Detecting genetic variation in microarray expression data (2007)
Greenhall, Jennifer A., Zapala, Matthew A., Cáceres, Mario, Libiger, Ondrej, Barlow, Carrolee, Schork, Nicholas J., ...
The use of high-density oligonucleotide arrays to measure the expression levels of thousands of genes in parallel has become commonplace. To take further advantage of the growing body of data, we...
Hovatta, Iiris, Zapala, Matthew A, Broide, Ron S, Schadt, Eric E, Libiger, Ondrej, Schork, Nicholas J, ...
Abstract Background Expression quantitative trait locus (eQTL) mapping is used to find loci that are responsible for the transcriptional activity of a particular gene. In recent eQTL studies,...
Mechanisms of aging in senescence-accelerated mice (2005)
Carter, Todd A, Greenhall, Jennifer A, Yoshida, Shigeo, Fuchs, Sebastian, Helton, Robert, Swaroop, Anand, ...
Abstract Background Progressive neurological dysfunction is a key aspect of human aging. Because of underlying differences in the aging of mice and humans, useful mouse models have been difficult to...
Aberrant recombination involving the granzyme locus occurs in Atm-/- T-cell lymphomas (2005)
Winrow, Christopher J., Pankratz, Daniel G., Vibat, Cecile Rose T., Bowen, T.J., Callahan, Marie A., Warren, Amy J., ...
Ataxia telangiectasia (A-T) is an autosomal recessive disease caused by loss of function of the serine/threonine protein kinase ATM (ataxia telangiectasia mutated). A-T patients have a 250–700-fold...
Software and methods for oligonucleotide and cDNA array data analysis (2002)
Zapala, Matthew A, Lockhart, Daniel J, Pankratz, Daniel G, Garcia, Anthony J, Barlow, Carrolee, Lockhart, David J
Abstract Two HTML-based programs were developed to analyze and filter gene-expression data: 'Bullfrog' for Affymetrix oligonucleotide arrays and 'Spot' for custom cDNA arrays. The programs provide...
Parallel Identification of New Genes in Saccharomyces cerevisiae (2002)
Oshiro, Guy, Wodicka, Lisa M., Washburn, Michael P., Yates, John R., Lockhart, David J., Winzeler, Elizabeth A.
Arrays of Arrays for High-Throughput Gene Expression Profiling (2001)
Zarrinkar, Patrick P., Mainquist, James K., Zamora, Matthew, Stern, David, Welsh, John B., Sapinoso, Lisa M., ...
Arrays of Arrays for High-Throughput Gene Expression Profiling (2001)
Zarrinkar, Patrick P., Mainquist, James K., Zamora, Matthew, Stern, David, Welsh, John B., Sapinoso, Lisa M., ...
Arrays of Arrays for High-Throughput Gene Expression Profiling (2001)
Zarrinkar, Patrick P., Mainquist, James K., Zamora, Matthew, Stern, David, Welsh, John B., Sapinoso, Lisa M., ...
Parallel genotyping of human SNPs using generic high-density oligonucleotide tag arrays. (2000)
Fan, Jian-Bing, Chen, Xiaoqiong, Halushka, Marc K., Berno, Anthony, Huang, Xiaohua, Ryder, Thomas, ...
Large scale human genetic studies require technologies for generating millions of genotypes with relative ease but also at a reasonable cost and with high accuracy. We describe a highly parallel...
Cell, Vol. 101, 249--258, April 28, 2000, Copyright 2000 by Cell Press (2000)
Functional And Genomic, Christopher K. Patil, Lisa Wodicka, David J. Lockhart, Jonathan S. Weissman, Peter Walter
roarrays. Rather than (Cox and Walter, 1996; Mori et al., 1996; Sidrauski et al., 1996; Sidrauski and Walter, 1997), and ultimately regulating only ER-resident chaperones and phospholipid...
Genome-wide Detection of Allelic Imbalance Using Human SNPs and High-density DNA Arrays (2000)
Mei, Rui, Galipeau, Patricia C., Prass, Cynthia, Berno, Anthony, Ghandour, Ghassan, Patil, Nila, ...
