A dynamic network of transcription in LPS-treated human subjects (2009)
Seok, Junhee, Xiao, Wenzhong, Moldawer, Lyle L, Davis, Ronald W, Covert, Markus W
Abstract Background Understanding the transcriptional regulatory networks that map out the coordinated dynamic responses of signaling proteins, transcription factors and target genes over time would...
Norman, Paul J., Abi-Rached, Laurent, Gendzekhadze, Ketevan, Hammond, John A., Moesta, Achim K., Sharma, Deepti, ...
Natural killer (NK) cells contribute to the essential functions of innate immunity and reproduction. Various genes encode NK cell receptors that recognize the major histocompatibility complex (MHC)...
Multiplex amplification of all coding sequences within 10 cancer genes by Gene-Collector (2007)
Fredriksson, Simon, Banér, Johan, Dahl, Fredrik, Chu, Angela, Ji, Hanlee, Welch, Katrina, ...
Herein we present Gene-Collector, a method for multiplex amplification of nucleic acids. The procedure has been employed to successfully amplify the coding sequence of 10 human cancer genes in one...
Multiplex amplification of all coding sequences within 10 cancer genes by Gene-Collector (2007)
Fredriksson, Simon, Banér, Johan, Dahl, Fredrik, Chu, Angela, Ji, Hanlee, Welsh, Katrina, ...
Herein we present Gene-Collector, a method for multiplex amplification of nucleic acids. The procedure has been employed to successfully amplify the coding sequence of 10 human cancer genes in one...
Multiplex amplification of all coding sequences within 10 cancer genes by Gene-Collector (2007)
Fredriksson, Simon, Banér, Johan, Dahl, Fredrik, Chu, Angela, Ji, Hanlee, Welch, Katrina, ...
Herein we present Gene-Collector, a method for multiplex amplification of nucleic acids. The procedure has been employed to successfully amplify the coding sequence of 10 human cancer genes in one...
Doostzadeh, Julie, Davis, Ronald W., Giaever, Guri N., Nislow, Corey, Langston, James W.
The yeast deletion collection includes ∼4700 strains deleted for both copies of every nonessential gene. This collection is a powerful resource for identifying the cellular pathways that...
Thiyagarajan, Sreedevi, Karhanek, Miloslav, Akhras, Michael, Davis, Ronald W, Pourmand, Nader
Abstract Background Here we describe PathogenMIPer, a software program for designing molecular inversion probe (MIP) oligonucleotides for use in pathogen identification and detection. The software...
Transcriptional Profiling of Aging in Human Muscle Reveals a Common Aging Signature (2006)
Jacob M. Zahn, Rebecca Sonu, Hannes Vogel, Emily Crane, Krystyna Mazan-Mamczarz, Ralph Rabkin, ...
We analyzed expression of 81 normal muscle samples from humans of varying ages, and have identified a molecular profile for aging consisting of 250 age-regulated genes. This molecular profile...
falciparum antigens by antigenic analysis of genomic and proteomic (2006)
Z. Bozdech, M. Llinas, B. L. Pulliam, E. D. Wong, J. Zhu, Z. Bozdech, ...
plasmodium
Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae (2006)
Kastenmayer, James P., Ni, Li, Chu, Angela, Kitchen, Lauren E., Au, Wei-Chun, Yang, Hui, ...
Genes with small open reading frames (sORFs;
Laser Extinction in Laminar Inverse Diffusion Flames (2005)
Macko, Kevin, Mikofski, Mark A, Fernandez-Pello, Carlos, Blevins, Linda G, Davis, Ronald W.
Measurements of line-of-sight laser extinction in a co-annular ethylene-air laminar inverse diffusion flame (IDF) were made to determine soot concentration. Extinction has frequently been used in the...
Genome-Wide Requirements for Resistance to Functionally Distinct DNA-Damaging Agents (2005)
William Lee, Michael Proctor, Patrick Flaherty, Michael I. Jordan, Adam P. Arkin, ...
The mechanistic and therapeutic differences in the cellular response to DNA-damaging compounds are not completely understood, despite intense study. To expand our knowledge of DNA damage, we assayed...
Genome-Wide Requirements for Resistance (2005)
To Functionally Distinct, William Lee, Michael Proctor, Patrick Flaherty, Michael I. Jordan, ...
this paper are as follows: CSM2 (P40465), DDC1 (Q08949), ELG1 (Q12050), LTE1 (P07866), MAG1 (P22134), MEC3 (Q02574), MMS1 (Q06211), MMS4 (P38257), MPH1 (P40562), MRE11 (P32829), MUS81 (Q04149), PSO2...
Allele quantification using molecular inversion probes (MIP) (2005)
Wang, Yuker, Moorhead, Martin, Karlin-Neumann, George, Falkowski, Matthew, Chen, Chunnuan, Siddiqui, Farooq, ...
Detection of genomic copy number changes has been an important research area, especially in cancer. Several high-throughput technologies have been developed to detect these changes. Features that are...
Hardenbol, Paul, Yu, Fuli, Belmont, John, MacKenzie, Jennifer, Bruckner, Carsten, Brundage, Tiffany, ...
Large-scale genetic studies are highly dependent on efficient and scalable multiplex SNP assays. In this study, we report the development of Molecular Inversion Probe technology with four-color,...
A Transcriptional Profile of Aging in the Human Kidney (2004)
Rebecca Sonu, Jacob M. Zahn, James Lund, Julie Wilhelmy, Lingli Wang, ...
A study of human aging in the kidney reveals similar changes in the transcriptional profile in cortex and medulla, suggesting that a common underlying aging process is taking place.
A Transcriptional Profile of Aging in the Human Kidney (2004)
Rebecca Sonu, Jacob M. Zahn, James Lund, Julie Wilhelmy, Lingli Wang, ...
In this study, we found 985 genes that change expression in the cortex and the medulla of the kidney with age. Some of the genes whose transcripts increase in abundance with age are known to be...
A study of the base sequence arrangements in DNA by electron microscopy (2004)
NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document. The study of base sequence arrangements in DNA molecules was accomplished by...
Integrative Analysis of the Mitochondrial Proteome in Yeast (2004)
Holger Prokisch, Curt Scharfe, David G. Camp, Wenzhong Xiao, Lior David, Christophe Andreoli, ...
Although individual approaches fall short, integrating multiple common genetic and biochemical approaches yields a description of mitochondrial proteins that is more than the sum of its parts.
Integrative Analysis of the Mitochondrial Proteome in Yeast (2004)
Holger Prokisch, Curt Scharfe, Wenzhong Xiao, Lior David, Christophe Andreoli, ...
In this study yeast mitochondria were used as a model system to apply, evaluate, and integrate different genomic approaches to define the proteins of an organelle. Liquid chromatography mass...
SNP Discovery in Pooled Samples With Mismatch Repair Detection (2004)
Fakhrai-Rad, Hossein, Zheng, Jianbiao, Willis, Thomas D., Wong, Kee, Suyenaga, Kent, Moorhead, Martin, ...
A targeted discovery effort is required to identify low frequency single nucleotide polymorphisms (SNPs) in human coding and regulatory regions. We here describe combining mismatch repair detection...
A multi-enzyme model for pyrosequencing (2004)
Agah, Ali, Aghajan, Mariam, Mashayekhi, Foad, Amini, Sasan, Davis, Ronald W., Plummer, James D., ...
