An introduction to statistical issues in High throughput screens (2008)
Sabatti, Chiara, Koppany Visnyei, Kornblum, H I
We describe the nature and goals of high-throughput screening experiments, focusing on the challenges they present from the view-point of statistical analysis. We suggest graphical displays to...
Markov models for inferring Copy Number Variations from genotype data (2008)
Hui Wang, Jan Veldink, Roel Opoff, Sabatti, Chiara
We develop an algorithm to analyze data from Illumina genotyping arrays for the detection of copy number variations in a single individual or in a random sample of individuals. We use a Hidden Markov...
Volume measures for linkage disequilibrium (2006)
Chen, Yuguo, Lin, Chia-Ho, Sabatti, Chiara
Abstract Background Defining measures of linkage disequilibrium (LD) that have good small sample properties and are applicable to multiallelic markers poses some challenges. The potential of volume...
Service, Susan, DeYoung, Joseph, Karayiorgou, Maria, Roos, J. Louw, Pretorious, Herman, Bedoya, Gabriel, ...
The genome-wide distribution of linkage disequilibrium (LD) determines the strategy for selecting markers for association studies, but it varies between populations. We assayed LD in large samples...
Service, Susan, DeYoung, Joseph, Karayiorgou, Maria, Roos, J. Louw, Pretorious, Herman, Bedoya, Gabriel, ...
The genome-wide distribution of linkage disequilibrium (LD) determines the strategy for selecting markers for association studies, but it varies between populations. We assayed LD in large samples...
Volume Measures for Linkage Disequilibrium (2006)
Chen, Yuguo, Lin, Chia-Ho, Sabatti, Chiara
We discuss the value of volume measures for linkage disequilibrium, showing how they are robust to small sample variation and easily generalized to multi-allelic markers. In particular we introduce...
Inferring protein domain interactions from databases of interacting proteins (2005)
Riley, Robert, Lee, Christopher, Sabatti, Chiara, Eisenberg, David
Abstract We describe domain pair exclusion analysis (DPEA), a method for inferring domain interactions from databases of interacting proteins. DPEA features a log odds score, E ij , reflecting...
Empirical Bayes Estimation of a Sparse Vector of Gene Expression Changes (2005)
Erickson, Stephen, Sabatti, Chiara
Gene microarray technology is often used to compare the expression of thousand of genes in two different cell lines. Typically, one does not expect measurable changes in transcription amounts for a...
Empirical Bayes Estimation of a Sparse Vector of Gene Expression Changes (2005)
Erickson, Stephen, Sabatti, Chiara
Gene microarray technology is often used to compare the expression of thousand of genes in two different cell lines. Typically, one does not expect measurable changes in transcription amounts for a...
Empirical Bayes Estimation of a Sparse Vector of Gene Expression Changes (2005)
Erickson, Stephen, Sabatti, Chiara
Gene microarray technology is often used to compare the expression of thousand of genes in two different cell lines. Typically, one does not expect measurable changes in transcription amounts for a...
Empirical Bayes Estimation of a Sparse Vector of Gene Expression Changes (2005)
Erickson, Stephen, Sabatti, Chiara
Gene microarray technology is often used to compare the expression of thousand of genes in two different cell lines. Typically, one does not expect measurable changes in transcription amounts for a...
Inferring genomic loss and location of tumor suppressor genes from high density genotypes (2005)
Wang, Hui, Lee, Yohan, Nelson, Stanley, Sabatti, Chiara
Novel technologies, such as the 10k Affymetrix genotyping array, allow scoring of genetic polymorphisms at a very high density across the genome. This allows researchers to conduct traditional...
Bayesian Gaussian Mixture Models for High Density Genotyping Arrays (2005)
Sabatti, Chiara, Lange, Kenneth
Affymetrix's SNP (single nucleotide polymorphism) genotyping chips have increased the scope and decreased the cost of gene mapping studies. Because each SNP is queried by mul- tiple DNA probes, the...
