Prediction of Contiguous Regions in the Amniote Ancestral Genome. - Aïda Ouangraoua; Frédéric Boyer; Andrew W. McPherson; Eric Tannier; Cédric Chauve (ISBRA, 2009)

Simultaneous Structural Variation Discovery in Multiple Paired-End Sequenced Genomes. - Fereydoun Hormozdiari; Iman Hajirasouliha; Andrew W. McPherson; Evan E. Eichler; Süleyman Cenk Sahinalp (RECOMB, 2011)

Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data. - Andrew W. McPherson; Chunxiao Wu; Iman Hajirasouliha; Fereydoun Hormozdiari; Faraz Hach; Anna Lapuk; Stanislav Volik; Sohrab P. Shah; Colin C. Collins; Süleyman Cenk Sahinalp (Bioinform., 2011)

deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data. - Andrew W. McPherson; Fereydoun Hormozdiari; Abdalnasser Zayed; Ryan Giuliany; Gavin Ha; Mark G. F. Sun; Malachi Griffith; Alireza Heravi Moussavi; Janine Senz; Nataliya Melnyk; Marina Pacheco; Marco A. Marra; et al. (PLoS Comput. Biol., 2011)

Discovery of Complex Genomic Rearrangements in Cancer Using High-Throughput Sequencing. - Andrew W. McPherson; Chunxiao Wu; Alexander Wyatt; Sohrab P. Shah; Colin C. Collins; Süleyman Cenk Sahinalp (RECOMB, 2012)

Joint Inference of Genome Structure and Content in Heterogeneous Tumor Samples. - Andrew W. McPherson; Andrew Roth; Cédric Chauve; Süleyman Cenk Sahinalp (RECOMB, 2015)

Clonality inference in multiple tumor samples using phylogeny. - Salem Malikic; Andrew W. McPherson; Nilgun Donmez; S. Cenk Sahinalp (Bioinform., 2015)

Joint Inference of Genome Structure and Content in Heterogeneous Tumour Samples. - Andrew W. McPherson; Andrew Roth; Gavin Ha; Sohrab P. Shah; Cédric Chauve; Süleyman Cenk Sahinalp (CoRR, 2015)

Computational identification of micro-structural variations and their proteogenomic consequences in cancer. - Yen-Yi Lin; Alexander Gawronski; Faraz Hach; Sujun Li; Ibrahim Numanagic; Iman Sarrafi; Swati Mishra 006; Andrew W. McPherson; Colin C. Collins; Milan Radovich; Haixu Tang; Süleyman Cenk Sahinalp (Bioinform., 2018)

CINner: Modeling and simulation of chromosomal instability in cancer at single-cell resolution. - Khanh N. Dinh; Ignacio Vázquez-García; Andrew Chan; Rhea Malhotra; Adam Weiner; Andrew W. McPherson; Simon Tavaré (PLoS Comput. Biol., 2025)