Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses (2009)
Fullwood, Melissa J., Wei, Chia-Lin, Liu, Edison T., Ruan, Yijun
Comprehensive understanding of functional elements in the human genome will require thorough interrogation and comparison of individual human genomes and genomic structures. Such an endeavor will...
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...
Identification of Cell Cycle-regulated Genes in Fission Yeast (2008)
Long Wang, Lim-soon Wong, Edison T. Liu, Mohan K. Balasubramanian, Jianhua Liu, Jianhua Liu
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...
ESR1and EGFgenetic variation in relation to breast cancer risk and survival (2008)
Einarsdóttir, Kristjana, Darabi, Hatef, Li, Yi, Low, Yen, Li, Yu, Bonnard, Carine, ...
Abstract Introduction Oestrogen exposure is a central factor in the development of breast cancer. Oestrogen receptor alpha (ESR1) is the main mediator of oestrogen effect in breast epithelia and has...
Evolution of the mammalian transcription factor binding repertoire via transposable elements (2008)
Bourque, Guillaume, Leong, Bernard, Vega, Vinsensius B., Chen, Xi, Lee, Yen Ling, Srinivasan, Kandhadayar G., ...
Identification of lineage-specific innovations in genomic control elements is critical for understanding transcriptional regulatory networks and phenotypic heterogeneity. We analyzed, from an...
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...
Tan, Jing, Yang, Xiaojing, Zhuang, Li, Jiang, Xia, Chen, Wei, Lee, Puay Leng, ...
Polycomb-repressive complex 2 (PRC2)-mediated histone methylation plays an important role in aberrant cancer gene silencing and is a potential target for cancer therapy. Here we show that...
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...
Whole-Genome Cartography of Estrogen Receptorα Binding Sites (2007)
Chin-Yo Lin, Jane S. Thomsen, Tao Zhang, Ming Xie, ...
Estrogen receptorα is nuclear hormone receptor involved in reproduction, cancer, and bone metabolism. Identification of its binding sites in the human genome will assist in understanding its precise...
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...
Effect of ATM, CHEK2 and ERBB2 TAGSNPs and haplotypes on endometrial cancer risk (2007)
Einarsdóttir, Kristjana, Humphreys, Keith, Bonnard, Carine, Li, Yuqing, Li, Yi, Chia, Kee Seng, ...
Family history of endometrial cancer increases the risk of developing the disease, but it is still largely unknown which germ-line genetic factors are involved in the aetiology of endometrial cancer....
Einarsdóttir, Kristjana, Rosenberg, Lena U, Humphreys, Keith, Bonnard, Carine, Palmgren, Juni, Li, Yuqing, ...
Abstract Background Mutations in the ataxia-telangiectasia mutated ( ATM ) and checkpoint kinase 2 ( CHEK2 ) genes and amplification of the v-erb-b2 avian erythroblastic leukemia viral oncogene...
Vega, Vinsensius B, Lin, Chin-Yo, Lai, Koon, Li Kong, Say, Xie, Min, Su, Xiaodi, ...
Abstract Background Transcription factor binding sites (TFBS) impart specificity to cellular transcriptional responses and have largely been defined by consensus motifs derived from a handful of...
Intrinsic molecular signature of breast cancer in a population-based cohort of 412 patients (2006)
Calza, Stefano, Hall, Per, Auer, Gert, Bjöhle, Judith, Klaar, Sigrid, Kronenwett, Ulrike, ...
Abstract Background Molecular markers and the rich biological information they contain have great potential for cancer diagnosis, prognostication and therapy prediction. So far, however, they have...
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...
Linkage Disequilibrium Mapping of CHEK2: Common Variation and Breast Cancer Risk (2006)
Kristjana Einarsdóttir, Keith Humphreys, Carine Bonnard, Juni Palmgren, Mark M. Iles, Arvid Sjölander, ...
Rare mutations in the CHEK2 gene are involved in familial breast cancer. This large study among Swedish women did not find an association between common CHEK2 variants and breast cancer.
Linkage Disequilibrium Mapping of CHEK2: Common Variation and Breast Cancer Risk (2006)
Kristjana Einarsdóttir, Keith Humphreys, Carine Bonnard, Juni Palmgren, Mark M. Iles, Arvid Sjölander, ...
Background Checkpoint kinase 2 (CHEK2) averts cancer development by promoting cell cycle arrest and activating DNA repair in genetically damaged cells. Previous investigation has established a role...
