Allele-Specific Amplification in Cancer Revealed by SNP Array Analysis. - Thomas LaFramboise; Barbara A. Weir; Xiaojun Zhao; Rameen Beroukhim; Cheng Li 016; David Harrington; William R. Sellers; Matthew Meyerson (PLoS Comput. Biol., 2005)

Inferring Loss-of-Heterozygosity from Unpaired Tumors Using High-Density Oligonucleotide SNP Arrays. - Rameen Beroukhim; Ming Lin; Yuhyun Park; Ke Hao; Xiaojun Zhao; Levi A. Garraway; Edward A. Fox; Ephraim P. Hochberg; Ingo K. Mellinghoff; Matthias D. Hofer; Aurelien Descazeaud; Mark A. Rubin; et al. (PLoS Comput. Biol., 2006)

Correction: Inferring Loss-of-Heterozygosity from Unpaired Tumors Using High-Density Oligonucleotide SNP Arrays. - Rameen Beroukhim; Ming Lin; Yuhyun Park; Ke Hao; Xiaojun Zhao; Levi A. Garraway; Edward A. Fox; Ephraim P. Hochberg; Ingo K. Mellinghoff; Matthias D. Hofer; Aurelien Descazeaud; Mark A. Rubin; et al. (PLoS Comput. Biol., 2007)

Major copy proportion analysis of tumor samples using SNP arrays. - Cheng Li 016; Rameen Beroukhim; Barbara A. Weir; Wendy Winckler; Levi A. Garraway; William R. Sellers; Matthew Meyerson (BMC Bioinform., 2008)

A Mathematical Methodology for Determining the Temporal Order of Pathway Alterations Arising during Gliomagenesis. - Yu-Kang Cheng; Rameen Beroukhim; Ross L. Levine; Ingo K. Mellinghoff; Eric C. Holland; Franziska Michor (PLoS Comput. Biol., 2012)

VariantBam: filtering and profiling of next-generational sequencing data using region-specific rules. - Jeremiah A. Wala; Cheng-Zhong Zhang; Matthew Meyerson; Rameen Beroukhim (Bioinform., 2016)

SeqLib: a C ++ API for rapid BAM manipulation, sequence alignment and sequence assembly. - Jeremiah A. Wala; Rameen Beroukhim (Bioinform., 2017)

Longitudinal molecular trajectories of diffuse glioma in adults. - Floris P. Barthel; Kevin C. Johnson; Frederick S. Varn; Anzhela D. Moskalik; Georgette Tanner; Emre Kocakavuk; Kevin J. Anderson; Olajide Abiola; Kenneth D. Aldape; Kristin D. Alfaro; Donat Alpar; Samirkumar B. Amin; et al. (Nat., 2019)

The evolutionary history of 2,658 cancers. - Moritz Gerstung; Clemency Jolly; Ignaty Leshchiner; Stefan C. Dentro; Santiago Gonzalez; Thomas J. Mitchell; Yulia Rubanova; Pavana Anur; Kaixian Yu; Maxime Tarabichi; Amit G. Deshwar; Jeff Wintersinger; et al. (Nat., 2020)

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. - Esther Rheinbay; Morten Muhlig Nielsen; Federico Abascal; Jeremiah Wala; Ofer Shapira; Grace Tiao; Henrik Hornshøj; Julian M. Hess; Randi Istrup Juul; Ziao Lin; Lars Feuerbach; Radhakrishnan Sabarinathan; et al. (Nat., 2020)

Quantification of aneuploidy in targeted sequencing data using ASCETS. - Liam F. Spurr; Mehdi Touat; Alison M. Taylor; Adrian M. Dubuc; Juliann Shih; David M. Meredith; William V. Pisano; Matthew Meyerson; Keith L. Ligon; Andrew D. Cherniack; Yvonne Y. Li; Rameen Beroukhim (Bioinform., 2021)

Tangent normalization for somatic copy-number inference in cancer genome analysis. - Galen F. Gao; Coyin Oh; Gordon Saksena; Davy Deng; Lindsay C. Westlake; Barbara A. Hill; Michael Reich; Steven E. Schumacher; Ashton C. Berger; Scott L. Carter; Andrew D. Cherniack; Matthew Meyerson; et al. (Bioinform., 2022)