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Journal articles on the topic 'OLIGONUCLEOTIDE FREQUENCIES'

Author: Grafiati

Published: 11 September 2023

Last updated: 31 July 2025

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1

Wang, G., D. D. Levy, M. M. Seidman, and P. M. Glazer. "Targeted mutagenesis in mammalian cells mediated by intracellular triple helix formation." Molecular and Cellular Biology 15, no. 3 (1995): 1759–68. http://dx.doi.org/10.1128/mcb.15.3.1759.

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As an alternative to standard gene transfer techniques for genetic manipulation, we have investigated the use of triple helix-forming oligonucleotides to target mutations to selected genes within mammalian cells. By treating monkey COS cells with oligonucleotides linked to psoralen, we have generated targeted mutations in a simian virus 40 (SV40) vector contained within the cells via intracellular triple helix formation. Oligonucleotide entry into the cells and sequence-specific triplex formation within the SV40 DNA deliver the psoralen to the targeted site. Photoactivation of the psoralen by

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2

Martindale, Colin, and Andrzej K. Konopka. "Oligonucleotide frequencies in DNA follow a Yule distribution." Computers & Chemistry 20, no. 1 (1996): 35–38. http://dx.doi.org/10.1016/s0097-8485(96)80005-2.

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3

Hong, Juan. "Prediction of oligonucleotide frequencies based upon dinucleotide frequencies obtained from the nearest neighbor analysis." Nucleic Acids Research 18, no. 6 (1990): 1625–28. http://dx.doi.org/10.1093/nar/18.6.1625.

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Tyagi, Antariksh, Sumit K. Bag, Virendra Shukla, Sribash Roy, and Rakesh Tuli. "Oligonucleotide Frequencies of Barcoding Loci Can Discriminate Species across Kingdoms." PLoS ONE 5, no. 8 (2010): e12330. http://dx.doi.org/10.1371/journal.pone.0012330.

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5

Goussarov, Gleb, Ilse Cleenwerck, Mohamed Mysara, et al. "PaSiT: a novel approach based on short-oligonucleotide frequencies for efficient bacterial identification and typing." Bioinformatics 36, no. 8 (2020): 2337–44. http://dx.doi.org/10.1093/bioinformatics/btz964.

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Abstract Motivation One of the most widespread methods used in taxonomy studies to distinguish between strains or taxa is the calculation of average nucleotide identity. It requires a computationally expensive alignment step and is therefore not suitable for large-scale comparisons. Short oligonucleotide-based methods do offer a faster alternative but at the expense of accuracy. Here, we aim to address this shortcoming by providing a software that implements a novel method based on short-oligonucleotide frequencies to compute inter-genomic distances. Results Our tetranucleotide and hexanucleot

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McFarland, JG, RH Aster, JB Bussel, JG Gianopoulos, RS Derbes, and PJ Newman. "Prenatal diagnosis of neonatal alloimmune thrombocytopenia using allele- specific oligonucleotide probes." Blood 78, no. 9 (1991): 2276–82. http://dx.doi.org/10.1182/blood.v78.9.2276.2276.

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Abstract The prediction of neonatal alloimmune thrombocytopenia (NATP) in affected families has, in the past, been based on information about gene frequencies of the antigen systems involved, parental phenotyping, and fetal platelet counts. We explored the feasibility of allele- specific oligonucleotide probe typing for PIA antigens to determine the risk of second or subsequent fetuses in families where one infant had a diagnosis of anti-PIA1-mediated NATP. A total of eight families at risk for delivering an affected fetus were studied with both serologic and oligonucleotide typing. The correl

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McFarland, JG, RH Aster, JB Bussel, JG Gianopoulos, RS Derbes, and PJ Newman. "Prenatal diagnosis of neonatal alloimmune thrombocytopenia using allele- specific oligonucleotide probes." Blood 78, no. 9 (1991): 2276–82. http://dx.doi.org/10.1182/blood.v78.9.2276.bloodjournal7892276.

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The prediction of neonatal alloimmune thrombocytopenia (NATP) in affected families has, in the past, been based on information about gene frequencies of the antigen systems involved, parental phenotyping, and fetal platelet counts. We explored the feasibility of allele- specific oligonucleotide probe typing for PIA antigens to determine the risk of second or subsequent fetuses in families where one infant had a diagnosis of anti-PIA1-mediated NATP. A total of eight families at risk for delivering an affected fetus were studied with both serologic and oligonucleotide typing. The correlation bet

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Obata, Fumiya, Koichi Ito, Takehisa Kaneko, et al. "HLA-DR gene frequencies in the Japanese population obtained by oligonucleotide genotyping." Tissue Antigens 38, no. 1 (1991): 124–32. http://dx.doi.org/10.1111/j.1399-0039.1991.tb02025.x.

