Eugenia Galeota

Eugenia Galeota
Istituto Italiano di Tecnologia | IIT · Center for Genomic Science

Postdoc/PhD Bioinformatics, MD Computer Science

About

26
Publications
4,416
Reads
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2,801
Citations
Additional affiliations
June 2014 - present
Istituto Italiano di Tecnologia
Position
  • PostDoc Position
Description
  • Semantic annotation of public data repositories to for the representation and analysis of large-scale epigenomics, transcriptional and regulatory NGS data
November 2013 - May 2014
San Raffaele Scientific Institute
Position
  • PostDoc Position
Description
  • Statistical analysis of public data (microarray experiments, copy number alterations, SNPs) to understand the involvement of the immune system in Cancer.
November 2009 - October 2013
University of Rome Tor Vergata
Position
  • PhD Student
Description
  • Analysis of protein-protein interaction networks and the dynamics of complex formation in self-organizing virtual cells.
Education
March 2006 - March 2008
Università degli Studi di Salerno
Field of study
  • Computer Science

Publications

Publications (26)
Article
Full-text available
Intracranial aneurysms (IAs) are very rare in children, and the characteristics of the T-cells in the IA wall are largely unknown. A comatose 7-years-old child was admitted to our center because of a subarachnoid hemorrhage due to a ruptured giant aneurysm of the right middle cerebral artery. Two days after the aneurysm clipping the patient was ful...
Article
Motivation Approaches such as chromatin immunoprecipitation followed by sequencing (ChIP-seq) represent the standard for the identification of binding sites of DNA-associated proteins, including transcription factors and histone marks. Public repositories of omics data contain a huge number of experimental ChIP-seq data, but their reuse and integra...
Article
Full-text available
To understand how a protective immune response against SARS-CoV-2 develops over time, we integrated phenotypic, transcriptional, and repertoire analyses on PBMCs from patients with mild and severe COVID-19 during and after infection and compared them to healthy donors (HDs). A type I IFN response signature marked all the immune populations from sev...
Article
The quantification of the kinetic rates of RNA synthesis, processing, and degradation are largely based on the integrative analysis of total and nascent transcription, the latter being quantified through RNA metabolic labeling. We developed INSPEcT-, a computational method based on the mathematical modeling of premature and mature RNA expression th...
Article
Full-text available
Public repositories of large-scale omics datasets represent a valuable resource for researchers. In fact, data re-analysis can either answer novel questions or provide critical data able to complement in-house experiments. However, despite the development of standards for the compilation of metadata, the identification and organization of samples s...
Article
Full-text available
The histone demethylase LSD1 is a key chromatin regulator that is often deregulated in cancer. Its ortholog, dLsd1 plays a crucial role in Drosophila oogenesis; however, our knowledge of dLsd1 function is insufficient to explain its role in the ovary. Here, we have performed genome-wide analysis of dLsd1 binding in the ovary, and we document that d...
Preprint
Full-text available
The kinetic rates of RNA synthesis, processing and degradation determine the dynamics of transcriptional regulation by governing both the abundance and the responsiveness to modulations of premature and mature RNA species. The study of RNA dynamics is largely based on the integrative analysis of total and nascent transcription, with the latter bein...
Article
Full-text available
N6-methyladenosine (m6A) is the most abundant RNA modification. It has been involved in the regulation of RNA metabolism, including degradation and translation, in both physiological and disease conditions. A recent study showed that m6A-mediated degradation of key transcripts also plays a role in the control of T cells homeostasis and IL-7 induced...
Article
Full-text available
Public repositories of large-scale biological data currently contain hundreds of thousands of experiments, including high-throughput sequencing and microarray data. The potential of using these resources to assemble data sets combining samples previously not associated is vastly unexplored. This requires the ability to associate samples with clear...
Article
Full-text available
Next-generation sequencing (NGS) technologies have deeply changed our understanding of cellular processes by delivering an astonishing amount of data at affordable prices; nowadays, many biology laboratories have already accumulated a large number of sequenced samples. However, managing and analyzing these data poses new challenges, which may easil...
Article
Full-text available
Background: To investigate in the NeoSphere trial the contribution of the immune system to pathological complete response in breast (pCRB) after neoadjuvant docetaxel with trastuzumab (TH), pertuzumab (TP) or both (THP), or monoclonal antibodies alone (HP). Patients and methods: Immune-gene mRNA expression (n=350, 83,8%), lymphocyte-infiltration...
Article
Full-text available
Cell organization is governed and maintained via specific interactions among its constituent macromolecules. Comparison of the experimentally determined protein interaction networks in different model organisms has revealed little conservation of the specific edges linking ortholog proteins. Nevertheless, some topological characteristics of the gra...
Conference Paper
Background: Genomic studies in estrogen-receptor (ER) positive breast cancer showed few commonly mutated genes and suggested that tumors with higher background of mutation rate were enriched in intrinsic aromatase-inhibitor-resistant tumors (Ellis MJ Nature 2012). Different combinations of proliferation (PROL) and estrogen-receptor related genes (E...
Article
Full-text available
IntAct (freely available at http://www.ebi.ac.uk/intact) is an open-source, open data molecular interaction database populated by data either curated from the literature or from direct data depositions. IntAct has developed a sophisticated web-based curation tool, capable of supporting both IMEx- and MIMIx-level curation. This tool is now utilized...
Article
Full-text available
The Proteomics Standard Initiative Common QUery InterfaCe (PSICQUIC) specification was created by the Human Proteome Organization Proteomics Standards Initiative (HUPO-PSI) to enable computational access to molecular-interaction data resources by means of a standard Web Service and query language. Currently providing >150 million binary interaction...
Article
Full-text available
The Molecular INTeraction Database (MINT, http://mint.bio.uniroma2.it/mint/) is a public repository for protein–protein interactions (PPI) reported in peer-reviewed journals. The database grows steadily over the years and at September 2011 contains approximately 235 000 binary interactions captured from over 4750 publications. The web interface all...
Article
Full-text available
One of the most pressing and interesting actual scientific challenges deals with the analysis and the understanding of complex network dynamics. In particular, a major trend is the definition of new frameworks for the analysis, the exploration and the detection of the dynamics at play in real dynamic networks. In this paper, we focus in particular...
Article
To study proteins in the context of a cellular system, it is essential that the molecules with which a protein interacts are identified and the functional consequence of each interaction is understood. A plethora of resources now exist to capture molecular interaction data from the many laboratories generating…

Questions

Question (1)
Question
I'm plotting a dataframe with the following commands:
pd <- position_dodge(width=0.4, height=NULL)
pl <- ggplot(mergendataframe, aes(VariableName, Coefficient, color=ModelName))
pl <- pl + geom_point(aes(shape=ModelName), size=4, position=pd)
I used the following lines to change axis text in bold and set a longer value for the ticks
pl <- pl + opts(axis.text.x = theme_text(face="bold"))
pl <- pl + opts(axis.text.y = theme_text(face="bold"))
pl <- pl+opts(axis.ticks.length=unit(0.5,"cm"))
if I try with
opts(axis.ticks.x = element_line(colour = 'red', size = 3, linetype = 'dashed'))
I get no element_line function error.

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