• Studies of genetic variation in natural populations at the sequence level usually show that most polymorphic sites are very asymmetrical in allele frequencies, with the rarer allele at a site near fixation. (genetics.org)
  • Gfeller K, Roth M, Meile L, Teuber M. Sequence and genetic organization of the 19.3-kb erythromycin- and dalfopristin-resistance plasmid pLME300 from Lactobacillus fermentum ROT1. (labome.org)
  • The new genetic revolution is fuelled by Deep Sequencing (or Next Generation Sequencing) apparatuses which, in essence, read billions of nucleotides per reaction. (abebooks.com)
  • These genetic results, sharpened by ORIEN's clinical data and the significant size of the sample set, accurately elucidate known drivers of cancer, identify new genetic alterations, and reveal novel potential therapeutic targets. (genomeweb.com)
  • Whole exome sequencing (WES) has been widely accepted as a robust and cost-effective approach for clinical genetic testing of small sequence variants. (biomedcentral.com)
  • However, it was impossible to identify the population of blue whales the individuals belonged to, due to the lack of strong population genetic signals in the mitochondrial control region sequences. (sljol.info)
  • This is a multi-institutional effort to aggregate detailed genetic (and molecular) data in connection with treatments and physician reported outcomes in patients with advanced cancer. (clinicaltrials.gov)
  • Incorporating genetic variant data into the electronic health record (EHR) in discrete computable fashion has vexed the informatics community for years. (cdc.gov)
  • Genetic sequence test results are typically communicated by the molecular laboratory and stored in the EHR as textual documents. (cdc.gov)
  • Rasmus Nielsen is certainly one of these researchers, and his work so far has merged many population genetic and phylogenetic aspects of biological research under the umbrella of molecular evolution. (springer.com)
  • In severe early-onset epilepsy, precise clinical and molecular genetic diagnosis is complex, as many metabolic and electro-physiological processes have been implicated in disease causation. (ox.ac.uk)
  • It also uncovers unexpected genetic mechanisms and emphasizes the power of WGS as a clinical tool for making molecular diagnoses, particularly for highly heterogeneous disorders. (ox.ac.uk)
  • This web-based application performed pairwise comparisons of HIV-1 protease and partial reverse transcriptase to measure sequence relatedness and identify sequences that were highly genetically similar at a genetic distance of ≤0.015 substitutions per site ( 6 , 7 ). (cdc.gov)
  • Genetic data in studies of systematics of Amazonian amphibians frequently reveal that purportedly widespread single species in reality comprise species complexes. (plos.org)
  • It is shown that more power can be achieved by increasing the length of sequence determined than by increasing the number of genomes sampled for the same total work. (genetics.org)
  • Interpreting relationships of human immunodeficiency virus type 1 (HIV-1) sequences can be challenging because of their rapidly evolving genomes, but it may also lead to a better understanding of the underlying biology. (washington.edu)
  • However, generating full scaffolds of N. gonorrhoeae genomes from short reads, and the assignment of molecular epidemiological information (NG-MLST, NG-MAST, and NG-STAR) to multiple assembled samples, is challenging due to required manual tasks such as annotating antimicrobial resistance determinants with standard nomenclature for a large number of genomes. (biomedcentral.com)
  • We present Gen2Epi, a pipeline that assembles short reads into full scaffolds and automatically assigns molecular epidemiological and AMR information to the assembled genomes. (biomedcentral.com)
  • For its evaluation, the Gen2Epi pipeline successfully assembled the WGS short reads from 1484 N. gonorrhoeae samples into full-length genomes for both chromosomes and plasmids and was able to assign in silico molecular determinant information to each dataset automatically. (biomedcentral.com)
  • Gen2Epi can be used to assemble short reads into full-length genomes and assign accurate molecular marker and AMR information automatically from NG-STAR, NG-MAST, and NG-MLST. (biomedcentral.com)
  • In order to manage and analyze the large amount of data generated from sequencing techniques, initiatives to develop appropriate tools and software have been undertaken by the N. gonorrhoeae scientific community worldwide [ 3 ] with a number of methods developed to assemble genomes, predict antimicrobial resistance (AMR), and investigate strain transmission through analysis of genomic molecular determinants. (biomedcentral.com)
  • We utilize DNA sequence data from the nuclear, chloroplast, and mitochondrial genomes to infer historical processes of biodiversification. (duke.edu)
  • Metasim is a sequencing simulator for genomes and metagenomes. (uni-tuebingen.de)
  • Detection of copy number variants (CNV) within WES data have become possible through the development of various algorithms and software programs that utilize read-depth as the main information. (biomedcentral.com)
  • Class assignments will familiarize students with biological data and tools for understanding this data and will help students gain a solid understanding of principles for design and analysis of algorithms. (ubc.ca)
  • Analysis of sub-type specific mutation data from the BC cohort demonstrates an increased mutational load in ECM-related proteins, particularly the myosins, along with increased TP53 clonality in the non-LAR subtypes. (aacrjournals.org)
  • Human pathology due to a deficient alpha-oxidation is mostly linked to mutations in the gene coding for the second enzyme of the sequence, phytanoyl-CoA hydroxylase. (labome.org)
  • ITHACA, N.Y.--( BUSINESS WIRE )-- Rheonix Inc. , a developer of fully automated molecular testing solutions, will highlight its Encompass Optimum ™ workstation at the Association for Molecular Pathology (AMP) Annual Meeting Nov. 10-12 in Charlotte, North Carolina. (businesswire.com)
  • Several studies have focused on the evolution of HIV-1, but there is little information to link sequence similarities and evolutionary histories of HIV-1 to the epidemiological information of the infected individual. (washington.edu)
