M
Matthew R. Jones
Researcher at Icahn School of Medicine at Mount Sinai
Publications - 8
Citations - 6640
Matthew R. Jones is an academic researcher from Icahn School of Medicine at Mount Sinai. The author has contributed to research in topics: GTPase-activating protein & Postsynaptic density. The author has an hindex of 7, co-authored 8 publications receiving 4205 citations.
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Journal ArticleDOI
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
TL;DR: 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.
Journal ArticleDOI
Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd
Zichen Wang,Caroline D. Monteiro,Kathleen M. Jagodnik,Kathleen M. Jagodnik,Kathleen M. Jagodnik,Nicolas F. Fernandez,Gregory W. Gundersen,Andrew D. Rouillard,Sherry L. Jenkins,Axel S. Feldmann,Kevin Hu,Michael G. McDermott,Qiaonan Duan,Neil R. Clark,Matthew R. Jones,Yan Kou,Troy Goff,Holly Woodland,Fabio M R. Amaral,Gregory L. Szeto,Oliver Fuchs,Sophia Miryam Schüssler-Fiorenza Rose,Sophia Miryam Schüssler-Fiorenza Rose,Shvetank Sharma,Uwe Schwartz,Xabier Bengoetxea Bausela,Maciej Szymkiewicz,Vasileios Maroulis,Anton Salykin,Carolina M. Barra,Candice D. Kruth,Nicholas J. Bongio,Vaibhav Mathur,Radmila D. Todoric,Udi Rubin,Apostolos Malatras,Carl T. Fulp,John A. Galindo,Ruta Motiejunaite,Christoph Jüschke,Philip C. Dishuck,Katharina Lahl,Mohieddin Jafari,Sara Aibar,Apostolos Zaravinos,Apostolos Zaravinos,Linda H. Steenhuizen,Lindsey R. Allison,Pablo Gamallo,Fernando de Andres Segura,Tyler Dae Devlin,Vicente Perez-Garcia,Avi Ma'ayan +52 more
TL;DR: This article reported a crowdsourcing project to annotate and reanalyse a large number of gene expression profiles from Gene Expression Omnibus (GEO) through a massive open online course on Coursera, over 70 participants from over 25 countries identify and annotate 2,460 single-gene perturbation signatures, 839 disease versus normal signatures, and 906 drug perturbations signatures.
Journal Article
Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd
Zichen Wang,Caroline D. Monteiro,Kathleen M. Jagodnik,Kathleen M. Jagodnik,Kathleen M. Jagodnik,Nicolas F. Fernandez,Gregory W. Gundersen,Andrew D. Rouillard,Sherry L. Jenkins,Axel S. Feldmann,Kevin Hu,Michael G. McDermott,Qiaonan Duan,Neil R. Clark,Matthew R. Jones,Yan Kou,Troy Goff,Holly Woodland,Fabio M R. Amaral,Gregory L. Szeto,Oliver Fuchs,Sophia Miryam Schüssler-Fiorenza Rose,Sophia Miryam Schüssler-Fiorenza Rose,Shvetank Sharma,Uwe Schwartz,Xabier Bengoetxea Bausela,Maciej Szymkiewicz,Vasileios Maroulis,Anton Salykin,Carolina M. Barra,Candice D. Kruth,Nicholas J. Bongio,Vaibhav Mathur,Radmila D. Todoric,Udi Rubin,Apostolos Malatras,Carl T. Fulp,John A. Galindo,Ruta Motiejunaite,Christoph Jüschke,Philip C. Dishuck,Katharina Lahl,Mohieddin Jafari,Sara Aibar,Apostolos Zaravinos,Apostolos Zaravinos,Linda H. Steenhuizen,Lindsey R. Allison,Pablo Gamallo,Fernando de Andres Segura,Tyler Dae Devlin,Vicente Perez-Garcia,Avi Ma'ayan +52 more
TL;DR: A crowdsourcing project to annotate and reanalyse a large number of gene expression profiles from Gene Expression Omnibus (GEO) and develops a web portal to serve these signatures for query, download and visualization.
Journal ArticleDOI
Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd
Zichen Wang,Caroline D. Monteiro,Kathleen M. Jagodnik,Nicolas F. Fernandez,Gregory W. Gundersen,Andrew D. Rouillard,Sherry L. Jenkins,Axel S. Feldmann,Kevin Hu,Michael G. McDermott,Qiaonan Duan,Neil R. Clark,Matthew R. Jones,Yan Kou,Troy Goff,Coursera Nasb students,Avi Ma'ayan +16 more
Journal ArticleDOI
GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions
Gregory W. Gundersen,Matthew R. Jones,Andrew D. Rouillard,Yan Kou,Caroline D. Monteiro,Axel S. Feldmann,Kevin Hu,Avi Ma'ayan +7 more
TL;DR: GEO2Enrichr opens a new avenue for adding functionality to major bioinformatics resources such GEO by integrating tools and resources without the need for a plug-in architecture, and helps researchers to quickly explore hypotheses with little technical overhead.