Now showing items 1-20 of 80

    • Draft genome of Chilean honeybee (Apis mellifera) gut strain Lactobacillus kunkeei MP2 

      Olmos, Alejandro [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile]; Henríquez-Piskulich, Patricia [Ceapi Mayor, Universidad Mayor, Chile]; Sanchez, Carolina [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile]; Rojas-Herrera, Marcelo [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile]; Moreno-Pino, Mario [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile]; Gómez, Marcela [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile]; Rodríguez Da Silva, Rafael [CEAPI Mayor, Universidad Mayor, Chile]; Maracaja-Coutinho, Vinicius [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile]; Aldea, Patricia [CEAPI Mayor, Universidad Mayor, Chile]; Trombert, Annette N. [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile] (American Society for Microbiology, 2014)
      Here, we report the first draft genome sequence of Lactobacillus kunkeei strain MP2, isolated from a Chilean honeybee gut. The sequenced genome has a total size of 1.58 Mb distributed into 44 contigs and 1,356 protein-coding ...
    • Deep Sequencing Reveals the Complete Genome and Evidence for Transcriptional Activity of the First Virus-Like Sequences Identified in Aristotelia chilensis (Maqui Berry) 

      Rojas-Herrera, Marcelo [Chile. Universidad Mayor. Centro de Genómica y Bioinformática]; Sanchez, Carolina [Chile. Universidad Mayor. Centro de Genómica y Bioinformática]; Undurraga, Soledad F. [Chile. Universidad Mayor. Centro de Genómica y Bioinformática]; Manque, Patricio [Chile. Universidad Mayor. Centro de Genómica y Bioinformática]; Maracaja-Coutinho, Vinicius [Chile. Universidad Mayor. Centro de Genómica y Bioinformática]; Polanco, Víctor [Chile. Universidad Mayor. Centro de Genómica y Bioinformática] (CIENCIAS, 2015)
      Here, we report the genome sequence and evidence for transcriptional activity of a virus-like element in the native Chilean berry tree Aristotelia chilensis. We propose to name the endogenous sequence as Aristotelia chilensis ...
    • High-Quality Draft Genome Sequence of Bacillus amyloliquefaciens Strain 629, an Endophyte from Theobroma cacao 

      SantAnna, Brena M. M.; Marbach, Phellippe P. A.; De Souza, Jorge T.; Rojas-Herrera, Marcelo [Univ Mayor, Ctr Genom & Bioinformat, Chile]; Roque, Milton R. A.; Queiroz, Artur T. L. (Chile. Universidad Mayor, 2015)
      Bacillus amyloliquefaciens strain 629 is an endophyte isolated from Theobroma cacao L. Here, we report the draft genome sequence (3.9 Mb) of B. amyloliquefaciens strain 629 containing 16 contigs (3,903,367 bp), 3,912 coding ...
    • High quality RNA extraction from Maqui berry for its application in next-generation sequencing 

      Villacreses, Javier [Chile. Universidad Mayor. Centro de Genómica y Bioinformática]; Blanc, Noelle [Chile. Universidad Mayor. Centro de Genómica y Bioinformática]; Espinoza, Loreto [Chile. Universidad Mayor. Centro de Genómica y Bioinformática]; Martínez, Camila [Chile. Universidad Mayor. Centro de Genómica y Bioinformática]; Pastor, Gabriela [Chile. Universidad Mayor. Centro de Genómica y Bioinformática]; Manque, Patricio [Chile. Universidad Mayor. Centro de Genómica y Bioinformática]; Undurraga, Soledad F. [Chile. Universidad Mayor. Centro de Genómica y Bioinformática]; Polanco, Víctor [Chile. Universidad Mayor. Centro de Genómica y Bioinformática]; Sánchez, Carolina [Chile. Universidad Mayor. Centro de Genómica y Bioinformática] (CIENCIAS, 2016)
      Maqui berry (Aristotelia chilensis) is a native Chilean species that produces berries that are exceptionally rich in anthocyanins and natural antioxidants. These natural compounds provide an array of health benefits for ...
    • Bioinformatic analyses of unique (orphan) core genes of the genus Acidithiobacillus: Functional inferences and use as molecular probes for genomic and metagenomic/transcriptomic interrogation 

