PID: the Pathway Interaction Database (2009)
Schaefer, Carl F., Anthony, Kira, Krupa, Shiva, Buchoff, Jeffrey, Day, Matthew, Hannay, Timo, ...
The Pathway Interaction Database (PID, http://pid.nci.nih.gov) is a freely available collection of curated and peer-reviewed pathways composed of human molecular signaling and regulatory events and...
PID: The Pathway Interaction Database (2008)
Carl F. Schaefer, Kira Anthony, Shiva Krupa, Jeffrey Buchoff, Matthew Day, Timo Hannay, ...
The Pathway Interaction Database (PID, "http://pid.nci.nih.gov":http://pid.nci.nih.gov) is a freely available collection of curated and peer-reviewed pathways composed of human molecular...
Systematic analysis of genetic alterations in tumors using Cancer Genome WorkBench (CGWB) (2007)
Zhang, Jinghui, Finney, Richard P., Rowe, William, Edmonson, Michael, Yang, Sei Hoon, Dracheva, Tatiana, ...
Systematic investigations of genetic changes in tumors are expected to lead to greatly improved understanding of cancer etiology. To meet the analytical challenges presented by such studies, we...
Mitsutaka Kadota, Howard H. Yang, Nan Hu, Chaoyu Wang, Ying Hu, Philip R. Taylor, ...
Several recent studies have shown a genetic influence on gene expression variation, including variation between the two chromosomes within an individual and variation between individuals at the...
Hu, Nan, Wang, Chaoyu, Hu, Ying, Yang, Howard H, Kong, Li-Hui, Lu, Ning, ...
Abstract Background Esophageal squamous cell carcinoma (ESCC) is a common malignancy worldwide. Comprehensive genomic characterization of ESCC will further our understanding of the carcinogenesis...
SNPdetector: A Software Tool for Sensitive and Accurate SNP Detection (2005)
Jinghui Zhang, David A. Wheeler, Imtiaz Yakub, Sharon Wei, Raman Sood, William Rowe, ...
Identification of single nucleotide polymorphisms (SNPs) and mutations is important for the discovery of genetic predisposition to complex diseases. PCR resequencing is the method of choice for de...
Cyberinfrastructure: Empowering a ”Third Way (2005)
Biomedicine has experienced explosive growth, fueled in parts by the substantial increase of government support, continued development of the biotechnology industry, and the increasing adoption of...
Zhang, Jinghui, Hunter, Kent W., Gandolph, Michael, Rowe, William L., Finney, Richard P., Kelley, Jenny M., ...
Understanding of the structure and the origin of genetic variation patterns in the laboratory inbred mouse provides insight into the utility of the mouse model for studying human complex diseases and...
ATG deserts define a novel core promoter subclass (2005)
Lee, Maxwell P., Howcroft, Kevin, Kotekar, Aparna, Yang, Howard H., Buetow, Kenneth H., Singer, Dinah S.
The MHC class I gene, PD1, has neither functional TATAA nor Initiator (Inr) elements in its core promoter and initiates transcription at multiple, dispersed sites over an extended region in vitro....
Large-scale analysis of non-synonymous coding region single nucleotide polymorphisms (2004)
Clifford, Robert J., Edmonson, Michael N., Nguyen, Cu, Buetow, Kenneth H.
Motivation: Single nucleotide polymorphisms (SNPs) are the most common form of genetic variant in humans. SNPs causing amino acid substitutions are of particular interest as candidates for loci...
Large-scale analysis of non-synonymous coding region single nucleotide polymorphisms (2004)
Clifford, Robert J., Edmonson, Michael N., Nguyen, Cu, Buetow, Kenneth H.
Motivation: Single nucleotide polymorphisms (SNPs) are the most common form of genetic variant in humans. SNPs causing amino acid substitutions are of particular interest as candidates for loci...
Zhining Wang, H. Shuen Lo, Howard Yang, Sheryl Gere, Ying Hu, Kenneth H. Buetow, ...
