Submitted Articles & Preprints

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2023

• N. E. Jiménez, V. Acuña, M. P. Cortés, D. Eveillard, A. Maass, Unveiling abundance-dependent metabolic phenotypes of a community. mSystems 8(5) (2023) e00492-23
• S. Kobayashi, J. Maldonado, A. Gaete, I. Araya, C. Aguado, N. Cumplido, S. Díaz, A. Espinoza, E. Fernández, F. Gajardo, F. González-Ordenes, K. Hauyon, P. Maldonado, R. Maldonado, I. Pochet, A. Riveros, P. Sandoval, A. Sepúlveda-González, C. Stuardo, P. Tapia-Reyes, C. Thornton, S. Undurraga, M. Varas, C. Valdivieso, School Earwig Genome Consortium, R.A. Guti ́errez, A. Orellana, M. Montecino, A. Maass, M. González, M. Allende, C. Hodar, P. Irles, DNA sequencing in the classroom: Complete genome sequence of two earwig (Dermaptera; Insecta) species. Biological Research 56 (1) (2023) 1-18.

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2022

• Andrea Sabina Llera et al. (A. Maass as part of the US-LACRN collaborators), The Transcriptomic Portrait of Locally Advanced Breast Cancer and Its Prognostic Value in a Multi-Country Cohort of Latin American Patients. Frontiers in Oncology 12 (2022) 1-21.
• A. Di Genova, G. Nardocci, R. Maldonado-Agurto, C. Hodar, C. Valdivieso, P. Morales, F. Gajardo, R. Marina, R. Gutiérrez, A. Orellana, V. Cambiazo, M. González, A. Glavic, M. Mendez, A. Maass, M. Allende, M. Montecino, Genome sequencing and transcriptomic analysis of the Atacama Desert fish Orestias ascotanensis reveals adaptation to high-altitude aquatic life. Genomics 114 (1) (2022) 305-315.
• C. Acuña-Castillo, M. Vidal, A. Inostroza-Molina, E. Vallejos-Vidal, R. Luraschi, M. Figueroa, C. Barrera-Ávalos, R. Vera, S. Vargas, D. Valdés, K. Maisey, M. Imarai, E. Leiva-Salcedo, A. Escobar, S. Reyes-Cerpa, A. Gaete, R. Palma-Vejares, D. Travisany, LE. Rojo, FE. Reyes-López, A. Sandino, First Identification of Reinfection by a Genetically Different Variant of SARS-CoV-2 in a Homeless Person from the Metropolitan Area of Santiago, Chile. J Environ Public Health (2022) 3859071.
• J.I. Arroyo, B. Diez, C.P. Kempes, G.B. West, P.A. Marquet, A general theory for temperature dependence in biology. Proceedings of the National Academy of Sciences 119 (30) (2022) e2119872119.

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2021

• G. Eshel, V. Araus, S. Undurraga, D. Soto, C Moraga, A. Montecinos, T. Moyano, J. Maldonado, F. Díaz, K. Varala, C. W. Nelson, O. Contreras-López, H. Pal-Gabor, T. Kraiser, G. Carrasco-Puga, R. Nilo, C. M. Zegar, A. Orellana, M. Montecino, A. Maass, M. L. Allende, R. DeSalle, D. W. Stevenson, M. González, C. Latorre, G. C. Coruzzi, R. A. Gutiérrez, Plant ecological genomics at the limits for life in the Atacama Desert. Proceedings of the National Academy of Sciences 118 (46) (2021) e2101177118.
• C. Beltrán-Pavez, S. Riquelme-Barrios, A. Oyarzún-Arrau, A. Gaete-Argel, R. González-Stegmaier, K. Cereceda-Solis, A. Aguirre, D. Travisany, R. Palma-Vejáres, G. P. Barriga, A. Gaggero, C. Martínez-Valdebenito, N. Le Corre, M. Ferrés, M. E. Balcells, J. Fernández, E. Ramírez, F. Villarroel, F. Valiente-Echeverría, R. Soto-Rifo, Insights into neutralizing antibody responses in individuals exposed to SARS-CoV-2 in Chile. Sci. Adv. (7) (2021) eabe6855.
• E. Barozet, C. Valenzuela, L. Cifuentes, R.A. Verdugo, L. Herrera, M. Acuña, E. Llop, M. Moraga, S. Berríos, A. Di Genova, D. Digman, A. Symon, S. Asenjo, P. López, M.L. Bustamante, P. Pezo-Valderrama, J. Suazo, F. Caba, M. Villalón, S. Alvarado, D. Cáceres, K. Salgado, P. Portales, N. Loira, A. Maass, The Chilean Socio-ethno-genomic cline. Biodemography and Social Biology (66) (2) (2021) 156-171.
• A. Altamirano, P. A. Saa, D. Garrido, Inferring composition and function of the human gut microbiome in time and space: A review of genome-scale metabolic modelling tools. Computational and Structural Biotechnology Journal (18) (2020) 3897–3904.
• J. Tamayo-Leiva, J. Cifuentes-Anticevic, P. Aparicio-Rizzo, J. Ignacio Arroyo, I. Masotti, B. Díez, Influence of estuarine water on the microbial community structure of Patagonian fjords. Frontiers in Marine Science 8, 611981

