Topslam: Waddington Landscape Recovery for Single Cell Experiments [article]

Max Zwiessele, Neil D Lawrence
2016 bioRxiv   pre-print
We present an approach to estimate the nature of the Waddington (or epigenetic) landscape that underlies a population of individual cells. Through exploiting high resolution single cell transcription experiments we show that cells can be located on a landscape that reflects their differentiated nature. Our approach makes use of probabilistic non-linear dimensionality reduction that respects the topology of our estimated epigenetic landscape. In simulation studies and analyses of real data we
more » ... w that the approach, known as topslam, outperforms previous attempts to understand the differentiation landscape. Hereby, the novelty of our approach lies in the correction of distances before extracting ordering information. This gives the advantage over other attempts, which have to correct for extracted time lines by post processing or additional data.
doi:10.1101/057778 fatcat:wnedwz6wrbajnjqm6uwb5f4f7u