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Journal articles on the topic 'Nucleotide sequence – Statistical methods'

Author: Grafiati

Published: 4 June 2021

Last updated: 17 February 2022

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1

Demongeot, Jacques, and Alexandra Henrion-Caude. "Footprints of a Singular 22-Nucleotide RNA Ring at the Origin of Life." Biology 9, no. 5 (2020): 88. http://dx.doi.org/10.3390/biology9050088.

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(1) Background: Previous experimental observations and theoretical hypotheses have been providing insight into a hypothetical world where an RNA hairpin or ring may have debuted as the primary informational and functional molecule. We propose a model revisiting the architecture of RNA-peptide interactions at the origin of life through the evolutionary dynamics of RNA populations. (2) Methods: By performing a step-by-step computation of the smallest possible hairpin/ring RNA sequences compatible with building up a variety of peptides of the primitive network, we inferred the sequence of a singu

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Yang, Z., S. Kumar, and M. Nei. "A new method of inference of ancestral nucleotide and amino acid sequences." Genetics 141, no. 4 (1995): 1641–50. http://dx.doi.org/10.1093/genetics/141.4.1641.

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Abstract A statistical method was developed for reconstructing the nucleotide or amino acid sequences of extinct ancestors, given the phylogeny and sequences of the extant species. A model of nucleotide or amino acid substitution was employed to analyze data of the present-day sequences, and maximum likelihood estimates of parameters such as branch lengths were used to compare the posterior probabilities of assignments of character states (nucleotides or amino acids) to interior nodes of the tree; the assignment having the highest probability was the best reconstruction at the site. The lysozy

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Farkaš, Tomáš, Jozef Sitarčík, Broňa Brejová, and Mária Lucká. "SWSPM: A Novel Alignment-Free DNA Comparison Method Based on Signal Processing Approaches." Evolutionary Bioinformatics 15 (January 2019): 117693431984907. http://dx.doi.org/10.1177/1176934319849071.

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Computing similarity between 2 nucleotide sequences is one of the fundamental problems in bioinformatics. Current methods are based mainly on 2 major approaches: (1) sequence alignment, which is computationally expensive, and (2) faster, but less accurate, alignment-free methods based on various statistical summaries, for example, short word counts. We propose a new distance measure based on mathematical transforms from the domain of signal processing. To tolerate large-scale rearrangements in the sequences, the transform is computed across sliding windows. We compare our method on several dat

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Diancourt, Laure, Virginie Passet, Christian Chervaux, Peggy Garault, Tamara Smokvina, and Sylvain Brisse. "Multilocus Sequence Typing of Lactobacillus casei Reveals a Clonal Population Structure with Low Levels of Homologous Recombination." Applied and Environmental Microbiology 73, no. 20 (2007): 6601–11. http://dx.doi.org/10.1128/aem.01095-07.

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ABSTRACT Robust genotyping methods for Lactobacillus casei are needed for strain tracking and collection management, as well as for population biology research. A collection of 52 strains initially labeled L. casei or Lactobacillus paracasei was first subjected to rplB gene sequencing together with reference strains of Lactobacillus zeae, Lactobacillus rhamnosus, and other species. Phylogenetic analysis showed that all 52 strains belonged to a single compact L. casei-L. paracasei sequence cluster, together with strain CIP107868 (= ATCC 334) but clearly distinct from L. rhamnosus and from a clu

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Xia, Xuhua. "Position Weight Matrix, Gibbs Sampler, and the Associated Significance Tests in Motif Characterization and Prediction." Scientifica 2012 (2012): 1–15. http://dx.doi.org/10.6064/2012/917540.

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Position weight matrix (PWM) is not only one of the most widely used bioinformatic methods, but also a key component in more advanced computational algorithms (e.g., Gibbs sampler) for characterizing and discovering motifs in nucleotide or amino acid sequences. However, few generally applicable statistical tests are available for evaluating the significance of site patterns, PWM, and PWM scores (PWMS) of putative motifs. Statistical significance tests of the PWM output, that is, site-specific frequencies, PWM itself, and PWMS, are in disparate sources and have never been collected in a single

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Pinheiro, M., V. Afreixo, G. Moura, A. Freitas, M. A. S. Santos, and J. L. Oliveira. "Statistical, Computational and Visualization Methodologies to Unveil Gene Primary Structure Features." Methods of Information in Medicine 45, no. 02 (2006): 163–68. http://dx.doi.org/10.1055/s-0038-1634061.

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Summary Objectives: Gene sequence features such as codon bias, codon context, and codon expansion (e.g. tri-nucleotide repeats) can be better understood at the genomic scale level by combining statistical methodologies with advanced computer algorithms and data visualization through sophisticated graphical interfaces. This paper presents the ANACONDA system, a bioinformatics application for gene primary structure analysis. Methods: Codon usage tables using absolute metrics and software for multivariate analysis of codon and amino acid usage are available in public databases. However, they do n

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Bilhère, Eric, Patrick M. Lucas, Olivier Claisse, and Aline Lonvaud-Funel. "Multilocus Sequence Typing of Oenococcus oeni: Detection of Two Subpopulations Shaped by Intergenic Recombination." Applied and Environmental Microbiology 75, no. 5 (2008): 1291–300. http://dx.doi.org/10.1128/aem.02563-08.

