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Formalizing and benchmarking open problems in single-cell genomics

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Open Problems in Single-Cell Analysis

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Formalizing and benchmarking open problems in single-cell genomics.

Visit the Open Problems Website.

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The team

Core (alphabetically):

  • Daniel Burkhardt (@dburkhardt), Cellarity
  • Robrecht Cannoodt (@rcannood), Data Intuitive
  • Scott Gigante (@scottgigante-immunai), Immunai
  • Christopher Lance (@xlancelottx), Helmholtz Munich
  • Malte Luecken (@LuckyMD), Helmholtz Munich
  • Angela Pisco (@aopisco), CZ Biohub

Task leaders (alphabetically):

Full tasks (>1 datasets, >5 methods):

  • Batch integration - Daniel Strobl (@danielStrobl)
  • Cell-cell communication - Daniel Dimitrov (@dbdimitrov)
  • Dimensionality reduction - Michael Vinyard (@mvinyard) and Luke Zappia (@lazappi)
  • Label projection - Nick Markov (@mxposed)
  • Spatial deconvolution - Alma Anderson (@almaan) and Giovanni Palla (@giovp)

Task stubs:

  • Data denoising - Wes Lewis (@weslewis)
  • Multimodal data integration - The Open Problems core team

Tasks in discussion:

  • ATAC denoising - Dominik Otto (@katosh)
  • Differential abundance - Emma Dann (@emdann)
  • Regulatory effect prediction - Qian (Alvin) Qin (@qinqian)

Supervision (alphabetically):

  • Jonathan Bloom (@jbloom22)
  • Smita Krishnaswamy, Yale
  • Fabian Theis, Helmholtz Munich

Chan Zuckerberg Initiative Support (alphabetically):

  • Jonah Cool
  • Fiona Griffin
  • Ivana Williams

Contributors:

See the long list of all those who contributed datasets, methods, metrics, or infrastructure code here

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Formalizing and benchmarking open problems in single-cell genomics

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