Genomics Bioinformatics Service

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Contact Information 935868945 sgb.bioinformatica@uab.cat | sgb.genomica@uab.cat | sgb@uab.cat http://sct.uab.cat/genomica-bioinformatica/en/content/presentation

Presentation

Introduction

The Genomics Bioinformatics Service Servei de Genòmica Bioinformàtica is a research support service for all members of the UAB, both from the campus and from the “esfera”, and also for other public and private institutions.
It was created by fusioning the expertise and the equipment from two services highly interconnected, genomics and bioinformatics, in order to promote them and improve in research and innovation.
The SGB has participated in a large variety of basic and applied research projects, both by performing experiments and assessing the experiment design and the analysis of results.

The fields of work of SGB are:

Biotechnology
Bioinformatics
Computational Genomics
Biomedicine
Nanotechnology
Metagenomics
Agrigenomics
Environment

Mission

Scientific and technical support to research groups at the UAB, UAB area and external ones, to boost research, innovation and trainingin the areas of Genomics and Bioinformatics.

Vision

Being a reference core facility for the scientific community at UAB and other universities and research centres and UAB area and for biotechnology companies, clinical and pharmaceutical industries.

Values

The bet for a quality service
Respect to our clients
The commitment to personalized and close service to the researcher

Strategic lines

Offer a quality service by optimizing available resources, ensuring confidentiality,compliance-oriented requirements and performing the activites while respecting the environment

Development, training, innovation and promotion of leading DNA and Microarray technologies and bioinformatic tools and procedures applied to genomic analysis.

Promote staff involvement and SGB values through theri motivation and awareness while ensuring their competence

Members

Services & Equipment

Publications of our users with the collaboration of the Genomics Bioinformatics Service

Unitat d'Antropologia del Departament de BABVE
Santos C, Lima M, Montiel R, Angles N, Pires L, Abade A, Aluja MP. Genetic structure and origen of peopling in the Azores Islands (Portugal): The view from mtDNA. Annals of Human Genetics 67: 433-456 (2003)
Santos C, Montiel R, Angles N, Lima M, Francalacci P, Malgosa A, Abade A, Aluja MP. Determination of Human Caucasian mitochondrial DNA haplogroups by means of hierarchical approach. Human Biology 76(3): 431-453 (2004)
Santos C, Montiel R, Sierra B, Bettencourt C, Fernandez E, Alvarez L, Lima M, Abade A, Aluja MP. Understanding differences between phylogenetic and pedigree-dervided mtDNA mutation rate: a model using families from the Azores Islands (Portugal). Mol. Biol. Evol.22(6): 1490-1505 (2005)
Santos C, Sierra B, Alvarez L, Ramos A, Fernández, Nogués R, Aluja MP. Frequency and Pattern of Heteroplasmy in the Control Region of Human Mitochondrial DNA.J.Mol.Evol. (2008)
Santos C, Montiel R, Arruda A, Alvarez L, Aluja MP, Lima M. Mutation patterns of mtDNA: Empirical inferences for the coding region.BMC Evolutionary Biology, 8:167 (2008)

Departament de Biologia Cel·lular
Camprubi C, Coll MD, Villatoro S, Gabau E, Kamli A, Martinez MJ, Poyatos D, Guitart M. Imprinting center analysis in Prader-Willi and Angelman syndrome patients with typical and atypical phenotypes. E J Med Genet 50 : 11-20 (2007)
Ferrando A, Ponsà M, Marmi J, Domingo-Roura X. Eurasian Otters, Lutra lutra, have a dominant mtDNA haplotype from the Iberian peninsula to Scandinavia. Journal of Heredity 95(5) : 430-435 (2004)
Ferrando A, Lecis R, Domingo-Roura X, Ponsà M. Genetic diversity and individual identification of reintroduced otters (Lutra lutra) in north-eastern Spain by DNA genotyping of sparints. Conserv Genet,9: 119-138(2008)

