Computational Biomedicine

Publications

Author links open overlay panelaA

Inigo Ayestaran*, Ana Galhoz*, Elmar Spiegel, Ben Sidders, Jonathan R. Dry, Frank Dondelinger, Andreas Bender, Ultan McDermott, Francesco Iorio, Michael P. Menden#
Identification of Intrinsic Drug Resistance and Its Biomarkers in High-Throughput Pharmacogenomic and CRISPR Screens
Cell Patterns 2020

Stefan Naulaerts, Michael P. Menden and Pedro J. Ballester#
Concise Polygenic Models for Cancer-Specific Identification of Drug-Sensitive Tumors from Their Multi-Omics Profiles
Biomolecules 2020

Mi Yang, Patricia Jaaks, Jonathan Dry, Mathew Garnett, Michael P. Menden* & Julio Saez-Rodriguez*#
Stratification and prediction of drug synergy based on target functional similarity
npj Systems Biology and Applications 2020

 Guo T*#, Luna A*, Rajapakse VN*, ChiekKoh C*, 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, Zhon Q, Varma S, Schmitt U, Qui P, Zhang Q, Zhu Y, Wild PJ, Garnett MJ, Bork P, Beck M, Liu K, Rodriguez JS, Elloumi F, Reinhold WC, Sander C, Pommier Y#, Aebersold R#
Quantitative proteome landscape of the NCI-60 cancer cell lines
iScience 2019

Keshava N*, Toh TS*, Yuan H, Yang B, Menden MP#, Wang D#
Defining subpopulations of differential drug response to reveal novel target populations.
npj Systems Bio & Applications 2019

Vlot AHC, Aniceto N, Menden MP, Ulrich-Merzenich G, Bender A.
Applying Drug Synergy Metrics to Oncology Combination Screening Data – Agreements, Disagreements, and Pitfalls.
Drug Discovery Today 2019

Menden MP*, Wang D*, Guan Y*, Mason M*, Szalai B*, Bulusu KC*, Yu T, Kang J, Jeon M, Wolfinger R, Nguyen T, Zaslavskiy M, AstraZeneca-Sanger Drug Combination DREAM Consortium, Jang IS, Ghazoui Z, Ahsen MA, Vogel R, Neto EC, Norman T, Tang EKY, Garnett MJ, Di Veroli G, Fawell S, Stolovitzky G, Guinney J, Dry JR, Saez-Rodriguez J.
A cancer pharmacogenomic screen powering crowed-sourced advancement of drug combination prediction. 
Nature Communications 2019

Menden MP*, Casale FP*, Stephan J, Bignell GR, Iorio F, McDermott U, Garnett MJ, Saez-Rodriguez J, Stegle O.
The germline genetic component of drug sensitivity in cancer cell lines. 
Nature Communications 2018

Cokelaer T, Chen E, Iorio F, Menden MP, Lightfoot H, Saez-Rodriguez J, Garnett MJ.
GDSCTools for Mining Pharmacogenomic Interactions in Cancer.
Bioinformatics – Oxford Academics 2018

Gönen et al. as part of the Broad-DREAM Community.
A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines.
Cell Systems 2017

Iorio F*, Knijnenburg TA*, Vis DJ*, Bignell GR*, Menden MP*, Schubert M, Aben N, Gonçalves E, Barthorpe S, Lightfoot H, Greninger P, van Dyk E, Chang H, de Silva H, Heyn HA, Deng X, Egan RK, Liu O, Mironenko T, Mitropoulos X, Richardson L, Wang J, Zhang T, Moran S, Saylos S, Soleimani M, Tamborero D, Lopez-Bigas N, Ross-Macdonald P, Esteller M, Gray N, Haber DA, Stratton MR, Benes CH, Wessels LFA, Saez-Rodriguez J, McDermott U, Garnett MJ.
A landscape of pharmacogenomic interactions in cancer.
Cell 2016

Stransky N*, Ghandi M*, Lehár J*, Amzallag A*, Menden MP*, Iorio F*, et al. (i.e. Cancer Cell Line Encyclopedia Consortium; Genomics of Drug Sensitivity in Cancer Consortium).
Pharmacogenomic agreement between two cancer cell line data sets.
Nature 2015

Cokelaer T, Bansal M, Bare C, Bila E, Bot BM, Chaibub Neto E, Eduati F, Gönen M, Hill SM, Hoff B, Karr JB, Küffner R, Menden MP, Meyer P, Norel R, Pratap A, Prill RJ, Weirauch MT, Costello JC, Stolovitzky G, Saez-Rodriguez J. DREAMTools: a Python package for scoring collaborative challenges.
F1000 2015

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, Friend S, Dearry A, Simeonov A, Tice RR, Rusyn I, Wright FA, Stolovitzky G, Xie Y, Saez-Rodriguez J, Niehs-Ncats-Unc Dream Toxicogenetics Collab T.
Prediction of human population responses to toxic compounds by a collaborative competition.
Nature Biotechnology 2015

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.
A community computational challenge to predict the activity of pairs of compounds.
Nature Biotechnology 2014

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.
A community effort to assess and improve drug sensitivity prediction algorithms.
Nature Biotechnology 2014

Menden MP, Iorio F, Garnett M, McDermott U, Benes CH, Ballester PJ, Saez-Rodriguez J. Machine learning prediction of cancer cell sensitivity to drugs based on genomic and chemical properties. PLoS One 2013

Iorio F, Rittman T, Ge H, Menden M, Saez-Rodriguez J.
Transcriptional data: a new gateway to drug repositioning?
Drug Discovery Today 2012

Millard BL, Niepel M, Menden MP, Muhlich JL, Sorger PK.
Adaptive informatics for multifactorial and high-content biological data.
Nature Methods 2011

Aranda B, Achuthan P, AlamHFaruque Y, Armean I, Bridge A, Derow C, Feuermann M, Ghanbarian AT, Kerrien S, Khadake J, Kerssemakers J, Leroy C, Menden M, Michaut M, Montecchi H, Palazzi L, Neuhauser SN, Orchard S, Perreau V, Roechert B, van Eijk K, Hermjakob H.
The IntAct molecular interaction database in 2010.
Nucleic Acids Research 2010

* equal contribution.

# corresponding author.