A 2O(n1-(1/d)log n) Time Algorithm for d-Dimensional Protein Folding in the HP-Model. - Bin Fu; Wei Wang 051 (ICALP, 2004)

Computational Analysis and Prediction of the Binding Motif and Protein Interacting Partners of the Abl SH3 Domain. - Tingjun Hou; Ken Chen 001; William A. McLaughlin; Benzhuo Lu; Wei Wang 051 (PLoS Comput. Biol., 2006)

High-throughput identification of interacting protein-protein binding sites. - Jo-Lan Chung; Wei Wang 051; Philip E. Bourne (BMC Bioinform., 2007)

On the detection of functionally coherent groups of protein domains with an extension to protein annotation. - William A. McLaughlin; Ken Chen 001; Tingjun Hou; Wei Wang 051 (BMC Bioinform., 2007)

Geometric Separators and Their Applications to Protein Folding in the HP-Model. - Bin Fu; Wei Wang 051 (SIAM J. Comput., 2007)

GBNet: Deciphering regulatory rules in the co-regulated genes using a Gibbs sampler enhanced Bayesian network approach. - Li Shen; Jie Liu; Wei Wang 051 (BMC Bioinform., 2008)

Prediction of regulatory elements in mammalian genomes using chromatin signatures. - Kyoung-Jae Won; Iouri Chepelev; Bing Ren; Wei Wang 051 (BMC Bioinform., 2008)

ChromaSig: A Probabilistic Approach to Finding Common Chromatin Signatures in the Human Genome. - Gary Chung Hon; Bing Ren; Wei Wang 051 (PLoS Comput. Biol., 2008)

Discovery and Annotation of Functional Chromatin Signatures in the Human Genome. - Gary Chung Hon; Wei Wang 051; Bing Ren (PLoS Comput. Biol., 2009)

A Novel Knowledge-driven Systems Biology Approach for Phenotype Prediction Upon Genetic Intervention. - Rui Chang; Wei Wang 051 (BIOCOMP, 2010)

Prediction of quantitative phenotypes based on genetic networks: a case study in yeast sporulation. - Li Shen; Iouri Chepelev; Jie Liu; Wei Wang 051 (BMC Syst. Biol., 2010)

Prediction of peptides binding to the PKA RIIα subunit using a hierarchical strategy. - Tingjun Hou; Youyong Li; Wei Wang 051 (Bioinform., 2011)

Recipes and mechanisms of cellular reprogramming: a case study on budding yeast Saccharomyces cerevisiae. - Shengchao Ding; Wei Wang 051 (BMC Syst. Biol., 2011)

Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking. - Tingjun Hou; Junmei Wang; Youyong Li; Wei Wang 051 (J. Comput. Chem., 2011)

Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations. - Tingjun Hou; Junmei Wang; Youyong Li; Wei Wang 051 (J. Chem. Inf. Model., 2011)

Systematic Search for Recipes to Generate Induced Pluripotent Stem Cells. - Rui Chang; Robert Shoemaker; Wei Wang 051 (PLoS Comput. Biol., 2011)

A Novel Knowledge-Driven Systems Biology Approach for Phenotype Prediction upon Genetic Intervention. - Rui Chang; Robert Shoemaker; Wei Wang 051 (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

STAR: an integrated solution to management and visualization of sequencing data. - Tao Wang; Jie Liu; Li Shen; Julian Tonti-Filippini; Yun Zhu; Haiyang Jia; Ryan Lister; John W. Whitaker; Joseph R. Ecker; A. Harvey Millar; Bing Ren; Wei Wang 051 (Bioinform., 2013)

Ensemble classifier based on context specific miRNA regulation modules: a new method for cancer outcome prediction. - Xionghui Zhou; Juan Liu; Xinghuo Ye; Wei Wang 051; Jianghui Xiong (BMC Bioinform., 2013)

