Computational Biology and Systems Biomedicine

Group leader: Dr. Marcos J. Araúzo-Bravo, Ph.D.

Biodonostia HRI. Ikerbasque Research Professor. marcos.arauzo@biodonostia.org

Strategic Objectives

  • Development of computational methods for the analysis and modeling of biological systems and their utilization for elucidating better understanding of stem cells, cellular reprogramming stem cells, diseases and aging mechanisms.
  • Study the interaction of biological networks (genetic, epigenetic, metabolic, and proteomic) in terms of their typology, perturbation response and dynamics.
  • Development of artificial vision methods for the automatic analysis and characterization of cellular and subcellular structures from static and dynamic images.
  • Development of data mining methods for medical histories analysis based on artificial intelligent technics to predict health condition, diseases and aging.
  • Synergetic integration of the “macroscopic” information provided by the medical histories data with the “microscopic” information provided by image data with the “molecular” information provided by the omics data for better understanding of human diseases and aging.
  • Exploration of how genetic variations between individuals influence their cell biological functions and – ultimately – disease, using a combination of iPSC technology and –omics data.

Main research lines

In mathematical modeling of biological systems

  • De novo prediction of genomic regulatory hot spots as building blocks for mathematical models of the cross-talk between genetic and epigenetic networks.
  • Biological network analysis. By perturbing network components, analyze the induced changes in their performance to understand the synergistic and antagonistic effects of the perturbations. Developing methods to identify the typology and the dynamics of the biological networks analyzing network properties such as the presence of motifs, and integrating systems engineering tools for the analysis of stability of controllability, robustness, response to perturbation and stochasticity. Application for better understanding of stem cells, cellular reprogramming, disease states, disease progression and aging mechanisms.
  • Identification and characterization of regulatory cores in pluripotent networks, in stem cells, in diseases and in aging.
  • Development of dynamical models to understand the genetic regulatory networks of pluripotent cells, cellular reprogramming, stem cells, diseases and aging.

In bioinformatics

  • Computational quality control of pluripotent cells by high throughput transcriptomics and epigenomics data analysis.
  • Integration of transcriptomics data form different platforms to create big corpus datasets.
  • Development of computational tools to exploit high throughput data, integrating omics data of different nature (transcriptomics, Chip-Seq, DNA methylomics, histone marks, microRNA expression and proteomics).
  • Implementation of data integrative approaches from different omic technologies to elucidate the cross-talk of the main molecular players of pluripotent cells, stem cells, diseases and aging.
  • Develop upstream and downstream statistical/machine learning analysis tools for mining next-generation sequencing data (RNAseq, ChIp-Seq of histone modification, and genome-wide DNA methylation.
  • Identification of targets for direct reprogramming
  • Identification of biomarkers for cancer research.
  • Search of DNA sequence patterns and DNA words for building DNA dictionaries and grammars.
  • Development of data mining methods for medical histories based on artificial intelligent strategies to predict health condition, diseases and aging.

Team Members

Name Surname
Center E-mail
Coloma Álvarez De Eulate López Donostialdea IHO elena.guimonolaizola@osakidetza.eus
Mikel Arrospide Elgarresta Biodonostia HRI mikel.arrospide@biodonostia.org
Javier Cabau Laporta Biodonostia HRI javier.cabau@biodonostia.org
Daniela Ivanova Gerovska Biodonostia HRI daniela.gerovska@biodonostia.org
Olga Ibañez Sole Biodonostia HRI olga.ibanez@biodonostia.org
Vadym Ivanchuk Onkologikoa ivanchuk.vadym@gmail.com
Shira Knafo CSIC, UPV/EHU s.knafo@ikerbasque.org
Alex Martínez Ascensión Biodonostia HRI  alex.martinez@biodonostia.org

 

Scientific Output

Originals

Published: 10 / 76

A mechanism for the segregation of age in mammalian neural stem cells.

Moore DL, Pilz GA, Arauzo-Bravo MJ, Barral Y, Jessberger S.

Science. 2015; 349: 1334-1338. FI: 33.611 (Q1).

Direct Induction of Trophoblast Stem Cells from Murine Fibroblasts.

Kubaczka C, Senner CE, Cierlitza M, Arauzo-Bravo MJ, Kuckenberg P, Peitz M, Hemberger M, Schorle H.

Cell Stem Cell. 2015; 17: 557-568. FI: 22.268 (Q1).

MicroRNA-199a-5p inhibition enhances the liver repopulation ability of human embryonic stem cell-derived hepatic cells.

Moebus S, Yang D, Yuan Q, Luedtke TH, Balakrishnan A, Sgodda M, Rani B, Kispert A, Arauzo-Bravo MJ, Vogel A, Manns MP, Ott M, Cantz T, Sharma AD.

