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Biología Computacional

Líneas de investigación

Contenidos con Investigacion Biología Computacional .

Biología Computacional

  • Uso de la Biología Computacional para investigación de mecanismos moleculares alterados en enfermedades crónicas (neurodegeneración y cancer) que puedan contribuir a prevenir, diagnosticar precozmente, y tratar la enfermedad de manera individualizada. 
  • Búsqueda e interpretación de vías de señalización, variantes génicas y genes biomarcadores obtenidos por técnicas de secuenciación profunda y técnicas de genotipado masivo.

Proyectos de investigación

Contenidos con Investigacion Biología Computacional .

  • 2022-2025: Modelos humanos neurales para estudiar la evolución celular y proteómica en la enfermedad de Alzheimer. PI22/00055. Proyecto de Acción Estratégica en Salud Intramural. PI I Liste, CoIP V. López-Alonso.
  • 2022-2024: CAM Ayudas para la contratación de técnico de Garantia Juvenil
  • 2022-2025: Medicina Personalizada (MedPer) en la detección precoz del deterioro cognitivo (DC) preclínico. Desarrollo de un modelo predictivo de riesgo. PMP22/00084. Proyectos de Investigación de Medicina Personalizada de Precisión de la Acción Estratégica en Salud. IP. A. Almeida Parra.
  • 2022-2025: Implicaciones de la proteína precursora amiloide (APP): neurodesarrollo y enfermedad de Alzheimer. PID2021-126715OB-I00. Programa Estatal de I+D+i Orientada a los Retos de la Sociedad. Ministerio de Ciencia e Innovación. PI I. Liste
  • From 2017-2022. Project MinE International groundbreaking genetic ALS research (www.projectmine.com).
  • 2020 – 2022: ELA-BASE: Una cohorte para un estudio piloto longitudinal de Medicina de Precisión en Esclerosis Lateral Amiotrófica (ELA). UFIECPY 354/19-TS.Actividad Singular dentro del Programa de prestación de servicios científico-técnicos en los centros del ISCIII. Programa Intramural 2019 ISCIII. PI Y. Campos.
  • 2020–2021: Spanish Ministry of Economy and Competitiveness: Ayudas para la contratación de estudiantes, Garantia Juvenil. V. López-Alonso
  • 01/04/2015 - 01/04/2021: New therapeutic strategies for resistant colorectal cancer. Fundación Científica de la Asociación Española Contra el Cáncer. CGB14142035THOM.  PI JM Rojas. 
  • 2017-2020: MicroRNAs y marcadores de metabolismo lipídico como potencial enlace entre la disfunción vascular y la patofisiología de la enfermedad de Alzheimer. SAF2016-78603-R MINECO. PI M Medina.
  • 2017-2020: Papel fisiológico de la proteína Shoc2/Sur8 y estudio de su implicación en patologías humanas. SAF2016-78852-R MINECO. PI JM Rojas.
  • 2019: Proyecto MinE: del análisis biocomputacional de genomas de pacientes con Esclerosis Lateral Amiotrófica al desarrollo de un modelo de motoneurona diferenciada a partir de células madre pluripotenciales inducidas obtenidas de cultivos de fibroblastos humanos de origen dérmico. GGVP 345/18 FUNDELA. IP Y Campos.
  • 2011-2013. IMBIOMEDvision: Promoting and Monitoring Biomedical Informatics in Europa Grant agreement no: 270107 Comisión Europea. IP V López-Alonso
  • 2011-2012. COMBIOMED. Red Temática de Investigación Cooperativa en Biomedicina Computacional RD07/0067/00 Fondo de Investigación Sanitaria. Instituto de Salud Carlos III. IP y Coordinación V. López-Alonso
     

Publicaciones destacadas

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Aβ42 Peptide Promotes Proliferation and Gliogenesis in Human Neural Stem Cells

Aβ42 Peptide Promotes Proliferation and Gliogenesis in Human Neural Stem Cells. Bernabeu-Zornoza A, Coronel R, Palmer C, Calero M, Martínez-Serrano A, Cano E, Zambrano A, Liste I. Mol Neurobiol. 2019 Jun;56(6):4023-4036. doi: 10.1007/s12035-018-1355-7. Epub 2018 Sep 27. PMID: 30259399.