Parallel Genotyping of Human SNPs Using Generic High-density Oligonucleotide Tag Arrays (2000)
Fan, Jian-Bing, Chen, Xiaoqiong, Halushka, Marc K., Berno, Anthony, Huang, Xiaohua, Ryder, Thomas, ...
Exploiting Chemical Libraries, Structure, and Genomics in the Search for Kinase Inhibitors (1998)
Kim, Sung-Hou, Meijer, Laurent, LeClerc, Sophie, Barnes, Georjana, Morgan, David O., Espinoza, F. Hernan, ...
Selective protein kinase inhibitors were developed on the basis of the unexpected binding mode of 2,6,9-trisubstituted purines to the adenosine triphosphate-binding site of the human cyclin-dependent...
Exploiting Chemical Libraries, Structure, and Genomics in the Search for Kinase Inhibitors (1998)
Lockhart, David J., Kim, Sung-Hou, Meijer, Laurent, LeClerc, Sophie, Barnes, Georjana, Morgan, David O., ...
Selective protein kinase inhibitors were developed on the basis of the unexpected binding mode of 2,6,9-trisubstituted purines to the adenosine triphosphate-binding site of the human cyclin-dependent...
Mutation Detection by Ligation to Complete n-mer DNA Arrays (1998)
Gunderson, Kevin L., Huang, Xiaohua C., Morris, Macdonald S., Lipshutz, Robert J., Lockhart, David J., Chee, Mark S.
Thesis (Ph. D.)--Stanford University, 1990.
Welsh, John B., Zarrinkar, Patrick P., Sapinoso, Lisa M., Kern, Suzanne G., Behling, Cynthia A., Monk, Bradley J., ...
Epithelial ovarian cancer is the leading cause of death from gynecologic cancer, in part because of the lack of effective early detection methods. Although alterations of several genes, such as...
Effects of environmental enrichment on gene expression in the brain
Rampon, Claire, Jiang, Cecilia H., Dong, Helin, Tang, Ya-Ping, Lockhart, David J., Schultz, Peter G., ...
An enriched environment is known to promote structural changes in the brain and to enhance learning and memory performance in rodents [Hebb, D. O. (1947) Am. Psychol. 2, 306–307]. To better...
Parallel analysis of genetic selections using whole genome oligonucleotide arrays
Cho, Raymond J., Fromont-Racine, Micheline, Wodicka, Lisa, Feierbach, Becket, Stearns, Timothy, Legrain, Pierre, ...
Thousands of genes have recently been sequenced in organisms ranging from Escherichia coli to human. For the majority of these genes, however, available sequence does not define a biological role....
Regional and strain-specific gene expression mapping in the adult mouse brain
Sandberg, Rickard, Yasuda, Rie, Pankratz, Daniel G., Carter, Todd A., Del Rio, Jo A., Wodicka, Lisa, ...
To determine the genetic causes and molecular mechanisms responsible for neurobehavioral differences in mice, we used highly parallel gene expression profiling to detect genes that are differentially...
Fields, Stanley, Kohara, Yuji, Lockhart, David J.
Complete genome sequences are providing a framework to allow the investigation of biological processes by the use of comprehensive approaches. Genome analysis also is having a dramatic impact on...
Software and methods for oligonucleotide and cDNA array data analysis
Zapala, Matthew A, Lockhart, Daniel J, Pankratz, Daniel G, Garcia, Anthony J, Barlow, Carrolee, Lockhart, David J
Two HTML-based programs were developed to analyze and filter gene-expression data. A background subtraction and normalization program for cDNA arrays was also built that provides an informative...
Parallel Identification of New Genes in Saccharomyces cerevisiae
Oshiro, Guy, Wodicka, Lisa M., Washburn, Michael P., Yates, John R., Lockhart, David J., Winzeler, Elizabeth A.
Short open reading frames (ORFs) occur frequently in primary genome sequence. Distinguishing bona fide small genes from the tens of thousands of short ORFs is one of the most challenging aspects of...
Elevated gene expression levels distinguish human from non-human primate brains
Cáceres, Mario, Lachuer, Joel, Zapala, Matthew A., Redmond, John C., Kudo, Lili, Geschwind, Daniel H., ...