A genome-wide computational screen was performed to identify tumorassociated alternative RNA splicing isoforms. A BLAST algorithm was used to compare 11,014 genes from RefSeq with 3,471,822 human...
Multiple Cross and Inbred Strain Haplotype Mapping of Complex-Trait Candidate Genes (2003)
Park, Yeong-Gwon, Clifford, Robert, Buetow, Kenneth H., Hunter, Kent W.
Identifying complex-trait candidate genes after initial low-resolution mapping has proven to be a difficult and labor-intensive undertaking, usually requiring years to develop and analyze congenic...
caCORE: A common infrastructure for cancer informatics (2003)
Covitz, Peter A., Hartel, Frank, Schaefer, Carl, De Coronado, Sherri, Fragoso, Gilberto, Sahni, Himanso, ...
Motivation:Sites with substantive bioinformatics operations are challenged to build data processing and delivery infrastructure that provides reliable access and enables data integration. Locally...
Allelic Variation in Gene Expression Is Common in the Human Genome (2003)
Lo, H. Shuen, Wang, Zhining, Hu, Ying, Yang, Howard H., Gere, Sheryl, Buetow, Kenneth H., ...
Variations in gene sequence and expression underlie much of human variability. Despite the known biological roles of differential allelic gene expression resulting from X-chromosome inactivation and...
Long-Range Heterogeneity at the 3' Ends of Human mRNAs (2002)
Iseli, Christian, Stevenson, Brian J., De Souza, Sandro J., Samaia, Helena B., Camargo, Anamaria A., Buetow, Kenneth H., ...
Long-Range Heterogeneity at the 3' Ends of Human mRNAs (2002)
Iseli, Christian, Stevenson, Brian J., De Souza, Sandro J., Samaia, Helena B., Camargo, Anamaria A., Buetow, Kenneth H., ...
Zhang, Jinghui, Rowe, William L., Struewing, Jeffery P., Buetow, Kenneth H.
We have developed a software analysis package, HapScope, which includes a comprehensive analysis pipeline and a sophisticated visualization tool for analyzing functionally annotated haplotypes. The...
Re: Detection of a Point Mutation in NQO1 (DTdiaphorase) in a Patient With Colon Cancer (1995)
ROSVOLD, ELIZABETH A., MCGLYNN, KATHERINE A., LUSTBADER, EDWARD D., BUETOW, KENNETH H.
Gastier, Julie M., Pulido, Jacqueline C., Sunden, Sara, Brody, Thomas, Buetow, Kenneth H., Murray, Jeffrey C., ...
Genetic markers based upon PCR amplification of short tandem repeat-containing sequence tagged sites (STSs) have become the standard for genetic mapping. We have completed a survey based on the...
Sheffield, Val. C., Weber, James L., Buetow, Kenneth H., Murray, Jeffrey C., Even, Dee Ann, Wiles, Kerry, ...
We report a collection of tri- and tetranucleotide repeat sequence polymorphic markers used to construct genome-wide human linkage maps. Using a strategy of marker selection to create libraries...
Loftus, Stacie K., Edwards, Sara J., Scherpbier-Heddema, Titia, Buetow, Kenneth H., Wasmuth, John J., Dixon, Michael J.
The distal region of chromosome 5q contains a large number of genes, including those implicated in a variety of Mendelian disorders. One of these, Treacher Collins syndrome (TCOF1), is an autosomal...
Multipoint gene mapping in man using seriation /--by Kenneth H. Buetow (1985)
Graduate School of Public Health
Buetow, Kenneth H., Edmonson, Michael, MacDonald, Richard, Clifford, Robert, Yip, Ping, Kelley, Jenny, ...
We describe here a system for the rapid identification, assay development, and characterization of gene-based single nucleotide polymorphisms (SNPs). This system couples informatics tools that mine...