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9

Bai, Yu, Yuki Iwasaki, Shigehiko Kanaya, Yue Zhao, and Toshimichi Ikemura. "A Novel Bioinformatics Method for Efficient Knowledge Discovery by BLSOM from Big Genomic Sequence Data." BioMed Research International 2014 (2014): 1–11. http://dx.doi.org/10.1155/2014/765648.

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With remarkable increase of genomic sequence data of a wide range of species, novel tools are needed for comprehensive analyses of the big sequence data. Self-Organizing Map (SOM) is an effective tool for clustering and visualizing high-dimensional data such as oligonucleotide composition on one map. By modifying the conventional SOM, we have previously developed Batch-Learning SOM (BLSOM), which allows classification of sequence fragments according to species, solely depending on the oligonucleotide composition. In the present study, we introduce the oligonucleotide BLSOM used for characteriz

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Abe, Takashi, Yuta Hamano, and Toshimichi Ikemura. "Visualization of Genome Signatures of Eukaryote Genomes by Batch-Learning Self-Organizing Map with a Special Emphasis onDrosophilaGenomes." BioMed Research International 2014 (2014): 1–8. http://dx.doi.org/10.1155/2014/985706.

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A strategy of evolutionary studies that can compare vast numbers of genome sequences is becoming increasingly important with the remarkable progress of high-throughput DNA sequencing methods. We previously established a sequence alignment-free clustering method “BLSOM” for di-, tri-, and tetranucleotide compositions in genome sequences, which can characterize sequence characteristics (genome signatures) of a wide range of species. In the present study, we generated BLSOMs for tetra- and pentanucleotide compositions in approximately one million sequence fragments derived from 101 eukaryotes, fo

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Chan, Chon-Kit Kenneth, Arthur L. Hsu, Sen-Lin Tang, and Saman K. Halgamuge. "Using Growing Self-Organising Maps to Improve the Binning Process in Environmental Whole-Genome Shotgun Sequencing." Journal of Biomedicine and Biotechnology 2008 (2008): 1–10. http://dx.doi.org/10.1155/2008/513701.

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Metagenomic projects using whole-genome shotgun (WGS) sequencing produces many unassembled DNA sequences and small contigs. The step of clustering these sequences, based on biological and molecular features, is called binning. A reported strategy for binning that combines oligonucleotide frequency and self-organising maps (SOM) shows high potential. We improve this strategy by identifying suitable training features, implementing a better clustering algorithm, and defining quantitative measures for assessing results. We investigated the suitability of each of di-, tri-, tetra-, and pentanucleot

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12

Liu, Shaolin, Nicholas A. Tinker, and Diane E. Mather. "Exact word matches in rice pseudomolecules." Genome 49, no. 8 (2006): 1047–51. http://dx.doi.org/10.1139/g06-055.

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Using pseudomolecules of assembled genomic sequence, we computed the frequencies of 6 to 24 bp oligonucleotide (oligo) "words" across the genome of rice (Oryza sativa L. subsp. japonica). All oligos of 10 or fewer basepairs were repeated at least 12 times in the genome. The percentage of unique (non-repeated) oligos ranged from 0.1% for 12 bp oligos to 76.0% for 24 bp oligos. For three 200 kb regions, we annotated each nucleotide position with the genome-wide frequency of the 18 bp oligo starting at that position. These frequencies formed landscapes consisting of high- and low-frequency zones.

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Harvey, D., J. J. Pointon, C. Sleator, et al. "Analysis of killer immunoglobulin-like receptor genes in ankylosing spondylitis." Annals of the Rheumatic Diseases 68, no. 4 (2008): 595–98. http://dx.doi.org/10.1136/ard.2008.095927.

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Objectives:To assess the possible association of killer immunoglobulin-like receptor (KIR) genes, specifically KIR3DL1, KIR3DS1 and KIR3DL2, with ankylosing spondylitis (AS).Methods:14 KIR genes were genotyped in 200 UK patients with AS and 405 healthy controls using multiplex polymerase chain reaction. Sequence-specific oligonucleotide probes were used to subtype 368 cases with AS and 366 controls for 12 KIR3DL2 alleles. Differences in KIR genotypes and KIR3DL2 allele frequencies were assessed using the χ2 test.Results:KIR3DL1 and KIR3DS1 gene frequencies were very similar in cases with AS an

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Keller-Seitz, Monika U., Ulrich Certa, Christian Sengstag, Friedrich E. Würgler, Mingzeng Sun, and Michael Fasullo. "Transcriptional Response of Yeast to Aflatoxin B1: Recombinational Repair InvolvingRAD51andRAD1." Molecular Biology of the Cell 15, no. 9 (2004): 4321–36. http://dx.doi.org/10.1091/mbc.e04-05-0375.