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ABSTRACT Oenococcus oeni is the acidophilic lactic acid bacterial species most frequently associated with malolactic fermentation of wine. Since the description of the species (formerly Leuconostoc oenos), characterization of indigenous strains and industrially produced cultures by diverse typing methods has led to divergent conclusions concerning the genetic diversity of strains. In the present study, a multilocus sequence typing (MLST) scheme based on the analysis of eight housekeeping genes was developed and tested on a collection of 43 strains of diverse origins. The eight targeted loci we

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Bedo, Justin, Benjamin Goudey, Jeremy Wazny, and Zeyu Zhou. "Information theoretic alignment free variant calling." PeerJ Computer Science 2 (July 25, 2016): e71. http://dx.doi.org/10.7717/peerj-cs.71.

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While traditional methods for calling variants across whole genome sequence data rely on alignment to an appropriate reference sequence, alternative techniques are needed when a suitable reference does not exist. We present a novel alignment and assembly free variant calling method based on information theoretic principles designed to detect variants have strong statistical evidence for their ability to segregate samples in a given dataset. Our method uses the context surrounding a particular nucleotide to define variants. Given a set of reads, we model the probability of observing a given nuc

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Timoshkina, Natalya N., Denis S. Kutilin, Inna A. Novikova, et al. "Features of iso-miR expression in colon tumor tissue." Journal of Clinical Oncology 38, no. 15_suppl (2020): e13518-e13518. http://dx.doi.org/10.1200/jco.2020.38.15_suppl.e13518.

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e13518 Background: With the advent of deep sequencing, enormous variability in miRNA biogenesis was detected, which means that many different sequences can potentially be generated from the same miRNA precursor, potentially having different targets and opposite changes in expression. These variable forms of micro-RNA that differ from the reference sequence are called iso-miR. To date, features of iso-miR expression have not been studied in patients with colorectal cancer (CRC). The aim of the study was to analyze the differential expression of iso-miR in the tumor and normal tissues of patient

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Abadi, Shiran, Oren Avram, Saharon Rosset, Tal Pupko, and Itay Mayrose. "ModelTeller: Model Selection for Optimal Phylogenetic Reconstruction Using Machine Learning." Molecular Biology and Evolution 37, no. 11 (2020): 3338–52. http://dx.doi.org/10.1093/molbev/msaa154.

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Abstract Statistical criteria have long been the standard for selecting the best model for phylogenetic reconstruction and downstream statistical inference. Although model selection is regarded as a fundamental step in phylogenetics, existing methods for this task consume computational resources for long processing time, they are not always feasible, and sometimes depend on preliminary assumptions which do not hold for sequence data. Moreover, although these methods are dedicated to revealing the processes that underlie the sequence data, they do not always produce the most accurate trees. Not

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Sethna, Zachary, Yuval Elhanati, Curtis G. Callan, Aleksandra M. Walczak, and Thierry Mora. "OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs." Bioinformatics 35, no. 17 (2019): 2974–81. http://dx.doi.org/10.1093/bioinformatics/btz035.

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Abstract Motivation High-throughput sequencing of large immune repertoires has enabled the development of methods to predict the probability of generation by V(D)J recombination of T- and B-cell receptors of any specific nucleotide sequence. These generation probabilities are very non-homogeneous, ranging over 20 orders of magnitude in real repertoires. Since the function of a receptor really depends on its protein sequence, it is important to be able to predict this probability of generation at the amino acid level. However, brute-force summation over all the nucleotide sequences with the cor

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Pozhylov, I., T. Rudnieva, T. Shevchenko, O. Shevchenko, and V. Tsvigun. "Phylogenetic analysis of coat protein gene of tomato mosaic virus isolates circulating in Ukraine." Bulletin of Taras Shevchenko National University of Kyiv. Series: Biology 77, no. 1 (2019): 44–50. http://dx.doi.org/10.17721/1728_2748.2019.77.44-50.

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Tomato mosaic virus (ToMV) induces highly infectious disease of vegetables, whereas use of virus-contaminated seed may lead to complete yield loss. This work was aimed at studying phylogenetic relationships of Ukrainian tomato isolates of ToMV with its known isolates by comparing nucleotide sequence of coat protein gene. ELISA, TEM, RT-PCR, sequence analysis using MEGA 5 software, and statistical methods. cDNAs of two novel Ukrainian isolates ToMV-ukr-5 and ToMV-ukr-10 corresponding to coat protein (CP) gene were sequenced and compared with other published ToMV sequences. On the constructed ph

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Tajima, F. "Simple methods for testing the molecular evolutionary clock hypothesis." Genetics 135, no. 2 (1993): 599–607. http://dx.doi.org/10.1093/genetics/135.2.599.

