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Investigación

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
     
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ILK mediates LPS-induced vascular adhesion receptor expression and subsequent leukocyte trans-endothelial migration

S Hortelano; R López-Fontal; PG Través; N Villa; C Grashoff; L Boscá; A Luque. 2010. ILK mediates LPS-induced vascular adhesion receptor expression and subsequent leukocyte trans-endothelial migration. Cardiovasc Res. 2010. May 1;86(2):283-92. https://doi.org/10.1093/cvr/cvq050.

DOI

Structural variation analysis of 6,500 whole genome sequences in amyotrophic lateral sclerosis

Al-Chalabi, Al Khleifat A, Iacoangeli A, van Vugt J, Moisse M, Zwamborn R, van der Spek R, Shatunov A, Cooper-Knock, Topp S, Byrne R, Gellera C, López Alonso V et al. “Structural variation analysis of 6,500 whole genome sequences in amyotrophic lateral sclerosis". NPJ Genomic Medicine 2022, 7(1). Q1.

Phage-Derived and Aberrant HaloTag Peptides Immobilized on Magnetic Microbeads for Amperometric Biosensing of Serum Autoantibodies and Alzheimer's Disease Diagnosis

Alejandro Valverde, Ana Montero-Calle, Beatriz Arévalo, Dr. Pablo San Segundo-Acosta, Dr. Verónica Serafín, Miren Alonso-Navarro, Guillermo Solís-Fernández, Prof. José M. Pingarrón, Dr. Susana Campuzano, Dr. Rodrigo Barderas. Phage-Derived and Aberrant HaloTag Peptides Immobilized on Magnetic Microbeads for Amperometric Biosensing of Serum Autoantibodies and Alzheimer's Disease Diagnosis. Analysis and Sensing. 2021; 1:161.

DOI

PGA1-induced apoptosis involves specific activation of H-Ras and N-Ras in cellular endomembranes

Anta B, Pérez-Rodríguez A, Castro J, García-Domínguez CA, Ibiza S, Martínez N, Durá LM, Hernández S, Gragera T, Peña-Jiménez D, Yunta M, Zarich N, Crespo P, Serrador JM, Santos E, Muñoz A, Oliva JL & Rojas-Cabañeros JM. PGA1-induced apoptosis involves specific activation of H-Ras and N-Ras in cellular endomembranes. Cell Death and Disease. 2016; 7(7):e2311. doi:10.1038/cddis.2016.219

DOI

A Two-Dimensional Human Minilung System (Model) for Respiratory Syncytial Virus Infections

A Two-Dimensional Human Minilung System (Model) for Respiratory Syncytial Virus Infections. Magro-Lopez E, Guijarro T, Martinez I, Martin-Vicente M, Liste I, Zambrano A. Viruses. 2017 Dec 10;9(12):379. doi: 10.3390/v9120379. PMID: 29232863; PMCID: PMC5744153.

PUBMED DOI

La Nutrición de yodo en España. Necesidades para el Futuro

Vila L, Lucas A, Donnay S, De la Vieja A, Wengrovicz S, Santiago P, Bandrés O, Velasco I, García-Fuentes E, Ares S, Moreno JC, Espada M, Muñoz JA, Galofré JC and Puig-Domingo M. La Nutrición de yodo en España. Necesidades para el Futuro. Endocrinología Diabetes y Nutrición 2019 67(1):61-69. PMID: 30962160. DOI: 10.1016/j.endinu.2019.02.009

DOI

Differentially Aquaporin 5 Expression in Submandibular Glands and Cerebral Cortex in Alzheimer's Disease

Antequera D, Carrero L, Cunha Alves V, Ferrer I, Hernández-Gallego J, Municio C, Carro E. Differentially Aquaporin 5 Expression in Submandibular Glands and Cerebral Cortex in Alzheimer's Disease. Biomedicines. 2022 Jul 8;10(7):1645. doi: 10.3390/biomedicines10071645.