Departament de Bioquímica i Biologia molecular
Vissi E, Clotet J, De Nadal E, Barcelo A, Bako E, Gergely P, Dombradi V, Ariño J. Functional analysis of the Neurospora crassa PZL-1 protein phosphatase by expression in budding and fission yeast.Yeast 18: 115-124 (2001)
Simón E, Barceló A, Ariño J. Mutagenesis analysis of the yeast Nha1 Na/H antiporter carboxy-terminal tail reveals residues required for function in cell cycle. FEBS Letters 545: 239-245 (2003)
Alberola TM, García-Martínez J, Antúnez O, Viladevall L, Barceló A, Ariño J, Pérez-Ortín JE. A new set of dna macrochips for the yeast Saccharomyces cerevisiae: features and uses. Intl. Microbiol. 7: 199-206 (2004)
Viladevall L, Serrano R, Ruiz A, Doménech G, Giraldo J, Barceló A, & Ariño J. Characterization Of The Calcium-Mediated Response To Alkaline Stress In Saccharomyces cerevisiae. Journal of Biological Chemistry 279: 43614-43624 (2004)
Muñoz I, Ruiz A, Marquina M, Barceló A, Albert, A, Ariño, J. Functional characterization of the yeast Ppz1 phosphatase inhibitory subunit Hal3. A mutagenesis study. Journal of Biological Chemistry 279: 42619-42627 (2004)
Garcia-Gomez JM, Tortajada S, Vicente J, Sáez C, Castells X, Luts J, Julià M, Juan A, Van Fuel S, Barcelo A, Ariño J, Arus C and Robles M. Genomics and metabolomics research for brain tumour diagnosis based on machine learning. Conference Information: 9th International Work-Conference on Artificial Neural Networks, Date: Jun 20-22, 2007 Donostia Source: COMPUTATIONAL AND AMBIENT INTELLIGENCE 4507: 1012-1019 (2007)
Serrano R, Martín H, Casamayor A, Ariño J. Signaling Alkaline pH sttress in the yeast Saccharomyces cerevisiae through the Wsc1 cell surface sensor and the Slt2 MAPK pathway. Journal of Biological Chemistry 281(52) : 39785-39795 (2006)
González A, Ruiz A, Serrano R, Ariño J, Casamayor A. Transcriptional profiling of the protein phosphatase 2C family in yeast provides insights into the unique functional roles of Ptc1. Journal of Biological Chemistry 281(46) : 35057-35069 (2006)
Rodríguez-Asiain A, Ruiz-Babot G, Romero W, Cubí R, Erazo T, Biondi RM, Bayascas JR, Aguilera J, Gómez N, Gil C, Claro E, Lizcano JM. Brain Specific Kinase-1 BRSK1/SAD-B associates with lipid rafts: modulation of kinase activity by lipid environment. Biochimica et Biophysica Acta 1811 (12) : 1124–1135 (2011)
Strategies for annotation and curation of translational databases: the eTUMOUR project. Julià-Sapé M, Lurgi M, Mier M, Estanyol F, Rafael X, Candiota AP, Barceló A, García A, Martínez-Bisbal MC, Ferrer-Luna R, Moreno-Torres Á, Celda B, Arús C.Database (Oxford). 2012 Nov 22;2012:bas035. doi: 10.1093/database/bas035. Print 2012. PMID: 23180768
Development of robust discriminant equations for assessing subtypes of glioblastoma biopsies. Castells X, Acebes JJ, Majós C, Boluda S, Julià-Sapé M, Candiota AP, Ariño J, Barceló A, Arús C. Br J Cancer. 2012 May 22;106(11):1816-25. doi: 10.1038/bjc.2012.174. Epub 2012 May 8. PMID: 22568967
