mathematics University of Chile, December 2023. Actual Job: Adjunt Professor Universidad Cardenal Silva Henríquez.
19. Nicolás Toro: (co-direction Olivier Jaillon) Ph.d. in Mathematics University of Chile and PhD in Bioinformatics University of Paris-Saclay, expected May 2027.
20. Diego Figueroa: (co-direction Beatriz Diez) Ph.d. Biological Sciences P. Catholic University in Chile, expected December 2027.

Direction of Engineering and Master Theses
1. Pierre-Paul Romagnoli: Mathematical Engineering, U. Chile, 1997.
2. Fernando Schwartz: Mathematical Engineering, U. Chile, 1999.
3. Andrés Moreira: Mathematical Engineering, U. Chile, 1999.
4. Rodrigo Radiscz: Electrical Engineering, U. Chile, 2000.
5. María Isabel Cortez: Mathematical Engineering, U. Chile, 2002. 3
6. Vicente Acuña: Mathematical Engineering and Master Computer Science, U. Chile, 2004.
7. Rodolfo Tapia: Mathematical Engineering, U. Chile, 2004.
8. Carito Vargas: Computer Science, U. Chile, 2004 (co-direction Gilles Didier).
9. Alvaro Coronel: Mathematical Engineering, U. Chile, 2005 (co-direction Pierre-Paul Romagnoli).
10. Felipe Torres: Mathematical Engineering, U. Chile, 2005.
11. José Luis González: Mathematical Engineering, U. Chile, 2005.
12. Alonso Silva: Mathematical Engineering, U. Chile, 2006.
13. Felipe Olmos: Mathematical Engineering and Computer Science, U. Chile, 2009 (co- direction Steffen Hartel and Nancy Hitschfeld).
14. Raul Aliaga: Mathematical Engineering and Computer Science, U. Chile, 2010 (co- direction Nancy Hitschfeld).
15. Sebastián Donoso: Mathematical Engineering, U. Chile, 2011.
16. Italo Cipriano: Mathematical Engineering, U. Chile, 2011.
17. Ángel Pardo: Mathematical Engineering, U. Chile, 2012.
18. Guillermo Rodríguez: Master in Biotechnology, U. Chile, 2013.
19. Rodolfo Gutiérrez: Master in Applied Mathematics and Mathematical Engineering, U. Chile, 2015.
20. Francisco Arana: Master in Applied Mathematics and Mathematical Engineering, U. Chile, 2016 (co-direction Vincent Delecroix).
21. Juan Marshall: Master in Applied Mathematics and Mathematical Engineering, U. Chile, 2017 (co-direction Vincent Delecroix).
22. Martín Ríos: Master in Applied Mathematics and Mathematical Engineering, U. Chile, 2017.
23. Christopher Cabezas, Master in Applied Mathematics and Mathematical Engineering, U. Chile, 2018.
24. Felipe Arbulu: Master in Applied Mathematics and Mathematical Engineering, U. Chile, November 2018.
25. Bastián Espinoza: Master in Applied Mathematics and Mathematical Engineering, U. Chile, April 2020.
26. Nicolás Bitar: Master in Applied Mathematics and Mathematical Engineering, U. Chile, May 2020 (co-direction Sebastián Donoso).
27. Vicente Saavedra: Master in Applied Mathematics and Mathematical Engineering, U. Chile, July 2022 (co-direction Sebastián Donoso).
28. Tristan Radic: Master in Applied Mathematics and Mathematical Engineering, U. Chile, May 2023 (co-direction Sebastián Donoso).
29. Felipe Hernández: Master in Applied Mathematics and Mathematical Engineering, U. Chile, July 2023 (co-direction Sebastián Donoso).
30. Nicolás Toro: Master in Applied Mathematics and Mathematical Engineering, U. Chile, November 2023 (co-direction Sebasti´an Donoso).
31. Juan Pablo Sepúlveda: Master in Applied Mathematics and Mathematical Engineering, U. Chile, September 2024 (co-direction Sebastián Donoso).