Little is known about how the human brain differs from that of our closest relatives. To investigate the genetic basis of human specializations in brain organization and cognition, we compared gene...
Stark effect spectroscopy of Rhodobacter sphaeroides and Rhodopseudomonas viridis reaction centers
Lockhart, David J., Boxer, Steven G.
The nature of the initially excited state of the primary electron donor or special pair has been investigated by Stark effect spectroscopy for reaction centers from the photosynthetic bacteria...
Parallel Genotyping of Human SNPs Using Generic High-density Oligonucleotide Tag Arrays
Fan, Jian-Bing, Chen, Xiaoqiong, Halushka, Marc K., Berno, Anthony, Huang, Xiaohua, Ryder, Thomas, ...
Large scale human genetic studies require technologies for generating millions of genotypes with relative ease but also at a reasonable cost and with high accuracy. We describe a highly parallel...
Arrays of Arrays for High-Throughput Gene Expression Profiling
Zarrinkar, Patrick P., Mainquist, James K., Zamora, Matthew, Stern, David, Welsh, John B., Sapinoso, Lisa M., ...
Gene expression profiling using DNA arrays is rapidly becoming an essential tool for research and drug discovery and may soon play a central role in disease diagnosis. Although it is possible to make...
Adult mouse brain gene expression patterns bear an embryologic imprint
Zapala, Matthew A., Hovatta, Iiris, Ellison, Julie A., Wodicka, Lisa, Del Rio, Jo A., Tennant, Richard, ...
The current model to explain the organization of the mammalian nervous system is based on studies of anatomy, embryology, and evolution. To further investigate the molecular organization of the adult...
Mechanisms of aging in senescence-accelerated mice
Carter, Todd A, Greenhall, Jennifer A, Yoshida, Shigeo, Fuchs, Sebastian, Helton, Robert, Swaroop, Anand, ...
Gene-expression analysis and polymorphism screening to study molecular senescence of the retina and hippocampus in two rare inbred mouse models of accelerated neurological senescence as well as a...
Inhibition of drug-resistant mutants of ABL, KIT, and EGF receptor kinases
Carter, Todd A., Wodicka, Lisa M., Shah, Neil P., Velasco, Anne Marie, Fabian, Miles A., Treiber, Daniel K., ...
To realize the full potential of targeted protein kinase inhibitors for the treatment of cancer, it is important to address the emergence of drug resistance in treated patients. Mutant forms of...
Welsh, John B., Zarrinkar, Patrick P., Sapinoso, Lisa M., Kern, Suzanne G., Behling, Cynthia A., Monk, Bradley J., ...
Epithelial ovarian cancer is the leading cause of death from gynecologic cancer, in part because of the lack of effective early detection methods. Although alterations of several genes, such as...
Effects of environmental enrichment on gene expression in the brain
Rampon, Claire, Jiang, Cecilia H., Dong, Helin, Tang, Ya-Ping, Lockhart, David J., Schultz, Peter G., ...
An enriched environment is known to promote structural changes in the brain and to enhance learning and memory performance in rodents [Hebb, D. O. (1947) Am. Psychol. 2, 306–307]. To better...
Parallel analysis of genetic selections using whole genome oligonucleotide arrays
Cho, Raymond J., Fromont-Racine, Micheline, Wodicka, Lisa, Feierbach, Becket, Stearns, Timothy, Legrain, Pierre, ...
Thousands of genes have recently been sequenced in organisms ranging from Escherichia coli to human. For the majority of these genes, however, available sequence does not define a biological role....
Regional and strain-specific gene expression mapping in the adult mouse brain
Sandberg, Rickard, Yasuda, Rie, Pankratz, Daniel G., Carter, Todd A., Del Rio, Jo A., Wodicka, Lisa, ...
To determine the genetic causes and molecular mechanisms responsible for neurobehavioral differences in mice, we used highly parallel gene expression profiling to detect genes that are differentially...
Fields, Stanley, Kohara, Yuji, Lockhart, David J.
Complete genome sequences are providing a framework to allow the investigation of biological processes by the use of comprehensive approaches. Genome analysis also is having a dramatic impact on...