Pyrosequencing is a DNA sequencing technique based on sequencing-by-synthesis enabling rapid real-time sequence determination. This technique employs four enzymatic reactions in a single tube to...
COSMIC: Carbon Monoxide and Soot in Microgravity Inverse Combustion (2003)
Mikofski, Mark A, Blevins, Linda G, Davis, Ronald W, Moore, Elizabeth F, Mulholland, George W
Almost seventy percent of fire related deaths are caused by the inhalation of toxins such as CO and soot that are produced when fires become underventilated.(1) Although studies have established the...
Identification and preliminary characterization of mouse Adam33 (2002)
Gunn, Teresa M, Azarani, Arezou, Kim, Philip H, Hyman, Richard W, Davis, Ronald W, Barsh, Gregory S
Abstract Background The metalloprotease-disintegrin family, or ADAM, proteins, are implicated in cell-cell interactions, cell fusion, and cell signaling, and are widely distributed among metazoan...
Multiplex Pyrosequencing (2002)
Pourmand, Nader, Elahi, Elahe, Davis, Ronald W., Ronaghi, Mostafa
We describe here the development of a new and simple single-tube multiplex Pyrosequencing assay. Genomic DNA or cDNA was employed to PCR amplify region(s) using biotinylated and normal primer(s)....
A Method For Parallel, Automated, Thermal Cycling of Submicroliter Samples (2001)
Nakane, Jonathan, Broemeling, David, Donaldson, Roger, Marziali, Andre, Willis, Thomas D., O'Keefe, Matthew, ...
A Method For Parallel, Automated, Thermal Cycling of Submicroliter Samples (2001)
Nakane, Jonathan, Broemeling, David, Donaldson, Roger, Marziali, Andre, Willis, Thomas D., O'Keefe, Matthew, ...
A Method For Parallel, Automated, Thermal Cycling of Submicroliter Samples (2001)
Nakane, Jonathan, Broemeling, David, Donaldson, Roger, Marziali, Andre, Willis, Thomas D., O'Keefe, Matthew, ...
Aharoni, Asaph, Keizer, Leopold C.P., Bouwmeester, Harro J., Sun, Zhongkui, Alvarez-Huerta, Mayte, Verhoeven, Harrie A., ...
Fruit flavor is a result of a complex mixture of numerous compounds. The formation of these compounds is closely correlated with the metabolic changes occurring during fruit maturation. Here, we...
DAtA: Database of Arabidopsis thaliana Annotation (2000)
Palm, Curtis J., Federspiel, Nancy A., Davis, Ronald W.
The Database of Arabidopsis thaliana Annotation (DAtA) was created to enable easy access to and analysis of all the Arabidopsis genome project annotation. The database was constructed using the...
Black-tailed deer habitat changes in a portion of the Mount St. Helens blast zone / (1999)
Thesis (M.A.)--Indiana State University, 1999.
An Automated Sample Preparation System for Large-Scale DNA Sequencing (1999)
Marziali, Andre, Willis, Thomas D., Federspiel, Nancy A., Davis, Ronald W.
An Automated Hydrodynamic Process for Controlled, Unbiased DNA Shearing (1998)
Thorstenson, Yvonne R., Hunicke-Smith, Scott P., Oefner, Peter J., Davis, Ronald W.
Underhill, Peter A., Jin, Li, Lin, Alice A., Mehdi, S. Qasim, Jenkins, Trefor, Vollrath, Douglas, ...
Galway, Moira E., Masucci, James D., Lloyd, Alan M., Walbot, Virginia, Davis, Ronald W., Schiefelbein, John W.
The control of cell fate was investigated in the root epidermis of Arabidopsis thaliana . Two distinct types of differentiated epidermal cells are normally present: root-hair-bearing Cells and...
LEUNG, PETER, DAVIS, RONALD W., YAO, C. C., CANNON, E. P., WAY, JAMES L.
Rhodanese and Sodium Thiosulfate Encapsulated in Mouse Carrier Erythrocytes, II. In Vivo Survivability and Alterations in Physiologic and Morphologic Characteristics. LEUNG, P., DAVIS, R. W., YAO, C....
Sadhale, Parag P., Sapolsky, Ronald, Davis, Ronald W., Butler, J.Scott, Platt, Terry
In general, synthetic RNA transcripts corresponding to the 3′ ends of Saccharomyces cerevisiae genes appear to be accurately cleaved and polyadenylated in vitro under appropriate conditions in...
Vollrath, Douglas, Davis, Ronald W.
Excellent resolution of chromosomal DNA molecules from Saccharomyces cerevisiae, Candida albicans and Schizosaccharomyces pombe has been obtained using alternating contour-clamped homogeneous...
"UO 87 137--UO 87 139."
Analysis of chromosomal integration and deletions of yeast plasmids (1977)
Cameron, John R., Philippsen, Peter, Davis, Ronald W.
Plasmid DNAs from six strains of Saccharomyces cerevisiae were compared. Three different plasmids were found, designated Scp 1, Scp 2 and Scp 3, with monomer lengths of 6. 19, 6.06 and 5.97 kilobases...
Thesis (M.A.)--Humboldt State University, 1976.
A study of the base sequence arrangements in DNA by electron microscopy (1969)
NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document. The study of base sequence arrangements in DNA molecules was accomplished by...
The Service Contract Act of 1965 and government procurement / (1969)
Thesis--Judge Advocate General's School, Charlottesville, Va., 1969.
Electron-microscopic visualization of deletion mutations (1968)
Davis, Ronald W., Davidson, Norman
Deletion mutants of λ coliphage were discovered by Kellenberger, Zichichi, and Weigle.(1) The deletions can be mapped by genetic recombination experiments. It is not known if the recombination maps...
Historical outline of the Kru Coast, Liberia, 1500 to the present /--by Ronald W. Davis. (1968)
Vita.
An arrayable flow-through microcentrifuge for high-throughput instrumentation
Marziali, Andre, Willis, Thomas D., Davis, Ronald W.
A compact, flow-through centrifugation system has been developed specifically for high-throughput centrifugation of large numbers of samples. The instrument is based on multiple high-speed rotors...
Population genetic implications from sequence variation in four Y chromosome genes
Shen, Peidong, Wang, Frank, Underhill, Peter A., Franco, Claudia, Yang, Wei-Hsien, Roxas, Adriane, ...
Some insight into human evolution has been gained from the sequencing of four Y chromosome genes. Primary genomic sequencing determined gene SMCY to be composed of 27 exons that comprise 4,620 bp of...
Prevalence of small inversions in yeast gene order evolution
Seoighe, Cathal, Federspiel, Nancy, Jones, Ted, Hansen, Nancy, Bivolarovic, Vesna, Surzycki, Ray, ...
Gene order evolution in two eukaryotes was studied by comparing the Saccharomyces cerevisiae genome sequence to extensive new data from whole-genome shotgun and cosmid sequencing of Candida albicans....
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....
Discovery and analysis of inflammatory disease-related genes using cDNA microarrays
Heller, Renu A., Schena, Mark, Chai, Andrew, Shalon, Dari, Bedilion, Tod, Gilmore, James, ...
cDNA microarray technology is used to profile complex diseases and discover novel disease-related genes. In inflammatory disease such as rheumatoid arthritis, expression patterns of diverse cell...
Jin, Li, Underhill, Peter A., Doctor, Vishal, Davis, Ronald W., Shen, Peidong, Cavalli-Sforza, L. Luca, ...
