Wei Wang

36 papers A* 1Journal 34Unranked 1
YearRankTypeTitle / Venue / Authors
2023 J jnl
Linear-Scaling Kernels for Protein Sequences and Small Molecules Outperform Deep Learning While Providing Uncertainty Quantitation and Improved Interpretability.
J. Chem. Inf. Model.
Jonathan Parkinson, Wei Wang
2023 J jnl
Scalable Gaussian process regression enables accurate prediction of protein and small molecule properties with uncertainty quantitation.
CoRR
Jonathan Parkinson, Wei Wang
2022 J jnl
Neural network facilitated ab initio derivation of linear formula: A case study on formulating the relationship between DNA motifs and gene expression.
CoRR
Chengyu Liu, Wei Wang
2021 J jnl
Deciphering the genetic code of DNA methylation.
Briefings Bioinform.
Mengchi Wang, Vu Ngo, Wei Wang
2020 J jnl
Engineering a Histone Reader Protein by Combining Directed Evolution, Sequencing, and Neural Network Based Ordinal Regression.
J. Chem. Inf. Model.
Jonathan Parkinson, Ryan Hard, Richard I. Ainsworth, Nan Li, Wei Wang
2019 J jnl
Biogenesis mechanisms of circular RNA can be categorized through feature extraction of a machine learning model.
Bioinform.
Chengyu Liu, Yu-Chen Liu, Hsien-Da Huang, Wei Wang
2019 J jnl
Finding de novo methylated DNA motifs.
Bioinform.
Vu Ngo, Mengchi Wang, Wei Wang
2017 J jnl
Contextual Regression: An Accurate and Conveniently Interpretable Nonlinear Model for Mining Discovery from Scientific Data.
CoRR
Chengyu Liu, Wei Wang
2016 J jnl
Computationally expanding infinium HumanMethylation450 BeadChip array data to reveal distinct DNA methylation patterns of rheumatoid arthritis.
Bioinform.
Shicai Fan, Chengzhe Li, Rizi Ai, Mengchi Wang, Gary S. Firestein, Wei Wang
2016 J jnl
MIEC-SVM: automated pipeline for protein peptide/ligand interaction prediction.
Bioinform.
Nan Li, Richard I. Ainsworth, Meixin Wu, Bo Ding, Wei Wang
2015 J jnl
A Transfer Learning Approach for Predictive Modeling of Degenerate Biological Systems.
Technometrics
Na Zou, Yun Zhu, Ji Zhu, Mustafa Gökçe Baydogan, Wei Wang, Jing Li
2015 J jnl
Integrative analysis of 111 reference human epigenomes Open.
Nat.
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, John W. Whitaker, Matthew D. Schultz, Lucas D. Ward, Abhishek Sarkar, Gerald T. Quon, Richard S. Sandstrom, Matthew L. Eaton, Yi-Chieh Wu, Andreas R. Pfenning, Xinchen Wang, Melina Claussnitzer, Yaping Liu, Cristian Coarfa, R. Alan Harris, Noam Shoresh, Charles B. Epstein, Elizabeta Gjoneska, Danny Leung, Wei Xie, R. David Hawkins, Ryan Lister, Chibo Hong, Philippe Gascard, Andrew J. Mungall, Richard A. Moore, Eric Chuah, Angela Tam, Theresa K. Canfield, R. Scott Hansen, Rajinder Kaul, Peter J. Sabo, Mukul S. Bansal, Annaick Carles, Jesse R. Dixon, Kyle Kai-How Farh, Soheil Feizi, Rosa Karlic, Ah-Ram Kim, Ashwinikumar Kulkarni, Daofeng Li, Rebecca F. Lowdon, GiNell Elliott, Tim R. Mercer, Shane J. Neph, Vitor Onuchic, Paz Polak, Nisha Rajagopal, Pradipta Ray, Richard C. Sallari, Kyle T. Siebenthall, Nicholas A. Sinnott-Armstrong, Michael Stevens, Robert E. Thurman, Jie Wu, Bo Zhang, Xin Zhou, Arthur E. Beaudet, Laurie A. Boyer, Philip L. De Jager, Peggy J. Farnham, Susan J. Fisher, David Haussler, Steven J. M. Jones, Wei Li, Marco A. Marra, Michael T. McManus, Shamil R. Sunyaev, James A. Thomson, Thea D. Tlsty, Li-Huei Tsai, Wei Wang, Robert A. Waterland, Michael Q. Zhang, Lisa H. Chadwick, Bradley E. Bernstein, Joseph F. Costello, Joseph R. Ecker, Martin Hirst, Alexander Meissner, Aleksandar Milosavljevic, Bing Ren, John A. Stamatoyannopoulos, Ting Wang, Manolis Kellis
2015 J jnl
Normalization and noise reduction for single cell RNA-seq experiments.
