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Items: 7

1.

eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks.

Clarke DJB, Kuleshov MV, Schilder BM, Torre D, Duffy ME, Keenan AB, Lachmann A, Feldmann AS, Gundersen GW, Silverstein MC, Wang Z, Ma'ayan A.

Nucleic Acids Res. 2018 Jul 2;46(W1):W171-W179. doi: 10.1093/nar/gky458.

2.

Clustergrammer, a web-based heatmap visualization and analysis tool for high-dimensional biological data.

Fernandez NF, Gundersen GW, Rahman A, Grimes ML, Rikova K, Hornbeck P, Ma'ayan A.

Sci Data. 2017 Oct 10;4:170151. doi: 10.1038/sdata.2017.151.

3.

GEN3VA: aggregation and analysis of gene expression signatures from related studies.

Gundersen GW, Jagodnik KM, Woodland H, Fernandez NF, Sani K, Dohlman AB, Ung PM, Monteiro CD, Schlessinger A, Ma'ayan A.

BMC Bioinformatics. 2016 Nov 15;17(1):461.

4.

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

Wang Z, Monteiro CD, Jagodnik KM, Fernandez NF, Gundersen GW, Rouillard AD, Jenkins SL, Feldmann AS, Hu KS, McDermott MG, Duan Q, Clark NR, Jones MR, Kou Y, Goff T, Woodland H, Amaral FMR, Szeto GL, Fuchs O, Schüssler-Fiorenza Rose SM, Sharma S, Schwartz U, Bausela XB, Szymkiewicz M, Maroulis V, Salykin A, Barra CM, Kruth CD, Bongio NJ, Mathur V, Todoric RD, Rubin UE, Malatras A, Fulp CT, Galindo JA, Motiejunaite R, Jüschke C, Dishuck PC, Lahl K, Jafari M, Aibar S, Zaravinos A, Steenhuizen LH, Allison LR, Gamallo P, de Andres Segura F, Dae Devlin T, Pérez-García V, Ma'ayan A.

Nat Commun. 2016 Sep 26;7:12846. doi: 10.1038/ncomms12846.

5.

The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins.

Rouillard AD, Gundersen GW, Fernandez NF, Wang Z, Monteiro CD, McDermott MG, Ma'ayan A.

Database (Oxford). 2016 Jul 3;2016. pii: baw100. doi: 10.1093/database/baw100. Print 2016.

6.

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update.

Kuleshov MV, Jones MR, Rouillard AD, Fernandez NF, Duan Q, Wang Z, Koplev S, Jenkins SL, Jagodnik KM, Lachmann A, McDermott MG, Monteiro CD, Gundersen GW, Ma'ayan A.

Nucleic Acids Res. 2016 Jul 8;44(W1):W90-7. doi: 10.1093/nar/gkw377. Epub 2016 May 3.

7.

GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions.

Gundersen GW, Jones MR, Rouillard AD, Kou Y, Monteiro CD, Feldmann AS, Hu KS, Ma'ayan A.

Bioinformatics. 2015 Sep 15;31(18):3060-2. doi: 10.1093/bioinformatics/btv297. Epub 2015 May 13.

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