Despite mounting genetic evidence implicating a recent origin of modern humans, the elucidation of early migratory gene-flow episodes remains incomplete. Geographic distribution of haplotypes may...
Lashkari, Deval A., McCusker, John H., Davis, Ronald W.
The recent ability to sequence whole genomes allows ready access to all genetic material. The approaches outlined here allow automated analysis of sequence for the synthesis of optimal primers in an...
Yeast microarrays for genome wide parallel genetic and gene expression analysis
Lashkari, Deval A., DeRisi, Joseph L., McCusker, John H., Namath, Allen F., Gentile, Cristl, Hwang, Seung Y., ...
We have developed high-density DNA microarrays of yeast ORFs. These microarrays can monitor hybridization to ORFs for applications such as quantitative differential gene expression analysis and...
Genomic evidence for a complete sexual cycle in Candida albicans
Tzung, Keh-Weei, Williams, Roy M., Scherer, Stewart, Federspiel, Nancy, Jones, Ted, Hansen, Nancy, ...
Candida albicans is a diploid fungus that has become a medically important opportunistic pathogen in immunocompromised individuals. We have sequenced the C. albicans genome to 10.4-fold coverage and...
Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid
Barnett, Melanie J., Fisher, Robert F., Jones, Ted, Komp, Caridad, Abola, A. Pia, Barloy-Hubler, Frédérique, ...
The symbiotic nitrogen-fixing soil bacterium Sinorhizobium meliloti contains three replicons: pSymA, pSymB, and the chromosome. We report here the complete 1,354,226-nt sequence of pSymA. In addition...
A genome-wide screen in Saccharomyces cerevisiae for genes affecting UV radiation sensitivity
Birrell, Geoff W., Giaever, Guri, Chu, Angela M., Davis, Ronald W., Brown, J. Martin
The recent completion of the deletion of essentially all of the ORFs in yeast is an important new resource for identifying the phenotypes of unknown genes. Each ORF is replaced with a cassette...
Identification and preliminary characterization of mouse Adam33
Gunn, Teresa M, Azarani, Arezou, Kim, Philip H, Hyman, Richard W, Davis, Ronald W, Barsh, Gregory S
Pourmand, Nader, Elahi, Elahe, Davis, Ronald W., Ronaghi, Mostafa
We describe here the development of a new and simple single-tube multiplex Pyrosequencing assay. Genomic DNA or cDNA was employed to PCR amplify region(s) using biotinylated and normal primer(s)....
DAtA: Database of Arabidopsis thaliana Annotation
Palm, Curtis J., Federspiel, Nancy A., Davis, Ronald W.
The Database of Arabidopsis thaliana Annotation (DAtA) was created to enable easy access to and analysis of all the Arabidopsis genome project annotation. The database was constructed using the...
Birrell, Geoff W., Brown, James A., Wu, H. Irene, Giaever, Guri, Chu, Angela M., Davis, Ronald W., ...
The recent completion of the deletion of all of the nonessential genes in budding yeast has provided a powerful new way of determining those genes that affect the sensitivity of this organism to...
The Ume6 regulon coordinates metabolic and meiotic gene expression in yeast
Williams, Roy M., Primig, Michael, Washburn, Brian K., Winzeler, Elizabeth A., Bellis, Michel, Sarrauste De Menthière, Cyril, ...
The Ume6 transcription factor in yeast is known to both repress and activate expression of diverse genes during growth and meiotic development. To obtain a more complete profile of the functions...
Metabolic specialization associated with phenotypic switching in Candida albicans
Lan, Chung-Yu, Newport, George, Murillo, Luis A., Jones, Ted, Scherer, Stewart, Davis, Ronald W., ...
Phase and antigenic variation are mechanisms used by microbial pathogens to stochastically change their cell surface composition. A related property, referred to as phenotypic switching, has been...
Parallel phenotypic analysis of sporulation and postgermination growth in Saccharomyces cerevisiae
Deutschbauer, Adam M., Williams, Roy M., Chu, Angela M., Davis, Ronald W.
We have quantitatively monitored the sporulation and germination efficiencies of ≈4,200 yeast deletion strains in parallel by using a molecular bar coding strategy. In a single study, we doubled...
Identification of the SAAT Gene Involved in Strawberry Flavor Biogenesis by Use of DNA Microarrays
Aharoni, Asaph, Keizer, Leopold C. P., Bouwmeester, Harro J., Sun, Zhongkui, Alvarez-Huerta, Mayte, Verhoeven, Harrie A., ...
Fruit flavor is a result of a complex mixture of numerous compounds. The formation of these compounds is closely correlated with the metabolic changes occurring during fruit maturation. Here, we...
Plant defense genes are regulated by ethylene
Ecker, Joseph R., Davis, Ronald W.
One of the earliest detectable events during plant-pathogen interaction is a rapid increase in ethylene biosynthesis. This gaseous plant stress hormone may be a signal for plants to activate defense...
Underhill, Peter A., Jin, Li, Lin, Alice A., Mehdi, S. Qasim, Jenkins, Trefor, Vollrath, Douglas, ...
Y chromosome haplotypes are particularly useful in deciphering human evolutionary history because they accentuate the effects of drift, migration, and range expansion. Significant acceleration of Y...
An Automated Hydrodynamic Process for Controlled, Unbiased DNA Shearing
Thorstenson, Yvonne R., Hunicke-Smith, Scott P., Oefner, Peter J., Davis, Ronald W.
An automated, inexpensive, easy-to-use, and reproducible technique for controlled, random DNA fragmentation has been developed. The technique is based on point–sink hydrodynamics that result when a...
An Automated Sample Preparation System for Large-Scale DNA Sequencing
Marziali, Andre, Willis, Thomas D., Federspiel, Nancy A., Davis, Ronald W.
Recent advances in DNA sequencing technologies, both in the form of high lane-density gels and automated capillary systems, will lead to an increased requirement for sample preparation systems that...
A Method For Parallel, Automated, Thermal Cycling of Submicroliter Samples
Nakane, Jonathan, Broemeling, David, Donaldson, Roger, Marziali, Andre, Willis, Thomas D., O'Keefe, Matthew, ...
A large fraction of the cost of DNA sequencing and other DNA-analysis processes results from the reagent costs incurred during cycle sequencing or PCR. In particular, the high cost of the enzymes and...
Chemogenomic profiling: Identifying the functional interactions of small molecules in yeast
Giaever, Guri, Flaherty, Patrick, Kumm, Jochen, Proctor, Michael, Nislow, Corey, Jaramillo, Daniel F., ...
We demonstrate the efficacy of a genome-wide protocol in yeast that allows the identification of those gene products that functionally interact with small molecules and result in the inhibition of...
Inhibition of gene expression in plant cells by expression of antisense RNA
Ecker, Joseph R., Davis, Ronald W.
Due to the paucity of mutations in biochemical pathways in plants, an alternative approach to classical genetics was tested by expressing antisense RNA in plant cells. A series of plasmids was...
Nitrate reductase from squash: cDNA cloning and nitrate regulation
Crawford, Nigel M., Campbell, Wilbur H., Davis, Ronald W.
The assimilation of nitrate in plants involves the reduction of nitrate to ammonia in two steps. The first step requires nitrate reductase, a nitrate-inducible enzyme. When seedlings of squash...
Cleavage of DNA by R1 Restriction Endonuclease Generates Cohesive Ends
Mertz, Janet E., Davis, Ronald W.
