Some bits about myself.

I am a prospective Ph.D. student in computer science at Harvard John A. Paulson School of Engineering and Applied Sciences in Hanspeter Pfister's Visual Computing Group.

I received my Bachelor's and Master's in bioinformatics from the Free University of Berlin and previously joined Peter J. Park's and Nils Gehlenborg's labs in the Department of Biomedical Informatics at Harvard Medical School as a visiting postgrad research fellow for one year.

From 2010 to 2015, I was a research assistant in Andreas Kurtz's knowledge management and stem cell group at the Berlin-Brandenburg Center for Regenerative Therapies at Charité - University Hospital Berlin. I have been the main web developer behind CellFinder and Semantic Body Browser and front-end engineer at hPSCreg.

I am deeply interested in understanding fundamental cellular processes and characteristics, especially cell fate and identity. I am seeking to make sense of the vast amount of diverse sequencing data combining the best from computational biology, computer science and data visualization to build intuitive and user-friendly applications that remove bottlenecks in biomedical research and aid clinical translation. I greatly enjoy working in interdisciplinary teams, evaluating different points of view to bridge gaps and think outside the box. Having lived and worked in South Korea, Japan, the United Kingdom, and the United States convinced me to never stop learning and seeking for more.

Research Projects

  1. SATORI

    A System for Ontology-Guided Visual Exploration of Biomedical Data Repositories.

    Responsibilities:
    • Data visualization
    • Semantic data integration
    • Web development
    Technologies:
    • JavaScript (D3)
    • Java
    • Solr
    • Neo4J
    • SVG
    • CSS3
    • HTML5
  2. Caleydo

    Caleydo is an open source visual analysis framework targeted at biomolecular data.

    Responsibilities:
    • Data visualization
    • Web development
    Technologies:
    • JavaScript (D3)
    • SVG
    • CSS3
    • HTML5
  3. Refinery Platform

    The Refinery Platform is a web-based data visualization and analysis system powered by an ISA-Tab-compatible data repository for public and private data sets. Analyses are implemented as Galaxy workflows and executed through the Galaxy API.

    Responsibilities:
    • Data set exploration
    • Web development
    Technologies:
    • JavaScript
    • Python
    • Java
    • Solr
    • Neo4J
    • SVG
    • CSS3
    • HTML5
    • PostgreSQL
  4. Human Pluripotent Stem Cell Registry

    The Human Pluripotent Stem Cell Registry (hPSCreg) was created to offer the research community, legislators, regulators and the general public at large an in-depth overview on the current status of human pluripotent stem cell research in Europe.

    Responsibilities:
    • Web design
    • Web development
    • Semantics
    Technologies:
    • JavaScript
    • PHP
    • CSS3
    • SVG
    • HTML5
    • MySQL
  5. Semantic Body Browser

    The Semantic Body Browser (SBB) is a web application for intuitively exploring the body of an organism from the organ to the sub-cellular level and visualising expression profiles by means of semantically annotated illustrations. It is used to comprehend biological and medical data related to the different body structures while relying on the strong pattern recognition capabilities of human users.

    Responsibilities:
    • Concept
    • Design
    • Implementation
    Technologies:
    • JavaScript
    • CSS3
    • SVG
    • PHP
    • RDFa
    • HTML5
    • R
  6. CellFinder

    CellFinder maps validated gene and protein expression, phenotype and images related to cell types. The data allow characterization and comparison of cell types and can be browsed by using the body browser and by searching for cells or genes. All cells are related to more complex systems such as tissues, organs and organisms and arranged according to their position in development.

    Responsibilities:
    • Concept
    • Web design
    • Web development
    Technologies:
    • PHP
    • JavaScript
    • HTML5
    • CSS3
    • MySQL
    • Omero
  7. StemReg

    The aims of the project are to explore the stem cell niche and epigenetic changes that accompany cellular senescence, to determined to what degree cellular senescence in vitro reflects processes that characterize stem cell ageing in vivo, to develop and apply biosensor technology for the sensitive detection and monitoring of senescence-associated changes of stem cells and their micro environment.

    Responsibilities:
    • Web design
    • Web development
    Technologies:
    • PHP
    • HTML5
    • CSS3

Publications

  1. Seltmann S*, Lekschas F*, Müller R*, Stachelscheid H*, Bittner MS, Zhang W, Kidane L, Seriola A, Veiga A, Stacey G and Kurtz A. (* Joint first authors)
    hPSCreg - the human pluripotent stem cell registry.
    Nucleic Acids Res., 2015. DOI | PubMed
  2. Amrani K, Stachelscheid H, Lekschas F, Kurtz A and Andrade-Navarro M.
    MGFM: a novel tool for detection of tissue and cell specific marker genes from microarray gene expression data.
    BMC Genomics, 2015, 16: 645. DOI | PubMed
  3. Lekschas F, Stachelscheid H, Seltmann S and Kurtz A.
    Semantic Body Browser: graphical exploration of an organism and spatially resolved expression data visualization.
    Bioinformatics, 2014, 31 (5), 794-796. DOI | PubMed
  4. Stachelscheid H*, Seltmann S*, Lekschas F*, Fontaine JF, Mah N, Neves M, Andrade-Navarro M, Leser U and Kurtz A. (* Joint first authors)
    CellFinder: A Cell Data Repository.
    Nucleic Acids Res., 2013, 42, D950-D958. DOI | PubMed
  5. Seltmann S, Stachelscheid H, Damaschun A, Jansen L, Lekschas F, Fontaine JF, Nguyen-Dobinsky TN, Leser U and Kurtz A.
    CELDA - an ontology for the comprehensive representation of cells in complex systems.
    BMC Bioinformatics, 2013, 14: 228. DOI | PubMed
  6. Neves M, Damaschun A, Mah N, Lekschas F, Seltmann S, Stachelscheid H, Fontaine JF, Kurtz A and Leser U.
    Preliminary evaluation of the CellFinder literature curation pipeline for gene expression in kidney cells and anatomical parts.
    Database, 2013: bat020. DOI | PubMed