Inferring Gene Networks from Microarray Data by Closed-loop Optimization (2009)
Frank Emmert-streib, Dongxiao Zhu
In this article we propose an inference algorithm for constructing gene networks from time series data of microarray experiments that optimizes the closed-loop formed by the data and the algorithm...
Reconstructing Condition-Specific Signal Transduction Hierarchy using Bayesian Networks (2009)
Dongxiao Zhu, Hua Li, Alfred O Hero
Bayesian networks (BNs) can simultaneously predict probabilistic causal relationships among biomolecules from noisy genome-wide measurements. However, optimal inference of Bayesian Network on the...
Abstract Background The gene shaving algorithm and many other clustering algorithms identify gene clusters showing high variation across samples. However, gene expression in many signaling pathways...
BAYESIAN HIERARCHICAL MODEL FOR ESTIMATING GENE ASSOCIATION NETWORK FROM MICROARRAY DATA (2008)
Estimating gene association networks from gene microarray data is the key to decipher complicated web of functional relationship between genes [1]. However, the process remains to be challenging due...
A statistical framework for consolidating "sibling" probe sets for Affymetrix GeneChip data (2008)
Li, Hua, Zhu, Dongxiao, Cook, Malcolm
Abstract Background Affymetrix GeneChip typically contains multiple probe sets per gene, defined as sibling probe sets in this study. These probe sets may or may not behave similar across treatments....
Chapter 1 De Novo Signaling Pathway Reconstruction From Multiple Data Sources (2008)
Dongxiao Zhu, Michael G. Rabbat, Alfred O. Hero, Robert Nowak, Mario Figueiredo, Dongxiao Zhu, ...
Signaling pathways are the primary means of regulating cell growth, metabolism, differentiation and apoptosis. The de novo signaling pathway reconstruction problem can be divided into two...
Bayesian Hierarchical Model for Large-Scale Covariance Matrix Estimation (2007)
Zhu, Dongxiao, Hero III, Alfred O.
Many bioinformatics problems implicitly depend on estimating large-scale covariance matrix. The traditional approaches tend to give rise to high variance and low accuracy due to “overfitting.” We...
Zhu, Dongxiao, Li, Youjuan, Li, Hua
Summary: Estimating pairwise correlation from replicated genome-scale (a.k.a. OMICS) data is fundamental to cluster functionally relevant biomolecules to a cellular pathway. The popular Pearson...
Zhu, Dongxiao, Hero, Alfred O, Qin, Zhaohui S, Swaroop, Anand
Many exploratory microarray data analysis tools such as gene clustering and relevance networks rely on detecting pairwise gene co-expression. Traditional screening of pairwise co-expression either...
Structural comparison of metabolic networks in selected single cell organisms (2005)
Abstract Background There has been tremendous interest in the study of biological network structure. An array of measurements has been conceived to assess the topological properties of these...
Network constrained clustering for gene microarray data (2005)
Gene Expression, Dongxiao Zhu, Alfred O Hero, Hong Cheng, Ritu Khanna
doi:10.1093/bioinformatics/bti655
BMC Bioinformatics BioMed Central (2005)
Dongxiao Zhu, Zhaohui S Qin, Dongxiao Zhu, Zhaohui S Qin
Research article Structural comparison of metabolic networks in selected single cell organisms
Masayuki Akimoto, Hong Cheng, Dongxiao Zhu, Joseph A. Brzezinski, Ritu Khanna, ...
doi:10.1073/pnas.0508214103 This information is current as of June 2007. High-resolution figures, a citation map, links to PubMed and Google Scholar, etc., can be found at:...
Dongxiao Zhu, Alfred O Hero, Zhaohui S Qin
Many exploratory microarray data analysis tools such as gene clustering and relevance networks rely on detecting pairwise gene co-expression. Traditional screening of pairwise co-expression either...
Network constrained clustering for gene microarray data (2005)
Zhu, Dongxiao, Hero, Alfred O., Cheng, Hong, Khanna, Ritu, Swaroop, Anand
Many bioinformatics problems can be tackled from a fresh angle offered by the network perspective. Directly inspired by metabolic network structural studies, we propose an improved gene clustering...
Network constrained clustering for gene microarray data (2005)
Zhu, Dongxiao, Hero, Alfred O, Cheng, Hong, Khanna, Ritu, Swaroop, Anand
Many bioinformatics problems can be tackled from a fresh angle offered by the network perspective. Directly inspired by metabolic network structural studies, we propose an improved gene clustering...
Akimoto, Masayuki, Cheng, Hong, Zhu, Dongxiao, Brzezinski, Joseph A., Khanna, Ritu, Filippova, Elena, ...
The Maf-family transcription factor Nrl is a key regulator of photoreceptor differentiation in mammals. Ablation of the Nrl gene in mice leads to functional cones at the expense of rods. We show that...
Akimoto, Masayuki, Cheng, Hong, Zhu, Dongxiao, Brzezinski, Joseph A., Khanna, Ritu, Filippova, Elena, ...
The Maf-family transcription factor Nrl is a key regulator of photoreceptor differentiation in mammals. Ablation of the Nrl gene in mice leads to functional cones at the expense of rods. We show that...
Paoletti, Andrew C., Parmely, Tari J., Tomomori-Sato, Chieri, Sato, Shigeo, Zhu, Dongxiao, Conaway, Ronald C., ...
Components of multiprotein complexes are routinely determined by using proteomic approaches. However, this information lacks functional content except when new complex members are identified. To...