Center for Genome Regulation

A FONDAP Center of Excellence

"Exploring the Genomic Landscape of Chile"

2012 Publications

1.     Van der Deen M, Akech J, Lapointe D, Gupta S, Young D, Montecino M, Galindo M, Lian J, Stein J, Stein G, van Wijnen A. 2012. Genomic promoter occupancy of runt-related transcription factor Runx2 in osteosarcoma cells identifies genes involved in cell adhesion and motility. J Biol Chem 287(7): 4503-17.

     2.     Nilo,R., Campos-Vargas,R., Orellana,A. 2012. Assessment of Prunus persica fruit softening using a proteomics approach. Journal of Proteomics. 75: 1618-1638.

     3.     Araya M, Nuñez H, Pavez L. Arredondo, Mendez M, Olivares M, Cisternas F, Pizarro F, Sierralta W, Uauy R, González M. 2012. Administration of high doses of copper to capuchin monkeys does not cause liver damage but induces transcriptional activation of hepatic proliferative responses. J Nutrition. Epub ahead of print, doi: 10.3945/jn.111.140103.

     4.     Zhang Z, Egaña JT, Reckhenrich AK, Schenck TL, Lohmeyer JA, Schantz JT, Machens HG, Schilling AF. 2012. Cell-based resorption assays for bone graft substitutes. Acta Biomater 8: 13-19.

     5.     Danner S, Kremer M, Petschnik AE, Nagel S, Zhang Z, Hopfner U,  Reckhenrich AK, Weber C, Schenck TL, Becker T, Kruse C, Machens HG, Egaña JT. 2012. The Use of Human Sweat Gland-derived Stem Cells for Enhancing Vascularization During Dermal Regeneration,Journal of Investigative Dermatology. 132: 1707-1716.

     6.     Holzer N, Braun KF, Ehnert S, Egaña JT, Schenck TL, Buchholz A, Schyschka L, Neumaier M, Benzing S, Stöckle U, Freude T, Nussler AK. 2012. Green tea protects human osteoblasts from cigarette smoke-induced injury: possible clinical implication. Langenbecks Arch Surg 397: 467-474.

     7.     Ehnert S, Braun KF, Buchholz A, Freude T, Egaña JT, Schenck TL, Schyschka L, Neumaier M, Döbele S, Stöckle U, Nussler A. 2012. Diallyl-disulfide is the 1 effective ingredient of garlic oil that protects primary human osteoblasts from damage due to cigarette smoke. Food Chemistry. 732: 724-729.

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

     9.     Travisany D, Di Genova A, Sepúlveda A, Bobadilla-Fazzini RA, Parada P, Maass A. 2012. Draft Genome Sequence of the Sulfobacillus thermosulfidooxidans Cutipay Strain, an Indigenous Bacterium Isolated from a Naturally Extreme Mining Environment in Northern Chile. J Bacteriol. 194: 6327-6328.

     10.     Acuña V, Vieira Milreu P, Cottret L, Marchetti-Spaccamela A, Stougie L, Sagot MF. 2012. Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks. Bioinformatics 28: 2474.

     11.      Acuña V, Birmeléa E,  Cottret L, Crescenzie P, Jourdan E,  Lacroix V,  Marchetti-Spaccamelag A, Marinoe A, Vieira Milreu P, Sagot MF, Stougie L. 2012. Telling stories: Enumerating maximal directed acyclic graphs with a constrained set of sources and targets. Theoretical Computer Science 457: 1/9/2015.

     12.     Loira N, Dulermo T, Nicaud JM, Sherman D. 2012. A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica. BMC Systems Biology. 6: 1-35.

     13.     Hong S, Jung U, Lee I. 2012. Decompositions of factor codes and embeddings between shift spaces with unequal entropies. Ergodic Theory and Dynamical Systems. doi:10.1017/etds.2012.131.

     14.     Moreno AA, Mukhtar MS, Blanco F, Boatwright JL, Moreno I, Jordan MR, Chen Y, Brandizzi F, Dong X, Orellana A, Pajerowska-Mukhtar KM. 2012. IRE1/bZIP60-Mediated Unfolded Protein Response Plays Distinct Roles in Plant Immunity and Abiotic Stress Responses. PloSOne 7: e31944.

     15.     Ding Z, Wang B, Moreno I, Dupláková N, Simon S, Carraro N, Reemmer J, Pěnčík A, Chen X, Tejos R, Skůpa P, Pollmann S, Mravec J, Petrášek J, Zažímalová E, Honys D, Rolčík J, Murphy A, Orellana A, Geisler M, Friml J. 2012. ER-localized auxin transporter PIN8 regulates auxin homeostasis and male gametophyte development in Arabidopsis. Nat Commun 3:914.

     16.     Handford M, Rodríguez-Furlán C, Marchant L, Segura M, Gómez D, Alvarez-Buylla E, Xiong GY, Pauly M, Orellana A. 2012. Arabidopsis thaliana AtUTr7 Encodes a Golgi-Localized UDP-Glucose/UDP-Galactose Transporter that Affects Lateral Root Emergence. Mol. Plant. 5:1263.

