Human-macaque comparisons illuminate variation in neutral substitution rates (2008)
Tyekucheva, Svitlana, Makova, Kateryna D, Karro, John E, Hardison, Ross C, Miller, Webb, Chiaromonte, Francesca
Abstract Background The evolutionary distance between human and macaque is particularly attractive for investigating local variation in neutral substitution rates, because substitutions can be...
A Macaque's-Eye View of Human Insertions and Deletions: Differences in Mechanisms (2007)
Erika M. Kvikstad, Svitlana Tyekucheva, Francesca Chiaromonte, Kateryna D. Makova
Insertions and deletions (indels) cause numerous genetic diseases and lead to pronounced evolutionary differences among genomes. The macaque sequences provide an opportunity to gain insights into the...
A macaque's-eye view of human insertions and deletions: differences in mechanisms (2007)
Erika M. Kvikstad, Svitlana Tyekucheva, Francesca Chiaromonte, Kateryna Makova
Insertions and deletions (indels) cause numerous genetic diseases and lead to pronounced evolutionary differences among genomes. The macaque sequences provide an opportunity to gain insights into the...
Gutiérrez, Rodrigo A, Lejay, Laurence V, Dean, Alexis, Chiaromonte, Francesca, Shasha, Dennis E, Coruzzi, Gloria M
Abstract Background Carbon (C) and nitrogen (N) metabolites can regulate gene expression in Arabidopsis thaliana . Here, we use multinetwork analysis of microarray data to identify molecular networks...
Genomic Environment Predicts Expression Patterns on the Human Inactive X Chromosome (2006)
Laura Carrel, Chungoo Park, Svitlana Tyekucheva, John Dunn, Francesca Chiaromonte, Kateryna D. Makova
What genomic landmarks render most genes silent while leaving others expressed on the inactive X chromosome in mammalian females? To date, signals determining expression status of genes on the...
Genomic Environment Predicts Expression Patterns on the Human Inactive X Chromosome (2006)
Laura Carrel, Chungoo Park, Svitlana Tyekucheva, John Dunn, Francesca Chiaromonte, Kateryna Makova
What genomic landmarks render most genes silent while leaving others expressed on the inactive X chromosome in mammalian females? To date, signals determining expression status of genes on the...
Genomic environment predicts expression patterns on the human inactive X chromosome. (2006)
Carrel, Laura, Park, Chungoo, Tyekucheva, Svitlana, Dunn, John, Chiaromonte, Francesca, Makova, Kateryna D, ...
What genomic landmarks render most genes silent while leaving others expressed on the inactive X chromosome in mammalian females? To date, signals determining expression status of genes on the...
Contour regression: A general approach to dimension reduction (2005)
Li, Bing, Zha, Hongyuan, Chiaromonte, Francesca
We propose a novel approach to sufficient dimension reduction in regression, based on estimating contour directions of small variation in the response. These directions span the orthogonal complement...
Contour regression: A general approach to dimension reduction (2005)
Li, Bing, Zha, Hongyuan, Chiaromonte, Francesca
We propose a novel approach to sufficient dimension reduction in regression, based on estimating contour directions of small variation in the response. These directions span the orthogonal complement...
Dimension reduction for the conditional mean in regressions with categorical predictors (2003)
Li, Bing, Cook, R. Dennis, Chiaromonte, Francesca
Consider the regression of a response Y on a vector of quantitative predictors $\X$ and a categorical predictor W. In this article we describe a first method for reducing the dimension of $\X$...
Clustering of Expression Data from Microarrays: (2002)
Francesco Bartolucci, Francesca Chiaromonte
A central aim of many statistical analyses of microarray data is to cluster genes according to their similarity in expression behavior. In this paper, we perform clustering based on the likelihood...
Sufficient dimensions reduction in regressions with categorical predictors (2002)
Chiaromonte, Francesca, Cook, R. Dennis, Li, Bing
In this article, we describe how the theory of sufficient dimension reduction, and a well-known inference method for it (sliced inverse regression), can be extended to regression analyses involving...
On Multivariate Structures and Exhaustive Reductions (1999)
Francesca Chiaromonte, Giovanni Dosi
Simplified representations of multivariate laws, and in particular those allowing one to decrease the dimension while preserving structural information, are of paramount importance in statistical...
Some Preliminary Experiments with the Financial "Toy-Room" (1999)
Francesca Chiaromonte, Mariele Bert E, Giovanni Dosi
We describe some preliminary experiments realized with the Financial "Toy-Room" (a microfounded simulation environment for decentralized trade in a homogeneous financial asset). The experiments are...
A Reduction Paradigm for Multivariate Laws (1997)
Francesca Chiaromonte, Giovanni Dosi
A reduction paradigm is a theoretical framework which provides a definition of structure for multivariate laws, and allows to simplify their representation and statistical analysis. The main idea is...