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2020

• N. Sanchez-Pi, L. Marti, A. Abreu, O. Bernard, C. de Vargas, D. Eveillard, A. Maass, P. Marquet, J. Sainte-Marie, J. Salomon, M. Schoenauer, M. Sebag, Artificial Intelligence, Machine Learning and Modeling for Understanding the Oceans and Climate Change. NeurIPS 2020 Workshop-Tackling Climate Change with Machine Learning.
• J. Ortiz-Severín, D. Travisany, A. Maass, V. Cambiazo, F.P. Chávez, Global proteomic profiling of Piscirickettsia salmonis and salmon macrophage-like cells during intracellular infection. Microorganisms (8) (12) (2020) 1845.

• C. Muñoz-Espinoza, A. Di Genova, A. Sánchez, J. Correa, A. Espinoza, C. Meneses, A. Maass, A. Orellana, P. Hinrichsen. Identification of SNPs and INDELs associated with berry size in table grapes using a transcriptomic approach (RNA-Seq). BMC-Plant Biology (355) (2020) 365.

• R. Verdugo, A. Di Genova, L. Herrera, M. Moraga, M. Acuña, S. Berrios, M. Acuña, C. Valenzuela, L. Bustamante, D. Digman, A. Symon, S. Asenjo, P. López, A. Blanco, J. Suazo, E. Barozet, F. Caba, M. Villalón, S. Alvarado, D. Cáceres, K. Salgado, P. Portales, A. Moreno-Estrada, Ch.R. Gignoux, C.D. Bustamante, C. Eng, S. Huntsman, E.G. Burchard, N. Loira, A. Maass, L. Cifuentes. Development of a small panel of SNPs to infer ancestry in Chileans that distinguishes Aymara and Mapuche components. Biological Research (53) (25) (2020) 542.

• D. Mandakovic, A. Cintolesi, J. Maldonado, M.P. Cortés, S. Mendoza, M. Aite, A. Gaete, F. Saitua, V. Cambiazo, A. Siegel, A. Maass, M. González, M. Latorre, Comparing two genome-scale metabolic models of microbacterium species isolated from the Atacama Desert. Scientific Reports (10) (2020) 5560.

• V. Acuña, R. Grossi, G. Italiano, L. Lima, R. Rizzi, G. Sacomoto, M.-F. Sagot, B. Sinaimeri, On bubble generators in directed graphs. Algorithmica (82) (2020) 898–914.

• D. Travisany, E. Goles, M. Latorre, M.-P. Cortés, A. Maass, Generation and robustness of boolean networks to model Clostridium difficile infection. Natural Computing (19) (2020) 111-134.

• J. M. Yáñez, G. Yoshida, A. Barria, R. Palma-Véjares, D. Travisany, D. Díaz, G. Cáceres, M. I. Cádiz, M. E. López, J. P. L’horente, A. Jedlicki, J. Soto, D. Salas, A. Maass, High-throughput single nucleotide polymorphism (SNP) discovery and validation through whole-genome resequencing of hundreds of individuals in Nile tilapia (Oreochromis niloticus). Marine Biotechnology (22) (1) (2020) 109–117.

• A. Zúñiga,P. Aravena, R. E. Pulgar, D. Travisany, J. Ortiz-Severín, F. P. Chávez, A. Maass, M. González, V. Cambiazo, Transcriptomic changes of Piscirickettsia salmonis during intracellular growth in a salmon macrophage-like cell line. Frontiers in Cellular and Infection Microbiology (9) (2020) Art. 426..

• M. P. Cortés, V. Acuña, D. Travisany, A. Siegel, A. Maass, M. Latorre, Integration of biological networks for Acidithiobacillus thiooxidans describes a modular gene regulatory organization of bioleaching pathways. Frontiers in Molecular Biosciences (6) (2020) Art. 155..

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2019

• J. Ortiz-Severín, D. Travisany, A. Maass, F. P. Chávez, V. Cambiazo,
  Piscirickettsia salmonis Cryptic Plasmids: Source of Mobile DNA and Virulence Factors. Pathogens (8)(4) (2019) 269.

• P.A. Saa, M. P. Cortés, D. Bustos, J. López, A. Maass, E. Agosín, Expanding metabolic capabilities using novel pathway designs: computational tools and applications. Biotechnology Journal (14) (9) (2019) 1800734.

• G. Caceres, M. E. López, M. I. Cádiz, G. Yoshida, A. Jedlicki, R. Palma-Véjares, D. Travisany, D. Díaz-Domínguez, A. Maass, J. P. L’horente, J. Soto, D. Salas, J. M. Yáñez, Fine mapping using whole-genome sequencing confirms anti Mullerian hormone as a major gene for sex determination in farmed Nile tilapia (Oreochromis niloticus L.). G3: Genes, Genomes and Genetics (9) (10) (2019) 3213-3223.