Tatiana Erazo, Ana Moreno, Gerard Ruiz-Babot, Arantza Rodríguez-Asiain, Nicholas A. Morrice, Josep Espadamala, Jose R. Bayascas, Nestor Gómez, Jose M. Lizcano. Canonical and Kinase ctivity-Independent Mechanisms for Extracellular Signal-Regulated Kinase 5 (ERK5) Nuclear Translocation Require Dissociation of Hsp90 from the ERK5-Cdc37 Complex. Mol Cell Biol. 33(8):1671-86 (2013)
Canonical and kinase activity-independent mechanisms for extracellular signal-regulated kinase 5 (ERK5) nuclear translocation require dissociation of Hsp90 from the ERK5-Cdc37 complex. Erazo T, Moreno A, Ruiz-Babot G, Rodríguez-Asiain A, Morrice NA, Espadamala J, Bayascas JR, Gómez N, Lizcano JM. Mol Cell Biol. 2013 Apr;33(8):1671-86. doi: 10.1128/MCB.01246-12. Epub 2013 Feb 19
Ptc6 is required for proper rapamycin-induced down-regulation of the genes coding for ribosomal and rRNA processing proteins in S. cerevisiae. González A, Casado C, Ariño J, Casamayor A. PLoS One. 2013 May 21;8(5):e64470. doi: 10.1371/journal.pone.0064470. Print 2013
Robustness of equations that define molecular subtypes of glioblastoma tumors based on five transcripts measured by RT-PCR.Castells X, Acebes JJ, Majós C, Boluda S, Julià-Sapé M, Candiota AP, Ariño J, Barceló A, Arús C. OMICS. 2015 Jan;19(1):41-51. doi: 10.1089/omi.2014.0077
Depletion of yeast PDK1 orthologs triggers a stress-like transcriptional response.Pastor-Flores D Ferrer-Dalmau J, Bahí A, Boleda M, Biondi RM, Casamayor BMC Genomics. 2015 Sep 21;16:719. doi: 10.1186/s12864-015-1903-8
Protein kinase Snf1 is involved in the proper regulation of the unfolded protein response in Saccharomyces cerevisiae. Ferrer-Dalmau J, Randez-Gil F, Marquina M, Prieto JA, Casamayor A.Biochem J. 2015 May 15;468(1):33-47. doi: 10.1042/BJ20140734
A novel sigma factor reveals a unique regulon controlling cell-specific recombination in Mycoplasma genitalium. Torres-Puig S, Broto A, Querol E, Piñol J, Pich OQ.Nucleic Acids Res. 2015 May 26;43(10):4923-36. doi: 10.1093/nar/gkv422. Epub 2015 Apr 29
The New Antitumor Drug ABTL0812 Inhibits the Akt/mTORC1 Axis by Upregulating Tribbles-3 Pseudokinase.Erazo T, Lorente M, López-Plana A, Muñoz-Guardiola P, Fernández-Nogueira P, García-Martínez JA, Bragado P, Fuster G, Salazar M, Espadaler J, Hernández-Losa J, Bayascas JR, Cortal M, Vidal L, Gascón P, Gómez-Ferreria M, Alfón J, Velasco G, Domènech C, Lizcano JM.Clin Cancer Res. 2015 Dec 15
The Saccharomyces cerevisiae Ptc1 protein phosphatase attenuates G2-M cell cycle blockage caused by activation of the cell wall integrity pathway. Tatjer L, González A, Serra-Cardona A, Barceló A, Casamayor A, Ariño J. Mol Microbiol. 2016 May 12. doi: 10.1111/mmi.13416
The New Antitumor Drug ABTL0812 Inhibits the Akt/mTORC1 Axis by Upregulating Tribbles-3 Pseudokinase Tatiana Erazo1, Mar Lorente2,3, Anna Lopez-Plana4, Pau Mu~noz-Guardiola1,5, Patricia Fernandez-Nogueira4, Jose A. García-Martínez5, Paloma Bragado4,Gemma Fuster4, María Salazar2, Jordi Espadaler5, Javier Fernandez-Losa6,Jose Ramon Bayascas7, Marc Cortal5, Laura Vidal8, Pedro Gascon4,8,Mariana Gomez-Ferreria5, Jose Alfon5, Guillermo Velasco2,3, Carles Domenech5, and Jose M. Lizcano1. 2508 Clin Cancer Res; 22(10) May 15, 2016

