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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
     
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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. 2021 144:108041. doi: 10.1016/j.bioelechem.2021.108041.

DOI

Spatial Proteomic Analysis of Isogenic Metastatic Colorectal Cancer Cells Reveals Key Dysregulated Proteins Associated with Lymph Node, Liver, and Lung Metastasis

Solís-Fernández G, Montero-Calle A, Martínez-Useros J, López-Janeiro Á, de los Ríos V, Sanz R, Dziakova J, Milagrosa E, Fernández-Aceñero MJ, Peláez-García A, et al. Spatial Proteomic Analysis of Isogenic Metastatic Colorectal Cancer Cells Reveals Key Dysregulated Proteins Associated with Lymph Node, Liver, and Lung Metastasis. Cells. 2022; 11(3):447

DOI

PKD phosphorylation and COP9/Signalosome modulate intracellular Spry2 protein stability

Martínez N, Gragera T, de Lucas MP, Cámara AB, Ballester A, Anta B, Fernández-Medarde A, López-Briones T, Ortega J, Peña-Jiménez D, Barbáchano A, Montero-Calle A, Cordero V, Barderas R, Iglesias T, Yunta M, Oliva JL, Muñoz A, Santos E, Zarich N & Rojas-Cabañeros JM. PKD phosphorylation and COP9/Signalosome modulate intracellular Spry2 protein stability. Oncogenesis. 2023; 12:20. doi.org/10.1038/s41389-023-00465-3

DOI

Decreased salivary lactoferrin levels are specific to Alzheimer's disease

González-Sánchez M, Bartolome F, Antequera D, Puertas-Martín V, González P, Gómez-Grande A, Llamas-Velasco S, Herrero-San Martín A, Pérez-Martínez D, Villarejo-Galende A, Atienza M, Palomar-Bonet M, Cantero JL, Perry G, Orive G, Ibañez B, Bueno H, Fuster V, Carro E. Decreased salivary lactoferrin levels are specific to Alzheimer's disease. EBioMedicine. 2020 Jul;57:102834. doi: 10.1016/j.ebiom.2020.102834.

DOI

Applied mathematics and nonlinear sciences in the war on cancer

Pérez-García VM, Fitzpatrick S, Pérez-Romasanta LA, Pesic M, Schucht P, Arana E, Sánchez-Gómez P. (2016) Applied mathematics and nonlinear sciences in the war on cancer. App. Math. Nonlin. Sci. 1(2): 423–436 doi: 10.21042/AMNS.2016.2.00036

DOI

Physiological effects of amyloid precursor protein and its derivatives on neural stem cell biology and signaling pathways involved

Coronel, R.; Palmer, C.; Bernabeu-Zornoza, A.; Monteagudo, M.; Rosca, A.; Zambrano, A.; Liste, I. (2019). Physiological effects of amyloid precursor protein and its derivatives on neural stem cell biology and signaling pathways involved. Neural Regen Res. 14, 1661-1671. doi: 10.4103/1673-5374.257511.

DOI

Insulin drives glucose-dependent insulinotropic peptide expression via glucose-dependent regulation of FoxO1 and LEF1/β-catenin

García-Martínez JM, Chocarro-Calvo A, De la Vieja A, García-Jiménez C. Insulin drives glucose-dependent insulinotropic peptide expression via glucose-dependent regulation of FoxO1 and LEF1/β-catenin. Biochim Biophys Acta. 2014 Nov; 1839(11):1141-50. (https://www.ncbi.nlm.nih.gov/pubmed/25091498) doi:10.1016/j.bbagrm.2014.07.020

PUBMED DOI

Impaired glucose metabolism reduces the neuroprotective action of adipocytokines in cognitively normal older adults with insulin resistance

Lopez-Vilaret KM, Cantero JL, Fernandez-Alvarez M, Calero M, Calero O, Lindín M, Zurrón M, Díaz F, Atienza M. Impaired glucose metabolism reduces the neuroprotective action of adipocytokines in cognitively normal older adults with insulin resistance. Aging (Albany NY). 2021 13(21):23936-23952. doi: 10.18632/aging.203668.