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The potent carcinogen aflatoxin B1is a weak mutagen but a strong recombinagen in Saccharomyces cerevisiae. Aflatoxin B1exposure greatly increases frequencies of both heteroallelic recombination and chromosomal translocations. We analyzed the gene expression pattern of diploid cells exposed to aflatoxin B1using high-density oligonucleotide arrays comprising specific probes for all 6218 open reading frames. Among 183 responsive genes, 46 are involved in either DNA repair or in control of cell growth and division. Inducible growth control genes include those in the TOR signaling pathway and SPO12

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Liu, Haipeng, and Darrell Irvine. "Immunostimulatory properties of dynamic oligonucleotide micelles (53.9)." Journal of Immunology 188, no. 1_Supplement (2012): 53.9. http://dx.doi.org/10.4049/jimmunol.188.supp.53.9.

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Abstract Synthetic immunostimulatory oligonucleotides such as double-stranded RNA or unmethylated cytosine-guanosine motifs (CpG-ODNs) mimic molecular signatures of pathogens and trigger an immunostimulatory cascade; as a result, these synthetic ODNs have been extensively studied as therapeutic agents for cancer and as vaccine adjuvants. Using a self-assembly approach, we designed lipo-CpG-ODN molecules composed of CpG oligos conjugated with diacyl lipid tails. These dynamic amphiphiles form compact micelles ~20 nm in diam. in water but can also disassemble and insert their acyl tails into the

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Armstrong, EG, and JTP Verhoeven. "Machine learning analyses of bacterial oligonucleotide frequencies to assess the benthic impact of aquaculture." Aquaculture Environment Interactions 12 (April 9, 2020): 131–37. http://dx.doi.org/10.3354/aei00353.

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Aquaculture is a rapidly expanding industry and is now one of the primary sources of all consumed seafood. Intensive aquaculture production is associated with organic enrichment, which occurs as organic material settles onto the seafloor, creating anoxic conditions which disrupt ecological processes. Bacteria are sensitive bioindicators of organic enrichment, and supervised classifiers using features derived from 16s rRNA gene sequences have shown potential to become useful in aquaculture environmental monitoring. Current taxonomy-based approaches, however, are time intensive and built upon em

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Bohlin, Jon, Eystein Skjerve, and David W. Ussery. "Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes." BMC Genomics 9, no. 1 (2008): 104. http://dx.doi.org/10.1186/1471-2164-9-104.

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Arnau, Vicente, Wladimiro Díaz-Villanueva, Jorge Mifsut Benet, et al. "Inference of the Life Cycle of Environmental Phages from Genomic Signature Distances to Their Hosts." Viruses 15, no. 5 (2023): 1196. http://dx.doi.org/10.3390/v15051196.

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The environmental impact of uncultured phages is shaped by their preferred life cycle (lytic or lysogenic). However, our ability to predict it is very limited. We aimed to discriminate between lytic and lysogenic phages by comparing the similarity of their genomic signatures to those of their hosts, reflecting their co-evolution. We tested two approaches: (1) similarities of tetramer relative frequencies, (2) alignment-free comparisons based on exact k = 14 oligonucleotide matches. First, we explored 5126 reference bacterial host strains and 284 associated phages and found an approximate thres

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Ameen, Reem, Salem H. Al Shemmari, and Steven G. E. Marsh. "HLA Haplotype Frequencies and Genetic Profiles of the Kuwaiti Population." Medical Principles and Practice 29, no. 1 (2019): 39–45. http://dx.doi.org/10.1159/000499593.

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Objective: The aim of this study was to assess the HLA haplotype frequencies and genetic profiles of the Kuwaiti population. Materials and Methods: Whole venous blood was obtained from 595 healthy, unrelated Kuwaiti volunteers. The study population was genotyped for HLA class I (HLA-A, HLA-B, and HLA-C) and class II (HLA-DRB1 and HLA-DQB1) loci using sequence-specific oligonucleotide (SSO) probe-based hybridization and high-resolution HLA genotyping. Haplotype frequencies were estimated using an implementation of the expectation maximization algorithm that resolves both phase and allelic ambig

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Osman, Awad E., Faviel F. Gonzalez-Galarza, Mohamed Mubasher, et al. "HLA-A, -B, -C, -DRB1, and -DQB1 Allele Lineages and Haplotype Frequencies among Saudis." Immunology and Immunogenetics Insights 6 (January 2014): III.S16769. http://dx.doi.org/10.4137/iii.s16769.