CBATEG
Alba R, Hearing P, Bosch A, Chillon M. Differential amplification of adenovirus vectors by flanking packaging signal with attB/attP-FC31 sequences: Implications for helper-dependent adenovirus production. Virology 367(1) 51-58 (2007)

Departament de Genètica i Microbiologia
Genètica
Baida A., S.M.. Farrington, P. Galofré, R. Marcos, A. Velázquez. Thyroid cancer susceptibility and THRA1 and BAT-40 repeats polymorphisms. Cancer Epidemiology Biomarkers and Prevention, 14(3): 638-642 (2005)
Marcos R., V. Martínez, A. Hernández, A. Creus, C. Sekaran, H. Tokunaga, D. Quinteros. Metabolic profile in workers occupationally exposed to arsenic. Role of GST polymorphisms. Journal of Occupational and Environmental Medicine, 48: 334-341 (2006)
Hernández A., N. Xamena, S. Gutiérrez, A. Velázquez, A. Creus, J. Surrallés, P. Galofré, R. Marcos. Basal and induced MN frequencies in different GST and NAT2 genetic backgrounds. Mutation Research (GTEM), 606: 12-20 (2006)
Kirsch-Volders M., R. Mateuca, M. Roelants, A. Tremp, E. Zeiger, S. Bonassi, N. Holland, W.P. Chang, P. Aka, M. De Boeck, L. Godderis, V. Haufroid, H. Ishikawa, B. Laffon, R. Marcos, L. Migliore, H. Norppa, J.P. Teixeira, A. Zijno, M. Fenech. The effects of GSTM1 and GSTT1polymorphisms on micronucleus frequencies in human lymphocytes in vivo. Cancer Epidemiology and Biomarkers Prevention, 15:1038-1042 (2006)
Hernández A., N. Xamena, J. Surrallés, C. Sekaran, H. Tokunaga, D. Quinteros, A. Creus, R. Marcos. Role of the Met287Thr polymorphism in the AS3MT gene on the metabolic arsenic profile. Mutation Research (FMMM) 637: 80-92 (2008)
Paiva L., R. Marcos, A. Creus, M. Coggan, A.J. Oakley, P.G. Board. Polymorphism of glutathione transferase Omega 1 in a population exposed to a high environmental arsenic burden. Pharmacogenetics and Genomics, 18: 1-10 (2008)
Espinoza F., D. Silverman, M. Kogevinas, A. Creus, F. Fernández, M. García-Closas, A. Tardón, R. García-Closas, C. Serra, A. Carrato, N. Rothman, M. Dosemeci, N. Malats, R. Marcos. Micronuclei assessment in the urothelial cells of women using hair dyes and its modulation by genetic polymorphisms. Cancer Letters (accepted) (2008)
Hernández, A., N. Xamena, C. Sekaran, H. Tokunaga, A. Sampayo-Reyes, A. Creus, R. Marcos. High arsenic metabolic efficiency in AS3MT 287Thr allele carriers. Pharmacogenetics and Genomics (accepted) (2008)
Baida A., P. Galofré, R. Marcos, A. Velázquez. Strong association of chromosome 1p12 loci with thyroid cancer susceptibility. Cancer Epidemiology Biomakkeres and Prevention (accepted) (2008)
Martínez-Fundichely A, Casillas S, Egea R, Ràmia M, Barbadilla A, Pantano L, Puig M, Cáceres M. InvFEST, a database integratin information of polymorphic inversions in the human genome. Nucleic Acids Research, 2014 Jan; 42 (Database Issue): D1027-32
Guillén Y, Rius N, Delprat A, Williford A, Muyas F, Puig M, Casillas S, Ràmia M, Egea R, Negre B, Mir G, Camps J, Moncunill V, Ruiz-Ruano FJ, Cabrero J, de Lima LG, Dias GB Ruiz JC, Kapusta A, Garcia-Mas J, Gut M, Gut IG, Torrents D, Camacho JP, Kuhn GC, Feschotte C, Clark AG, Betrán E, Barbadilla A, Ruiz A. Genomics of ecological adaptation in cactophilic Drosophila. Genome Biol Evol. 2014 Dec 31; 7 (1): 349-66
Microbiologia
Abella M, Campoy S, Erill I, Rojo F, Barbé J. Cohabitativn of two different lexA regulons in Pseudomonas putida. Journal of Bacteriology 189(24) :8855-8862 (2007)

Universitat de Barcelona (UB)
Maes T, Barceló A, Buesa C. Cloning and Characterization of human gene family homologous to C. elegans unc-53. Genomics 80 (1): 21-30 (2002)
Carreras C, Pont S, Maffucci F, Pascual M, Barceló A, Bentivegna F, Cardona L, Alegre F, SanFelix M, Fernández G, Aguilar A. Genetic structuring of immature loggerhead sea turtles (Caretta caretta) in the Mediterranean Sea reflects water circulation patterns. Marine Biology 149:1269-1279 (2006)

Institut Català de Nanotecnologia
Morales-Narváez E, Montón H, Fomicheva A, Merkoçi A. Mejora de Señal en Microarrays de Anticuerpos Usando Puntos Cuánticos Nanocristales: Aplicación a la Revisión Potencial de Biomarcadores de Enfermedad de Alzheimer. Anal Chem [Epub antes de la impresión] (2012)
Óxido de grafeno como agente revelador de patógenos: detección con una respuesta de tipo digital. Morales-Narváez E, Hassan AR, Merkoçi A. Angew Chem Int Ed Engl. 2013 16 de diciembre; 52 (51): 13779-83. doi: 10.1002 / anie.201307740. Epub 2013 Nov 7

CRESA (Centro de Recerca En Sanitat Animal)
Identificación de micrornas en cerdos PCV2 subclínicamente infectados por secuenciación de alto rendimiento Núñez-Hernández F, Pérez LJ, Muñoz M, Vera G, Tomás A, Egea R, Córdoba S, Segalés J, Sánchez A, Núñez JI Vet Res. 2015 Mar 3, 46: 18. doi: 10.1186 / s13567-014-0141-4
La microbiota nasal de cerdo al destete puede influir en el desarrollo de la enfermedad de Glässer durante el período de cría. Correa-Fiz F, Fraile L, Aragón V. BMC Genómica. 2016 26 de mayo; 17 (1): 404. doi: 10.1186 / s12864-016-2700-8.

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