检索结果-内蒙古大学图书馆

Francisella tularensis subsp. novicida isolated from a human in Arizona

BMC Research Notes 2009年第1期2卷 1-6页

作者： Birdsell, Dawn N Stewart, Tasha Vogler, Amy J Lawaczeck, Elisabeth Diggs, Alisa Sylvester, Tammy L Buchhagen, Jordan L Auerbach, Raymond K Keim, Paul Wagner, David M Center for Microbial Genetics and Genomics Northern Arizona University Flagstaff AZ 86011-4073 United States Maricopa County Department of Public Health Phoenix AZ 85012 United States Arizona Department of Health Services Phoenix AZ 85007 United States Translational Genomics Research Institute Phoenix AZ 85004 United States Program in Computational Biology and Bioinformatics Yale University New Haven CT 06520 United States

Background. Francisella tularensis is the etiologic agent of tularemia and is classified as a select agent by the Centers for Disease Control and Prevention. Currently four known subspecies of F. tularensis that differ in virulence and geographical distribution are recognized:tularensis (type A), holarctica (type B), mediasiatica, and novicida. Because of the Select Agent status and differences in virulence and geographical location, the molecular analysis of any clinical case of tularemia is of particular interest. We analyzed an unusual Francisella clinical isolate from a human infection in Arizona using multiple DNA-based approaches. Findings. We report that the isolate is F. tularensis subsp. novicida, a subspecies that is rarely isolated. Conclusion. The rarity of this novicida subspecies in clinical settings makes each case study important for our understanding of its role in disease and its genetic relationship with other F. tularensis subspecies. © 2009 Wagner et al;licensee BioMed Central Ltd.

关键词： Clinical Isolate Coccidioidomycosis Tularemia Francisella Tularensis Tularensis Subsp

来源：评论

学校读者我要写书评

暂无评论

Worm Perturb-Seq: massively parallel whole-animal RNAi and RNA-seq

引用

Nature Communications 2025年第1期16卷 1-21页

作者： Hefei Zhang Xuhang Li Shivani Nanda Albertha J. M. Walhout Dongyuan Song Jingyi Jessica Li Onur Yukselen Alper Kucukural Manuel Garber Department of Systems Biology University of Massachusetts Chan Medical School Worcester MA USA Bioinformatics Interdepartmental Ph.D. Program University of California Los Angeles CA USA Department of Statistics and Data Science Department of Biostatistics Department of Computational Medicine and Department of Human Genetics University of California Los Angeles CA USA Via Scientific Inc. Cambridge MA USA Department of Genomics and Computational Biology University of Massachusetts Chan Medical School Worcester MA USA

Transcriptomes provide highly informative molecular phenotypes that, combined with gene perturbation, can connect genotype to phenotype. An ultimate goal is to perturb every gene and measure transcriptome changes, however, this is challenging, especially in whole animals. Here, we present ‘Worm Perturb-Seq (WPS)’, a method that provides high-resolution RNA-sequencing profiles for hundreds of replicate perturbations at a time in living animals. WPS introduces multiple experimental advances combining strengths of Caenhorhabditis elegans genetics and multiplexed RNA-sequencing with a novel analytical framework, EmpirDE. EmpirDE leverages the unique power of large transcriptomic datasets and improves statistical rigor by using gene-specific empirical null distributions to identify DEGs. We apply WPS to 103 nuclear hormone receptors (NHRs) and find a striking ‘pairwise modularity’ in which pairs of NHRs regulate shared target genes. We envision the advances of WPS to be useful not only for C. elegans, but broadly for other models, including human cells.

关键词：

来源：评论

学校读者我要写书评

暂无评论

RETRACTION: RETRACTED: Crystal structure of a Baeyer-Villiger flavin-containing monooxygenase from Staphylococcus aureus MRSA strain MU50 (Retraction of 2014)

引用

PROTEINS-STRUCTURE FUNCTION AND bioinformatics 2018年第2期86卷 269-269页

作者： Hwang, William C. Xu, Qingping Wu, Bainan Godzik, Adam Bioinformatics Core Joint Center for Structural Genomics (JCSG) La Jolla California 92037 Bioinformatics and Systems Biology Program Sanford-Burnham Medical Research Institute La Jolla California 92037.

