A Bayesian Variable Selection Approach to Major League Baseball Hitting Metrics (2009)
McShane, Blakeley B., Braunstein, Alexander, Piette, James, Jensen, Shane T.
Numerous statistics have been proposed for the measure of offensive ability in major league baseball. While some of these measures may offer moderate predictive power in certain situations, it is...
Jensen, Shane T, Soi, Sameer, Wang, Li-San
Abstract Background Large-scale statistical analyses have become hallmarks of post-genomic era biological research due to advances in high-throughput assays and the integration of large biological...
Bayesian testing of many hypothesis x many genes: a study of sleep apnea (2009)
Jensen, Shane T, Erkan, Ibrahim, Arnardottir, Erna S, Small, Dylan S
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Bayesian Testing of Many Hypotheses X Many Genes: A Study of Sleep Apnea (2009)
Jensen, Shane T., Erkan, Ibrahim, Arnardottir, Erna S., Small, Dylan S.
Substantial statistical research has recently been devoted to the analysis of large-scale microarray experiments which provide a measure of the simultaneous expression of thousands of genes in a...
Hierarchical Bayesian Modeling of Hitting Performance in Baseball (2009)
Jensen, Shane T., McShane, Blake, Wyner, Abraham J.
We have developed a sophisticated statistical model for predicting the hitting performance of Major League baseball players. The Bayesian paradigm provides a principled method for balancing past...
A transcription factor affinity-based code for mammalian transcription initiation (2009)
Megraw, Molly, Pereira, Fernando, Jensen, Shane T., Ohler, Uwe, Hatzigeorgiou, Artemis G.
The recent arrival of large-scale cap analysis of gene expression (CAGE) data sets in mammals provides a wealth of quantitative information on coding and noncoding RNA polymerase II transcription...
BIOINFORMATICS ORIGINAL PAPER (2008)
Shane T. Jensen, Lei Shen, Jun S. Liu
Vol. 21 no. 20 2005, pages 3832–3839 doi:10.1093/bioinformatics/bti628 Combining phylogenetic motif discovery and motif clustering to predict co-regulated genes
BIOINFORMATICS ORIGINAL PAPER Sequence analysis (2008)
GAME: detecting cis-regulatory elements using a genetic algorithm Vol. 22 no. 13 2006, pages 1577–1584 doi:10.1093/bioinformatics/btl147
1. THE BIOLOGY OF TRANSCRIPTION REGULATION (2008)
Shane T. Jensen, X. Shirley Liu, Qing Zhou, Jun S. Liu, Shane T. Jensen
Abstract. The Bayesian approach together with Markov chain Monte Carlo techniques has provided an attractive solution to many important bioinformatics problems such as multiple sequence alignment,...
Changes in the Distribution of Income Volatility (2008)
Jensen, Shane T., Shore, Stephen H.
Recent research has documented a significant rise in the volatility (e.g., expected squared change) of individual incomes in the U.S. since the 1970s. Existing measures of this trend abstract from...
BIOINFORMATICS ORIGINAL PAPER Sequence analysis (2008)
GAME: detecting cis-regulatory elements using a genetic algorithm Vol. 22 no. 13 2006, pages 1577–1584 doi:10.1093/bioinformatics/btl147
1 Implementation Details for JASPAR and Combined Applications (2008)
Our Bayesian hierarchical clustering model is implemented by a Gibbs sampling program which is available as suite of Perl scripts that can run on any platform which has Perl installed. Our suite of...
An Interaction-Dependent Model for Transcription Factor Binding (2008)
Li-san Wang, Shane T. Jensen, Sridhar Hannenhalli
Abstract. Transcriptional regulation is accomplished by several transcription factor proteins that bind to specific DNA elements in the relative vicinity of the gene, and interact with each other and...
Yan, Bin, Chen, Guang, Saigal, Kunal, Yang, Xinping, Jensen, Shane T, Van Waes, Carter, ...
Abstract Background Aberrant activation of the nuclear factor kappaB (NF- κ B) pathway has been previously implicated as a crucial signal promoting tumorigenesis. However, how NF- κ B acts as a key...
Bayesball: A Bayesian Hierarchical Model for Evaluating Fielding in Major League Baseball (2008)
Jensen, Shane T., Shirley, Kenny, Wyner, Abraham J.
