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Items: 14

1.

Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines.

Guo T, Luna A, Rajapakse VN, Koh CC, Wu Z, Liu W, Sun Y, Gao H, Menden MP, Xu C, Calzone L, Martignetti L, Auwerx C, Buljan M, Banaei-Esfahani A, Ori A, Iskar M, Gillet L, Bi R, Zhang J, Zhang H, Yu C, Zhong Q, Varma S, Schmitt U, Qiu P, Zhang Q, Zhu Y, Wild PJ, Garnett MJ, Bork P, Beck M, Liu K, Saez-Rodriguez J, Elloumi F, Reinhold WC, Sander C, Pommier Y, Aebersold R.

iScience. 2019 Nov 22;21:664-680. doi: 10.1016/j.isci.2019.10.059. Epub 2019 Oct 31.

2.

Defining subpopulations of differential drug response to reveal novel target populations.

Keshava N, Toh TS, Yuan H, Yang B, Menden MP, Wang D.

NPJ Syst Biol Appl. 2019 Oct 3;5:36. doi: 10.1038/s41540-019-0113-4. eCollection 2019.

3.

Applying synergy metrics to combination screening data: agreements, disagreements and pitfalls.

Vlot AHC, Aniceto N, Menden MP, Ulrich-Merzenich G, Bender A.

Drug Discov Today. 2019 Dec;24(12):2286-2298. doi: 10.1016/j.drudis.2019.09.002. Epub 2019 Sep 10. Review.

PMID:
31518641
4.

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen.

Menden MP, Wang D, Mason MJ, Szalai B, Bulusu KC, Guan Y, Yu T, Kang J, Jeon M, Wolfinger R, Nguyen T, Zaslavskiy M; AstraZeneca-Sanger Drug Combination DREAM Consortium, Jang IS, Ghazoui Z, Ahsen ME, Vogel R, Neto EC, Norman T, Tang EKY, Garnett MJ, Veroli GYD, Fawell S, Stolovitzky G, Guinney J, Dry JR, Saez-Rodriguez J.

Nat Commun. 2019 Jun 17;10(1):2674. doi: 10.1038/s41467-019-09799-2.

5.

The germline genetic component of drug sensitivity in cancer cell lines.

Menden MP, Casale FP, Stephan J, Bignell GR, Iorio F, McDermott U, Garnett MJ, Saez-Rodriguez J, Stegle O.

Nat Commun. 2018 Aug 23;9(1):3385. doi: 10.1038/s41467-018-05811-3.

6.

GDSCTools for mining pharmacogenomic interactions in cancer.

Cokelaer T, Chen E, Iorio F, Menden MP, Lightfoot H, Saez-Rodriguez J, Garnett MJ.

Bioinformatics. 2018 Apr 1;34(7):1226-1228. doi: 10.1093/bioinformatics/btx744.

7.

A Landscape of Pharmacogenomic Interactions in Cancer.

Iorio F, Knijnenburg TA, Vis DJ, Bignell GR, Menden MP, Schubert M, Aben N, Gonçalves E, Barthorpe S, Lightfoot H, Cokelaer T, Greninger P, van Dyk E, Chang H, de Silva H, Heyn H, Deng X, Egan RK, Liu Q, Mironenko T, Mitropoulos X, Richardson L, Wang J, Zhang T, Moran S, Sayols S, Soleimani M, Tamborero D, Lopez-Bigas N, Ross-Macdonald P, Esteller M, Gray NS, Haber DA, Stratton MR, Benes CH, Wessels LFA, Saez-Rodriguez J, McDermott U, Garnett MJ.

Cell. 2016 Jul 28;166(3):740-754. doi: 10.1016/j.cell.2016.06.017. Epub 2016 Jul 7.

8.

Erratum: Prediction of human population responses to toxic compounds by a collaborative competition.