      González, Carolina [Chile. Universidad Andres Bello. Facultad de Ciencias Biológicas]; Lazcano, Marcelo [Chile. Universidad Andres Bello. Facultad de Ciencias Biológicas]; Valdés, Jorge [Chile. Universidad Mayor. Centro de Genómica y Bioinformática]; Holmes, David S. [Chile. Universidad Andres Bello. Facultad de Ciencias Biológicas] (Facultad de Ciencias, 2016)
      Using phylogenomic and gene compositional analyses, five highly conserved gene families have been detected in the core genome of the phylogenetically coherent genus Acidithiobacillus of the class Acidithiobacillia. These ...
    • Chloropicophyceae, a new class of picophytoplanktonic prasinophytes 

      Lopes dos Santos, Adriana [Univ Mayor, Fac Ciencias, Ctr Genom & Bioinformat, Chile]; Pollina, Thibaut; Gourvil, Priscillia; Corre, Erwan; Marie, Dominique; Luis Garrido, José; Rodríguez, Francisco; Noel, Mary-Helene; Vaulot, Daniel; Eikrem, Wenche (Chile. Universidad Mayor, 2016)
      Prasinophytes are a paraphyletic group of nine lineages of green microalgae that are currently classified either at the class or order level or as clades without formal taxonomic description. Prasinophyte clade VII comprises ...
    • Draft Genome Sequences of Five Enterococcus Species Isolated from the Gut of Patients with Suspected Clostridium Difficile Infection. Genome Announcement 

      Castro-Nallar, Eduardo [Chile. Universidad Andrés Bello. Facultad de Ciencias Biológicas. Centro de Bioinformática y Biología Integrativa]; Valenzuela, Sandro L. [Chile. Universidad Andrés Bello. Facultad de Ciencias Biológicas. Centro de Bioinformática y Biología Integrativa]; Baquedano, Sebastián [Chile. Universidad Mayor. Facultad de Ciencias. Escuela de Tecnología Médica]; Sánchez, Carolina [Chile. Universidad Mayor. Centro de Genómica y Bioinformática]; Fernández, Fabiola [Chile. Universidad Mayor. Centro de Genómica y Bioinformática]; Trombert, Annette Nicole [Chile. Universidad Mayor. Centro de Genómica y Bioinformática] (Facultad de Ciencias, 2017)
      We present draft genome sequences of five Enterococcus species from patients suspected of Clostridium difficile infection. Genome completeness was confirmed by presence of bacterial orthologs (97%). Gene searches using ...
    • Gadolinium Chloride Rescues Niemann-Pick Type C Liver Damage 

      Cortez, Cristián [Univ Mayor, Fac Sci, Ctr Genom & Bioinformat, Santiago 8580745, Chile]; Klein, Andrés D.; Esteban Oyarzún, Juan; Zanlungo, Silvana (MDPI, 2018)
      Niemann-Pick type C (NPC) disease is a rare neurovisceral cholesterol storage disorder that arises from loss of function mutations in the NPC1 or NPC2 genes. Soon after birth, some patients present with an aggressive ...
    • Improved ontology for eukaryotic single-exon coding sequences in biological databases 

      Holmes, David S. [Univ Mayor, Fac Ciencias, Ctr Genom & Bioinformat, Santiago, Chile]; Jorquera, Roddy; González, Carolina; Clausen, Philip; Petersen, Bent (OXFORD UNIV PRESS, 2018)
      Efficient extraction of knowledge from biological data requires the development of structured vocabularies to unambiguously define biological terms. This paper proposes descriptions and definitions to disambiguate the term ...
    • MicroRNA Profiling and Bioinformatics Target Analysis in Dorsal Hippocampus of Chronically Stressed Rats: Relevance to Depression Pathophysiology 