Mentoring of Postdocs:
1. Song Shao. Actual job: Associate Professor, University of Science en Technology of China, China.
2. Michael Schraudner. Actual job: researcher Center for Mathematical Modeling, Chile.
3. José Aliste. Actual job: Assistant Professor Universidad Andrés Bello, Chile.
4. Nicolás Loira. Actual job: Independent Engineer, Chile.
5. Mahsa Allahbakhshi. Actual Job: Lecturer Pontificia Universidad Católica, Chile
6. Philippe Bordron. Actual job: Research Engineer, CNRS, France.
7. Pierre Guillon. Actual job: Assistant Professor Universidad de Valparaíso, Chile.
8. Soonjo Hong. Actual job: Researcher National Institute for Mathematical Sciences, Daejeon, Korea.
9. Maryam Hosseini. Actual job: Researcher Institute for Research in Fundamental Sciences, Iran.
10. Yuki Yayama. Actual job: Associate Professor Universidad Bio-Bio, Chile.
11. Congping Lin. Actual job: Associate Professor Wuhan Center for Mathematical Sciences, China.
12. Siming Tu. Actual job: Associate Professor Sun Yatsen University, China.
13. Lei Jin. Postdoc Fondecyt 2019-2021.
14. Yixiaio Qiao. Postdoc Fondecyt 2020-2021.
15. Natalia Jiménez. Postdoc Center for Genome Regulation 2019-2022.
16. Iganacio Arroyo, Postdoc Center for Mathematical Modeling 2020-2022.
17. Laura Jiménez, Postdoc Center for Mathematical Modeling 2022-2024.

Organization of International Conferences and Schools:

1. CIMPA–UNESCO Summer School on Symbolic Dynamics and Applications, Temuco, Chile, January 1997.
2. Workshop on Dynamics and Randomness, Santiago, Chile, December 2000.
3. Workshop on Dynamics and Randomness II, Santiago, Chile, December 2002.
4. CIMPA Summer School on Mathematical and Computational Methods in Biology, Valdivia, Chile, January 2004.
5. Workshop on Information and Randomness, Santiago, Chile, December 2004.
6. III Chilean Workshop on Bioinformatics, Santiago, Chile, September 2005.
7. Workshop on Information and Randomness, Santiago, Chile, December 2006.
8. School on Information and Randomness, Santiago, Chile, December 2008.
9. Mathematical Modeling in Geobiometallurgy, Santiago, Chile, October 2009.
10. School on Information and Randomness, Pucón, Chile, December 2010.
11. Bioinformatics Workshop on Metabolomics Analysis of Massive Data Sets, Santiago, Chile, September 2011.
12. AUTOMATA 2011, 17th International Workshop on Cellular Automata and Discrete Complex Systems, Santiago, Chile, November 2011.
13. Premier Congrès Franco-Chilien en Dynamique et Combinatoire, Cap Hornu, Baie de Somme, France, January 2012.
14. ICGEB-Chile Theoretical and Practical Course Advances in Bioinformatics Tools for the Analysis of High-throughput Omics Data, Santiago, Chile, July 2012.
15. School on Information and Randomness, Puerto Varas, Chile, December 2012.
16. SubTile 2013 “Pavages : systèmes dynamiques, combinatoire, théorie des nombres, décidabilité, géométrie discrète, géométrie non-commutative”, Marseille, France, Jan- uary 2013.
17. Workshop on Integrative Omics, Pucón, Chile, December 2013.
18. School on Information and Randomness, Puerto Varas, Chile, December 2014.
19. Workshop i-Plant Chile, Santiago, Chile, December 2015.
20. 3rd International Conference on Integrative Salmonid Biology, Puerto Varas, Chile, April 2016.
21. School on Information and Randomness, Santiago, Chile, December 2016.
22. Symbolic Dynamics Session, Mathematical Congress for the Americas, Montreal, Canada, July 2017.
23. Tara South America Meeting: The Tara Ocean Program: Structuring International
Scientific Cooperation with South America, Concepci´on, Chile, September 2017.
24. Workshop on Systems Biology: different views of the metabolism, Valpara´?so, Chile, November 2018.
25. Workshop Ocean and Climate Nexus: Road to COP25, Paris, France, October 2019.
26. The Eighth Pacic Rim Conference in Mathematics, Berkeley, USA, August 2020.
27. Series of Online Workshops: Expanding Dynamics-Creative Online Ventures in Dynamics, 2020-2021.
28. EMALCA Chile Online School, January 2022.
29. Workshop SymBioDiversity 2022, May 2022.
30. Pucón Meeting CMM, August 2022.
31. School Combinatorial and Geometric Approaches on Dynamics, November 2022.
32. Make Health Latam - Chile, Valpara´?so, Chile, January 2023.
33. Workshop Towards a modern analysis of omics data of the Ocean: CEODOS and Atlant-Eco expeditions, Valpara´?so, Chile, May 2023.
34. Workshop The Metabolic Club I, Santiago, Chile, January 2024.
35. Pucón Symposium 2024, Puerto Varas, September, 2024.
36. Large scale omics-sciences, mathematical modeling and remote sensing - Side event at COP16, Cali, Colombia, October 2024.
37. Dyadisc 7, Joint Workshop Brazil-France-Chile in Dynamical Systems, Valpara´?so, Chile, December 2024.
38. Workshop The Metabolic Club II, Santiago, Chile, January 2025.