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There are few reported studies on Saudi population for human leukocyte antigens (HLA) genes. We investigated allele lineages (two-digit) and haplotype frequencies of HLA-A, -B, -C, -DRB1, and -DQB1 loci in 499 healthy unrelated individuals, selected from potential bone marrow transplant (BMT) families’ donors at King Fahad Medical City (KFMC), Saudi Arabia (SA). Genotyping was performed by Sequence Specific Oligonucleotide Probe (SSOP) utilizing a Luminex-based method. Allele lineages and haplotype frequencies were evaluated along with principal component analysis (PCA) to compare findings wit

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Ikemura, Toshimichi, Yuki Iwasaki, Kennosuke Wada, Yoshiko Wada, and Takashi Abe. "AI-based search for convergently expanding, advantageous mutations in SARS-CoV-2 by focusing on oligonucleotide frequencies." PLOS ONE 17, no. 8 (2022): e0273860. http://dx.doi.org/10.1371/journal.pone.0273860.

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Among mutations that occur in SARS-CoV-2, efficient identification of mutations advantageous for viral replication and transmission is important to characterize and defeat this rampant virus. Mutations rapidly expanding frequency in a viral population are candidates for advantageous mutations, but neutral mutations hitchhiking with advantageous mutations are also likely to be included. To distinguish these, we focus on mutations that appear to occur independently in different lineages and expand in frequency in a convergent evolutionary manner. Batch-learning SOM (BLSOM) can separate SARS-CoV-

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Zhang, Jing, Jun Hu, Xiu-fan Shi, Huai Cao, and Wei-bo Liu. "Detection of potential positive regulatory motifs of transcription in yeast introns by comparative analysis of oligonucleotide frequencies." Computational Biology and Chemistry 27, no. 4-5 (2003): 497–506. http://dx.doi.org/10.1016/j.compbiolchem.2003.09.005.

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23

Quddus, Faiza, and Sayyeda Saba Batool. "Exploring HLA-DQA & HLA-DQB Polymorphisms in Local Population of Pakistan." TSF Journal of Biology 1, no. 1 (2023): 19–34. http://dx.doi.org/10.69547/tsfjb.v1i1.9.

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Human leukocyte antigens (HLA) are pivotal in immune regulation, crucial in organ transplants. Allelic frequencies at HLA-DQA1 and HLA-DQB1 were compared across age, gender, patient/donor status, blood group, cities, and ethnicity in 100 participants. DNA extracted from blood samples underwent quantification, hybridization, and sequence-specific oligonucleotide (SSO) typing. Match IT DNA software analyzed SSO typing, and statistical tools including Student's T-test and Analysis of Variance (ANOVA) assessed data, utilizing GraphPad Prism 6 and Microsoft Excel. Findings revealed varying allele f

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Mehta, S. C., B. P. Mishra, and M. S. Sahani. "Genetic differentiation of Indian camel (Camelus dromedarius) breeds using random oligonucleotide primers." Animal Genetic Resources Information 39 (April 2006): 77–88. http://dx.doi.org/10.1017/s1014233900002157.

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SummaryThe camel population in India is facing a severe decline which demands that immediate steps are taken to ensure its conservation. Characterisation is an integral part of the conservation program. The Polymerase Chain Reaction-Randomly Amplified Polymorphic DNA profile of unrelated camels of the Bikaneri (29), Jaisalmeri (30) and Kachchhi (18) breeds were analyzed. Reproducible polymorphic bands with varying frequencies among the three breeds of camel were obtained with five oligonucleotide primers. A total of 75 bands were amplified, of which 27 (36%) were polymorphic. The probability o

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Blake, Jonathan D., and R. D. Blake. "The use of multi-dimensional scaling to investigate similarities between non-random oligonucleotide frequencies in introns and exons." Computers & Chemistry 17, no. 2 (1993): 177–84. http://dx.doi.org/10.1016/0097-8485(93)85008-z.

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Mahdi, Rami N., and Eric C. Rouchka. "RBF-TSS: Identification of Transcription Start Site in Human Using Radial Basis Functions Network and Oligonucleotide Positional Frequencies." PLoS ONE 4, no. 3 (2009): e4878. http://dx.doi.org/10.1371/journal.pone.0004878.

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Wills, Mark R., Andrew J. Carmichael, Michael P. Weekes, et al. "Human Virus-Specific CD8+ CTL Clones Revert from CD45ROhigh to CD45RAhigh In Vivo: CD45RAhighCD8+ T Cells Comprise Both Naive and Memory Cells." Journal of Immunology 162, no. 12 (1999): 7080–87. http://dx.doi.org/10.4049/jimmunol.162.12.7080.

