Lance D. Miller

Differential Friendly Neighbors Algorithm for Differential Relationships Based Gene Selection and Classification using Microarray Data (2008)

R. Krishna, Murthy Karuturi, Silvia Wong, Wing-kin Sung, Lance D. Miller

Abstract — Identifying biologically relevant genes in a given tumor classification problem is as important as accurately classifying the samples. Differential expression may not always achieve this...

Resource A Global Map of p53 Transcription-Factor Binding Sites in the (2008)

Human Genome, Chia-lin Wei, Qiang Wu, Vinsensius B. Vega, Kuo Ping Chiu, Patrick Ng, ...

The ability to derive a whole-genome map of transcription-factor binding sites (TFBS) is crucial for elucidating gene regulatory networks. Herein, we describe a robust approach that couples chromatin...

LOMA: A fast method to generate efficient tagged-random primers despite amplification bias of random PCR on pathogens (2008)

Lee, Wah, Wong, Christopher W, Leong, Wan, Miller, Lance D, Sung, Wing

Abstract Background Pathogen detection using DNA microarrays has the potential to become a fast and comprehensive diagnostics tool. However, since pathogen detection chips currently utilize random...

Whole-Genome Cartography of Estrogen Receptor α Binding Sites (2007)

Chin-Yo Lin, Vinsensius B. Vega, Jane S. Thomsen, Tao Zhang, Say Li Kong, Min Xie, ...

Using a chromatin immunoprecipitation-paired end diTag cloning and sequencing strategy, we mapped estrogen receptor α (ERα) binding sites in MCF-7 breast cancer cells. We identified 1,234 high...

Optimization and clinical validation of a pathogen detection microarray (2007)

Wong, Christopher W, Heng, Charlie, Wan Yee, Leong, Soh, Shirlena WL, Kartasasmita, Cissy B, Simoes, Eric AF, ...

Abstract DNA microarrays used as 'genomic sensors' have great potential in clinical diagnostics. Biases inherent in random PCR-amplification, cross-hybridization effects, and inadequate microarray...

Inhibitory effects of estrogen receptor beta on specific hormone-responsive gene expression and association with disease outcome in primary breast cancer (2007)

Lin, Chin-Yo, Ström, Anders, Li Kong, Say, Kietz, Silke, Thomsen, Jane S, Tee, Jason BS, ...

Abstract Introduction The impact of interactions between the two estrogen receptor (ER) subtypes, ERα and ERβ, on gene expression in breast cancer biology is not clear. The goal of this study was...

Expression genomics in breast cancer research: microarrays at the crossroads of biology and medicine (2007)

Miller, Lance D, Liu, Edison T

Abstract Genome-wide expression microarray studies have revealed that the biological and clinical heterogeneity of breast cancer can be partly explained by information embedded within a complex but...

Hormone-replacement therapy influences gene expression profiles and is associated with breast-cancer prognosis: a cohort study (2006)

Hall, Per, Ploner, Alexander, Bjöhle, Judith, Huang, Fei, Lin, Chin-Yo, Liu, Edison T, ...

Abstract Background Postmenopausal hormone-replacement therapy (HRT) increases breast-cancer risk. The influence of HRT on the biology of the primary tumor, however, is not well understood. Methods...

Identifying gene expression changes in breast cancer that distinguish early and late relapse among uncured patients (2006)

Broët, Philippe, Kuznetsov, Vladimir A., Bergh, Jonas, Liu, Edison T., Miller, Lance D.

Motivation: In recent years, microarray technology has revealed many tumor-expressed genes prognostic of clinical outcomes in early-stage breast cancer patients. However, in the presence of cured...

Transcriptome Analysis of Zebrafish Embryogenesis Using Microarrays (2005)

Sinnakaruppan Mathavan, Alicia Mak, Lance D. Miller, Kunde R. Govindarajan, ...

Zebrafish (Danio rerio) is a well-recognized model for the study of vertebrate developmental genetics, yet at the same time little is known about the transcriptional events that underlie zebrafish...

Correlation test to assess low-level processing of high-density oligonucleotide microarray data (2005)

Ploner, Alexander, Miller, Lance D, Hall, Per, Bergh, Jonas, Pawitan, Yudi

Abstract Background There are currently a number of competing techniques for low-level processing of oligonucleotide array data. The choice of technique has a profound effect on subsequent...