• D. Travisany, A. Ayala-Raso, A. Di Genova, L. Monsalve, M. Bernales, J.-P. Martínez, M. González-Aguero, B. Defilippi, S. Cherian, A. Maass, L. Fuentes-Viveros, RNA-Seq analysis and transcriptome assembly of raspberry fruit (Rubus idaeus ¨Heritage¨) revealed several candidate genes involved in fruit development and ripening. Scientia Horticulturae (254) (2019) 26-34.

• L. Heirendt, S. Arreckx, T. Pfau, S.N. Mendoza, A. Richelle, A. Heinken, H. S. Har- aldsdottir, S. M. Keating, V. Vlasov, J. Wachowiak, S. Magnusdottir, C. Yu Ng, G. Preciat, A. Zagare, S. H.J. Chan, M. K. Aurich, C. M. Clancy, J. Modamio, J. T. Sauls, A. Noronha, A. Bordbar, B. Cousins, D. C. El Assal, S. Ghaderi, M. Ahookhosh, M. Ben Guebila, I. Apaolaza, A. Kostromins, H. M. Le, D. Ma, Y. Sun, L. V. Valcarcel, L. Wang, J. T. Yurkovich, P. T. Vuong, L. P. El Assal, S. Hinton, W. A. Bryant, F. J. Arag ́on Artacho, F. J. Planes, E. Stalidzans, A. Maass, S. Vempala, M. Hucka, M. A. Saunders, C. D. Maranas, N. E. Lewis, T. Sauter, B. O. Palsson, I. Thiele, R. M.T. Fleming, Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0. Nature Protocols 14 (2019) 639–702.

• E. A. Vidal, T. Moyano, B. Bustos, E. Pérez-Palma, C. Moraga, A. Montecinos, L. Azócar, D. Soto, E. Riveras, M. Vidal, A. Di Genova, K. Puschel, P. Nurnberg, S. Buch, J. Hampe, M. Allende, V. Cambiazo, M. González, C. Hodar, M. Montecino, C. Muñoz, A. Orellana, A. Reyes-Jara, D. Travisany, P. Vizoso, M. Moraga, S. Eyheramendy, A. Maass, G. V. De Ferrari, J. F. Miquel, R. A. Gutiérrez, Whole Genome Sequence of Mapuche-Huilliche Native Americans. Scientific Reports (9) (2019) 2132.

• B. Fernández-Gómez, J. Maldonado, D. Mandakovic, A. Gaete, R.A. Gutiérrez, A. Maass, V. Cambiazo, M. González, Plant genotype effect on taxonomy and function of the rhizosphere in Andean grassland soils. Scientific Reports (9) (2019) 1042.

• M.E. López, L. Benestan, J.S. Moore, C. Perrier, J. Gilbey, A. Di Genova, A. Maass, R. Neira, J.P. Lhorente, K. Correa, D. Díaz, L. Bernatchez, J.M. Yáñez, Independent and parallel genomic signatures of selection underlying domestication in two Atlantic salmon (Salmo salar L.) populations. Evolutionary Applications (12) (2019) 137-156.

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2018

• K. Meacham, M.-P. Cortés, E. Wiggins, A. Maass, M. Latorre, M. Ralle, J. Burkhead, Altered zinc balance in the Atp7b mouse model of Wilson Disease reveals a mechanism of copper toxicity in Wilson Disease. Metallomics (10) (2018) 59-69.

• S. Narum, A. Di Genova, S. Micheletti, A. Maass, Divergent life history traits and cryptic phenotypes elucidated by the Chinook salmon genome. Proc. R. Soc. B 285 (1883) (2018) 20180935.

• M. Aite, M. Chevallier, C. Frioux, C. Trottier, J. Got, M. P. Cortés, N. Loira, G. Carrier, O. Dameron, N. Guillaudeux, M. Latorre, S. Mendoza, G. V. Markov, A. Maass, A. Siegel, Traceability, reproducibility and wiki-exploration for “à-la-carte” reconstructions of genome-scale metabolic models. Plos Computational Biology 14 (5) (2018) e1006146.

• A. Di Genova, G. A. Ruz, M.-F. Sagot, A. Maass, Fast-SG: An alignment-free algo- rithm for hybrid assembly. Giga Science 7 (5) (2018) giy048.

• D. Mandakovic, C. Rojas, J. Maldonado, M. Latorre, D. Travisany, E. Delage, A. Bihouée, G. Jean, F. P. Díaz, B. Fernández-Gómez, P. Cabrera, A. Gaete, H. Pal-Gabor, C. Latorre, R. Gutiérrez, A. Maass, V. Cambiazo, S.A. Navarrete, D. Eveillard, M. González, Structure and co-occurrence patterns in microbial communities under acute environmental stress: untangling ecological factors fostering resilience. Scientific Reports 8 (1) (2018) 5875.

