检索结果-内蒙古大学图书馆

SPARSE: Quadratic time simultaneous alignment and folding of rnas without sequence-based heuristics

17th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2013

作者： Will, Sebastian Schmiedl, Christina Miladi, Milad Möhl, Mathias Backofen, Rolf Bioinformatics Department of Computer Science University of Freiburg Germany Bioinformatics Department of Computer Science University of Leipzig Germany University of Freiburg Germany University of Freiburg Germany Centre for Non-coding RNA in Technology and Health Bagsvaerd Denmark

ISBN: (纸本)9783642371943

Motivation: There is increasing evidence of pervasive transcription, resulting in hundreds of thousands of ncrnas of unknown function. Standard computational analysis tasks for inferring functional annotations like clustering require fast and accurate rna comparisons based on sequence and structure similarity. The gold standard for the latter is Sankoff's algorithm [3], which simultaneously aligns and folds rnas. Because of its extreme time complexity of O(n6), numerous faster "Sankoff-style" approaches have been suggested. Several such approaches introduce heuristics based on sequence alignment, which compromises the alignment quality for rnas with sequence identities below 60% [1]. Avoiding such heuristics, as e.g. in LocArna [4], has been assumed to prohibit time complexities better than O(n 4), which strongly limits large-scale applications. © 2013 Springer-Verlag.

关键词： Alignment

来源：评论

学校读者我要写书评

暂无评论

50 shades of rule composition from chemical reactions to higher levels of abstraction

引用

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 2014年 8738卷 115-135页

作者： Andersen, Jakob Lykke Flamm, Christoph Merkle, Daniel Stadler, Peter F. Department of Mathematics and Computer Science University of Southern Denmark Denmark Institute for Theoretical Chemistry University of Vienna Austria Bioinformatics Group Department of Computer Science and Interdisciplinary Center for Bioinformatics Leipzig Germany Max Planck Institute for Mathematics in the Sciences Leipzig Germany Fraunhofer Institute for Cell Therapy and Immunology Leipzig Germany Center for Non-coding RNA in Technology and Health University of Copenhagen Denmark Santa Fe Institute United States

ISBN: (纸本)9783319103976

Graph rewriting has been applied quite successfully to model chemical and biological systems at different levels of abstraction. A particularly powerful feature of rule-based models that are rigorously grounded in category theory, is, that they admit a well-defined notion of rule composition, hence, provide their users with an intrinsic mechanism for compressing trajectories and coarse grained representations of dynamical aspects. The same formal framework, however, also allows the detailed analysis of transitions in which the final and initial states are known, but the detailed stepwise mechanism remains hidden. To demonstrate the general principle we consider here how rule composition is used to determine accurate atom maps for complex enzyme reactions. This problem not only exemplifies the paradigm but is also of considerable practical importance for many down-stream analyses of metabolic networks and it is a necessary prerequisite for predicting atom traces for the analysis of isotope labelling experiments. © Springer International Publishing Switzerland 2014.

关键词： Biological systems

来源：评论

学校读者我要写书评

暂无评论

Identification of valid reference genes for microrna expression studies in a hepatitis B virus replicating liver cell line

引用

BMC Research Notes 2016年第1期9卷 1-7页

作者： Jacobsen, Kari Stougaard Nielsen, Kirstine Overgaard Winther, Thilde Nordmann Glebe, Dieter Pociot, Flemming Hogh, Birthe Department of Paediatrics Hvidovre Hospital University of Copenhagen Copenhagen Denmark Department of Paediatrics Center for Non-Coding RNA in Technology and Health Herlev Hospital University of Copenhagen Copenhagen Denmark Institute of Medical Virology National Reference Center for Hepatitis B and D Viruses German Center for Infection Research Biomedical Research Center Seltersberg Justus-Liebig University Giessen Giessen Germany

Background: Micrornas are regulatory molecules and suggested as non-invasive biomarkers for molecular diagnostics and prognostics. Altered expression levels of specific micrornas are associated with hepatitis B virus infection and hepatocellular carcinoma. We previously identified differentially expressed micrornas with liver-specific target genes in plasma from children with chronic hepatitis B. To further understand the biological role of these micrornas in the pathogenesis of chronic hepatitis B, we have used the human liver cell line HepG2, with and without HBV replication, after transfection of hepatitis B virus expression vectors. RT-qPCR is the preferred method for microrna studies, and a careful normalisation strategy, verifying the optimal set of reference genes, is decisive for correctly evaluating microrna expression levels. The aim of this study was to provide valid reference genes for the human HCC-derived cell line HepG2. Results: A panel of 739 micrornas was screened to identify the most stably expressed micrornas, followed by a PubMed search identifying micrornas previously used as reference genes. Sixteen candidate reference genes were validated by RT-qPCR. Reference gene stabilities were calculated first by standard deviations of ΔCt values and then by geNorm and NormFinder analyses, taking into account the amplification efficiency of each microrna primer set. The optimal set of reference genes was verified by a target analysis using RT-qPCR on miR-215-5p. Conclusion: We identified miR-24-3p, miR-151a-5p, and miR-425-5p as the most valid combination of reference genes for microrna RT-qPCR studies in our hepatitis B virus replicating HepG2 cell model. © 2016 Jacobsen et al.