Invitations to International Conferences (last 15 years)

1. Workshop on Ergodic Theory and Dynamical System, Poland, June 2006.
2. Aperiodic Order: new connections and old problems revisited, Marseille, France, Septem- ber 2007.
3. Mathematical Sciences Research Institute, Berkeley, California: 2008. Program in Ergodic Theory and Additive Combinatorics (August 30, 2008 to November 21, 2008)
4. I Discrete Mathematics Workshop, Salta, Argentina, March 2009.
5. Workshop in “Dynamical Numbers: Interplay between Dynamical Systems and Number Theory”, Bonn, Germany, June 2009.
6. Pyrenees International Workshop on Statistics, Probability and Operations Research, SPO 09, Jaca, Spain, September 2009.
7. Math-Info 2010, Towards new interactions between mathematics and computer science, Marseille, France, February 2010 (Invited Speaker FRUMAM).
8. Workshop on Dynamical Systems and Related Topics in honor of Dan Rudolph, U. Maryland, USA, April 2010.
9. Nonlinear Dynamics: New Directions, Guanajuato, Mexico, May 2010.
10. Dynamical Systems Meeting, Lower Silesia, Poland, May 2010.
11. XIV Brazilian School of Probability and Clay Mathematical Institute Summer School, Buzios, Brazil, August 2010.
12. 13th Mons Theoretical Computer Science Days, Amiens, France, September 2010.
13. Workshop on Dynamical Systems and Related Topics with a special session in honor of Mike Boyle on his 60th birthday, U. Maryland, USA, April 2011.
14. Trends in Dynamics, Chicago, USA, April 2011.
15. International Conference on Measurable and Topological Dynamics and Related Topics, Yellow-Mountains, China, June 2011.
16. XII Latin American Workshop on Nonlinear Phenomena (LAWNP-2011), San Luis Potosí, Mexico, October 2011.
17. Ergodic Theory with Connections to Arithmetic, Heraklion, Greece, June 2013
18. Mathematical Congress of the Americas, Guanajuato, Mexico, August 2013.
19. Ergodic Theory and Dynamical Systems Conference, Torun, Poland, May 2014.
20. Workshop on Functional Analysis and Dynamical Systems, Florianópolis, Brazil, Febru- ary 2015.
21. Congrès SMAI 2015, 7e Biennale Française des Mathématiques Appliquées et Industrielles, Les Karellis, Savoie, France, June 2015.
22. Combinatorics Meets Ergodic Theory, Banff International Research Station for Mathematical Innovation and Discovery, Banff, Canada, July 2015.
23. 2nd Workshop on Combinatorics, Number Theory and Dynamical Systems, IMPA, Rio de Janeiro, August 2015.
24. CIMPA School Dynamics on Cantor Sets, Salta, Argentina, November 2015.
25. Ergodic Theory and Dynamical Systems Conference (In honor of the 60th birthday of T. Downarowicz), Wroclaw, Poland, May 2016.
26. The 7th Pacific RIM Conference on Mathematics, Seoul, Korea, June 2016. 19
27. 6th Pingree Park Dynamics Workshop, Foundations and Frontiers in Symbolic Dynamics, Pingree Park, Colorado, USA, July 17-20, 2017.
28. Structures et Modèles Discrets, Rouen, France, September 27-29, 2017.
29. Oberwolfach Workshop: Spectral Structures and Topological Methods in Mathematical Quasicrystals, Oberwolfach, Germany, October 1-7, 2017.
