Center for Human and Clinical Genetics - LUMC

(Centrum voor Humane en Klinische Genetica)

BioInformatics Groups and Aims

LGTC - Next-generation Sequencing Analysis

The group primarily works on analysis of next-generation sequencing (NGS) data, as well as providing advice to NGS users. This includes knowledge of how to handle different platforms and applications, as well as keeping up to date with current NGS analysis tools. We also develop our own in-house analysis pipelines and tools. An additional project of this group includes support of CORE_TF, a web site for identification of conserved and over-represented transcription factor binding sites in ChIP and expression data.

  • Michiel van Galen: data analysis support and tool developer
  • Jaap van der Heijden: genome variation data analysis and tool developer
  • Yuching Lai: genome variation data analysis and tool developer
  • Henk Buermans: micro-RNA data analysis and tool developer
  • Matthew Hestand: coordinator, data analysis support, and tool developer

  • Microarray Analysis

    The group works on different aspects of microarray data analysis, including platform comparison, sample size determination, and study design. In addition to expression profiling, we work on the analysis of different types of microarray data, e.g. array-CGH, SNP arrays, and methylation arrays. We develop new statistical tools for optimizing study design and for the analysis and integration of microarray experiments and apply them to genomics projects carried out within our institute.

  • Peter-Bram 't Hoen: developer and superuser of microarray analysis tools
  • Maarten van Iterson: statistical methods and tools for design, analysis, and integration of genomic experiments
  • Judith Boer: coordinator, developer, and superuser of microarray analysis tools

  • Databases and Annotation

    The group works on the development and maintenance of the web-based locus-specific database LOVD (Leiden Open source sequence Variation Database) and on proper nomenclature of sequence variations. This latter aspect, in the Mutalyzer package, also aims to determine the functional effects of sequence variations (under development).

  • Ivo Fokkema: LOVD and HCG database developer
  • Jacopo Celli: LOVD database set-up and curator support
  • Gerard Schaafsma: LOVD tool developer
  • Jeroen Laros: Development of algorithms and tools for sequence (variant) analysis and annotation
  • Peter Taschner: coordinator

  • BioSemantics

    The BioSemantics group investigates and develops new ways to analyse biological data and information through computational means. A prime focus is methodology for discovering hidden biological relations from text, biological databases, and knowledge held by experts; resources that go beyond a single researcher or a single group. In Leiden we focus on applying this research ('meta-analysis') to help build better hypotheses for a number of cases within the Human Genetics department. Thereby we establish a feedback loop between computer scientists, software developers and biologists. The group is a collaboration between the Center for Human and Clinical Genetics at theLeiden University Medical Center and the Medical Informatics department of the ErasmusMC University Medical Center of Rotterdam.

    LUMC members:
  • Herman van Haagen: research and tool developer
  • Bharat Singh: software developement
  • Peter-Bram 't Hoen: 'user expert' of BioSemantic methods
  • Marco Roos: project coordination and bioinformatics research, e-science liaison
  • Barend Mons: founder and senior advisor, founder of the Concept Web Alliance

  • BioInformatics Courses and Tutorials

  • DNA chip and array technology: "Analysis of microarray gene expression data" -Lectures & Practicals
  • Next-gen sequencing technology: "Next generation sequencing (NGS) data analysis "
  • Getting started in R: information for first time R users including several practicals for microarray data analysis

  • Tools originating from the department

  • Anni 2.1: a multipurpose text-mining tool for the life sciences
  • CORE_TF: Conserved and Over-REpresented Transcription Factor binding sites
  • LOVD: Leiden Open source sequence Variation Database
  • MaRe: Microarray Retriever
  • Mutalyzer: Sequence variant nomenclature check
  • SIM: Integrated Analysis on two human genomic datasets
  • SSPA: Sample Size and Power Analysis for Microarray Data

  • WWW-links originating from the department

  • Leiden Muscular Dystrophy data pages  (incl. muscular dystrophy mutation databases)
    Duchenne and Becker muscular dystrophy (DMD / BMD), Limb-Girdle muscular dystrophy (SCARMD, LGMD), diagnostic techniques
  • Classifying unclassified BRCA1/BRCA2 variants found in the Dutch population
  • ArrayNL platform: DNA chip & micro-array technology in Nederland

  • Vacancies and Internships

    Besides the listed vacancies we welcome you to contact any of the coordinators to inquery about positions or internships.

    If you have any comments or suggestions be sure to let us know.  mail to Matthew Hestand

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