Yi Kuo Yu

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc RAId_DbS: peptide identification using database searches with realistic statistics
    Gelio Alves
    National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA
    Biol Direct 2:25. 2007
  2. ncbi request reprint On a class of integrals of Legendre polynomials with complicated arguments--with applications in electrostatics and biomolecular modeling
    Yi Kuo Yu
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Physica A 326:522-33. 2003
  3. pmc Protein database searches using compositionally adjusted substitution matrices
    Stephen F Altschul
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    FEBS J 272:5101-9. 2005
  4. ncbi request reprint Robust accurate identification of peptides (RAId): deciphering MS2 data using a structured library search with de novo based statistics
    Gelio Alves
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD 20894, USA
    Bioinformatics 21:3726-32. 2005
  5. pmc Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST
    E Michael Gertz
    National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
    BMC Biol 4:41. 2006
  6. pmc Calibrating E-values for MS2 database search methods
    Gelio Alves
    National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA
    Biol Direct 2:26. 2007
  7. ncbi request reprint Replica model for an unusual directed polymer in 1+1 dimensions and prediction of the extremal parameter of gapped sequence alignment statistics
    Yi Kuo Yu
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 69:061904. 2004
  8. pmc Retrieval accuracy, statistical significance and compositional similarity in protein sequence database searches
    Yi Kuo Yu
    National Center for Biotechnology Information, National Library of Medicine, NIH, DHHS, Bethesda, MD 20894, USA
    Nucleic Acids Res 34:5966-73. 2006
  9. pmc The compositional adjustment of amino acid substitution matrices
    Yi Kuo Yu
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Proc Natl Acad Sci U S A 100:15688-93. 2003
  10. pmc Detection of co-eluted peptides using database search methods
    Gelio Alves
    National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, 20894, USA
    Biol Direct 3:27. 2008

Detail Information

Publications43

  1. pmc RAId_DbS: peptide identification using database searches with realistic statistics
    Gelio Alves
    National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA
    Biol Direct 2:25. 2007
    ..The peptide identification performance and statistical accuracy of RAId_DbS are assessed and compared with several other search tools. The executables and data related to RAId_DbS are freely available upon request...
  2. ncbi request reprint On a class of integrals of Legendre polynomials with complicated arguments--with applications in electrostatics and biomolecular modeling
    Yi Kuo Yu
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Physica A 326:522-33. 2003
    ..In fact, with this solution, a more robust foundation is laid for the Generalized Born method in modeling the dynamics of biomolecules...
  3. pmc Protein database searches using compositionally adjusted substitution matrices
    Stephen F Altschul
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    FEBS J 272:5101-9. 2005
    ..In a typical database search, at least one of these criteria is satisfied by over half the related sequence pairs. Compositional substitution matrix adjustment is now available in NCBI's protein-protein version of blast...
  4. ncbi request reprint Robust accurate identification of peptides (RAId): deciphering MS2 data using a structured library search with de novo based statistics
    Gelio Alves
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD 20894, USA
    Bioinformatics 21:3726-32. 2005
    ..The characteristics of the noise can only be uncovered once a spectrum is given. We wish to overcome such issues...
  5. pmc Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST
    E Michael Gertz
    National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
    BMC Biol 4:41. 2006
    ..Until recently, composition-based statistics were available only for protein-protein searches. They are now available as a command line option for recent versions of TBLASTN and as an option for TBLASTN on the NCBI BLAST web server...
  6. pmc Calibrating E-values for MS2 database search methods
    Gelio Alves
    National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA
    Biol Direct 2:26. 2007
    ..Although each search engine has its strength, combining the strengths of various search engines is not yet realizable largely due to the lack of a unified statistical framework that is applicable to any method...
  7. ncbi request reprint Replica model for an unusual directed polymer in 1+1 dimensions and prediction of the extremal parameter of gapped sequence alignment statistics
    Yi Kuo Yu
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 69:061904. 2004
    ..We have obtained the conditions under which the more important extremal parameter lambda, characterizing the alignment score statistics, becomes predictable...
  8. pmc Retrieval accuracy, statistical significance and compositional similarity in protein sequence database searches
    Yi Kuo Yu
    National Center for Biotechnology Information, National Library of Medicine, NIH, DHHS, Bethesda, MD 20894, USA
    Nucleic Acids Res 34:5966-73. 2006
    ..A version of the BLAST protein database search program, modified to employ this new measure, outperforms the baseline program in both retrieval and statistical accuracy on ASTRAL, a SCOP-based test set...
  9. pmc The compositional adjustment of amino acid substitution matrices
    Yi Kuo Yu
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Proc Natl Acad Sci U S A 100:15688-93. 2003
    ..Composition-specific substitution matrix adjustment is shown to be of utility for comparing compositionally biased proteins, including those of organisms with nucleotide-biased, and therefore codon-biased, genomes or isochores...
  10. pmc Detection of co-eluted peptides using database search methods
    Gelio Alves
    National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, 20894, USA
    Biol Direct 3:27. 2008
    ....
