Education and Presentations

    Software, Web Applications, and Online Databases

    CellNet: network biology-based computational platform to assess establishment of cell type specific gene regulatory networks in user-provided gene expression profiles.

    • StemSite database of regulators of the developmental origin of mouse hematopoietic stem cells.

    • WUHMMM (Washington University Hidden Markov Model): an algorithm for detecting DNA copy number variants from oligonucleotide array comparative genomic hybridization (aCGH) data. This package also contains an algorithm for assigning discrete CNV-region genotypes when multiple samples are available and data visualization tools. No longer updated or supported.


    • A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo. Stem Cell Research. 2018 Aug;31:201-215. GSE114220

    • Deconstructing transcriptional heterogeneity in pluripotent stem cells. Nature. 2014 Dec 4;516(7529):56-61. GSE60749

    • Dissecting Engineered Cell Types and Enhancing Cell Fate Conversion via CellNet. Cell. 2014 Aug 14;158(4):889-902. GSE59037

    • The transcriptional landscape of hematopoietic stem cell ontogeny. Cell Stem Cell. 2012 Nov 2;11(5):701-14. StemSite and GSE37000

    • The impact of copy number variation on local gene expression in mouse hematopoietic stem and progenitor cells. Nature Genetics. 2009 Apr;41(4):430-7. GSE10656

    • wuHMM: a robust algorithm to detect DNA copy number variation using long oligonucleotide microarray data. Nucleic Acids Research. 2008 Apr;36(7):e4. GSE10511