PUBMED DOI

Reduced Salivary Lactoferrin Levels in Early-Onset Alzheimer's Disease

Antequera D, Carrero L, Gonzalez-Sanchez M, Cantero JL, Orive G, Municio C, Carro E. Reduced Salivary Lactoferrin Levels in Early-Onset Alzheimer's Disease. Aging Dis. 2024 May 7;15(3):945-947. doi: 10.14336/AD.2023.0819.

DOI

Immune profiling of gliomas reveals a connection with Tau function and the tumor vasculature

Cejalvo T*, Gargini R*, Segura-Collar B, Mata P, Herránz B, Cantero D, Ruano Y, García-Pérez D, Pérez-Núñez A, Ramos A, Hernández-Laín A, Cruz Martín-Soberón M, Sánchez-Gómez P# and Sepúlveda-Sánchez JM# (# Co-corresponding author) (* Co-1st author). (2020) Immune profiling of gliomas reveals a connection with Tau function and the tumor vasculature. Cancers. 12-11, pp.E3230. PMID: 33147752doi: 10.3390/cancers12113230

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European mitochondrial DNA haplogroups and metabolic disorders in HIV/HCV-coinfected patients on highly active antiretroviral therapy

European mitochondrial DNA haplogroups and metabolic disorders in HIV/HCV-coinfected patients on highly active antiretroviral therapy. Micheloud D, Berenguer J, Guzmán-Fulgencio M, Campos Y, García-Álvarez M, Catalán P, Cosín J, Miralles P, López JC, Resino S.J Acquir Immune Defic Syndr. 2011 ; 58:371-8. DOI: 10.1097/QAI.0b013e31822d2629

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European mitochondrial DNA haplogroups and liver fibrosis in HIV and hepatitis C virus coinfected patients

European mitochondrial DNA haplogroups and liver fibrosis in HIV and hepatitis C virus coinfected patients. García-Álvarez M, Guzmán-Fulgencio M, Berenguer J, Micheloud D, Campos Y, López JC, Cosín J, Miralles P, Alvarez E, Resino S. AIDS. 2011;25:1619-926. DOI: 10.1097/QAD.0b013e328349820f

DOI

Neurogenesis is increased in human neural stem cells by Aβ40 peptide

Bernabeu-Zornoza, A.; Coronel, R.; Palmer, C.; Martín, A.; López-Alonso, V.; Liste, I. (2022). Neurogenesis is increased in human neural stem cells by Aβ40 peptide. Int J Mol Sci. 23, 5820. doi: 10.3390/ijms23105820.

DOI

Toxicity of nanoplastics for zebrafish embryos, what we know and where to go next

Torres-Ruiz M*, De la Vieja A, Gonzalez MD, Lopez ME, Castaño-Calvo A, Cañas-Portilla AI. Toxicity of nanoplastics for zebrafish embryos, what we know and where to go next. Science of the Total Environment 2021 797:149125. PMID: 34346375. doi: 10.1016/j.scitotenv.2021.149125

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Colocalization Analysis of Peripheral Myelin Protein-22 and Lamin-B1 in the Schwann Cell Nuclei of Wt and TrJ Mice

Di Tomaso MV, Vázquez Alberdi L, Olsson D, Cancela S, Fernández A, Rosillo JC, Reyes Ábalos AL, Álvarez Zabaleta M, Calero M, Kun A. Colocalization Analysis of Peripheral Myelin Protein-22 and Lamin-B1 in the Schwann Cell Nuclei of Wt and TrJ Mice. Biomolecules. 2022 12(3):456. doi: 10.3390/biom12030456.

DOI

The transcription factor LEF1 interacts with NFIX and switches isoforms during adult hippocampal neural stem cell quiescence

Garcia-Corzo L, Calatayud-Baselga I, Casares-Crespo L, Mora-Martinez C, Julian Escribano-Saiz J, Hortiguela R, et al. The transcription factor LEF1 interacts with NFIX and switches isoforms during adult hippocampal neural stem cell quiescence. Front Cell Dev Biol. 2022;10:912319. Q1

ΔNp73 and its effector targets promote colorectal peritoneal carcinosis and predict survival. The Journal of Pathology.