  • In the field of molecular evolution, inferences about past evolutionary events are made using molecular data from currently living species. (springer.com)
  • Most studies in molecular evolution rely heavily on statistical procedures based on stochastic process modelling and advanced computational methods including high-dimensional numerical optimization and Markov Chain Monte Carlo. (springer.com)
  • This book provides an overview of the statistical theory and methods used in studies of molecular evolution. (springer.com)
  • This book is suitable for statisticians seeking to learn more about applications in molecular evolution and molecular evolutionary biologists with an interest in learning more about the theory behind the statistical methods applied in the field. (springer.com)
  • Most relevant statistical concepts are introduced in the book in the context of their application in molecular evolution, and the book should be accessible for most biology graduate students with an interest in quantitative methods and theory. (springer.com)
  • His is an associate editor of the Journal of Molecular Evolution and has published more than fifty original papers in peer-reviewed journals on the topic of this book. (springer.com)
  • I find Statistical Methods in Molecular Evolution very interesting and useful. (springer.com)
  • This book gives an overview of his interests and current achievements in molecular evolution. (springer.com)
  • The high level of internal consistency found in our analyses suggests that the Bayesian statistical model employed is an adequate fit for both the geological and morphological data, and provides evidence from real data that the framework used can accurately model the evolution of discrete morphological traits coded from fossil and extant taxa. (royalsocietypublishing.org)
  • It may be less widely appreciated by molecular evolutionary biologists that the statistical phylogenetic revolution in molecular evolution has also been mirrored in the increasing application of statistical phylogenetic reasoning in macroevolutionary and systematic studies of the fossil record [ 14 - 17 ]. (royalsocietypublishing.org)
  • The divergence time of 5.5 million years between humans and chimpanzees also corresponds to the P. humanus-P. schaeffi divergence, and hence was used as a calibration point for molecular clocks. (abc.net.au)
  • The continual improvement of models and methods for statistical phylogenetic inference from molecular sequence data is well documented [ 4 , 5 ], and in recent years, it is arguably the case that molecular phylogenetics has taken primacy over the fossil record in providing a timescale for evolutionary history [ 1 ]. (royalsocietypublishing.org)
  • Sequencing delivers objective data on taxa of incredible diversity but mostly without a solid taxonomic foundation and should help pave the road for the eventual formal naming of new species. (wikisource.org)
  • Our results provide an estimate of the distribution of fitness effects of weakly selected mutations and provide a possible explanation for why the molecular clock is fairly constant across taxa and time. (sussex.ac.uk)
  • Graph generated 15 March 2017 using data from PubMed using criteria . (cancerindex.org)
  • HIV-1 sequence data reported in Wisconsin during 2014-2017 for persons with HIV infection diagnosed through August 15, 2017, were analyzed using Secure HIV-TRACE (Secure HIV TRAnsmission Cluster Engine). (cdc.gov)
  • The breadth and scope of the ORIEN Avatar clinical and molecular data enables the discovery of a wide array of DNA and RNA biomarkers, including those biomarkers associated with response to immuno-oncology agents. (genomeweb.com)
  • In a previous study, we presented the clinical and molecular findings in 140 FCCM individuals. (cdc.gov)
  • Rheonix will present data from a user-defined assay for sexually transmitted infections (STIs), as well as data that demonstrates new capabilities of its system in next-generation sequencing (NGS) library preparation. (businesswire.com)
  • Due to the rapid development of "-omics" technology, such as DNA microarrays [ 1 ] and next-generation sequencing (NGS) [ 2 , 3 ], scientists are now able to quantify large numbers of transcripts from organisms simultaneously. (biomedcentral.com)
  • Data generated by this effort demonstrates that, in addition to detecting the presence of viral RNA, the system can distinguish early immunoglobulin M (IgM) antibodies from late immunoglobulin G (IgG) antibodies, thus providing more information on a patient's stage of infection. (businesswire.com)
  • Using standard phylogenetic and phenetic techniques on 100 HIV-1 subtype B sequences, we were able to show some correlation between the viral sequences and the geographic area of infection and the risk of men who engage in sex with men. (washington.edu)
  • To help identify more subtle relationships between the viral sequences, the method of multidimensional scaling (MDS) was performed. (washington.edu)
  • That method identified statistically significant correlations between the viral sequences and the risk factors of men who engage in sex with men and individuals who engage in sex with injection drug users or use injection drugs themselves. (washington.edu)
  • Prevention recommendations generated from national data (e.g., targeting preexposure prophylaxis for HIV-negative persons at high risk and implementing measures to maintain viral suppression among persons with HIV infection) also are relevant in a lower HIV-morbidity state. (cdc.gov)
  • We used DNA microarray data available on-line. (uci.edu)
  • Based on microarray data from Stanford Microarray Database, two hNAT pairs were found to display significant inverse expression patterns before and after insulin injection. (mendeley.com)
  • Methods for estimating divergence times from molecular data have improved dramatically over the past decade, yet there are few studies examining alternative taxon sampling effects on node age estimates. (hindawi.com)
  • Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of necessary materials and reagents, step-by-step, readily reproducible protocols, and key tips on troubleshooting and avoiding known pitfalls. (abebooks.com)
  • 2008. (Methods in Molecular Biology, Volume 452). (koeltz.com)