30. Workshop: Entropies and Soficity, Lyon, France, January 15-19, 2018.
31. Ergodic aspects of modern dynamics in honour of Mariusz Lemanczyk on his 60th birthday, Bedlewo, Poland, June 10-16, 2018.
32. Workshop : Dynamiques et Analyse Discr`ete, Analyse spectrale de sous-shifts, Amiens, France, July 9-11, 2018.
33. 7th International Conference on Nonlinear Science and Complexity, San Luís Potosí, Mexico, August 14-17, 2018.
34. Chile-Japan Academic Forum, Nikko, Japan, September 25-28, 2018.
35. Thirteenth International Conference on Computability, Complexity and Randomness (CCR 2018), Santiago, Chile, December 17-21, 2018.
36. Climate and Data at Harvard Workshop, Radcliffe Institute for Advanced Study, Cambridge, USA, January 28-29, 2019.
37. Banff Workshop on Symbolic Dynamics, Oaxaca, Mexico, May 12-17, 2019.
38. EMALCA Mexico 2019, San Lu´?s Potos´?, Mexico, June 10-14, 2019.
39. Numeration, Shr¨odinger Institute, Viena, Austria, July 8-12, 2019.
40. ICIAM - International Conference on Industrial and Applied Mathematics, Valencia, España, July 15-19, 2019.
41. Groups and Graphs, Designs and Dynamics, Yichang and Shanghai, China, August 19-25, 2019.
42. Minisymposium on Discrete Dynamical Systems, Jiaotong University, Shanghai, August 26-28, 2019.
43. Nilpotent structures in topological dynamics, ergodic theory and combinatorics, Bedlewo, Poland, June 7-13, 2020. (postponed 2021)
44. DynamicsDays - XL, Nice, France, August 24-28, 2020. (postponed 2021)
45. MCA2021, Buenos Aires, July 12-23, 2021.
46. UN-Ocean Conference, side Event Understanding the Ocean Microbiome, June 28, 2022.
47. Workshop All Atlantic Marine Ecosystems: a science to policy debate, Lisbone, Portugal, October 3, 2022.
48. Workshop Seascape: theories and advances processes driving community, assembly, biodiversity and ecosystem, functioning, Sesimbra, Portugal, October 4-7, 2022.
49. Conference Nilpotent structures in topological dynamics, ergodic theory and combinatorics, Banach Center, Poland, June 4-9, 2023.
50. Conference ISME-LATAM, Universidad Nacional de Quilmes, August 7-10, 2023.
51. Workshop Aspects of Aperiodic Order, Oberwolfach Center, Germany, August 27-September 2, 2023.
52. Workshop Low Complexity Dynamical Systems, Brin Mathematics Research Center University of Maryland, October 2-6, 2023.
53. Integrating Ecological Theories From a First Principles Perspective, Santa Fe Institute of Complex Systems, October 17-19, 2023.
54. Thematic Month Discrete Mathematics & Computer Science: Groups, Dynamics, Complexity, Words, CIRM, Marseille, France, February 12-16, 2024.
55. Synergy summer school 2024 “Seascape”, Naples, Italy, June 24-29, 2024.
56. Conference NU Trends in Ergodic Theory, Northwestern University, US, August 5-9, 2024.
57. 21st IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), Natal, Brazil, August 27-29, 2024.
58. Workshop “Algométabionte”, Roscoff, France, October 3-4, 2024.
59. Workshop on Random Dynamical Systems in Biology, Chicago, US, November 4-8, 2024.

