A Comparison of Some Robust Procedures for Estimating a Linear Discriminant Function, (9999)
A number of methods have been suggested for robustly estimating a linear discriminant function. These include substitution of robust estimates for the mean and covariance matrix and methods which...
using a mixed-effects model with (2009)
Clustering of time-course gene expression data
Hongzhe Li, Ninning Liu, Grace K. Rajendran, Thomas J. Gernon, Jason K. Rockhill, Jeffrey L. Schwartz, ...
Li, H., Liu, N., Rajendran, G. K., Gernon, T. J., Rockhill, J. K., Schwartz, J. L. and Gu, Y. A Role for Endogenous and Radiation-Induced DNA Double-Strand Breaks in p53-Dependent Apoptosis during...
H. Li, Y. Luan, Hongzhe Li, Yihui Luan
In functional genomics, one important problem is to relate the microarray gene expression profiles to various clinical phenotypes from patients. The success has been demonstrated in molecular...
Microarray time course (MTC) gene expression data are commonly collected to study the dynamic nature of biological processes. One important problem is to identify genes that show different expression...
Group additive regression models for genomic data analysis (2008)
One important problem in genomic research is to identify genomic features such as gene expression data or DNA single nucleotide polymorphisms (SNPs) that are related to clinical phenotypes. Often...
Network-constrained regularization and variable selection for analysis of genomic data (2008)
Motivation: Graphs or networks are common ways of depicting information. In biology in particular, many different biological processes are represented by graphs, such as regulatory networks or...
Contact: hongzhe@mail.med.upenn.edu
Group SCAD regression analysis for microarray time course gene expression data (2007)
Wang, Lifeng, Chen, Guang, Li, Hongzhe
Motivation: Since many important biological systems or processes are dynamic systems, it is important to study the gene expression patterns over time in a genomic scale in order to capture the...
A Markov random field model for network-based analysis of genomic data (2007)
Motivation: A central problem in genomic research is the identification of genes and pathways involved in diseases and other biological processes. The genes identified or the univariate test...
Nonparametric pathway-based regression models for analysis of genomic data (2007)
High-throughout genomic data provide an opportunity for identifying pathways and genes that are related to various clinical phenotypes. Besides these genomic data, another valuable source of data is...
Li, Hongzhe, Rajendran, Grace K, Liu, Ninning, Ware, Carol, Rubin, Brian P, Gu, Yansong
Abstract Introduction Estrogen and insulin-like growth factor-1 (IGF-1) play important roles in mammary gland development and breast cancer. SirT1 is a highly conserved protein deacetylase that can...
Nonparametric pathway-based regression models for analysis of genomic data (2007)
High-throughout genomic data provide an opportunity for identifying pathways and genes that are related to various clinical phenotypes. Besides these genomic data, another valuable source of data is...
Large-scale microarray gene expression data provide the possibility of constructing genetic networks or biological pathways. Gaussian graphical models have been suggested to provide an effective...
Nonparametric pathway-based regression models for analysis of genomic data (2006)
High-throughout genomic data provide an opportunity for identifying pathways and genes that are related to various clinical phenotypes. Besides these genomic data, another valuable source of data is...
Address for correspondence: (2005)
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for...
BIOINFORMATICS ORIGINAL PAPER (2005)
Gene Expression, Jiang Gui, Hongzhe Li
doi:10.1093/bioinformatics/bti422 Penalized Cox regression analysis in the high-dimensional and low-sample size settings, with applications to microarray gene expression data
Motivation: An important area of research in the postgenomics era is to relate high-dimensional genetic or genomic data to various clinical phenotypes of patients. Due to large variability in time to...
Large-scale microarray gene expression data provide the possibility of constructing genetic networks or biological pathways. Gaussian graphical models have been suggested to provide an effective...
Large-scale microarray gene expression data provide the possibility of constructing genetic networks or biological pathways. Gaussian graphical models have been suggested to provide an effective...
Motivation: An important area of research in the postgenomics era is to relate high-dimensional genetic or genomic data to various clinical phenotypes of patients. Due to large variability in time to...
Motivation: An important application of microarray technology is to relate gene expression profiles to various clinical phenotypes of patients. Success has been demonstrated in molecular...
Time course studies of gene expression are essential in biomedical research to understand biological phenomena that evolve in a temporal fashion. Microarray technology makes it possible to study...
Partial Cox Regression Analysis for High-Dimensional Microarray Gene Expression Data (2004)
An important application of microarray technology is to predict various clinical phenotypes based on the gene expression profile. Success has been demonstrated in molecular classification of cancer...
An important application of microarray technology is to relate gene expression profiles to various clinical phenotypes of patients. Success has been demonstrated in molecular classification of cancer...
Dimension Reduction Methods for Microarrays with Application to Censored Survival Data (2004)
Recent research has shown that gene expression profiles can potentially be used for predicting phenotypes such as cancer types and survival time in biomedical research. Microarray technology which...
Dimension reduction methods for microarrays with application to censored survival data (2004)
Motivation: Recent research has shown that gene expression profiles can potentially be used for predicting various clinical phenotypes, such as tumor class, drug response and survival time. While...
Seldin, Michael F., Morii, Takanobu, Collins-Schramm, Heather E., Chima, Bill, Kittles, Rick, Criswell, Lindsey A., ...
Theoretically, markers that distinguish European from West African ancestry can be used to examine the origin of chromosomal segments in individual African Americans. In this study, putative...
Dimension reduction methods for microarrays with application to censored survival data (2004)
Motivation: Recent research has shown that gene expression profiles can potentially be used for predicting various clinical phenotypes such as tumor class, drug response, and survival time. While...