R1 restriction endonuclease cleaves duplex DNA at a specific sequence, probably 6 nucleotide pairs in length, by making two single-strand staggered cleavages, generating 5′-phosphoryl and...
The diploid genome sequence of Candida albicans
Jones, Ted, Federspiel, Nancy A., Chibana, Hiroji, Dungan, Jan, Kalman, Sue, Magee, B. B., ...
We present the diploid genome sequence of the fungal pathogen Candida albicans. Because C. albicans has no known haploid or homozygous form, sequencing was performed as a whole-genome shotgun of the...
Integrative Analysis of the Mitochondrial Proteome in Yeast
Prokisch, Holger, Scharfe, Curt, Camp, David G, Xiao, Wenzhong, David, Lior, Andreoli, Christophe, ...
In this study yeast mitochondria were used as a model system to apply, evaluate, and integrate different genomic approaches to define the proteins of an organelle. Liquid chromatography mass...
Viable Molecular Hybrids of Bacteriophage Lambda and Eukaryotic DNA
Thomas, Marjorie, Cameron, John R., Davis, Ronald W.
A bacteriophage λ strain has been constructed and a method developed by which DNA from potentially any source can be covalently inserted through EcoRI cohesive ends into the middle of the λ DNA....
SNP Discovery in Pooled Samples With Mismatch Repair Detection
Fakhrai-Rad, Hossein, Zheng, Jianbiao, Willis, Thomas D., Wong, Kee, Suyenaga, Kent, Moorhead, Martin, ...
A targeted discovery effort is required to identify low frequency single nucleotide polymorphisms (SNPs) in human coding and regulatory regions. We here describe combining mismatch repair detection...
Characterization of synthetic DNA bar codes in Saccharomyces cerevisiae gene-deletion strains
Eason, Robert G., Pourmand, Nader, Tongprasit, Waraporn, Herman, Zelek S., Anthony, Kevin, Jejelowo, Olufisayo, ...
Incorporation of strain-specific synthetic DNA tags into yeast Saccharomyces cerevisiae gene-deletion strains has enabled identification of gene functions by massively parallel growth rate analysis....
A Transcriptional Profile of Aging in the Human Kidney
Rodwell, Graham E. J, Sonu, Rebecca, Zahn, Jacob M, Lund, James, Wilhelmy, Julie, Wang, Lingli, ...
In this study, we found 985 genes that change expression in the cortex and the medulla of the kidney with age. Some of the genes whose transcripts increase in abundance with age are known to be...
A multi-enzyme model for pyrosequencing
Agah, Ali, Aghajan, Mariam, Mashayekhi, Foad, Amini, Sasan, Davis, Ronald W., Plummer, James D., ...
Pyrosequencing is a DNA sequencing technique based on sequencing-by-synthesis enabling rapid real-time sequence determination. This technique employs four enzymatic reactions in a single tube to...
Dean, Bill B., Kolattukudy, P. E., Davis, Ronald W.
The disorder of potato tubers (Solanum tuberosum var. Russet Burbank) called “hollow heart” is manifested by the occurrence of hollow regions in internal parts of the tuber. The structure and...
Elevated evolutionary rates in the laboratory strain of Saccharomyces cerevisiae
Gu, Zhenglong, David, Lior, Petrov, Dmitri, Jones, Ted, Davis, Ronald W., Steinmetz, Lars M.
By using the maximum likelihood method, we made a genome-wide comparison of the evolutionary rates in the lineages leading to the laboratory strain (S288c) and a wild strain (YJM789) of Saccharomyces...
Hardenbol, Paul, Yu, Fuli, Belmont, John, MacKenzie, Jennifer, Bruckner, Carsten, Brundage, Tiffany, ...
Large-scale genetic studies are highly dependent on efficient and scalable multiplex SNP assays. In this study, we report the development of Molecular Inversion Probe technology with four-color,...
Apidianakis, Yiorgos, Mindrinos, Michael N., Xiao, Wenzhong, Lau, Gee W., Baldini, Regina L., Davis, Ronald W., ...
Insights into the host factors and mechanisms mediating the primary host responses after pathogen presentation remain limited, due in part to the complexity and genetic intractability of host...
Effect of Flooding on Starch Accumulation in Chloroplasts of Sunflower (Helianthus annuus L.) 1
Wample, Robert L., Davis, Ronald W.
Chloroplasts in leaves of sunflower (Helianthus annuus L. cv hybrid 894) whose roots were flooded for 4 days showed an increase in the level of starch in chloroplasts when examined with the electron...
Microbes on the human vaginal epithelium
Hyman, Richard W., Fukushima, Marilyn, Diamond, Lisa, Kumm, Jochen, Giudice, Linda C., Davis, Ronald W.
Using solely a gene-based procedure, PCR amplification of the 16S ribosomal RNA gene coupled with very deep sequencing of the amplified products, the microbes on 20 human vaginal epithelia of healthy...
Genome-Wide Requirements for Resistance to Functionally Distinct DNA-Damaging Agents
Lee, William, St.Onge, Robert P, Proctor, Michael, Flaherty, Patrick, Jordan, Michael I, Arkin, Adam P, ...
The mechanistic and therapeutic differences in the cellular response to DNA-damaging compounds are not completely understood, despite intense study. To expand our knowledge of DNA damage, we assayed...
Significance analysis of time course microarray experiments
Storey, John D., Xiao, Wenzhong, Leek, Jeffrey T., Tompkins, Ronald G., Davis, Ronald W.
Characterizing the genome-wide dynamic regulation of gene expression is important and will be of much interest in the future. However, there is currently no established method for identifying...
Global Analysis of ATM Polymorphism Reveals Significant Functional Constraint
Thorstenson, Yvonne R., Shen, Peidong, Tusher, Virginia G., Wayne, Tierney L., Davis, Ronald W., Chu, Gilbert, ...
ATM, the gene that is mutated in ataxia-telangiectasia, is associated with cerebellar degeneration, abnormal proliferation of small blood vessels, and cancer. These clinically important...
Allele quantification using molecular inversion probes (MIP)
Wang, Yuker, Moorhead, Martin, Karlin-Neumann, George, Falkowski, Matthew, Chen, Chunnuan, Siddiqui, Farooq, ...
Detection of genomic copy number changes has been an important research area, especially in cancer. Several high-throughput technologies have been developed to detect these changes. Features that are...
Faham, Malek, Zheng, Jianbiao, Moorhead, Martin, Fakhrai-Rad, Hossein, Namsaraev, Eugeni, Wong, Kee, ...
Identification of the genetic basis of common disease may require comprehensive sequence analysis of coding regions and regulatory elements in patients and controls to find genetic effects caused by...
A high-resolution map of transcription in the yeast genome
David, Lior, Huber, Wolfgang, Granovskaia, Marina, Toedling, Joern, Palm, Curtis J., Bofkin, Lee, ...
There is abundant transcription from eukaryotic genomes unaccounted for by protein coding genes. A high-resolution genome-wide survey of transcription in a well annotated genome will help relate...
Transcriptional Profiling of Aging in Human Muscle Reveals a Common Aging Signature
Zahn, Jacob M, Sonu, Rebecca, Vogel, Hannes, Crane, Emily, Mazan-Mamczarz, Krystyna, Rabkin, Ralph, ...
We analyzed expression of 81 normal muscle samples from humans of varying ages, and have identified a molecular profile for aging consisting of 250 age-regulated genes. This molecular profile...
Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae
Kastenmayer, James P., Ni, Li, Chu, Angela, Kitchen, Lauren E., Au, Wei-Chun, Yang, Hui, ...
Genes with small open reading frames (sORFs;
Mechanisms of Haploinsufficiency Revealed by Genome-Wide Profiling in Yeast
Deutschbauer, Adam M., Jaramillo, Daniel F., Proctor, Michael, Kumm, Jochen, Hillenmeyer, Maureen E., Davis, Ronald W., ...
Haploinsufficiency is defined as a dominant phenotype in diploid organisms that are heterozygous for a loss-of-function allele. Despite its relevance to human disease, neither the extent of...
Direct electrical detection of DNA synthesis
Pourmand, Nader, Karhanek, Miloslav, Persson, Henrik H. J., Webb, Chris D., Lee, Thomas H., Zahradníková, Alexandra, ...
Rapid, sequence-specific DNA detection is essential for applications in medical diagnostics and genetic screening. Electrical biosensors that use immobilized nucleic acids are especially promising in...
PathogenMIPer: a tool for the design of molecular inversion probes to detect multiple pathogens
Thiyagarajan, Sreedevi, Karhanek, Miloslav, Akhras, Michael, Davis, Ronald W, Pourmand, Nader
Introns Regulate RNA and Protein Abundance in Yeast
Juneau, Kara, Miranda, Molly, Hillenmeyer, Maureen E., Nislow, Corey, Davis, Ronald W.
The purpose of introns in the architecturally simple genome of Saccharomyces cerevisiae is not well understood. To assay the functional relevance of introns, a series of computational analyses and...
An arrayable flow-through microcentrifuge for high-throughput instrumentation
Marziali, Andre, Willis, Thomas D., Davis, Ronald W.
A compact, flow-through centrifugation system has been developed specifically for high-throughput centrifugation of large numbers of samples. The instrument is based on multiple high-speed rotors...
Population genetic implications from sequence variation in four Y chromosome genes
Shen, Peidong, Wang, Frank, Underhill, Peter A., Franco, Claudia, Yang, Wei-Hsien, Roxas, Adriane, ...
Some insight into human evolution has been gained from the sequencing of four Y chromosome genes. Primary genomic sequencing determined gene SMCY to be composed of 27 exons that comprise 4,620 bp of...
Prevalence of small inversions in yeast gene order evolution
Seoighe, Cathal, Federspiel, Nancy, Jones, Ted, Hansen, Nancy, Bivolarovic, Vesna, Surzycki, Ray, ...
Gene order evolution in two eukaryotes was studied by comparing the Saccharomyces cerevisiae genome sequence to extensive new data from whole-genome shotgun and cosmid sequencing of Candida albicans....
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....
Discovery and analysis of inflammatory disease-related genes using cDNA microarrays
Heller, Renu A., Schena, Mark, Chai, Andrew, Shalon, Dari, Bedilion, Tod, Gilmore, James, ...
cDNA microarray technology is used to profile complex diseases and discover novel disease-related genes. In inflammatory disease such as rheumatoid arthritis, expression patterns of diverse cell...
Jin, Li, Underhill, Peter A., Doctor, Vishal, Davis, Ronald W., Shen, Peidong, Cavalli-Sforza, L. Luca, ...
Despite mounting genetic evidence implicating a recent origin of modern humans, the elucidation of early migratory gene-flow episodes remains incomplete. Geographic distribution of haplotypes may...
Lashkari, Deval A., McCusker, John H., Davis, Ronald W.
The recent ability to sequence whole genomes allows ready access to all genetic material. The approaches outlined here allow automated analysis of sequence for the synthesis of optimal primers in an...
Yeast microarrays for genome wide parallel genetic and gene expression analysis
Lashkari, Deval A., DeRisi, Joseph L., McCusker, John H., Namath, Allen F., Gentile, Cristl, Hwang, Seung Y., ...
We have developed high-density DNA microarrays of yeast ORFs. These microarrays can monitor hybridization to ORFs for applications such as quantitative differential gene expression analysis and...
Genomic evidence for a complete sexual cycle in Candida albicans
Tzung, Keh-Weei, Williams, Roy M., Scherer, Stewart, Federspiel, Nancy, Jones, Ted, Hansen, Nancy, ...
Candida albicans is a diploid fungus that has become a medically important opportunistic pathogen in immunocompromised individuals. We have sequenced the C. albicans genome to 10.4-fold coverage and...
Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid
Barnett, Melanie J., Fisher, Robert F., Jones, Ted, Komp, Caridad, Abola, A. Pia, Barloy-Hubler, Frédérique, ...
The symbiotic nitrogen-fixing soil bacterium Sinorhizobium meliloti contains three replicons: pSymA, pSymB, and the chromosome. We report here the complete 1,354,226-nt sequence of pSymA. In addition...
A genome-wide screen in Saccharomyces cerevisiae for genes affecting UV radiation sensitivity
Birrell, Geoff W., Giaever, Guri, Chu, Angela M., Davis, Ronald W., Brown, J. Martin
The recent completion of the deletion of essentially all of the ORFs in yeast is an important new resource for identifying the phenotypes of unknown genes. Each ORF is replaced with a cassette...
Identification and preliminary characterization of mouse Adam33
Gunn, Teresa M, Azarani, Arezou, Kim, Philip H, Hyman, Richard W, Davis, Ronald W, Barsh, Gregory S
Pourmand, Nader, Elahi, Elahe, Davis, Ronald W., Ronaghi, Mostafa
We describe here the development of a new and simple single-tube multiplex Pyrosequencing assay. Genomic DNA or cDNA was employed to PCR amplify region(s) using biotinylated and normal primer(s)....
DAtA: Database of Arabidopsis thaliana Annotation
Palm, Curtis J., Federspiel, Nancy A., Davis, Ronald W.
The Database of Arabidopsis thaliana Annotation (DAtA) was created to enable easy access to and analysis of all the Arabidopsis genome project annotation. The database was constructed using the...
Birrell, Geoff W., Brown, James A., Wu, H. Irene, Giaever, Guri, Chu, Angela M., Davis, Ronald W., ...
The recent completion of the deletion of all of the nonessential genes in budding yeast has provided a powerful new way of determining those genes that affect the sensitivity of this organism to...
The Ume6 regulon coordinates metabolic and meiotic gene expression in yeast
Williams, Roy M., Primig, Michael, Washburn, Brian K., Winzeler, Elizabeth A., Bellis, Michel, Sarrauste De Menthière, Cyril, ...
The Ume6 transcription factor in yeast is known to both repress and activate expression of diverse genes during growth and meiotic development. To obtain a more complete profile of the functions...
Metabolic specialization associated with phenotypic switching in Candida albicans
Lan, Chung-Yu, Newport, George, Murillo, Luis A., Jones, Ted, Scherer, Stewart, Davis, Ronald W., ...
Phase and antigenic variation are mechanisms used by microbial pathogens to stochastically change their cell surface composition. A related property, referred to as phenotypic switching, has been...
Parallel phenotypic analysis of sporulation and postgermination growth in Saccharomyces cerevisiae
Deutschbauer, Adam M., Williams, Roy M., Chu, Angela M., Davis, Ronald W.
We have quantitatively monitored the sporulation and germination efficiencies of ≈4,200 yeast deletion strains in parallel by using a molecular bar coding strategy. In a single study, we doubled...
