Nicola Rinaldi

Nicola Rinaldi
Massachusetts Institute of Technology | MIT · Department of Biology

22.86
 · 
PhD
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Introduction
Currently a stay-at-home mom, working on a book about hypothalamic amenorrhea, tentatively titled, "No Period. Now What? -- A Guide to Recovering Your Health and Fertility"
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Research items (12)
Article
Transforming growth factor (TGF)-beta has a central role in driving many of the pathological processes that characterize pulmonary fibrosis. Inhibition of the integrin alpha(v)beta6, a key activator of TGF-beta in lung, is an attractive therapeutic strategy, as it may be possible to inhibit TGF-beta at sites of alpha(v)beta6 up-regulation without a...
Article
Chromatin regulators play fundamental roles in the regulation of gene expression and chromosome maintenance, but the regions of the genome where most of these regulators function has not been established. We explored the genome-wide occupancy of four different chromatin regulators encoded in Saccharomyces cerevisiae. The results reveal that the his...
Article
Full-text available
DNA-binding transcriptional regulators interpret the genome's regulatory code by binding to specific sequences to induce or repress gene expression. Comparative genomics has recently been used to identify potential cis-regulatory sequences within the yeast genome on the basis of phylogenetic conservation, but this information alone does not reveal...
Article
The transcriptional regulatory networks that specify and maintain human tissue diversity are largely uncharted. To gain insight into this circuitry, we used chromatin immunoprecipitation combined with promoter microarrays to identify systematically the genes occupied by the transcriptional regulators HNF1alpha, HNF4alpha, and HNF6, together with RN...
Article
Full-text available
We describe an algorithm for discovering regulatory networks of gene modules, GRAM (Genetic Regulatory Modules), that combines information from genome-wide location and expression data sets. A gene module is defined as a set of coexpressed genes to which the same set of transcription factors binds. Unlike previous approaches that relied primarily o...
Article
Gene arrays demonstrate a promising ability to characterize expression levels across the entire genome but suffer from significant levels of measurement noise. We present a rigorous new approach to estimate transcript levels and ratios from one or more gene array experiments, given a model of measurement noise and available prior information. The B...
Article
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We have determined how most of the transcriptional regulators encoded in the eukaryote Saccharomyces cerevisiaeassociate with genes across the genome in living cells. Just as maps of metabolic networks describe the potential pathways that may be used by a cell to accomplish metabolic processes, this network of regulator-gene interactions describes...
Article
Gene arrays demonstrate a promising ability to characterize expression levels across the entire genome, but they su#er from significant levels of measurement noise. We present a statistical technique to estimate transcript levels or transcript level ratios from one or more gene array experiments, incorporating a model of measurement noise and prior...
Conference Paper
We present a new statistically optimal approach to estimate transcript levels and ratios from one or more gene array experiments. The Bayesian Estimation of Array Measurements (BEAM) technique uses a model of measurement noise and prior information to estimate biological expression levels. It provides a principled method to deal with negative expre...
Article
Genome-wide location analysis was used to determine how the yeast cell cycle gene expression program is regulated by each of the nine known cell cycle transcriptional activators. We found that cell cycle transcriptional activators that function during one stage of the cell cycle regulate transcriptional activators that function during the next stag...
Article
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METHODS Epitope Tagging of Strains Regulators were tagged by inserting multiple copies of the Myc epitope coding sequence into the normal chomosomal loci of these genes. The plasmid pWZV88 (1) was used as a template to generate PCR products containing the Myc epitope coding sequence and a selectable marker (TRP) flanked by homologous regions design...