Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq
Jul 27, 2020·


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Dr. Bo Li
†
Joshua Gould
Yiming Yang
S. sarkizova
M. tabaka
O. ashenberg
Y. rosen
M. slyper
M. s. kowalczyk
A. c. villani
T. l. tickle
N. hacohen
O. rozenblatt rosen
†
,A. regev
†
·
0 min readAbstract
Massively parallel single-cell and single-nucleus RNA-seq (sc/snRNA-seq) have opened the way to systematic tissue atlases in health and disease, but as the scale of data generation is growing, so does the need for computational pipelines for scaled analysis. Here, we developed Cumulus, a cloud-based framework for analyzing large scale sc/snRNA-seq datasets. Cumulus combines the power of cloud computing with improvements in algorithm implementations to achieve high scalability, low cost, user-friendliness, and integrated support for a comprehensive set of features. We benchmark Cumulus on the Human Cell Atlas Census of Immune Cells dataset of bone marrow cells and show that it substantially improves efficiency over conventional frameworks, while maintaining or improving the quality of results, enabling large-scale studies.
Type
Publication
Nature Methods

Authors
Principal Scientist II
Dr. Bo Li is a Principal Scientist II at AI for Biology and Translation (AIBT), Genentech, Inc. His research focuses on three major topics: Science, Technology and Computational Methods. For Science, his team works on lung cancer and especially small cell lung cancer. For Technology, his team evaluates and adopts cutting-edge high-throughput data generation technologies, such as Cellanome and SBX sequencing. For Computational Methods, his team develops novel computational and deep learning tools for enabling insight discovery from high-throughput multi-modal data.
Before joining in Genentech, he was an Assistant Professor of Medicine at Harvard Medical School and the director of Bioinformatics and Computational Biology at Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital.
He received his Ph.D. in computer science from UW-Madison and completed two postdoctoral trainings with Dr. Lior Pachter at UC Berkeley and Dr. Aviv Regev at Broad Institute.
He is best known for developing RSEM, an impactful RNA-seq transcript quantification software. RSEM is cited 22,602 times (Google Scholar) and adopted by several big consortia such as TCGA, ENCODE, GTEx and TOPMed.

Authors
Senior Research Software Engineer
Joshua Gould is a senior research software engineer in Li Lab.

Authors
Bioinformatics Software Engineer
Yiming Yang is a bioinformatics software engineer in Li Lab.
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