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The project MinE databrowser: bringing large-scale whole-genome sequencing in ALS to researchers and the public

van der Spek RAA, van Rheenen W, Pulit SL, Kenna KP, van den Berg LH, Veldink JH, et al. The project MinE databrowser: bringing large-scale whole-genome sequencing in ALS to researchers and the public. Amyotroph Lateral Scler Frontotemporal Degener. 2019,20(5-6):432-40. Q1

Brain and immune system-derived extracellular vesicles mediate regulation of complement system, extracellular matrix remodeling, brain repair and antigen tolerance in Multiple sclerosis

Torres Iglesias G, Fernández-Fournier M, Botella L, Piniella D, Laso-García F, Gómez-de Frutos MC, Chamorro B, Puertas I, Tallón Barranco A, Fuentes B, de Leciñana MA, Alonso-López E, Bravo SB, Miranda-Carús ME, Montero-Calle A, Barderas R, Díez-Tejedor E, Gutiérrez-Fernández M, Otero-Ortega L. Brain and immune system-derived extracellular vesicles mediate regulation of complement system, extracellular matrix remodeling, brain repair and antigen tolerance in Multiple sclerosis. Brain, Behavior, and Immunity. 2023; 113:44

DOI

Salivary lactoferrin is associated with cortical amyloid-beta load, cortical integrity, and memory in aging

Reseco L, Atienza M, Fernandez-Alvarez M, Carro E, Cantero JL. Salivary lactoferrin is associated with cortical amyloid-beta load, cortical integrity, and memory in aging. Alzheimers Res Ther. 2021 Sep 6;13(1):150. doi: 10.1186/s13195-021-00891-8.

DOI

Preclinical test of dacomitinib, an irreversible EGFR inhibitor, confirms its effectiveness for glioblastoma

Zahonero C, Aguilera P, Ramírez-Castillejo C, Pajares M, Bolós MV, Cantero C, Pérez-Núñez A, Hernández-Laín A, Sánchez-Gómez P*, Sepúlveda JM*. (*Co-corresponding authors) (2015) Preclinical test of dacomitinib, an irreversible EGFR inhibitor, confirms its effectiveness for glioblastoma. Mol. Can. Ther. 14(7):1548-58. PMID: 25939761 doi: 10.1158/1535-7163.MCT-14-0736

DOI

Whole-Genome Sequences of Seven Listeria monocytogenes Strains from Different Stages of a Poultry Meat Production Chain

Lopez-Alonso V, Ortiz S, Martinez-Suarez JV. Whole-Genome Sequences of Seven Listeria monocytogenes Strains from Different Stages of a Poultry Meat Production Chain. Microbiol Resour Announc. 2019,8(11). Q4

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. (2018). Role of amyloid precursor protein (APP) and its derivatives in the biology and cell fate specification of neural stem cells. Mol Neurobiol. 55, 7107-7117. doi: 10.1007/s12035-018-0914-2.

DOI

Medial Temporal Lobe Involvement in Human Prion Diseases: Implications for the Study of Focal Non Prion Neurodegenerative Pathology

Rábano A, Guerrero Márquez C, Juste RA, Geijo MV, Calero M. Medial Temporal Lobe Involvement in Human Prion Diseases: Implications for the Study of Focal Non Prion Neurodegenerative Pathology. Biomolecules. 2021 Mar 10;11(3):413. doi: 10.3390/biom11030413.

DOI

Flat clathrin lattices are linked to metastatic potential in colorectal cancer

Cresens C, Solís-Fernández G, Tiwari A, Nuyts R, Hofkens J, Barderas R, Rocha S. Flat clathrin lattices are linked to metastatic potential in colorectal cancer. iScience. 2023; 26: 107327

DOI

NIS mediates iodide uptake in the female reproductive tract and is a poor prognostic factor in ovarian cancer

Riesco-Eizaguirre G, Leoni SG, Mendiola M, Estévez-Cebrero MA, Gallego MI, Redondo A, Hardisson D, Santisteban P, De la Vieja A. NIS mediates iodide uptake in the female reproductive tract and is a poor prognostic factor in ovarian cancer. J Clin Endocrinol Metab. 2014 Jul; 99(7):E1199-208. (https://www.ncbi.nlm.nih.gov/pubmed/24708099) doi: 10.1210/jc.2013-4249

PUBMED DOI

Standardizing salivary lactoferrin measurements to obtain a robust diagnostic biomarker for Alzheimer's disease

Bartolome F, Orive G, Carro E. Standardizing salivary lactoferrin measurements to obtain a robust diagnostic biomarker for Alzheimer's disease. Alzheimers Dement (Amst). 2021 May 2;13(1):e12173. doi: 10.1002/dad2.12173.

