Collaborative Computational Tools for a Human Cell Atlas

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Projects

The goal of the Human Cell Atlas project is to create a shared, open reference atlas of all cells in the healthy human body as a resource for studies of health and disease. This global endeavor will generate a large variety of molecular and imaging data across a wide range of modalities and spatial scales. To analyze, interpret, and disseminate these data, these 85 projects will focus on creating new computational tools, algorithms, visualizations, and benchmark datasets. In the spirit of open, collaborative development, researchers will work together and share progress with each other to evaluate the strengths of different approaches.

Bioconductor

Bioconductor is a widely-used collection of open-source software packages for the genomics community, and these projects focus on enabling these tools to work with Human Cell Atlas data, and better handle the scale and complexity of the data likely to be encountered.

Cell States

Projects that aim to determine how a particular cell type can vary in gene expression related to stages of the cell cycle.

Cell Types

Projects focused on the fundamental problem of defining a cell type from single-cell RNA sequencing data, possibly alongside other data modalities, including both algorithmic and ontological challenges.

Compression

These projects leverage information theory to design better compression and feature extraction methods for single-cell RNA sequencing data, enabling cheaper storage of larger datasets, and possibly new insights into the structure of the data itself.

Imaging

Approaches using imaging map the spatial distribution of gene expression within cells and across cells within tissues. Computational tools here focus on new algorithms for visualizing and extracting features from these data, and sharing them with other researchers.

Latent Spaces

This group of projects models the diversity of measurements obtained from single-cell RNA sequencing as arising from some latent, low-dimensional representation, and focuses on how to best learn and interpret that representation.

Manifolds

These projects use concepts from manifold learning to better integrate datasets coming from a variety of sources, normalizing across variability due to noise in order to highlight the signal.

Multiomics

Projects that incorporate different characteristics of cells, like protein expression, epigenetics, and morphology, into the definition of cell type.

Populations

Approaches to population-scale single-cell genomics, including new experimental techniques for higher-throughput measurements, and approaches to solving the related computational challenges.

Portals

Projects building portals to data and analyses, including interactive user experiences for browing datasets and interacting with analysis pipelines, as well as novel visualizations to make new kinds of algorithms easier to understand.

Scale

These projects leverage new distributed computing methods to enable large-scale computation on the massive single-cell RNA sequencing datasets that the Human Cell Atlas will generate.

Trajectories

Projects that aim to understand the lineages of cell differentiation — the paths between cell types — based on patterns in gene expression.

