DREAM Publications
October 29, 2013

2013 Publications

Robert M Plenge, Jeffrey D Greenberg, Lara M Mangravite, Jonathan M J Derry, Eli A Stahl, Marieke J H Coenen, Anne Barton, Leonid Padyukov, Lars Klareskog, Peter K Gregersen, Xavier Mariette, Larry W Moreland, S Louis Bridges Jr, Niek de Vries, Tom W J Huizinga, Henk-Jan Guchelaar, International Rheumatoid Arthritis Consortium (INTERACT), Stephen H Friend & Gustavo Stolovitzky
Crowdsourcing genetic prediction of clinical utility in the Rheumatoid Arthritis Responder Challenge
Nature Genetics 45,468-469 (2013) doi:10.1038/ng.2623

Bilal E, Dutkowski J, Guinney J, Jang IS, Logsdon BA, et al. (2013)
Improving Breast Cancer Survival Analysis through Competition-Based Multidimensional Modeling
PLoS Comput Biol 9(5): e1003047. doi:10.1371/journal.pcbi.1003047

Pablo Meyer, Geoffrey Siwo, Danny Zeevi, Eilon Sharon, Raquel Norel, DREAM6 Promoter Prediction Consortium, Eran Segal and Gustavo Stolovitzky
Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach
Genome Res 2013. 23: 1928-1937. doi:10.1101/gr.157420.113

Margolin, a. a. and Bilal, E.Huang, E. Norman, T. C. and Ottestad, L. and Mecham, B. H. and Sauerwine, B. and Kellen, M. R. and Mangravite, L. M. and Furia, M. D. and Vollan, H. K. M. and Rueda, O. M. and Guinney, J. and Deflaux, N. a. and Hoff, B. and and Schildwachter, X. and Russnes, H. G. and Park, D. and Vang, V. O. and Pirtle, T. and Youseff, L. and Citro, C. and Curtis, C. and Kristensen, V. N. and Hellerstein, J. and Friend, S. H. and Stolovitzky, G. and Aparicio, S. and Caldas, C. and Borresen-Dale, A.-L.
Systematic Analysis of Challenge-Driven Improvements in Molecular Prognostic Models for Breast Cancer
Sci. Transl. Med. 5, 181re1 (2013). doi:10.1126/scitranslmed.3006112

Cheng, W.-Y. and Yang, T.-H. O. and Anastassiou, D.
Development of a Prognostic Model for Breast Cancer Survival in an Open Challenge Environment
Sci. Transl. Med. 5, 181ra50 (2013). doi:10.1126/scitranslmed.3005974

Biehl M, Bunte K, Schneider P (2013)
Analysis of Flow Cytometry Data by Matrix Relevance Learning Vector Quantization
PLoS ONE 8(3): e59401. doi:10.1371/journal.pone.0059401

Aghaeepour N, Finak G, The FlowCAP Consortium, et al
Critical assessment of automated flow cytometry data analysis techniques
Nat Methods. 2013 Feb 10. doi:10.1038/nmeth.2365

Weirauch, M. T., Cote, A., Norel, R., Annala, M., Zhao, Y., Riley, T. R., Saez-Rodriguez, J., Cokelaer, T., Vedenko, A., Talukder, S., DREAM5 Consortium, Bussemaker H.J., Morris, Q.D., Bulyk, M,L,Stolovitsky G., Hughes, T.R.
Evaluation of methods for modeling transcription factor sequence specificity
Nature Biotechnology 31, 126–134 (2013) doi:10.1038/nbt.2486

Daemen, et al.
Modeling precision treatment of breast cancer,
Genome Biology (2013) doi:10.1186/gb-2013-14-10-r110