Reconstructing Ancestral Haplotypes with a Dictionary Model (2005)
Ayers, Kristen L, Sabatti, Chiara, Lange, Kenneth
We propose a dictionary model for haplotypes. According to the model, a haplotype is con- structed by randomly concatenating haplotype segments from a given dictionary of segments. A haplotype block...
Bayesian Sparse Hidden Components Analysis for Transcription Regulation Networks (2005)
Sabatti, Chiara, James, Gareth
We describe a framework where DNA sequence information and expression arrays data are used in concert to analyze the effects of a collection of regulatory proteins on genomic expres- sion levels. The...
Empirical Bayes estimation of a sparse vector of gene expression changes (2005)
Erickson, Stephen W, Sabatti, Chiara
Gene microarray technology is often used to compare the expression of thousand of genes in two different cell lines. Typically, one does not expect measurable changes in transcription amounts for a...
A Vocabulon Study of E.Coli Regulatory Sites with Feedback to Expression Array Analysis (2003)
The identification of binding sites for regulatory proteins in the up-stream region of genes is an important ingredient towards the understanding of transcription regulation. In recent years, novel...
Genomewide Motif Identification Using a Dictionary Model (2002)
Sabatti, Chiara, Lange, Kenneth
This paper surveys and extends models and algorithms for identifying binding sites in non-coding regions of DNA. These sites control the transcription of genes into messenger RNA in preparation for...
Sabatti, Chiara, Service, Susan, Freimer, Nelson
Population based linkage disequilibrium genome screens represent one of the most recent approaches for the lo- calization of genes responsible for complex diseases. One open problem in this context...
Thresholding Rules for Recovering a Sparse Signal From Microarray Experiments (2001)
Chiara Sabatti, Stanislav L. Karsten, Daniel Geschwind
We consider array experiments that compare expression levels of a high number of genes in two cell lines with few repetitions and with no subject e#ect. We develop a statistical model that...
Thresholding rules for recovering a sparse signal from microarray experiments (2001)
Sabatti, Chiara, Karsten, Stanislav L., Geschwind, Daniel
We consider array experiments that compare expression levels of a high number of genes in two cell lines with few repetitions and with no subject effect. We develop a statistical model that...
Bayesian Analysis of Haplotypes for Linkage Disequilibrium Mapping (2000)
Jun S. Liu, Chiara Sabatti, Jun Teng
Haplotype analysis of disease chromosomes can help identify probable historical recombination events and, consequently, localize a disease gene. Most available analyses use only marginal and pairwise...
Group transformations and dimensionality reduction in transition rules for MCMC / (1998)
Submitted to the Department of Statistics.
Karsten, Stanislav L., Sabatti, Chiara, Gill, Lisa H., Geschwind, Daniel H.
Archival formalin-fixed, paraffin-embedded and ethanol-fixed tissues represent a potentially invaluable resource for gene expression analysis, as they are the most widely available material for...
Co-expression pattern from DNA microarray experiments as a tool for operon prediction
Sabatti, Chiara, Rohlin, Lars, Oh, Min-Kyu, Liao, James C.
The prediction of operons, the smallest unit of transcription in prokaryotes, is the first step towards reconstruction of a regulatory network at the whole genome level. Sequence information, in...
Network component analysis: Reconstruction of regulatory signals in biological systems
Liao, James C., Boscolo, Riccardo, Yang, Young-Lyeol, Tran, Linh My, Sabatti, Chiara, Roychowdhury, Vwani P.
High-dimensional data sets generated by high-throughput technologies, such as DNA microarray, are often the outputs of complex networked systems driven by hidden regulatory signals. Traditional...
Bayesian Analysis of Haplotypes for Linkage Disequilibrium Mapping
Liu, Jun S., Sabatti, Chiara, Teng, Jun, Keats, Bronya J.B., Risch, Neil
Haplotype analysis of disease chromosomes can help identify probable historical recombination events and localize disease mutations. Most available analyses use only marginal and pairwise allele...