Software and methods for oligonucleotide and cDNA array data analysis
Zapala, Matthew A, Lockhart, Daniel J, Pankratz, Daniel G, Garcia, Anthony J, Barlow, Carrolee, Lockhart, David J
Two HTML-based programs were developed to analyze and filter gene-expression data. A background subtraction and normalization program for cDNA arrays was also built that provides an informative...
Parallel Identification of New Genes in Saccharomyces cerevisiae
Oshiro, Guy, Wodicka, Lisa M., Washburn, Michael P., Yates, John R., Lockhart, David J., Winzeler, Elizabeth A.
Short open reading frames (ORFs) occur frequently in primary genome sequence. Distinguishing bona fide small genes from the tens of thousands of short ORFs is one of the most challenging aspects of...
Elevated gene expression levels distinguish human from non-human primate brains
Cáceres, Mario, Lachuer, Joel, Zapala, Matthew A., Redmond, John C., Kudo, Lili, Geschwind, Daniel H., ...
Little is known about how the human brain differs from that of our closest relatives. To investigate the genetic basis of human specializations in brain organization and cognition, we compared gene...
Stark effect spectroscopy of Rhodobacter sphaeroides and Rhodopseudomonas viridis reaction centers
Lockhart, David J., Boxer, Steven G.
The nature of the initially excited state of the primary electron donor or special pair has been investigated by Stark effect spectroscopy for reaction centers from the photosynthetic bacteria...
Parallel Genotyping of Human SNPs Using Generic High-density Oligonucleotide Tag Arrays
Fan, Jian-Bing, Chen, Xiaoqiong, Halushka, Marc K., Berno, Anthony, Huang, Xiaohua, Ryder, Thomas, ...
Large scale human genetic studies require technologies for generating millions of genotypes with relative ease but also at a reasonable cost and with high accuracy. We describe a highly parallel...
Arrays of Arrays for High-Throughput Gene Expression Profiling
Zarrinkar, Patrick P., Mainquist, James K., Zamora, Matthew, Stern, David, Welsh, John B., Sapinoso, Lisa M., ...
Gene expression profiling using DNA arrays is rapidly becoming an essential tool for research and drug discovery and may soon play a central role in disease diagnosis. Although it is possible to make...
Adult mouse brain gene expression patterns bear an embryologic imprint
Zapala, Matthew A., Hovatta, Iiris, Ellison, Julie A., Wodicka, Lisa, Del Rio, Jo A., Tennant, Richard, ...
The current model to explain the organization of the mammalian nervous system is based on studies of anatomy, embryology, and evolution. To further investigate the molecular organization of the adult...
Mechanisms of aging in senescence-accelerated mice
Carter, Todd A, Greenhall, Jennifer A, Yoshida, Shigeo, Fuchs, Sebastian, Helton, Robert, Swaroop, Anand, ...
Gene-expression analysis and polymorphism screening to study molecular senescence of the retina and hippocampus in two rare inbred mouse models of accelerated neurological senescence as well as a...
Inhibition of drug-resistant mutants of ABL, KIT, and EGF receptor kinases
Carter, Todd A., Wodicka, Lisa M., Shah, Neil P., Velasco, Anne Marie, Fabian, Miles A., Treiber, Daniel K., ...
To realize the full potential of targeted protein kinase inhibitors for the treatment of cancer, it is important to address the emergence of drug resistance in treated patients. Mutant forms of...
Hovatta, Iiris, Zapala, Matthew A, Broide, Ron S, Schadt, Eric E, Libiger, Ondrej, Schork, Nicholas J, ...
Gene expression profiles of five brain regions from six inbred mouse strains suggest that many regulatory networks are highly specific to particular brain regions.
Detecting genetic variation in microarray expression data
Greenhall, Jennifer A., Zapala, Matthew A., Cáceres, Mario, Libiger, Ondrej, Barlow, Carrolee, Schork, Nicholas J., ...
The use of high-density oligonucleotide arrays to measure the expression levels of thousands of genes in parallel has become commonplace. To take further advantage of the growing body of data, we...