Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd

Autor: Zichen Wang, Caroline D. Monteiro, Kathleen M. Jagodnik, Nicolas F. Fernandez, Gregory W. Gundersen, Andrew D. Rouillard, Sherry L. Jenkins, Axel S. Feldmann, Kevin S. 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 M. 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 E. Rubin, Apostolos Malatras, Carl T. Fulp, John A. Galindo, Ruta Motiejunaite, Christoph Jüschke, Philip C. Dishuck, Katharina Lahl, Mohieddin Jafari, Sara Aibar, Apostolos Zaravinos, Linda H. Steenhuizen, Lindsey R. Allison, Pablo Gamallo, Fernando de Andres Segura, Tyler Dae Devlin, Vicente Pérez-García, Avi Ma’ayan

Publikováno v: Nature Communications, Vol 7, Iss 1, Pp 1-11 (2016)

A wealth of gene expression data is publicly available, yet is little use without additional human curation. Ma’ayan and colleagues report a crowdsourcing project involving over 70 participants to annotate and analyse thousands of human disease-rel

Externí odkaz: https://doaj.org/article/a8f2b28d890e4a0e99fc75b9634da8c0

Systems Analysis Implicates WAVE2 Complex in the Pathogenesis of Developmental Left-Sided Obstructive Heart Defects

Autor: Avi Ma'ayan, Nahid Turan, Bradley L. Demarest, Brent W. Bisgrove, Richard P. Lifton, Zichen Wang, Christine E. Seidman, Alessandro Giardini, Alexander Lachmann, Wendy K. Chung, Richard B. Kim, George A. Porter, Amy E. Roberts, Bruce D. Gelb, Andrew D. Rouillard, Martin Tristani-Firouzi, Sunita S. Shankaran, Deepak Srivastava, Nicolas F. Fernandez, Jonathan J. Edwards, Jane W. Newburger, Martina Brueckner, Elizabeth Goldmuntz, Daniel Bernstein, John E. Deanfield, H. Joseph Yost

Publikováno v: JACC: Basic to Translational Science

Visual Abstract
Highlights • Combining CHD phenotype–driven gene set enrichment and CRISPR knockdown screening in zebrafish is an effective approach to identifying novel CHD genes. • Mutations affecting genes coding for the WAVE2 protein c

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a00bbf51d3f8f2297e9e92eefd2a0be6
http://europepmc.org/articles/PMC7188873

Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd

Autor: Sophia Miryam Schüssler-Fiorenza Rose, Anton Salykin, Xabier Bengoetxea Bausela, Linda H. Steenhuizen, Qiaonan Duan, Oliver Fuchs, Christoph Jüschke, Neil R. Clark, Caroline D. Monteiro, Pablo Gamallo, Apostolos Zaravinos, Vicente Perez-Garcia, Carl T. Fulp, Kathleen M. Jagodnik, Nicolas F. Fernandez, Tyler Dae Devlin, Philip C. Dishuck, Apostolos Malatras, Candice D. Kruth, Avi Ma'ayan, Gregory W. Gundersen, Sherry L. Jenkins, Katharina Lahl, Maciej Szymkiewicz, Holly Woodland, Vaibhav Mathur, Yan Kou, Michael G. McDermott, Sara Aibar, Uwe Schwartz, Mohieddin Jafari, Nicholas J. Bongio, Carolina M. Barra, Shvetank Sharma, Vasileios Maroulis, John A. Galindo, Udi Rubin, Fabio M R. Amaral, Ruta Motiejunaite, Kevin Hu, Zichen Wang, Fernando de Andres Segura, Matthew R. Jones, Axel S. Feldmann, Troy Goff, Radmila D. Todoric, Andrew D. Rouillard, Lindsey R. Allison, Gregory L. Szeto

Publikováno v: Nature Communications, Vol 7, Iss 1, Pp 1-11 (2016)
Nature Communications
RUIdeRA. Repositorio Institucional de la UCLM
instname
Wang, Z, Monteiro, C D, Jagodnik, K M, Fernandez, N F, Gundersen, G W, Rouillard, A D, Jenkins, S L, Feldmann, A S, Hu, K S, McDermott, M G, Duan, Q, Clark, N R, Jones, M R, Kou, Y, Goff, T, Woodland, H, Amaral, F M R, Szeto, G L, Fuchs, O, Schüssler-Fiorenza Rose, S M, Sharma, S, Schwartz, U, Bausela, X B, Szymkiewicz, M, Maroulis, V, Salykin, A, Barra, C M, Kruth, C D, Bongio, N J, Mathur, V, Todoric, R D, Rubin, U E, Malatras, A, Fulp, C T, Galindo, J A, Motiejunaite, R, Jüschke, C, Dishuck, P C, Lahl, K, Jafari, M, Aibar, S, Zaravinos, A, Steenhuizen, L H, Allison, L R, Gamallo, P, De Andres Segura, F, Dae Devlin, T, Pérez-García, V & Ma'ayan, A 2016, ' Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd ', Nature Communications, vol. 7, 12846 . https://doi.org/10.1038/ncomms12846
Nature

Gene expression data are accumulating exponentially in public repositories. Reanalysis and integration of themed collections from these studies may provide new insights, but requires further human curation. Here we report a crowdsourcing project to a

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5c9c9491a70ded33061255f09b66ada8
https://doaj.org/article/a8f2b28d890e4a0e99fc75b9634da8c0

Could advances in representation learning in Artificial Intelligence provide the new paradigm for data integration in drug discovery?

Autor: Pankaj K. Agarwal, Deepak K. Rajpal, Vinaya Vijayan, Andrew D. Rouillard

Publikováno v: Expert opinion on drug discovery. 14(3)

The goal of data integration in drug discovery is to enable cross-dataset analyses that strengthen or fill gaps in our knowledge of biological, pharmacological, or clinical phenomena. For example, ...

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::22d97df1d369399aefc114fbacc2bfa0
https://pubmed.ncbi.nlm.nih.gov/30696299

Abstract B1-25: Data integration for illuminating the druggable genome

Autor: Andrew D. Rouillard, Avi Ma'ayan

Publikováno v: Cancer Research. 75:B1-25

Introduction: The druggable genome is defined as a set of roughly 3000 genes encoding proteins for which drugs can be readily designed to modify their activity. Nearly half of the genes of the druggable genome are G protein-coupled receptors (GPCRs),

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::ba680d138cb8d3cab1245c47792d2d81
https://doi.org/10.1158/1538-7445.compsysbio-b1-25