DOI

The activity of interleukin-4 receptor alpha-chain promoter is regulated by a GT box element

13. Dorado B, Martín-Saavedra FM, Jerez MJ, Ballester S. The activity of interleukin-4 receptor alpha-chain promoter is regulated by a GT box element. Molecular Immunology (2006) 43-11, pp.1808-1816. ISSN 0161-5890 doi:10.1016/j.molimm.2005.10.016

PUBMED DOI

Novel Functions of the Neurodegenerative-Related Gene Tau in Cancer

Gargini R*, Segura-Collar B*, Sánchez-Gómez P. (* Co-1st author) (2019) Novel Functions of the Neurodegenerative-Related Gene Tau in Cancer. Front Aging Neurosci. 11:231. PMID: 31551755 doi: 10.3389/fnagi.2019.00231

DOI

Effects of chlorpyrifos on cell death and cellular phenotypic specification of human neural stem cells

Sandoval, L., Rosca, A., Oniga, A., Zambrano, A., Ramos, J.J., González, M.C., Liste, I., Motas, M. (2019). Effects of chlorpyrifos on cell death and cellular phenotypic specification of human neural stem cells. Sci Total Environ. 683, 445-454. doi: 10.1016/j.scitotenv.2019.05.270.

DOI

Unraveling autoimmune and neurodegenerative diseases by amperometric serological detection of antibodies against aquaporin-4

Arévalo B, Blázquez M, Serafín V, Montero-Calle A, Calero M, Valverde A, Barderas R, Campuzano S, Yáñez-Sedeño P, Pingarrón JM. Unraveling autoimmune and neurodegenerative diseases by amperometric serological detection of antibodies against aquaporin-4. Bioelectrochemistry. 2022 144:108041. doi: 10.1016/j.bioelechem.2021.108041.

DOI

Oligomeric and Fibrillar Species of Abeta42 Diversely Affect Human Neural Stem Cells

Bernabeu-Zornoza A, Coronel R, Palmer C, Lopez-Alonso V, Liste I. Oligomeric and Fibrillar Species of Abeta42 Diversely Affect Human Neural Stem Cells. Int J Mol Sci. 2021,22(17). Q1

The Molecular Misreading of APP and UBB Induces a Humoral Immune Response in Alzheimer’s Disease Patients with Diagnostic Ability

Montero-Calle, A., San Segundo-Acosta, P., Garranzo-Asensio, M., Rábana, A, Barderas, R. The Molecular Misreading of APP and UBB Induces a Humoral Immune Response in Alzheimer’s Disease Patients with Diagnostic Ability. Mol Neurobiol 57, 1009–1020 (2020)

DOI

The CSN3 subunit of the COP9 signalosome interacts with the HD region of Sos1 regulating stability of this GEF protein.

Zarich N, Anta B, Fernández-Medarde A, Ballester A, de Lucas MP, Cámara AB, Anta B, Oliva JL, Rojas-Cabañeros JM & Santos E. The CSN3 subunit of the COP9 signalosome interacts with the HD region of Sos1 regulating stability of this GEF protein. Oncogenesis. 2019; 8(1):2. doi:10.1038/s41389-018-0111-1

DOI

Induction of DNA double-strand breaks and cellular senescence by human respiratory syncytial virus

Induction of DNA double-strand breaks and cellular senescence by human respiratory syncytial virus. Martínez I, García-Carpizo V, Guijarro T, García-Gomez A, Navarro D, Aranda A, Zambrano A. Virulence. 2016 May 18;7(4):427-42. doi: 10.1080/21505594.2016.1144001. Epub 2016 Jan 25. PMID: 26809688; PMCID: PMC4871660.

PUBMED DOI

Role of Iodide Metabolism in physiology and cancer

De la Vieja A* and Santisteban P. Role of Iodide Metabolism in physiology and cancer. Endocrine-Related Cancer 2018 25(4):R225-R245. PMID: 29437784. doi: 10.1530/ERC-17-0515.