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Abstract Simple statistical methods for testing the molecular evolutionary clock hypothesis are developed which can be applied to both nucleotide and amino acid sequences. These methods are based on the chi-square test and are applicable even when the pattern of substitution rates is unknown and/or the substitution rate varies among different sites. Furthermore, some of the methods can be applied even when the outgroup is unknown. Using computer simulations, these methods were compared with the likelihood ratio test and the relative rate test. The results indicate that the powers of the presen

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ORLOV, YURIY L., RENE TE BOEKHORST, and IRINA I. ABNIZOVA. "STATISTICAL MEASURES OF THE STRUCTURE OF GENOMIC SEQUENCES: ENTROPY, COMPLEXITY, AND POSITION INFORMATION." Journal of Bioinformatics and Computational Biology 04, no. 02 (2006): 523–36. http://dx.doi.org/10.1142/s0219720006001801.

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Identifying regions of DNA with extreme statistical characteristics is an important aspect of the structural analysis of complete genomes. Linguistic methods, mainly based on estimating word frequency, can be used for this as they allow for the delineation of regions of low complexity. Low complexity may be due to biased nucleotide composition, by tandem- or dispersed repeats, by palindrome-hairpin structures, as well as by a combination of all these features. We developed software tools in which various numerical measures of text complexity are implemented, including combinatorial and linguis

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Ji, Yanrong, Zhihan Zhou, Han Liu, and Ramana V. Davuluri. "DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome." Bioinformatics 37, no. 15 (2021): 2112–20. http://dx.doi.org/10.1093/bioinformatics/btab083.

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Abstract Motivation Deciphering the language of non-coding DNA is one of the fundamental problems in genome research. Gene regulatory code is highly complex due to the existence of polysemy and distant semantic relationship, which previous informatics methods often fail to capture especially in data-scarce scenarios. Results To address this challenge, we developed a novel pre-trained bidirectional encoder representation, named DNABERT, to capture global and transferrable understanding of genomic DNA sequences based on up and downstream nucleotide contexts. We compared DNABERT to the most widel

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Yang, Ziheng. "Statistical Properties of a DNA Sample Under the Finite-Sites Model." Genetics 144, no. 4 (1996): 1941–50. http://dx.doi.org/10.1093/genetics/144.4.1941.

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Statistical properties of a DNA sample from a random-mating population of constant size are studied under the finite-sites model. It is assumed that there is no migration and no recombination occurs within the locus. A Markov process model is used for nucleotide substitution, allowing for multiple substitutions at a single site. The evolutionary rates among sites are treated as either constant or variable. The general likelihood calculation using numerical integration involves intensive computation and is feasible for three or four sequences only; it may be used for validating approximate algo

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Wang, Mengchi, David Wang, Kai Zhang, Vu Ngo, Shicai Fan, and Wei Wang. "Motto: Representing Motifs in Consensus Sequences with Minimum Information Loss." Genetics 216, no. 2 (2020): 353–58. http://dx.doi.org/10.1534/genetics.120.303597.

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Sequence analysis frequently requires intuitive understanding and convenient representation of motifs. Typically, motifs are represented as position weight matrices (PWMs) and visualized using sequence logos. However, in many scenarios, in order to interpret the motif information or search for motif matches, it is compact and sufficient to represent motifs by wildcard-style consensus sequences (such as [GC][AT]GATAAG[GAC]). Based on mutual information theory and Jensen-Shannon divergence, we propose a mathematical framework to minimize the information loss in converting PWMs to consensus seque

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Mirzaev, K. B., D. V. Ivashchenko, I. V. Volodin, et al. "New Pharmacogenetic Markers to Predict the Risk of Bleeding During Taking of Direct Oral Anticoagulants." Rational Pharmacotherapy in Cardiology 16, no. 5 (2020): 670–77. http://dx.doi.org/10.20996/1819-6446-2020-10-05.

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Aim. To search for new pharmacogenetic biomarkers of bleeding risk in patients taking rivaroxaban and dabigatran for different indications: atrial fibrillation, endoprosthesis of large joints of lower limbs.Material and methods. The study enrolled 29 patients (17 patients received dabigatran and 12 –rivaroxaban), who had hemorrhagic complications during taking direct oral anticoagulants. To find new pharmacogenetic biomarkers of bleeding risk, a next generation sequencing (NGS) was performed for selected candidate genes.Results. Among the patients with bleeding who received dabigatran, 13 vari

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Korotkov, Eugene V., Yulia M. Suvorova, Dmitrii O. Kostenko, and Maria A. Korotkova. "Multiple Alignment of Promoter Sequences from the Arabidopsis thaliana L. Genome." Genes 12, no. 2 (2021): 135. http://dx.doi.org/10.3390/genes12020135.

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In this study, we developed a new mathematical method for performing multiple alignment of highly divergent sequences (MAHDS), i.e., sequences that have on average more than 2.5 substitutions per position (x). We generated sets of artificial DNA sequences with x ranging from 0 to 4.4 and applied MAHDS as well as currently used multiple sequence alignment algorithms, including ClustalW, MAFFT, T-Coffee, Kalign, and Muscle to these sets. The results indicated that most of the existing methods could produce statistically significant alignments only for the sets with x < 2.5, whereas MAHDS coul

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Zhu, Huisheng, Brent E. Allman, and Katia Koelle. "Fitness Estimation for Viral Variants in the Context of Cellular Coinfection." Viruses 13, no. 7 (2021): 1216. http://dx.doi.org/10.3390/v13071216.

