Ruslan I Sadreyev

Summary

Affiliation: University of Texas Southwestern Medical Center
Country: USA

Publications

  1. ncbi Effects of glutamate agonists on the isolated neurons from the locomotor network of the mollusc Clione limacina
    Ruslan I Sadreyev
    A N Belozersky Institute of Physico Chemical Biology, Moscow State University, Moscow 119899, Russia
    Neuroreport 13:2235-9. 2002
  2. ncbi Considering scores between unrelated proteins in the search database improves profile comparison
    Ruslan I Sadreyev
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390 9050, USA
    BMC Bioinformatics 10:399. 2009
  3. ncbi COMPASS server for homology detection: improved statistical accuracy, speed and functionality
    Ruslan I Sadreyev
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390 9050, USA
    Nucleic Acids Res 37:W90-4. 2009
  4. ncbi Estimates of statistical significance for comparison of individual positions in multiple sequence alignments
    Ruslan I Sadreyev
    Howard Hughes Medical Institute, Department of Biochemistry, University of Texas Southwestern Medical Center, 5323, Harry Hines Blvd, Dallas, TX 75390 9050, USA
    BMC Bioinformatics 5:106. 2004
  5. ncbi Exploring dynamics of protein structure determination and homology-based prediction to estimate the number of superfamilies and folds
    Ruslan I Sadreyev
    Howard Hughes Medical Institute, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390 8816, USA
    BMC Struct Biol 6:6. 2006
  6. ncbi COMPASS server for remote homology inference
    Ruslan I Sadreyev
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390 9050, USA
    Nucleic Acids Res 35:W653-8. 2007
  7. ncbi A tale of two ferredoxins: sequence similarity and structural differences
    S Sri Krishna
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390 9050, USA
    BMC Struct Biol 6:8. 2006
  8. ncbi A comprehensive system for evaluation of remote sequence similarity detection
    Yuan Qi
    Department of Biochemistry, University of Texas Southwestern Medical Center, 5323, Harry Hines Blvd, Dallas, TX 75390 9050, USA
    BMC Bioinformatics 8:314. 2007
  9. ncbi Structure similarity measure with penalty for close non-equivalent residues
    Ruslan I Sadreyev
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390 9050, USA
    Bioinformatics 25:1259-63. 2009
  10. ncbi PROCAIN server for remote protein sequence similarity search
    Yong Wang
    Biomedical Engineering Program, University of Texas Southwestern Medical Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390 9050, USA
    Bioinformatics 25:2076-7. 2009