PUBMED DOI

Increased YKL-40 but Not C-Reactive Protein Levels in Patients with Alzheimer's Disease

Blanco-Palmero VA, Rubio-Fernández M, Antequera D, Villarejo-Galende A, Molina JA, Ferrer I, Bartolome F, Carro E. Increased YKL-40 but Not C-Reactive Protein Levels in Patients with Alzheimer's Disease. Biomedicines. 2021 Aug 27;9(9):1094. doi: 10.3390/biomedicines9091094.

DOI

Grb2 is a negative modulator of the intrinsic Ras-GEF activity of hSos1

Zarich N, Oliva JL, Martínez N, Jorge R, Ballester A, Gutiérrez-Eisman S, García-Vargas S, Rojas JM. Grb2 is a negative modulator of the intrinsic Ras-GEF activity of hSos1. Molecular Biology of the Cell (2006) 17-8, pp.3591-3597.PMCID: PMC1525251 doi:10.1091/mbc.E05-12-1104

PUBMED DOI

Oncogenic dependence of glioma cells to Kish/TMEM167A regulation of vesicular trafficking

Portela M#, Segura B#, Argudo I, Sáiz A, Gargini R, Sánchez-Gómez P*, Casas-Tintó S*. (* Co-corresponding authors) (# Co-1st author) (2019) Oncogenic dependence of glioma cells to Kish/TMEM167A regulation of vesicular trafficking. GLIA 67(2):404-417. PMID: 30506943 doi: 10.1002/glia.23551

DOI

Brain organoid as a model to study the role of mitochondria in neurodevelopmental disorders: Achievements and weaknesses

Coronel, R.; García-Moreno, E.; Siendones, E.; Barrero, M.J.; Martinez-Delgado, B.; Santos-Ocaña, C.; Liste, I.; Cascajo- Almenara, M.V. (2024). Brain organoid as a model to study the role of mitochondria in neurodevelopmental disorders: Achievements and weaknesses. Front Cell Neurosci. 18. doi: 10.3389/fncel.2024.1403734.

DOI

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. eCollection 2021.

DOI

ATXN1 repeat expansions confer risk for amyotrophic lateral sclerosis and contribute to TDP-43 mislocalization

Tazelaar GHP, Boeynaems S, De Decker M, van Vugt J, Kool L, Goedee HS, et al. ATXN1 repeat expansions confer risk for amyotrophic lateral sclerosis and contribute to TDP-43 mislocalization. Brain Commun. 2020,2(2):fcaa064. Q1

Magnetic microbeads-based amperometric immunoplatform for the rapid and sensitive detection of N6-methyladenosine to assist in metastatic cancer cells discrimination

Eloy Povedano, María Gamella, Rebeca M. Torrente-Rodríguez, Ana Montero-Calle, María Pedrero, Guillermo Solís-Fernández, Fernando Navarro-Villoslada, Rodrigo Barderas, Susana Campuzano, José M. Pingarrón. Magnetic microbeads-based amperometric immunoplatform for the rapid and sensitive detection of N6-methyladenosine to assist in metastatic cancer cells discrimination. Biosensors and Bioelectronics. 2021; 171:112708

DOI

SOS GEFs in health and disease

Baltanás FC, Zarich N, Rojas- Cabañeros JM & Santos E. SOS GEFs in health and disease. BBA-Reviews on Cancer. 2020; 188445. doi: 10.1016/j.bbcan.2020.188445

DOI

Thyroid hormone increases bulk histones expression by enhancing translational efficiency

Thyroid hormone increases bulk histones expression by enhancing translational efficiency. Zambrano A, García-Carpizo V, Villamuera R, Aranda A. Mol Endocrinol. 2015 Jan;29(1):68-75. doi: 10.1210/me.2014-1235. PMID: 25422881; PMCID: PMC5414774.

PUBMED DOI

Epidemiological bases and molecular mechanisms linking obesity, diabetes, and cancer

Gutiérrez-Salmerón M, Chocarro-Calvo A, García-Martínez JM, de la Vieja A, García-Jiménez C. Epidemiological bases and molecular mechanisms linking obesity, diabetes, and cancer. Endocrinol Diabetes Nutr. 2017 Feb; 64(2):109-117. (https://www.ncbi.nlm.nih.gov/pubmed/28440775) doi:10.1016/j.endinu.2016.10.005

PUBMED DOI

Salivary lactoferrin as biomarker for Alzheimer's disease: Brain-immunity interactions

Bermejo-Pareja F, Del Ser T, Valentí M, de la Fuente M, Bartolome F, Carro E. Salivary lactoferrin as biomarker for Alzheimer's disease: Brain-immunity interactions. Alzheimers Dement. 2020 Aug;16(8):1196-1204. doi: 10.1002/alz.12107.