Pastor-Morate D, Amigo-Morán L, Garranzo-Asensio M, Rejas-González R, Carnicero P, Rodríguez N, Pérez-Robledo JP, Barderas R, Prieto-Nieto I, Domínguez G. ΔNp73 and its effector targets promote colorectal peritoneal carcinosis and predict survival. The Journal of Pathology. 2024;263:328.

DOI

Regulation of CBP andTip60 coordinates histone acetylation at local and global level during Ras-induced transformation

Sánchez-Molina S, Estarás C, Oliva JL, Akizu N, Asensio-Juan E, Rojas JM & Martínez-Balbás MA. Regulation of CBP andTip60 coordinates histone acetylation at local and global level during Ras-induced transformation. Carcinogenesis 2014; 35(10):2194-202. doi:10.1093/carcin/bgu111

DOI

Establishment and characterization of a rainbow trout heart endothelial cell line with susceptibility to viral hemorrhagic septicemia virus (VHSV) Fish Shellfish

A Luque; A González-Granja; L González; C Tafalla. 2014. Establishment and characterization of a rainbow trout heart endothelial cell line with susceptibility to viral hemorrhagic septicemia virus (VHSV) Fish Shellfish Immunol. 2014 May;38(1):255-64. https://doi.org/10.1016/j.fsi.2014.03.027.

DOI

Role of Amyloid Precursor Protein (APP) and Its Derivatives in the Biology and Cell Fate Specification of Neural Stem Cells

Coronel R, Bernabeu-Zornoza A, Palmer C, Muñiz-Moreno M, Zambrano A, Cano E, Liste I. Mol Neurobiol. 2018 Sep;55(9):7107-7117. doi: 10.1007/s12035-018-0914-2. Epub 2018 Jan 30. PMID: 29383688

PUBMED DOI

Epigenetic silencing of OR and TAS2R genes expression in human orbitofrontal cortex at early stages of sporadic Alzheimer's disease

Alves VC, Figueiro-Silva J, Ferrer I, Carro E. Epigenetic silencing of OR and TAS2R genes expression in human orbitofrontal cortex at early stages of sporadic Alzheimer's disease. Cell Mol Life Sci. 2023 Jul 5;80(8):196. doi: 10.1007/s00018-023-04845-1.

DOI

Synthesis, structural analysis, and biological evaluation of thioxoquinazoline derivatives as phosphodiesterase 7 inhibitors

Castaño T, Wang H, Campillo NE, Ballester S, González-García C, Hernández J, Pérez C, Cuenca J, Pérez-Castillo A, Martínez A, Huertas O, Gelpí JL, Luque FJ, Ke H and Gil C. Synthesis, structural analysis, and biological evaluation of thioxoquinazoline derivatives as phosphodiesterase 7 inhibitors. ChemMedChem. (2009) 4-5, pp.866-876.PMCID: PMC2952885 doi:10.1002/cmdc.200900043

PUBMED DOI

Cellular plasticity and tumor microenvironment in gliomas: the struggle to hit a moving target

Gargini R, Segura-Co llar B, Sánchez-Gómez P. (2020) Cellular plasticity and tumor microenvironment in gliomas: the struggle to hit a moving target. Cancers. 12(6): E1622. PMID: 32570988 doi: 10.3390/cancers12061622

DOI

Oligomeric and fibrillar species of Aβ42 diversely affect human neural stem cells

Bernabeu-Zornoza, A.; Coronel, R.; Palmer, C.; López-Alonso, V.; Liste, I. (2021). Oligomeric and fibrillar species of Aβ42 diversely affect human neural stem cells. Int J Mol Sci. 22, 9537. doi: 10.3390/ijms22179537.