Identification of cell cycle-regulated genes in fission yeast (2005)

Xu Peng, Lance D. Miller, Kui Lin, Yonghui Jia, Pinar Kondu, ...

Cell cycle progression is both regulated and accompanied by periodic changes in the expression levels of a large number of genes. To investigate cell cycle-regulated transcriptional programs in the...

Discovery of estrogen receptor α target genes and response elements in breast tumor cells (2004)

Lin, Chin-Yo, Ström, Anders, Vega, Vinsensius, Li Kong, Say, Li Yeo, Ai, Thomsen, Jane S, ...

Abstract Background Estrogens and their receptors are important in human development, physiology and disease. In this study, we utilized an integrated genome-wide molecular and computational approach...

Multi-tissue gene-expression analysis in a mouse model of thyroid hormone resistance (2004)

Miller, Lance D, McPhie, Peter, Suzuki, Hideyo, Kato, Yasuhito, Liu, Edison T, Cheng, Sheue-yann

Abstract Background Resistance to thyroid hormone (RTH) is caused by mutations of the thyroid hormone receptor β (TRβ) gene. To understand the transcriptional program underlying TRβ mutant-induced...

BEARR: batch extraction and analysis of cis-regulatory regions (2004)

Vinsensius B. Vega, Dhinoth Kumar Bangarusamy, Lance D. Miller, Edison T. Liu, Chin-yo Lin

Transcription factors play important roles in regulatingbiologicalanddiseaseprocesses.Microarraytechnology has enabled researchers to simultaneously monitor changes in the expression of thousands of...

Tracking the Evolution of the SARS Coronavirus Using High-Throughput, High-Density Resequencing Arrays (2004)

Wong, Christopher W., Albert, Thomas J., Vega, Vinsensius B., Norton, Jason E., Cutler, David J., Richmond, Todd A., ...

Mutations in the SARS-Coronavirus (SARS-CoV) can alter its clinical presentation, and the study of its mutation patterns in human populations can facilitate contact tracing. Here, we describe the...

BEARR: Batch Extraction and Analysis of cis-Regulatory Regions (2004)

Vega, Vinsensius B., Bangarusamy, Dhinoth Kumar, Miller, Lance D., Liu, Edison T., Lin, Chin-Yo

Transcription factors play important roles in regulating biological and disease processes. Microarray technology has enabled researchers to simultaneously monitor changes in the expression of...

Optimal gene expression analysis by microarrays (2002)

Lance D. Miller, Philip M. Long, Limsoon Wong, Sayan Mukherjee, Lisa M. Mcshane, Edison T. Liu

DNA microarrays make possible the rapid and comprehensive assessment of the transcriptional activity of a cell, and as such have proven valuable in assessing the molecular contributors to biological...

Optimal gene expression analysis by microarrays (2002)

Lance D. Miller, Philip M. Long, Limsoon Wong, Sayan Mukherjee, Lisa M. Mcshane, Edison T. Liu

DNA microarrays make possible the rapid and comprehensive assessment of the transcriptional activity of a cell, and as such have proven valuable in assessing the molecular contributors to biological...

Silencing of Wnt Signaling and Activation of Multiple Metabolic Pathways in Response to Thyroid Hormone-Stimulated Cell Proliferation

Miller, Lance D., Park, Kyung Soo, Guo, Qingbin M., Alkharouf, Nawal W., Malek, Renae L., Lee, Norman H., ...

To investigate the transcriptional program underlying thyroid hormone (T3)-induced cell proliferation, cDNA microarrays were used to survey the temporal expression profiles of 4,400 genes. Of 358...

Identification of White Spot Syndrome Virus Latency-Related Genes in Specific-Pathogen-Free Shrimps by Use of a Microarray

Khadijah, Siti, Neo, Soek Ying, Hossain, M. S., Miller, Lance D., Mathavan, S., Kwang, Jimmy

To investigate whether specific-pathogen-free (SPF) shrimps are asymptomatic carriers of white spot syndrome virus (WSSV), we used a WSSV-specific DNA microarray to measure WSSV gene expression in...