DOI

Ocoxin Modulates Cancer Stem Cells and M2 Macrophage Polarization in Glioblastoma

Hernández SanMiguel, E.; Gargini, R.; Cejalvo, T., Segura-Collar B, Núñez-Hervada P, Hortigüela R, Sepúlveda-Sánchez JM, Hernández-Laín A, Pérez-Núñez A, Sanz E, Sánchez Gómez, P. (2019) Ocoxin Modulates Cancer Stem Cells and M2 Macrophage Polarization in Glioblastoma. Oxid.Med.Cell. Longev. pp.9719730. PMID: 31467641. doi: 10.1155/2019/9719730

DOI

Impact of environmental neurotoxic: current methods and usefulness of human stem cells

Rosca, A.; Coronel, R.; Moreno, M.; González, R.; Oniga, A.; Martín, A.; López, V.; González, M.C.; Liste, I. (2020). Impact of environmental neurotoxic: current methods and usefulness of human stem cells. Heliyon. 6, e05773. doi: 10.1016/j.heliyon.2020.e05773.

DOI

Genomic Characterization of Host Factors Related to SARS-CoV-2 Infection in People with Dementia and Control Populations: The GR@ACE/DEGESCO Study

de Rojas I, Hernández I, Montrreal L, Quintela I, Calero M, Royo JL, Huerto Vilas R, González-Pérez A, Franco-Macías E, Macías J, Menéndez-González M, Frank-García A, Diez-Fairen M, Lage C, García-Madrona S, Aguilera N, García-González P, Puerta R, Sotolongo-Grau O, Alonso-Lana S, Rábano A, Arias Pastor A, Pastor AB, Corma-Gómez A, Martín Montes A, Martínez Rodríguez C, Buiza-Rueda D, Periñán MT, Rodriguez-Rodriguez E, Alvarez I, Rosas Allende I, Pineda JA, Bernal Sánchez-Arjona M, Fernández-Fuertes M, Mendoza S, Del Ser T, Gr Ace/Degesco Consortium, Garcia-Ribas G, Sánchez-Juan P, Pastor P, Bullido MJ, Álvarez V, Real LM, Mir P, Piñol-Ripoll G, García-Alberca JM, Medina M, Orellana A, Butler CR, Marquié M, Sáez ME, Carracedo Á, Tárraga L, Boada M, Ruiz A. Genomic Characterization of Host Factors Related to SARS-CoV-2 Infection in People with Dementia and Control Populations: The GR@ACE/DEGESCO Study. J Pers Med. 2021 11(12):1318. doi: 10.3390/jpm11121318.

DOI

Impact of environmental neurotoxic: current methods and usefulness of human stem cells

Rosca A, Coronel R, Moreno M, Gonzalez R, Oniga A, Martin A, et al. Impact of environmental neurotoxic: current methods and usefulness of human stem cells. Heliyon. 2020,6(12):e05773. Q1

Bringing to Light the Importance of the miRNA Methylome in Colorectal Cancer Prognosis Through Electrochemical Bioplatforms

Povedano E, Ruiz-Valdepeñas Montiel V, Sebuyoya R, Torrente-Rodríguez RM, Garranzo-Asensio M, Montero-Calle A, Pingarrón JM, Barderas R, Bartosik M, Campuzano S. Bringing to Light the Importance of the miRNA Methylome in Colorectal Cancer Prognosis Through Electrochemical Bioplatforms. Analytical Chemistry 2024;96:4580

DOI

Minilungs from Human Embryonic Stem Cells to Study the Interaction of Streptococcus pneumoniae with the Respiratory Tract