Interleukin 9: A candidate gene for asthma
Nicolaides, Nicholas C., Holroyd, Kenneth J., Ewart, Susan L., Eleff, Scott M., Kiser, Matthew B., Dragwa, Carl R., ...
Asthma is a complex heritable inflammatory disorder of the airways associated with clinical signs of atopy and bronchial hyperresponsiveness. Recent studies localized a major gene for asthma to...
An anatomy of normal and malignant gene expression
Boon, Kathy, Osório, Elisson C., Greenhut, Susan F., Schaefer, Carl F., Shoemaker, Jennifer, Polyak, Kornelia, ...
A gene's expression pattern provides clues to its role in normal physiology and disease. To provide quantitative expression levels on a genome-wide scale, the Cancer Genome Anatomy Project (CGAP)...
HapScope: a software system for automated and visual analysis of functionally annotated haplotypes
Zhang, Jinghui, Rowe, William L., Struewing, Jeffery P., Buetow, Kenneth H.
We have developed a software analysis package, HapScope, which includes a comprehensive analysis pipeline and a sophisticated visualization tool for analyzing functionally annotated haplotypes. The...
Long-Range Heterogeneity at the 3′ Ends of Human mRNAs
Iseli, Christian, Stevenson, Brian J., De Souza, Sandro J., Samaia, Helena B., Camargo, Anamaria A., Buetow, Kenneth H., ...
The publication of a draft of the human genome and of large collections of transcribed sequences has made it possible to study the complex relationship between the transcriptome and the genome. In...
Clifford, Robert, Edmonson, Michael, Hu, Ying, Nguyen, Cu, Scherpbier, Titia, Buetow, Kenneth H.
SNPs (Single-Nucleotide Polymorphisms), the most common DNA variant in humans, represent a valuable resource for the genetic analysis of cancer and other illnesses. These markers may be used in a...
Allelic Variation in Gene Expression Is Common in the Human Genome
Lo, H. Shuen, Wang, Zhining, Hu, Ying, Yang, Howard H., Gere, Sheryl, Buetow, Kenneth H., ...
Variations in gene sequence and expression underlie much of human variability. Despite the known biological roles of differential allelic gene expression resulting from X-chromosome inactivation and...
Multiple Cross and Inbred Strain Haplotype Mapping of Complex-Trait Candidate Genes
Park, Yeong-Gwon, Clifford, Robert, Buetow, Kenneth H., Hunter, Kent W.
Identifying complex-trait candidate genes after initial low-resolution mapping has proven to be a difficult and labor-intensive undertaking, usually requiring years to develop and analyze congenic...
Zhang, Jinghui, Hunter, Kent W., Gandolph, Michael, Rowe, William L., Finney, Richard P., Kelley, Jenny M., ...
Understanding of the structure and the origin of genetic variation patterns in the laboratory inbred mouse provides insight into the utility of the mouse model for studying human complex diseases and...
ATG deserts define a novel core promoter subclass
Lee, Maxwell P., Howcroft, Kevin, Kotekar, Aparna, Yang, Howard H., Buetow, Kenneth H., Singer, Dinah S.
The MHC class I gene, PD1, has neither functional TATAA nor Initiator (Inr) elements in its core promoter and initiates transcription at multiple, dispersed sites over an extended region in vitro....
SNPdetector: A Software Tool for Sensitive and Accurate SNP Detection
Zhang, Jinghui, Wheeler, David A, Yakub, Imtiaz, Wei, Sharon, Sood, Raman, Rowe, William, ...
Identification of single nucleotide polymorphisms (SNPs) and mutations is important for the discovery of genetic predisposition to complex diseases. PCR resequencing is the method of choice for de...
Buetow, Kenneth H., Shiang, Rita, Yang, Ping, Nakamura, Yusuke, Lathrop, G. Mark, White, Raymond, ...
Utilizing the CEPH reference panel and genotypic data for 53 markers, we have constructed a 20-locus multipoint genetic map of human chromosome 4. New RFLPs are reported for four loci. The map...
