GeNets

a unified web platform for network-based genomic analyses

Taibo Li, April Kim, Joseph Rosenbluh, Heiko Horn, Liraz Greenfeld, David An, Andrew Zimmer, Arthur Liberzon, Jon Bistline, Ted Natoli, Yang Li, Aviad Tsherniak, Rajiv Narayan, Aravind Subramanian, Ted Liefeld, Bang Wong, Dawn Thompson, Sarah Calvo, Steve Carr, Jesse Boehm & 5 others Jake Jaffe, Jill Mesirov, Nir Hacohen, Aviv Regev, Kasper Lage

Research output: Contribution to journalArticleResearchpeer-review

5 Citations (Scopus)

Abstract

Functional genomics networks are widely used to identify unexpected pathway relationships in large genomic datasets. However, it is challenging to compare the signal-to-noise ratios of different networks and to identify the optimal network with which to interpret a particular genetic dataset. We present GeNets, a platform in which users can train a machine-learning model (Quack) to carry out these comparisons and execute, store, and share analyses of genetic and RNA-sequencing datasets.

Original languageEnglish
Number of pages4
JournalNature Methods
DOIs
Publication statusPublished - 18 Jun 2018
Externally publishedYes

Keywords

  • functional genomics
  • genetics research
  • network topology
  • systems biology

Cite this

Li, Taibo ; Kim, April ; Rosenbluh, Joseph ; Horn, Heiko ; Greenfeld, Liraz ; An, David ; Zimmer, Andrew ; Liberzon, Arthur ; Bistline, Jon ; Natoli, Ted ; Li, Yang ; Tsherniak, Aviad ; Narayan, Rajiv ; Subramanian, Aravind ; Liefeld, Ted ; Wong, Bang ; Thompson, Dawn ; Calvo, Sarah ; Carr, Steve ; Boehm, Jesse ; Jaffe, Jake ; Mesirov, Jill ; Hacohen, Nir ; Regev, Aviv ; Lage, Kasper. / GeNets : a unified web platform for network-based genomic analyses. In: Nature Methods. 2018.
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abstract = "Functional genomics networks are widely used to identify unexpected pathway relationships in large genomic datasets. However, it is challenging to compare the signal-to-noise ratios of different networks and to identify the optimal network with which to interpret a particular genetic dataset. We present GeNets, a platform in which users can train a machine-learning model (Quack) to carry out these comparisons and execute, store, and share analyses of genetic and RNA-sequencing datasets.",
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Li, T, Kim, A, Rosenbluh, J, Horn, H, Greenfeld, L, An, D, Zimmer, A, Liberzon, A, Bistline, J, Natoli, T, Li, Y, Tsherniak, A, Narayan, R, Subramanian, A, Liefeld, T, Wong, B, Thompson, D, Calvo, S, Carr, S, Boehm, J, Jaffe, J, Mesirov, J, Hacohen, N, Regev, A & Lage, K 2018, 'GeNets: a unified web platform for network-based genomic analyses', Nature Methods. https://doi.org/10.1038/s41592-018-0039-6

GeNets : a unified web platform for network-based genomic analyses. / Li, Taibo; Kim, April; Rosenbluh, Joseph; Horn, Heiko; Greenfeld, Liraz; An, David; Zimmer, Andrew; Liberzon, Arthur; Bistline, Jon; Natoli, Ted; Li, Yang; Tsherniak, Aviad; Narayan, Rajiv; Subramanian, Aravind; Liefeld, Ted; Wong, Bang; Thompson, Dawn; Calvo, Sarah; Carr, Steve; Boehm, Jesse; Jaffe, Jake; Mesirov, Jill; Hacohen, Nir; Regev, Aviv; Lage, Kasper.

In: Nature Methods, 18.06.2018.

Research output: Contribution to journalArticleResearchpeer-review

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T2 - a unified web platform for network-based genomic analyses

AU - Li, Taibo

AU - Kim, April

AU - Rosenbluh, Joseph

AU - Horn, Heiko

AU - Greenfeld, Liraz

AU - An, David

AU - Zimmer, Andrew

AU - Liberzon, Arthur

AU - Bistline, Jon

AU - Natoli, Ted

AU - Li, Yang

AU - Tsherniak, Aviad

AU - Narayan, Rajiv

AU - Subramanian, Aravind

AU - Liefeld, Ted

AU - Wong, Bang

AU - Thompson, Dawn

AU - Calvo, Sarah

AU - Carr, Steve

AU - Boehm, Jesse

AU - Jaffe, Jake

AU - Mesirov, Jill

AU - Hacohen, Nir

AU - Regev, Aviv

AU - Lage, Kasper

PY - 2018/6/18

Y1 - 2018/6/18

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KW - genetics research

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KW - systems biology

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