RNA Viral Community in Human Feces: Prevalence of Plant Pathogenic Viruses (2006)
Tao Zhang, Mya Breitbart, Wah Heng Lee, Jin-Quan Run, Chia Lin Wei, ...
A comparative metagenomic analysis of RNA viruses in the human gut identifies the vast majority as plant pathogens.
RNA Viral Community in Human Feces: Prevalence of Plant Pathogenic Viruses (2006)
Tao Zhang, Mya Breitbart, Wah Heng Lee, Jin-Quan Run, Chia Lin Wei, ...
The human gut is known to be a reservoir of a wide variety of microbes, including viruses. Many RNA viruses are known to be associated with gastroenteritis; however, the enteric RNA viral community...
Genome-wide analysis of mammalian promoter architecture and evolution (2006)
Carninci, Piero, Sandelin, Albin, Lenhard, Boris, Katayama, Shintaro, Shimokawa, Kazuro, Ponjavic, Jasmina, ...
Mammalian promoters can be separated into two classes, conserved TATA box–enriched promoters, which initiate at a well-defined site, and more plastic, broad and evolvable CpG-rich promoters. We...
Genome-wide analysis of mammalian promoter architecture and evolution (2006)
Carninci, Piero, Sandelin, Albin, Lenhard, Boris, Katayama, Shintaro, Shimokawa, Kazuro, Ponjavic, Jasmina, ...
Mammalian promoters can be separated into two classes, conserved TATA box enriched promoters, which initiate at a well-defined site, and more plastic, broad and evolvable CpG-rich promoters. We have...
Genome-wide analysis of mammalian promoter architecture and evolution (2006)
Carninci, Piero, Sandelin, Albin, Lenhard, Boris, Katayama, Shintaro, Shimokawa, Kazuro, Ponjavic, Jasmina, ...
Mammalian promoters can be separated into two classes, conserved TATA box–enriched promoters, which initiate at a well-defined site, and more plastic, broad and evolvable CpG-rich promoters. We...
Genome-wide analysis of mammalian promoter architecture and evolution (2006)
Carninci, Piero, Sandelin, Albin, Lenhard, Boris, Katayama, Shintaro, Shimokawa, Kazuro, Ponjavic, Jasmina, ...
Mammalian promoters can be separated into two classes, conserved TATA box–enriched promoters, which initiate at a well-defined site, and more plastic, broad and evolvable CpG-rich promoters. We...
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...
Effect of ATM, CHEK2 and ERBB2 tagSNPs and haplotypes on endometrial cancer risk (2006)
Einarsdóttir, Kristjana, Humphreys, Keith, Bonnard, Carine, Li, Yuqing, Li, Yi, Chia, Kee Seng, ...
Family history of endometrial cancer increases the risk of developing the disease, but it is still largely unknown which germ-line genetic factors are involved in the aetiology of endometrial cancer....
Pawitan, Yudi, Bjöhle, Judith, Amler, Lukas, Borg, Anna-Lena, Egyhazi, Suzanne, Hall, Per, ...
Abstract Introduction Adjuvant breast cancer therapy significantly improves survival, but overtreatment and undertreatment are major problems. Breast cancer expression profiling has so far mainly...
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...
SARS Transmission Pattern in Singapore Reassessed by Viral Sequence Variation Analysis (2005)
Jianjun Liu, Siew Lan Lim, Yijun Ruan, Ai Ee Ling, Christian Drosten, ...
Mass spectrometry-based sequence analysis provides a sensitive and accurate method to characterize genetic variation of the SARS coronavirus in clinical samples.
SARS Transmission Pattern in Singapore Reassessed by Viral Sequence Variation Analysis (2005)
Jianjun Liu, Siew Lan Lim, Yijun Ruan, Ai Ee Ling, Christian Drosten, ...
Background Epidemiological investigations of infectious disease are mainly dependent on indirect contact information and only occasionally assisted by characterization of pathogen sequence variation...
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...
Expression genomics and drug development: Towards predictive pharmacology (2005)
Expression genomics can be defined as the study of the dynamic transciptome and its regulatory elements. Technologies are available that can assess transcripts on a genome-wide scale over time and...
BRCA1-mediated repression of select X chromosome genes (2004)
Jazaeri, Amir A, Chandramouli, Gadisetti VR, Aprelikova, Olga, Nuber, Ulrike A, Sotiriou, Christos, Liu, Edison T, ...
Abstract Recently BRCA1 has been implicated in the regulation of gene expression from the X chromosome. In this study the influence of BRCA1 on expression of X chromosome genes was investigated....