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Animal models are frequently used to characterize the within-host dynamics of emerging zoonotic viruses. More recent studies have also deep-sequenced longitudinal viral samples originating from experimental challenges to gain a better understanding of how these viruses may evolve in vivo and between transmission events. These studies have often identified nucleotide variants that can replicate more efficiently within hosts and also transmit more effectively between hosts. Quantifying the degree to which a mutation impacts viral fitness within a host can improve identification of variants that

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Tao, Qiqing, Jose Barba-Montoya, Louise A. Huuki, Mary Kathleen Durnan, and Sudhir Kumar. "Relative Efficiencies of Simple and Complex Substitution Models in Estimating Divergence Times in Phylogenomics." Molecular Biology and Evolution 37, no. 6 (2020): 1819–31. http://dx.doi.org/10.1093/molbev/msaa049.

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Abstract The conventional wisdom in molecular evolution is to apply parameter-rich models of nucleotide and amino acid substitutions for estimating divergence times. However, the actual extent of the difference between time estimates produced by highly complex models compared with those from simple models is yet to be quantified for contemporary data sets that frequently contain sequences from many species and genes. In a reanalysis of many large multispecies alignments from diverse groups of taxa, we found that the use of the simplest models can produce divergence time estimates and credibili

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Pavesi, Angelo. "Origin, Evolution and Stability of Overlapping Genes in Viruses: A Systematic Review." Genes 12, no. 6 (2021): 809. http://dx.doi.org/10.3390/genes12060809.

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During their long evolutionary history viruses generated many proteins de novo by a mechanism called “overprinting”. Overprinting is a process in which critical nucleotide substitutions in a pre-existing gene can induce the expression of a novel protein by translation of an alternative open reading frame (ORF). Overlapping genes represent an intriguing example of adaptive conflict, because they simultaneously encode two proteins whose freedom to change is constrained by each other. However, overlapping genes are also a source of genetic novelties, as the constraints under which alternative ORF

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Said Mohammed, Khadija, Nelson Kibinge, Pjotr Prins, et al. "Evaluating the performance of tools used to call minority variants from whole genome short-read data." Wellcome Open Research 3 (September 13, 2018): 21. http://dx.doi.org/10.12688/wellcomeopenres.13538.2.

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Background: High-throughput whole genome sequencing facilitates investigation of minority virus sub-populations from virus positive samples. Minority variants are useful in understanding within and between host diversity, population dynamics and can potentially assist in elucidating person-person transmission pathways. Several minority variant callers have been developed to describe low frequency sub-populations from whole genome sequence data. These callers differ based on bioinformatics and statistical methods used to discriminate sequencing errors from low-frequency variants. Methods: We ev

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Arnedo-Pac, Claudia, Loris Mularoni, Ferran Muiños, Abel Gonzalez-Perez, and Nuria Lopez-Bigas. "OncodriveCLUSTL: a sequence-based clustering method to identify cancer drivers." Bioinformatics 35, no. 22 (2019): 4788–90. http://dx.doi.org/10.1093/bioinformatics/btz501.

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Abstract Motivation Identification of the genomic alterations driving tumorigenesis is one of the main goals in oncogenomics research. Given the evolutionary principles of cancer development, computational methods that detect signals of positive selection in the pattern of tumor mutations have been effectively applied in the search for cancer genes. One of these signals is the abnormal clustering of mutations, which has been shown to be complementary to other signals in the detection of driver genes. Results We have developed OncodriveCLUSTL, a new sequence-based clustering algorithm to detect

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Whelan, Simon. "The genetic code can cause systematic bias in simple phylogenetic models." Philosophical Transactions of the Royal Society B: Biological Sciences 363, no. 1512 (2008): 4003–11. http://dx.doi.org/10.1098/rstb.2008.0171.

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Phylogenetic analysis depends on inferential methodology estimating accurately the degree of divergence between sequences. Inaccurate estimates can lead to misleading evolutionary inferences, including incorrect tree topology estimates and poor dating of historical species divergence. Protein coding sequences are ubiquitous in phylogenetic inference, but many of the standard methods commonly used to describe their evolution do not explicitly account for the dependencies between sites in a codon induced by the genetic code. This study evaluates the performance of several standard methods on dat

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Adam, Krisztian, Zoltan Gyorgypal, and Zoltan Hegedus. "DNA Readout Viewer (DRV): visualization of specificity determining patterns of protein-binding DNA segments." Bioinformatics 36, no. 7 (2019): 2286–87. http://dx.doi.org/10.1093/bioinformatics/btz906.