Murray, Jeffrey C., Buetow, Kenneth H., Donovan, Mark, Hornung, Sigrid, Motulsky, Arno G., Disteche, Christine, ...
Linkage disequilibrium was observed between newly identified DNA polymorphisms and a previously described protein polymorphism for plasminogen. This finding implies that the two types of...
Buetow, Kenneth H., Edmonson, Michael, MacDonald, Richard, Clifford, Robert, Yip, Ping, Kelley, Jenny, ...
We describe here a system for the rapid identification, assay development, and characterization of gene-based single nucleotide polymorphisms (SNPs). This system couples informatics tools that mine...
Interleukin 9: A candidate gene for asthma
Nicolaides, Nicholas C., Holroyd, Kenneth J., Ewart, Susan L., Eleff, Scott M., Kiser, Matthew B., Dragwa, Carl R., ...
Asthma is a complex heritable inflammatory disorder of the airways associated with clinical signs of atopy and bronchial hyperresponsiveness. Recent studies localized a major gene for asthma to...
An anatomy of normal and malignant gene expression
Boon, Kathy, Osório, Elisson C., Greenhut, Susan F., Schaefer, Carl F., Shoemaker, Jennifer, Polyak, Kornelia, ...
A gene's expression pattern provides clues to its role in normal physiology and disease. To provide quantitative expression levels on a genome-wide scale, the Cancer Genome Anatomy Project (CGAP)...
HapScope: a software system for automated and visual analysis of functionally annotated haplotypes
Zhang, Jinghui, Rowe, William L., Struewing, Jeffery P., Buetow, Kenneth H.
We have developed a software analysis package, HapScope, which includes a comprehensive analysis pipeline and a sophisticated visualization tool for analyzing functionally annotated haplotypes. The...
Long-Range Heterogeneity at the 3′ Ends of Human mRNAs
Iseli, Christian, Stevenson, Brian J., De Souza, Sandro J., Samaia, Helena B., Camargo, Anamaria A., Buetow, Kenneth H., ...
The publication of a draft of the human genome and of large collections of transcribed sequences has made it possible to study the complex relationship between the transcriptome and the genome. In...
Clifford, Robert, Edmonson, Michael, Hu, Ying, Nguyen, Cu, Scherpbier, Titia, Buetow, Kenneth H.
SNPs (Single-Nucleotide Polymorphisms), the most common DNA variant in humans, represent a valuable resource for the genetic analysis of cancer and other illnesses. These markers may be used in a...
Allelic Variation in Gene Expression Is Common in the Human Genome
Lo, H. Shuen, Wang, Zhining, Hu, Ying, Yang, Howard H., Gere, Sheryl, Buetow, Kenneth H., ...
Variations in gene sequence and expression underlie much of human variability. Despite the known biological roles of differential allelic gene expression resulting from X-chromosome inactivation and...
Multiple Cross and Inbred Strain Haplotype Mapping of Complex-Trait Candidate Genes
Park, Yeong-Gwon, Clifford, Robert, Buetow, Kenneth H., Hunter, Kent W.
Identifying complex-trait candidate genes after initial low-resolution mapping has proven to be a difficult and labor-intensive undertaking, usually requiring years to develop and analyze congenic...
Zhang, Jinghui, Hunter, Kent W., Gandolph, Michael, Rowe, William L., Finney, Richard P., Kelley, Jenny M., ...
Understanding of the structure and the origin of genetic variation patterns in the laboratory inbred mouse provides insight into the utility of the mouse model for studying human complex diseases and...
Zhang, Jinghui, Rowe, William L., Clark, Andrew G., Buetow, Kenneth H.
Knowledge of human haplotype structure has important implications for strategies of disease-gene mapping and for understanding human evolutionary history. Many attributes of SNPs and haplotypes...