Invited Positions (longer than two weeks)

1. Institut de Mathématiques de Luminy, CNRS-France (about 15 months from 1994 to 2010).
2. University of Marne la Vallée, Paris-Est, France: 1998, 2000, 2001, 2009, 2010, 2012, 2013 (4 months,“Bézout Chair”), 2015, 2020.
3. University of Haute Picardie Jules Verne, France: 1999, 2000, 2002, 2005, 2014 (3 months, “Poste Rouge CNRS”), 2016, 2018 (3 months, “Poste Rouge CNRS”), 2021 (3 months, “Poste Rouge CNRS”), 2022, 2023.
4. U. Toulouse III, Paul Sabatier, France: 2012.
5. INRIA-Rennes, France: 2012, 2013, 2016, 2018, 2022, 2024.
6. University of Nantes, France: 2019, 2021, 2022, 2023, 2024.
7. University of Bourgogne, France: 2002, 2004.
8. University of Nice, France: 2020.
9. University of Maryland at College Park, USA: 1995, 2004, 2010.
10. Northwestern University, USA: 2011, 2012, 2014, 2015, 2023, 2024.
11. Mathematical Sciences Research Institute, Berkeley, California: 2008. Program in Ergodic Theory and Additive Combinatorics (August 30, 2008 to November 21, 2008).
12. University of Science and Technology of China: 2001, 2006, 2011, 2014, 2019.
13. Fudan University, China: 2019.
14. Jiatong University, China: 2019.
15. Max Planck Institute Bonn, Germany: 2004 and 2009 for activity “Dynamical Numbers: Interplay between Dynamical Systems and Number Theory”.
16. University Charles at Prague, Check Republic: 1997.
17. University of Sao Pablo, Brasil: 1997.
18. CIMAT, Guanajuato, Mexico: 2018, 2019, 2020. 2022.
19. Instituto de Física, Universidad Autónoma San Luis Potosí, Mexico: 1998, 2001, 2019.

Patents:

1. A. Maass, A. Aravena, M. González, S. Martínez, P. Parada, K. Ehrenfeld, Method for the design of oligonucleotides for molecular biology techniques.
*South Africa, Number: ZA 2006/06828, Date: 24/01/2008;
*USA, Number: US 7853408B2, Date: 14/12/2010;
*Australia, Number: AU 2006203551, Date: 15/09/2011;
*Mexico, Number: MX 305872, Date: 04/12/2012;
*Argentina, Number: AR 054923B1, Date: 21/10/2013.

2. R. Badilla, A. Maass, P. Parada, A. Aravena, M. González, S. Martínez, K. Ehrenfeld, P. Moreno, DNA fragments array from biomining microorganisms and method for detection of them.
 *South Africa, Number: ZA 2006/09650, Date: 23/10/2007;
 *Argentina, Number: AR 057612B1, Date: 09/09/2010;
 *Peru, Number: PE 5838, Date: 29/10/2010;
 *USA, Number: US 7915031B2, Date: 29/03/2011;
 *Australia, Number: AU 2006241345, Date: 26/09/2013;
 *Mexico, Number: MX 307357, Date: 13/02/2013.
 *Chile, Number: 55273, Date: 04/01/2018;