Partial Cox regression analysis for high-dimensional microarray gene expression data (2004)
Motivation: An important application of microarray technology is to predict various clinical phenotypes based on the gene expression profile. Success has been demonstrated in molecular classification...
Seldin, Michael F., Morii, Takanobu, Collins-Schramm, Heather E., Chima, Bill, Kittles, Rick, Criswell, Lindsey A., ...
Theoretically, markers that distinguish European from West African ancestry can be used to examine the origin of chromosomal segments in individual African Americans. In this study, putative...
Nuclear families with multiple affected sibs are often collected for genetic linkage analysis of complex diseases. Once linkage evidence is established, dense markers are often typed in the linked...
Dimension reduction methods for microarrays with application to censored survival data (2004)
Motivation: Recent research has shown that gene expression profiles can potentially be used for predicting various clinical phenotypes such as tumor class, drug response, and survival time. While...
A Hidden Markov Modeling Approach for Admixture Mapping Based on Case-Control Haplotype Data (2003)
Zhang, Chun, Chen, Kun, Seldin, Michael F, Li, Hongzhe
Admixture mapping is potentially a powerful method for mapping genes for complex human diseases, when the disease frequency due to a particular disease susceptible gene is different between founding...
The additive genetic gamma frailty model has been proposed for genetic linkage analysis for complex diseases to account for variable age of onset and possible covariates effects. To avoid...
Responses of inferior colliculus neurons to sinusoidal amplitude modulation in chinchillas / (2003)
Thesis (Ph. D.)--Arizona State University, 2003.
Kernel Cox regression models for linking gene expression profiles to censored survival data (2003)
In functional genomics, one important problem is to relate the microarray gene expression profiles to various clinical phenotypes from patients. The success has been demonstrated in molecular...
Clustering of time-course gene expression data using a mixed-effects model with B-splines (2003)
Motivation: Time-course gene expression data are often measured to study dynamic biological systems and gene regulatory networks. To account for time dependency of the gene expression measurements...
Complex human diseases are often due to multiple disease genes with variable age of onset, as well as both genetic and environmental risk factors. In order to simultaneously consider two possible...
Complex human diseases are often due to multiple disease genes with variable age of onset, as well as both genetic and environmental risk factors. In order to simultaneously consider two possible...
Complex human diseases are often due to multiple disease genes with variable age of onset, as well as both genetic and environmental risk factors. In order to simultaneously consider two possible...
Complex human diseases are often due to multiple disease genes with variable age of onset, as well as both genetic and environmental risk factors. In order to simultaneously consider two possible...
We derive a multivariate survival model for age of onset data of a sibship from an additive genetic gamma frailty model constructed basing on the inheritance vectors, and investigate the properties...
Cluster-Rasch models for microarray gene expression data (2001)
Abstract Background We propose two different formulations of the Rasch statistical models to the problem of relating gene expression profiles to the phenotypes. One formulation allows us to...
Cluster-rasch models for microarray gene expression data (2001)
Background: We propose two different formulations of the Rasch statistical models to the problem of relating gene expression profiles to the phenotypes. One formulation allows us to investigate...
Seldin, Michael F., Morii, Takanobu, Collins-Schramm, Heather E., Chima, Bill, Kittles, Rick, Criswell, Lindsey A., ...
Theoretically, markers that distinguish European from West African ancestry can be used to examine the origin of chromosomal segments in individual African Americans. In this study, putative...
AAA ATPases regulate membrane association of yeast oxysterol binding proteins and sterol metabolism
Wang, Penghua, Zhang, Yong, Li, Hongzhe, Chieu, Hai Kee, Munn, Alan L, Yang, Hongyuan
The yeast genome encodes seven oxysterol binding protein homologs, Osh1p–Osh7p, which have been implicated in regulating intracellular lipid and vesicular transport. Here, we show that both Osh6p...
Ethnic-Difference Markers for Use in Mapping by Admixture Linkage Disequilibrium
Collins-Schramm, Heather E., Phillips, Carolyn M., Operario, Darwin J., Lee, Jane S., Weber, James L., Hanson, Robert L., ...
Mapping by admixture linkage disequilibrium (MALD) is a potentially powerful technique for the mapping of complex genetic diseases. The practical requirements of this method include (a) a set of...
Seldin, Michael F., Morii, Takanobu, Collins-Schramm, Heather E., Chima, Bill, Kittles, Rick, Criswell, Lindsey A., ...
Theoretically, markers that distinguish European from West African ancestry can be used to examine the origin of chromosomal segments in individual African Americans. In this study, putative...
AAA ATPases regulate membrane association of yeast oxysterol binding proteins and sterol metabolism
Wang, Penghua, Zhang, Yong, Li, Hongzhe, Chieu, Hai Kee, Munn, Alan L, Yang, Hongyuan
The yeast genome encodes seven oxysterol binding protein homologs, Osh1p–Osh7p, which have been implicated in regulating intracellular lipid and vesicular transport. Here, we show that both Osh6p...
Complex human diseases are often due to multiple disease genes with variable age of onset, as well as both genetic and environmental risk factors. In order to simultaneously consider two possible...
HLA-A amino acid polymorphism and delayed kidney allograft function
Kamoun, Malek, Holmes, John H., Israni, Ajay K., Kearns, Jane D., Teal, Valerie, Yang, Wei Peter, ...
Delayed allograft function (DGF) is a common adverse event in postrenal transplantation. The etiology of DGF is thought to include both nonimmunologic (donor age, cold ischemia time, and recipient...