Enrichr: a comprehensive gene set enrichment analysis web server 2016 update
Maxim V. Kuleshov,Matthew R. Jones,Andrew D. Rouillard,Nicolas F. Fernandez,Qiaonan Duan,Zichen Wang,Simon Koplev,Sherry L. Jenkins,Kathleen M. Jagodnik,Alexander Lachmann,Michael G. McDermott,Caroline D. Monteiro,Gregory W. Gundersen,Avi Ma'ayan +13 more
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TLDR
A significant update to one of the tools in this domain called Enrichr, a comprehensive resource for curated gene sets and a search engine that accumulates biological knowledge for further biological discoveries is presented.Abstract:
Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a significant update to one of the tools in this domain called Enrichr. Enrichr currently contains a large collection of diverse gene set libraries available for analysis and download. In total, Enrichr currently contains 180 184 annotated gene sets from 102 gene set libraries. New features have been added to Enrichr including the ability to submit fuzzy sets, upload BED files, improved application programming interface and visualization of the results as clustergrams. Overall, Enrichr is a comprehensive resource for curated gene sets and a search engine that accumulates biological knowledge for further biological discoveries. Enrichr is freely available at: http://amp.pharm.mssm.edu/Enrichr.read more
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Cells of the adult human heart.
Monika Litviňuková,Monika Litviňuková,Carlos Talavera-López,Carlos Talavera-López,Henrike Maatz,Daniel Reichart,Daniel Reichart,Catherine L. Worth,Eric L. Lindberg,Masatoshi Kanda,Masatoshi Kanda,Krzysztof Polanski,Matthias Heinig,Michael Lee,Emily R. Nadelmann,Kenny Roberts,Liz Tuck,Eirini S. Fasouli,Daniel M. DeLaughter,Barbara McDonough,Barbara McDonough,Barbara McDonough,Hiroko Wakimoto,Joshua M. Gorham,Sara Samari,Krishnaa T. Mahbubani,Kourosh Saeb-Parsy,Giannino Patone,Joseph J. Boyle,Hongbo Zhang,Hongbo Zhang,Hao Zhang,Anissa Viveiros,Gavin Y. Oudit,Omer Ali Bayraktar,Jonathan G. Seidman,Christine E. Seidman,Christine E. Seidman,Christine E. Seidman,Michela Noseda,Michela Noseda,Norbert Hubner,Sarah A. Teichmann,Sarah A. Teichmann +43 more
TL;DR: The state-of-the-art analyses of large-scale single-cell and single-nucleus transcriptomes are used to construct a cellular atlas of the human heart that will aid further research into cardiac physiology and disease and provides a valuable reference for future studies.
Journal ArticleDOI
iPSC-Derived Human Microglia-like Cells to Study Neurological Diseases
Edsel M. Abud,Ricardo Ramirez,Eric S. Martinez,Luke M. Healy,Cecilia H.H. Nguyen,Sean A. Newman,Andriy V. Yeromin,Vanessa M. Scarfone,Samuel E. Marsh,Cristhian Fimbres,Chad A. Caraway,Gianna M. Fote,Abdullah M. Madany,Anshu Agrawal,Rakez Kayed,Karen H. Gylys,Michael D. Cahalan,Brian J. Cummings,Jack P. Antel,Ali Mortazavi,Monica J. Carson,Wayne W. Poon,Mathew Blurton-Jones +22 more
TL;DR: iMGLs were used to examine the effects of Aβ fibrils and brain-derived tau oligomers on AD-related gene expression and to interrogate mechanisms involved in synaptic pruning, and whole-transcriptome analysis demonstrates that they are highly similar to cultured adult and fetal human microglia.
Journal ArticleDOI
Pooled CRISPR screening with single-cell transcriptome readout
Paul Datlinger,André F. Rendeiro,Christian Schmidl,Thomas Krausgruber,Peter Traxler,Johanna Klughammer,Linda C. Schuster,Amelie Kuchler,Donát Alpár,Christoph Bock,Christoph Bock,Christoph Bock +11 more
TL;DR: This method forCRISPR droplet sequencing (CROP-seq) enables pooled CRISPR screens with single-cell transcriptome resolution, which will facilitate high-throughput functional dissection of complex regulatory mechanisms and heterogeneous cell populations.
Journal ArticleDOI
Context-Dependent and Disease-Specific Diversity in Protein Interactions within Stress Granules.
Sebastian Markmiller,Sahar Soltanieh,Kari L. Server,Raymond H. Mak,Wenhao Jin,Mark Y. Fang,En-Ching Luo,Florian Krach,Dejun Yang,Anindya Sen,Amit Fulzele,Jacob M. Wozniak,David Gonzalez,David Gonzalez,Mark W. Kankel,Fen-Biao Gao,Eric J. Bennett,Eric Lécuyer,Gene W. Yeo +18 more
TL;DR: Stress granules (SGs) are transient ribonucleoprotein (RNP) aggregates that form during cellular stress and are increasingly implicated in human neurodegeneration as mentioned in this paper.
A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response
Britt Adamson,Thomas M. Norman,Marco Jost,Min Y. Cho,James K. Nuñez,Yuwen Chen,Jacqueline E. Villalta,Luke A. Gilbert,Max A. Horlbeck,Marco Y. Hein,Ryan A. Pak,Andrew N. Gray,Carol A. Gross,Oren Parnas,Jonathan S. Weissman,Atray Dixit,Aviv Regev +16 more
TL;DR: Insight is provided into how the three sensors of ER homeostasis monitor distinct types of stress and the ability of Perturb-seq to dissect complex cellular responses are highlighted.
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