DOI

Controlled release microspheres loaded with BMP7 suppress primary tumors from human glioblastoma

González-Gómez P, Crecente-Campo J, Zahonero C, de la Fuente M, Hernández-Laín A, Mira H*, Sánchez-Gómez P*, García-Fuentes M* (* Co-corresponding authors). (2015) Controlled release microspheres loaded with BMP7 suppress primary tumors from human glioblastoma. Oncotarget, 6 (13): 10950-10963. PMID: 25860932 doi: 10.18632/oncotarget.3459

DOI

Advances in Alzheimer’s disease research: Human cerebral organoids

Mateos-Martínez, P.; González-Sastre, R.; Coronel, R.; Rosca, A.; Martín-Benito, S.; Bernabeu-Zornoza, A.; López-Alonso, V.; Liste, I. (2023). Advances in Alzheimer’s disease research: Human cerebral organoids. Am J Biomed Sci & Res. 18, AJBSR.MS.ID.002421. doi: 10.34297/AJBSR.2023.18.002421.

DOI

Validation of a novel and accurate ApoE4 assay for automated chemistry analyzers

Veiga S, Rodríguez-Martín A, Garcia-Ribas G, Arribas I, Menacho-Román M, Calero M. Validation of a novel and accurate ApoE4 assay for automated chemistry analyzers. Sci Rep. 2020 10(1):2138. doi: 10.1038/s41598-020-58841-7.

DOI

Advances in Alzheimer’s Disease Research: Human Cerebral Organoids

Mateos P., González R., Coronel R., Rosca A, Martín S., Bernabeu A, López-Alonso V and Liste I. Advances in Alzheimer’s Disease Research: Human Cerebral Organoids. American Journal of Biomedical Science & Research. 2023; 715:719.

Multiomics Profiling of Alzheimer’s Disease Serum for the Identification of Autoantibody Biomarkers

San Segundo-Acosta P, Montero-Calle A, Jernbom-Falk A, Alonso-Navarro M, Pin E, Andersson E, Hellström C, Sánchez-Martínez M, Rábano A, Solís-Fernández G, Peláez-García A, Martínez-Useros J, Fernández-Aceñero MJ, Månberg A, Nilsson P, Barderas R. Multiomics Profiling of Alzheimer’s Disease Serum for the Identification of Autoantibody Biomarkers. Journal of Proteome Research 2021 20 (11), 5115-5130.

DOI

Kynurenic Acid Levels are Increased in the CSF of Alzheimer's Disease Patients

González-Sánchez M, Jiménez J, Narváez A, Antequera D, Llamas-Velasco S, Martín AH, Arjona JAM, Munain AL, Bisa AL, Marco MP, Rodríguez-Núñez M, Pérez-Martínez DA, Villarejo-Galende A, Bartolome F, Domínguez E, Carro E. Kynurenic Acid Levels are Increased in the CSF of Alzheimer's Disease Patients. Biomolecules. 2020 Apr 8;10(4):571. doi: 10.3390/biom10040571.

DOI

EGFR-dependent mechanisms in glioblastoma: towards a better therapeutic strategy

Zahonero C and Sánchez-Gómez P. (2014) EGFR-dependent mechanisms in glioblastoma: towards a better therapeutic strategy. Cel. Mol. Life Sci. 71 (18): 3465-88. PMID: 24671641 doi: 10.1007/s00018-014-1608-1

DOI

Working Group on Disorders Related to Iodine Deficiency and Thyroid Dysfunction of the Spanish Society of Endocrinology and Nutrition. Iodine supplementation during pregnancy and lactation. Position statement of the working group on disorders related to iodine deficiency and thyroid dysfunction of the Spanish Society of Endocrinology and Nutrition