3. K.Ehrenfeld, J. Ugalde, A. Aravena, N. Loira, A. Maass, P. Parada, R. Badilla, Array of nucleotidic sequences for the detection and identication of genes that codify proteins with activities relevant in biotechnology present in a microbiological sample, and method for using this array.
 *South Africa, Number: ZA 2008/02344, Date: 26/11/2008;
 *Mexico, Number: MX 298861, Date: 03/05/2012;
 *Peru, Number: PE 6669, Date: 23/11/2012;
 *USA, Number: US 8207324B2, Date: 26/06/2012.
 *Australia, Number: AU 2008201183, Date: 29/08/2013;
 *Chile, Number: 49170, Date: 13/06/2013;
 *Chine, Number: CN 101275168B, Date: 05/06/2013;
 *Japan, Number: 5377870, Date: 04/10/2013;

4. P. Parada, K. Ehrenfeld, I. Pacheco, A. Maass, A. Aravena, M. González, S. Martínez,
Method for the identication and quantication of microorganisms useful in biomining processes.
 *South Africa, Number: ZA 2006/07131, Date: 30/05/2007;
 *Chile, Number: 46739, Date: 31/08/2010;
 *Australia, Number: AU 2006204629, Date: 27/09/2012;
 *Argentina, Number: AR 055140B1, Date: 26/08/2013.
 *Mexico, Number: MX 307267, Date: 08/02/2013;
 *USA, Number: US 8492093B2, Date: 23/07/2013

5. A. Maass, P. Moreno, M. Budinich, P. Parada, L. Padilla, M. Barreto, Method to increase the production of extracellular polymeric substances (EPS) in a Acidithiobacillus ferrooxidans culture by the inhibition of enzymes of tricarboxilic acid cycle.
 *South Africa, Number: ZA 2011/01564, Date: 29/02/2012;
 *Chile, Number: 50961, Date: 15/06/2015.
 *USA, Number: US 8927246B2, Date: 06/01/2015;

Startups:

1. Founder Partner of Diagnofast: a startup for the development of bio-identification kits to specifically recognise microorganisms, 2018 (www.diagnofast.cl)..

Transfer Projects:

Oceanography:
1. CNRS Research Federation “GO-SEE - Global Ocean Systems Ecology and Evolution”, 2018-2028. Main Coordinator in Chile.
2. Project INRIA -Challenge: OceanIA, 2020-2024 (coordinated by INRIA-Chile). Main Researcher, coordinator at CMM.

Aquaculture Sector:
1. Project: Sequencing and Assembly of Salmon Chinook. Funded by Columbia River Inter-Tribal Fisch Commission.
2. Project: Sequencing and Assembly of Atlantic Salmon. Funded by ICSASG-Consortium (Chile-Norway-Canada).
3. Project: Development of an integrative strategy for the genetic improvement of the resistance against Salmon Rickettsial Syndrome (Piscirickettsia salmonis) in salmonid species using molecular information. Funded by Fondef-Conicyt (Main Institutions: U. Chile-Aquainnovo), 2015-2016. Director Bioinformatics Team.
4. Project: Developmet of a biotechnological platform for exporting genetic services to improve warm water aquaculture species production in America applying genomic selection. Funded by INNOVA-Corfo (Main Institution: Aquainnovo), 2015-2016. Director Bioinformatics Team.
5. Project: Salmonid genomics: identification of genes related to protein and vegetal oil usage in Atlantic salmon and rainbow trout nutrition. Funded by INNOVA-Corfo 07CN13PBT-41 (coordinated by Medical School U. Chile), 2008-2011. Director Bioinformatics Team.

Agriculture Sector:
1. Project: Kits to detect bacterial contaminants in the wine production. Bioinformatics part. Funded by INNOVA-Corfo (coordinated by V. Cambiazo, INTA-U. Chile), 2014- 2016. Deputy Director of the project and Director Bioinformatics Team. Generated Product: Fast-Wine, today is commercialised to more than 6 wineries in Chile.
2. Project: Bioidentification system for industrial relevant microorganisms: application to avian and winery sectors. Funded by Fundación Copec-Universidad Católica, in cooperation with Viña San Pedro, July 2007 to December 2008. Director.
3. Project: Identification of genes related to berry development and growth in seedless table grapes by means of functional genomics. Funded by Fondef G07I1002 (coordinated by INIA), 2008-2012. Director Bioinformatics Team.
4. Project: Implementation of a platform for the bioinformatics analysis and storage of databases of genomics information coming from different vegetables of interest for the programs of genetic improvement at La Platina-INIA. Funded by INIA, 2010. Director.
5. Project: Implementation of a database with the potato genome and transcriptomics data of genotypes DM and RH and bioinformatics analysis. Funded by INIA, 2011. Director.

