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
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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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DissertationDOI
Functional Genomics of Ageing and Its Modulation by Diet
TL;DR: Functional genomics approaches are applied to genomic data such as transcriptomics and interactomics to gain insights into the ageing process which can be manipulated by targeting ageing genes via genetic modifications, environmental factors, or pharmacological interventions.
Journal ArticleDOI
An ensemble learning approach for modeling the systems biology of drug-induced injury
Joaquim Aguirre-Plans,Janet Piñero,Terezinha Souza,Giulia Callegaro,Steven J. Kunnen,Ferran Sanz,Narcis Fernandez-Fuentes,Narcis Fernandez-Fuentes,Laura I. Furlong,Emre Guney,Baldo Oliva +10 more
TL;DR: In this article, an ensemble learning approach based on different features (CMap gene expression, chemical structures, drug targets) was developed to predict drugs that might cause DILI and gain a better understanding of the mechanisms linked to the adverse reaction.
Posted ContentDOI
Predicting Tumor Cell Response to Synergistic Drug Combinations Using a Novel Simplified Deep Learning Model
TL;DR: A new simplified deep learning model, DeepSignalingSynergy, is proposed, built on a small set of cancer signaling pathways, which can mimic the integration of multi-omics data and drug target/mechanism in a more biological meaningful and explainable manner.
Journal ArticleDOI
The vagal ganglia transcriptome identifies candidate therapeutics for airway hyperreactivity.
Leah R. Reznikov,David K. Meyerholz,Mahmoud H. Abou Alaiwa,Mahmoud H. Abou Alaiwa,Shin-Ping Kuan,Yan-Shin J. Liao,Nicholas L. Bormann,Thomas B. Bair,Margaret P. Price,Margaret P. Price,David A. Stoltz,Michael J. Welsh +11 more
TL;DR: The data suggest that transcriptome profiling of the vagal ganglia might be a novel strategy to identify potential asthma therapeutics.
Journal ArticleDOI
Uncovering cancer gene regulation by accurate regulatory network inference from uninformative data
Deniz Seçilmiş,Thomas Hillerton,Daniel Morgan,Andreas Tjärnberg,Sven Nelander,Torbjörn E. M. Nordling,Erik L. L. Sonnhammer +6 more
TL;DR: A gene reduction pipeline is developed in which uninformative genes are eliminated from the system using a selection criterion based on SNR, until reaching an informative subset, allowing inference of accurate subset GRNs.
References
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Journal ArticleDOI
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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