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Abstract Summary The sequence specific recognition of DNA by regulatory proteins typically occurs by establishing hydrogen bonds and non-bonded contacts between chemical sub-structures of nucleotides and amino acids forming the compatible interacting surfaces. The recognition process is also influenced by the physicochemical and conformational character of the target oligonucleotide motif. Although the role of these mechanisms in DNA-protein interactions is well-established, bioinformatical methods rarely address them directly, instead binding specificity is mostly assessed at nucleotide level

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Wang, Kai, Pei-sheng Yan, and Li-xin Cao. "Chitinase from a Novel Strain ofSerratia marcescensJPP1 for Biocontrol of Aflatoxin: Molecular Characterization and Production Optimization Using Response Surface Methodology." BioMed Research International 2014 (2014): 1–8. http://dx.doi.org/10.1155/2014/482623.

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Chitinase is one of the most important mycolytic enzymes with industrial significance, and produced by a number of organisms. A chitinase producing isolateSerratia marcescensJPP1 was obtained from peanut hulls in Jiangsu Province, China, and exhibited antagonistic activity against aflatoxins. In this study, we describe the optimization of medium composition with increased production of chitinase for the selected bacteria using statistical methods: Plackett-Burman design was applied to find the key ingredients, and central composite design of response surface methodology was used to optimize th

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Cardoso, Gisele Antoniazzi, Marco Antonio Tonus Marinho, Raquel Dietsche Monfardini, Ana Maria Lima de Azeredo Espin, and Tatiana Teixeira Torres. "Evolution of genes involved in feeding preference and metabolic processes in Calliphoridae (Diptera: Calyptratae)." PeerJ 4 (October 27, 2016): e2598. http://dx.doi.org/10.7717/peerj.2598.

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Background The genotype-phenotype interactions among traits governing feeding preference are of fundamental importance to behavioral genetics and evolutionary biology. The genetic basis of behavioral traits has been explored in different taxa using different approaches. However, the complex nature of the genetic mechanisms undergirding behavior is poorly understood. Here, we present an evolutionary study of candidate genes related to parasitism in Calliphoridae (Diptera: Calyptratae). Closely related species in this family exhibit distinct larval feeding habits, most notably necro-saprophagy a

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Ghosh, Sujoy, Juan C. Vivar, Mark A. Sarzynski, et al. "Integrative pathway analysis of a genome-wide association study of V̇o2max response to exercise training." Journal of Applied Physiology 115, no. 9 (2013): 1343–59. http://dx.doi.org/10.1152/japplphysiol.01487.2012.

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We previously reported the findings from a genome-wide association study of the response of maximal oxygen uptake (V̇o2max) to an exercise program. Here we follow up on these results to generate hypotheses on genes, pathways, and systems involved in the ability to respond to exercise training. A systems biology approach can help us better establish a comprehensive physiological description of what underlies V̇o2maxtrainability. The primary material for this exploration was the individual single-nucleotide polymorphism (SNP), SNP-gene mapping, and statistical significance levels. We aimed to ge

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Said Mohammed, Khadija, Nelson Kibinge, Pjotr Prins, et al. "Evaluating the performance of tools used to call minority variants from whole genome short-read data." Wellcome Open Research 3 (March 5, 2018): 21. http://dx.doi.org/10.12688/wellcomeopenres.13538.1.

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Background: High-throughput whole genome sequencing facilitates investigation of minority sub-populations from virus positive samples. Minority variants are useful in understanding within and between host diversity, population dynamics and can potentially help to elucidate person-person transmission chains. Several minority variant callers have been developed to describe the minority variants sub-populations from whole genome sequence data. However, they differ on bioinformatics and statistical approaches used to discriminate sequencing errors from low-frequency variants. Methods: We evaluated

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Novikova, Inna A., Denis S. Kutilin, Natalya N. Timoshkina, et al. "YsRNA aberrant expression in colorectal cancer patients." Journal of Clinical Oncology 38, no. 15_suppl (2020): e13525-e13525. http://dx.doi.org/10.1200/jco.2020.38.15_suppl.e13525.

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e13525 Background: Cancer is a disease characterized by uncontrolled cell proliferation. DNA replication is the main driving force behind cell proliferation in both normal development and cancer. Non-coding Y-RNAs are important factors in initiating DNA replication in the nuclei of human cells. Excessive expression of Y-RNA is characteristic of tumors of the bladder, cervix, kidney, lung and prostate. It has also been shown that the level of small RNAs formed from the 3'- and 5'-ends of Y-RNA is significantly higher in patients with certain types of cancer compared to healthy people, therefore

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Choi, Seunghyuk, and Eunok Paek. "MutCombinator: identification of mutated peptides allowing combinatorial mutations using nucleotide-based graph search." Bioinformatics 36, Supplement_1 (2020): i203—i209. http://dx.doi.org/10.1093/bioinformatics/btaa504.

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Abstract Motivation Proteogenomics has proven its utility by integrating genomics and proteomics. Typical approaches use data from next-generation sequencing to infer proteins expressed. A sample-specific protein sequence database is often adopted to identify novel peptides from matched mass spectrometry-based proteomics; nevertheless, there is no software that can practically identify all possible forms of mutated peptides suggested by various genomic information sources. Results We propose MutCombinator, which enables us to practically identify mutated peptides from tandem mass spectra allow

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Lynch, Michael, and Wei-Chin Ho. "The Limits to Estimating Population-Genetic Parameters with Temporal Data." Genome Biology and Evolution 12, no. 4 (2020): 443–55. http://dx.doi.org/10.1093/gbe/evaa056.