A Classification of Cellular Processes Through Aggregation of Single-Cell Gene Expression Trajectories
Lead Investigator Josh Stuart
Institution University of California, Santa Cruz, United States
Focus Trajectories
A Comprehensive Benchmark Dataset for Comparison of Approaches Used to Infer Cell State Transition Dynamics
Lead Investigator Sahand Hormoz
Institution Dana-Farber Cancer Institute, United States
Focus Trajectories
A Force-Directed Graph Interface for HCA Data Visualization and Exploration
Lead Investigator Allon Klein
Institution Harvard University, United States
Focus Trajectories
A Notebook-Based Analysis Workspace for the Human Cell Atlas
Lead Investigator Jill Mesirov
Institution University of California, San Diego, United States
Focus Portals
A Pilot Tertiary Analysis Portal for the Human Cell Atlas
Lead Investigator Kerstin Meyer
Institution Wellcome Sanger Institute, United States
Focus Portals
A Pilot Tertiary Analysis Portal for the Human Cell Atlas
Lead Investigator Irene Papatheodorou
Institution EMBL-EBI, United Kingdom
Focus Portals
Accelerating Cross-Sample Analysis of Single-Cell Genomic Data with Adam and Apache Spark
Lead Investigator Anthony Joseph
Institution University of California, Berkeley, United States
Focus Scale
Aligning Biological Manifolds for Integrated Analysis of Single-Cell Data
Lead Investigator Oliver Stegle
Institution EMBL-EBI, United Kingdom
Focus Manifolds
Aligning Biological Manifolds for Integrated Analysis of Single-Cell Data
Lead Investigator Rahul Satija
Institution New York Genome Center, United States
Focus Manifolds
An Integrative Analysis Pipeline for Sequencing and Imaging-Based Gene Expression Data
Lead Investigator Guo-Cheng Yuan
Institution Dana-Farber Cancer Institute, United States
Focus Multiomics
An Interactive Environment for Exploratory Analysis of Large Single-Cell Datasets
Lead Investigator Matt Thomson
Institution California Institute of Technology, United States
Focus Scale
An Open, Extensible, Benchmark Platform To Evaluate Computational Tools for Single-Cell Differential Expression
Lead Investigator Matthew Stephens
Institution University of Chicago, United States
Focus Cell Types
Analysis of Molecular and Cellular Interactions by Combining Network Algorithms and Human Insight
Lead Investigator Benjamin Raphael
Institution Princeton University, United States
Focus Cell Types
Bayesian Sparse Matrix Factorization for Multimodal Integration
Lead Investigator Elana Fertig
Institution Johns Hopkins University, United States
Focus Latent Spaces
Benchmarking Single-Cell RNA-sequencing Methods
Lead Investigator Holger Heyn
Institution Fundació Centre de Regulació Genòmica (CRG-CNAG), Spain
Focus Cell Types
Bioinformatic Tools to Assess and Evaluate Identity at Single-Cell Resolution
Lead Investigator Samantha Morris
Institution Washington University, United States
Focus Cell Types
Cell Dynamics Portal
Lead Investigator Chris Sander
Institution Dana-Farber Cancer Institute, United States
Focus Trajectories
Cell Lineage Tracing Using Somatic Microsatellite Mutations
Lead Investigator Peter Park
Institution Harvard University, United States
Focus Trajectories
Cellbench: Generating Data and Software for Comparing Single-Cell Analysis Methods
Lead Investigator Matthew Ritchie
Institution Walter and Eliza Hall Institute, Australia
Focus Multiomics
Combining Crowdsourcing and Machine Learning for Image Segmentation and to Define Cell Type
Lead Investigator Arjun Raj
Institution University of Pennsylvania, United States
Focus Latent Spaces
Comparative Workbench for Atlas Data
Lead Investigator Mark Arends
Institution University of Edinburgh, United Kingdom
Focus Imaging
Comparative Workbench for Atlas Data
Lead Investigator Albert Burger
Institution Heriot-Watt University, United Kingdom
Focus Imaging
Compression of Structural, Cartographic, and Multimodal Cell Data
Lead Investigator Lav Varshney
Institution University of Illinois, Urbana-Champaign, United States
Focus Compression
Computational Inference of the Impact of Perturbations on Cell State
Lead Investigator Gerald Quon
Institution University of California, Davis, United States
Focus Cell States
Computational Methods for Single-Cell Analysis of Genetic Effects on Gene Expression
Lead Investigator Alexis Battle
Institution Johns Hopkins University, United States
Focus Populations
Computational Methods for Single-Cell Regulomics and Integrative Multiomics
Lead Investigator William Greenleaf
Institution Stanford University, United States
Focus Multiomics
Computational Tools for Traversing Genes to Cells to Disease
Lead Investigator Benjamin Neale
Institution Massachusetts General Hospital, United States
Focus Scale
Deep Space Exploration: Machine Learning to Understand and Annotate Image-Based Transcriptomics
Lead Investigator James Zou
Institution Stanford University, United States
Focus Imaging
Detection and Visualization of Temporal Partitioned Cellular States Using Single-Cell Analysis
Lead Investigator Benedict Anchang
Institution Stanford University, United States
Focus Cell States