A reduction paradigm for multivariate laws /--by Francesca Chiaromonte. (1996)
Thesis (Ph. D.)--University of Minnesota, 1996.
Modeling a Decentralized Asset Market: An Introduction to the Financial "Toy-Room"
Francesca Chiaromonte, Giovanni Dosi
In this paper, we describe a micro-founded simulation enviroment for decentralized trade in financial asset. Within the philosophy of computer simulated "artificial markets", this enviroments allows...
A Speculative Centralized Asset Market with Adaptive Heterogenous Agents
Francesca Chiaromonte, Nicolas Jonard, Giovanni Dosi
-
Association between divergence and interspersed repeats in mammalian noncoding genomic DNA
Chiaromonte, Francesca, Yang, Shan, Elnitski, Laura, Yap, Von Bing, Miller, Webb, Hardison, Ross C.
The amount of noncoding genomic DNA sequence that aligns between human and mouse varies substantially in different regions of their genomes, and the amount of repetitive DNA also varies. In this...
Patterns of Insertions and Their Covariation With Substitutions in the Rat, Mouse, and Human Genomes
Yang, Shan, Smit, Arian F., Schwartz, Scott, Chiaromonte, Francesca, Roskin, Krishna M., Haussler, David, ...
The rates at which human genomic DNA changes by neutral substitution and insertion of certain families of transposable elements covary in large, megabase-sized segments. We used the rat, mouse, and...
Insertions and Deletions Are Male Biased Too: A Whole-Genome Analysis in Rodents
Makova, Kateryna D., Yang, Shan, Chiaromonte, Francesca
It is presently accepted that, in mammals, due to the greater number of cell divisions in the male germline than in the female germline, nucleotide substitutions occur more frequently in males. The...
Regulatory Potential Scores From Genome-Wide Three-Way Alignments of Human, Mouse, and Rat
Kolbe, Diana, Taylor, James, Elnitski, Laura, Eswara, Pallavi, Li, Jia, Miller, Webb, ...
We generalize the computation of the Regulatory Potential (RP) score from two-way alignments of human and mouse to three-way alignments of human, mouse, and rat. This requires overcoming technical...
Gene Length and Proximity to Neighbors Affect Genome-Wide Expression Levels
Chiaromonte, Francesca, Miller, Webb
Steady-state levels of mRNA in cells theoretically depend on the rate and efficiency of transcription and posttranscriptional processing, on mRNA stability, on transcriptional interference from other...
Hardison, Ross C., Roskin, Krishna M., Yang, Shan, Diekhans, Mark, Kent, W. James, Weber, Ryan, ...
Six measures of evolutionary change in the human genome were studied, three derived from the aligned human and mouse genomes in conjunction with the Mouse Genome Sequencing Consortium, consisting of...
Distinguishing Regulatory DNA From Neutral Sites
Elnitski, Laura, Hardison, Ross C., Li, Jia, Yang, Shan, Kolbe, Diana, Eswara, Pallavi, ...
We explore several computational approaches to analyzing interspecies genomic sequence alignments, aiming to distinguish regulatory regions from neutrally evolving DNA. Human–mouse genomic...
King, David C., Taylor, James, Elnitski, Laura, Chiaromonte, Francesca, Miller, Webb, Hardison, Ross C.
Techniques of comparative genomics are being used to identify candidate functional DNA sequences, and objective evaluations are needed to assess their effectiveness. Different analytical methods...
Genomic Environment Predicts Expression Patterns on the Human Inactive X Chromosome
Carrel, Laura, Park, Chungoo, Tyekucheva, Svitlana, Dunn, John, Chiaromonte, Francesca, Makova, Kateryna D
What genomic landmarks render most genes silent while leaving others expressed on the inactive X chromosome in mammalian females? To date, signals determining expression status of genes on the...
Association between divergence and interspersed repeats in mammalian noncoding genomic DNA
Chiaromonte, Francesca, Yang, Shan, Elnitski, Laura, Yap, Von Bing, Miller, Webb, Hardison, Ross C.
The amount of noncoding genomic DNA sequence that aligns between human and mouse varies substantially in different regions of their genomes, and the amount of repetitive DNA also varies. In this...
Patterns of Insertions and Their Covariation With Substitutions in the Rat, Mouse, and Human Genomes
Yang, Shan, Smit, Arian F., Schwartz, Scott, Chiaromonte, Francesca, Roskin, Krishna M., Haussler, David, ...
The rates at which human genomic DNA changes by neutral substitution and insertion of certain families of transposable elements covary in large, megabase-sized segments. We used the rat, mouse, and...
Insertions and Deletions Are Male Biased Too: A Whole-Genome Analysis in Rodents
Makova, Kateryna D., Yang, Shan, Chiaromonte, Francesca
It is presently accepted that, in mammals, due to the greater number of cell divisions in the male germline than in the female germline, nucleotide substitutions occur more frequently in males. The...
