Statistical Significance of Probabilistic Sequence Alignment and Related Local Hidden Markov Models. - Yi-Kuo Yu; Terence Hwa (J. Comput. Biol., 2001)

Hybrid alignment: high-performance with universal statistics. - Yi-Kuo Yu; Ralf Bundschuh; Terence Hwa (Bioinform., 2002)

Scale-free networks versus evolutionary drift. - Teresa M. Przytycka; Yi-Kuo Yu (Comput. Biol. Chem., 2004)

Robust accurate identification of peptides (RAId): deciphering MS2 data using a structured library search with de novo based statistics. - Gelio Alves; Yi-Kuo Yu (Bioinform., 2005)

The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions. - Yi-Kuo Yu; Stephen F. Altschul (Bioinform., 2005)

Information Flow in Interaction Networks. - Aleksandar Stojmirovic; Yi-Kuo Yu (J. Comput. Biol., 2007)

The effectiveness of position- and composition-specific gap costs for protein similarity searches. - Aleksandar Stojmirovic; E. Michael Gertz; Stephen F. Altschul; Yi-Kuo Yu (ISMB, 2008)

ITM Probe: analyzing information flow in protein networks. - Aleksandar Stojmirovic; Yi-Kuo Yu (Bioinform., 2009)

Geometric Aspects of Biological Sequence Comparison. - Aleksandar Stojmirovic; Yi-Kuo Yu (J. Comput. Biol., 2009)

Robust and accurate data enrichment statistics via distribution function of sum of weights. - Aleksandar Stojmirovic; Yi-Kuo Yu (Bioinform., 2010)

Compositional Adjustment of Dirichlet Mixture Priors. - Xugang Ye; Yi-Kuo Yu; Stephen F. Altschul (J. Comput. Biol., 2010)

The Construction and Use of Log-Odds Substitution Scores for Multiple Sequence Alignment. - Stephen F. Altschul; John C. Wootton; Elena Zaslavsky; Yi-Kuo Yu (PLoS Comput. Biol., 2010)

ppiTrim: constructing non-redundant and up-to-date interactomes. - Aleksandar Stojmirovic; Yi-Kuo Yu (Database J. Biol. Databases Curation, 2011)

CytoITMprobe: a network information flow plugin for Cytoscape - Aleksandar Stojmirovic; Alexander Bliskovsky; Yi-Kuo Yu (CoRR, 2011)

On the Inference of Dirichlet Mixture Priors for Protein Sequence Comparison. - Xugang Ye; Yi-Kuo Yu; Stephen F. Altschul (J. Comput. Biol., 2011)

The Complexity of the Dirichlet Model for Multiple Alignment Data. - Yi-Kuo Yu; Stephen F. Altschul (J. Comput. Biol., 2011)

CytoSaddleSum: a functional enrichment analysis plugin for Cytoscape based on sum-of-weights scores. - Aleksandar Stojmirovic; Alexander Bliskovsky; Yi-Kuo Yu (Bioinform., 2012)

Information Flow in Interaction Networks II: Channels, Path Lengths, and Potentials. - Aleksandar Stojmirovic; Yi-Kuo Yu (J. Comput. Biol., 2012)

Mass spectrometry-based protein identification with accurate statistical significance assignment. - Gelio Alves; Yi-Kuo Yu (Bioinform., 2015)

Log-odds sequence logos. - Yi-Kuo Yu; John A. Capra; Aleksandar Stojmirovic; David Landsman; Stephen F. Altschul (Bioinform., 2015)

Confidence assignment for mass spectrometry based peptide identifications via the extreme value distribution. - Gelio Alves; Yi-Kuo Yu (Bioinform., 2016)

MiCId GUI: The Graphical User Interface for MiCId, a Fast Microorganism Classification and Identification Workflow with Accurate Statistics and High Recall. - Aleksey Y. Ogurtsov; Gelio Alves; Alex Rubio; Brendan Joyce; Björn Andersson; Roger Karlsson; Edward R. B. Moore; Yi-Kuo Yu (J. Comput. Biol., 2024)