• W. Mardones, A. Di Genova, M.P. Cortés, D. Travisany, E. Callegari, A. Maass, J. Eyzaguirre, The genome sequence of the soft-rot fungus Penicillium purpurogenum reveals a high gene dosage for lignocellulolytic enzymes. Micology 9 (1) (2018) 59-69.

• A. Hart, M.P. Cortés, M. Latorre, S. Martínez, Codon usage bias reveals genomic adaptations to environmental conditions in an acidophilic consortium. PLoS ONE 13(5): e0195869.

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2017

• The FAASG Consortium: D.J. Macqueen, C.R. Primmer, R.D. Houston, B.F. Nowak, L. Bernatchez, S. Bergseth, W.S. Davidson, C. Gallardo-Escárate, T. Goldammer, Y. Guiguen, P. Iturra, J.W. Kijas, B.F. Koop, S. Lien, A. Maass, S.A.M. Martin, P. McGinnity, M. Montecino, K.A. Naish, K.M. Nichols, K. Olafsson, S.W. Omholt, Y. Palti, G.S. Plastow, C.E. Rexroad, M.L. Rise, R.J. Ritchie, S.R. Sandve, P.M. Schulte, A. Tello, R. Vidal, J. Olav Vik, A. Wargelius, J.M. Yáñez, Functional Analysis of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture. BMC-Genomics 18 (1) (2017) 484 .

• Thomas F, Bordron P, Eveillard D and Michel G (2017) Gene Expression Analysis of Zobellia galactanivorans during the Degradation of Algal Polysaccharides Reveals both Substrate-Specific and Shared Transcriptome-Wide Responses. Front. Microbiol. 8:1808.

• Pastenes, Luis et al. “Global Gene Expression Analysis Provides Insight into Local Adaptation to Geothermal Streams in Tadpoles of the Andean Toad Rhinella Spinulosa.” Scientific Reports 7 (2017): 1966.

• N. Loira, S. Mendoza, M.P. Cortés, D. Travisany, A. Di Genova, N. Gajardo, N. Ehrenfeld, A. Maass, Reconstruction of the microalga Nannochloropsis salina genome-scale metabolic model with applications to lipid production. BMC-Systems Biology 11 (1) (2017) 66.

• K. Correa, J. P. Lhorente, L. Bassinic, M. E. López, A. Di Genova, A. Maass, W. S. Davidson, J. M. Yáñez, Genome wide association study for resistance to Caligus rogercresseyi in Atlantic salmon (Salmo salar L.) using a 50K SNP genotyping array. Aquaculture 472 (1) (2017) 61-65.

• A. Hart, S. Martínez, An entropy-based technique for classifying bacterial chromosomes according to synonymous codon usage, J. Math. Biol. 74 (2017), no. 7, 1611–1625.

• M.P. Cortés, S. Mendoza, D. Travisany, A. Gaete, A. Siegel, V. Cambiazo, A.  Maass, Analysis of Piscirickettsia salmonis Metabolism Using Genome-Scale Reconstruction, Modeling, and Testing. Front. Microbiol. 8 (2017):2462.

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2016

• R. Andrade, M. Wannagat, C.C. Klein, V. Acuña, A. Marchetti-Spaccamela, P.V. Milreu, L. Stougie, M.-F. Sagot, Enumeration of minimal stoichiometric precursor sets in metabolic networks. Algorithmics for Molecular Biology  11 (1) (2016) 25.

• S. DebRoy, M. Saldana, D. Travisany, A. Montano, J. Galloway-Pena, N. Horstmann, H. Yao, M. González, A. Maass, M. Latorre, S. Shelburne, A Multi-Serotype Approach Clarifies the Catabolite Control protein A Regulon in the Major Human Pathogen Group A Streptococcus. Scientific Reports 6 (2016) 32442.

• H. Hefzi, KS. Ang, M. Hanscho, A. Bordbar, D. Ruckerbauer, M. Lakshmanan, CA. Orellana, DB. Hizal, Y. Huang, D. Ley, VS. Martinez, S. Kyriakopoulos, NE. Jiménez, DC. Zielinski, L. Quek, T. Wulff, J. Arnsdorf, S. Li, JS Lee, G. Paglia, N. Loira, P. N. Spahn, LE. Pedersen, JM. Gutierrez, H. Nagarajan, A. Thomas, AM. Abdel-Haleem, J. Zanghellini, HF. Kildegaard, ZP. Gerdtzen, MJ. Betenbaugh, BØ. Palsson, MR. Andersen, LK. Nielsen, N. Borth, DY Lee, NE. Lewis. A community built, genome-scale reconstruction of CHO cell metabolism recapitulates cell physiology and responses to bioprocess treatments. Cell Systems 3 (5) (2016) 434-443.