      Vidal, Elena A. [Univ Mayor, Fac Ciencias, Ctr Genom & Bioinformat, Santiago, Chile]; Muñoz-Llanos, Mauricio; García-Pérez, María A.; Xu, Xiaojiang; Tejos-Bravo, Macarena; Moyano, Tomás C.; Gutiérrez, Rodrigo A.; Aguayo, Felipe I.; Pacheco, Anibal; García-Rojo, Gonzalo; Aliaga, Esteban; Rojas, Paulina S.; Cidlowski, John A.; Fiedler, Jenny L. (FRONTIERS MEDIA SA, 2018)
      Studies conducted in rodents subjected to chronic stress and some observations in humans after psychosocial stress, have allowed to establish a link between stress and the susceptibility to many complex diseases, including ...
    • Effect of yeast (Xanthophyllomyces dendrorhous) and plant (Saint John's wort, lemon balm, and rosemary) extract based functional diets on antioxidant and immune status of Atlantic salmon (Salmo salar) subjected to crowding stress 

      Reyes-Cerpa, Sebastián [Univ Mayor, Fac Ciencias, Ctr Genom & Bioinformat, Santiago, Chile]; Pérez-Stuardo, Diego [Univ Mayor, Fac Ciencias, Ctr Genom & Bioinformat, Santiago, Chile]; Vallejos-Vidal, Eva; González-Brown, María José; Morales-Reyes, Jonathan; Vargas, Deborah; Imarai, Mónica; Cifuentes, Víctor; Spencer, Eugenio; Sandino, Ana María; Reyes-López, Felipe E. (ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD, 2018)
      Salmon farming may face stress due to the intensive culture conditions with negative impacts on overall performance. In this aspect, functional feed improves not only the basic nutritional requirements but also the health ...
    • Transcriptional profiling of embryos lacking the lipoprotein receptor SR-B1 reveals a regulatory circuit governing a neurodevelopmental or metabolic decision during neural tube closure 

      Murgas, Leandro [Univ Mayor, Network Biol Lab, Ctr Genom & Bioinformat, Fac Sci, Santiago, Chile]; Contreras, Sebastián [Univ Mayor, Network Biol Lab, Ctr Genom & Bioinformat, Fac Sci, Santiago, Chile]; Martin, Alberto J. M. [Univ Mayor, Network Biol Lab, Ctr Genom & Bioinformat, Fac Sci, Santiago, Chile]; Santander, Nicolás; Lizama, Carlos; Molina, Paz; Quiroz, Alonso; Rivera, Katherine; Salas-Pérez, Francisca; Godoy, Alejandro; Rigotti, Attilio; Busso, Dolores (BMC, 2018)
      Background: The high-density lipoprotein receptor SR-B1 mediates cellular uptake of several lipid species, including cholesterol and vitamin E. During early mouse development, SR-B1 is located in the maternal-fetal interface, ...
    • RIP-MD: a tool to study residue interaction networks in protein molecular dynamics 

      Contreras-Riquelme, Sebastián [Univ Mayor, Fac Ciencias, Ctr Genom & Bioinformat, Network Biol Lab, Santiago, Chile]; Martín, Alberto J. M. [Univ Mayor, Fac Ciencias, Ctr Genom & Bioinformat, Network Biol Lab, Santiago, Chile]; Garate, José-Antonio; Pérez-Acle, Tomás (PEERJ INC, 2018)
      Protein structure is not static; residues undergo conformational rearrangements and, in doing so, create, stabilize or break non-covalent interactions. Molecular dynamics (MD) is a technique used to simulate these movements ...
    • SMZ/SNZ and gibberellin signaling are required for nitrate-elicited delay of flowering time in Arabidopsis thaliana 

      Vidal, Elena A. [Univ Mayor, Fac Ciencias, Ctr Genom & Bioinformat, Santiago, Chile]; Gras, Diana E.; Undurraga, Soledad F.; Riveras, Eleodoro; Moreno, Sebastián; Domínguez-Figueroa, José; Alabadi, David; Blazquez, Miguel A.; Medina, Joaquín; Gutiérrez, Rodrigo A. (OXFORD UNIV PRESS, 2018)
      The reproductive success of plants largely depends on the correct programming of developmental phase transitions, particularly the shift from vegetative to reproductive growth. The timing of this transition is finely ...
    • Rule-Based Models and Applications in Biology 