BRCA1-mediated repression of select X chromosome genes (2004)
Jazaeri,Amir A, Chandramouli,Gadisetti VR, Aprelikova,Olga, Nuber,Ulrike A, Sotiriou,Christos, Liu,Edison T, ...
Recently BRCA1 has been implicated in the regulation of gene expression from the X chromosome. In this study the influence of BRCA1 on expression of X chromosome genes was investigated. Complementary...
Ng, Lisa FP, Hibberd, Martin L, Ooi, Eng-Eong, Tang, Kin-Fai, Neo, Soek-Ying, Tan, Jenny, ...
Abstract Background The molecular basis of severe acute respiratory syndrome (SARS) coronavirus (CoV) induced pathology is still largely unclear. Many SARS patients suffer respiratory distress...
Vega, Vinsensius B, Ruan, Yijun, Liu, Jianjun, Lee, Wah, Wei, Chia, Se-Thoe, Su, ...
Abstract Background The SARS coronavirus is the etiologic agent for the epidemic of the Severe Acute Respiratory Syndrome. The recent emergence of this new pathogen, the careful tracing of its...
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...
BRCA1-mediated repression of select X chromosome genes (2004)
Jazaeri, Amir A, Chandramouli, Gadisetti VR, Aprelikova, Olga, Nuber, Ulrike A, Sotiriou, Christos, Liu, Edison T, ...
Recently BRCA1 has been implicated in the regulation of gene expression from the X chromosome. In this study the influence of BRCA1 on expression of X chromosome genes was investigated. Complementary...
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...
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...
Bajic, Vladimir B., Tan, Sin Lam, Chong, Allen, Tang, Suisheng, Ström, Anders, Gustafsson, Jan-Åke, ...
We present a unique program for identification of estrogen response elements (EREs) in genomic DNA and related analyses. The detection algorithm was tested on several large datasets and makes one...
Defining the galaxy of gene expression in breast cancer (2002)
Liu, Edison T, Sotiriou, Christos
Abstract Recent reports detailing the expression profiles of primary breast cancer have pointed to the utility of this approach in defining subclasses with distinct molecular configurations and...
Prevalence and spectrum of p53 mutations associated with smoking in breast cancer (2002)
Conway, Kathleen, Edmiston, Sharon N., Cui, Lisa, Drouin, S. Scott, Pang, Jingzhong, He, Mei, ...
To explore the role of smoking in breast cancer, we undertook a population-based study to evaluate the prevalence and spectrum of p53 mutations in the breast tumors of smokers and nonsmokers. We...
Prevalence and spectrum of p53 mutations associated with smoking in breast cancer (2002)
Conway, Kathleen, Edmiston, Sharon N., Cui, Lisa, Drouin, S. Scott, Pang, Jingzhong, He, Mei, ...
To explore the role of smoking in breast cancer, we undertook a population-based study to evaluate the prevalence and spectrum of p53 mutations in the breast tumors of smokers and nonsmokers. We...
Prevalence and spectrum of p53 mutations associated with smoking in breast cancer (2002)
Conway, Kathleen, Edmiston, Sharon N., Cui, Lisa, Drouin, S. Scott, Pang, Jingzhong, He, Mei, ...
To explore the role of smoking in breast cancer, we undertook a population-based study to evaluate the prevalence and spectrum of p53 mutations in the breast tumors of smokers and nonsmokers. We...
Sotiriou, Christos, Powles, Trevor J, Dowsett, Mitch, Jazaeri, Amir A, Feldman, Andrew L, Assersohn, Laura, ...
Abstract Background Drug resistance in breast cancer is a major obstacle to successful chemotherapy. In this study we used cDNA microarray technology to examine gene expression profiles obtained from...
Prevalence and spectrum of p53 mutations associated with smoking in breast cancer (2002)
Conway, Kathleen, Edmiston, Sharon N., Cui, Lisa, Drouin, S. Scott, Pang, Jingzhong, He, Mei, ...
To explore the role of smoking in breast cancer, we undertook a population-based study to evaluate the prevalence and spectrum of p53 mutations in the breast tumors of smokers and nonsmokers. We...
Prevalence and spectrum of p53 mutations associated with smoking in breast cancer (2002)
Conway, Kathleen, Edmiston, Sharon N., Cui, Lisa, Drouin, S. Scott, Pang, Jingzhong, He, Mei, ...