The use of statistical modeling in baseball has received substantial attention recently in both the media and academic community. We focus on a relatively under-explored topic: the use of...
Adaptive Paired Comparison Design (2008)
Mark E. Glickman, Shane T. Jensen
An important aspect of paired comparison experiments is the decision of how to form pairs in advance of collecting data. A weakness of typical paired comparison experimental designs is the diculty in...
Prior Distributions for Partitions in Bayesian Nonparametrics (2008)
Prior distributions for unknown data distributions play an important role in nonparametric Bayesian statistics. A commonly-used prior distribution for an unknown data distribution is the Dirichlet...
Tuteja, Geetu, Jensen, Shane T., White, Peter, Kaestner, Klaus H.
Foxa2 is a critical transcription factor that controls liver development and plays an important role in hepatic gluconeogensis in adult mice. Here, we use genome-wide location analysis for Foxa2 to...
Evaluating Throwing Ability in Baseball (2007)
Carruth, Matthew, Jensen, Shane T.
We present a quantitative analysis of throwing ability for major league outfielders and catchers. We use detailed game event data to tabulate success and failure events in outfielder and catcher...
Clustering of genes into regulons using integrated modeling-COGRIM (2007)
Chen, Guang, Jensen, Shane T, Stoeckert, Christian J
Abstract We present a Bayesian hierarchical model and Gibbs Sampling implementation that integrates gene expression, ChIP binding, and transcription factor motif data in a principled and robust...
Bayesian Clustering of Transcription Factor Binding Motifs (2006)
Genes are often regulated in living cells by proteins called transcription factors (TFs) that bind directly to short segments of DNA in close proximity to specific genes. These binding sites have a...
Bayesian variable selection and data integration for biological regulatory networks (2006)
Jensen, Shane T., Chen, Guang, Stoeckert, Christian J.
A substantial focus of research in molecular biology are gene regulatory networks: the set of transcription factors and target genes which control the involvement of different biological processes in...
MicroRNA promoter element discovery in Arabidopsis (2006)
Megraw, Molly, Baev, Vesselin, Rusinov, Ventsislav, Jensen, Shane T., Kalantidis, Kriton, Hatzigeorgiou, Artemis G.
In this study we present a method of identifying Arabidopsis miRNA promoter elements using known transcription factor binding motifs. We provide a comparative analysis of the representation of these...
GAME: detecting cis-regulatory elements using a genetic algorithm (2006)
Motivation: Identification of a transcription factor binding sites is an important aspect of the analysis of genetic regulation. Many programs have been developed for the de novo discovery of a...
MicroRNA promoter element discovery in Arabidopsis (2006)
Megraw, Molly, Baev, Vesselin, Rusinov, Ventsislav, Jensen, Shane T., Kalantidis, Kriton, Hatzigeorgiou, Artemis G.
In this study we present a method of identifying Arabidopsis miRNA promoter elements using known transcription factor binding motifs. We provide a comparative analysis of the representation of these...
MicroRNA promoter element discovery in Arabidopsis (2006)
Megraw, Molly, Baev, Vesselin, Rusinov, Ventsislav, Jensen, Shane T., Kalantidis, Kriton, Hatzigeorgiou, Artemis G.
In this study we present a method of identifying Arabidopsis miRNA promoter elements using known transcription factor binding motifs. We provide a comparative analysis of the representation of these...
Combining phylogenetic motif discovery and motif clustering to predict co-regulated genes (2005)
Jensen, Shane T., Shen, Lei, Liu, Jun S.
Motivation: We present a sequence-based framework and algorithm PHYLOCLUS for predicting co-regulated genes. In our approach, de novo discovery methods are used to find motifs conserved by evolution...
Combining phylogenetic motif discovery and motif clustering to predict co-regulated genes (2005)
Jensen, Shane T., Shen, Lei, Liu, Jun S.
Motivation: We present a sequence-based framework and algorithm PHYLOCLUS for predicting co-regulated genes. In our approach, de novo discovery methods are used to find motifs conserved by evolution...
Patrick Eichenberger, Masaya Fujita, Shane T. Jensen, Erin M. Conlon, David Z. Rudner, Stephanie T. Wang, ...
A comprehensive genomic analysis of sporulation in Bacillus subtilis reveals a coordinated program of gene activation and repression, which involves 383 genes.