J. Hepatol. 2015; 62: 101-110. FI: 11.336 (Q1).

Human primordial germ cell commitment in vitro associates with a unique PRDM14 expression profile.

Sugawa F, Arauzo-Bravo MJ, Yoon J, Kim KP, Aramaki S, Wu G, Stehling,M, Psathaki OE, Huebner K, Schoeler HR.

Embo J. 2015; 34: 1009-1024. FI: 10.434 (Q1).

Oct4-induced oligodendrocyte progenitor cells enhance functional recovery in spinal cord injury model.

Kim JB, Lee H, Araúzo-Bravo MJ, Hwang K, Nam D, Park MR, Zaehres H, Park KI, Lee SJ.

Embo J.2015; 34: 2971-2983. FI: 10.434 (Q1).

Hypoxia Induces Pluripotency in Primordial Germ Cells by HIF1 alpha Stabilization and Oct4 Deregulation.

Lopez-Iglesias P, Alcaina Y, Tapia N, Sabour D, Arauzo-Bravo MJ, Sainz de la Maza D, Berra E, Nunez A, Nistal M, Ortega S, Donovan PJ, Schoeler HR, De Miguel MP.

Antioxid. Redox Signal. 2015; 22: 205-223. FI: 7.407 (Q1).

Universal Cardiac Induction of Human Pluripotent Stem Cells in Two and Three-Dimensional Formats: Implications for In Vitro Maturation.

Zhang, M, Schulte JS, Heinick A, Piccini I, Rao J, Quaranta R, Zeuschner D, Malan D, Kim KP, Roepke A, Sasse P, Arauzo-Bravo M, Seebohm G, Schoeler H, Fabritz L, Kirchhof P, Mueller FU, Greber B.

Stem Cells. 2015; 33: 1456-1469. FI: 6.523 (Q1).

Erythroid differentiation of human induced pluripotent stem cells is independent of donor cell type of origin.

Dorn I, Klich K, Arauzo-Bravo MJ, Radstaak M, Santourlidis S, Ghanjati F, Radke TF, Psathaki OE, Hargus G, Kramer J, Einhaus M, Kim JB, Koegler G, Wernet P, Schoeler HR, Schlenke P, Zaehres H.

Haematologica. 2015; 100: 32-41. FI: 5.814 (Q1).

Perivascular Mesenchymal Stem Cells From the Adult Human Brain Harbor No Instrinsic Neuroectodermal but High Mesodermal Differentiation Potential.

Lojewski X, Srimasorn S, Rauh J, Francke S, Wobus M, Taylor V, Arauzo-Bravo MJ, Hallmeyer-Elgner S, Kirsch M, Schwarz S, Schwarz J, Storch A, Hermann A.

Stem Cells Transl. Med. 2015; 4: 1223-1233. FI: 5.709 (Q1).

Methods for extracellular vesicles isolation in a hospital setting.

Saenz-Cuesta M, Arbelaiz A, Oregi A, Irizar H, Osorio-Querejeta I, Munoz-Culla M, Banales JM, Falcon-Perez JM, Olascoaga J, Otaegui D.

Front. Immunol. 2015; 6. FI: 5.695 (Q1).

Reviews

Published: 1 / 1

Measuring the impact of informal elderly caregiving: a systematic review of tools.

Mosquera I, Vergara I, Larrañaga I, Machón M, del Río M, Calderón C.

Quality Of Life Research. 2016; 25: 1059-1092. FI: 2,344 (Q1).

Editorials

Published: 0 / 0

Letters

Published: 0 / 0

Others

Published: 2 / 2

Armonización de bases de datos para el estudio de la fragilidad en personas mayores: Estudio INTAFRADE.

Machón M, Egüés N, Martínez N, Abellán van Kan G, Calderón-Larrañaga A, Aldaz P, Poblador-Plou B, Vrotsou K, Clerencia-Sierra M, Prados-Torres A, Vergara I.

Revista Espanola De Geriatria Y Gerontologia. 2016; 51: 29-36.

Situación actual de la investigación sobre las condiciones de vida y el estado de salud de las personas mayores en España.

Machón-Sobrado M, Vergara-Mitxeltorena I, Dorronsoro-Iraeta M, Larrañaga-Larrañaga N, Vrotsou K, Larrañaga-Padilla I.

Enfermería Clínica. 2016; 26: 15-22.

Projects

Projects 1 / 1

Asociación entre el “Dietary Inflammatory Index” (DII) y los biomarcadores proinflamatorios en el envejecimiento y su relación con la fragilidad.

Investigador principal: María Nerea Egüés Olazábal. Entidad financiadora: Gobierno Vasco, Departamento de Salud. Año inicio: 2014. Año final: 2017.