Developing Single-Cell Interactomes to Identify Molecular Determinants of Single-Cell State
Lead Investigator Andrea Califano
Institution Columbia University, United States
Focus Cell States
Diffusion and Deep-Learning Based Methods for Exploratory Data Analysis
Lead Investigator Smita Krinshnaswamy
Institution Yale University, United States
Focus Latent Spaces
Efficient and Scalable Single-Cell RNA-seq Analysis Pipeline Exploiting Bayesian Non-Negative Matrix Factorization
Lead Investigator Gad Getz
Institution Massachusetts General Hospital, United States
Focus Scale
Efficient Tools for Quantifying and Simulating Transcript-Level Abundance in Single-Cell RNA-seq
Lead Investigator Robert Patro
Institution Stony Brook University, United States
Focus Latent Spaces
Enhancing the Accessibility of Large Single-Cell Datasets in R / Bioconductor
Lead Investigator John Marioni
Institution EMBL-EBI, United Kingdom
Focus Bioconductor
Flexible Statistical Methods for Differential Analysis of Single-Cell Datasets
Lead Investigator Mark Robinson
Institution University of Zurich, Switzerland
Focus Cell Types
Genome-Wide Hypothesis Generation for Single-Cell Expression via Latent Spaces
Lead Investigator Casey Greene
Institution University of Pennsylvania, United States
Focus Latent Spaces
Human Cell Atlas Integration with the Cytoscape Ecosystem for Analysis of scRNA-seq Data
Lead Investigator John Morris
Institution University of California, San Francisco, United States
Focus Portals
Human Cell Atlas Methods Registry
Lead Investigator Timothy Tickle
Institution The Broad Institute of MIT and Harvard, United States
Focus Portals
Identifying Genetic Markers: Dimension Reduction and Feature Selection for Sparse Data
Lead Investigator Anna Gilbert
Institution University of Michigan, United States
Focus Cell Types
Image Data Resources and Applications for the Human Cell Atlas
Lead Investigator Eric Banks
Institution The Broad Institute of MIT and Harvard, United States
Focus Imaging
Image Data Resources and Applications for the Human Cell Atlas
Lead Investigator Jason Swedlow
Institution University of Dundee, United Kingdom
Focus Imaging
Inferring the Tree of Cells
Lead Investigator Martin Hemberg
Institution Wellcome Sanger Institute, United Kingdom
Focus Trajectories
Integrating Single-Cell Profiles Across Modalities Using Manifold Alignment
Lead Investigator Joshua Welch
Institution University of Michigan, United States
Focus Manifolds
Integrative Multivariate Computational Methods for Single-Cell Assays
Lead Investigator Kim-Anh Le Cao
Institution University of Melbourne, Australia
Focus Multiomics
Interactive Identification of Trajectories in Single-Cell RNA-seq
Lead Investigator Fabian Theis
Institution Helmholtz Zentrum München, Germany
Focus Trajectories
Joint Analysis of Single-Cell and Bulk RNA Data via Matrix Factorization
Lead Investigator Clayton Scott
Institution University of Michigan, United States
Focus Cell Types
Joint Manifold Learning for Integrated Analysis of Single-Cell Data
Lead Investigator John Marioni
Institution EMBL-EBI, United Kingdom
Focus Manifolds
Machine Learning Approaches to Intersect Cellular Images and Single-Cell RNA-seq Data
Lead Investigator Barbara Engelhardt
Institution Princeton University, United States
Focus Multiomics
Machine Learning Methods for Fully Exploiting Heterogeneous, Multimodal Data
Lead Investigator Liam Paninski
Institution Columbia University, United States
Focus Multiomics
Methods to Enable Multiplexing of Single-Cell RNA-seq Experiments in Population Scale
Lead Investigator Hyun Min Kang
Institution University of Michigan, United States
Focus Populations
Nonparametric Manifold Learning for Imputation and Alignment in Single-Cell RNA-sequencing Data
Lead Investigator Barbara Engelhardt
Institution Princeton University, United States
Focus Manifolds
Pan-Omics Single-Cell Data Integration for Joint Cell Type Identification
Lead Investigator Ken Chen
Institution MD Anderson Cancer Center, United States
Focus Manifolds
Portal for the Interactive Analysis of Single-Cell RNA-seq Data
Lead Investigator Bart Deplancke
Institution EPFL, France
Focus Portals
Probabilistic Methods for Cell Classification
Lead Investigator Kenneth Harris
Institution University College London, United Kingdom
Focus Imaging
Quantization and Compressive Learning Methods for Omics Data
Lead Investigator Mikel Hernaez
Institution University of Illinois, Urbana-Champaign, United States
Focus Compression
Quantization and Compressive Learning Methods for Omics Data
Lead Investigator Olgica Milenkovic
Institution University of Illinois, Urbana-Champaign, United States
Focus Compression
Quantization and Compressive Learning Methods for Omics Data
Lead Investigator Idoia Ochoa
Institution University of Illinois, Urbana-Champaign, United States
Focus Compression
Rapid Exploration, Interpretation, and Comparison of Discrete Basis Vectors Contributing to Transcriptional Signatures of Single-Cells
Lead Investigator Loyal Goff
Institution Johns Hopkins University, United States
Focus Latent Spaces
Reconstruction of Cellular Trajectories via Optimal Transport