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Abstract The ability to obtain genome-wide sequences of very large numbers of individuals from natural populations raises questions about optimal sampling designs and the limits to extracting information on key population-genetic parameters from temporal-survey data. Methods are introduced for evaluating whether observed temporal fluctuations in allele frequencies are consistent with the hypothesis of random genetic drift, and expressions for the expected sampling variances for the relevant statistics are given in terms of sample sizes and numbers. Estimation methods and aspects of statistical

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Ritter, Deborah, Kimberly Walker, Myoung Kwon, et al. "Whole genome sequencing of sporadic Burkitt lymphoma in HIV-infected and uninfected patients." Journal of Clinical Oncology 31, no. 15_suppl (2013): 8577. http://dx.doi.org/10.1200/jco.2013.31.15_suppl.8577.

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8577 Background: Burkitt Lymphoma is defined by canonical translocations between MYC and immunoglobulin IgH, IgK or IgL (8:14, 8:2, 8:22, respectively), and is commonly associated with HIV. The identification of HIV from sequenced samples is critical to understanding HIV-associated Burkitt Lymphoma. While recent novel gene mutations (ID3 and TCF3) have been implicated in functional roles, concomitant genomic structural variants and the interaction of HIV with structural variation is less well defined. Methods: We sequenced the whole genomes of 15 patients with 100bp paired-end reads on Illumin

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Ling, Guy, Danielle Miller, Rasmus Nielsen, and Adi Stern. "A Bayesian Framework for Inferring the Influence of Sequence Context on Point Mutations." Molecular Biology and Evolution 37, no. 3 (2019): 893–903. http://dx.doi.org/10.1093/molbev/msz248.

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Abstract The probability of point mutations is expected to be highly influenced by the flanking nucleotides that surround them, known as the sequence context. This phenomenon may be mainly attributed to the enzyme that modifies or mutates the genetic material, because most enzymes tend to have specific sequence contexts that dictate their activity. Here, we develop a statistical model that allows for the detection and evaluation of the effects of different sequence contexts on mutation rates from deep population sequencing data. This task is computationally challenging, as the complexity of th

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Martin, Michael G., Meagan Jacoby, Jin Shao, Elena Deych, Timothy Graubert, and Matthew J. Walter. "BRCA1 and BRCA2 Nucleotide Variants in Young Women with Therapy Related Acute Myeloid Leukemia." Blood 114, no. 22 (2009): 1102. http://dx.doi.org/10.1182/blood.v114.22.1102.1102.

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Abstract Abstract 1102 Poster Board I-124 Background Therapy-related acute myeloid leukemia (t-AML) is a lethal iatrogenic complication of radiation therapy and chemotherapy. It is unclear whether t-AML represents a truly stochastic event, or if individuals have different degrees of susceptibility. It has been shown that women diagnosed with breast cancer younger than 50 are at the highest risk of developing subsequent AML compared to age-matched controls (RR 4.14). This may either reflect more aggressive therapy given to younger women or differences in their ability to tolerate chemotherapy,

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Cunningham, Scott A., Nicholas Chia, Patricio R. Jeraldo, et al. "Comparison of Whole-Genome Sequencing Methods for Analysis of Three Methicillin-Resistant Staphylococcus aureus Outbreaks." Journal of Clinical Microbiology 55, no. 6 (2017): 1946–53. http://dx.doi.org/10.1128/jcm.00029-17.

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ABSTRACT Whole-genome sequencing (WGS) can provide excellent resolution in global and local epidemiological investigations of Staphylococcus aureus outbreaks. A variety of sequencing approaches and analytical tools have been used; it is not clear which is ideal. We compared two WGS strategies and two analytical approaches to the standard method of SmaI restriction digestion pulsed-field gel electrophoresis (PFGE) for typing S. aureus . Forty-two S. aureus isolates from three outbreaks and 12 reference isolates were studied. Near-complete genomes, assembled de novo with paired-end and long-mate

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Demin, М. V., D. C. Tikhomirov, B. V. Biderman, et al. "Cytomegalovirus after allogeneic hematopoietic stem cell transplantation: reactivation or reinfection?" Clinical Microbiology and Antimicrobial Chemotherapy 23, no. 2 (2021): 138–45. http://dx.doi.org/10.36488/cmac.2021.2.138-145.

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Objective. To determine type of cytomegalovirus (CMV) infection (reactivation of a virus strain that was present before transplantation or re-infection with another virus strain) in allogeneic hematopoietic stem cell recipients by sequencing. Materials and Methods. Clinical and laboratory data of 179 recipients of allogeneic hematopoietic stem cells collected from 2014 to 2018 were analyzed for CMV DNA in clinical specimens before and after transplantation. A total of 14 patients (28 samples) were included in the study. The CMV UL139 gene encoding viral glycoprotein was chosen for virus genoty

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Pylypenko, L., V. Blok, and M. Phillips. "Phylogenetic Affi nities of the Globodera pallida Inferred From the mtDNA cyt-b Gene Polymorphism." Agricultural Science and Practice 1, no. 2 (2014): 3–11. http://dx.doi.org/10.15407/agrisp1.02.003.