To explore the role of smoking in breast cancer, we undertook a population-based study to evaluate the prevalence and spectrum of p53 mutations in the breast tumors of smokers and nonsmokers. We...
Prevalence and spectrum of p53 mutations associated with smoking in breast cancer (2002)
Conway, Kathleen, Edmiston, Sharon N., Cui, Lisa, Drouin, S. Scott, Pang, Jingzhong, He, Mei, ...
To explore the role of smoking in breast cancer, we undertook a population-based study to evaluate the prevalence and spectrum of p53 mutations in the breast tumors of smokers and nonsmokers. We...
Prevalence and spectrum of p53 mutations associated with smoking in breast cancer (2002)
Conway, Kathleen, Edmiston, Sharon N., Cui, Lisa, Drouin, S. Scott, Pang, Jingzhong, He, Mei, ...
To explore the role of smoking in breast cancer, we undertook a population-based study to evaluate the prevalence and spectrum of p53 mutations in the breast tumors of smokers and nonsmokers. We...
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...
Gene expression profiles of BRCA1-linked, BRCA2-linked, and sporadic ovarian cancers (2002)
Amir A. Jazaeri, Cindy J. Yee, Christos Sotiriou, Kelly R. Brantley, Jeff Boyd, Edison T. Liu
are responsible for 5%–10 % of epithelial ovarian cancers, but the molecular pathways affected by these mutations are unknown. We used complementary DNA (cDNA) microarrays to compare gene...
Prevalence and spectrum of p53 mutations associated with smoking in breast cancer (2002)
Conway, Kathleen, Edmiston, Sharon N., Cui, Lisa, Drouin, S. Scott, Pang, Jingzhong, He, Mei, ...
To explore the role of smoking in breast cancer, we undertook a population-based study to evaluate the prevalence and spectrum of p53 mutations in the breast tumors of smokers and nonsmokers. We...
Edgerton, Mary E., Taylor, Ronald, Powell, John I., Hunter, Lawrence, Simon, Richard, Liu, Edison T.
One of the challenges to the effective utilization of cDNA microarray analysis in mouse models of oncogenesis is the choice of a critical set of probes that are informative for human disease. Given...
Shan, Liang, He, Mei, Yu, Minshu, Qiu, Cunping, Lee, Norman H., Liu, Edison T., ...
cDNA microarray analysis was used to examine gene expression profiles in normal female Sprague–Dawley rat mammary gland and in carcinomas induced by the cooked meat-derived carcinogen...
Gene Expression Profiles of BRCA1-Linked, BRCA2-Linked, and Sporadic Ovarian Cancers (2002)
Jazaeri, Amir A., Yee, Cindy J., Sotiriou, Christos, Brantley, Kelly R., Boyd, Jeff, Liu, Edison T.
Background: Germline mutations in BRCA1 and BRCA2 are responsible for 5%–10% of epithelial ovarian cancers, but the molecular pathways affected by these mutations are unknown. We used complementary...
Prevalence and spectrum of p53 mutations associated with smoking in breast cancer (2002)
Conway, Kathleen, Edmiston, Sharon N., Cui, Lisa, Drouin, S. Scott, Pang, Jingzhong, He, Mei, ...
To explore the role of smoking in breast cancer, we undertook a population-based study to evaluate the prevalence and spectrum of p53 mutations in the breast tumors of smokers and nonsmokers. We...
BRCA1 function in T lymphocytes: a cellular specificity of a different kind (2000)
Abstract Recent work by Mak et al demonstrates that mice carrying a T-cell-specific disruption of the brca1 gene display markedly impaired T-lymphocyte development and proliferation in the absence of...
Breast cancer research: where we are and where we should go (2000)
No abstract available.
Biologic and Biochemical Analyses of p16INK4a Mutations From Primary Tumors (1999)
Yarbrough, Wendell G., Buckmire, Robert A., Bessho, Mika, Liu, Edison T.
BACKGROUND: Point mutations in the tumor suppressor gene p16INK4a (also known as p16, CDKN2, MTS1, and INK4a) are found in many tumor types. Because the function of the products of these naturally...
erbB-2, p53, and Efficacy of Adjuvant Therapy in Lymph Node-Positive Breast Cancer (1998)
Thor, Ann D., Berry, Donald A., Budman, Daniel R., Muss, Hyman B., Kute, Timothy, Henderson, I. Craig, ...
Background: We have previously reported that high expression of the erbB-2 gene (also known as HER-2/neu and ERBB2) in breast cancer is associated with patient response to dose-intensive treatment...