Patrick Eichenberger, Masaya Fujita, Shane T. Jensen, Erin M. Conlon, David Z. Rudner, Stephanie T. Wang, ...
Asymmetric division during sporulation by Bacillus subtilis generates a mother cell that undergoes a 5-h program of differentiation. The program is governed by a hierarchical cascade consisting of...
Computational Discovery of Gene Regulatory Binding Motifs: A Bayesian Perspective (2004)
Jensen, Shane T., Liu, X. Shirley, Zhou, Qing, Liu, Jun S.
The Bayesian approach together with Markov chain Monte Carlo techniques has provided an attractive solution to many important bioinformatics problems such as multiple sequence alignment, microarray...
BioOptimizer: a Bayesian scoring function approach to motif discovery (2004)
Motivation: Transcription factors (TFs) bind directly to short segments on the genome, often within hundreds to thousands of base pairs upstream of gene transcription start sites, to regulate gene...
BioOptimizer: a bayesian scoring function approach to motif discovery (2004)
Motivation: Transcription factors (TF) bind directly to short segments on the genome, often within hundreds to thousands of base pairs upstream of gene transcription start sites, to regulate genes'...
BioOptimizer: a bayesian scoring function approach to motif discovery (2004)
Motivation: Transcription factors (TF) bind directly to short segments on the genome, often within hundreds to thousands of base pairs upstream of gene transcription start sites, to regulate genes'...
Mark F. Lenzenweger, Shane T. Jensen, Donald B. Rubin
Heterogeneity in the performance of persons affected with schizophrenia or schizotypic psychopathology on various laboratory tasks has long been recognized, both for its consistency across tasks and...
Thesis title: “Statistical methods for elucidating cell regulation” Winner of the Leonard J. Savage Award for best thesis in application methodology from the International Society for Bayesian...
Eichenberger, Patrick, Fujita, Masaya, Jensen, Shane T, Conlon, Erin M, Rudner, David Z, Wang, Stephanie T, ...
Asymmetric division during sporulation by Bacillus subtilis generates a mother cell that undergoes a 5-h program of differentiation. The program is governed by a hierarchical cascade consisting of...
Eichenberger, Patrick, Fujita, Masaya, Jensen, Shane T, Conlon, Erin M, Rudner, David Z, Wang, Stephanie T, ...
Asymmetric division during sporulation by Bacillus subtilis generates a mother cell that undergoes a 5-h program of differentiation. The program is governed by a hierarchical cascade consisting of...
MicroRNA promoter element discovery in Arabidopsis
Megraw, Molly, Baev, Vesselin, Rusinov, Ventsislav, Jensen, Shane T., Kalantidis, Kriton, Hatzigeorgiou, Artemis G.
In this study we present a method of identifying Arabidopsis miRNA promoter elements using known transcription factor binding motifs. We provide a comparative analysis of the representation of these...
Clustering of genes into regulons using integrated modeling-COGRIM
Chen, Guang, Jensen, Shane T, Stoeckert, Christian J
COGRIM, an implementation that integrates gene expression, ChIP binding and transcription factor motif data, is described and applied to both unicellular and mammalian organisms.
Yan, Bin, Chen, Guang, Saigal, Kunal, Yang, Xinping, Jensen, Shane T, Van Waes, Carter, ...
Detailed analysis of NFκB regulons in 1,265 genes differentially expressed in head and neck cancer cell lines differing in p53 status revealed a cross talk between NFkB and specific signaling...
Tuteja, Geetu, Jensen, Shane T., White, Peter, Kaestner, Klaus H.
Foxa2 is a critical transcription factor that controls liver development and plays an important role in hepatic gluconeogensis in adult mice. Here, we use genome-wide location analysis for Foxa2 to...
Changes in the Distribution of Income Volatility
Shane T. Jensen, Stephen H. Shore
Recent research has documented a significant rise in the volatility (e.g., expected squared change) of individual incomes in the U.S. since the 1970s. Existing measures of this trend abstract from...
A transcription factor affinity-based code for mammalian transcription initiation
Megraw, Molly, Pereira, Fernando, Jensen, Shane T., Ohler, Uwe, Hatzigeorgiou, Artemis G.
The recent arrival of large-scale cap analysis of gene expression (CAGE) data sets in mammals provides a wealth of quantitative information on coding and noncoding RNA polymerase II transcription...