  11. pmc Information flow in interaction networks II: channels, path lengths, and potentials
    Aleksandar Stojmirović
    National Central for Biotechnology Information, National Library of Medicine, National Institute of Health, Bethesda, Maryland, USA
    J Comput Biol 19:379-403. 2012
    ..Through examples involving the yeast pheromone response pathway, we illustrate the versatility and stability of our new framework...
  12. pmc The construction and use of log-odds substitution scores for multiple sequence alignment
    Stephen F Altschul
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS Comput Biol 6:e1000852. 2010
    ..We illustrate how simple BILD score based strategies can enhance the recognition of DNA binding domains, including the Api-AP2 domain in Toxoplasma gondii and Plasmodium falciparum...
  13. pmc RAId_aPS: MS/MS analysis with multiple scoring functions and spectrum-specific statistics
    Gelio Alves
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS ONE 5:e15438. 2010
    ..The web link is http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/raid_aps/index.html. Relevant binaries for Linux, Windows, and Mac OS X are available from the same page...
  14. pmc On the inference of dirichlet mixture priors for protein sequence comparison
    Xugang Ye
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    J Comput Biol 18:941-54. 2011
    ..We apply our methods as well to real data, and infer Dirichlet mixtures that describe the data better than does a mixture derived using previous approaches...
  15. ncbi request reprint The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions
    Yi Kuo Yu
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD 20894, USA
    Bioinformatics 21:902-11. 2005
    ..RESULTS: This paper presents the mathematical details underlying the compositional adjustment of amino acid or DNA substitution matrices...
  16. pmc CytoITMprobe: a network information flow plugin for Cytoscape
    Aleksandar Stojmirović
    National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA
    BMC Res Notes 5:237. 2012
    ..However, plugins for Cytoscape with these features do not yet exist. To provide the Cytoscape users the possibility of integrating ITM Probe into their workflows, we developed CytoITMprobe, a new Cytoscape plugin...
  17. pmc RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration
    Gelio Alves
    National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA
    BMC Genomics 9:505. 2008
    ..Integration of such information with peptide searches facilitates speedy, dynamic information retrieval that may significantly benefit clinical laboratory studies...
  18. pmc The complexity of the dirichlet model for multiple alignment data
    Yi Kuo Yu
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    J Comput Biol 18:925-39. 2011
    ..Although our results are confined to the Dirichlet model, they may cast light as well on the complexity of Dirichlet mixture models, which have been applied fruitfully to the study of protein multiple sequence alignments...
  19. ncbi request reprint Information flow in interaction networks
    Aleksandar Stojmirović
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    J Comput Biol 14:1115-43. 2007
    ....
  20. pmc Using dissociation energies to predict observability of b- and y-peaks in mass spectra of short peptides
    O I Obolensky
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Rapid Commun Mass Spectrom 26:915-20. 2012
    ..We propose using dissociation energies (as opposed to proton affinities) as a predictor of observability of different m/z peaks in spectra of short peptides...
  21. pmc PSI-BLAST pseudocounts and the minimum description length principle
    Stephen F Altschul
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD 20894, USA
    Nucleic Acids Res 37:815-24. 2009
    ..A new method for calculating pseudocounts that significantly improves PSI-BLAST's; retrieval accuracy is now employed by default...
  22. pmc ppiTrim: constructing non-redundant and up-to-date interactomes
    Aleksandar Stojmirović
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Database (Oxford) 2011:bar036. 2011
    ..Database URL: http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads/ppiTrim.html...
  23. pmc Assigning statistical significance to proteotypic peptides via database searches
    Gelio Alves
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Proteomics 74:199-211. 2011
    ..The advantage of including proteotypic information is evidenced by its superior retrieval performance when compared to regular database searches...
  24. pmc Improving peptide identification sensitivity in shotgun proteomics by stratification of search space
    Gelio Alves
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, United States
    J Proteome Res 12:2571-81. 2013
    ..Our results show that this scheme can significantly improve retrieval performance compared to those of search strategies that assign equal Bonferroni correction factors to all qualified peptides...
  25. pmc Enhancing peptide identification confidence by combining search methods
    Gelio Alves
    National Center for Biotechnology Information, Library of Medicine, NIH, Bethesda, MD 20894, USA
    J Proteome Res 7:3102-13. 2008
    ..The data related to this study are freely available upon request...
  26. pmc Scale-free networks versus evolutionary drift
    Teresa M Przytycka
    NCBI NLM NIH 8600 Rockville Pike, Bethesda, MD 20894, USA
    Comput Biol Chem 28:257-64. 2004
    ..Instead they adhere quite closely to the Yule distribution. This finding indicates that the direct applicability of scale-free models in understanding the evolution of biological network may not be as wide as it has been hoped for...