Collaborators

Detail Information

Publications20

  1. ncbi Effects of glutamate agonists on the isolated neurons from the locomotor network of the mollusc Clione limacina
    Ruslan I Sadreyev
    A N Belozersky Institute of Physico Chemical Biology, Moscow State University, Moscow 119899, Russia
    Neuroreport 13:2235-9. 2002
    ....
  2. ncbi Considering scores between unrelated proteins in the search database improves profile comparison
    Ruslan I Sadreyev
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390 9050, USA
    BMC Bioinformatics 10:399. 2009
    ..Here we analyze a novel approach to estimate the statistical significance of profile similarity: the explicit consideration of background score distributions for each database template (subject)...
  3. ncbi COMPASS server for homology detection: improved statistical accuracy, speed and functionality
    Ruslan I Sadreyev
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390 9050, USA
    Nucleic Acids Res 37:W90-4. 2009
    ..URL: http://prodata.swmed.edu/compass...
  4. ncbi Estimates of statistical significance for comparison of individual positions in multiple sequence alignments
    Ruslan I Sadreyev
    Howard Hughes Medical Institute, Department of Biochemistry, University of Texas Southwestern Medical Center, 5323, Harry Hines Blvd, Dallas, TX 75390 9050, USA
    BMC Bioinformatics 5:106. 2004
    ....
  5. ncbi Exploring dynamics of protein structure determination and homology-based prediction to estimate the number of superfamilies and folds
    Ruslan I Sadreyev
    Howard Hughes Medical Institute, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390 8816, USA
    BMC Struct Biol 6:6. 2006
    ..random sample of all sequence families? Do targets solved by structural genomic initiatives (SGI) provide such a sample? What are approximate total numbers of structure-based superfamilies and folds among soluble globular domains?..
  6. ncbi COMPASS server for remote homology inference
    Ruslan I Sadreyev
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390 9050, USA
    Nucleic Acids Res 35:W653-8. 2007
    ..To illustrate the value of this tool for protein structure-functional prediction, we present two examples of detecting distant homologs for uncharacterized protein families. Available at http://prodata.swmed.edu/compass...
  7. ncbi A tale of two ferredoxins: sequence similarity and structural differences
    S Sri Krishna
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390 9050, USA
    BMC Struct Biol 6:8. 2006
    ..Profile-based methods for sequence comparison, such as PSI-BLAST and HMMer, suggest statistically significant similarity between these domains...
  8. ncbi A comprehensive system for evaluation of remote sequence similarity detection
    Yuan Qi
    Department of Biochemistry, University of Texas Southwestern Medical Center, 5323, Harry Hines Blvd, Dallas, TX 75390 9050, USA
    BMC Bioinformatics 8:314. 2007
    ....
  9. ncbi Structure similarity measure with penalty for close non-equivalent residues
    Ruslan I Sadreyev
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390 9050, USA
    Bioinformatics 25:1259-63. 2009
    ....
  10. ncbi PROCAIN server for remote protein sequence similarity search
    Yong Wang
    Biomedical Engineering Program, University of Texas Southwestern Medical Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390 9050, USA
    Bioinformatics 25:2076-7. 2009
    ..AVAILABILITY: http://prodata.swmed.edu/procain/...
  11. ncbi Quality of alignment comparison by COMPASS improves with inclusion of diverse confident homologs
    Ruslan I Sadreyev
    Howard Hughes Medical Institute, and Department of Biochemistry, University of Texas Southwestern Medical Center, 5323, Harry Hines Blvd, Dallas, TX 75390-9050, USA
    Bioinformatics 20:818-28. 2004
    ..Our results suggest that at any level of profile diversity, one should include in the multiple alignment as many confident sequence homologs as possible in order to produce the most accurate results...
  12. ncbi PROCAIN: protein profile comparison with assisting information
    Yong Wang
    Biomedical Engineering Program, University of Texas Southwestern Medical Center, Dallas, TX 75390 9050, USA
    Nucleic Acids Res 37:3522-30. 2009
    ..ProCAIn, relevant databases and tools can be downloaded from: http://prodata.swmed.edu/procain/download. The web server can be accessed at http://prodata.swmed.edu/procain/procain.php...
  13. ncbi Profile-profile comparisons by COMPASS predict intricate homologies between protein families
    Ruslan I Sadreyev
    Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050, USA
    Protein Sci 12:2262-72. 2003
    ....
  14. ncbi Accurate statistical model of comparison between multiple sequence alignments
    Ruslan I Sadreyev
    Howard Hughes Medical Institute, Dallas, TX 75390 9050, USA
    Nucleic Acids Res 36:2240-8. 2008
    ..Third, we apply this random model to database searches and show that it surpasses conventional models in the accuracy of detecting remote protein similarities...
  15. ncbi CASP5 assessment of fold recognition target predictions
    Lisa N Kinch
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390 9050, USA
    Proteins 53:395-409. 2003
    ..We also compared the results of manual groups to those of automatic servers evaluated in parallel by CAFASP, showing that the top performing automated server structure predictions approached those of the best manual predictors...
  16. ncbi Discrete-continuous duality of protein structure space
    Ruslan I Sadreyev
    Howard Hughes Medical Institute, 5323 Harry Hines Blvd, Dallas, TX 75390 9050, USA
    Curr Opin Struct Biol 19:321-8. 2009
    ..However, for a geometric similarity measure, it is usually possible to find a reasonable cutoff that yields paths connecting any two structures through intermediates...
  17. ncbi Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations
    Stefan F Pinter
    Howard Hughes Medical Institute, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
    Genome Res 22:1864-76. 2012
    ..This suggests that PRC2 and H3K27 methylation spread along a gradient unique to XCI. We propose that XCI is governed by a hierarchy of defined Polycomb stations that spread H3K27 methylation in cis...
  18. ncbi Phenotypic categorization of genetic skin diseases reveals new relations between phenotypes, genes and pathways
    Ruslan I Sadreyev
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390 9050, USA
    Bioinformatics 25:2891-6. 2009
    ..This interaction may mediate glucose-dependent regulation of TGF-beta signaling, providing a clue to the known association between angiopathies and diabetes and implying new gene candidates for mutational analysis and drug targeting...
  19. ncbi Xist RNA is a potent suppressor of hematologic cancer in mice
    Eda Yildirim
    Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
    Cell 152:727-42. 2013
    ..Thus, Xist RNA not only is required to maintain XCI but also suppresses cancer in vivo...
  20. ncbi X-chromosome hyperactivation in mammals via nonlinear relationships between chromatin states and transcription
    Eda Yildirim
    Howard Hughes Medical Institute, Boston, Massachusetts, USA
    Nat Struct Mol Biol 19:56-61. 2012
    ..Thus, Xa upregulation involves combined increases of active histone marks and Pol II occupancy, without invoking X-specific dependencies between chromatin states and transcription...