The scientist in me.

I create visual exploratory systems for biologists to help them make sense of their data. I am interested in how the ever-increasing amount of biomedical information can be efficiently visualized and managed at various scales.

Projects

  1. 4D Nucleome

    Active

    The 4D Nucleome program is a collaboration of doctors, biologists, and computational scientists working together to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development as well as various diseases. We are developing visualization methods and tools for exploring and analyzing the large amounts of datasets generated throughout the program.

    Responsibilities:
    • Data visualization
    • Data exploration
    Technologies:
    • JavaScript (ES6, D3, WebGL)
    • Python
    • SVG
    • CSS3
    • HTML5
  2. Connectomics

    Active

    Connectomics is the production and study of connectomes: comprehensive maps of connections within the mouse brain or eye. This project focuses on the segmentation, visualization and analysis of brain scans in electron and optical microscopy in the multi-terabyte range.

    Responsibilities:
    • Data compression
    Technologies:
    • Python
    Publications:
  3. The Refinery Platform is a web-based system for data management, data visualization, and analysis of biomedical data sets powered by an ISA-Tab-compatible data repository. Analyses are implemented as Galaxy workflows and executed through the Galaxy API.

    Responsibilities:
    • Data set exploration
    • Data set search
    • Web development
    Technologies:
    • JavaScript (ES6, D3)
    • Python
    • Java
    • Solr
    • Neo4J
    • PostgreSQL
    • SVG
    • CSS3
    • HTML5
    Publications:
  4. Caleydo is an open source visual analysis framework targeted at biomolecular data.

    Responsibilities:
    • Data visualization
    • Web development
    Technologies:
    • JavaScript (D3)
    • SVG
    • CSS3
    • HTML5
  5. 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 Web
    Technologies:
    • JavaScript
    • PHP
    • CSS3
    • SVG
    • HTML5
    • MySQL
    Publications:
  6. 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. CellFinder incorporates complex data exploration tools using visualization and analysis tools.

    Responsibilities:
    • Concepts
    • Web design
    • Web development
    Technologies:
    • PHP
    • JavaScript
    • MySQL
    • Omero
    • HTML5
    • CSS3

Publications

  1. 11
    Lekschas F, Bach B, Kerpedjiev P, Gehlenborg N, and Pfister H.
    HiPiler: Visual Exploration Of Large Genome Interaction Matrices With Interactive Small Multiples.
    IEEE Transactions on Visualization and Computer Graphics (InfoVis 17), 2018.
  2. 10
    Lekschas F and Gehlenborg N.
    SATORI: A System for Ontology-Guided Visual Exploration of Biomedical Data Repositories.
    Bioinformatics, btx739, 2017 .
  3. 9
    Dekker j, Belmont AS, Guttman M, Leshyk VO, Lis JT, Lomvardas S, Mirny LA, O'Shea CC, Park PJ, Ren B, Politz JCR, Shendure J, Zhong S, and the 4D Nucleome Network.
    The 4D nucleome project.
    Nature, 2017, 549, 219-226.
  4. 8
    Matejek B, Haehn D, Lekschas F, Mitzenmacher M, and Pfister H.
    Compresso: Efficient Compression of Segmentation Data For Connectomics.
    Proceedings of the International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI 2017), 2017, 781-788.
  5. 7
    Kerpedjiev P, Abdenur N, Lekschas F, McCallum C, Dinkla K, Strobelt H, Luber J, Ouellette S, Ahzir A, Kumar N, Hwang J, Alver B, Pfister H, Mirny L, Park P, and Gehlenborg N.
    HiGlass: Web-based Visual Comparison And Exploration Of Genome Interaction Maps.
    bioRxiv, 2017.
  6. 6
    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., 2016, 44 (D1), D757-D763.
  7. 5
    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.
  8. 4
    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.
  9. 3
    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., 2014, 42 (D1), D950-D958.
  10. 2
    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.
  11. 1
    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.

Theses

  1. 2
    Ontology-guided exploration of biomedical data repositories.
    Master of Science, Freie Universität Berlin, 2016.
  2. 1
    Semantic Body Browser: A web-based tool for graphically exploring an organism’s body in respect to the CELDA ontology.
    Bachelor of Science, Freie Universität Berlin, 2012.

Talks

  1. 3
    Paper Talk, IEEE VIS (InfoVis), Phoenix (Oct 2017)
  2. 2
    Invited Talk, Harvard - Novartis Machine Learning and Computational Meeting, Cambridge (Sep 2017)
  3. 1
    Session Talk, 4D Nucleome Annual Meeting, Bethesda (Sep 2017)

Reviews