DOI

Radio-Iodide Treatment: From Molecular Aspects to the Clinical View

De la Vieja A* and Riesco-Eizaguirre G. Radio-Iodide Treatment: From Molecular Aspects to the Clinical View. Cancers 2021 13(5):995. PMID: 33673669. doi: 10.3390/cancers13050995

DOI

Blood DNAMethylation Patterns in Older Adults With Evolving Dementia

Pérez RF, Alba-Linares JJ, Tejedor JR, Fernández AF, Calero M, Román-Domínguez A, Borrás C, Viña J, Ávila J, Medina M, Fraga MF. Blood DNAMethylation Patterns in Older Adults With Evolving Dementia. J Gerontol A Biol Sci Med Sci. 2022 77(9):1743-1749. doi: 10.1093/gerona/glac068.

DOI

Prevalence and Population Diversity of Listeria monocytogenes Isolated from Dairy Cattle Farms in the Cantabria Region of Spain

Varsaki A, Ortiz S, Santorum P, López P, López-Alonso V, Hernández M, Abad D, Rodríguez-Grande J, Ocampo-Sosa AA, Martínez-Suárez JV. Prevalence and Population Diversity of Listeria monocytogenes Isolated from Dairy Cattle Farms in the Cantabria Region of Spain. Animals (Basel). 2022 Sep 19;12(18):2477. Q1

Functional Proteomics Characterization of the Role of SPRYD7 in Colorectal Cancer Progression and Metastasis

Montero-Calle A, Jiménez de Ocaña S, Benavente-Naranjo R, Rejas-González R, Bartolomé RA, Martínez-Useros J, Sanz R, Dziaková J, Fernández-Aceñero MJ, Mendiola M, et al. Functional Proteomics Characterization of the Role of SPRYD7 in Colorectal Cancer Progression and Metastasis. Cells. 2023; 12:2548.

DOI

Shoc2/Sur8 protein regulates neurite outgrowth

León G, Sánchez-Ruiloba L, Perez-Rodriguez A, Gragera T, Martinez N, Hernandez S, Anta B, Calero O, Garcia-Domínguez CA, Dura LM, Peña-J Jimenez D, Castro J, Zarich N, Sanchez-Gomez P, Calero M, Iglesias T, Oliva JL & Rojas JM. Shoc2/Sur8 protein regulates neurite outgrowth. PloS ONE. 2014; 9(12):e114837. doi:10.1371/journal.pone.0114837

DOI

Detrimental pro-senescence effects of vitamin D on lung fibrosis

Guijarro T, Magro-Lopez E, Manso J, Garcia-Martinez R, Fernandez-Aceñero MJ, Liste I, Zambrano A. Mol Med. 2018 Dec 19;24(1):64. doi: 10.1186/s10020-018-0064-z. PMID: 30567504; PMCID: PMC6299997.

PUBMED DOI

Beta1 integrin establishes endothelial cell polarity and arteriolar lumen formation via a Par3-dependent mechanism

Zovein AC, Luque A, Turlo KA, Hofmann JJ, Yee KM, Becker MS, Fassler R, Mellman I, Lane TF, Iruela-Arispe ML. Beta1 integrin establishes endothelial cell polarity and arteriolar lumen formation via a Par3-dependent mechanism. Dev Cell. 2010 Jan 19;18(1):39-51. Los dos mpriemros autores han contribuido igualmente en este trabajo. doi: 10.1016/j.devcel.2009.12.006.

DOI

Effects of lung and airway epithelial maturation cocktail on the structure of lung bud organoids

Effects of lung and airway epithelial maturation cocktail on the structure of lung bud organoids. Magro-Lopez E, Palmer C, Manso J, Liste I, Zambrano A. Stem Cell Res Ther. 2018 Jul 11;9(1):186. doi: 10.1186/s13287-018-0943-9. PMID: 29996941; PMCID: PMC6042463.

PUBMED DOI

Salivary Lactoferrin Expression in a Mouse Model of Alzheimer's Disease

Antequera D, Moneo D, Carrero L, Bartolome F, Ferrer I, Proctor G, Carro E. Salivary Lactoferrin Expression in a Mouse Model of Alzheimer's Disease. Front Immunol. 2021 Sep 30;12:749468. doi: 10.3389/fimmu.2021.749468.