• S. Lien, B. F. Koop, S. R. Sandve, J. R. Miller, M. P. Kent, T. Nome, T. R. Hvidsten, J. Leong, D. Minkley, A. Zimin, F. Grammes, H. Grove, A. Gjuvsland, B. Walenz, R. A. Hermansen, K. von Schalburg, E. B. Rondeau, A. Di Genova, J. K. A. Samy, J. O. Vik, M. D. Vigeland, L. Caler, U. Grimholt, S. Jentoft, D. I. Vage, P. de Jong, T. Moen, M. Baranski, Y. Palti, D. R. Smith, J. A. Yorke, A. J. Nederbragt, A. Tooming-Klunderud, K. S. Jakobsen, X. Jiang, D. Fan, Y. Hu, D. A. Liberles, R. Vidal, P. Iturra, S. J.M. Jones, I. Jonassen, A. Maass, S. W. Omholt, W. S. Davidson, Atlantic salmon genome provides insights into rediploidization. Nature 533 (2016) 200-205.

• M. Latorre, M. P. Cortés, D. Travisany, A. Di Genova, M. Budinich, A. Reyes, C. Hödar, P. Parada, M. González, R. A. Robadilla-Fazzine, V. Cambiazo, A. Maass, Bioleaching potential of a bacterial consortium. Bioresource Technology 218 (2016) 659-666.

• C. Muñoz-Espinoza, A. Di Genova, J. Correa, R. Silva, A. Maass, M. González-Agüero, A. Orellana, P Hinrichsen, Transcriptomic profiling of grapevine genotypes in early stages of berry development reveals candidate markers associated to berry weight. BMC-Plant Biology 16 (1) (2016) 104.

• J.M. Yáñez, S. Naswa, M.E. López, L. Bassini, K. Correa, J. Gilbey, L. Bernatchez, A. Norris, R. Neira, J.P. Lhorente, P.S. Schnable, S. Newman, A. Mileham, N. Deeb, A. Di Genova, A. Maass, High-throughput single nucleotide polymorphism (SNP) discovery in Atlantic salmon (Salmo salar): validation in farmed and wild American and European populations. Molecular Ecology Resources 16 (2016) 1002-1011.

• P. Bordron, M. Latorre, M.P. Cortés, M. González, A. Siegel, A. Maass, D. Eveillard, Putative bacterial interactions from metagenomics knowledge with an integrative systems ecology approach. Microbiology Open 5 (1) (2016) 106–117.

• C. Álvarez, A. Aravena, T. Tapia, E. Rozenblum, L. M. Solís, A. Corvalán, M. Camus, M. Álvarez, D. Munroe, A. Maass, P. Carvallo, Different Array CGH profiles within hereditary FFPE breast cancer tumors associated to BRCA1 expression and overall survival. BMC-Cancer 16 (1) (2016) 219.

• V. Acuña, A. Aravena, C. Guziolowski, D. Eveillard, A. Siegel, A. Maass, Deciphering transcriptional regulations coordinating the response to environmental changes. BMC- Bioinformatics 17 (2016) 1–12.

• M. Latorre, N. Ehrenfeld, M. P. Cortés, D. Travisany, M. Budinich, A. Aravena, M. González, R. A Bobadilla-Fazzini, P. Parada, A. Maass, Global transcriptional responses of A. ferrooxidans Wneelen under different sulfide minerals. Bioresource Technology 200 (2016) 29-34.

• S. Martínez, A stationary distribution associated to a set of laws whose initial states are grouped into classes. An application in genomics. Journal of Applied Probability 53 (2016) 315-326.

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2015

• Damian Smedley et al., The BioMart Community Portal: an innovative alternative to large, centralized data repositories. Nucleid Acid Research 43 (1) (2015) 589–598.

• K. Correa, J. P. Lhorente, M. E. López, L. Bassini, S. Naswa, N. Deeb, A. di Genova, A. Maass, W. S. Davidson, J. M. Yáñez, Genome-wide association analysis reveals genetic architecture of the resistance to Piscirickettsia salmonis in Atlantic salmon (Salmo salar L.). BMC-Genomics 16 (2015) 854.

• R. Pulgar, D. Travisany, A. Zuñiga, M. González, A. Maass, V. Cambiazo, Complete genome sequence of the fish pathogen Piscirickettsia salmonis LF-89 (ATCC VR-1361). Journal of Biotechnology 212 (2015) 30–31.

• R. Pulgar, C. Hödar, D. Travisany, A. Zuñiga, C. Domínguez, A. Maass, M. González, V. Cambiazo, Transcriptional response of Atlantic salmon families to Piscirickettsia salmonis infection highlights the relevance of the iron-deprivation defence system. BMC Genomics 16 (2015) 495.

• M. Zhao, C. Andrieu-Soler, L. Kowalczuk, M.P. Cortés, M. Berdugo, M. Dernighogossian, J.C. Jeanny, B. Goldenberg, M. Savoldelli, M. El Sanharawi, M.C. Naud, W.F. van Ijcken, R. Pescini-Gobert, D. Martinet, A. Maass, J. Wijnholds, P. Crisanti, C. Rivolta, F. Behar-Cohen, A new CRB1 rat mutation links Müller glial cells to retinal telangiectasia. The Journal of Neuroscience 35 (2015) 6093-6106.