  27. pmc Compositional adjustment of Dirichlet mixture priors
    Xugang Ye
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    J Comput Biol 17:1607-20. 2010
    ..We have implemented this method, and can compositionally adjust to good precision a 20-component Dirichlet mixture prior for proteins in under half a second on a standard workstation...
  28. pmc Cysteine-cysteine contact preference leads to target-focusing in protein folding
    Mihaela E Sardiu
    Stowers Institute for Medical Research, Kansas City, Missouri, USA
    Biophys J 93:938-51. 2007
    ..The concept of target-focusing also provides a qualitative understanding of a correlation between the rates of protein folding and parameters such as contact order and total contact distance...
  29. ncbi request reprint Electrostatics of charged dielectric spheres with application to biological systems
    T P Doerr
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike MSC 6075, Bethesda, Maryland 20894, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 73:061902. 2006
    ..With modest additions, the model also describes an electrorheological fluid. Such a system provides the cleanest opportunity to apply the model...
  30. pmc ITM Probe: analyzing information flow in protein networks
    Aleksandar Stojmirović
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Bioinformatics 25:2447-9. 2009
    ..With a click, the user may send the resulting protein list for enrichment analysis to facilitate hypothesis formation or confirmation...
  31. pmc Using dissociation energies to predict observability of b- and y-peaks in mass spectra of short peptides. II. Results for hexapeptides with non-polar side chains
    O I Obolensky
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Rapid Commun Mass Spectrom 27:152-6. 2013
    ....
  32. pmc Rigorous treatment of electrostatics for spatially varying dielectrics based on energy minimization
    O I Obolensky
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 79:041907. 2009
    ..The simplicity of application of the formalism to real problems is shown with analytical and numerical examples...
  33. pmc Robust and accurate data enrichment statistics via distribution function of sum of weights
    Aleksandar Stojmirović
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Bioinformatics 26:2752-9. 2010
    ..Others either mandate extensive simulations to obtain statistics or assume normal weight distribution. In addition, most methods have difficulty assigning correct statistical significance to terms with few entities...
  34. pmc Molecular Isotopic Distribution Analysis (MIDAs) with Adjustable Mass Accuracy
    Gelio Alves
    National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, 20894, USA
    J Am Soc Mass Spectrom 25:57-70. 2014
    ..MIDAs can be accessed freely through a user-friendly web-interface at http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/midas/index.html. ..
  35. pmc Geometric aspects of biological sequence comparison
    Aleksandar Stojmirović
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    J Comput Biol 16:579-610. 2009
    ..Numerous examples are provided to illustrate the concepts introduced and their potential applications...
  36. pmc CytoSaddleSum: a functional enrichment analysis plugin for Cytoscape based on sum-of-weights scores
    Aleksandar Stojmirović
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Bioinformatics 28:893-4. 2012
    ..Furthermore, query results are written as Cytoscape attributes allowing easy saving, retrieval and integration into network-based data analysis workflows...
  37. pmc Combining independent, weighted P-values: achieving computational stability by a systematic expansion with controllable accuracy
    Gelio Alves
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS ONE 6:e22647. 2011
    ..ncbi.nlm.nih.gov/CBBresearch/Yu/downloads/CoinedPValues.html...
  38. pmc Simple electrostatic model applicable to biomolecular recognition
    T P Doerr
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, MSC 6075, Bethesda, Maryland 20894 6075, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 81:031925. 2010
    ....
  39. pmc The effectiveness of position- and composition-specific gap costs for protein similarity searches
    Aleksandar Stojmirović
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Bioinformatics 24:i15-23. 2008
    ....
  40. ncbi request reprint Heat conduction process on community networks as a recommendation model
    Yi Cheng Zhang
    Physics Department, University of Fribourg, 1700 Fribourg, Switzerland
    Phys Rev Lett 99:154301. 2007
    ..The performance is assessed by comparing with traditional recommendation methods using real data...
  41. ncbi request reprint Toward an accurate statistics of gapped alignments
    Maik Kschischo
    University of Applied Sciences Koblenz, RheinAhrCampus Remagen, Südallee 2, 53424 Remagen, Germany
    Bull Math Biol 67:169-91. 2005
    ..Although the result demonstrated uses a simple match-mismatch scoring system, it is expected to be a good starting point for more general scoring functions...
  42. ncbi request reprint Hybrid alignment: high-performance with universal statistics
    Yi Kuo Yu
    Department of Physics, Florida Atlantic University, 777 Glades Road, Boca Raton 33431 0991, USA
    Bioinformatics 18:864-72. 2002
    ..Hybrid alignment is thereby established as a high performance alignment algorithm with well-characterized, universal statistics...
  43. ncbi request reprint Score statistics of global sequence alignment from the energy distribution of a modified directed polymer and directed percolation problem
    Mihaela E Sardiu
    Department of Physics, Florida Atlantic University, Boca Raton, Florida 33431, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 72:061917. 2005
    ..Nevertheless, the possibility of characterizing score statistics for modest system size (sequence lengths), via proper reparametrization of alignment scores, is illustrated...