Lead Investigator Philippe Rigollet
Institution Massachusetts Institute of Technology, United States
Focus Trajectories
Scalable Interactive Analysis of Single-Cell Data with Apache Spark
Lead Investigator Uri Laserson
Institution Ichann at Mount Sinai, United States
Focus Scale
Search Tools for Larger scRNA-seq References
Lead Investigator Martin Hemberg
Institution Wellcome Sanger Institute, United Kingdom
Focus Portals
Semantically-Coherent & Statistically-Comparable Representation of Reference Cell Types
Lead Investigator Richard Scheuermann
Institution J. Craig Venter Institute, United States
Focus Cell Types
Semi-Supervised Generative Autoencoder Models for Single-Cell Data
Lead Investigator Merja Heinaniemi
Institution University of Eastern Finland, Finland
Focus Latent Spaces
Single-Cell Expression Visualization and its Integration into UCSC Xena
Lead Investigator Max Haeussler
Institution University of California, Santa Cruz, United States
Focus Portals
Single-Cell RNA-seq Analysis of Immune Activation Using Iteratively Adjusted Surrogate Variable Analysis
Lead Investigator Duygu Ucar
Institution Jackson Laboratory, United States
Focus Populations
Spectral Phenotyping
Lead Investigator Cynthia McMurray
Institution Lawerence Berkley National Lab, United States
Focus Imaging
Statistical Analysis and Comprehension of the Human Cell Atlas in R / Bioconductor: Access and Scalable Infrastructure
Lead Investigator Vincent Carey
Institution Brigham and Women’s Hospital, United States
Focus Bioconductor
Statistical Analysis and Comprehension of the Human Cell Atlas in R / Bioconductor: Access and Scalable Infrastructure
Lead Investigator Raphael Gottardo
Institution Fred Hutchinson Cancer Research Center, United States
Focus Bioconductor
Statistical Analysis and Comprehension of the Human Cell Atlas in R / Bioconductor: Access and Scalable Infrastructure
Lead Investigator Kasper Hansen
Institution Johns Hopkins University, United States
Focus Bioconductor
Statistical Analysis and Comprehension of the Human Cell Atlas in R / Bioconductor: Access and Scalable Infrastructure
Lead Investigator Wolfgang Huber
Institution EMBL-EBI, United Kingdom
Focus Bioconductor
Statistical Analysis and Comprehension of the Human Cell Atlas in R / Bioconductor: Access and Scalable Infrastructure
Lead Investigator Rafael Irizarry
Institution Dana-Farber Cancer Institute, United States
Focus Bioconductor
Statistical Analysis and Comprehension of the Human Cell Atlas in R / Bioconductor: Access and Scalable Infrastructure
Lead Investigator Martin Morgan
Institution Roswell Park Alliance Foundation, United States
Focus Bioconductor
Statistical Analysis and Comprehension of the Human Cell Atlas in R / Bioconductor: Access and Scalable Infrastructure
Lead Investigator Davide Risso
Institution Cornell University, United States
Focus Bioconductor
Statistical Methods for Characterizing Gene Regulatory Networks from Single-Cell Sequencing Data
Lead Investigator Harri Lahdesmaki
Institution Aalto University, Finland
Focus Cell States
Strategies for Lineage Trajectory Reconstruction with Single-Cell Multiomic Data
Lead Investigator Luca Pinello
Institution Massachusetts General Hospital, United States
Focus Trajectories
Subpopulation Identification from Single-Cell RNA-seq Data
Lead Investigator Peng Qiu
Institution Georgia Institute of Technology, United States
Focus Cell Types
The Draft Human Immune Census
Lead Investigator Jimmie Ye
Institution University of California, San Francisco, United States
Focus Populations
The Rosetta Project: Translating Data Across Single-Cell Technologies to Define Human Cell Types
Lead Investigator Anne Carpenter
Institution University of Michigan, United States
Focus Multiomics
Tools for Classification and Data Interaction with Labeled RNA-seq Data
Lead Investigator Colin Dewey
Institution University of Wisconsin-Madison, United States
Focus Cell Types
Tools for Integrated Analysis of Single-Cell Epigenomic and Transcriptomic Data
Lead Investigator Eran Mukamel
Institution University of California, San Diego, United States
Focus Multiomics
Tools for Integrating Single-Cell RNA-seq Studies with Genome-Wide Association Studies
Lead Investigator Xiang Zhou
Institution University of Michigan, United States
Focus Populations
Tools to Understand the Variation Within a Cell Type Using Evolutionary Tradeoff Theory
Lead Investigator Uri Alon
Institution Weizmann Institute of Science, Israel
Focus Cell States
UCSC Single-Cell Browser for the Visualization of Human Cell Atlas Data
Lead Investigator Jingchun Zhu
Institution University of California, Santa Cruz, United States
Focus Portals
Video Analysis: Efficiently Tracking and Detecting Life Cycle Phase Transitions for Live Cells
Lead Investigator Danna Gurari
Institution University of Texas, United States
Focus Imaging
Visualizing & Quantifying Mesoscale Structure & Organization in Human Cells
Lead Investigator Carolyn Larabell
Institution University of California, San Francisco, United States
Focus Imaging

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