NCBI logo Computational Biology Branch
PubMed Entrez BLAST OMIM Books TaxBrowser Structure
  Search for

back to NCBI homepage
back to NCBI homepage

spacer gif
Staff Scientist
Computational Biology Branch
Building 38A, Room 6S604
8600 Rockville Pike
Bethesda, MD 20894

Tel: (301) 594-5693

Curriculum vitae

Research Interests:

  • Comparative analysis of mammalian genomes
  • Genome organization and evolution of mammalian noncoding genome sequences
  • Evolution of noncoding RNA genes
  • Transcriptional and posttranscriptional regulation of gene expression
  • RNA-RNA interactions and regulation of gene expression
  • DNA and RNA signals involved in the regulation of tissue-specific expression
  • Mutation accumulation and genomic deleterious mutation rates

Selected Publications:

  • Zhang F, Kang Y, Saha S, Shabalina SA, Kashina A (2010). Differential Arginylation of Actin Isoforms is Regulated by Coding-Sequence-Dependent Degradation. Science (in press).
  • Shabalina SA, Ogurtsov AY, Spiridonov AN, Novichkov PS, Spiridonov NA, Koonin EV (2010). Distinct patterns of expression and evolution of intronless and intron-containing mammalian genes. Mol. Biol. Evol., 27, 1745-1749.
  • Matveeva OV, Kang Y, Nechipurenko YD, Nemtsov VA, Shabalina SA (2010). Efficient method for the design of siRNAs and shRNAs. PLoS One, 5, e10180.
  • Losada L, Ronning CM, DeShazer D, Woods D, Fedorova N, Kim HS, Shabalina SA, Pearson TR, Brinkac L, Tan P, Nandi T, Crabtree J, Badger J, Beckstrom-Sternberg S, Saqib M, Schutzer SE, Keim P, Nierman WC (2010). Continuing evolution of Burkholderia mallei through genome reduction and large-scale rearrangements. Genome Biol. Evol., 2, 102-116.
  • Fozo EM, Makarova KS, Shabalina SA, Yutin N, Koonin EV, Storz G (2010). Abundance of type I toxin-antitoxin systems in bacteria: searches for new candidates and discovery of novel families. Nucleic Acids Res., 38, 3743-3759.
  • Resch AM, Ogurtsov AY, Rogozin IB, Shabalina SA, Koonin EV (2009). Evolution of alternative and constitutive regions of mammalian 5'UTRs. BMC Genomics, 10, 162.
  • Nackley AG, Shabalina SA, Lambert JE, Conrad MS, Gibson D, Spiridonov AN, Satterfield SK, Diatchenko L (2009). Low Enzymatic Activity Haplotypes of the Human Catechol-O-Methyltransferase Gene: Enrichment for Marker SNPs. PLoS ONE, 4, e5237.
  • Shabalina SA, Zaykin D, Ogurtsov AY, Gris P, Gauthier J, Shibata K, Sama S, Chivileva I, Belfer I, Spiridonov NA, Max MB, Goldman D, Fillingim RB, Maixner W, Diatchenko L (2009). Expansion of the Human .-Opioid Receptor Gene Architecture: Novel Functional Variants. Hum. Mol. Genet., 18, 1037-1051.
  • Ogurtsov AY, Mari.o-Ram.rez L, Johnson GR, Landsman D, Shabalina SA, Spiridonov NA (2008). Expression patterns of protein kinases correlate with gene architecture and evolutionary rates. PLoS ONE, 3, e3599. Shabalina SA and Koonin EV (2008). Evolution and origin of the eukaryotic microRNA system. Trends Ecol. Evol., 23, 578-587.
  • Wang P, Lyman RF, Shabalina SA, Mackay TF, Anholt RR (2007). Association of polymorphisms in odorant-binding protein genes with variation in olfactory response to benzaldehyde in Drosophila. Genetics, 177, 1655-1665.
  • Diatchenko L, Nackley AG, Chivileva I, Shabalina SA, Maixner W (2007). Genetic Architecture of Human Pain Perception. Trends Genet., 23, 605-613.
  • Resch AM, Carmel L, Marino-Ramirez L, Ogurtsov AY, Shabalina SA, Rogozin IB, Koonin EV (2007). Evidence of positive and negative selection in synonymous sites of mammalian genes. Mol. Biol. Evol., 24, 1821-1831.
  • Matveeva O, Nechipurenko Y, Rossi L, Moore B, Saetrom P, Ogurtsov AY, Atkins JF, Shabalina SA (2007). Comparative analysis of experimental databases and algorithms for functional siRNA design. Nucleic Acids Res., 35, e63.
  • Nackley AG, Shabalina SA, Tchivileva I, Satterfield KS, Korchinskyy O, Maixner W. Diatchenko L (2006). Common human catechol-O-methyltransferase haplotype modulates protein expression by altering mRNA secondary structure. Science, 314, 1930-1933.
  • Diatchenko L, Anderson AD, Slade GD, Fillingim RB, Shabalina SA, Bhalang K, Sigurdsson A., Higgins T, Sama S, Belfer I, Goldman D., Max MB, Weir B, Maixner W (2006). Three major haplotypes of the adrenergic receptor .2 define psychological profile and risk of development of a common musculoskeletal pain disorder. Am. J. Med. Genet. B Neuropsychiatr. Genet., 141, 449-462.
  • Shabalina SA, Ogurtsov AY, Spiridonov NA (2006). A Periodic pattern of mRNA secondary structure created by the genetic code. Nucleic Acids Res., 34, 2428-2437.
  • Makarova KS, Grishin NV, Shabalina SA, Wolf YI, Koonin EV (2006). A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biology Direct, 1, 7.
  • Ogurtsov AY, Shabalina SA, Kondrashov AS, Roytberg MA (2006). Analysis of internal loops within the RNA secondary structure in an almost quadratic time. Bioinformatics, 22, 1317-1324.
