Definition, conservation and epigenetics of housekeeping and tissue-enriched genes (2009)
She, Xinwei, Rohl, Carol A, Castle, John C, Kulkarni, Amit V, Johnson, Jason M, Chen, Ronghua
Abstract Background Housekeeping genes (HKG) are constitutively expressed in all tissues while tissue-enriched genes (TEG) are expressed at a much higher level in a single tissue type than in others....
Christopher K. Raymond, John Castle, Philip Garrett-engele, Christopher D. Armour, Zhengyan Kan, Nicholas Tsinoremas, ...
Molecular medicine requires the precise definition of drug targets, and tools are now in place to provide genome-wide information on the expression and alternative splicing patterns of any known...
Su, Wan-Lin, Modrek, Barmak, GuhaThakurta, Debraj, Edwards, Stephen, Shah, Jyoti K, Kulkarni, Amit V, ...
Abstract Background Studies have shown that genetic and sex differences strongly influence gene expression in mice. Given the diversity and complexity of transcripts produced by alternative splicing,...
Mapping the Genetic Architecture of Gene Expression in Human Liver (2008)
Eric E. Schadt, Cliona Molony, Eugene Chudin, Ke Hao, Xia Yang, Pek Y. Lum, ...
Genetic variants that are associated with common human diseases do not lead directly to disease, but instead act on intermediate, molecular phenotypes that in turn induce changes in higher-order...
Jason M. Johnson, Elizabeth M. Meiering, Joel E. Wright, Jorge Pardo, Andre Rosowsky, Gerhard Wagner
: The antitumor compound PT523 [N R -(4-amino-4-deoxypteroyl)-N # -hemiphthaloyl-L-ornithine] was found to have an inhibition constant (K i ) of 0.35 ( 0.10 pM against human dihydrofolate reductase...
Levine, David M, Haynor, David R, Castle, John C, Stepaniants, Sergey B, Pellegrini, Matteo, Mao, Mao, ...
Abstract Background Interpretation of lists of genes or proteins with altered expression is a critical and time-consuming part of microarray and proteomics research, but relatively little attention...
Position-specific chemical modification of siRNAs reduces "off-target" transcript silencing (2006)
Jackson, Aimee L., Burchard, Julja, Leake, Devin, Reynolds, Angela, Schelter, Janell, Guo, Jie, ...
Transfected siRNAs regulate numerous transcripts sharing limited complementarity to the RNA duplex. This unintended (“off-target”) silencing can hinder the use of RNAi to define gene function....
Position-specific chemical modification of siRNAs reduces "off-target" transcript silencing (2006)
Jackson, Aimee L., Burchard, Julja, Leake, Devin, Reynolds, Angela, Schelter, Janell, Guo, Jie, ...
Transfected siRNAs regulate numerous transcripts sharing limited complementarity to the RNA duplex. This unintended (“off-target”) silencing can hinder the use of RNAi to define gene function....
Position-specific chemical modification of siRNAs reduces "off-target" transcript silencing (2006)
Jackson, Aimee L., Burchard, Julja, Leake, Devin, Reynolds, Angela, Schelter, Janell, Guo, Jie, ...
Transfected siRNAs regulate numerous transcripts sharing limited complementarity to the RNA duplex. This unintended (“off-target”) silencing can hinder the use of RNAi to define gene function....
RAYMOND, CHRISTOPHER K., ROBERTS, BRIAN S., GARRETT-ENGELE, PHILLIP, LIM, LEE P., JOHNSON, JASON M.
There has been a surge of interest in the biology of microRNAs and the technology of RNA interference. We describe a simple, robust, inexpensive assay for quantitative analysis of microRNAs and...
Kan, Zhengyan, Garrett-Engele, Philip W., Johnson, Jason M., Castle, John C.
To better decipher the functional impact of alternative splicing, we classified alternative splicing events in 10 818 pairs of human and mouse genes based on conservation at genome and transcript...
Schadt, Eric E, Edwards, Stephen W, GuhaThakurta, Debraj, Holder, Dan, Ying, Lisa, Svetnik, Vladimir, ...
Abstract Background Computational and microarray-based experimental approaches were used to generate a comprehensive transcript index for the human genome. Oligonucleotide probes designed from...