     17.     Chiu TY, Christiansen K, Moreno I, Lao J, Loque´ D, Orellana A, Heazlewood JL, Clark G, Roux SJ. 2012. AtAPY1 and AtAPY2 Function as Golgi-Localized Nucleoside Diphosphatases in Arabidopsis thaliana. Plant Cell Phys 53: 1913.

     18.     Ordenes VR, Moreno I, Maturana D, Norambuena L, Trewavas AJ, Orellana A. 2012. In vivo analysis of the calcium signature in the plant Golgi apparatus reveals unique dynamics. Cell Calcium 52:397.

     19.     Alvarez JM, Vidal EA, Gutiérrez RA. 2012. Integration of local and systemic signaling pathways for plant N responses. Current Opinion in Plant Biology 15:493-574.

     20.     Gutiérrez RA. 2012. Systems biology for enhanced plant nitrogen nutrition. Science 336:1763-1753.

     21.     Reckhenrich AK, Koch C, Egaña JT, Plank C. 2012. The use of non-viral gene vectors for bioactive poly-(D,L-Lactide) implant surfaces in bone tissue engineering. European Cells and Materials 23:441-448.

     22.     López G, Latorre M, Reyes-Jara A, Cambiazo V, González M. 2012. Transcriptomic response of Enterococcus faecalis to iron excess. Biometals 25:737-747.

     23.     Vázquez MC, Balboa E, Alvarez AR, Zanlungo S. 2012. Oxidative Stress: A Pathogenic Mechanism for Niemann-Pick Type C Disease. Oxid Med Cell Longev 10.1155/2012/205713.

     24.     Vázquez MC, Martínez P, Alvarez AR, González M, Zanlungo S. 2012. Increased copper levels in in vitro and in vivo models of Niemann-Pick C disease. Biometals 25:777-86.

     25.     Mera-Adasme R, Mendizábal F, Gonzalez M, Miranda-Rojas S, Olea-Azar C, Sundhol D. 2012. Computational studies of the metal-binding site of the wild-type and the H46R Mutant of the copper, zinc superoxide dismutase. Inorganic Chemistry J 51:5561-5568.

     26.     Araya M, Núñez H, Pavez L, Arredondo M, Méndez M, Olivares M, Cisternas F, Pizarro F, Sierralta W, Uauy R, González M. 2012. Administration of high doses of copper to capuchin monkeys does not cause liver damage but induces transcriptional activation of hepatic proliferative responses. 2012. J Nutrition 142:233-237.

     27.     Hinrichs MV, Torrejon M, Montecino M, Olate J. 2012. Ric-8: different cellular roles for a heterotrimeric G-protein GEF. J Cell Biochem 113:2797-2805.

     28.     Ugarte G, Opazo T, Leisewitz F, van Zundert B, Montecino M. 2012. Runx1 and C/EBP transcription factors directly up-regulate P2X3 gene transcription. J Cell Physiol 227:1645-1652.

     29.     Assar R, Leisewitz AV, Garcia A, Inestrosa NC, Montecino M, Sherman DJ. 2012. Reusing and composing models of cell fate regulation of human bone precursor cells. Biosystems 108:63-72.

     30.     Medina R, Ghule P, Cruzat F, Montecino M, Stein J, van Wijnen A, Stein G. 2012. Epigenetic control of cell cycle-dependent histone gene expression is a principal component of the abbreviated pluripotent cell cycle. Mol Cell Biol 32:3860-3871.

     31.     Villegas R, Martin SM, O’Donnell K, Carrillo S, Sagasti A, Allende ML. 2012. Dynamics of degeneration and regeneration of zebrafish peripheral axons reveals a requirement for extrinsic cell types. Neural Dev 7:19.

     32.     Quezada M, Alvarez M, Peña OA, Henríquez S, d’Alençon CA, Lange S, Oliva B, Owen GI, Allende ML. 2012. Antiangiogenic, antimigratory and antiinflammatory effects of 2-Methoxyestradiol in zebrafish larvae. Comp Biochem Physiol Part C. 157:141-149.

     33.     Milla L, Cortés C, Hodar C, Oñate M, Cambiazo V, Burgess S, Palma V. 2012. Yeast-based assay identifies novel Shh/Gli target genes in vertebrate development. BMC Genomics 13:2-9.

     34.     Rapacioli M, Botelho J, Cerda G, Duarte S, Elliot M, Palma V, Flores V. 2012. Sonic hedgehog (Shh)/Gli modulates the spatial organization of neuroepithelial cell proliferation in the developing chick optic tectum. BMC Neuroscience 3:117-125.

     35.     Milla L, González-Ramírez CN, Palma V. 2012. Sonic Hedgehog in cancer stem cells: a novel link with autophagy. Biological Research 45:223-230.

     36.     Puelma T, Gutiérrez RA, Soto A. 2012. Discriminative local subspaces in gene expression data for effective gene function prediction. Bioinformatics 17:2256-2264.