Sempere J, Rossi SA, Chamorro-Herrero I, González-Camacho F, de Lucas MP, Rojas-Cabañeros JM, Taborda CP, Zaragoza O, Yuste J & Zambrano A. Minilungs from Human Embryonic Stem Cells to Study the Interaction of Streptococcus pneumoniae with the Respiratory Tract. Microbiology Spectrum. 2022; 10(3):e00453-22. doi: 10.1128/spectrum.00453-22

DOI

The thyroid hormone receptor β induces DNA damage and premature senescence

The thyroid hormone receptor β induces DNA damage and premature senescence. Zambrano A, García-Carpizo V, Gallardo ME, Villamuera R, Gómez-Ferrería MA, Pascual A, Buisine N, Sachs LM, Garesse R, Aranda A. J Cell Biol. 2014 Jan 6;204(1):129-46. doi: 10.1083/jcb.201305084. PMID: 24395638; PMCID: PMC3882795.

PUBMED DOI

From obesity to diabetes and cancer: epidemiological links and role of therapies

García-Jiménez C, Gutiérrez-Salmerón M, Chocarro-Calvo A, García-Martínez JM, Castaño A, De la Vieja A. From obesity to diabetes and cancer: epidemiological links and role of therapies. Br J Cancer. 2016 Mar 29; 114(7):716-22. (https://www.ncbi.nlm.nih.gov/pubmed/26908326) doi: 10.1038/bjc.2016.37

PUBMED DOI

Aquaporin 5 in Alzheimer's disease: a link between oral and brain pathology?

Municio C, Carro E. Aquaporin 5 in Alzheimer's disease: a link between oral and brain pathology? Neural Regen Res. 2023 Jul;18(7):1491-1492. doi: 10.4103/1673-5374.361545.

DOI

The Netrin-4/ Neogenin-1 axis promotes neuroblastoma cell survival and migration

Villanueva AA, Falcón P, Espinoza N, R LS, Milla LA, Hernández-SanMiguel E, Torres VA, Sanchez-Gomez P, Palma V. (2017) The Netrin-4/ Neogenin-1 axis promotes neuroblastoma cell survival and migration. Oncotarget 8(6):9767-9782. PMID: 28038459 doi: 18632/oncotarget.14213

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Analysis of Benzalkonium Chloride Resistance and Potential Virulence of Listeria monocytogenes Isolates Obtained from Different Stages of a Poultry Production Chain in Spain

Lopez-Alonso V, Ortiz S, Corujo A, Martinez-Suarez JV. Analysis of Benzalkonium Chloride Resistance and Potential Virulence of Listeria monocytogenes Isolates Obtained from Different Stages of a Poultry Production Chain in Spain. J Food Prot. 2020,83(3):443-51. Q2

Physiological and pathological effects of amyloid-β species in neural stem cell biology

Bernabeu-Zornoza, A.; Coronel, R.; Palmer, C.; Monteagudo, M.; Zambrano, A.; Liste, I. (2019). Physiological and pathological effects of amyloid-β species in neural stem cell biology. Neural Regen Res. 14, 2035-2042. doi: 10.4103/1673-5374.262571.

DOI

Selenium Increases Thyroid-Stimulating Hormone-Induced Sodium/Iodide Symporter Expression Through Thioredoxin/Apurinic/Apyrimidinic Endonuclease 1-Dependent Regulation of Paired Box 8 Binding Activity. Antioxid Redox Signal. 2016 May 20; 24(15):855-66. (*co-corresponding authors) (IF: 6,337)

Leoni SG, Sastre-Perona A, De la Vieja A, Santisteban P. Selenium Increases Thyroid-Stimulating Hormone-Induced Sodium/Iodide Symporter Expression Through Thioredoxin/Apurinic/Apyrimidinic Endonuclease 1-Dependent Regulation of Paired Box 8 Binding Activity. Antioxid Redox Signal. 2016 May 20; 24(15):855-66. (https://www.ncbi.nlm.nih.gov/pubmed/26908326) doi: 10.1089/ars.2014.6228

PUBMED 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 .