Search results for "genomic data"

Genomic Testing for Human Health and Disease Across the Life Cycle: Applications and Ethical, Legal, and Social Challenges

2019

The expanding use of genomic technologies encompasses all phases of life, from the embryo to the elderly, and even the posthumous phase. In this paper, we present the spectrum of genomic healthcare applications, and describe their scope and challenges at different stages of the life cycle. The integration of genomic technology into healthcare presents unique ethical issues that challenge traditional aspects of healthcare delivery. These challenges include the different definitions of utility as applied to genomic information; the particular characteristics of genetic data that influence how it might be protected, used and shared; and the difficulties applying existing models of informed con…

Pathway network inference from gene expression data

2014

[EN] Background: The development of high-throughput omics technologies enabled genome-wide measurements of the activity of cellular elements and provides the analytical resources for the progress of the Systems Biology discipline. Analysis and interpretation of gene expression data has evolved from the gene to the pathway and interaction level, i.e. from the detection of differentially expressed genes, to the establishment of gene interaction networks and the identification of enriched functional categories. Still, the understanding of biological systems requires a further level of analysis that addresses the characterization of the interaction between functional modules. Results: We presen…

Ancestry and demography and descendants of Iron Age nomads of the Eurasian Steppe

2017

During the 1st millennium before the Common Era (BCE), nomadic tribes associated with the Iron Age Scythian culture spread over the Eurasian Steppe, covering a territory of more than 3,500 km in breadth. To understand the demographic processes behind the spread of the Scythian culture, we analysed genomic data from eight individuals and a mitochondrial dataset of 96 individuals originating in eastern and western parts of the Eurasian Steppe. Genomic inference reveals that Scythians in the east and the west of the steppe zone can best be described as a mixture of Yamnaya-related ancestry and an East Asian component. Demographic modelling suggests independent origins for eastern and western g…

Genomic Databases Characteristics

2013

Penalized regression and clustering in high-dimensional data

The main goal of this Thesis is to describe numerous statistical techniques that deal with high-dimensional genomic data. The Thesis begins with a review of the literature on penalized regression models, with particular attention to least absolute shrinkage and selection operator (LASSO) or L1-penalty methods. L1 logistic/multinomial regression models are used for variable selection and discriminant analysis with a binary/categorical response variable. The Thesis discusses and compares several methods that are commonly utilized in genetics, and introduces new strategies to select markers according to their informative content and to discriminate clusters by offering reduced panels for popul…

A Common Genetic Origin for Early Farmers from Mediterranean Cardial and Central European LBK Cultures

2015

Olalde, Iñigo et al.

Ten millennia of hepatitis B virus evolution

2021

Hepatitis B virus (HBV) has been infecting humans for millennia and remains a global health problem, but its past diversity and dispersal routes are largely unknown. We generated HBV genomic data from 137 Eurasians and Native Americans dated between ~10,500 and ~400 years ago. We date the most recent common ancestor of all HBV lineages to between ~20,000 and 12,000 years ago, with the virus present in European and South American hunter-gatherers during the early Holocene. After the European Neolithic transition, Mesolithic HBV strains were replaced by a lineage likely disseminated by early farmers that prevailed throughout western Eurasia for ~4000 years, declining around the end of the 2nd…

According to the CPLL proteome sheriffs, not all aperitifs are created equal!

2014

Combinatorial peptide ligand libraries (CPLLs) have been adopted for investigating the proteome of a popular aperitif in Northern Italy, called "Amaro Branzi", stated to be an infusion of a secret herbal mixture, of which some ingredients are declared on the label, namely Angelica officinalis, Gentiana lutea and orange peel, sweetened by a final addition of honey. In order to assess the genuineness of this commercial liqueur, we have prepared extracts of the three vegetable ingredients, assessed their proteomes, and compared them to the one found in the aperitif. The amaro's proteome was identified via prior capture with CPLLs at two different pH values (2.2 and 4.8). Via mass spectrometry …

Detection of batch effects in liquid chromatography-mass spectrometry metabolomic data using guided principal component analysis.

2014

Metabolomics based on liquid chromatography-mass spectrometry (LC-MS) is a powerful tool for studying dynamic responses of biological systems to different physiological or pathological conditions. Differences in the instrumental response within and between batches introduce unwanted and uncontrolled data variation that should be removed to extract useful information. This work exploits a recently developed method for the identification of batch effects in high throughput genomic data based on the calculation of a delta statistic through principal component analysis (PCA) and guided PCA. Its applicability to LC-MS metabolomic data was tested on two real examples. The first example involved t…

Reconfigurable Accelerator for the Word-Matching Stage of BLASTN

2013

BLAST is one of the most popular sequence analysis tools used by molecular biologists. It is designed to efficiently find similar regions between two sequences that have biological significance. However, because the size of genomic databases is growing rapidly, the computation time of BLAST, when performing a complete genomic database search, is continuously increasing. Thus, there is a clear need to accelerate this process. In this paper, we present a new approach for genomic sequence database scanning utilizing reconfigurable field programmable gate array (FPGA)-based hardware. In order to derive an efficient structure for BLASTN, we propose a reconfigurable architecture to accelerate the…