      Bustos, Álvaro; Fuenzalida, Ignacio; Santibáñez, Rodrigo; Pérez-Acle, Tomás; Martin, Alberto J M [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile] (Humana Press, 2018-11-13)
      Complex systems are governed by dynamic processes whose underlying causal rules are difficult to unravel. However, chemical reactions, molecular interactions, and many other complex systems can be usually represented as ...
    • Pleione: A tool for statistical and multi-objective calibration of Rule-based models 

      Martin, Alberto J. M. [Univ Mayor, Fac Ciencias, Network Biol Lab, Ctr Genom & Bioinformat]; Santibáñez, Rodrigo [Univ Mayor, Fac Ciencias, Network Biol Lab, Ctr Genom & Bioinformat]; Garrido, Daniel (NATURE PUBLISHING GROUP, 2019)
      Mathematical models based on Ordinary Differential Equations (ODEs) are frequently used to describe and simulate biological systems. Nevertheless, such models are often difficult to understand. Unlike ODE models, Rule-Based ...
    • Identification of Modules With Similar Gene Regulation and Metabolic Functions Based on Co-expression Data 

      Pérez-Rueda, Ernesto [Univ Mayor, Fac Ciencias, Ctr Genom & Bioinformat, Santiago, Chile]; Galán-Vásquez, Edgardo (FRONTIERS MEDIA SA, 2019)
      Biological systems respond to environmental perturbations and to a large diversity of compounds through gene interactions, and these genetic factors comprise complex networks. In particular, a wide variety of gene co-expression ...
    • Whole Genome Sequence, Variant Discovery and Annotation in Mapuche-Huilliche Native South Americans 

      Vizoso, Paula [Univ Mayor, Fac Ciencias, Ctr Propagac Conservac Vegetal CEPROVEG, Santiago, Chile]; Vidal, Elena A. [Univ Mayor, Fac Ciencias, Ctr Geneim Bioinformat, Santiago, Chile]; Moyano, Tomás C.; Bustos, Bernabe, I; Pérez-Palma, Eduardo; Moraga, Carol; Riveras, Eleodoro; Montecinos, Alejandro; Azocar, Lorena; Soto, Daniela C.; Vidal, Mabel; Di Genoval, Alex; Puschel, Klaus; Nurnberg, Peter; Buch, Stephan; Hampe, Jochen; Allende, Miguel L.; Cambiazo, Veronica; González, Mauricio; Hodar, Christian; Montecino, Martin; Muñoz-Espinoza, Claudia; Orellana, Ariel; Reyes-Jara, Angelica; Travisanyl, Dante; Moraga, Mauricio; Eyheramendy, Susana; Maass, Alejandro; De Ferrari, Giancarlo, V; Mique, Juan Francisco; Gutiérrez, Rodrigo A. (NATURE PUBLISHING GROUP, 2019)
      Whole human genome sequencing initiatives help us understand population history and the basis of genetic diseases. Current data mostly focuses on Old World populations, and the information of the genomic structure of Native ...
    • Intermediate-Salinity Systems at High Altitudes in the Peruvian Andes Unveil a High Diversity and Abundance of Bacteria and Viruses 

      Pérez-Rueda, Ernesto [Univ Mayor, Fac Ciencias, Ctr Genom & Bioinformat]; Gildardo Castelan-Sánchez, Hugo; Elorrieta, Paola; Romoacca, Pedro; Linan-Torres, Arturo; Luis Sierra, Jose; Vera, Ingrid; Alberto Batista-Garcia, Ramon; Tenorio-Salgado, Silvia; Lizama-Uc, Gabriel; Antonieta Quispe-Ricalde, Maria; Davila-Ramos, Sonia (MDPI, 2019)
      Intermediate-salinity environments are distributed around the world. Here, we present a snapshot characterization of two Peruvian thalassohaline environments at high altitude, Maras and Acos, which provide an excellent ...
    • Tracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomes 

      Pérez-Rueda, E. [Univ Mayor, Fac Ciencias, Ctr Genom & Bioinformat, Santiago, Chile]; Santos-Zavaleta, A.; Sánchez-Pérez, M.; Velazquez-Ramírez, D. A.; Collado-Vides, J. (BMC, 2019)
      Background: Crl, identified for curli production, is a small transcription factor that stimulates the association of the sigma(S) factor (RpoS) with the RNA polymerase core through direct and specific interactions, increasing ...


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