Search results for "genomic"

Efficacy and safety of cyclic pyranopterin monophosphate substitution in severe molybdenum cofactor deficiency type A: a prospective cohort study.

2015

Summary Background Molybdenum cofactor deficiency (MoCD) is characterised by early, rapidly progressive postnatal encephalopathy and intractable seizures, leading to severe disability and early death. Previous treatment attempts have been unsuccessful. After a pioneering single treatment we now report the outcome of the complete first cohort of patients receiving substitution treatment with cyclic pyranopterin monophosphate (cPMP), a biosynthetic precursor of the cofactor. Methods In this observational prospective cohort study, newborn babies with clinical and biochemical evidence of MoCD were admitted to a compassionate-use programme at the request of their treating physicians. Intravenous…

Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment.

2007

Abstract Background Similarity of sequences is a key mathematical notion for Classification and Phylogenetic studies in Biology. It is currently primarily handled using alignments. However, the alignment methods seem inadequate for post-genomic studies since they do not scale well with data set size and they seem to be confined only to genomic and proteomic sequences. Therefore, alignment-free similarity measures are actively pursued. Among those, USM (Universal Similarity Metric) has gained prominence. It is based on the deep theory of Kolmogorov Complexity and universality is its most novel striking feature. Since it can only be approximated via data compression, USM is a methodology rath…

Guest Editors' Introduction to the Special Section on Algorithms in Bioinformatics

2008

CORENup: a combination of convolutional and recurrent deep neural networks for nucleosome positioning identification

2020

Abstract Background Nucleosomes wrap the DNA into the nucleus of the Eukaryote cell and regulate its transcription phase. Several studies indicate that nucleosomes are determined by the combined effects of several factors, including DNA sequence organization. Interestingly, the identification of nucleosomes on a genomic scale has been successfully performed by computational methods using DNA sequence as input data. Results In this work, we propose CORENup, a deep learning model for nucleosome identification. CORENup processes a DNA sequence as input using one-hot representation and combines in a parallel fashion a fully convolutional neural network and a recurrent layer. These two parallel …

PVAmpliconFinder: a workflow for the identification of human papillomaviruses from high-throughput amplicon sequencing

2019

Abstract Background The detection of known human papillomaviruses (PVs) from targeted wet-lab approaches has traditionally used PCR-based methods coupled with Sanger sequencing. With the introduction of next-generation sequencing (NGS), these approaches can be revisited to integrate the sequencing power of NGS. Although computational tools have been developed for metagenomic approaches to search for known or novel viruses in NGS data, no appropriate tool is available for the classification and identification of novel viral sequences from data produced by amplicon-based methods. Results We have developed PVAmpliconFinder, a data analysis workflow designed to rapidly identify and classify kno…

Highlights of the 1st Student Symposium on Computational Genomics

2017

On 30 November 2016, over 70 junior researchers in computational biology from diverse countries met in Mainz, Germany, for the 1st Student Symposium on Computational Genomics. Overall, the symposium was a great success and featured four outstanding keynote lectures, nine selected student talks, and over 38 poster presentations. This report briefly highlights the scientific outcomes and activities of this student-driven event.

CRISPR sequences are sometimes erroneously translated and can contaminate public databases with spurious proteins containing spaced repeats

2020

© The Author(s) 2020.

pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components

2019

AbstractBackgroundPrincipal component analysis (PCA) is frequently useentirely written ind in genomics applications for quality assessment and exploratory analysis in high-dimensional data, such as RNA sequencing (RNA-seq) gene expression assays. Despite the availability of many software packages developed for this purpose, an interactive and comprehensive interface for performing these operations is lacking.ResultsWe developed the pcaExplorer software package to enhance commonly performed analysis steps with an interactive and user-friendly application, which provides state saving as well as the automated creation of reproducible reports. pcaExplorer is implemented in R using the Shiny fra…

Enforcing Conceptual Modeling to improve the understanding of human genome

2010

It is widely accepted that the use of Conceptual Modeling techniques in modern Software Engineering leads to a more accurate description of the problem domain. The application of these techniques in the context of challenging domains as the human genome is a fascinating task. The relevant biological concepts should be properly addressed through the creation of the corresponding conceptual schema. This schema will improve the description of the global process followed from a DNA sequence to a fully functional protein. Once the conceptual model is established, the corresponding database is created. The database is intended to act as a unified repository of integrated information that will all…

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…