Yi-Kuo Yu

发表

The effectiveness of position- and composition-specific gap costs for protein similarity searches

E. Michael Gertz, Aleksandar Stojmirovic, Stephen F. Altschul, 2008, ISMB.

Geometric Aspects of Biological Sequence Comparison

Aleksandar Stojmirovic, Yi-Kuo Yu, 2009, J. Comput. Biol..

Hybrid alignment: high-performance with universal statistics

Terence Hwa, Yi-Kuo Yu, Ralf Bundschuh, 2002, Bioinform..

Confidence assignment for mass spectrometry based peptide identifications via the extreme value distribution

Yi-Kuo Yu, Gelio Alves, Yi-Kuo Yu, 2016, Bioinform..

RAId: Knowledge‐Integrated Proteomics Web Service with Accurate Statistical Significance Assignment

Yi-Kuo Yu, Gelio Alves, Aleksey Y Ogurtsov, 2019, Proteomics.

RAId{\_}DbS: Method for Peptide ID using Database Search with Accurate Statistics

Aleksey Y. Ogurtsov, Yi-Kuo Yu, Gelio Alves, 2007 .

Sequence Alignment in Bioinformatics

Yi-Kuo Yu, 2004 .

Challenges of information retrieval and evaluation in data-centric biology.

Yi-Kuo Yu, 2011, Omics : a journal of integrative biology.

Mass spectrometry-based protein identification with accurate statistical significance assignment

Yi-Kuo Yu, Gelio Alves, Yi-Kuo Yu, 2014, Bioinform..

High Performance Alignment with Universal Statistics: the Hybrid Method and Open Problems

Yi-Kuo Yu, Elizabeth Raley, 2001 .

RAId_deNovo: giving the score distribution of all possible peptides for statistical inference in peptide identifications

Aleksey Y. Ogurtsov, Yi-Kuo Yu, Gelio Alves, 2008 .

The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions

Stephen F. Altschul, Yi-Kuo Yu, S. Altschul, 2005, Bioinform..

ITM Probe: analyzing information flow in protein networks

Aleksandar Stojmirovic, Yi-Kuo Yu, Yi-Kuo Yu, 2009, Bioinform..

Assigning statistical significance to proteotypic peptides via database searches.

Yi-Kuo Yu, Gelio Alves, Aleksey Y Ogurtsov, 2011, Journal of proteomics.

Enhancing Peptide Identification Confidence by Combining Search Methods

Yi-Kuo Yu, Gelio Alves, Guanghui Wang, 2008, Journal of proteome research.

Heat conduction process on community networks as a recommendation model.

Yi-Cheng Zhang, Yi-Kuo Yu, Marcel Blattner, 2007, Physical review letters.

Publisher’s Note: Heat Conduction Process on Community Networks as a Recommendation Model [Phys. Rev. Lett.99, 154301 (2007)]

Yi-Cheng Zhang, Yi-Kuo Yu, Marcel Blattner, 2007 .

RAId_aPS: MS/MS Analysis with Multiple Scoring Functions and Spectrum-Specific Statistics

Aleksey Y. Ogurtsov, Yi-Kuo Yu, Gelio Alves, 2008, PloS one.

RAId_deNovo: using de novo based spectrum-specific statistics to combine search results from multiple scoring functions and more

Aleksey Y. Ogurtsov, Yi-Kuo Yu, Gelio Alves, 2008 .

Information Flow in Interaction Networks II: Channels, Path Lengths, and Potentials

Aleksandar Stojmirovic, Yi-Kuo Yu, 2012, J. Comput. Biol..

Information Flow in Interaction Networks

Aleksandar Stojmirovic, Yi-Kuo Yu, Yi-Kuo Yu, 2011, J. Comput. Biol..

Information channels in protein interaction networks

Yi-Kuo Yu, Aleksandar Stojmirović, 2009 .

CytoITMprobe: a network information flow plugin for Cytoscape

Aleksandar Stojmirovic, Yi-Kuo Yu, Alexander Bliskovsky, 2011, BMC Research Notes.

Compositional Adjustment of Dirichlet Mixture Priors

Xugang Ye, Stephen F. Altschul, Yi-Kuo Yu, 2010, J. Comput. Biol..

Robust accurate identification of peptides (RAId): deciphering MS2 data using a structured library search with de novo based statistics

Yi-Kuo Yu, Gelio Alves, Yi-Kuo Yu, 2005, Bioinform..

Robust and accurate data enrichment statistics via distribution function of sum of weights

Aleksandar Stojmirovic, Yi-Kuo Yu, Yi-Kuo Yu, 2010, Bioinform..

Simple electrostatic model applicable to biomolecular recognition.

Yi-Kuo Yu, T P Doerr, 2010, Physical review. E, Statistical, nonlinear, and soft matter physics.

Decoding Information from noisy, redundant, and intentionally-distorted sources

Yi-Cheng Zhang, Paolo Laureti, Yi-Kuo Yu, 2006 .