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Abstract It has been generally believed that human CD8+ memory cells are principally found within the CD45ROhigh population. There are high frequencies of CD8+ memory CTL specific for the human CMV tegument phosphoprotein pp65 in PBMC of long-term virus carriers; the large population of memory CTL specific for a given pp65 peptide contains individual CTL clones that have greatly expanded. In this study, we found high frequencies of pp65 peptide-specific memory CTL precursors in the CD45ROhighCD45RA− population, but also appreciable frequencies in the CD45RAhigh subpopulation. Because the major

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Huang, Xin, Kushi Kushekhar, Ilja Nolte, et al. "Multiple HLA class I and II associations in classical Hodgkin lymphoma and EBV status defined subgroups." Blood 118, no. 19 (2011): 5211–17. http://dx.doi.org/10.1182/blood-2011-04-342998.

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AbstractThe pathogenesis of classical Hodgkin lymphoma (cHL) involves environmental and genetic factors. To explore the role of the human leukocyte antigen (HLA) genes, we performed a case-control genotyping study in 338 Dutch cHL patients and more than 5000 controls using a PCR-based sequence-specific oligonucleotide probe hybridization approach. HLA-A68 and HLA-DR11 (5) were significantly increased in the cHL patient population compared with the controls. Three class II associations were observed in the EBV− cHL population with an increase of HLA-DR15 (2) and a decrease of HLA-DR4 and HLA-DR

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Zeiny, Sarmad M. "The correlation between HLA class II and β-thalassemia major in Al-Karama teaching hospital". Journal of the Faculty of Medicine Baghdad 58, № 4 (2016): 366–70. http://dx.doi.org/10.32007/jfacmedbagdad.584287.

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Background: Thalassemia is a form of inherited autosomal recessive blood disorder characterized by abnormal formation of hemoglobin.Objective: Determine frequencies & association of HLA class II alleles (DRB1& DQB1) in Iraqi β-thalassemia major patients.Patients: seventy unrelated randomly selected β-thalassemia major patients, and one hundred unrelated randomly selected healthy individuals, composed the control group.Methods: low resolution PCR-SSO (Sequence Specific Oligonucleotide) technique was used for HLA typing.Results: HLA DQB1*5 give significance importance as an etiological r

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Takahashi, Chikara, Amelia Au-Yeung, Johnny Gutierrez, Shadi Toghi-Eshghi, Rod Mathews, and William O’Gorman. "Evaluation of oligonucleotide conjugated antibodies as reporter molecules in single-cell assays." Journal of Immunology 204, no. 1_Supplement (2020): 86.35. http://dx.doi.org/10.4049/jimmunol.204.supp.86.35.

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Abstract Multiplexing in conventional flow and mass cytometric analysis has been constrained by both the number of available reporter molecules as well as signal spillover between these molecules. Monoclonal antibodies(mAbs) conjugated to oligonucleotides have been used in the design of ultrasensitive immunoassays but the multiplexing potential of these reagents have only recently been realized. The Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) method is established and uses oligo-conjugated mAbs and single-cell RNA sequencing technology to simultaneously enable the

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Doddapaneni, Harsha, Sara Javornik Cregeen, Richard Sucgang, et al. "Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals." PLOS ONE 16, no. 8 (2021): e0244468. http://dx.doi.org/10.1371/journal.pone.0244468.

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The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC q

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Goldberg, A. C., J. M. Chiarella, M. L. C. Marin, et al. "Molecular typing of HLA class II antigens in a São Paulo population." Genetics and Molecular Biology 21, no. 3 (1998): 301–5. http://dx.doi.org/10.1590/s1415-47571998000300001.

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In the present paper we show data obtained from a normal population with a racially mixed profile typical of the city of São Paulo, State of São Paulo. Data were generated with polymerase chain reaction using sequence specific primers (PCR-SSP) for HLA-DRB and polymerase chain reaction followed by hybridization with sequence specific oligonucleotide probes (PCR-SSO) for HLA-DQA1 and HLA-DQB1 loci. HLA-DRB, DQA1, DQB1 and haplotype frequencies as well as common linkage disequilibria were found. This population was also shown to be in genetic equilibrium according to the Hardy-Weinberg law. HLA-

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Zhang, Siyu, Pei Du, Xueying Lu, et al. "Frequent numerical and structural chromosome changes in early generations of synthetic hexaploid wheat." Genome 65, no. 4 (2022): 205–17. http://dx.doi.org/10.1139/gen-2021-0074.

