| A periodic pattern of mRNA secondary structure created by the genetic code SA Shabalina, AY Ogurtsov, NA Spiridonov Nucleic acids research 34 (8), 2428-2437, 2006 | 244 | 2006 |
| Computational models with thermodynamic and composition features improve siRNA design SA Shabalina, AN Spiridonov, AY Ogurtsov BMC bioinformatics 7, 1-16, 2006 | 200 | 2006 |
| Comparison of approaches for rational siRNA design leading to a new efficient and transparent method O Matveeva, Y Nechipurenko, L Rossi, B Moore, P Sætrom, AY Ogurtsov, ... Nucleic acids research 35 (8), e63, 2007 | 188 | 2007 |
| Expansion of the human μ-opioid receptor gene architecture: novel functional variants SA Shabalina, DV Zaykin, P Gris, AY Ogurtsov, J Gauthier, K Shibata, ... Human molecular genetics 18 (6), 1037-1051, 2009 | 182 | 2009 |
| Selective constraint in intergenic regions of human and mouse genomes SA Shabalina, AY Ogurtsov, VA Kondrashov, AS Kondrashov Trends in Genetics 17 (7), 373-376, 2001 | 170 | 2001 |
| Distinct patterns of expression and evolution of intronless and intron-containing mammalian genes SA Shabalina, AY Ogurtsov, AN Spiridonov, PS Novichkov, ... Molecular biology and evolution 27 (8), 1745-1749, 2010 | 141 | 2010 |
| Role of mRNA structure in the control of protein folding G Faure, AY Ogurtsov, SA Shabalina, EV Koonin Nucleic acids research 44 (22), 10898-10911, 2016 | 116 | 2016 |
| Widespread positive selection in synonymous sites of mammalian genes AM Resch, L Carmel, L Mariño-Ramírez, AY Ogurtsov, SA Shabalina, ... Molecular biology and evolution 24 (8), 1821-1831, 2007 | 108 | 2007 |
| Comparative analysis of orthologous eukaryotic mRNAs: potential hidden functional signals SA Shabalina, AY Ogurtsov, IB Rogozin, EV Koonin, DJ Lipman Nucleic Acids Research 32 (5), 1774-1782, 2004 | 108 | 2004 |
| Positive selection at sites of multiple amino acid replacements since rat–mouse divergence GA Bazykin, FA Kondrashov, AY Ogurtsov, S Sunyaev, AS Kondrashov Nature 429 (6991), 558-562, 2004 | 88 | 2004 |
| Evolution of alternative and constitutive regions of mammalian 5'UTRs AM Resch, AY Ogurtsov, IB Rogozin, SA Shabalina, EV Koonin BMC genomics 10, 1-14, 2009 | 86 | 2009 |
| Bioinformatical assay of human gene morbidity FA Kondrashov, AY Ogurtsov, AS Kondrashov Nucleic acids research 32 (5), 1731-1737, 2004 | 79 | 2004 |
| OWEN: aligning long collinear regions of genomes AY Ogurtsov, MA Roytberg, SA Shabalina, AS Kondrashov Bioinformatics 18 (12), 1703-1704, 2002 | 76 | 2002 |
| Variation in human chromosome 21 ribosomal RNA genes characterized by TAR cloning and long-read sequencing JH Kim, AT Dilthey, R Nagaraja, HS Lee, S Koren, D Dudekula, ... Nucleic acids research 46 (13), 6712-6725, 2018 | 71 | 2018 |
| Indel-based evolutionary distance and mouse–human divergence AY Ogurtsov, S Sunyaev, AS Kondrashov Genome Research 14 (8), 1610-1616, 2004 | 67 | 2004 |
| Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites FA Kondrashov, AY Ogurtsov, AS Kondrashov Journal of Theoretical Biology 240 (4), 616-626, 2006 | 58 | 2006 |
| Evolution at protein ends: major contribution of alternative transcription initiation and termination to the transcriptome and proteome diversity in mammals SA Shabalina, AY Ogurtsov, NA Spiridonov, EV Koonin Nucleic acids research 42 (11), 7132-7144, 2014 | 52 | 2014 |
| Analysis of similarity within 142 pairs of orthologous intergenic regions of Caenorhabditis elegans and Caenorhabditis briggsae CT Webb, SA Shabalina, AY Ogurtsov, AS Kondrashov Nucleic acids research 30 (5), 1233-1239, 2002 | 50 | 2002 |
| Optimization of duplex stability and terminal asymmetry for shRNA design OV Matveeva, Y Kang, AN Spiridonov, P Sætrom, VA Nemtsov, ... PloS one 5 (4), e10180, 2010 | 49 | 2010 |
| Analysis of internal loops within the RNA secondary structure in almost quadratic time AY Ogurtsov, SA Shabalina, AS Kondrashov, MA Roytberg Bioinformatics 22 (11), 1317-1324, 2006 | 47 | 2006 |