Familial Tumor Syndrome Associated With a Germline Nonfunctional p16INK4a Allele (1996)
Yarbrough, Wendell G., Aprelikova, Olga, Pei, Hong, Olshan, Andrew F., Liu, Edison T.
Risk of Miscarriage and a Common Variant of the Estrogen Receptor Gene (1993)
Taylor, Jack A., Wilcox, Allen J., Bowes, Watson A., Li, Yu, Liu, Edison T., You, Ming
An inherited variant of the estrogen receptor gene was previously suggested to be a major determinant of a woman's risk of miscarriage. The authors tested this hypothesis in a case-control study of...
Burck, Kathy B., Liu, Edison T., Larrick, James W.
Incluye bibliografía e índice
BRCA1-associated growth arrest is RB-dependent
Aprelikova, Olga N., Fang, Bruno S., Meissner, Eric G., Cotter, Shane, Campbell, Mel, Kuthiala, Aalok, ...
BRCA1 is a susceptibility gene for breast and ovarian cancer with growth-inhibitory activity for which the mechanism of action remains unclear. When introduced into cells, BRCA1 inhibits growth of...
Identification of a large Myc-binding protein that contains RCC1-like repeats
Guo, Qingbin, Xie, Jingwu, Dang, Chi V., Liu, Edison T., Bishop, J. Michael
The protooncogene MYC plays an important role in the regulation of cellular proliferation, differentiation, and apoptosis and has been implicated in a variety of human tumors. MYC and the closely...
Axl-Gas6 Interaction Counteracts E1A-Mediated Cell Growth Suppression and Proapoptotic Activity
Lee, Wei-Ping, Liao, Yong, Robinson, Dan, Kung, Hsing-Jien, Liu, Edison T., Hung, Mien-Chie
The adenovirus type 5 early region 1A gene (E1A) has previously been known as an immortalization oncogene because E1A is required for transforming oncogenes, such as ras and E1B, to transform cells...
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...
Sotiriou, Christos, Powles, Trevor J, Dowsett, Mitch, Jazaeri, Amir A, Feldman, Andrew L, Assersohn, Laura, ...
Initiating oncogenic event determines gene-expression patterns of human breast cancer models
Desai, Kartiki V., Xiao, Nianqing, Wang, Weili, Gangi, Lisa, Greene, John, Powell, John I., ...
Molecular expression profiling of tumors initiated by transgenic overexpression of c-myc, c-neu, c-ha-ras, polyoma middle T antigen (PyMT) or simian virus 40 T/t antigen (T-ag) targeted to the mouse...
BRCA1 function in T lymphocytes: a cellular specificity of a different kind
Recent work by Mak et al demonstrates that mice carrying a T-cell-specific disruption of the brca1 gene display markedly impaired T-lymphocyte development and proliferation in the absence of any...
Defining the galaxy of gene expression in breast cancer
Liu, Edison T, Sotiriou, Christos
Recent reports detailing the expression profiles of primary breast cancer have pointed to the utility of this approach in defining subclasses with distinct molecular configurations and clinical...
Characterization of Mice Deficient in the Src Family Nonreceptor Tyrosine Kinase Frk/rak
Chandrasekharan, Subhashini, Qiu, Ting Hu, Alkharouf, Nawal, Brantley, Kelly, Mitchell, James B., Liu, Edison T.
Frk/rak belongs to a novel family of Src kinases with epithelial tissue-specific expression. Although developmental expression patterns and functional overexpression in vitro have associated these...
Bajic, Vladimir B., Tan, Sin Lam, Chong, Allen, Tang, Suisheng, Ström, Anders, Gustafsson, Jan-Åke, ...
We present a unique program for identification of estrogen response elements (EREs) in genomic DNA and related analyses. The detection algorithm was tested on several large datasets and makes one...
Sotiriou, Christos, Neo, Soek-Ying, McShane, Lisa M., Korn, Edward L., Long, Philip M., Jazaeri, Amir, ...
Comprehensive gene expression patterns generated from cDNA microarrays were correlated with detailed clinico-pathological characteristics and clinical outcome in an unselected group of 99...
Detection of Severe Acute Respiratory Syndrome Coronavirus in Blood of Infected Patients
Ng, Lisa F. P., Wong, Michelle, Koh, Susie, Ooi, Eng-Eong, Tang, King-Fai, Leong, Hoe-Nam, ...
