Juan L. Mateo

Juan L. Mateo

Associate Professor

University of Oviedo

Biography

Juan Luis Mateo Cerdán is Associate Professor in the Department of Computer Science at the University of Oviedo. His research is focused on Machine Learning and Data Mining with application to biological problems, specially in Genomics.

Before he was at the University of Heidelberg from 2010 to 2016. There, in the Centre for Organismal Studies, was part of Joachim Wittbrodt’s lab where he worked along with biologists applying his data analysis skills to different problems. At the same time he acquired an invaluable knowledge and experience in several kinds of molecular biology experiments.

His research and teaching activity began at the University of Castilla-La Mancha, in the Sistemas Inteligentes y Minería de Datos (SIMD) group led by José Antonio Gámez Marín and José Miguel Puerta Callejón.

Interests
  • Bioinformatics
  • Genomics
  • Data Mining
  • Machine Learning
Education
  • PhD in Advanced Computer Technology, 2010

    University of Castilla-La Mancha

  • Master in Advanced Computer Technology, 2008

    University of Castilla-La Mancha

  • Engineering in Computer Science, 2002

    University of Castilla-La Mancha

  • Technical Engineering in Computer Science, 2000

    University of Castilla-La Mancha

Recent Publications

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Software

ACEofBASEs (a careful evaluation of BaseEdits) standalone

ACEofBASEs is a tool to determine sites to be editted with the CRISPR/Cas9 technology in a input sequence and predict its potential off-target sites. The online version of ACEofBASEs is available at http://aceofbases.cos.uni-heidelberg.de/

The standalone version has a command line interface designed to allow search of large volume of sequences and higher flexibility. Also advisable if the target genome is not publicly available.

Access ACEofBASEs standalone from my bitbucket site.

CCTop (CRISPR/Cas9 target online predictor) standalone

CCTop is a tool to determine suitable CRISPR target sites in a given query sequence(s) and predict its potential off-target sites. The online version of CCTop is available at http://cctop.cos.uni-heidelberg.de/

The standalone version has a command line interface designed to allow search of large volume of sequences and higher flexibility. Also advisable if the target genome is not publicly available.

Access CCTop standalone from my bitbucket site.

iDEAR (iDamID Enrichment Analysis with R)

iDEAR identifies the binding profile of a transcription factor (or any DNA binding protein) from iDamIDseq data according to our publication in Development.

Access iDEAR from my bitbucket site.

Teaching

Currently I teach at the University of Oviedo the following subjects:

  • Sistemas Inteligentes (Grado en Ingeniería Informática del Software)
  • Programming Methodology (Grado en Ingeniería Informática en Tecnologías de la Información)
  • Bioinformática (Máster Universitario en Biotecnología Aplicada a la Conservación y Gestión Sostenible de Recursos Vegetales)

Previously

  • Repositorios de Información (Grado en Ingeniería Informática del Software)
  • Sistemas Operativos (Grado en Ingeniería Informática en Tecnologías de la Información)
  • Tecnologías y Paradigmas de la Programación (Grado en Ingeniería Informática en Tecnologías de la Información)
  • Arquitectura del Software (Grado en Ingeniería Informática del Software)

At the University of Heidelberg I’ve taught these subjects (2014-2016):

  • Introduction to Statistical Analysis for Biologists with R (Bachelor in the Faculty of Biosciences)
  • Data Analysis with R (Bachelor in the Faculty of Biosciences)
  • Introduction to Genetics (Bachelor in the Faculty of Biosciences)
  • Statistics for Biology: design, analysis and visualization (Core course in the HBIGS International PhD Program in Molecular and Cellular Biology)

At the University of Castilla-La Mancha I taught these subjects (2006-2010):

  • Minería de Datos (Ingeniería Informática)
  • Bioinformática (Ingeniería Informática)
  • Metodología de la Programación (Ingeniería Informática)
  • Estructuras de Datos y de la Información (Ingeniería Informática)

Contact

  • +34 985 10 2943
  • Jesús Arias de Velasco s/n, 33005 Oviedo, Spain
  • Geology Faculty, 7th floor, Room 7-1