Castle, John, Garrett-Engele, Phil, Armour, Christopher D, Duenwald, Sven J, Loerch, Patrick M, Meyer, Michael R, ...
Abstract Microarrays offer a high-resolution means for monitoring pre-mRNA splicing on a genomic scale. We have developed a novel, unbiased amplification protocol that permits labeling of entire...
Protein family annotation in a multiple alignment viewer (2003)
Johnson, Jason M., Mason, Keith, Moallemi, Ciamac, Xi, Hualin, Somaroo, Shyamal, Huang, Enoch S.
Summary: The Pfaat protein family alignment annotation tool is a Java-based multiple sequence alignment editor and viewer designed for protein family analysis. The application merges display features...
Structure and function prediction from sequence in bacterial protein families / (1999)
Thesis (Ph. D., Committee on Higher Degrees)--Harvard University, 1999.
Jason M. Johnson, George M. Church
The emergence of drug-resistant strains of bacteria is a signi®cant and growing human health problem. Active ef¯ux pumps with broad speci-®city are involved in the intrinsic and acquired
Predicting ligand-binding function in families of bacterial receptors
Johnson, Jason M., Church, George M.
The three-dimensional fold of a new protein sequence can often be inferred directly from sequence homology to a protein of known structure. The function of a new protein sequence is more difficult to...
Castle, John, Garrett-Engele, Phil, Armour, Christopher D, Duenwald, Sven J, Loerch, Patrick M, Meyer, Michael R, ...
A novel, unbiased amplification protocol has been developed that permits labeling of entire transcripts. Also, hybridization conditions, probe characteristics, and analysis algorithms were optimized...
Schadt, Eric E, Edwards, Stephen W, GuhaThakurta, Debraj, Holder, Dan, Ying, Lisa, Svetnik, Vladimir, ...
A combination of microarray data with extensive genome annotations resulted in a set of 28,456 experimentally supported transcripts, providing the first experiment-driven annotation of the human...
Kan, Zhengyan, Garrett-Engele, Philip W., Johnson, Jason M., Castle, John C.
To better decipher the functional impact of alternative splicing, we classified alternative splicing events in 10 818 pairs of human and mouse genes based on conservation at genome and transcript...
RAYMOND, CHRISTOPHER K., ROBERTS, BRIAN S., GARRETT-ENGELE, PHILLIP, LIM, LEE P., JOHNSON, JASON M.
There has been a surge of interest in the biology of microRNAs and the technology of RNA interference. We describe a simple, robust, inexpensive assay for quantitative analysis of microRNAs and...
Young, Juan I., Hong, Eugene P., Castle, John C., Crespo-Barreto, Juan, Bowman, Aaron B., Rose, Matthew F., ...
Rett syndrome (RTT) is a postnatal neurodevelopmental disorder characterized by the loss of acquired motor and language skills, autistic features, and unusual stereotyped movements. RTT is caused by...
The Long-term Effects of Gastric Bypass on Vitamin D Metabolism
Johnson, Jason M., Maher, James W., DeMaria, Eric J., Downs, Robert W., Wolfe, Luke G., Kellum, John M.
Routine monitoring of 25-OH-vitamin D and parathormone levels at annuals visits for gastric bypass patients disclosed a high incidence of vitamin D insufficiency and secondary hyperparathyroidism....
Predicting ligand-binding function in families of bacterial receptors
Johnson, Jason M., Church, George M.
The three-dimensional fold of a new protein sequence can often be inferred directly from sequence homology to a protein of known structure. The function of a new protein sequence is more difficult to...
Castle, John, Garrett-Engele, Phil, Armour, Christopher D, Duenwald, Sven J, Loerch, Patrick M, Meyer, Michael R, ...
A novel, unbiased amplification protocol has been developed that permits labeling of entire transcripts. Also, hybridization conditions, probe characteristics, and analysis algorithms were optimized...
Schadt, Eric E, Edwards, Stephen W, GuhaThakurta, Debraj, Holder, Dan, Ying, Lisa, Svetnik, Vladimir, ...
A combination of microarray data with extensive genome annotations resulted in a set of 28,456 experimentally supported transcripts, providing the first experiment-driven annotation of the human...