• W. Huanga, C. Ojaimia, J. T. Fallona, D. Travisany, A. Maass, L. Ivanova, A. Tomova, D. González-Acuña, H. P. Godfrey, F. C. Cabello, Genome Sequence of Borrelia chilensis VA1, a South American member of the Lyme Borreliosis Group. Genome announcements of the ASM 3 (2015), e01535-14.

• M. J. Arismendi, R. Almada, P. Pimentel, P. Hinrichsen, M. Pinto, A. Di Genova, D. Travisany, A. Maass, B. Sagredo, Characterization of root transcriptome dynamics in Prunus sp. rootstocks with contrasting response to hypoxia. Tree Genome and Genetics 11 (2015) 1–16.

• N. Loira, A. Zhukova, DJ. Sherman, A template-based method for genome-scale metabolic model reconstruction. Journal of Bioinformatics and Computational Biology 13 (2015) 1-19.

• R. Assar, A. Maass, J. Fernández, E. Kofman, M. A. Montecino, Modeling cell decisions in bone formation. In Analysis, Modelling, Optimization and Numerical Techniques, G. O. Tost and O. Vasilieva, Eds. Springer International Publishing, pp. 235-245 (2015).

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2014

• A. Hart, S. Martínez, Markovianness and conditional independence in annotated bacterial DNA. Stat. Appl. Genet. Mol. Biol. 13 (2014) 693-716.

• R. A. Bobadilla-Fazzini, M. P. Cortés, A. Maass, P. Parada, Sulfobacillus thermo sulfidooxidans strain Cutipay enhances chalcopyrite bioleaching under moderate thermophilic conditions in the presence of chloride ion. AMB Express 4 (2014) 84-88.

• D. Travisany, M. P. Cortés, M. Latorre. A. Di Genova, M. Budinich, R.A. Bobadilla-Fazzini, P. Parada, M. González, A. Maass, A new genome of Acidithiobacillus thiooxidans provides insights into adaptation to bioleaching environment. Research in Microbiology 165 (2014) 743-752.

• F. Abarca, P. Parada, P. Martínez, A. Maass, T. Pérez-Acle, Structure prediction and stability analysis of Licanantase: a trimeric acid-stable coiled-coil lipoprotein from Acidithiobacillus thiooxidans. PeerJ (2014) 2:e457.

• R. Assar, A. Maass, M. Montecino, DJ. Sherman, Describing acclimatization by hybrid systems and reconciliation: condition changes alter biological system behavior models. Biosystems 121 (2014) 43–53 .

• T. Downarowicz, D. Travisany, M. Montecino, A. Maass, Symbolic extensions applied to multiscale structure of genomes. Acta Biotheoretica 62 (2014) 145–169.

• A. Di Genova, A. Miyasaka, P. Vizoso, D. Travisany, C. Moraga, C. Muñoz, M. Pinto, P. Hinrichsen, A. Orellana, A. Maass, Whole genome comparison between table and wine grapes reveals a comprehensive catalog of structural variants. BMC Plant Biology 14 (2014) 7–20.

• M. Latorre, J. Galloway-Peña, J. Hyeob Roh, M. Budinich, A. Reyes-Jara, B. E. Murray, A. Maass, M. González, Enterococcus faecalis reconfigures its gene regulatory network activation under copper exposure. Metallomics 6 (2014) 572–581.

• C. Hodar, A. Zuñiga, R. Pulgar, D. Travisany, C. Chacón, M. Pino, A. Maass, V Cambiazo, Comparative gene expression analysis of Dtg, a novel target of the Dppsignaling pathway in the early Drosophila melanogaster embryo. Gene 535 (2014) 210-217.
• P.V. Milreu, C.C. Klein, L. Cottret, V. Acuña, E. Birmelé, M. Borassi, C. Junot, A. Marchetti-Spaccamela, A. Marino, L. Stougie, F. Jourdan, P. Crescenzi, V. Lacroix, M.-F. Sagot, Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure, Bioinformatics, 30 (1) (2014), 61-70.

• V. Acuña, A. Aravena, A. Maass, A. Siegel, Modeling parsimonious putative regulatory networks: complexity and heuristic approaches. 15th International Conference on Verification, Model Checking, and Abstract Interpretation (VMCAI) January 19–21, 2014, San Diego, USA. Lecture Notes in Computer Science 8318, 322–336 (2014).
• A. Zimmer, C. Durand, N. Loira, P. Durrens, DJ. Sherman, P. Marullo, QTL Dissection of lag phase in wine fermentation reveals a new translocation responsible for Saccharomyces cerevisiae adaptation to sulfite. PLoS ONE 9 (2014), 9:e86298.

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2013

• M. González-Aguero, M. García-Rojas, A. Di Genova, J. Correa, A. Maass, A. Orellana, P. Hinrichsen, Identification of two putative reference genes from grapevine suitable for gene expression analysis in berry and related tissues derived from RNA-Seq data. BMC Genomics 14 (2013) 878.