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The mitochondrial cytochrome b gene marker was used to investigate the genetic variability of G. pallida populations of different origins and selection on three sources of resistance. Aim. To sequence the mitochon- drial gene cyt-b and to clarify its application as a genetic marker for intraspecifi c genetic diversity study, phylogenetic analysis and nematode virulence assessment. Methods. The cysts of nematodes were used as a source for DNA extraction. Polymerase chain reaction was performed using the specifi c primers of INRAcytbL and INRAcytbR, followed by the amplifi ed product sequencing.

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Jiang, Jyun-Yu, Chelsea J. T. Ju, Junheng Hao, Muhao Chen, and Wei Wang. "JEDI: circular RNA prediction based on junction encoders and deep interaction among splice sites." Bioinformatics 37, Supplement_1 (2021): i289—i298. http://dx.doi.org/10.1093/bioinformatics/btab288.

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Abstract Motivation Circular RNA (circRNA) is a novel class of long non-coding RNAs that have been broadly discovered in the eukaryotic transcriptome. The circular structure arises from a non-canonical splicing process, where the donor site backspliced to an upstream acceptor site. These circRNA sequences are conserved across species. More importantly, rising evidence suggests their vital roles in gene regulation and association with diseases. As the fundamental effort toward elucidating their functions and mechanisms, several computational methods have been proposed to predict the circular st

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Zhou, Jing-Bo, Yao Xiong, Ke An, Zhi-Qiang Ye, and Yun-Dong Wu. "IDRMutPred: predicting disease-associated germline nonsynonymous single nucleotide variants (nsSNVs) in intrinsically disordered regions." Bioinformatics 36, no. 20 (2020): 4977–83. http://dx.doi.org/10.1093/bioinformatics/btaa618.

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Abstract Motivation Despite of the lack of folded structure, intrinsically disordered regions (IDRs) of proteins play versatile roles in various biological processes, and many nonsynonymous single nucleotide variants (nsSNVs) in IDRs are associated with human diseases. The continuous accumulation of nsSNVs resulted from the wide application of NGS has driven the development of disease-association prediction methods for decades. However, their performance on nsSNVs in IDRs remains inferior, possibly due to the domination of nsSNVs from structured regions in training data. Therefore, it is highl

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Doroshchenko, E. K., O. V. Lisak, V. A. Rar, O. V. Suntsova, Yu S. Savinova, and I. V. Kozlova. "Species and Genetic Diversity of Representatives of the Anaplasmataceae Family Found in the Sympatry Zone of the Ixodes, Dermacentor and Haemaphysalis Genera Ticks." Acta Biomedica Scientifica 4, no. 2 (2019): 127–35. http://dx.doi.org/10.29413/abs.2019-4.2.18.

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Introduction.On the territory of the Ekhirit-Bulagatsky district of the Irkutsk region zones of sympatry of four Ixodes ticks species are found, where the species and genetic diversity of infectious agents transmitted through tick bites may be more pronounced than in foci with a mono-dominant type of ticks’ population. In this connection, the study of the species and genetic diversity of representatives of the Anaplasmataceae family in the sympatry zone of the Ixodes ticks of closely related species was of scientific interest.Objective:To study the species and genetic diversity of members of t

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Kdkhodazadeh, Mahdi, Mehrdad Hajilooi, Behzad Houshmand, Sara Khazaei, Leila Gholami, and Sara Alijani. "Evaluation of PECAM-1 Gene Polymorphism in Patients with Periodontal Disease and Healthy Individuals." ISRN Dentistry 2012 (March 5, 2012): 1–5. http://dx.doi.org/10.5402/2012/751920.

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Objective. Our aim in this paper was to investigate the possible genetic association between three Ser563Asn, Leu125Val and Arg670Gly polymorphisms of the PECAM-1 gene and periodontitis. Methods. Genomic DNA was isolated from whole blood of 105 periodontal patient (52 with chronic periodontitis and 53 with aggressive periodontitis) and 101 healthy individuals. Samples were genotyped and analyzed for the three single-nucleotide polymorphisms (SNPs) of PECAM-1 using polymerase chain reaction with sequence-specific primers (PCR-SSPs). Results. A statistically significant difference was found betw

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Ke, Yaobin, Jiahua Rao, Huiying Zhao, Yutong Lu, Nong Xiao, and Yuedong Yang. "Accurate prediction of genome-wide RNA secondary structure profile based on extreme gradient boosting." Bioinformatics 36, no. 17 (2020): 4576–82. http://dx.doi.org/10.1093/bioinformatics/btaa534.

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Abstract Motivation RNA secondary structure plays a vital role in fundamental cellular processes, and identification of RNA secondary structure is a key step to understand RNA functions. Recently, a few experimental methods were developed to profile genome-wide RNA secondary structure, i.e. the pairing probability of each nucleotide, through high-throughput sequencing techniques. However, these high-throughput methods have low precision and cannot cover all nucleotides due to limited sequencing coverage. Results Here, we have developed a new method for the prediction of genome-wide RNA seconda

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Kameda, Takuro, Kotaro Shide, Haruko Shimoda, et al. "Absence of Somatically Acquired JAK1 Mutations in Adult T-Cell Leukemia/Lymphoma." Blood 114, no. 22 (2009): 1921. http://dx.doi.org/10.1182/blood.v114.22.1921.1921.