  • Shabalina SA, Spiridonov AN, Ogurtsov AY (2006). Computational models with thermodynamic and composition features improve siRNA design. BMC Bioinformatics, 7, 65.
  • Yampolsky L, Allen CD, Shabalina SA, Kondrashov AS (2005). Persistence time of loss-of-function mutations at non-essential loci affecting eye color in Drosophila melanogaster. Genetics, 171, 2133-2138.
  • Diatchenko L, Slade GD, Nackley AG, Bhalang K, Sigurdsson A, Belfer I, Goldman D, Xu K, Shabalina SA, Shagin D, Max MB, Makarov SS, Maixner W (2005). Genetic basis for individual variations in pain perception and the development of a chronic pain condition. Hum. Mol. Genet., 14, 135-143.
  • Shabalina SA, Ogurtsov AY, Rogozin IB, Koonin EV, Lipman DJ (2004). Comparative analysis of orthologous eukaryotic mRNAs: potential hidden functional signals. Nucleic Acids Res., 32, 1774-1782.
  • Shabalina SA, Spiridonov NA (2004). The mammalian transcriptome and the function of non-coding DNA sequences. Genome Biol., 5, 105.
  • Matveeva OV, Foley BT , Nemtsov VA, Gesteland RF, Matsufuji S, Atkins JF, Ogurtsov AY, Shabalina SA (2004). Identification of regions in multiple sequence alignments thermodynamically suitable for targeting by consensus oligonucleotides: application to HIV genome. BMC Bioinformatics, 5, 44.
  • Kolker E, Makarova KS, Shabalina SA, Picone AF, Purvine S, Holzman T, Cherny T, Armbruster D, Munson RS, Kolesov G, Frishman D, Galperin MY (2004) Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae. Nucleic Acids Res., 32, 2353-2361.
  • Glazko GV, Koonin EV, Rogozin IB, Shabalina SA (2003). A significant fraction of conserved noncoding DNA in human and mouse consists of predicted matrix attachment regions. Trends Genet.,19, 119-124.
  • Silva JC, Shabalina SA, Harris JL, Spouge AS, Kondrashov AS (2003). Conserved fragments of transposable elements in intergenic regions: evidence for widespread recruitment of Mir and L2-derived sequences within the mouse and human genomes. Genetical Research, 82, 1-18.
  • Matveeva OV, Shabalina SA, Nemtsov VA, Tsodikov AD, Gesteland RF, Atkins JF (2003) Thermodynamic calculations and statistical correlations for oligo-probes design. Nucleic Acids Res., 31, 4211-4217.
  • Matveeva OV, Mathews DH, Tsodikov AD, Shabalina SA, Gesteland RF, Atkins JF, Freier SM (2003). Thermodynamic criteria for high hit rate antisense oligonucleotide design. Nucleic Acids Res., 31, 4989-4994.
  • Shabalina SA, Ogurtsov AY, Lipman DJ, Kondrashov SA (2003). Patterns in interspecies similarity correlate with nucleotide composition in mammalian 3'UTRs.
  • Nucleic Acids Res., 31, 5433-5439
  • Webb CT, Shabalina SA, Ogurtsov AY, Kondrashov AS (2002). Analysis of similarity within 142 pairs of orthologous intergenic regions of Caenorhabditis elegans and Caenorhabditis briggsae. Nucleic Acids Res., 30, 1233-1239.
  • Kondrashov AS, Shabalina SA (2002). Classification of common conserved sequences in mammalian intergenic regions. Hum. Mol. Genet., 11, 669-674.
  • Shabalina SA (2002). Regions of intermolecular complementarity in Escherichia coli 16S rRNA, mRNA, and tRNA molecules. Mol. Biol., 36, 359-364.
  • Ogurtsov AY, Roytberg MA, Shabalina SA, Kondrashov AS (2002). OWEN: aligning long collinear regions of genomes. Bioinformatics, 18, 1703-1704.
  • Roytberg MA, Ogurtsov AY, Shabalina SA, Kondrashov AS (2002). A hierarchical approach to aligning collinear regions of genomes. Bioinformatics, 18, 1673-1680.
  • Shabalina SA, Ogurtsov AY, Kondrashov VA, Kondrashov AS (2001). Selective constraint in intergenic regions of human and mouse genomes. Trends Genet., 17, 373-376.
  • Matveeva OV, Tsodikov AD, Giddings M, Freier SM, Wyatt JR, Spiridonov AN, Shabalina SA, Gesteland RF, Atkins JF (2000). Identification of sequence motifs in oligonucleotides whose presence is correlated with antisense activity. Nucleic Acids Res., 28, 2862-2865.
  • Yampolsky LY, Webb CT, Shabalina SA, Kondrashov AS (1999). Rapid accumulation of a vertically transmitted parasite triggered by relaxation of natural selection among hosts. Evolutionary Ecology Research, 1, 581-589.
  • Shabalina SA, Kondrashov AS (1999). Pattern of selective constraint in C. elegans and C. briggsae genomes. Genetical Research, 74, 23-30.
  • Kondrashov AS, Yampolsky LYu, Shabalina SA (1998). On the sympatric origin of species by means of natural selection. In: Endless Forms: Species and Speciation (D. J. Howarth and S. H. Berlocher, eds.), 90-98, Oxford Univ. Press.
  • Shabalina SA, Yampolsky LY, Kondrashov AS (1997). Decline of fitness in panmictic populations of Drosophila melanogaster maintained under relaxed natural selection. Proc. Natl. Acad. Sci. USA, 94, 13034-13039.

Disclaimer      Privacy statement

Revised: 25 August 2010.