Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data. - Jiang Qian; C. Jimmy Lin; Nicholas M. Luscombe; Haiyuan Yu; Mark Gerstein (Bioinform., 2003)

Protein Interaction Prediction by Integrating Genomic Features and Protein Interaction Network Analysis. - Long J. Lu; Yu Xia 002; Haiyuan Yu; Alexander Rives; Haoxin Lu; Falk Schubert; Mark Gerstein (Data Analysis and Visualization in Genomics and Proteomics, 2005)

Inferring protein-protein interactions using interaction network topologies. - Alberto Paccanaro; Valery Trifonov; Haiyuan Yu; Mark Gerstein (IJCNN, 2005)

An algebraic multigrid method for finite element systems on criss-cross grids. - Shi Shu; Jinchao Xu; Ying Yang 014; Haiyuan Yu (Adv. Comput. Math., 2006)

Predicting interactions in protein networks by completing defective cliques. - Haiyuan Yu; Alberto Paccanaro; Valery Trifonov; Mark Gerstein (Bioinform., 2006)

The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks. - Kevin Y. Yip; Haiyuan Yu; Philip M. Kim; Martin H. Schultz; Mark Gerstein (Bioinform., 2007)

Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications. - Haiyuan Yu; Ronald Jansen; Gustavo Stolovitzky; Mark Gerstein (Bioinform., 2007)

The Importance of Bottlenecks in Protein Networks: Correlation with Gene Essentiality and Expression Dynamics. - Haiyuan Yu; Philip M. Kim; Emmett Sprecher; Valery Trifonov; Mark Gerstein (PLoS Comput. Biol., 2007)

Genome-scale analysis of interaction dynamics reveals organization of biological networks. - Jishnu Das; Jaaved Mohammed; Haiyuan Yu (Bioinform., 2012)

HINT: High-quality protein interactomes and their applications in understanding human disease. - Jishnu Das; Haiyuan Yu (BMC Syst. Biol., 2012)

INstruct: a database of high-quality 3D structurally resolved protein interactome networks. - Michael J. Meyer; Jishnu Das; Xiujuan Wang; Haiyuan Yu (Bioinform., 2013)

Superconvergence and asymptotic expansion for semidiscrete bilinear finite volume element approximation of the parabolic problem. - Cunyun Nie; Shi Shu; Haiyuan Yu; Yuyue Yang (Comput. Math. Appl., 2013)

Target Essentiality and Centrality Characterize Drug Side Effects. - Xiujuan Wang; Bram Thijssen; Haiyuan Yu (PLoS Comput. Biol., 2013)

A high order composite scheme for the second order elliptic problem with nonlocal boundary and its fast algorithm. - Cunyun Nie; Shi Shu; Haiyuan Yu; Qianjiang An (Appl. Math. Comput., 2014)

Some error estimates on the large jump asymptotic approach for the interface problem. - Cunyun Nie; Haiyuan Yu (Appl. Math. Comput., 2015)

BISQUE: locus- and variant-specific conversion of genomic, transcriptomic and proteomic database identifiers. - Michael J. Meyer; Philip Geske; Haiyuan Yu (Bioinform., 2016)

Error estimates on a finite volume method for diffusion problems with interface on rectangular grids. - Jie Peng; Shi Shu; Haiyuan Yu; Chunsheng Feng; Mingxian Kan; Ganghua Wang (Appl. Math. Comput., 2017)

Superconvergence and asymptotic expansions for bilinear finite volume element approximation on non-uniform grids. - Cunyun Nie; Shi Shu; Haiyuan Yu; Wenhua Xia (J. Comput. Appl. Math., 2017)

GeMSTONE: orchestrated prioritization of human germline mutations in the cloud. - Siwei Chen; Juan F. Beltrán; Clara Esteban-Jurado; Sebastià Franch-Expósito; Sergi Castellví-Bel; Steven Lipkin; Xiaomu Wei; Haiyuan Yu (Nucleic Acids Res., 2017)

Leveraging genetic interactions for adverse drug-drug interaction prediction. - Sheng Qian; Siqi Liang 002; Haiyuan Yu (PLoS Comput. Biol., 2019)

Revealing new therapeutic opportunities through drug target prediction: a class imbalance-tolerant machine learning approach. - Siqi Liang 002; Haiyuan Yu; Jonathan D. Wren (Bioinform., 2020)

A Difference Scheme and Its Error Analysis for a Poisson Equation with Nonlocal Boundary Conditions. - Chunsheng Feng; Cunyun Nie; Haiyuan Yu; Liping Zhou; Karthikeyan Rajagopal (Complex., 2020)

SAAMBE-SEQ: a sequence-based method for predicting mutation effect on protein-protein binding affinity. - Gen Li; Swagata Pahari; Adithya Krishna Murthy; Siqi Liang 002; Robert Fragoza; Haiyuan Yu; Emil Alexov (Bioinform., 2021)

Combining views for newly sequenced organisms. - Yingying Zhang; Shayne D. Wierbowski; Haiyuan Yu (Nat. Mach. Intell., 2021)

A monotone finite volume element scheme for diffusion equations on triangular grids. - Cunyun Nie; Haiyuan Yu (Comput. Math. Appl., 2022)