Tracking the Evolution of the SARS Coronavirus Using High-Throughput, High-Density Resequencing Arrays

Wong, Christopher W., Albert, Thomas J., Vega, Vinsensius B., Norton, Jason E., Cutler, David J., Richmond, Todd A., ...

Mutations in the SARS-Coronavirus (SARS-CoV) can alter its clinical presentation, and the study of its mutation patterns in human populations can facilitate contact tracing. Here, we describe the...

Multi-tissue gene-expression analysis in a mouse model of thyroid hormone resistance

Miller, Lance D, McPhie, Peter, Suzuki, Hideyo, Kato, Yasuhito, Liu, Edison T, Cheng, Sheue-yann

Gene-expression analysis in cerebellum, heart and white adipose tissue from a knock-in mouse that harbors a human mutation and faithfully reproduces human resistance to thyroid hormone, uncovered...

BEARR: Batch Extraction and Analysis of cis-Regulatory Regions

Vega, Vinsensius B., Bangarusamy, Dhinoth Kumar, Miller, Lance D., Liu, Edison T., Lin, Chin-Yo

Transcription factors play important roles in regulating biological and disease processes. Microarray technology has enabled researchers to simultaneously monitor changes in the expression of...

Discovery of estrogen receptor α target genes and response elements in breast tumor cells

Lin, Chin-Yo, Ström, Anders, Vega, Vinsensius Berlian, Li Kong, Say, Li Yeo, Ai, Thomsen, Jane S, ...

Microarray analysis has identified 89 estrogen target genes. The cis-regulatory elements found upstream of those genes are not well conserved in mouse and human.

Transcriptome Analysis of Zebrafish Embryogenesis Using Microarrays

Mathavan, Sinnakaruppan, Lee, Serene G. P, Mak, Alicia, Miller, Lance D, Murthy, Karuturi Radha Krishna, Govindarajan, Kunde R, ...

Zebrafish (Danio rerio) is a well-recognized model for the study of vertebrate developmental genetics, yet at the same time little is known about the transcriptional events that underlie zebrafish...

An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival

Miller, Lance D., Smeds, Johanna, George, Joshy, Vega, Vinsensius B., Vergara, Liza, Ploner, Alexander, ...

Perturbations of the p53 pathway are associated with more aggressive and therapeutically refractory tumors. However, molecular assessment of p53 status, by using sequence analysis and...

Identification of Cell Cycle-regulated Genes in Fission YeastD⃞

Peng, Xu, Karuturi, R. Krishna Murthy, Miller, Lance D., Lin, Kui, Jia, Yonghui, Kondu, Pinar, ...

Cell cycle progression is both regulated and accompanied by periodic changes in the expression levels of a large number of genes. To investigate cell cycle-regulated transcriptional programs in the...

Silencing of Wnt Signaling and Activation of Multiple Metabolic Pathways in Response to Thyroid Hormone-Stimulated Cell Proliferation

Miller, Lance D., Park, Kyung Soo, Guo, Qingbin M., Alkharouf, Nawal W., Malek, Renae L., Lee, Norman H., ...

To investigate the transcriptional program underlying thyroid hormone (T3)-induced cell proliferation, cDNA microarrays were used to survey the temporal expression profiles of 4,400 genes. Of 358...

Identification of White Spot Syndrome Virus Latency-Related Genes in Specific-Pathogen-Free Shrimps by Use of a Microarray

Khadijah, Siti, Neo, Soek Ying, Hossain, M. S., Miller, Lance D., Mathavan, S., Kwang, Jimmy

To investigate whether specific-pathogen-free (SPF) shrimps are asymptomatic carriers of white spot syndrome virus (WSSV), we used a WSSV-specific DNA microarray to measure WSSV gene expression in...

Tracking the Evolution of the SARS Coronavirus Using High-Throughput, High-Density Resequencing Arrays

Wong, Christopher W., Albert, Thomas J., Vega, Vinsensius B., Norton, Jason E., Cutler, David J., Richmond, Todd A., ...

Mutations in the SARS-Coronavirus (SARS-CoV) can alter its clinical presentation, and the study of its mutation patterns in human populations can facilitate contact tracing. Here, we describe the...