Scale-free networks versus evolutionary drift

Teresa M. Przytycka, Yi-Kuo Yu, T. Przytycka, 2004, Comput. Biol. Chem..

The Construction and Use of Log-Odds Substitution Scores for Multiple Sequence Alignment

John C. Wootton, Stephen F. Altschul, Yi-Kuo Yu, 2010, PLoS Comput. Biol..

ppiTrim: constructing non-redundant and up-to-date interactomes

Aleksandar Stojmirovic, Yi-Kuo Yu, Yi-Kuo Yu, 2011, Database J. Biol. Databases Curation.

A graphical user interface for RAId, a knowledge integrated proteomics analysis suite with accurate statistics

Yi-Kuo Yu, Gelio Alves, Brendan Joyce, 2018, BMC Research Notes.

On the Inference of Dirichlet Mixture Priors for Protein Sequence Comparison

Xugang Ye, Stephen F. Altschul, Yi-Kuo Yu, 2011, J. Comput. Biol..

Exploring induced pluripotency in human fibroblasts via construction, validation, and application of a gene regulatory network

Yi-Kuo Yu, Mehdi B Hamaneh, Yi-Kuo Yu, 2019, PloS one.

The Complexity of the Dirichlet Model for Multiple Alignment Data

Stephen F. Altschul, Yi-Kuo Yu, 2011, J. Comput. Biol..

Log-odds sequence logos

Aleksandar Stojmirovic, David Landsman, Stephen F. Altschul, 2015, Bioinform..

Statistical Significance of Probabilistic Sequence Alignment and Related Local Hidden Markov Models

Terence Hwa, Yi-Kuo Yu, T. Hwa, 2001, J. Comput. Biol..

CytoSaddleSum: a functional enrichment analysis plugin for Cytoscape based on sum-of-weights scores

Aleksandar Stojmirovic, Yi-Kuo Yu, Alexander Bliskovsky, 2012, Bioinform..

Combining Independent, Weighted P-Values: Achieving Computational Stability by a Systematic Expansion with Controllable Accuracy

Yi-Kuo Yu, Gelio Alves, Yi-Kuo Yu, 2011, PloS one.

Calibrating E-values for MS2 database search methods

Yi-Kuo Yu, Gelio Alves, Guanghui Wang, 2007, Biology Direct.

Accuracy Evaluation of the Unified P-Value from Combining Correlated P-Values

Yi-Kuo Yu, Gelio Alves, Yi-Kuo Yu, 2014, PloS one.

Statistical significance and extremal ensemble of gapped local hybrid alignment

Terence Hwa, Ralf Bundschuh, Yi-Kuo Yu, 2002 .

Identification of Microorganisms by High Resolution Tandem Mass Spectrometry with Accurate Statistical Significance

Aleksey Y. Ogurtsov, Steven K. Drake, Yi-Kuo Yu, 2015, Journal of The American Society for Mass Spectrometry.

Electrostatics of charged dielectric spheres with application to biological systems.

Yi-Kuo Yu, T P Doerr, 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.

Relating Diseases by Integrating Gene Associations and Information Flow through Protein Interaction Network

Yi-Kuo Yu, Mehdi Bagheri Hamaneh, Yi-Kuo Yu, 2014, PloS one.

Score statistics of global sequence alignment from the energy distribution of a modified directed polymer and directed percolation problem.

Yi-Kuo Yu, Gelio Alves, Mihaela E. Sardiu, 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

A metric measure for weight matrices of variable lengths—with applications to clustering and classification of hidden Markov models

Yi-Kuo Yu, 2007 .

Improving series convergence: the simple pendulum and beyond

Yi-Kuo Yu, Yi-Kuo Yu, T P Doerr, 2018, European journal of physics.

Improving peptide identification sensitivity in shotgun proteomics by stratification of search space.

Yi-Kuo Yu, Gelio Alves, Yi-Kuo Yu, 2013, Journal of proteome research.

Buyer feedback as a filtering mechanism for reputable sellers

František Slanina, Paolo Laureti, Yi-Kuo Yu, 2002 .

PSI-BLAST pseudocounts and the minimum description length principle

Alejandro A. Schäffer, Richa Agarwala, E. Michael Gertz, 2008, Nucleic acids research.

Ranked solutions to a class of combinatorial optimizations - with applications in mass spectrometry based peptide sequencing

Yi-Kuo Yu, Gelio Alves, Timothy P. Doerr, 2005 .

RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration

Yi-Kuo Yu, Gelio Alves, Aleksey Y Ogurtsov, 2008, BMC Genomics.

Detection of co-eluted peptides using database search methods

Yi-Kuo Yu, Gelio Alves, Guanghui Wang, 2008, Biology Direct.

Policy and data-intensive scientific discovery in the beginning of the 21st century.

Eugene Kolker, Bartha M Knoppers, Vural Ozdemir, 2011, Omics : a journal of integrative biology.

RAId_DbS: Peptide Identification using Database Searches with Realistic Statistics

Yi-Kuo Yu, Gelio Alves, Aleksey Y Ogurtsov, 2007, Biology Direct.