Characterizing Binding of Small Molecules. II. Evaluating the Potency of Small Molecules to Combat Resistance Based on Docking Structures. - Bo Ding; Nan Li; Wei Wang 051 (J. Chem. Inf. Model., 2013)

Characterization of Small Molecule Binding. I. Accurate Identification of Strong Inhibitors in Virtual Screening. - Bo Ding; Jian Wang; Nan Li; Wei Wang 051 (J. Chem. Inf. Model., 2013)

RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State. - Nisha Rajagopal; Wei Xie; Yan Li; Uli Wagner 002; Wei Wang 051; John A. Stamatoyannopoulos; Jason Ernst; Manolis Kellis; Bing Ren (PLoS Comput. Biol., 2013)

Normalization and noise reduction for single cell RNA-seq experiments. - Bo Ding; Lina Zheng; Yun Zhu; Nan Li; Haiyang Jia; Rizi Ai; Andre Wildberg; Wei Wang 051 (Bioinform., 2015)

Using Hierarchical Virtual Screening To Combat Drug Resistance of the HIV-1 Protease. - Nan Li; Richard I. Ainsworth; Bo Ding; Tingjun Hou; Wei Wang 051 (J. Chem. Inf. Model., 2015)

Integrative analysis of 111 reference human epigenomes Open. - Roadmap Epigenomics Consortium; Anshul Kundaje; Wouter Meuleman; Jason Ernst; Misha Bilenky; Angela Yen; Alireza Heravi Moussavi; Pouya Kheradpour; ZhiZhuo Zhang; Jianrong Wang; Michael J. Ziller; Viren Amin; et al. (Nat., 2015)

A Transfer Learning Approach for Predictive Modeling of Degenerate Biological Systems. - Na Zou 001; Yun Zhu; Ji Zhu; Mustafa Gökçe Baydogan; Wei Wang 051; Jing Li 016 (Technometrics, 2015)

Computationally expanding infinium HumanMethylation450 BeadChip array data to reveal distinct DNA methylation patterns of rheumatoid arthritis. - Shicai Fan; Chengzhe Li; Rizi Ai; Mengchi Wang; Gary S. Firestein; Wei Wang 051 (Bioinform., 2016)

MIEC-SVM: automated pipeline for protein peptide/ligand interaction prediction. - Nan Li; Richard I. Ainsworth; Meixin Wu; Bo Ding; Wei Wang 051 (Bioinform., 2016)

Contextual Regression: An Accurate and Conveniently Interpretable Nonlinear Model for Mining Discovery from Scientific Data. - Chengyu Liu; Wei Wang 051 (CoRR, 2017)

Biogenesis mechanisms of circular RNA can be categorized through feature extraction of a machine learning model. - Chengyu Liu; Yu-Chen Liu; Hsien-Da Huang; Wei Wang 051 (Bioinform., 2019)

Finding de novo methylated DNA motifs. - Vu Ngo; Mengchi Wang; Wei Wang 051 (Bioinform., 2019)

Engineering a Histone Reader Protein by Combining Directed Evolution, Sequencing, and Neural Network Based Ordinal Regression. - Jonathan Parkinson; Ryan Hard; Richard I. Ainsworth; Nan Li; Wei Wang 051 (J. Chem. Inf. Model., 2020)

Deciphering the genetic code of DNA methylation. - Mengchi Wang; Vu Ngo; Wei Wang 051 (Briefings Bioinform., 2021)

Neural network facilitated ab initio derivation of linear formula: A case study on formulating the relationship between DNA motifs and gene expression. - Chengyu Liu; Wei Wang 051 (CoRR, 2022)

Scalable Gaussian process regression enables accurate prediction of protein and small molecule properties with uncertainty quantitation. - Jonathan Parkinson; Wei Wang 051 (CoRR, 2023)

Linear-Scaling Kernels for Protein Sequences and Small Molecules Outperform Deep Learning While Providing Uncertainty Quantitation and Improved Interpretability. - Jonathan Parkinson; Wei Wang 051 (J. Chem. Inf. Model., 2023)