DOI

Beta interferon restricts the inflammatory potential of CD4+ cells through the boost of the Th2 phenotype, the inhibition of Th17 response and the prevalence of naturally occurring T regulatory cells

Martín-Saavedra FM, González-García C, Bravo B and Ballester S. Beta interferon restricts the inflammatory potential of CD4+ cells through the boost of the Th2 phenotype, the inhibition of Th17 response and the prevalence of naturally occurring T regulatory cells. Molecular Immunology (2008)45-15, pp.4008-4019. ISSN 0161-5890 doi:10.1016/j.molimm.2008.06.006

PUBMED DOI

The IDH-Tau-EGFR triad defines the neovascular landscape of diffuse gliomas by controlling mesenchymal differentiation

Gargini R*, Segura-Collar B*, Hernández-SanMiguel E, Garcia-Escudero V, Romero-Bravo A, Herránz B, Núñez FJ, Cantero D, García-Pérez D, Ayuso-Sacido A, Seoane J, Sepúlveda-Sánchez JM, Hernández-Laín A, Castro MG, García-Escudero R, Ávila J* and Sánchez-Gómez P*. (* Co-corresponding author) (* Co-1st author) (2020) The IDH-Tau-EGFR triad defines the neovascular landscape of diffuse gliomas by controlling mesenchymal differentiation. Sci. Transl. Med.12 (527). PMID: 31969485 doi: 10.1126/scitranslmed.aax1501

DOI

Aβ42 peptide promotes proliferation and gliogenesis in human neural stem cells

Bernabeu-Zornoza, A.; Coronel, R.; Palmer, C.; Calero, M.; Martínez-Serrano, A.; Cano, E.; Zambrano, A.; Liste, I. (2019). Aβ42 peptide promotes proliferation and gliogenesis in human neural stem cells. Mol Neurobiol. 56, 4023-4036. doi: 10.1007/s12035-018-1355-7.

DOI

Diagnostic accuracy of cerebrospinal fluid biomarkers in genetic prion diseases

Schmitz M, Villar-Piqué A, Hermann P, Escaramís G, Calero M, Chen C, Kruse N, Cramm M, Golanska E, Sikorska B, Liberski PP, Pocchiari M, Lange P, Stehmann C, Sarros S, Martí E, Baldeiras I, Santana I, Žáková D, Mitrová E, Dong XP, Collins S, Poleggi A, Ladogana A, Mollenhauer B, Kovacs GG, Geschwind MD, Sánchez-Valle R, Zerr I, Llorens F. Diagnostic accuracy of cerebrospinal fluid biomarkers in genetic prion diseases. Brain. 2022 145(2):700-712. doi: 10.1093/brain/awab350.

DOI

Anchorage of VEGF to the extracellular matrix conveys differential signaling responses to endothelial cells

TT Chen; A Luque; S Lee; SM Anderson; T Segura; ML Iruela-Arispe. 2010. Anchorage of VEGF to the extracellular matrix conveys differential signaling responses to endothelial cells. J Cell Biol. 2010 Feb 22;188(4):595-609. https://doi.org/10.1083/jcb.200906044.

DOI

Neurogenesis Is Increased in Human Neural Stem Cells by A40 Peptide

Bernabeu-Zornoza A, Coronel R, Palmer C, Lopez-Alonso V, Liste I. Neurogenesis Is Increased in Human Neural Stem Cells by A40 Peptide. Int. J. Mol. Sci. 2022, 23, 5820. Q1

Metabolic Reprogramming Helps to Define Different Metastatic Tropisms in Colorectal Cancer

Montero-Calle A, Gomez de Cedron M, Quijada-Freire A, Solís-Fernandez G, López-Alonso V, Espinosa-Salinas I, Pelaez-García A, Fernandez-Aceñero MJ, Ramírez de Molina A, Barderas R. Metabolic Reprogramming Helps to Define Different Metastatic Tropisms in Colorectal Cancer. Front. Oncol. 2022; 12

DOI

SPROUTY-2 represses the epithelial phenotype of colon carcinoma cells via upregulation of ZEB1 mediated by ETS1 and miR-200/miR-150