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Modern hexaploid wheat (Triticum aestivum L.; AABBDD) has evolved from a hybrid of tetraploid wheat (closely related to Triticum turgidum L. ssp. durum (Desf.) Husn., AABB) and goatgrass (Aegilops tauschii Coss., DD). Variations in chromosome structure and ploidy have played important roles in wheat evolution. How these variations occur and their role in expanding the genetic diversity of modern wheat remain largely unknown. Synthetic hexaploid wheat (SHW) can be used to investigate chromosome variations that occur during the early generations of existence. SHW lines derived by crossing durum

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Theobald, M., and D. Bunjes. "Pretransplant detection of human minor histocompatibility antigen- specific naive and memory interleukin-2-secreting T cells within class I major histocompatibility complex (MHC)-restricted CD8+ and class II MHC-restricted CD4+ T-cell subsets." Blood 82, no. 1 (1993): 298–306. http://dx.doi.org/10.1182/blood.v82.1.298.bloodjournal821298.

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Recent studies have shown that host-reactive interleukin-2 (IL-2)- secreting donor T lymphocytes (TI) are critically involved in the development of acute graft-versus-host disease (GVHD) after allogeneic HLA-identical sibling bone marrow transplantation (BMT). To further characterize the responding TI, we determined the frequency of pretransplant IL-2-secreting TI-precursors (TI-p) between eight HLA-A, - B, -C, -DR, and -DQ-identical sibling donor-host pairs in both the graft-versus-host (GVH) and the host-versus-graft (HVG) direction. High frequencies of pretransplant host-reactive donor TI-p

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Okubo, H., K. Itou, S. Tanaka, N. Watanabe, N. Kashiwagi, and F. Obata. "Analysis of the HLA-DR gene frequencies in Japanese cases of juveniles rheumatoid arthritis and rheumatoid arthritis by oligonucleotide DNA typing." Rheumatology International 13, no. 2 (1993): 65–69. http://dx.doi.org/10.1007/bf00307736.

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Louie, Wilson, Max W. Shen, Zakir Tahiry, et al. "Machine learning based CRISPR gRNA design for therapeutic exon skipping." PLOS Computational Biology 17, no. 1 (2021): e1008605. http://dx.doi.org/10.1371/journal.pcbi.1008605.

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Restoring gene function by the induced skipping of deleterious exons has been shown to be effective for treating genetic disorders. However, many of the clinically successful therapies for exon skipping are transient oligonucleotide-based treatments that require frequent dosing. CRISPR-Cas9 based genome editing that causes exon skipping is a promising therapeutic modality that may offer permanent alleviation of genetic disease. We show that machine learning can select Cas9 guide RNAs that disrupt splice acceptors and cause the skipping of targeted exons. We experimentally measured the exon ski

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Louie, Wilson, Max W. Shen, Zakir Tahiry, et al. "Machine learning based CRISPR gRNA design for therapeutic exon skipping." PLOS Computational Biology 17, no. 1 (2021): e1008605. http://dx.doi.org/10.1371/journal.pcbi.1008605.

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Restoring gene function by the induced skipping of deleterious exons has been shown to be effective for treating genetic disorders. However, many of the clinically successful therapies for exon skipping are transient oligonucleotide-based treatments that require frequent dosing. CRISPR-Cas9 based genome editing that causes exon skipping is a promising therapeutic modality that may offer permanent alleviation of genetic disease. We show that machine learning can select Cas9 guide RNAs that disrupt splice acceptors and cause the skipping of targeted exons. We experimentally measured the exon ski

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Chan, Kai-Chieh, Che-Ming Wu, Wan-Ling Ho, and Ping-Chin Lai. "Association of Ménière Disease with Human Leukocyte Antigen in Taiwanese Population." Ear, Nose & Throat Journal 97, no. 12 (2018): 396–402. http://dx.doi.org/10.1177/014556131809701208.

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The etiology of Ménière disease (MD) is multifactorial; genetic factors seem to play an important role. The associations between MD and human leukocyte antigen (HLA) status have been studied previously in several populations and have shown that the HLA alleles imparting susceptibility varied. In the present study, we explored HLA status in Taiwanese patients with definitive MD. HLA was typed via polymerase chain reaction, sequence-specific oligonucleotide genotyping in 35 patients with MD diagnosed using the criteria of the American Academy of Otolaryngology–Head and Neck Surgery and 70 unrela

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Bahgat, Dina M. R., Alaa A. Gad, Walid R. Kosmass, Mariam R. Fadel, and Fatma H. Abdelraouf. "Frequency of class 1 human leukocyte antigen allele subtypes in Egyptian patients with idiopathic uveitis." Journal of the Egyptian Ophthalmological Society 116, no. 1 (2023): 42–49. http://dx.doi.org/10.4103/ejos.ejos_91_22.