Identification of the SAAT Gene Involved in Strawberry Flavor Biogenesis by Use of DNA Microarrays
Aharoni, Asaph, Keizer, Leopold C. P., Bouwmeester, Harro J., Sun, Zhongkui, Alvarez-Huerta, Mayte, Verhoeven, Harrie A., ...
Fruit flavor is a result of a complex mixture of numerous compounds. The formation of these compounds is closely correlated with the metabolic changes occurring during fruit maturation. Here, we...
Plant defense genes are regulated by ethylene
Ecker, Joseph R., Davis, Ronald W.
One of the earliest detectable events during plant-pathogen interaction is a rapid increase in ethylene biosynthesis. This gaseous plant stress hormone may be a signal for plants to activate defense...
Underhill, Peter A., Jin, Li, Lin, Alice A., Mehdi, S. Qasim, Jenkins, Trefor, Vollrath, Douglas, ...
Y chromosome haplotypes are particularly useful in deciphering human evolutionary history because they accentuate the effects of drift, migration, and range expansion. Significant acceleration of Y...
An Automated Hydrodynamic Process for Controlled, Unbiased DNA Shearing
Thorstenson, Yvonne R., Hunicke-Smith, Scott P., Oefner, Peter J., Davis, Ronald W.
An automated, inexpensive, easy-to-use, and reproducible technique for controlled, random DNA fragmentation has been developed. The technique is based on point–sink hydrodynamics that result when a...
An Automated Sample Preparation System for Large-Scale DNA Sequencing
Marziali, Andre, Willis, Thomas D., Federspiel, Nancy A., Davis, Ronald W.
Recent advances in DNA sequencing technologies, both in the form of high lane-density gels and automated capillary systems, will lead to an increased requirement for sample preparation systems that...
A Method For Parallel, Automated, Thermal Cycling of Submicroliter Samples
Nakane, Jonathan, Broemeling, David, Donaldson, Roger, Marziali, Andre, Willis, Thomas D., O'Keefe, Matthew, ...
A large fraction of the cost of DNA sequencing and other DNA-analysis processes results from the reagent costs incurred during cycle sequencing or PCR. In particular, the high cost of the enzymes and...
Chemogenomic profiling: Identifying the functional interactions of small molecules in yeast
Giaever, Guri, Flaherty, Patrick, Kumm, Jochen, Proctor, Michael, Nislow, Corey, Jaramillo, Daniel F., ...
We demonstrate the efficacy of a genome-wide protocol in yeast that allows the identification of those gene products that functionally interact with small molecules and result in the inhibition of...
Inhibition of gene expression in plant cells by expression of antisense RNA
Ecker, Joseph R., Davis, Ronald W.
Due to the paucity of mutations in biochemical pathways in plants, an alternative approach to classical genetics was tested by expressing antisense RNA in plant cells. A series of plasmids was...
Nitrate reductase from squash: cDNA cloning and nitrate regulation
Crawford, Nigel M., Campbell, Wilbur H., Davis, Ronald W.
The assimilation of nitrate in plants involves the reduction of nitrate to ammonia in two steps. The first step requires nitrate reductase, a nitrate-inducible enzyme. When seedlings of squash...
Cleavage of DNA by R1 Restriction Endonuclease Generates Cohesive Ends
Mertz, Janet E., Davis, Ronald W.
R1 restriction endonuclease cleaves duplex DNA at a specific sequence, probably 6 nucleotide pairs in length, by making two single-strand staggered cleavages, generating 5′-phosphoryl and...
The diploid genome sequence of Candida albicans
Jones, Ted, Federspiel, Nancy A., Chibana, Hiroji, Dungan, Jan, Kalman, Sue, Magee, B. B., ...
We present the diploid genome sequence of the fungal pathogen Candida albicans. Because C. albicans has no known haploid or homozygous form, sequencing was performed as a whole-genome shotgun of the...
Integrative Analysis of the Mitochondrial Proteome in Yeast
Prokisch, Holger, Scharfe, Curt, Camp, David G, Xiao, Wenzhong, David, Lior, Andreoli, Christophe, ...
In this study yeast mitochondria were used as a model system to apply, evaluate, and integrate different genomic approaches to define the proteins of an organelle. Liquid chromatography mass...
Viable Molecular Hybrids of Bacteriophage Lambda and Eukaryotic DNA
Thomas, Marjorie, Cameron, John R., Davis, Ronald W.
A bacteriophage λ strain has been constructed and a method developed by which DNA from potentially any source can be covalently inserted through EcoRI cohesive ends into the middle of the λ DNA....
SNP Discovery in Pooled Samples With Mismatch Repair Detection
Fakhrai-Rad, Hossein, Zheng, Jianbiao, Willis, Thomas D., Wong, Kee, Suyenaga, Kent, Moorhead, Martin, ...
A targeted discovery effort is required to identify low frequency single nucleotide polymorphisms (SNPs) in human coding and regulatory regions. We here describe combining mismatch repair detection...
Characterization of synthetic DNA bar codes in Saccharomyces cerevisiae gene-deletion strains
Eason, Robert G., Pourmand, Nader, Tongprasit, Waraporn, Herman, Zelek S., Anthony, Kevin, Jejelowo, Olufisayo, ...
Incorporation of strain-specific synthetic DNA tags into yeast Saccharomyces cerevisiae gene-deletion strains has enabled identification of gene functions by massively parallel growth rate analysis....
A Transcriptional Profile of Aging in the Human Kidney
Rodwell, Graham E. J, Sonu, Rebecca, Zahn, Jacob M, Lund, James, Wilhelmy, Julie, Wang, Lingli, ...
In this study, we found 985 genes that change expression in the cortex and the medulla of the kidney with age. Some of the genes whose transcripts increase in abundance with age are known to be...
A multi-enzyme model for pyrosequencing
Agah, Ali, Aghajan, Mariam, Mashayekhi, Foad, Amini, Sasan, Davis, Ronald W., Plummer, James D., ...
Pyrosequencing is a DNA sequencing technique based on sequencing-by-synthesis enabling rapid real-time sequence determination. This technique employs four enzymatic reactions in a single tube to...
Dean, Bill B., Kolattukudy, P. E., Davis, Ronald W.
The disorder of potato tubers (Solanum tuberosum var. Russet Burbank) called “hollow heart” is manifested by the occurrence of hollow regions in internal parts of the tuber. The structure and...
Elevated evolutionary rates in the laboratory strain of Saccharomyces cerevisiae
Gu, Zhenglong, David, Lior, Petrov, Dmitri, Jones, Ted, Davis, Ronald W., Steinmetz, Lars M.
By using the maximum likelihood method, we made a genome-wide comparison of the evolutionary rates in the lineages leading to the laboratory strain (S288c) and a wild strain (YJM789) of Saccharomyces...
Hardenbol, Paul, Yu, Fuli, Belmont, John, MacKenzie, Jennifer, Bruckner, Carsten, Brundage, Tiffany, ...
Large-scale genetic studies are highly dependent on efficient and scalable multiplex SNP assays. In this study, we report the development of Molecular Inversion Probe technology with four-color,...
Apidianakis, Yiorgos, Mindrinos, Michael N., Xiao, Wenzhong, Lau, Gee W., Baldini, Regina L., Davis, Ronald W., ...
Insights into the host factors and mechanisms mediating the primary host responses after pathogen presentation remain limited, due in part to the complexity and genetic intractability of host...
Application of genome-wide expression analysis to human health and disease
Cobb, J. Perren, Mindrinos, Michael N., Miller-Graziano, Carol, Calvano, Steve E., Baker, Henry V., Xiao, Wenzhong, ...