The above article from Proteins: Structure, Function, and bioinformatics, published online on 5 August 2014 in Wiley Online Library (http://***/doi/10.1002/prot.24661/full), has been retracted by agreement between William C. Hwang, Qingping Xu, Bainan Wu, Adam Godzik, the Editor‐in‐Chief, Bertrand E. Garcia‐Moreno, and Wiley Periodicals, Inc. The retraction has been agreed because submission was made without agreement from co‐author Adam Godzik.

关键词： Baeyer-Villiger reaction FMO antibiotics resistance methicillin vancomycin

来源：评论

学校读者我要写书评

暂无评论

Spliceosomal genes in the *** genome:a comparison with those in ***,***,*** and ***

引用

Protein & Cell 2011年第5期2卷 395-409页

作者： Bing Yu Petra Fey Karen E.Kestin-Pilcher Alexei Fedorov Ashwin Prakash Rex L.Chisholm Jane Y.Wu Department of Molecular and Clinical Genetics Royal Prince Alfred Hospital and Sydney Medical School(Central)the University of SydneyNSW 2006Australia dictyBase Center for Genetic MedicineNorthwestern UniversityChicagoIL 60611USA Department of Neurology and Lurie Comprehensive Cancer Center Center for Genetic MedicineNorthwestern University Feinberg Medical SchoolChicagoIL 60611USA Department of Medicine and Program in Bioinformatics and Proteomics/Genomics The University of ToledoToledoOH 43614USA

Little is known about pre-mRNA splicing in Dictyostelium discoideum although its genome has been completely *** analysis suggests that pre-mRNA splicing plays an important role in *** gene expression as two thirds of its genes contain at least one *** curation of the genome to date has revealed 40 genes in *** with clear evidence of alternative splicing,supporting the existence of alternative splicing in this unicellular *** identified 160 candidate U2-type spliceosomal proteins and related factors in *** based on 264 known human genes involved in *** small ribonucleoproteins(snRNPs),PRP19 complex proteins and late-acting proteins are highly conserved in *** and throughout the *** non-snRNP and hnRNP families,*** orthologs are closer to those in ***,*** and *** than to their counterparts in *** splicing regulators,including SR proteins and CUGbinding proteins,were found in ***,but not in *** comprehensive catalog of spliceosomal proteins provides useful information for future studies of splicing in *** where the efficient genetic and biochemical manipulation will also further our general understanding of pre-mRNA splicing.

关键词： pre-mRNA splicing spliceosomal genes Dictyostelium discoideum comparative genomics splicing regulators

来源：评论

学校读者我要写书评

暂无评论

Correcting base-assignment errors in repeat regions of shotgun assembly

Correcting base-assignment errors in repeat regions of shotg...

引用

作者： Zhi, Degui Keich, Uri Pevzner, Pavel Heber, Steffen Tang, Haixu Bioinformatics Program University of California San Diego San Diego CA 92093 Department of Computer Science 4130 Upson Hall Cornell University Ithaca NY 14853 Department of Computer Science and Engineering University of California San Diego San Diego CA 92093 North Carolina State University Raleigh NC 27695-7566 School of Informatics Center for Genomics and Bioinformatics Indiana University Bloomington IN 47408

Accurate base-assignment in repeat regions of a whole genome shotgun assembly is an unsolved problem. Since reads in repeat regions cannot be easily attributed to a unique location in the genome, current assemblers may place these reads arbitrarily. As a result, the base-assignment error rate in repeats is likely to be much higher than that in the rest of the genome. We developed an iterative algorithm, EULER-AIR, that is able to correct base-assignment errors in finished genome sequences in public databases. The Wolbachia genome is among the best finished genomes. Using this genome project as an example, we demonstrated that EULER-AIR can 1) discover and correct base-assignment errors, 2) provide accurate read assignments, 3) utilize finishing reads for accurate base-assignment and 4) provide guidance for designing finishing experiments. In the genome of Wolbachia, EULER-AIR found 16 positions with ambiguous base-assignment and two positions with erroneous bases. Besides Wolbachia, many other genome sequencing projects have significantly fewer finishing reads and, hence, are likely to contain more base-assignment errors in repeats. We demonstrate that EULER-AIR is a software tool that can be used to find and correct base-assignment errors in a genome assembly project. © 2007 IEEE.