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Bacground Idiopathic uveitis is the most common uveitis type and is viewed as an inconclusive diagnosis for patients as well as physicians. Human leukocyte antigen (HLA) typing helps in understanding the pathogenesis of several diseases. Limited knowledge is known regarding the association of HLA with idiopathic uveitis. Aim This was a cross-sectional observational case–control study evaluating HLA-A and HLA-B allelic and phenotypic frequencies in patients with idiopathic uveitis. Patients and methods HLA-A and HLA-B molecular typing by PCR-sequence-specific oligonucleotide probes and LIRAS in

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Al Yafei, Zain, Abdelhafidh Hajjej, Marion Alvares, et al. "Analysis of the Origin of Emiratis as Inferred from a Family Study Based on HLA-A, -C, -B, -DRB1, and -DQB1 Genes." Genes 14, no. 6 (2023): 1159. http://dx.doi.org/10.3390/genes14061159.

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In this study, we investigated HLA class I and class II allele and haplotype frequencies in Emiratis and compared them to those of Asian, Mediterranean, and Sub-Saharan African populations. Methods: Two-hundred unrelated Emirati parents of patients selected for bone marrow transplantation were genotyped for HLA class I (A, B, C) and class II (DRB1, DQB1) genes using reverse sequence specific oligonucleotide bead-based multiplexing. HLA haplotypes were assigned with certainty by segregation (pedigree) analysis, and haplotype frequencies were obtained by direct counting. HLA class I and class II

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van Helden, J., B. André, and J. Collado-Vides. "Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies 1 1Edited by G. von Heijne." Journal of Molecular Biology 281, no. 5 (1998): 827–42. http://dx.doi.org/10.1006/jmbi.1998.1947.

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Sahin Tekin, Melisa, Goknur Yorulmaz, Emel Yantir, Eren Gunduz, and Ertugrul Colak. "A Novel Finding of an HLA Allele’s and a Haplotype’s Relationship with SARS-CoV-2 Vaccine-Associated Subacute Thyroiditis." Vaccines 10, no. 12 (2022): 1986. http://dx.doi.org/10.3390/vaccines10121986.

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Subacute thyroiditis (SAT) is a thyroid disease associated with viral infections. Its relationship with major histocompatibility complex (MHC) antigens was shown before. SAT cases triggered by different types of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines have been reported. In this study, human leukocyte antigen (HLA) genotypes of 27 SAT patients (13 vaccine-associated (V-SAT) and 14 non-SARS-CoV-2-infection non-vaccine-associated (non-V-SAT)) were compared with those of 362 healthy donors. HLA analyses were performed with low-resolution DNA-based sequence-specific o

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Du, Wei-Dong, Gang Chen, Hui-Min Cao, et al. "A Simple Oligonucleotide Biochip Capable of Rapidly Detecting Known Mitochondrial DNA Mutations in Chinese Patients with Leber’S Hereditary Optic Neuropathy (LHON)." Disease Markers 30, no. 4 (2011): 181–90. http://dx.doi.org/10.1155/2011/340723.

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Leber's hereditary optic neuropathy (LHON) is a maternally transmitted disease. Clinically, no efficient assay protocols have been available. In this study, we aimed to develop an oligonucleotide biochip specialized for detection of known base substitution mutations in mitochondrial DNA causing LHON and to investigate frequencies of LHON relevant variants in Anhui region of China. Thirty-two pairs of oligonucleotide probes matched with the mutations potentially linked to LHON were covalently immobilized. Cy5-lablled targets were amplified from blood DNA samples by a multiplex PCR method. Two k

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Thonnard, Joëlle, Marianne Philippe, Ming-Yu Cao, et al. "HLA Class II-Associated Genetic Susceptibility in Idiopathic Progressive Sensorineural Hearing Loss." Annals of Otology, Rhinology & Laryngology 105, no. 8 (1996): 628–33. http://dx.doi.org/10.1177/000348949610500808.

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To investigate the association between genes in the major histocompatibility complex and inner ear disease susceptibility at the DNA level, high-resolution genotyping for HLA class II (HLA-DR, -DQ, -DP) was performed by polymerase chain reaction-sequence-specific oligonucleotide reverse dot blot and polymerase chain reaction-restriction fragment length polymorphism analysis in 34 patients with idiopathic progressive sensorineural hearing loss (PSHL) and in 214 controls. The frequencies of DRB1*0301, DRB3*0101, DQB1*0201, and DPB1*0401 were significantly increased in patients with idiopathic PS

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Bohlin, Jon. "Genomic Signatures in Microbes—Properties and Applications." Scientific World JOURNAL 11 (2011): 715–25. http://dx.doi.org/10.1100/tsw.2011.70.