The application of genome-wide expression analysis to a large-scale, multicentered program in critically ill patients poses a number of theoretical and technical challenges. We describe here an...
Effect of Flooding on Starch Accumulation in Chloroplasts of Sunflower (Helianthus annuus L.) 1
Wample, Robert L., Davis, Ronald W.
Chloroplasts in leaves of sunflower (Helianthus annuus L. cv hybrid 894) whose roots were flooded for 4 days showed an increase in the level of starch in chloroplasts when examined with the electron...
Microbes on the human vaginal epithelium
Hyman, Richard W., Fukushima, Marilyn, Diamond, Lisa, Kumm, Jochen, Giudice, Linda C., Davis, Ronald W.
Using solely a gene-based procedure, PCR amplification of the 16S ribosomal RNA gene coupled with very deep sequencing of the amplified products, the microbes on 20 human vaginal epithelia of healthy...
Genome-Wide Requirements for Resistance to Functionally Distinct DNA-Damaging Agents
Lee, William, St.Onge, Robert P, Proctor, Michael, Flaherty, Patrick, Jordan, Michael I, Arkin, Adam P, ...
The mechanistic and therapeutic differences in the cellular response to DNA-damaging compounds are not completely understood, despite intense study. To expand our knowledge of DNA damage, we assayed...
Significance analysis of time course microarray experiments
Storey, John D., Xiao, Wenzhong, Leek, Jeffrey T., Tompkins, Ronald G., Davis, Ronald W.
Characterizing the genome-wide dynamic regulation of gene expression is important and will be of much interest in the future. However, there is currently no established method for identifying...
Global Analysis of ATM Polymorphism Reveals Significant Functional Constraint
Thorstenson, Yvonne R., Shen, Peidong, Tusher, Virginia G., Wayne, Tierney L., Davis, Ronald W., Chu, Gilbert, ...
ATM, the gene that is mutated in ataxia-telangiectasia, is associated with cerebellar degeneration, abnormal proliferation of small blood vessels, and cancer. These clinically important...
Faham, Malek, Zheng, Jianbiao, Moorhead, Martin, Fakhrai-Rad, Hossein, Namsaraev, Eugeni, Wong, Kee, ...
Identification of the genetic basis of common disease may require comprehensive sequence analysis of coding regions and regulatory elements in patients and controls to find genetic effects caused by...
Allele quantification using molecular inversion probes (MIP)
Wang, Yuker, Moorhead, Martin, Karlin-Neumann, George, Falkowski, Matthew, Chen, Chunnuan, Siddiqui, Farooq, ...
Detection of genomic copy number changes has been an important research area, especially in cancer. Several high-throughput technologies have been developed to detect these changes. Features that are...
A high-resolution map of transcription in the yeast genome
David, Lior, Huber, Wolfgang, Granovskaia, Marina, Toedling, Joern, Palm, Curtis J., Bofkin, Lee, ...
There is abundant transcription from eukaryotic genomes unaccounted for by protein coding genes. A high-resolution genome-wide survey of transcription in a well annotated genome will help relate...
Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae
Kastenmayer, James P., Ni, Li, Chu, Angela, Kitchen, Lauren E., Au, Wei-Chun, Yang, Hui, ...
Genes with small open reading frames (sORFs;
Mechanisms of Haploinsufficiency Revealed by Genome-Wide Profiling in Yeast
Deutschbauer, Adam M., Jaramillo, Daniel F., Proctor, Michael, Kumm, Jochen, Hillenmeyer, Maureen E., Davis, Ronald W., ...
Haploinsufficiency is defined as a dominant phenotype in diploid organisms that are heterozygous for a loss-of-function allele. Despite its relevance to human disease, neither the extent of...
Direct electrical detection of DNA synthesis
Pourmand, Nader, Karhanek, Miloslav, Persson, Henrik H. J., Webb, Chris D., Lee, Thomas H., Zahradníková, Alexandra, ...
Rapid, sequence-specific DNA detection is essential for applications in medical diagnostics and genetic screening. Electrical biosensors that use immobilized nucleic acids are especially promising in...
Transcriptional Profiling of Aging in Human Muscle Reveals a Common Aging Signature
Zahn, Jacob M, Sonu, Rebecca, Vogel, Hannes, Crane, Emily, Mazan-Mamczarz, Krystyna, Rabkin, Ralph, ...
We analyzed expression of 81 normal muscle samples from humans of varying ages, and have identified a molecular profile for aging consisting of 250 age-regulated genes. This molecular profile...
Introns Regulate RNA and Protein Abundance in Yeast
Juneau, Kara, Miranda, Molly, Hillenmeyer, Maureen E., Nislow, Corey, Davis, Ronald W.
The purpose of introns in the architecturally simple genome of Saccharomyces cerevisiae is not well understood. To assay the functional relevance of introns, a series of computational analyses and...
PathogenMIPer: a tool for the design of molecular inversion probes to detect multiple pathogens
Thiyagarajan, Sreedevi, Karhanek, Miloslav, Akhras, Michael, Davis, Ronald W, Pourmand, Nader
Rapid and Highly Informative Diagnostic Assay for H5N1 Influenza Viruses
Pourmand, Nader, Diamond, Lisa, Garten, Rebecca, Erickson, Julianna P., Kumm, Jochen, Donis, Ruben O., ...
A highly discriminative and information-rich diagnostic assay for H5N1 avian influenza would meet immediate patient care needs and provide valuable information for public health interventions, e.g.,...
PathogenMip Assay: A Multiplex Pathogen Detection Assay
Akhras, Michael S., Thiyagarajan, Sreedevi, Villablanca, Andrea C., Davis, Ronald W., Nyrén, Pål, Pourmand, Nader
The Molecular Inversion Probe (MIP) assay has been previously applied to a large-scale human SNP detection. Here we describe the PathogenMip Assay, a complete protocol for probe production and...
Prediction of protein orientation upon immobilization on biological and nonbiological surfaces
Talasaz, AmirAli H., Nemat-Gorgani, Mohsen, Liu, Yang, Ståhl, Patrik, Dutton, Robert W., Ronaghi, Mostafa, ...
We report on a rapid simulation method for predicting protein orientation on a surface based on electrostatic interactions. New methods for predicting protein immobilization are needed because of the...
Laudanski, Krzysztof, Miller-Graziano, Carol, Xiao, Wenzhong, Mindrinos, Michael N., Richards, Daniel R., De, Asit, ...
Monitoring genome-wide, cell-specific responses to human disease, although challenging, holds great promise for the future of medicine. Patients with injuries severe enough to develop multiple organ...
Multiplex amplification of all coding sequences within 10 cancer genes by Gene-Collector
Fredriksson, Simon, Banér, Johan, Dahl, Fredrik, Chu, Angela, Ji, Hanlee, Welch, Katrina, ...
Herein we present Gene-Collector, a method for multiplex amplification of nucleic acids. The procedure has been employed to successfully amplify the coding sequence of 10 human cancer genes in one...
A Haplotype Framework for Cystic Fibrosis Mutations in Iran
Elahi, Elahe, Khodadad, Ahmad, Kupershmidt, Ilya, Ghasemi, Fereshteh, Alinasab, Babak, Naghizadeh, Ramin, ...
This is the first comprehensive profile of cystic fibrosis transmembrane conductance regulator (CFTR) mutations and their corresponding haplotypes in the Iranian population. All of the 27 CFTR exons...