关键词： Error analysis

来源：评论

学校读者我要写书评

暂无评论

Determinants of translation speed are randomly distributed across transcripts resulting in a universal scaling of protein synthesis times

引用

Physical Review E 2018年第2期97卷 022409-022409页

作者： Ajeet K. Sharma Nabeel Ahmed Edward P. O’Brien Department of Chemistry Pennsylvania State University University Park Pennsylvania 16802 USA Bioinformatics and Genomics Graduate Program The Huck Institutes of the Life Sciences Pennsylvania State University University Park Pennsylvania 16802 USA

Ribosome profiling experiments have found greater than 100-fold variation in ribosome density along mRNA transcripts, indicating that individual codon elongation rates can vary to a similar degree. This wide range of elongation times, coupled with differences in codon usage between transcripts, suggests that the average codon translation-rate per gene can vary widely. Yet, ribosome run-off experiments have found that the average codon translation rate for different groups of transcripts in mouse stem cells is constant at 5.6 AA/s. How these seemingly contradictory results can be reconciled is the focus of this study. Here, we combine knowledge of the molecular factors shown to influence translation speed with genomic information from Escherichia coli, Saccharomyces cerevisiae and Homo sapiens to simulate the synthesis of cytosolic proteins in these organisms. The model recapitulates a near constant average translation rate, which we demonstrate arises because the molecular determinants of translation speed are distributed nearly randomly amongst most of the transcripts. Consequently, codon translation rates are also randomly distributed and fast-translating segments of a transcript are likely to be offset by equally probable slow-translating segments, resulting in similar average elongation rates for most transcripts. We also show that the codon usage bias does not significantly affect the near random distribution of codon translation rates because only about 10% of the total transcripts in an organism have high codon usage bias while the rest have little to no bias. Analysis of Ribo-Seq data and an in vivo fluorescent assay supports these conclusions.

关键词： Gene expression Bacteria Genes Proteins Markovian processes Monte Carlo methods

来源：评论

学校读者我要写书评

暂无评论

VirusT5: Harnessing Large Language Models to Predicting SARS-CoV-2 Evolution

arXiv

引用

arXiv 2024年

作者： Marathe, Vishwajeet Bajracharya, Deewan Yan, Changhui The Department of Computer Science Department of North Dakota State University FargoND58102 United States The Genomics Phenomics and Bioinformatics Program of North Dakota State University FargoND58102 United States The Department of Computer Science and the Genomics Phenomics and Bioinformatics Program of North Dakota State University FargoND58102 United States

During a virus's evolution, various regions of the genome are subjected to distinct levels of functional constraints. Combined with factors like codon bias and DNA repair efficiency, these constraints contribute to unique mutation patterns within the genome or a specific gene. In this project, we harnessed the power of Large Language Models (LLMs) to predict the evolution of SARS-CoV-2. By treating the mutation process from one generation to the next as a translation task, we trained a transformer model, called VirusT5, to capture the mutation patterns underlying SARS-CoV-2's evolution. We evaluated the VirusT5's ability to detect these mutation patterns including its ability to identify mutation hotspots and explored the potential of using VirusT5 to predict future virus strains. Our findings demonstrate the feasibility of using a large language model to model viral evolution as a translation process. This study establishes the groundbreaking concept of "mutation-as-translation," paving the way for new methodologies and tools in combating viral threats. © 2024, CC BY.

关键词： Genome

来源：评论

学校读者我要写书评

暂无评论

Parsimonious reconstruction of network evolution

Parsimonious reconstruction of network evolution

引用

Lecture Notes in Computer Science

作者： Patro, Rob Sefer, Emre Malin, Justin Marçais, Guillaume Navlakha, Saket Kingsford, Carl Center for Bioinformatics and Computational Biology University of Maryland College Park MD 20742 United States Department of Computer Science University of Maryland College Park MD 20742 United States Computational Biology Bioinformatics and Genomics Concentration Biological Sciences Graduate Program University of Maryland College Park MD 20742 United States Program in Applied Mathematics Statistics and Scientific Computation University of Maryland College Park MD 20742 United States School of Computer Science Carnegie Mellon University Pittsburgh PA 15213 United States

ISBN: (纸本)9783642230370

We consider the problem of reconstructing a maximally parsimonious history of network evolution under models that support gene duplication and loss and independent interaction gain and loss. We introduce a combinatorial framework for encoding network histories, and we give a fast procedure that, given a set of duplication histories, in practice finds network histories with close to the minimum number of interaction gain or loss events. In contrast to previous studies, our method does not require knowing the relative ordering of unrelated duplication events. Results on simulated histories suggest that common ancestral networks can be accurately reconstructed using this parsimony approach. © 2011 Springer-Verlag.

