Author

David Wadden

Broad Institute

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 2 Genomics· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 3 Research Focus:benchmarking· 2 Assay:bulk RNA-seq· 2 Research Focus:differential expression· 2 Research Focus:gene regulatory network inference· 2 Approach:benchmark study· 1 Research Focus:database / resource· 1 Research Focus:drug response / drug discovery· 1

Frequent Co-Authors

Aravind SubramanianiD· 3 shared David L. LahriD· 3 shared Rajiv Narayan· 3 shared Corey Flynn· 2 shared David E. RootiD· 2 shared Ian C. P. SmithiD· 2 shared Jacob K. Asiedu· 2 shared John G. DoenchiD· 2 shared

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2017-2018 · peak 2/yr

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3 shared papersBioinformatics

Aravind SubramanianORCID

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3 papers

Recent·Most cited

The GCTx format and cmap{Py, R, M} packages: resources for the optimized storage and integrated traversal of dense matrices of data and annotations

Oana M. Enache, David L. Lahr, Ted E. Natoli, Lev Litichevskiy, David Wadden, Corey Flynn, Joshua Gould, Jacob K. Asiedu, Rajiv Narayan, Aravind Subramanian

The paper introduces the GCTx format and associated software packages for efficiently storing and analyzing large dense matrices of perturbation data and annotations.

bioRxiv · Jan 3, 2018 · PreprintBioinformatics

Evaluation of RNAi and CRISPR technologies by large-scale gene expression profiling in the Connectivity Map

Ian C. P. Smith, Peyton Greenside, Ted E. Natoli, David L. Lahr, David Wadden, Itay Tirosh, Rajiv Narayan, David E. Root, Todd R. Golub, Aravind Subramanian, John G. Doench

The paper evaluates RNAi and CRISPR technologies by analyzing gene expression profiles in the Connectivity Map, finding that RNAi has strong off-target effects while CRISPR is more accurate.

PLoS Biology · Nov 30, 2017Peer-reviewedBioinformatics

A Next Generation Connectivity Map: L1000 Platform And The First 1,000,000 Profiles

Aravind Subramanian, Rajiv Narayan, Steven M. Corsello, David D. Peck, Ted Natoli, Xiaodong Lü, Joshua Gould, John F. Davis, Andrew A. Tubelli, Jacob K. Asiedu, David L. Lahr, Jodi Hirschman, Zihan Liu, Melanie K. Donahue, Bina Julian, , Todd R. Golub

The paper introduces the L1000 platform, a high-throughput gene expression profiling method, and reports 1.3 million perturbational profiles expanding the Connectivity Map for drug mechanism discovery and functional annotation.

Cell · Nov 1, 2017Peer-reviewedGenomics