Donnay S, Arena J, Lucas A, Velasco I, Ares S; Working Group on Disorders Related to Iodine Deficiency and Thyroid Dysfunction of the Spanish Society of Endocrinology and Nutrition.. Iodine supplementation during pregnancy and lactation. Position statement of the working group on disorders related to iodine deficiency and thyroid dysfunction of the Spanish Society of Endocrinology and Nutrition. Endocrinol Nutr. 2014 Jan; 61(1):27-34. (https://www.ncbi.nlm.nih.gov/pubmed/24035326) doi:10.1016/j.endonu.2013.05.004

PUBMED DOI

Treatment of Parkinson’s disease using human stem cells

Palmer, C.; Coronel, R.; Liste, I. (2016). Treatment of Parkinson’s disease using human stem cells. J Stem Cell Res Med. 1, 71-77. doi: 10.15761/JSCRM.1000113.

DOI

Spanish CJD Surveillance Group. Human prion disease surveillance in Spain, 1993-2018: an overview

De Pedro-Cuesta J, Almazán-Isla J, Tejedor-Romero L, Ruiz-Tovar M, Avellanal F, Rábano A, Calero M, García López FJ; Spanish CJD Surveillance Group. Human prion disease surveillance in Spain, 1993-2018: an overview. Prion. 2021. 15(1):94-106. doi: 10.1080/19336896.2021.1933873.

DOI

Human neural stem cells in developmental neurotoxicology: Current scenario and future prospects. Alternative Methods in Neurotoxicology

Rosca A., Coronel R., López-Alonso V, Liste I, González-Caballero M. Carmen. Human neural stem cells in developmental neurotoxicology: Current scenario and future prospects. Alternative Methods in Neurotoxicology. Advances in Neurotoxicology. 2023; 197:226.

In-depth quantitative proteomics analysis revealed C1GALT1 depletion in ECC-1 cells mimics an aggressive endometrial cancer phenotype observed in cancer patients with low C1GALT1 expression

Montero-Calle A, López-Janeiro Á, Mendes ML, Perez-Hernandez D, Echevarría I, Ruz-Caracuel I, Heredia-Soto V, Mendiola M, Hardisson D, Argüeso P, Peláez-García A, Guzman-Aranguez A, Barderas R. In-depth quantitative proteomics analysis revealed C1GALT1 depletion in ECC-1 cells mimics an aggressive endometrial cancer phenotype observed in cancer patients with low C1GALT1 expression. Cell Oncol. 46, 697–715 (2023).

DOI

Annexin A5 prevents amyloid-β-induced toxicity in choroid plexus: implication for Alzheimer's disease

Bartolome F, Krzyzanowska A, de la Cueva M, Pascual C, Antequera D, Spuch C, Villarejo-Galende A, Rabano A, Fortea J, Alcolea D, Lleo A, Ferrer I, Hardy J, Abramov AY, Carro E. Annexin A5 prevents amyloid-β-induced toxicity in choroid plexus: implication for Alzheimer's disease. Sci Rep. 2020 Jun 10;10(1):9391. doi: 10.1038/s41598-020-66177-5.

DOI

A new link between diabetes and cancer: enhanced Wnt/beta-catening signaling by high glucose

García-Jiménez C, Garcia-Martinez JM, Chocarro-Calvo A, and De la Vieja A. A new link between diabetes and cancer: enhanced Wnt/beta-catening signaling by high glucose. Journal of Molecular Endocrinology 2014 52(1): R51-R66. (https://www.ncbi.nlm.nih.gov/pubmed/24049067) doi: 10.1530/JME-13-0152

PUBMED DOI

DYRK1A destabilizes EGFR and reduces EGFR-dependent glioblastoma growth

Pozo Zahonero, Fernández P, Liñares JM, Ayuso A, Hagiwara M, Pérez A, Ricoy JR, Hernández-Laín A, Sepúlveda JM, Sánchez-Gómez P. (2013) Inhibition of DYRK1A destabilizes EGFR and reduces EGFR-dependent glioblastoma growth. J. Clin. Invest. 123(6):2475-87. PMID: 23635774 doi: 10.1172/JCI63623