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Abstract Abstract 1921 Poster Board I-944 Background: Janus kinase 1 (JAK1) plays a critical role in lymphocyte proliferation and differentiation. Somatic JAK1 mutations are found in 18% of adult precursor T acute lymphoblastic leukemias (T-ALL). Some of the mutations were shown to induce the phosphorylation of JAK1 and STAT5 and lead to cytokine-independent proliferation. These data suggest that dysregulation of JAK1 can be involved in the development or progression of T-ALL (Flex et al. J Exp Med. 2008;205:751-758). Adult T-cell leukemia/lymphoma (ATLL) is a type of T-cell neoplasm, and the

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Sinha, Shweta, Jagtar Singh, and Surinder Kumar Jindal. "Association of Interleukin 7 Receptor (rs1494555 and rs6897932) Gene Polymorphisms with Asthma in a North Indian Population." Allergy & Rhinology 6, no. 3 (2015): ar.2015.6.0137. http://dx.doi.org/10.2500/ar.2015.6.0137.

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Background Interleukin 7R (IL-7R), a cytokine receptor gene, plays an important role in the development of innate and adaptive inflammatory response in asthma etiology. Objective IL-7R is a heterodimeric protein composed of α chain and γ chain. The α chain of IL-7R has a range of single nucleotide polymorphisms, which give rise to nonsynonymous amino-acid substitutions that might result in an increased production of inflammatory cytokines and cause asthma. Methods A case-control study was conducted with a total of 964 subjects, including 483 healthy controls and 481 patients with asthma. DNA s

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Ghazaryan, Hovsep, Roksana Zakharyan, Martin Petrek, et al. "Expression of micro-RNAs miR-31, miR-146a, miR-181c and miR-155 and their target gene IL-2 are altered in schizophrenia: a case-control study." F1000Research 8 (December 10, 2019): 2077. http://dx.doi.org/10.12688/f1000research.19900.1.

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Background: Schizophrenia is a severe psychiatric disorder with a heterogeneous clinical phenotype. The association of interleukins and other cytokines and their receptors with schizophrenia has been previously reported. Additionally, a number of studies have reported altered mico-RNA (miRNA) expression in schizophrenia and other psychiatric disorders. The aim of our study was to explore the possible association of miR-31, miR-146a, miR-181c and miR-155 with schizophrenia pathogenesis, as well as their link to IL2 gene expression in disease. Methods: For this case-control study, 225 patients w

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Lourenco, Daniela, Shogo Tsuruta, Yutaka Masuda, and Ignacy Misztal. "384 Genetic and Genomic Analysis in Livestock with Increasing Datasets." Journal of Animal Science 98, Supplement_4 (2020): 137–38. http://dx.doi.org/10.1093/jas/skaa278.253.

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Abstract In animal breeding and genetics, statistical methods have been used for several decades to identify animals with the best genetic potential. One of the foundations for computing accurate estimated breeding values (EBV) is the amount of data that is used in the evaluation system — as the more data points one animal has, the more accurate its EBV is going to be. However, the animal breeding and genetics field periodically faces a big data paradox, where efficient methods have to be developed to handle the amount of data collected over time, given the computing capacity becomes the limit

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Liu, Li, Jianjun Huang, Baomin Wei, et al. "Multiomics Analysis of Genetics and Epigenetics Reveals Pathogenesis and Therapeutic Targets for Atrial Fibrillation." BioMed Research International 2021 (March 25, 2021): 1–36. http://dx.doi.org/10.1155/2021/6644827.

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Objective. This study is aimed at understanding the molecular mechanisms and exploring potential therapeutic targets for atrial fibrillation (AF) by multiomics analysis. Methods. Transcriptomics and methylation data of AF patients were retrieved from the Gene Expression Omnibus (GEO). Differentially expressed genes (DEGs) and differentially methylated sites between AF and normal samples were screened. Then, highly expressed and hypomethylated and lowly expressed and hypermethylated genes were identified for AF. Weighted gene coexpression network analysis (WGCNA) was presented to construct AF-r

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McCrone, John T., and Adam S. Lauring. "Measurements of Intrahost Viral Diversity Are Extremely Sensitive to Systematic Errors in Variant Calling." Journal of Virology 90, no. 15 (2016): 6884–95. http://dx.doi.org/10.1128/jvi.00667-16.

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ABSTRACTWith next-generation sequencing technologies, it is now feasible to efficiently sequence patient-derived virus populations at a depth of coverage sufficient to detect rare variants. However, each sequencing platform has characteristic error profiles, and sample collection, target amplification, and library preparation are additional processes whereby errors are introduced and propagated. Many studies account for these errors by usingad hocquality thresholds and/or previously published statistical algorithms. Despite common usage, the majority of these approaches have not been validated

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