Regulatory Potential Scores From Genome-Wide Three-Way Alignments of Human, Mouse, and Rat
Kolbe, Diana, Taylor, James, Elnitski, Laura, Eswara, Pallavi, Li, Jia, Miller, Webb, ...
We generalize the computation of the Regulatory Potential (RP) score from two-way alignments of human and mouse to three-way alignments of human, mouse, and rat. This requires overcoming technical...
Gene Length and Proximity to Neighbors Affect Genome-Wide Expression Levels
Chiaromonte, Francesca, Miller, Webb
Steady-state levels of mRNA in cells theoretically depend on the rate and efficiency of transcription and posttranscriptional processing, on mRNA stability, on transcriptional interference from other...
Hardison, Ross C., Roskin, Krishna M., Yang, Shan, Diekhans, Mark, Kent, W. James, Weber, Ryan, ...
Six measures of evolutionary change in the human genome were studied, three derived from the aligned human and mouse genomes in conjunction with the Mouse Genome Sequencing Consortium, consisting of...
Distinguishing Regulatory DNA From Neutral Sites
Elnitski, Laura, Hardison, Ross C., Li, Jia, Yang, Shan, Kolbe, Diana, Eswara, Pallavi, ...
We explore several computational approaches to analyzing interspecies genomic sequence alignments, aiming to distinguish regulatory regions from neutrally evolving DNA. Human–mouse genomic...
King, David C., Taylor, James, Elnitski, Laura, Chiaromonte, Francesca, Miller, Webb, Hardison, Ross C.
Techniques of comparative genomics are being used to identify candidate functional DNA sequences, and objective evaluations are needed to assess their effectiveness. Different analytical methods...
Genomic Environment Predicts Expression Patterns on the Human Inactive X Chromosome
Carrel, Laura, Park, Chungoo, Tyekucheva, Svitlana, Dunn, John, Chiaromonte, Francesca, Makova, Kateryna D
What genomic landmarks render most genes silent while leaving others expressed on the inactive X chromosome in mammalian females? To date, signals determining expression status of genes on the...
Gutiérrez, Rodrigo A, Lejay, Laurence V, Dean, Alexis, Chiaromonte, Francesca, Shasha, Dennis E, Coruzzi, Gloria M
Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis and indicate that regulation by carbon/nitrogen metabolites occurs at...
Experimental validation of predicted mammalian erythroid cis-regulatory modules
Wang, Hao, Zhang, Ying, Cheng, Yong, Zhou, Yuepin, King, David C., Taylor, James, ...
Multiple alignments of genome sequences are helpful guides to functional analysis, but predicting cis-regulatory modules (CRMs) accurately from such alignments remains an elusive goal. We predict...
Taylor, James, Tyekucheva, Svitlana, King, David C., Hardison, Ross C., Miller, Webb, Chiaromonte, Francesca
Genomic sequence signals—such as base composition, presence of particular motifs, or evolutionary constraint—have been used effectively to identify functional elements. However, approaches based...
A Macaque's-Eye View of Human Insertions and Deletions: Differences in Mechanisms
Kvikstad, Erika M, Tyekucheva, Svitlana, Chiaromonte, Francesca, Makova, Kateryna D
Insertions and deletions (indels) cause numerous genetic diseases and lead to pronounced evolutionary differences among genomes. The macaque sequences provide an opportunity to gain insights into the...
Finding cis-regulatory elements using comparative genomics: Some lessons from ENCODE data
King, David C., Taylor, James, Zhang, Ying, Cheng, Yong, Lawson, Heather A., Martin, Joel, ...
Identification of functional genomic regions using interspecies comparison will be most effective when the full span of relationships between genomic function and evolutionary constraint are...
Augmenting the bootstrap to analyze high dimensional genomic data
Svitlana Tyekucheva, Francesca Chiaromonte
Inverse covariance, Large-p-small-n , Resampling, Genomics, 62G09, 62P10,
The genome-wide determinants of human and chimpanzee microsatellite evolution
Kelkar, Yogeshwar D., Tyekucheva, Svitlana, Chiaromonte, Francesca, Makova, Kateryna D.
Mutation rates of microsatellites vary greatly among loci. The causes of this heterogeneity remain largely enigmatic yet are crucial for understanding numerous human neurological diseases and genetic...
Dimension reduction in regression without matrix inversion
Bing Li, Francesca Chiaromonte
Regressions in which the fixed number of predictors p exceeds the number of independent observational units n occur in a variety of scientific fields. Sufficient dimension reduction provides a...
Sufficient Dimension Reduction and Graphics in Regression
Francesca Chiaromonte, R. Cook
Sufficient dimension reduction, graphical displays, regression analysis,