关键词： Genes

来源：评论

学校读者我要写书评

暂无评论

Enhancing healthcare AI stability with edge computing and machine learning for extubation prediction

引用

Scientific Reports 2025年第1期15卷 1-11页

作者： Kuo-Yang Huang Ching-Hsiung Lin Che-Liang Chung Ying-Lin Hsu Huang-Chi Chen Ming-Hwarng Horng Ching-Sen Liu Jia-Lang Xu Division of Chest Medicine Department of Internal Medicine Changhua Christian Hospital Changhua Taiwan Institute of Genomics and Bioinformatics National Chung Hsing University Taichung Taiwan Ph.D. Program in Medical Biotechnology National Chung Hsing University Taichung Taiwan Division of Chest Medicine Department of Internal Medicine Yuanlin Christian Hospital Changhua Taiwan Institute of Statistics National Chung Hsing University Taichung Taiwan Department of Applied Mathematics National Chung Hsing University Taichung Taiwan Department of Computer Science and Information Engineering Chaoyang University of Technology Taichung Taiwan

The advancement of the Internet of Medical Things (IoMT) has revolutionized data acquisition and processing in critical care settings. Given the pivotal role of ventilators, accurately predicting extubation outcomes is essential to optimize patient care. This study presents an edge computing-based framework that incorporates machine learning algorithms to predict ventilator extubation success using real-time data collected directly from ventilators. The system was deployed on edge devices to enable on-site inference with minimal latency. Among the evaluated models, Random Forest and XGBoost, the latter demonstrated superior predictive performance under both holdout and tenfold cross-validation schemes. Notably, the edge-based architecture reduced server data transmissions by 83.33%, while improving system stability, resilience, and sustainability. This paper details the model evaluation and demonstrates the feasibility and efficiency of edge intelligence in ventilator weaning decision support.

关键词：

来源：评论

学校读者我要写书评

暂无评论

OP0153 BROADENING OUR UNDERSTANDING OF THE GENETICS OF JUVENILE IDIOPATHIC ARTHRITIS: INTERROGATION OF THREE DIMENSIONAL CHROMATIN STRUCTURES WITHIN JIA-ASSOCIATED RISK LOCI

引用

Annals of the Rheumatic Diseases 2019年 78卷 151-152页

作者： Haeja Kessler Evan Tarbell Yungki Park Jim Jarvis University at Buffalo Pediatrics Buffalo United States of America University at Buffalo Biochemistry Buffalo United States of America University at Buffalo Genetics Genomics and Bioinformatics Program Buffalo United States of America

Background Our group has shown that, like most complex traits, the risk loci for juvenile idiopathic arthritis (JIA) identified on genome-wide association studies (GWAS) and genetic fine mapping studies are highly enriched for enhancers. Enhancers are regulatory elements that fine-tune gene expression to specific physiologic circumstances. Enhancers do not always regulate the nearest gene, and may regulate more than one gene. Enhancers typically regulate genes within the same chromatin loop, or topologically associated domain (TAD). Objectives To gain a better understanding of the genetics of JIA by examining the broader chromatin architecture that encompasses the known risk haplotypes. Methods We used publically available chromatin conformation HiC data and the online JuiceBox software suite to query known JIA risk haplotypes for evidence of physical interactions between putative enhancers within the haplotypes and immunologically relevant genes. We specifically queried 20 haplotypes in which H3K4me1/H3K27ac marks were prominent within both lymphoid and myeloid cells. We queried data from GM12787 (B cell), K562 (lymphoblast), and THP-1 (monocyte/macrophage) cells, as well as human cord blood T cells. To identify TADs associated with specific enhancers, we used a 5KB resolution (which allowed us to visualize chromatin loops as peaks), setting the cursor at the center of each putative enhancer. We also identified the genes within the identified chromatin loop domains and used gene ontology (GO) analyses to identify functional associations among genes within the TADs incorporating the JIA risk loci. Results We identified at least one chromatin loop structure in all 20 of the JIA risk haplotypes for each of the 4 cell lines we queried. These loops were not cell type specific. That is, almost identical loops structures could be seen in each of the cell lines at each of the loci, suggesting that these enhancers regulate a broad range of common leukocyte functions. The TA

关键词：

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：