Eduati F, Mangravite LM, Wang T, Tang H, Bare JC, Huang R, Norman T, Kellen M, Menden MP, Yang J, Zhan X, Zhong R, Xiao G, Xia M, Abdo N, Kosyk O; NIEHS-NCATS-UNC DREAM Toxicogenetics Collaboration, Friend S, Dearry A, Simeonov A, Tice RR, Rusyn I, Wright FA, Stolovitzky G, Xie Y, Saez-Rodriguez J.

Nat Biotechnol. 2015 Oct;33(10):1109. doi: 10.1038/nbt1015-1109a. No abstract available.

PMID:
26448092
9.

Prediction of human population responses to toxic compounds by a collaborative competition.

Eduati F, Mangravite LM, Wang T, Tang H, Bare JC, Huang R, Norman T, Kellen M, Menden MP, Yang J, Zhan X, Zhong R, Xiao G, Xia M, Abdo N, Kosyk O; NIEHS-NCATS-UNC DREAM Toxicogenetics Collaboration, Friend S, Dearry A, Simeonov A, Tice RR, Rusyn I, Wright FA, Stolovitzky G, Xie Y, Saez-Rodriguez J.

Nat Biotechnol. 2015 Sep;33(9):933-40. doi: 10.1038/nbt.3299. Epub 2015 Aug 10. Erratum in: Nat Biotechnol. 2015 Oct;33(10):1109. Friend, Stephen; Dearry, Allen; Simeonov, Anton; Tice, Raymond R; Rusyn, Ivan; Wright, Fred A; Stolovitzky, Gustavo; Xie, Yang; and Saez-Rodriguez, Julio [Added].

10.

DREAMTools: a Python package for scoring collaborative challenges.

Cokelaer T, Bansal M, Bare C, Bilal E, Bot BM, Chaibub Neto E, Eduati F, de la Fuente A, Gönen M, Hill SM, Hoff B, Karr JR, Küffner R, Menden MP, Meyer P, Norel R, Pratap A, Prill RJ, Weirauch MT, Costello JC, Stolovitzky G, Saez-Rodriguez J.

Version 2. F1000Res. 2015 Oct 9 [revised 2016 Jan 1];4:1030. doi: 10.12688/f1000research.7118.2. eCollection 2015.

11.

A community computational challenge to predict the activity of pairs of compounds.

Bansal M, Yang J, Karan C, Menden MP, Costello JC, Tang H, Xiao G, Li Y, Allen J, Zhong R, Chen B, Kim M, Wang T, Heiser LM, Realubit R, Mattioli M, Alvarez MJ, Shen Y; NCI-DREAM Community, Gallahan D, Singer D, Saez-Rodriguez J, Xie Y, Stolovitzky G, Califano A; NCI-DREAM Community.

Nat Biotechnol. 2014 Dec;32(12):1213-22. doi: 10.1038/nbt.3052. Epub 2014 Nov 17.

12.

A community effort to assess and improve drug sensitivity prediction algorithms.

Costello JC, Heiser LM, Georgii E, Gönen M, Menden MP, Wang NJ, Bansal M, Ammad-ud-din M, Hintsanen P, Khan SA, Mpindi JP, Kallioniemi O, Honkela A, Aittokallio T, Wennerberg K; NCI DREAM Community, Collins JJ, Gallahan D, Singer D, Saez-Rodriguez J, Kaski S, Gray JW, Stolovitzky G.

Nat Biotechnol. 2014 Dec;32(12):1202-12. doi: 10.1038/nbt.2877. Epub 2014 Jun 1.

13.

Machine learning prediction of cancer cell sensitivity to drugs based on genomic and chemical properties.

Menden MP, Iorio F, Garnett M, McDermott U, Benes CH, Ballester PJ, Saez-Rodriguez J.

PLoS One. 2013 Apr 30;8(4):e61318. doi: 10.1371/journal.pone.0061318. Print 2013.

14.

Adaptive informatics for multifactorial and high-content biological data.

Millard BL, Niepel M, Menden MP, Muhlich JL, Sorger PK.

Nat Methods. 2011 Jun;8(6):487-93. doi: 10.1038/nmeth.1600. Epub 2011 Apr 24.

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