Search results for "GENOMICS"
showing 10 items of 1255 documents
Variations in Substitution Rate in Human and Mouse Genomes
2003
We present a method to quantify spatial fluctuations of the substitution rate on different length scales throughout genomes of eukaryotes. The fluctuations on large length scales are found to be predominantly a consequence of a coarse-graining effect of fluctuations on shorter length scales. This is verified for both the mouse and the human genome. We also found that both species show similar standard deviation of fluctuations even though their mean substitution rate differs by a factor of two. Our method furthermore allows to determine time-resolved substitution rate maps from which we can compute auto-correlation functions in order to quantify how fast the spatial fluctuations in substitu…
Comparing DNA sequence collections by direct comparison of compressed text indexes
2012
Popular sequence alignment tools such as BWA convert a reference genome to an indexing data structure based on the Burrows-Wheeler Transform (BWT), from which matches to individual query sequences can be rapidly determined. However the utility of also indexing the query sequences themselves remains relatively unexplored. Here we show that an all-against-all comparison of two sequence collections can be computed from the BWT of each collection with the BWTs held entirely in external memory, i.e. on disk and not in RAM. As an application of this technique, we show that BWTs of transcriptomic and genomic reads can be compared to obtain reference-free predictions of splice junctions that have h…
Inverted Repeats in Viral Genomes
2004
We investigate 738 complete genomes of viruses to detect the presence of short inverted repeats. The number of inverted repeats found is compared with the prediction obtained for a Bernoullian and for a Markovian control model. We find as a statistical regularity that the number of observed inverted repeats is often greater than the one expected in terms of a Bernoullian or Markovian model in several of the viruses and in almost all those with a genome longer than 30,000 bp.
Statistical properties of thermodynamically predicted RNA secondary structures in viral genomes
2008
By performing a comprehensive study on 1832 segments of 1212 complete genomes of viruses, we show that in viral genomes the hairpin structures of thermodynamically predicted RNA secondary structures are more abundant than expected under a simple random null hypothesis. The detected hairpin structures of RNA secondary structures are present both in coding and in noncoding regions for the four groups of viruses categorized as dsDNA, dsRNA, ssDNA and ssRNA. For all groups hairpin structures of RNA secondary structures are detected more frequently than expected for a random null hypothesis in noncoding rather than in coding regions. However, potential RNA secondary structures are also present i…
Deep metazoan phylogeny: When different genes tell different stories
2013
11 páginas, 4 figuras, 1 tabla.
New Vocabulary for Bacterial Communication
2019
Abstract Quorum sensing (QS) is widely accepted as a procedure that bacteria use to converse. However, prevailing thinking places acyl homoserine lactones (AHLs) at the forefront of this communication pathway in Gram‐negative bacteria. With the advent of high‐throughput genomics and the subsequent influx of bacterial genomes, bioinformatics analysis has determined that the genes encoding AHL biosynthesis, originally discovered to be indispensable for QS (LuxI‐like proteins and homologues), are often absent in QS‐capable bacteria. Instead, the sensing protein (LuxR‐like proteins) is present with an apparent inability to produce any outgoing AHL signal. Recently, several signals for these Lux…
Genomic characterization of undifferentiated sarcomatoid carcinoma of the pancreas
2022
Undifferentiated sarcomatoid carcinoma (USC) of the pancreas is a rare but especially aggressive variant of pancreatic ductal adenocarcinoma (PDAC), composed of at least 80% of sarcomatoid cells. This study aimed to elucidate its clinicopathological and molecular features. The study cohort included 10 patients with pancreatic USC. Clinicopathological parameters were determined for each patient. The molecular profile was investigated using next-generation sequencing (NGS). Histologically, all tumors were hypercellular neoplasms with spindle-shaped or sarcomatoid cells. All patients showed vascular and perineural invasion. Most patients had a poor prognosis. NGS showed important similarities …
Histone Code and Higher-Order Chromatin Folding: A Hypothesis
2016
AbstractHistone modifications alone or in combination are thought to modulate chromatin structure and function; a concept termed histone code. By combining evidence from several studies, we investigated if the histone code can play a role in higher-order folding of chromatin. Firstly using genomic data, we analyzed associations between histone modifications at the nucleosome level. We could dissect the composition of individual nucleosomes into five predicted clusters of histone modifications. Secondly, by assembling the raw reads of histone modifications at various length scales, we noticed that the histone mark relationships that exist at nucleosome level tend to be maintained at the high…
Genetics of Inflammation in Age-Related Atherosclerosis: Its Relevance to Pharmacogenomics
2007
In response to tissue injury elicited by trauma or infection, the inflammatory response, as a complex network of molecular and cellular interactions, sets an answer directed to facilitate a return to physiological homeostasis and tissue repair. The role of the genetic background and the subsequent predisposition toward the extent of the inflammatory response is determined by gene variability encoding endogenous mediators involved in the inflammatory pathway. Due to its clinical relevance, the genetics of inflammation in aging will be studied using an inflammatory disease like atherosclerosis as an example. Several studies have reported a significant difference in distribution, between patie…
Genome-wide scan for selection signatures reveals novel insights into the adaptive capacity in local North African cattle
2020
International audience; Natural-driven selection is supposed to have left detectable signatures on the genome of North African cattle which are often characterized by the fixation of genetic variants associated with traits under selection pressure and/or an outstanding genetic differentiation with other populations at particular loci. Here, we investigate the population genetic structure and we provide a first outline of potential selection signatures in North African cattle using single nucleotide polymorphism genotyping data. After comparing our data to African, European and indicine cattle populations, we identified 36 genomic regions using three extended haplotype homozygosity statistic…