Kan, Zhengyan, Garrett-Engele, Philip W., Johnson, Jason M., Castle, John C.
To better decipher the functional impact of alternative splicing, we classified alternative splicing events in 10 818 pairs of human and mouse genes based on conservation at genome and transcript...
Young, Juan I., Hong, Eugene P., Castle, John C., Crespo-Barreto, Juan, Bowman, Aaron B., Rose, Matthew F., ...
Rett syndrome (RTT) is a postnatal neurodevelopmental disorder characterized by the loss of acquired motor and language skills, autistic features, and unusual stereotyped movements. RTT is caused by...
RAYMOND, CHRISTOPHER K., ROBERTS, BRIAN S., GARRETT-ENGELE, PHILLIP, LIM, LEE P., JOHNSON, JASON M.
There has been a surge of interest in the biology of microRNAs and the technology of RNA interference. We describe a simple, robust, inexpensive assay for quantitative analysis of microRNAs and...
The Long-term Effects of Gastric Bypass on Vitamin D Metabolism
Johnson, Jason M., Maher, James W., DeMaria, Eric J., Downs, Robert W., Wolfe, Luke G., Kellum, John M.
Routine monitoring of 25-OH-vitamin D and parathormone levels at annuals visits for gastric bypass patients disclosed a high incidence of vitamin D insufficiency and secondary hyperparathyroidism....
Position-specific chemical modification of siRNAs reduces “off-target” transcript silencing
Jackson, Aimee L., Burchard, Julja, Leake, Devin, Reynolds, Angela, Schelter, Janell, Guo, Jie, ...
Transfected siRNAs regulate numerous transcripts sharing limited complementarity to the RNA duplex. This unintended (“off-target”) silencing can hinder the use of RNAi to define gene function....
Levine, David M, Haynor, David R, Castle, John C, Stepaniants, Sergey B, Pellegrini, Matteo, Mao, Mao, ...
A comparison of five different measures of pathway expression and a public map of pathway expression in human tissues are presented.
Transcripts Targeted by the MicroRNA-16 Family Cooperatively Regulate Cell Cycle Progression▿ †
Linsley, Peter S., Schelter, Janell, Burchard, Julja, Kibukawa, Miho, Martin, Melissa M., Bartz, Steven R., ...
microRNAs (miRNAs) are abundant, ∼21-nucleotide, noncoding regulatory RNAs. Each miRNA may regulate hundreds of mRNA targets, but the identities of these targets and the processes they regulate are...
Mapping the Genetic Architecture of Gene Expression in Human Liver
Schadt, Eric E, Molony, Cliona, Chudin, Eugene, Hao, Ke, Yang, Xia, Lum, Pek Y, ...
Genetic variants that are associated with common human diseases do not lead directly to disease, but instead act on intermediate, molecular phenotypes that in turn induce changes in higher-order...
Exon and junction microarrays detect widespread mouse strain- and sex-bias expression differences
Su, Wan-Lin, Modrek, Barmak, GuhaThakurta, Debraj, Edwards, Stephen, Shah, Jyoti K, Kulkarni, Amit V, ...
ACC2 Is Expressed at High Levels Human White Adipose and Has an Isoform with a Novel N-Terminus
Castle, John C., Hara, Yoshikazu, Raymond, Christopher K., Garrett-Engele, Philip, Ohwaki, Kenji, Kan, Zhengyan, ...
Acetyl-CoA carboxylases ACC1 and ACC2 catalyze the carboxylation of acetyl-CoA to malonyl-CoA, regulating fatty-acid synthesis and oxidation, and are potential targets for treatment of metabolic...
Castle, John C., Hara, Yoshikazu, Raymond, Christopher K., Garrett-Engele, Philip, Ohwaki, Kenji, Kan, Zhengyan, ...
A postnatal switch of CELF and MBNL proteins reprograms alternative splicing in the developing heart
Kalsotra, Auinash, Xiao, Xinshu, Ward, Amanda J., Castle, John C., Johnson, Jason M., Burge, Christopher B., ...
From a large-scale screen using splicing microarrays and RT-PCR, we identified 63 alternative splicing (AS) events that are coordinated in 3 distinct temporal patterns during mouse heart development....