Topslam: Waddington Landscape Recovery for Single Cell Experiments

Max ZwiesseleNeil D. Lawrence
, 2016.

Abstract

We present an approach to estimating 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 show that the approach, known as , 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.

Cite this Paper


BibTeX
@Misc{Zwiessele:topslam16, title = {Topslam: Waddington Landscape Recovery for Single Cell Experiments}, author = {Max Zwiessele and Neil D. Lawrence}, year = {2016}, doi = {10.1101/057778}, abstract = {We present an approach to estimating 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 show that the approach, known as , 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.} }
Endnote
%0 Generic %T Topslam: Waddington Landscape Recovery for Single Cell Experiments %A Max Zwiessele %A Neil D. Lawrence %D 2016 %F Zwiessele:topslam16 %R 10.1101/057778 %X We present an approach to estimating 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 show that the approach, known as , 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.
RIS
TY - GEN TI - Topslam: Waddington Landscape Recovery for Single Cell Experiments AU - Max Zwiessele AU - Neil D. Lawrence DA - 2016/06/20 ID - Zwiessele:topslam16 DO - 10.1101/057778 AB - We present an approach to estimating 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 show that the approach, known as , 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. ER -
APA
Zwiessele, M. & Lawrence, N.D.. (2016). Topslam: Waddington Landscape Recovery for Single Cell Experiments. doi:10.1101/057778

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