Juneau, Kara, Palm, Curtis, Miranda, Molly, Davis, Ronald W.
Knowing gene structure is vital to understanding gene function, and accurate genome annotation is essential for understanding cellular function. To this end, we have developed a genome-wide assay for...
Akhras, Michael S., Unemo, Magnus, Thiyagarajan, Sreedevi, Nyrén, Pål, Davis, Ronald W., Fire, Andrew Z., ...
We combined components of a previous assay referred to as Molecular Inversion Probe (MIP) with a complete gap filling strategy, creating a versatile powerful one-primer multiplex amplification...
Pourmand, Nader, Caramuta, Stefano, Villablanca, Andrea, Mori, Silvia, Karhanek, Miloslav, Wang, Shan X., ...
The analysis of short tandem repeats (STRs) plays an important role in forensic science, human identification, genetic mapping, and disease diagnostics. Traditional STR analysis utilizes gel- or...
Multigene amplification and massively parallel sequencing for cancer mutation discovery
Dahl, Fredrik, Stenberg, Johan, Fredriksson, Simon, Welch, Katrina, Zhang, Michael, Nilsson, Mats, ...
We have developed a procedure for massively parallel resequencing of multiple human genes by combining a highly multiplexed and target-specific amplification process with a high-throughput parallel...
Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789
Wei, Wu, McCusker, John H., Hyman, Richard W., Jones, Ted, Ning, Ye, Cao, Zhiwei, ...
We sequenced the genome of Saccharomyces cerevisiae strain YJM789, which was derived from a yeast isolated from the lung of an AIDS patient with pneumonia. The strain is used for studies of fungal...
Apidianakis, Yiorgos, Mindrinos, Michael N., Xiao, Wenzhong, Tegos, George P., Papisov, Michail I., Hamblin, Michael R., ...
Despite recent advances in our understanding the pathophysiology of trauma, the basis of the predisposition of trauma patients to infection remains unclear. A Drosophila melanogaster/Pseudomonas...
Pervasive and Persistent Redundancy among Duplicated Genes in Yeast
Dean, E. Jedediah, Davis, Jerel C., Davis, Ronald W., Petrov, Dmitri A.
The loss of functional redundancy is the key process in the evolution of duplicated genes. Here we systematically assess the extent of functional redundancy among a large set of duplicated genes in...
High Throughput Automated Allele Frequency Estimation by Pyrosequencing
Doostzadeh, Julie, Shokralla, Shadi, Absalan, Farnaz, Jalili, Roxana, Mohandessi, Sharareh, Langston, James W., ...
Pyrosequencing is a DNA sequencing method based on the principle of sequencing-by-synthesis and pyrophosphate detection through a series of enzymatic reactions. This bioluminometric, real-time DNA...
High-Resolution, In Vivo Magnetic Resonance Imaging of Drosophila at 18.8 Tesla
Null, Brian, Liu, Corey W., Hedehus, Maj, Conolly, Steven, Davis, Ronald W.
High resolution MRI of live Drosophila was performed at 18.8 Tesla, with a field of view less than 5 mm, and administration of manganese or gadolinium-based contrast agents. This study demonstrates...
Sinha, Himanshu, David, Lior, Pascon, Renata C., Clauder-Münster, Sandra, Krishnakumar, Sujatha, Nguyen, Michelle, ...
Several quantitative trait loci (QTL) mapping strategies can successfully identify major-effect loci, but often have poor success detecting loci with minor effects, potentially due to the confounding...
Superoxide anions regulate TORC1 and its ability to bind Fpr1:rapamycin complex
Neklesa, Taavi K., Davis, Ronald W.
The small natural product rapamycin, when bound to FKBP12, is a potent inhibitor of an evolutionarily conserved Target of Rapamycin Complex 1 (TORC1), which plays a central role in mediating cellular...
Mapping Gene Associations in Human Mitochondria using Clinical Disease Phenotypes
Scharfe, Curt, Lu, Henry Horng-Shing, Neuenburg, Jutta K., Allen, Edward A., Li, Guan-Cheng, Klopstock, Thomas, ...
Nuclear genes encode most mitochondrial proteins, and their mutations cause diverse and debilitating clinical disorders. To date, 1,200 of these mitochondrial genes have been recorded, while no...
Multiplex protein assays based on real-time magnetic nanotag sensing
Osterfeld, Sebastian J., Yu, Heng, Gaster, Richard S., Caramuta, Stefano, Xu, Liang, Han, Shu-Jen, ...
Magnetic nanotags (MNTs) are a promising alternative to fluorescent labels in biomolecular detection assays, because minute quantities of MNTs can be detected with inexpensive giant magnetoresistive...
Talasaz, AmirAli H., Powell, Ashley A., Huber, David E., Berbee, James G., Roh, Kyung-Ho, Yu, Wong, ...
The enumeration of rare circulating epithelial cells (CEpCs) in the peripheral blood of metastatic cancer patients has shown promise for improved cancer prognosis. Moving beyond enumeration,...
Label-free biosensing with functionalized nanopipette probes
Umehara, Senkei, Karhanek, Miloslav, Davis, Ronald W., Pourmand, Nader
Nanopipette technology can uniquely identify biomolecules such as proteins based on differences in size, shape, and electrical charge. These differences are determined by the detection of changes in...
High-throughput, high-accuracy array-based resequencing
Zheng, Jianbiao, Moorhead, Martin, Weng, Li, Siddiqui, Farooq, Carlton, Victoria E. H., Ireland, James S., ...
Although genomewide association studies have successfully identified associations of many common single-nucleotide polymorphisms (SNPs) with common diseases, the SNPs implicated so far account for...
Neklesa, Taavi K., Davis, Ronald W.
TORC1 is a central regulator of cell growth in response to amino acid availability, yet little is known about how it is regulated. Here, we performed a reverse genetic screen in yeast for genes...
Targeted cell detection based on microchannel gating
Javanmard, Mehdi, Talasaz, AmirAli H., Nemat-Gorgani, Mohsen, Pease, Fabian, Ronaghi, Mostafa, Davis, Ronald W.
Currently, microbiological techniques such as culture enrichment and various plating techniques are used for detection of pathogens. These expensive and time consuming methods can take several days....
Esfandyarpour, Hesaam, Zheng, Bo, Pease, R. Fabian W., Davis, Ronald W.
For the past three decades, Sanger’s method has been the primary DNA sequencing technology; however, inherent limitations in cost and complexity have limited its usage in personalized medicine and...
A dynamic network of transcription in LPS-treated human subjects
Seok, Junhee, Xiao, Wenzhong, Moldawer, Lyle L, Davis, Ronald W, Covert, Markus W
Wheeler, Heather E., Metter, E. Jeffrey, Tanaka, Toshiko, Absher, Devin, Higgins, John, Zahn, Jacob M., ...
Kidneys age at different rates, such that some people show little or no effects of aging whereas others show rapid functional decline. We sequentially used transcriptional profiling and expression...
Meiotic recombination generates rich diversity in NK cell receptor genes, alleles, and haplotypes
Norman, Paul J., Abi-Rached, Laurent, Gendzekhadze, Ketevan, Hammond, John A., Moesta, Achim K., Sharma, Deepti, ...
Natural killer (NK) cells contribute to the essential functions of innate immunity and reproduction. Various genes encode NK cell receptors that recognize the major histocompatibility complex (MHC)...