Multistage Sequencing by Hybridization. - Semyon Kruglyak (J. Comput. Biol., 1998)

A New Estimator of Significance of Correlation in Time Series Data. - Semyon Kruglyak; Haixu Tang (J. Comput. Biol., 2001)

Compressing Genomic Sequence Fragments Using SlimGene. - Christos Kozanitis; Christopher T. Saunders; Semyon Kruglyak; Vineet Bafna; George Varghese (J. Comput. Biol., 2011)

Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms. - Come Raczy; Roman Petrovski; Christopher T. Saunders; Ilya Chorny; Semyon Kruglyak; Elliott H. Margulies; Han-Yu Chuang; Morten Källberg; Swathi A. Kumar; Arnold Liao; Kristina M. Little; Michael P. Strömberg; et al. (Bioinform., 2013)

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. - Xiaoyu Chen; Ole Schulz-Trieglaff; Richard Shaw; Bret Barnes; Felix Schlesinger; Morten Källberg; Anthony J. Cox; Semyon Kruglyak; Christopher T. Saunders (Bioinform., 2016)

Accurate human genome analysis with element avidity sequencing. - Andrew Carroll; Alexey Kolesnikov; Daniel E. Cook; Lucas Brambrink; Kelly N. Wiseman; Sophie M. Billings; Semyon Kruglyak; Bryan R. Lajoie; Junhua Zhao; Shawn E. Levy; Cory Y. McLean; Kishwar Shafin; et al. (BMC Bioinform., 2025)