• S. Kumar Sharma, …, A. Di Genova, …, A. Maass, …, G. J. Bryan, Construction of reference chromosome-scale pseudomolecules for potato: Integrating the potato genome with genetic and physical maps. G3-Genes, Genomes and Genetics 3 (11) (2013) 20131-2047.

• P. Bordron, D. Eveillard, A. Maass, A. Siegel, S. Thiele, An ASP application in integrative biology: identification of functional genes units. 12th International Conference on Logic Programming and Nonmonotonic Reasoning – LPNMR 2013. Lecture Notes in Computer Science series 8148 (2013) 206–218.

• R. Bobadilla-Fazzini, M. P. Cortés, L. Padilla, D. Maturana, M. Budinich, A. Maass, P. Parada, Stoichiometric Modeling of Oxidation of Reduced Inorganic Sulfur Compounds (RISCs) in Acidithiobacillus thiooxidans. Biotechnology and Bioengineering 110 (8) (2013) 2242-2251.

• E. Utreras, D. Henríquez, E. Contreras-Vallejos, C. Olmos, A. Di Genova, A. Maass, A.B. Kulkarni, Ch. González-Billault, Cdk5 regulates Rap1 activity through phosphorylation of C3G. Neurochemestry International 62 (6) (2013) 848-853.

• D. Bórquez, C. Olmos, S. Álvarez, A. Di Genova, A. Maass, C. González-Billault, Bioinformatic survey for new physiological substrates of Cyclin-dependent kinase 5. Genomics 101 (4) (2013) 221-228.

• P. Martínez, S. Gálvez, N. Ohtsuka, M. Budinich, M. Paz Cortés, C. Serpell, K. Nakahigashi, A. Hirayama, M. Tomita, T. Soga, S. Martínez, A. Maass, P. Parada, Metabolomic study of Chilean biomining bacteria Acidithiobacillus ferrooxidans Wenelen and Acidithiobacillus thiooxidans Licanantay. Metabolomics 9 (1) (2013) 247-257.

• P. Collet. S. Martínez, S. Méléard, J. San Martín, Stochastic behavior for a chemostat and long-time behavior. Adv. Appl. Probab. 45 (3) (2013) 822-837.

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2012

• D. Travisany, A. Di Genova, A. Sepúlveda, R. A. Bobadilla Fazzini, P. Parada, A. Maass, Draft genome sequence of Sulfobacillus thermosulfidooxidans Cutipay strain, indigenous bacteria isolated from naturally extreme mining environment in the north of Chile. Journal of Bacteriology 194 (22) (2012) 6327-6328.

• N. Loira, T. Dulermo, JM. Nicaud, DJ. Sherman, A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica. BMC Systems Bbiology 6 (2012) 35-42.

• A. Hart, S. Martínez, F. Olmos. A Gibbs approach to Chargaff’s second parity rule. J. Stat. Phys. 148 (2012) 408-422.

• C. Hodar, P. Moreno, A. di Genova, M. Latorre, A. Reyes-Jara, A. Maass, M. González, V. Cambiazo, Genome wide identification of A. ferrooxidans (ATCC 23270) transcription factors and comparative analysis of ArsR and MerR metal regulators. Biometals 25 (2012) 75-93.

• V. Acuña, E. Birmelé, L. Cottret, P. Crescenzi, F. Jourdan, V. Lacroix, A. Marchetti-Spaccamela, A. Marino, P.V. Milreu, M.-F. Sagot, L. Stougie, Telling Stories in Metabolic Networks. Theoretical Computer Science 457 (2012) 1-9.

• V. Acuña, L. Cottret, P.V. Milreu, A. Marchetti-Spaccamela, L. Stougie, M.-F. Sagot, Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks. Bioinformatics 28 (2012) 2474-2483.

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2011

• The Potato Genome Sequencing Consortium* (A. di Genova among authors), Genome sequence and analysis of the tuber crop potato. Nature 475 (2011) 189–195.

• M. Latorre, F. Olivares, A. Reyes-Jara, G. López, M. González, cutC is induced late during copper exposure and can modify intracellular copper content in Enterococcus faecalis. Biochem Biophys Res Commun. 406 (2011) 633-637.

• J.M. Guberman et al. (A. di Genova among authors), BioMart Central Portal: An Open Database Network for the Biological Community. DATABASE journal (2011).

• A. di Genova, A. Aravena, Luis Zapata, A. Maass, M. González, P. Iturra, SalmonDB: A bioinformatics resource for Salmo salar and Oncorhynchus mykiss. DATABASE journal (2011) doi: 10.1093/database/bar050..

• A. Hart, S. Martínez. Statistical testing of Chargaff’s second parity rule in bacterial genome sequences. Stochastic Models 27 (2011) 272-317.

• T. Huillet,  S. Martínez, Discrete evolutionary genetics: multiplicative fitnesses and the mutation-fitness balance. Appl. Math. 2 (2011) 11-22.