Multi-tissue gene-expression analysis in a mouse model of thyroid hormone resistance

Miller, Lance D, McPhie, Peter, Suzuki, Hideyo, Kato, Yasuhito, Liu, Edison T, Cheng, Sheue-yann

Gene-expression analysis in cerebellum, heart and white adipose tissue from a knock-in mouse that harbors a human mutation and faithfully reproduces human resistance to thyroid hormone, uncovered...

BEARR: Batch Extraction and Analysis of cis-Regulatory Regions

Vega, Vinsensius B., Bangarusamy, Dhinoth Kumar, Miller, Lance D., Liu, Edison T., Lin, Chin-Yo

Transcription factors play important roles in regulating biological and disease processes. Microarray technology has enabled researchers to simultaneously monitor changes in the expression of...

Discovery of estrogen receptor α target genes and response elements in breast tumor cells

Lin, Chin-Yo, Ström, Anders, Vega, Vinsensius Berlian, Li Kong, Say, Li Yeo, Ai, Thomsen, Jane S, ...

Microarray analysis has identified 89 estrogen target genes. The cis-regulatory elements found upstream of those genes are not well conserved in mouse and human.

Identification of Cell Cycle-regulated Genes in Fission YeastD⃞

Peng, Xu, Karuturi, R. Krishna Murthy, Miller, Lance D., Lin, Kui, Jia, Yonghui, Kondu, Pinar, ...

Cell cycle progression is both regulated and accompanied by periodic changes in the expression levels of a large number of genes. To investigate cell cycle-regulated transcriptional programs in the...

Transcriptome Analysis of Zebrafish Embryogenesis Using Microarrays

Mathavan, Sinnakaruppan, Lee, Serene G. P, Mak, Alicia, Miller, Lance D, Murthy, Karuturi Radha Krishna, Govindarajan, Kunde R, ...

Zebrafish (Danio rerio) is a well-recognized model for the study of vertebrate developmental genetics, yet at the same time little is known about the transcriptional events that underlie zebrafish...

An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival

Miller, Lance D., Smeds, Johanna, George, Joshy, Vega, Vinsensius B., Vergara, Liza, Ploner, Alexander, ...

Perturbations of the p53 pathway are associated with more aggressive and therapeutically refractory tumors. However, molecular assessment of p53 status, by using sequence analysis and...

Expression genomics in breast cancer research: microarrays at the crossroads of biology and medicine

Miller, Lance D, Liu, Edison T

Genome-wide expression microarray studies have revealed that the biological and clinical heterogeneity of breast cancer can be partly explained by information embedded within a complex but ordered...

Whole-Genome Cartography of Estrogen Receptor α Binding Sites

Lin, Chin-Yo, Vega, Vinsensius B, Thomsen, Jane S, Zhang, Tao, Kong, Say Li, Xie, Min, ...

Using a chromatin immunoprecipitation-paired end diTag cloning and sequencing strategy, we mapped estrogen receptor α (ERα) binding sites in MCF-7 breast cancer cells. We identified 1,234 high...

Optimization and clinical validation of a pathogen detection microarray

Wong, Christopher W, Heng, Charlie Lee Wah, Wan Yee, Leong, Soh, Shirlena WL, Kartasasmita, Cissy B, Simoes, Eric AF, ...

New design and optimization of pathogen detection microarrays is shown to allow robust and accurate detection of a range of pathogens. The customized microarray platform includes a method for...

CDKN1C (p57KIP2) Is a Direct Target of EZH2 and Suppressed by Multiple Epigenetic Mechanisms in Breast Cancer Cells

Yang, Xiaojing, Karuturi, R. K. Murthy, Sun, Feng, Aau, Meiyee, Yu, Kun, Shao, Rongguang, ...

CDKN1C (encoding tumor suppressor p57KIP2) is a cyclin-dependent kinase (CDK) inhibitor whose family members are often transcriptionally downregulated in human cancer via promoter DNA methylation. In...

CT-X antigen expression in human breast cancer

Grigoriadis, Anita, Caballero, Otavia L., Hoek, Keith S., Da Silva, Leonard, Chen, Yao-Tseng, Shin, Sandra J., ...

Cancer/testis (CT) genes are predominantly expressed in human germ line cells, but not somatic tissues, and frequently become activated in different cancer types. Several CT antigens have already...