Severe acute respiratory syndrome (SARS) has caused major outbreaks worldwide, resulting in an urgent need to obtain sensitive and accurate diagnosis of this disease. PCR-based detection methods were...
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...
Wei, Chia-Lin, Ng, Patrick, Chiu, Kuo Ping, Wong, Chee Hong, Ang, Chin Chin, Lipovich, Leonard, ...
Complete genome annotation relies on precise identification of transcription units bounded by a transcription initiation site (TIS) and a polyadenylation site (PAS). To facilitate this process, we...
Mutational dynamics of the SARS coronavirus in cell culture and human populations isolated in 2003
Vega, Vinsensius B, Ruan, Yijun, Liu, Jianjun, Lee, Wah Heng, Wei, Chia Lin, Se-Thoe, Su Yun, ...
BRCA1-mediated repression of select X chromosome genes
Jazaeri, Amir A, Chandramouli, Gadisetti VR, Aprelikova, Olga, Nuber, Ulrike A, Sotiriou, Christos, Liu, Edison T, ...
Recently BRCA1 has been implicated in the regulation of gene expression from the X chromosome. In this study the influence of BRCA1 on expression of X chromosome genes was investigated. Complementary...
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.
SARS Transmission Pattern in Singapore Reassessed by Viral Sequence Variation Analysis
Liu, Jianjun, Lim, Siew Lan, Ruan, Yijun, Ling, Ai Ee, Ng, Lisa F. P, Drosten, Christian, ...
Mass spectrometry-based sequence analysis provides a sensitive and accurate method to characterize genetic variation of the SARS coronavirus in clinical samples
Systematic Deletion Analysis of Fission Yeast Protein Kinases†
Bimbó, Andrea, Jia, Yonghui, Poh, Siew Lay, Karuturi, R. Krishna Murthy, Den Elzen, Nicole, Peng, Xu, ...
Eukaryotic protein kinases are key molecules mediating signal transduction that play a pivotal role in the regulation of various biological processes, including cell cycle progression, cellular...
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...
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...
RNA Viral Community in Human Feces: Prevalence of Plant Pathogenic Viruses
Zhang, Tao, Breitbart, Mya, Lee, Wah Heng, Run, Jin-Quan, Wei, Chia Lin, Soh, Shirlena Wee Ling, ...
The human gut is known to be a reservoir of a wide variety of microbes, including viruses. Many RNA viruses are known to be associated with gastroenteritis; however, the enteric RNA viral community...
Cozma, Diana, Lukes, Luanne, Rouse, Jessica, Qiu, Ting Hu, Liu, Edison T., Hunter, Kent W.
The epistatically interacting modifier loci (Apmt1 and Apmt2) accelerate the polyoma Middle-T (PyVT)-induced mammary tumor. To identify potential candidate genes loci, a combined bioinformatics 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...
Zhao, Yan, Tan, Jing, Zhuang, Li, Jiang, Xia, Liu, Edison T., Yu, Qiang
Inhibitors of histone deacetylases (HDACIs) are a new generation of anticancer agents that selectively kill tumor cells. However, the molecular basis for their tumor selectivity is not well...
Linkage Disequilibrium Mapping of CHEK2: Common Variation and Breast Cancer Risk
Einarsdóttir, Kristjana, Humphreys, Keith, Bonnard, Carine, Palmgren, Juni, Iles, Mark M, Sjölander, Arvid, ...
Rare mutations in the CHEK2 gene are involved in familial breast cancer. This large study among Swedish women did not find an association between common CHEK2 variants and breast cancer.
BRCA1-associated growth arrest is RB-dependent
Aprelikova, Olga N., Fang, Bruno S., Meissner, Eric G., Cotter, Shane, Campbell, Mel, Kuthiala, Aalok, ...
BRCA1 is a susceptibility gene for breast and ovarian cancer with growth-inhibitory activity for which the mechanism of action remains unclear. When introduced into cells, BRCA1 inhibits growth of...
Identification of a large Myc-binding protein that contains RCC1-like repeats
Guo, Qingbin, Xie, Jingwu, Dang, Chi V., Liu, Edison T., Bishop, J. Michael
The protooncogene MYC plays an important role in the regulation of cellular proliferation, differentiation, and apoptosis and has been implicated in a variety of human tumors. MYC and the closely...
