`

Timezone: »

 
A sandbox for prediction and integration of DNA, RNA, and proteins in single cells
Malte Luecken · Daniel Burkhardt · Robrecht Cannoodt · Christopher Lance · Aditi Agrawal · Hananeh Aliee · Ann Chen · Louise Deconinck · Angela Detweiler · Alejandro Granados · Shelly Huynh · Laura Isacco · Yang Kim · Dominik Klein · BONY DE KUMAR · Sunil Kuppasani · Heiko Lickert · Aaron McGeever · Honey Mekonen · Joaquin Melgarejo · Maurizio Morri · Michaela Müller · Norma Neff · Sheryl Paul · Bastian Rieck · Kaylie Schneider · Scott Steelman · Michael Sterr · Daniel Treacy · Alexander Tong · Alexandra-Chloe Villani · Guilin Wang · Jia Yan · Ce Zhang · Angela Pisco · Smita Krishnaswamy · Fabian Theis · Jonathan M Bloom

The last decade has witnessed a technological arms race to encode the molecular states of cells into DNA libraries, turning DNA sequencers into scalable single-cell microscopes. Single-cell measurement of chromatin accessibility (DNA), gene expression (RNA), and proteins has revealed rich cellular diversity across tissues, organisms, and disease states. However, single-cell data poses a unique set of challenges. A dataset may comprise millions of cells with tens of thousands of sparse features. Identifying biologically relevant signals from the background sources of technical noise requires innovation in predictive and representational learning. Furthermore, unlike in machine vision or natural language processing, biological ground truth is limited. Here we leverage recent advances in multi-modal single-cell technologies which, by simultaneously measuring two layers of cellular processing in each cell, provide ground truth analogous to language translation. We define three key tasks to predict one modality from another and learn integrated representations of cellular state. We also generate a novel dataset of the human bone marrow specifically designed for benchmarking studies. The dataset and tasks are accessible through an open-source framework that facilitates centralized evaluation of community-submitted methods.

Author Information

Malte Luecken (Helmholtz Center Munich)

* Computational biologist * Multimodal single-cell data integration challenge organizer * Single-cell data integration * Benchmarking

Daniel Burkhardt (Cellarity)
Robrecht Cannoodt (Data Intuitive)
Christopher Lance (Helmholtz Center Munich)
Aditi Agrawal (Chan Zuckerberg Biohub)
Hananeh Aliee (Computational Biology)

I am a postdoctoral researcher in computational biology working in the ngroup of Prof. Fabian Theis. I did my phd in Computer Science.

Ann Chen (Chan Zuckerberg Biohub)
Louise Deconinck (Ghent University)
Angela Detweiler
Alejandro Granados
Shelly Huynh (University of California, Santa Cruz)
Laura Isacco (Cellarity)
Yang Kim
Dominik Klein (Helmholtz Munich)
BONY DE KUMAR (Yale University)
Sunil Kuppasani (Rutgers University)
Heiko Lickert
Aaron McGeever
Honey Mekonen
Joaquin Melgarejo
Maurizio Morri
Michaela Müller
Norma Neff
Sheryl Paul
Bastian Rieck (Institute of AI for Health, Helmholtz Centre Munich)
Kaylie Schneider (Friedman School of Nutrition Science and Policy, Tufts University)
Scott Steelman
Michael Sterr (None)
Daniel Treacy (Cellarity)
Alexander Tong (Yale University; MILA; UdeM)
Alexandra-Chloe Villani
Guilin Wang (Yale University)
Jia Yan
Ce Zhang (Yale University)
Angela Pisco
Smita Krishnaswamy (Yale University)
Fabian Theis (Helmholtz Munich)
Jonathan M Bloom (Cellarity)

More from the Same Authors

  • 2021 : Multimodal Single-Cell Data Integration + Q&A »
    Daniel Burkhardt · Smita Krishnaswamy · Malte Luecken · Debora Marks · Angela Pisco · Bastian Rieck · Jian Tang · Alexander Tong · Fabian Theis · Guy Wolf
  • 2020 : Closing Remarks »
    Frederic Chazal · Smita Krishnaswamy · Roland Kwitt · Karthikeyan Natesan Ramamurthy · Bastian Rieck · Yuhei Umeda · Guy Wolf
  • 2020 Workshop: Learning Meaningful Representations of Life (LMRL.org) »
    Elizabeth Wood · Debora Marks · Ray Jones · Adji Bousso Dieng · Alan Aspuru-Guzik · Anshul Kundaje · Barbara Engelhardt · Chang Liu · Edward Boyden · Kresten Lindorff-Larsen · Mor Nitzan · Smita Krishnaswamy · Wouter Boomsma · Yixin Wang · David Van Valen · Orr Ashenberg
  • 2020 Workshop: Topological Data Analysis and Beyond »
    Bastian Rieck · Frederic Chazal · Smita Krishnaswamy · Roland Kwitt · Karthikeyan Natesan Ramamurthy · Yuhei Umeda · Guy Wolf
  • 2020 : Opening Remarks »
    Frederic Chazal · Smita Krishnaswamy · Roland Kwitt · Karthikeyan Natesan Ramamurthy · Bastian Rieck · Yuhei Umeda · Guy Wolf
  • 2020 Poster: Uncovering the Topology of Time-Varying fMRI Data using Cubical Persistence »
    Bastian Rieck · Tristan Yates · Christian Bock · Karsten Borgwardt · Guy Wolf · Nicholas Turk-Browne · Smita Krishnaswamy
  • 2020 Spotlight: Uncovering the Topology of Time-Varying fMRI Data using Cubical Persistence »
    Bastian Rieck · Tristan Yates · Christian Bock · Karsten Borgwardt · Guy Wolf · Nicholas Turk-Browne · Smita Krishnaswamy
  • 2019 : Cell »
    Anne Carpenter · Jian Zhou · Maria Chikina · Alexander Tong · Ben Lengerich · Aly Abdelkareem · Gokcen Eraslan · Stephen Ra · Daniel Burkhardt · Frederick A Matsen IV · Alan Moses · Zhenghao Chen · Marzieh Haghighi · Alex Lu · Geoffrey Schau · Jeff Nivala · Miriam Shiffman · Hannes Harbrecht · Levi Masengo Wa Umba · Joshua Weinstein
  • 2019 : Phenotype »
    Nir HaCohen · David Reshef · Matthew Johnson · Sam Morris · Aurel Nagy · Gokcen Eraslan · Meromit Singer · Eliezer Van Allen · Smita Krishnaswamy · Casey Greene · Scott Linderman · Alexander Wiltschko · Dylan Kotliar · James Zou · Brendan Bulik-Sullivan
  • 2019 Poster: Wasserstein Weisfeiler-Lehman Graph Kernels »
    Matteo Togninalli · Elisabetta Ghisu · Felipe Llinares-Lopez · Bastian Rieck · Karsten Borgwardt
  • 2019 Spotlight: Wasserstein Weisfeiler-Lehman Graph Kernels »
    Matteo Togninalli · Elisabetta Ghisu · Felipe Llinares-López · Bastian Rieck · Karsten Borgwardt
  • 2019 Poster: Visualizing the PHATE of Neural Networks »
    Scott Gigante · Adam S Charles · Smita Krishnaswamy · Gal Mishne
  • 2018 Poster: Geometry Based Data Generation »
    Ofir Lindenbaum · Jay Stanley · Guy Wolf · Smita Krishnaswamy
  • 2018 Spotlight: Geometry Based Data Generation »
    Ofir Lindenbaum · Jay Stanley · Guy Wolf · Smita Krishnaswamy