On pairwise distances and median score of three genomes under DCJ. - Sergey Aganezov Jr.; Max A. Alekseyev (BMC Bioinform., 2012)

Scaffold assembly based on genome rearrangement analysis. - Sergey Aganezov Jr.; Nadia Sitdykova; Max A. Alekseyev (Comput. Biol. Chem., 2015)

Multi-genome Scaffold Co-assembly Based on the Analysis of Gene Orders and Genomic Repeats. - Sergey Aganezov Jr.; Max A. Alekseyev (ISBRA, 2016)

Transcriptome sequencing based annotation and homologous evidence based scaffolding of Anguilla japonica draft genome. - Yu-Chen Liu; Sheng-Da Hsu; Chih-Hung Chou; Wei-Yun Huang; Yu-Hung Chen; Chia-Yu Liu; Guan-Jay Lyu; Shao-Zhen Huang; Sergey Aganezov Jr.; Max A. Alekseyev; Chung-Der Hsiao; Hsien-Da Huang (BMC Genom., 2016)

Reconstruction of Ancestral Genomes in Presence of Gene Gain and Loss. - Pavel Avdeyev; Shuai Jiang; Sergey Aganezov Jr.; Fei Hu; Max A. Alekseyev (J. Comput. Biol., 2016)

On problem of orienting ordered scaffolds. - Sergey Aganezov Jr.; Max A. Alekseyev (ICCABS, 2017)

Orientation of Ordered Scaffolds. - Sergey Aganezov Jr.; Max A. Alekseyev (RECOMB-CG, 2017)

CAMSA: a tool for comparative analysis and merging of scaffold assemblies. - Sergey Aganezov Jr.; Max A. Alekseyev (BMC Bioinform., 2017)

Recovering rearranged cancer chromosomes from karyotype graphs. - Sergey Aganezov; Ilya Zban; Vitaly Aksenov; Nikita Alexeev; Michael C. Schatz (BMC Bioinform., 2019)

Chromothripsis Rearrangements Are Informed by 3D-Genome Organization. - Natalia Petukhova; Alexey Zabelkin; Vitaly Dravgelis; Sergey Aganezov; Nikita Alexeev (RECOMB-CG, 2022)

Orienting Ordered Scaffolds: Complexity and Algorithms. - Sergey Aganezov; Pavel Avdeyev; Nikita Alexeev; Yongwu Rong; Max A. Alekseyev (SN Comput. Sci., 2022)