Axl-Gas6 Interaction Counteracts E1A-Mediated Cell Growth Suppression and Proapoptotic Activity
Lee, Wei-Ping, Liao, Yong, Robinson, Dan, Kung, Hsing-Jien, Liu, Edison T., Hung, Mien-Chie
The adenovirus type 5 early region 1A gene (E1A) has previously been known as an immortalization oncogene because E1A is required for transforming oncogenes, such as ras and E1B, to transform cells...
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...
Sotiriou, Christos, Powles, Trevor J, Dowsett, Mitch, Jazaeri, Amir A, Feldman, Andrew L, Assersohn, Laura, ...
Initiating oncogenic event determines gene-expression patterns of human breast cancer models
Desai, Kartiki V., Xiao, Nianqing, Wang, Weili, Gangi, Lisa, Greene, John, Powell, John I., ...
Molecular expression profiling of tumors initiated by transgenic overexpression of c-myc, c-neu, c-ha-ras, polyoma middle T antigen (PyMT) or simian virus 40 T/t antigen (T-ag) targeted to the mouse...
BRCA1 function in T lymphocytes: a cellular specificity of a different kind
Recent work by Mak et al demonstrates that mice carrying a T-cell-specific disruption of the brca1 gene display markedly impaired T-lymphocyte development and proliferation in the absence of any...
Defining the galaxy of gene expression in breast cancer
Liu, Edison T, Sotiriou, Christos
Recent reports detailing the expression profiles of primary breast cancer have pointed to the utility of this approach in defining subclasses with distinct molecular configurations and clinical...
Characterization of Mice Deficient in the Src Family Nonreceptor Tyrosine Kinase Frk/rak
Chandrasekharan, Subhashini, Qiu, Ting Hu, Alkharouf, Nawal, Brantley, Kelly, Mitchell, James B., Liu, Edison T.
Frk/rak belongs to a novel family of Src kinases with epithelial tissue-specific expression. Although developmental expression patterns and functional overexpression in vitro have associated these...
Bajic, Vladimir B., Tan, Sin Lam, Chong, Allen, Tang, Suisheng, Ström, Anders, Gustafsson, Jan-Åke, ...
We present a unique program for identification of estrogen response elements (EREs) in genomic DNA and related analyses. The detection algorithm was tested on several large datasets and makes one...
Sotiriou, Christos, Neo, Soek-Ying, McShane, Lisa M., Korn, Edward L., Long, Philip M., Jazaeri, Amir, ...
Comprehensive gene expression patterns generated from cDNA microarrays were correlated with detailed clinico-pathological characteristics and clinical outcome in an unselected group of 99...
Detection of Severe Acute Respiratory Syndrome Coronavirus in Blood of Infected Patients
Ng, Lisa F. P., Wong, Michelle, Koh, Susie, Ooi, Eng-Eong, Tang, King-Fai, Leong, Hoe-Nam, ...
Severe acute respiratory syndrome (SARS) has caused major outbreaks worldwide, resulting in an urgent need to obtain sensitive and accurate diagnosis of this disease. PCR-based detection methods were...
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...
Wei, Chia-Lin, Ng, Patrick, Chiu, Kuo Ping, Wong, Chee Hong, Ang, Chin Chin, Lipovich, Leonard, ...
Complete genome annotation relies on precise identification of transcription units bounded by a transcription initiation site (TIS) and a polyadenylation site (PAS). To facilitate this process, we...
Mutational dynamics of the SARS coronavirus in cell culture and human populations isolated in 2003
Vega, Vinsensius B, Ruan, Yijun, Liu, Jianjun, Lee, Wah Heng, Wei, Chia Lin, Se-Thoe, Su Yun, ...
BRCA1-mediated repression of select X chromosome genes
Jazaeri, Amir A, Chandramouli, Gadisetti VR, Aprelikova, Olga, Nuber, Ulrike A, Sotiriou, Christos, Liu, Edison T, ...
Recently BRCA1 has been implicated in the regulation of gene expression from the X chromosome. In this study the influence of BRCA1 on expression of X chromosome genes was investigated. Complementary...
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.
SARS Transmission Pattern in Singapore Reassessed by Viral Sequence Variation Analysis
Liu, Jianjun, Lim, Siew Lan, Ruan, Yijun, Ling, Ai Ee, Ng, Lisa F. P, Drosten, Christian, ...
Mass spectrometry-based sequence analysis provides a sensitive and accurate method to characterize genetic variation of the SARS coronavirus in clinical samples
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...
Systematic Deletion Analysis of Fission Yeast Protein Kinases†
Bimbó, Andrea, Jia, Yonghui, Poh, Siew Lay, Karuturi, R. Krishna Murthy, Den Elzen, Nicole, Peng, Xu, ...
