Assembly-Free and Alignment-Free Sample Identification Using Genome Skims. - Shahab Sarmashghi; Kristine Bohmann; M. Thomas P. Gilbert; Vineet Bafna; Siavash Mirarab (RECOMB, 2018)

APPLES: Fast Distance-Based Phylogenetic Placement. - Metin Balaban; Shahab Sarmashghi; Siavash Mirarab (RECOMB, 2019)

A Note on Computing Interval Overlap Statistics. - Shahab Sarmashghi; Vineet Bafna (RECOMB, 2019)

Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT. - Shahab Sarmashghi; Metin Balaban; Eleonora Rachtman; Behrouz Touri; Siavash Mirarab; Vineet Bafna (PLoS Comput. Biol., 2021)

Uncertainty Quantification Using Subsampling for Assembly-Free Estimates of Genomic Distance and Phylogenetic Relationships. - Eleonora Rachtman; Shahab Sarmashghi; Vineet Bafna; Siavash Mirarab (RECOMB, 2022)