Bioinform.
Bo Ding, Lina Zheng, Yun Zhu, Nan Li, Haiyang Jia, Rizi Ai, Andre Wildberg, Wei Wang
2015 J jnl
Using Hierarchical Virtual Screening To Combat Drug Resistance of the HIV-1 Protease.
J. Chem. Inf. Model.
Nan Li, Richard I. Ainsworth, Bo Ding, Tingjun Hou, Wei Wang
2013 J jnl
Characterization of Small Molecule Binding. I. Accurate Identification of Strong Inhibitors in Virtual Screening.
J. Chem. Inf. Model.
Bo Ding, Jian Wang, Nan Li, Wei Wang
2013 J jnl
Characterizing Binding of Small Molecules. II. Evaluating the Potency of Small Molecules to Combat Resistance Based on Docking Structures.
J. Chem. Inf. Model.
Bo Ding, Nan Li, Wei Wang
2013 J jnl
Ensemble classifier based on context specific miRNA regulation modules: a new method for cancer outcome prediction.
BMC Bioinform.
Xionghui Zhou, Juan Liu, Xinghuo Ye, Wei Wang, Jianghui Xiong
2013 J jnl
RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State.
PLoS Comput. Biol.
Nisha Rajagopal, Wei Xie, Yan Li, Uli Wagner, Wei Wang, John A. Stamatoyannopoulos, Jason Ernst, Manolis Kellis, Bing Ren
2013 J jnl
STAR: an integrated solution to management and visualization of sequencing data.
Bioinform.
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
2011 J jnl
A Novel Knowledge-Driven Systems Biology Approach for Phenotype Prediction upon Genetic Intervention.
IEEE ACM Trans. Comput. Biol. Bioinform.
Rui Chang, Robert Shoemaker, Wei Wang
2011 J jnl
Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations.
J. Chem. Inf. Model.
Tingjun Hou, Junmei Wang, Youyong Li, Wei Wang
2011 J jnl
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.
J. Comput. Chem.
Tingjun Hou, Junmei Wang, Youyong Li, Wei Wang
2011 J jnl
Prediction of peptides binding to the PKA RIIα subunit using a hierarchical strategy.
Bioinform.
Tingjun Hou, Youyong Li, Wei Wang
2011 J jnl
Recipes and mechanisms of cellular reprogramming: a case study on budding yeast Saccharomyces cerevisiae.
BMC Syst. Biol.
Shengchao Ding, Wei Wang
2011 J jnl
Systematic Search for Recipes to Generate Induced Pluripotent Stem Cells.
PLoS Comput. Biol.
Rui Chang, Robert Shoemaker, Wei Wang
2010 — conf
A Novel Knowledge-driven Systems Biology Approach for Phenotype Prediction Upon Genetic Intervention.
BIOCOMP
Rui Chang, Wei Wang
2010 J jnl
Prediction of quantitative phenotypes based on genetic networks: a case study in yeast sporulation.
BMC Syst. Biol.
Li Shen, Iouri Chepelev, Jie Liu, Wei Wang
2009 J jnl
Discovery and Annotation of Functional Chromatin Signatures in the Human Genome.
PLoS Comput. Biol.
Gary Chung Hon, Wei Wang, Bing Ren
2008 J jnl
ChromaSig: A Probabilistic Approach to Finding Common Chromatin Signatures in the Human Genome.
PLoS Comput. Biol.
Gary Chung Hon, Bing Ren, Wei Wang
2008 J jnl
GBNet: Deciphering regulatory rules in the co-regulated genes using a Gibbs sampler enhanced Bayesian network approach.
BMC Bioinform.
Li Shen, Jie Liu, Wei Wang
2008 J jnl
Prediction of regulatory elements in mammalian genomes using chromatin signatures.
BMC Bioinform.
Kyoung-Jae Won, Iouri Chepelev, Bing Ren, Wei Wang
2007 J jnl
Geometric Separators and Their Applications to Protein Folding in the HP-Model.
SIAM J. Comput.
Bin Fu, Wei Wang
2007 J jnl
High-throughput identification of interacting protein-protein binding sites.
BMC Bioinform.
Jo-Lan Chung, Wei Wang, Philip E. Bourne
2007 J jnl
On the detection of functionally coherent groups of protein domains with an extension to protein annotation.
BMC Bioinform.
William A. McLaughlin, Ken Chen, Tingjun Hou, Wei Wang
2006 J jnl
Computational Analysis and Prediction of the Binding Motif and Protein Interacting Partners of the Abl SH3 Domain.
PLoS Comput. Biol.
Tingjun Hou, Ken Chen, William A. McLaughlin, Benzhuo Lu, Wei Wang
2004 A* conf
A 2
ICALP
Bin Fu, Wei Wang