ATG deserts define a novel core promoter subclass
Lee, Maxwell P., Howcroft, Kevin, Kotekar, Aparna, Yang, Howard H., Buetow, Kenneth H., Singer, Dinah S.
The MHC class I gene, PD1, has neither functional TATAA nor Initiator (Inr) elements in its core promoter and initiates transcription at multiple, dispersed sites over an extended region in vitro....
SNPdetector: A Software Tool for Sensitive and Accurate SNP Detection
Zhang, Jinghui, Wheeler, David A, Yakub, Imtiaz, Wei, Sharon, Sood, Raman, Rowe, William, ...
Identification of single nucleotide polymorphisms (SNPs) and mutations is important for the discovery of genetic predisposition to complex diseases. PCR resequencing is the method of choice for de...
Buetow, Kenneth H., Shiang, Rita, Yang, Ping, Nakamura, Yusuke, Lathrop, G. Mark, White, Raymond, ...
Utilizing the CEPH reference panel and genotypic data for 53 markers, we have constructed a 20-locus multipoint genetic map of human chromosome 4. New RFLPs are reported for four loci. The map...
Murray, Jeffrey C., Buetow, Kenneth H., Donovan, Mark, Hornung, Sigrid, Motulsky, Arno G., Disteche, Christine, ...
Linkage disequilibrium was observed between newly identified DNA polymorphisms and a previously described protein polymorphism for plasminogen. This finding implies that the two types of...
Identification of Key Processes Underlying Cancer Phenotypes Using Biologic Pathway Analysis
Efroni, Sol, Schaefer, Carl F., Buetow, Kenneth H.
Cancer is recognized to be a family of gene-based diseases whose causes are to be found in disruptions of basic biologic processes. An increasingly deep catalogue of canonical networks details the...
Molecular Profiling of Clinical Tissue Specimens : Feasibility and Applications
Emmert-Buck, Michael R., Strausberg, Robert L., Krizman, David B., Bonaldo, M. Fatima, Bonner, Robert F., Bostwick, David G., ...
Kadota, Mitsutaka, Yang, Howard H, Hu, Nan, Wang, Chaoyu, Hu, Ying, Taylor, Philip R, ...
Several recent studies have shown a genetic influence on gene expression variation, including variation between the two chromosomes within an individual and variation between individuals at the...
Molecular Profiling of Clinical Tissue Specimens: Feasibility and Applications
Emmert-Buck, Michael R., Strausberg, Robert L., Krizman, David B., Bonaldo, M. Fatima, Bonner, Robert F., Bostwick, David G., ...
Godwin, Andrew K., Vanderveer, Lisa, Schultz, David C., Lynch, Henry T., Altomare, Deborah A., Buetow, Kenneth H., ...
Linkage analysis in familial breast and ovarian cancer and studies of allelic deletion in sporadic ovarian tumors have identified a region on chromosome 17q containing a candidate tumor-suppressor...
Systematic analysis of genetic alterations in tumors using Cancer Genome WorkBench (CGWB)
Zhang, Jinghui, Finney, Richard P., Rowe, William, Edmonson, Michael, Yang, Sei Hoon, Dracheva, Tatiana, ...
Systematic investigations of genetic changes in tumors are expected to lead to greatly improved understanding of cancer etiology. To meet the analytical challenges presented by such studies, we...
Superposition of Transcriptional Behaviors Determines Gene State
Efroni, Sol, Carmel, Liran, Schaefer, Carl G., Buetow, Kenneth H.
We introduce a novel technique to determine the expression state of a gene from quantitative information measuring its expression. Adopting a productive abstraction from current thinking in molecular...
PID: the Pathway Interaction Database
Schaefer, Carl F., Anthony, Kira, Krupa, Shiva, Buchoff, Jeffrey, Day, Matthew, Hannay, Timo, ...
The Pathway Interaction Database (PID, http://pid.nci.nih.gov) is a freely available collection of curated and peer-reviewed pathways composed of human molecular signaling and regulatory events and...