Barbáchano A, Fernández-Barral A, Pereira F, Segura MF, Ordóñez-Morán P, Carrillo-de Santa Pau E, González-Sancho JM, Hanniford D, Martínez N, Costales-Carrera A, Real FX, Pálmer HG, Rojas JM, Hernando E & Muñoz A. SPROUTY-2 represses the epithelial phenotype of colon carcinoma cells via upregulation of ZEB1 mediated by ETS1 and miR-200/miR-150. Oncogene. 2016; 35(23):2991-3003. doi:10.1038/onc.2015.366

DOI

Radio-Iodide Treatment: From Molecular Aspects to the Clinical View

Gutiérrez-Salmerón M, García-Martínez JM, Martinez-Useros J, Fernandez-Aceñedo MJ, Viollet B, Olivier S, Chauha J, Lucena SR, De la Vieja A, Goding CR and Chocarro-Calvo A* and García-Jiménez C*. Paradoxical activation of AMPK by glucose drives selective EP300 activity in colorectal cancer. Plos Biology 2020 6: e3000732. PMID 32603375. DOI: 10.1371/journal.pbio.3000732

PUBMED DOI

Amyloid-β impairs mitochondrial dynamics and autophagy in Alzheimer's disease experimental models

de la Cueva M, Antequera D, Ordoñez-Gutierrez L, Wandosell F, Camins A, Carro E, Bartolome F. Amyloid-β impairs mitochondrial dynamics and autophagy in Alzheimer's disease experimental models. Sci Rep. 2022 Jun 16;12(1):10092. doi: 10.1038/s41598-022-13683-3.

DOI

Beta-interferon unbalances the peripheral T cell proinflammatory response in experimental autoimmune encephalomyelitis

Martín-Saavedra FM, Flores N, Dorado B, Eguiluz C, Bravo B, García-Merino A and Ballester S. Beta-interferon unbalances the peripheral T cell proinflammatory response in experimental autoimmune encephalomyelitis. Molecular immunology (2007) 44-14, pp.3597-3607. ISSN 0161-5890 doi:10.1016/j.molimm.2007.03.002

PUBMED DOI

The EGFR-TMEM167A-p53 Axis Defines the Aggressiveness of Gliomas

Segura-Collar B, Gargini R, Tovar-Ambel E, Hernández-SanMiguel E, Epifano C, Pérez de Castro I, Hernández-Laín A, Casas-Tintó S, Sánchez-Gómez P. (2020) The EGFR-TMEM167A-p53 Axis Defines the Aggressiveness of Gliomas. Cancers 12(1):208. PMID: 31947645 doi: 10.3390/cancers12010208

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Neuronal and glial differentiation of human neural stem cells is regulated by amyloid precursor protein (APP) levels

Coronel, R.; Lachgar, M.; Bernabeu-Zornoza, A.; Palmer, C.; Domínguez-Alvaro, M.; Revilla, A.; Ocaña, I.; Fernández, A.; Martínez-Serrano, A.; Cano, E.; Liste, I. (2019). Neuronal and glial differentiation of human neural stem cells is regulated by amyloid precursor protein (APP) levels. Mol Neurobiol. 56, 1248-1261. doi: 10.1007/s12035-018-1167-9.

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Survival Patterns of Human Prion Diseases in Spain, 1998-2018: Clinical Phenotypes and Etiological Clues

Tejedor-Romero L, López-Cuadrado T, Almazán-Isla J, Calero M, García López FJ, de Pedro-Cuesta J. Survival Patterns of Human Prion Diseases in Spain, 1998-2018: Clinical Phenotypes and Etiological Clues. Front Neurosci. 2022 15:773727. doi: 10.3389/fnins.2021.773727.

DOI

Contenidos con Investigacion Biología Computacional .

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La Unidad de Biología Computacional de la UFIEC tiene como línea de investigación principal la aplicación de métodos computacionales para la interpretación funcional de los datos obtenidos por las tecnologías de alto rendimiento, y la posibilidad de integración de esta información con los datos clínicos para aplicaciones diagnósticas y terapéuticas de enfermedades crónicas.

 

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Contenidos con Investigacion Biología Computacional .