Eukaryotic protein kinases are key molecules mediating signal transduction that play a pivotal role in the regulation of various biological processes, including cell cycle progression, cellular...
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...
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...
Zhao, Yan, Tan, Jing, Zhuang, Li, Jiang, Xia, Liu, Edison T., Yu, Qiang
Inhibitors of histone deacetylases (HDACIs) are a new generation of anticancer agents that selectively kill tumor cells. However, the molecular basis for their tumor selectivity is not well...
RNA Viral Community in Human Feces: Prevalence of Plant Pathogenic Viruses
Zhang, Tao, Breitbart, Mya, Lee, Wah Heng, Run, Jin-Quan, Wei, Chia Lin, Soh, Shirlena Wee Ling, ...
The human gut is known to be a reservoir of a wide variety of microbes, including viruses. Many RNA viruses are known to be associated with gastroenteritis; however, the enteric RNA viral community...
Cozma, Diana, Lukes, Luanne, Rouse, Jessica, Qiu, Ting Hu, Liu, Edison T., Hunter, Kent W.
The epistatically interacting modifier loci (Apmt1 and Apmt2) accelerate the polyoma Middle-T (PyVT)-induced mammary tumor. To identify potential candidate genes loci, a combined bioinformatics and...
Linkage Disequilibrium Mapping of CHEK2: Common Variation and Breast Cancer Risk
Einarsdóttir, Kristjana, Humphreys, Keith, Bonnard, Carine, Palmgren, Juni, Iles, Mark M, Sjölander, Arvid, ...
Rare mutations in the CHEK2 gene are involved in familial breast cancer. This large study among Swedish women did not find an association between common CHEK2 variants and breast cancer.
Intrinsic molecular signature of breast cancer in a population-based cohort of 412 patients
Calza, Stefano, Hall, Per, Auer, Gert, Bjöhle, Judith, Klaar, Sigrid, Kronenwett, Ulrike, ...
Vega, Vinsensius B, Lin, Chin-Yo, Lai, Koon Siew, Li Kong, Say, Xie, Min, Su, Xiaodi, ...
Refinement of the functional human estrogen receptor binding site model using a multi-platform genome-wide approach reveals extended binding specificity signal.
Einarsdóttir, Kristjana, Rosenberg, Lena U, Humphreys, Keith, Bonnard, Carine, Palmgren, Juni, Li, Yuqing, ...
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...
Core Biopsies Can Be Used to Distinguish Differences in Expression Profiling by cDNA Microarrays
Sotiriou, Christos, Khanna, Chand, Jazaeri, Amir A., Petersen, David, Liu, Edison T.
The primary focus of this work was to determine the feasibility of obtaining representative expression array profiles from clinical core biopsies. For this purpose we performed six 16-gauge needle...
Tan, Jing, Yang, Xiaojing, Zhuang, Li, Jiang, Xia, Chen, Wei, Lee, Puay Leng, ...
Polycomb-repressive complex 2 (PRC2)-mediated histone methylation plays an important role in aberrant cancer gene silencing and is a potential target for cancer therapy. Here we show that...
ESR1 and EGF genetic variation in relation to breast cancer risk and survival
Einarsdóttir, Kristjana, Darabi, Hatef, Li, Yi, Low, Yen Ling, Li, Yu Qing, Bonnard, Carine, ...
Lam, Siew Hong, Mathavan, Sinnakarupan, Tong, Yan, Li, Haixia, Karuturi, R. Krishna Murthy, Wu, Yilian, ...
The ability to perform large-scale, expression-based chemogenomics on whole adult organisms, as in invertebrate models (worm and fly), is highly desirable for a vertebrate model but its feasibility...
De-Novo Identification of PPARγ/RXR Binding Sites and Direct Targets during Adipogenesis
Hamza, Mohamed Sabry, Pott, Sebastian, Vega, Vinsensius B., Thomsen, Jane S., Kandhadayar, Gopalan Srinivasan, Ng, Patrick Wei Pern, ...
Evolution of the mammalian transcription factor binding repertoire via transposable elements
Bourque, Guillaume, Leong, Bernard, Vega, Vinsensius B., Chen, Xi, Lee, Yen Ling, Srinivasan, Kandhadayar G., ...
Identification of lineage-specific innovations in genomic control elements is critical for understanding transcriptional regulatory networks and phenotypic heterogeneity. We analyzed, from an...