DOI

Genetic Diversity, Antimicrobial Resistance and Survival upon Manure Storage of Campylobacter jejuni Isolated from Dairy Cattle Farms in the Cantabric Coast of Spain

Varsaki, A.; Ortiz, S.; Santorum, P.; López, P.; López-Alonso, V.; Martínez-Suárez, J.V. Genetic Diversity, Antimicrobial Resistance and Survival upon Manure Storage of Campylobacter jejuni Isolated from Dairy Cattle Farms in the Cantabric Coast of Spain. Zoonotic Dis. 2022, 2, 82–94

Alzheimer’s Disease Neuroimaging Initiative. Long runs of homozygosity are associated with Alzheimer's disease

Moreno-Grau S, Fernández MV, de Rojas I, Garcia-González P, Hernández I, Farias F, Budde JP, Quintela I, Madrid L, González-Pérez A, Montrreal L, Alarcón-Martín E, Alegret M, Maroñas O, Pineda JA, Macías J; GR@ACE study group; DEGESCO consortium, Marquié M, Valero S, Benaque A, Clarimón J, Bullido MJ, García-Ribas G, Pástor P, Sánchez-Juan P, Álvarez V, Piñol-Ripoll G, García-Alberca JM, Royo JL, Franco-Macías E, Mir P, Calero M, Medina M, Rábano A, Ávila J, Antúnez C, Real LM, Orellana A, Carracedo Á, Sáez ME, Tárraga L, Boada M, Cruchaga C, Ruiz A; Alzheimer’s Disease Neuroimaging Initiative. Long runs of homozygosity are associated with Alzheimer's disease. Transl Psychiatry. 2021 11(1):142. doi: 10.1038/s41398-020-01145-1.

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Endothelial-specific deficiency of megalin in the brain protects mice against high-fat diet challenge

Bartolome F, Antequera D, de la Cueva M, Rubio-Fernandez M, Castro N, Pascual C, Camins A, Carro E. Endothelial-specific deficiency of megalin in the brain protects mice against high-fat diet challenge. J Neuroinflammation. 2020 Jan 14;17(1):22. doi: 10.1186/s12974-020-1702-2.

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Pursuing precision in medicine and nutrition: the rise of electrochemical biosensing at the molecular level

Campuzano S, Barderas R, Moreno-Casbas MT, Almeida A. Pursuing precision in medicine and nutrition: the rise of electrochemical biosensing at the molecular level. Anal Bioanal Chem 416, 2151–2172 (2024)

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Glucose-Induced b-Catenin Acetylation Enhances Wnt Signaling in Cancer

Chocarro-Calvo A, Garcia-Martinez JM, Ardila-González S, De la Vieja A and García-Jiménez C*. Glucose-Induced b-Catenin Acetylation Enhances Wnt Signaling in Cancer. Molecular Cell 2013 49(3):474-486. PMID: 23273980. doi: 10.1016/j.molcel.2012.11.022

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Experimental Radiation System for Effects Assessment in Biological in Vitro and in Vivo Models

V. Ramos, P. Marina, M. Torres-Ruiz, O. J. Suárez, V. López, I. Liste, M. de Alba. "Experimental Radiation System for Effects Assessment in Biological in Vitro and in Vivo Models," 2021 Photonics & Electromagnetics Research Symposium (PIERS), 2021, pp. 2800-2807, doi: 10.1109/PIERS53385.2021.9695112

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TREM2 expression in the brain and biological fluids in prion diseases

Diaz-Lucena D, Kruse N, Thüne K, Schmitz M, Villar-Piqué A, da Cunha JEG, Hermann P, López-Pérez Ó, Andrés-Benito P, Ladogana A, Calero M, Vidal E, Riggert J, Pineau H, Sim V, Zetterberg H, Blennow K, Del Río JA, Marín-Moreno A, Espinosa JC, Torres JM, Sánchez-Valle R, Mollenhauer B, Ferrer I, Zerr I, Llorens F. TREM2 expression in the brain and biological fluids in prion diseases. Acta Neuropathol. 2021 141(6):841-859. doi: 10.1007/s00401-021-02296-1.

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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 .