Research Topics
| Yi Kuo YuSummaryAffiliation: National Institutes of Health Country: USA Publications
| Collaborators
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Detail Information
Publications
CytoITMprobe: a network information flow plugin for CytoscapeAleksandar Stojmirović
National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA
BMC Res Notes 5:237. 2012..abstract:..- RAId_DbS: peptide identification using database searches with realistic statisticsGelio 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... 
On a class of integrals of Legendre polynomials with complicated arguments--with applications in electrostatics and biomolecular modelingYi 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...- Protein database searches using compositionally adjusted substitution matricesStephen 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... 
Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLASTE 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...- Calibrating E-values for MS2 database search methodsGelio Alves
National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA
Biol Direct 2:26. 2007..We also address the importance of using spectrum-specific statistics and possible improvement on the current calibration protocol. The spectra used for statistical (E-value) calibration are freely available upon request... - Detection of co-eluted peptides using database search methodsGelio Alves
National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, 20894, USA
Biol Direct 3:27. 2008..OPEN PEER REVIEW: Reviewed by Vlad Petyuk (nominated by Arcady Mushegian), King Jordan and Shamil Sunyaev. For the full reviews, please go to the Reviewers' comments section... - Information flow in interaction networksAleksandar 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.... - Information flow in interaction networks II: channels, path lengths, and potentialsAleksandar 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... - The construction and use of log-odds substitution scores for multiple sequence alignmentStephen 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... - RAId_aPS: MS/MS analysis with multiple scoring functions and spectrum-specific statisticsGelio 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... - On the inference of dirichlet mixture priors for protein sequence comparisonXugang 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... - RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integrationGelio 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... - The complexity of the dirichlet model for multiple alignment dataYi 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... - The effectiveness of position- and composition-specific gap costs for protein similarity searchesAleksandar Stojmirović
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Bioinformatics 24:i15-23. 2008.... - Using dissociation energies to predict observability of b- and y-peaks in mass spectra of short peptidesO 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... - PSI-BLAST pseudocounts and the minimum description length principleStephen 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... - Enhancing peptide identification confidence by combining search methodsGelio 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... - Assigning statistical significance to proteotypic peptides via database searchesGelio 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... - ppiTrim: constructing non-redundant and up-to-date interactomesAleksandar 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... - Scale-free networks versus evolutionary driftTeresa 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... - Compositional adjustment of Dirichlet mixture priorsXugang 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... - Electrostatics of charged dielectric spheres with application to biological systemsT 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... - Cysteine-cysteine contact preference leads to target-focusing in protein foldingMihaela 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... - The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositionsYi-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... 
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 chainsO 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....- CytoSaddleSum: a functional enrichment analysis plugin for Cytoscape based on sum-of-weights scoresAleksandar 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... - Geometric aspects of biological sequence comparisonAleksandar 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... - Rigorous treatment of electrostatics for spatially varying dielectrics based on energy minimizationO 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... - Robust and accurate data enrichment statistics via distribution function of sum of weightsAleksandar 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... - The compositional adjustment of amino acid substitution matricesYi-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... - Replica model for an unusual directed polymer in 1+1 dimensions and prediction of the extremal parameter of gapped sequence alignment statisticsYi-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... - Robust accurate identification of peptides (RAId): deciphering MS2 data using a structured library search with de novo based statisticsGelio Alves
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD 20894, USA
Bioinformatics 21:3726-32. 2005..Other important features of RAId include its potential in de novo sequencing alone and the ease of incorporating post-translational modifications... - Simple electrostatic model applicable to biomolecular recognitionT 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.... - Combining independent, weighted P-values: achieving computational stability by a systematic expansion with controllable accuracyGelio 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... - Retrieval accuracy, statistical significance and compositional similarity in protein sequence database searchesYi-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... - ITM Probe: analyzing information flow in protein networksAleksandar Stojmirović
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Bioinformatics 25:2447-9. 2009..AVAILABILITY: ITM Probe web service and documentation can be found at www.ncbi.nlm.nih.gov/CBBresearch/qmbp/mn/itm_probe... - Toward an accurate statistics of gapped alignmentsMaik 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... - Score statistics of global sequence alignment from the energy distribution of a modified directed polymer and directed percolation problemMihaela 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... - Heat conduction process on community networks as a recommendation modelYi 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... - Hybrid alignment: high-performance with universal statisticsYi 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...