Health:
1. Project: Genomics of Chilean populations: genetic profiles necessaries in clinic research, public health and forensic medicine. Funded by Fondef D10I1007 (coordinated by Medical School U. Chile), 2012-2014. Director Bioinformatics Team.
2. Project: Academic industrial network for the development of applications of probability and information theory to biosciences. Funded by Programa Bicentenario en Ciencia y Tecnología. Cooperation with “Centro para el análisis de la función génica en el desarrollo neuronal”, Fac. Medicine, U. Chile and “Centro de Regulación Celular y Patologías Joaquín V. Luco”, Facultad de Biología, P.U. Católica de Chile, March 2008- June 2009. Director.
3. Project: Molecular profile of breast cancer at clinical stages II and III in Latinamerican women receiving a standard reference treatment. Funded by National Cancer Institute USA (coordinated by GOCCHI), 2012-2014. Director Bioinformatics Team.

Mining:
1. Project: Development of a scientific-technological capacity in mathematical modeling and simulation for the control of biological networks in productive processes: application to bacterial bioleaching. Funded by BioSigma S.A. and FONDEF D04I1257, December 2005 to August 2008. Director.
2. Project: Information biomining laboratory: organization and statistical processing of biomining data, modeling and networks. Funded by BioSigma S.A. (joint venture Codelco/Nippon Mining & Metals). January 2003 to June 2010. Director.
3. Project: Application of metabolomics to the mining industry to improve processes associated with the bioleaching of mineral resources. Funded by INNOVA-Corfo 09CN14- 585 (coordinated by Biosigma S.A.), 2010-2012. Director Bioinformatics Team.

International Cooperation Projects:

1. Project INRIA -Challenge: OceanIA, 2020-2024 (coordinated by INRIA-Chile). Main Researcher.
2. Associate Research Team INRIA "SymBioDiversity" 2020-2022. Main Researcher.
3. CNRS Research Federation \GO-SEE - Global Ocean Systems Ecology and Evolution", 2018-2028. Main Researcher.
4. Project MathAmsud "Dynamics of Cantor systems: computability, combinatorial and geometric aspects", 2017-2018. Main Researcher.
5. Project INRIA-Conicyt French Cooperation "Intégration dynamique de données grandeechelle et heterogenes en biologie moleculaire: application a l'identication de régulateurs de la bio-lixiviation du cuivre minier", 2011-2012. Main Researcher. Associate Research Team INRIA 2011-2013, 2014-2016.
6. Project PICS-CNRS French Cooperation \Dynamics and Combinatorics", U. Chile-U. Picardie Jules Verne-U. Marne la Vallée, 2009-2011. Main Researcher.
7. Project CNRS-Conicyt French Cooperation "Study of linearly recurrent tilings, combinatorial and ergodic aspects", U. Chile-U.Picardie Jules Verne-U. Marne la Vallée, 2004. Main Researcher.
8. Project ECOS-Conicyt French Cooperation "Tiling systems and standardness", U.Chile-U. Bourgogne-Institut de Math. de Luminy-U.Picardie Jules Verne-U. Marne la Vallée, 2004-2006. Main Researcher.
9. Project ECOS-Conicyt French Cooperation "Algebraic aspects and complexity of topological dynamical systems", U. Chile-Institut de Math. de Luminy-U.Picardie Jules Verne-U. Marne la Vallée, 2000-2002. Main Researcher.
10. Project CNRS-Conicyt French Cooperation "Discrete Dynamical Systems, Complexity and Automata", U. Chile-Institut de Math. de Luminy, 1997-1999. Main Researcher.