Kao, Katy C., Yang, Young-Lyeol, Boscolo, Riccardo, Sabatti, Chiara, Roychowdhury, Vwani, Liao, James C.
Cells adjust gene expression profiles in response to environmental and physiological changes through a series of signal transduction pathways. Upon activation or deactivation, the terminal regulators...
Inferring protein domain interactions from databases of interacting proteins
Riley, Robert, Lee, Christopher, Sabatti, Chiara, Eisenberg, David
A new method for inferring domain interactions from databases of interacting proteins was used to deduce 3,005 high-confidence domain interactions from over 177,000 potential interactions.
Homozygosity and linkage disequilibrium.
We illustrate how homozygosity of haplotypes can be used to measure the level of disequilibrium between two or more markers. An excess of either homozygosity or heterozygosity signals a departure...
False discovery rate in linkage and association genome screens for complex disorders.
Sabatti, Chiara, Service, Susan, Freimer, Nelson
We explore the implications of the false discovery rate (FDR) controlling procedure in disease gene mapping. With the aid of simulations, we show how, under models commonly used, the simple step-down...
Karsten, Stanislav L., Sabatti, Chiara, Gill, Lisa H., Geschwind, Daniel H.
Archival formalin-fixed, paraffin-embedded and ethanol-fixed tissues represent a potentially invaluable resource for gene expression analysis, as they are the most widely available material for...
Co-expression pattern from DNA microarray experiments as a tool for operon prediction
Sabatti, Chiara, Rohlin, Lars, Oh, Min-Kyu, Liao, James C.
The prediction of operons, the smallest unit of transcription in prokaryotes, is the first step towards reconstruction of a regulatory network at the whole genome level. Sequence information, in...
Network component analysis: Reconstruction of regulatory signals in biological systems
Liao, James C., Boscolo, Riccardo, Yang, Young-Lyeol, Tran, Linh My, Sabatti, Chiara, Roychowdhury, Vwani P.
High-dimensional data sets generated by high-throughput technologies, such as DNA microarray, are often the outputs of complex networked systems driven by hidden regulatory signals. Traditional...
Bayesian Analysis of Haplotypes for Linkage Disequilibrium Mapping
Liu, Jun S., Sabatti, Chiara, Teng, Jun, Keats, Bronya J.B., Risch, Neil
Haplotype analysis of disease chromosomes can help identify probable historical recombination events and localize disease mutations. Most available analyses use only marginal and pairwise allele...
Kao, Katy C., Yang, Young-Lyeol, Boscolo, Riccardo, Sabatti, Chiara, Roychowdhury, Vwani, Liao, James C.
Cells adjust gene expression profiles in response to environmental and physiological changes through a series of signal transduction pathways. Upon activation or deactivation, the terminal regulators...
Inferring protein domain interactions from databases of interacting proteins
Riley, Robert, Lee, Christopher, Sabatti, Chiara, Eisenberg, David
A new method for inferring domain interactions from databases of interacting proteins was used to deduce 3,005 high-confidence domain interactions from over 177,000 potential interactions.
Homozygosity and linkage disequilibrium.
We illustrate how homozygosity of haplotypes can be used to measure the level of disequilibrium between two or more markers. An excess of either homozygosity or heterozygosity signals a departure...
False discovery rate in linkage and association genome screens for complex disorders.
Sabatti, Chiara, Service, Susan, Freimer, Nelson
We explore the implications of the false discovery rate (FDR) controlling procedure in disease gene mapping. With the aid of simulations, we show how, under models commonly used, the simple step-down...
Empirical Bayes Estimation of a Sparse Vector of Gene Expression Changes
Stephen Erickson, Chiara Sabatti
Gene microarray technology is often used to compare the expression of thousand of genes in two different cell lines. Typically, one does not expect measurable changes in transcription amounts for a...