Inferring the Mutational History of a Tumor Using Multi-State Perfect Phylogeny Mixtures

M. El-Kebir, G. Satas, L. Oesper, B.J. Raphael.   Cell Systems (2016) 3(1):43-53.

Comet: A Statistical Approach to Identify Combinations of Mutually Exclusive Alterations in Cancer

M.D.M. Leiserson, H-T. Wu, F. Vandin, B.J. Raphael.   Genome Biology (2015) 16:160. 

Reconstruction of Clonal Trees and Tumor Composition from Multi-sample Sequencing Data

M. El-Kebir, L. Oesper, H. Acheson-Field, B.J. Raphael   Bioinformatics (Special Issue: Proceedings of ISMB) (2015) 31(12):i62-i70. 

Pan-cancer Network Analysis Identifies Combinations of Rare Somatic Mutations Across Pathways and Protein Complexes

M.D.M Leiserson, F. Vandin, H. Wu, J.R. Dobson, J.V. Eldridge, J.L. Thomas, A. Papoutsaki, Y. Kim, B. Niu, M. McLellan, M.S. Lawrence, A. Gonzalez-Perez, D. Tamborero, Y. Cheng, G.A. Ryslik, N. Lopez-Bigas, G. Getz, L. Ding, B.J Raphael.    Nature Genetics (2015) 47(2):106-114. 

Analyzing Combinations of Somatic Mutations in Cancer Genomes

M.D.M. Leiserson and B.J. Raphael.   In Integrating Omics Data G.C.Tseng, D. Ghosh, X.J. Zhou (Eds). Cambridge University Press (2015) 

Quantifying Tumor Heterogeneity in Whole-Genome and Whole-Exome Sequencing Data

L. Oesper, G. Satas, B.J. Raphael.   Bioinformatics (2014) 30(24):3532-40. 

A Combinatorial Approach for Analyzing Intra-tumor Heterogeneity from High-throughput Sequencing Data

I. Hajirasouliha, A. Mahmoody, B.J. Raphael.   Bioinformatics 30 (12): i78-i86.  Special issue for the 22nd Annual International Conference on Intelligent Systems in Molecular Biology (ISMB 2014) 

Identifying Driver Mutations in Sequenced Cancer Genomes: Computational Approaches to Enable Precision Medicine

B.J. Raphael, J.R. Dobson, L. Oesper, F. Vandin.   Genome Medicine (2014) 6:5

Reconstructing Mutational History in Multiply Sampled Tumors Using Perfect Phylogeny Mixtures

I. Hajirasouliha, B.J. Raphael.    14th Workshop on Algorithms in Bioinformatics (WABI) (2014) Lecture Notes in Computer Science
Vol 8701: 354-367.

Network Analysis of GWAS Data

M.D.M. Leiserson, J.V. Eldridge, S. Ramachandran, B.J. Raphael.    Current Opinion in Genetics & Development (2013) 23: 602–610

THetA: Inferring Intra-tumor Heterogeneity from High-throughput DNA Sequencing Data

L. Oesper, A. Mahmoody, B.J. Raphael.    Genome Biology (2013) 14:R80