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2010

• W. Davidson, B. Koop, S. Jones, P. Iturra, R. Vidal, A. Maass, I. Jonassen, S. Lien, S. Omholt, Sequencing the genome of the Atlantic salmon (Salmo salar). Genome Biology (2010) 11: 403.

• C. Hodar, R. Assar, M. Colombres, A. Aravena, L. Pavez, M. González, S. Martínez, N. C. Inestrosa, A. Maass, Genome-wide identification of new Wnt/β-catenin target genes in the human genome using CART method. BMC Genomics (2010) 11:348.

• J. Briche, Y. Lacroix, A. Maass, Adaptation d’un algorithme génétique pour la reconstruction de réseaux de régulation génétique: COGARE. Revue d’Intelligence Artificielle 24 (2010) 7-26.

• A. Reyes-Jara, M. Latorre, G. López, A. Bourgogne, B.E. Murray, V. Cambiazo, M. González, Genome-wide transcriptome analysis of the adaptive response of Enterococcus faecalis to copper exposure. BioMetals 23 (6) (2010)1105-1112.

• T. Del Pozo, V. Cambiazo, M. González, Gene expression profiling analysis of copper homeostasis in Arabidopsis thaliana. Biochem Biophys Res Commun. 393 (2) (2010) 248-252.

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2009

• M. Arrázola, L. Varela-Nallar, M. Colombres, R. Assar, A. Aravena, A. Maass, S. Martínez, N. C. Inestrosa, Calcium /calmodulin-dependent protein kinase type IV (CaMKIV) is a target gene of the Wnt/β-catenin signaling pathway. Journal of Cellular Physiology 221 (2009) 658-667.

• N. Ehrenfeld, A. Aravena, A. Reyes-Jara, N. Barreto, R. Assar, A. Maass, P. Parada, Design and use of oligonucleotide microarrays for identification of Biomining microorganisms. Advanced Materials Research 71-73 (2009) 155-158.

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2008

• G. Levicán, J. A. Ugalde, N. Ehrenfeld, A. Maass, P. Parada, Comparative genomic analysis of carbon and nitrogen assimilation mechanisms in three indigenous bioleaching bacteria: predictions and validations. BMC-Genomics 9 (2008) 581.

• R. Uauy, A. Maass, M. Araya, Estimating risk from copper excess in human populations. The American Journal of Clinical Nutrition 88 (2008) 867S-871S.

• M. González, A. Reyes-Jara, M. Suazo, WJ. Jo, C. Vulpe, Expression of copper-related genes in response to copper load.  The American Journal of Clinical Nutrition 88 (2008) 830S-834S.

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2007

• G. Didier, C. Guziolowski-Vargas, Mapping sequences by parts, Algorithms Mol. Biol., 2, 1, 11, 2007

• P. Moreno, A. Maass, B. Andrews, J. Asenjo, Gene regulation of metabolic pathways: a continuous model for Escherichia coli carbon sources uptake, 8th International Conference on Systems Biology 2007, Long Beach, California. (poster)

• N. Ehrenfeld, G. Levican, S. Galvez, R. Assar, I. Pacheco I., A. Aravena, A. Maass, P. Parada, Estudio genómico y transcriptómico de una cepa nativa de Acidithiobacillus ferrooxidans crecida en presencia de distintos sustratos minerales. In XXIX Congreso Chileno de Microbiología, 2007.

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2006

• E. Pécou, A. Maass, D. Remenik, J. Briche, M González, A mathematical model for copper homeostasis in Enterococcus hirae , Mathematical Biosciences 203, 2, 222-239, 2006.

• Hart, S. Martínez, L. Videla, A simple maximization model inspired by algorithms for the organization of genetic candidates in bacterial DNA, Advances in Applied Probability 38, 4, 1071-1097, 2006. Presented as invited lecture at International Workshop on Applied Probability, Connecticut, May 2006.

• V. Acuña, G. Didier, A. Maass, Coding with variable block maps, Theoretical Computer Science 369, 1-3, 396-405, 2006.

• M. González, A. Reyes, M. Suazo, T. del Pozo, C. Hodar, E. Pécou, A. Maass, Cellular metabolism of copper in pro- and eukaryotes: comparative analysis of their transcriptional regulation mechanisms, Placenta 27, 1, 29-29, 2006. (poster).

• A. Reyes, A. Leiva, V. Cambiazo, MA. Mendez, M. González, Cop-like operon: structure and organization in species of the Lactobacillale order. Biol Res. 2006. 39:87-93.

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2005

• A. Maass, E. Pécou, Sa. Martínez, Mathematical and computational methods in biology, Collection Travaux en Cours 65, Hermann Editeurs, Paris, 2005, 300 p.

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2004

• A. Moreira, A. Maass, TIP: Protein Backtranslation Aided by Genetic Algorithms, Bioinformatics 20, 13, 2148-2149, 2004.

• AD. Armendariz, M. González, L. Loguinov, CD. Vulpe. Gene expression profiling in chronic copper overload reveals up regulation of Prnp and APP. Physiol Genomics. 2004. 20:45-54.