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The ratio of genomic oligonucleotide frequencies relative to the mean genomic AT/GC content has been shown to be similar for closely related species and, therefore, said to reflect a “genomic signature”. The genomic signature has been found to be more similar within genomes than between closely related genomes. Furthermore, genomic signatures of closely related organisms are, in turn, more similar than more distantly related organisms. Since the genomic signature is remarkably stable within a genome, it can be extracted from only a fraction of the genomic DNA sequence. Genomic signatures, ther

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Nikaein, A., D. Cluff, R. Fishbeck, L. Dombrausky, and J. Fay. "Serologic and oligonucleotide typing of HLA antigens, MLC and helper and cytotoxic T cell frequencies in selection of unrelated bone marrow transplant donors." Human Immunology 40 (January 1994): 25. http://dx.doi.org/10.1016/0198-8859(94)91708-6.

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Calamita, Zamir, Andrea Bronhara Pelá, Márcia Gamberini, et al. "HLA among Brazilian patients with spontaneous chronic urticaria and positive autologous serum skin test." Anais Brasileiros de Dermatologia 87, no. 4 (2012): 578–83. http://dx.doi.org/10.1590/s0365-05962012000400010.

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BACKGROUND: An association between class I and II alleles of the major histocompatibility complex and idiopathic chronic urticaria has previously been observed in different populations, but there are still no studies on Brazilian populations in this regard. OBJECTIVE: The involvement of the major histocompatibility complex classes I and II (loci A, B and DR) in Brazilian patients with idiopathic chronic urticaria and a positive autologous serum skin test was investigated and compared with a healthy population group. METHODS: DNA was extracted from the blood of 42 patients with idiopathic chron

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Pearce, Richard J., Chris Drakeley, Daniel Chandramohan, Frank Mosha, and Cally Roper. "Molecular Determination of Point Mutation Haplotypes in the Dihydrofolate Reductase and Dihydropteroate Synthase of Plasmodium falciparum in Three Districts of Northern Tanzania." Antimicrobial Agents and Chemotherapy 47, no. 4 (2003): 1347–54. http://dx.doi.org/10.1128/aac.47.4.1347-1354.2003.

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ABSTRACT The antimalarial combination of sulfadoxine and pyrimethamine (SP) was introduced as first-line treatment for uncomplicated malaria in Tanzania during 2001 following 18 years of second-line use. The genetic determinants of in vitro resistance to the two drugs individually are shown to be point mutations at seven sites in the dihydrofolate reductase gene (dhfr) conferring resistance to pyrimethamine and five sites in the dihydropteroate synthase (dhps) gene conferring resistance to sulfadoxine. Different combinations of mutations within each gene confer differing degrees of insensitivi

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Vickerman, M. M., S. Iobst, A. M. Jesionowski, and S. R. Gill. "Genome-Wide Transcriptional Changes in Streptococcus gordonii in Response to Competence Signaling Peptide." Journal of Bacteriology 189, no. 21 (2007): 7799–807. http://dx.doi.org/10.1128/jb.01023-07.

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ABSTRACT Streptococcus gordonii is a primary colonizer of the multispecies biofilm on tooth surfaces forming dental plaque and a potential agent of endocarditis. The recent completion of the genome sequence of the naturally competent strain Challis allowed the design of a spotted oligonucleotide microarray to examine a genome-wide response of this organism to environmental stimuli such as signal peptides. Based on temporal responses to synthetic competence signaling peptide (CSP) as indicated by transformation frequencies, the S. gordonii transcriptome was analyzed at various time points after

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Revenko, Alexey, Larissa S. Carnevalli, Charles Sinclair, et al. "Direct targeting of FOXP3 in Tregs with AZD8701, a novel antisense oligonucleotide to relieve immunosuppression in cancer." Journal for ImmunoTherapy of Cancer 10, no. 4 (2022): e003892. http://dx.doi.org/10.1136/jitc-2021-003892.

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BackgroundThe Regulatory T cell (Treg) lineage is defined by the transcription factor FOXP3, which controls immune-suppressive gene expression profiles. Tregs are often recruited in high frequencies to the tumor microenvironment where they can suppress antitumor immunity. We hypothesized that pharmacological inhibition of FOXP3 by systemically delivered, unformulated constrained ethyl-modified antisense oligonucleotides could modulate the activity of Tregs and augment antitumor immunity providing therapeutic benefit in cancer models and potentially in man.MethodsWe have identified murine Foxp3

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