A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles.
Aravind Subramanian,Rajiv Narayan,Steven M. Corsello,Steven M. Corsello,David Peck,Ted Natoli,Xiaodong Lu,Joshua Gould,John F. Davis,Andrew A. Tubelli,Jacob K. Asiedu,David L. Lahr,Jodi E. Hirschman,Zihan Liu,Melanie Donahue,Bina Julian,Mariya Khan,David Wadden,Ian Smith,Daniel D. Lam,Arthur Liberzon,Courtney Toder,Mukta Bagul,Marek Orzechowski,Oana M. Enache,Federica Piccioni,Sarah A. Johnson,Nicholas J. Lyons,Alice H. Berger,Alice H. Berger,Alykhan F. Shamji,Angela N. Brooks,Angela N. Brooks,Anita Vrcic,Corey Flynn,Jacqueline Rosains,David Y. Takeda,David Y. Takeda,Roger Hu,Desiree Davison,Justin Lamb,Kristin Ardlie,Larson Hogstrom,Peyton Greenside,Nathanael S. Gray,Nathanael S. Gray,Paul A. Clemons,Serena J. Silver,Xiaoyun Wu,Wen-Ning Zhao,Wen-Ning Zhao,Willis Read-Button,Xiaohua Wu,Stephen J. Haggarty,Stephen J. Haggarty,Lucienne Ronco,Jesse S. Boehm,Stuart L. Schreiber,Stuart L. Schreiber,Stuart L. Schreiber,John G. Doench,Joshua A. Bittker,David E. Root,Bang Wong,Todd R. Golub +64 more
TLDR
The expanded CMap is reported, made possible by a new, low-cost, high-throughput reduced representation expression profiling method that is shown to be highly reproducible, comparable to RNA sequencing, and suitable for computational inference of the expression levels of 81% of non-measured transcripts.About:
This article is published in Cell.The article was published on 2017-11-30 and is currently open access. It has received 1943 citations till now.read more
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A data-driven drug repositioning framework discovered a potential therapeutic agent targeting COVID-19
Yiyue Ge,Tingzhong Tian,Huang S,Fangping Wan,J Li,Shuya Li,Hui Yang,Lixiang Hong,Nian Wu,Enming Yuan,Lili Cheng,Yipin Lei,Hantao Shu,Xiaolong Feng,Ziyuan Jiang,Ying Chi,Xiling Guo,Lunbiao Cui,Liang Xiao,Zeng Li,Chunhao Yang,Zehong Miao,Haidong Tang,Ligong Chen,Hainian Zeng,Dan Zhao,Fengcai Zhu,Xiaokun Shen,Jianyang Zeng +28 more
TL;DR: The in silico screening followed by wet-lab validation indicated that a poly-ADP-ribose polymerase 1 (PARP1) inhibitor, CVL218, currently in Phase I clinical trial, may be repurposed to treat COVID-19 and proposed several possible mechanisms to explain the antiviral activities of PARP1 inhibitors against SARS-CoV-2.
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Diverse compounds from pleuromutilin lead to a thioredoxin inhibitor and inducer of ferroptosis
Evijola Llabani,Robert W. Hicklin,Hyang Yeon Lee,Stephen E. Motika,Lisa A. Crawford,Eranthie Weerapana,Paul J. Hergenrother +6 more
TL;DR: A set of stereochemically complex and structurally diverse compounds were created from the diterpene natural product pleuromutilin using the complexity-to-diversity strategy, identifying a compound that induces rapid ferroptotic death of cancer cells.
Journal ArticleDOI
Artificial Intelligence in Cancer Research and Precision Medicine
TL;DR: Artificial intelligence (AI) is rapidly reshaping cancer research and personalized clinical care Availability of high-dimensionality datasets coupled with advances in high-performance computing, as well as innovative deep learning architectures, has led to an explosion of AI use in various aspects of oncology research as discussed by the authors.
Journal ArticleDOI
Why Hypothesis Testers Should Spend Less Time Testing Hypotheses.
TL;DR: How shifting the focus to nonconfirmatory research can tie together many loose ends of psychology’s reform movement and help us to develop strong, testable theories, as Paul Meehl urged is discussed.
Journal ArticleDOI
Quantifying Drug Combination Synergy along Potency and Efficacy Axes.
Christian T. Meyer,David J. Wooten,B. Bishal Paudel,B. Bishal Paudel,Joshua A. Bauer,Joshua A. Bauer,Keisha N. Hardeman,Keisha N. Hardeman,David Westover,Christine M. Lovly,Leonard A. Harris,Darren R. Tyson,Vito Quaranta +12 more
TL;DR: Multi-dimensional synergy of combinations (MuSyC), a formalism based on a generalized, multi-dimensional Hill equation, which decouples synergistic potency and efficacy, is developed to transform the enterprise of drug-combination screens by precisely guiding translation of combinations toward dose reduction, improved efficacy, or both.
References
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Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
Aravind Subramanian,Pablo Tamayo,Vamsi K. Mootha,Sayan Mukherjee,Benjamin L. Ebert,Michael A. Gillette,Amanda G. Paulovich,Scott L. Pomeroy,Todd R. Golub,Eric S. Lander,Jill P. Mesirov +10 more
TL;DR: The Gene Set Enrichment Analysis (GSEA) method as discussed by the authors focuses on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation.
Journal Article
Visualizing Data using t-SNE
TL;DR: A new technique called t-SNE that visualizes high-dimensional data by giving each datapoint a location in a two or three-dimensional map, a variation of Stochastic Neighbor Embedding that is much easier to optimize, and produces significantly better visualizations by reducing the tendency to crowd points together in the center of the map.
Journal ArticleDOI
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
TL;DR: The Gene Expression Omnibus (GEO) project was initiated in response to the growing demand for a public repository for high-throughput gene expression data and provides a flexible and open design that facilitates submission, storage and retrieval of heterogeneous data sets from high-power gene expression and genomic hybridization experiments.
Journal ArticleDOI
BLAT—The BLAST-Like Alignment Tool
TL;DR: How BLAT was optimized is described, which is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences.
Journal ArticleDOI
Adjusting batch effects in microarray expression data using empirical Bayes methods
TL;DR: This paper proposed parametric and non-parametric empirical Bayes frameworks for adjusting data for batch effects that is robust to outliers in small sample sizes and performs comparable to existing methods for large samples.
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