SAMSON: a software package for the biopolymer primary structure analysis. - Nafisa N. Nazipova; Svetlana A. Shabalina; Aleksey Y. Ogurtsov; Alexey S. Kondrashov; Mikhail A. Roytberg; G. V. Buryakov; S. E. Vernoslov (Comput. Appl. Biosci., 1995)

OWEN: aligning long collinear regions of genomes. - Aleksey Y. Ogurtsov; Mikhail A. Roytberg; Svetlana A. Shabalina; Alexey S. Kondrashov (Bioinform., 2002)

A hierarchical approach to aligning collinear regions of genomes. - Mikhail A. Roytberg; Aleksey Y. Ogurtsov; Svetlana A. Shabalina; Alexey S. Kondrashov (Bioinform., 2002)

Identification of regions in multiple sequence alignments thermodynamically suitable for targeting by consensus oligonucleotides: application to HIV genome. - Olga V. Matveeva; Brian T. Foley; Vladimir A. Nemtsov; Raymond F. Gesteland; Senya Matsufuji; John F. Atkins; Aleksey Y. Ogurtsov; Svetlana A. Shabalina (BMC Bioinform., 2004)

Analysis of internal loops within the RNA secondary structure in almost quadratic time. - Aleksey Y. Ogurtsov; Svetlana A. Shabalina; Alexey S. Kondrashov; Mikhail A. Roytberg (Bioinform., 2006)

Computational models with thermodynamic and composition features improve siRNA design. - Svetlana A. Shabalina; Alexey N. Spiridonov; Aleksey Y. Ogurtsov (BMC Bioinform., 2006)

The role of periodic mRNA secondary structure and RNA-RNA interactions in biological regulation and complexity. - Svetlana A. Shabalina; Aleksey Y. Ogurtsov; Anna Kashina; Nikolay A. Spiridonov (CMSR@ECCB, 2014)

Optimization of signal-to-noise ratio for efficient microarray probe design. - Olga V. Matveeva; Yury D. Nechipurenko; Evgeniy Riabenko; Chikako Ragan; Nafisa N. Nazipova; Aleksey Y. Ogurtsov; Svetlana A. Shabalina (Bioinform., 2016)

MiCId GUI: The Graphical User Interface for MiCId, a Fast Microorganism Classification and Identification Workflow with Accurate Statistics and High Recall. - Aleksey Y. Ogurtsov; Gelio Alves; Alex Rubio; Brendan Joyce; Björn Andersson; Roger Karlsson; Edward R. B. Moore; Yi-Kuo Yu (J. Comput. Biol., 2024)