关键词： Hepatitis B virus microrna Normalisation Reference genes RT-qPCR

来源：评论

学校读者我要写书评

暂无评论

Comparative ncrna gene and structure prediction using foldalign and foldalignM

引用

Current Protocols in Bioinformatics 2012年第SUPPL.39期39卷

作者： Havgaard, Jakob Kaur, Simranjeet Gorodkin, Jan Center for Non-Coding RNA in Technology and Health Department of Veterinary Clinical and Animal Sciences University of Copenhagen Copenhagen Denmark

This unit describes how to use Foldalign and FoldalignM to make structural alignments of non-protein-coding-rna (ncrna). These tools can be used to find new ncrnas, to find the structure of novel ncrnas, and to improv... 详细信息

关键词： ncrna ncrna gene finding non-coding rna rna multiple sequence alignment rna structural alignment rna structure prediction

来源：评论

学校读者我要写书评

暂无评论

Methane and Co2 Consumption from a Synthetic Waste Gas by Microbial Communities in Enriched Seawater

SSRN

引用

SSRN 2024年

作者： Frigaard, Niels-Ulrik Seemann, Stefan E. Marine Biological Section Department of Biology University of Copenhagen Helsingør Denmark Center for non-coding RNA in Technology and Health Department of Veterinary and Animal Sciences University of Copenhagen Frederiksberg Denmark

Methane (CH4) and carbon dioxide (CO2) occur as undesirable waste products in carbon-based fuel productions. Bothgases are major greenhouse gases with CH4 being much more potent than CO2. For this reason, excess CH4 from varioussources is often flared into CO2 rather than releasing the CH4 into the atmosphere, however, some CH4 is still emitteddue to the inefficiency of flare combustion. We have explored how natural microbial communities can be manipulatedinto consuming both CH4 and CO2 from a gas stream and converting the gases into microbial biomass. Natural seawaterwas enriched with inorganic nutrients and injected with a continuous gas stream containing CH4 (4.7% v/v) and CO2(1% v/v) over a period of several days, either in the dark or in the light. Microbial communities established thatcontained methanotrophic bacteria consuming CH4, and cyanobacteria and microalgae consuming CO2. The measureof chemotaxonomic markers revealed that the growth of phototrophs increased greatly only in the light with an earlydominance by cyanobacteria later overtaken by microalgae, and that the growth of methanotrophs increased greatlyonly in the dark. The microbial communities were characterized using near-full-length 16S/18S rrna gene ampliconsequencing with the Nanopore technology. In the incubated cultures, the microbial diversity was drastically lower ascompared to the natural communities. The most abundant microalgae were green algae belonging to Picochlorum,Tetraselmis, Chlamydomonas, and Nannochloris, and the most abundant cyanobacteria were related to Geitlerinemasp. PCC 7105, Symphothece sp. PCC 7002 and Cyanobium sp. PCC 6307 (based on the SILVA reference database).Methylomicrobium and Methylobacter were the most abundant methanotrophs in the dark-incubated cultures, whereasMethylomonas methanica was identified as the single methanotroph with notable abundance under light ***, for optimal CH4 and CO2 consumption it may be necessary to physically separate

关键词： Microalgae

来源：评论

学校读者我要写书评

暂无评论

ATP-P2 receptor signaling transduction in the regulation of glucose and lipid metabolism

ATP-P2 receptor signaling transduction in the regulation of ...

引用

第六次国际暨第十五次全国膜生物学学术研讨会

作者： Jichun Yang Department of Physiology and Pathophysiology School of Basic Medical SciencesKey Laboratory of Molecular Cardiovascular Sciences of the Ministry of EducationCenter for Non-coding RNA MedicinePeking University Health Science Center

Mitochondrial dysfunction including decreased ATP production and increased ROS production plays important roles in the pathogenesis of *** the past decade,our research had been focused on determining the roles and mechanisms of ATP production in the regulation of hepatic gluconeogenesis and *** hepatocytes,ATP can be released to function as a signaling molecule by binding to and activating P2 receptor (ATP receptor).ATP activates P2X receptor subtype to increase influx of extracellular calcium,and activates P2Y receptor subtype to increase calcium release from internal calcium storage such as ***,ATP-triggered slight increase in cellular calcium activates CaM to phosphorylate

关键词： ATP-P2 receptor signaling transduction in the regulation of glucose and lipid metabolism

来源：评论

学校读者我要写书评

暂无评论

The DrugPattern tool for drug set enrichment analysis and its prediction for beneficial effects of oxLDL on type 2 diabetes

引用

Journal of Genetics and Genomics 2018年第7期45卷 389-397页

作者： Chuanbo Huang Weili Yang Junpei wang Yuan Zhou Bin Geng Georgios Kararigas Jichun Yang Qinghua Cui Department of Biomedical Informatics Department of Physiology and Pathophysiology MOE Key Lab of Cardiovascular Sciences School of Basic Medical Sciences Center for Non-Coding RNA Medicine Peking UniversityBeijing 100191China School of Mathematics Sciences Huaqiao University Quanzhou 362021 China Hypertension Center Fuwai Hospital Chinese Academy of Medical Sciences and Peking Union Medical CollegeState Key Laboratory of Cardiovascular Disease National Center for Cardiovascular Diseases Beijing 100037 China Charit-Universitatsmedizin Berlin. Corporate Member of Freie Universitat Berlin Humboldt-Universitat zu Berlin Berlin Institute of Health Institute of Gender in Medicine and Center for Cardiovascular Research. DZHK (German Centre for Cardiovascular Research) 10115 Berlin Germany Center of Bioinformatics Key Laboratory for Neuro-lnformation of Ministry of Education School of Life Science and Technology University of Electronic Science and Technology of China Chengdu 610054 China

Enrichment analysis methods, e.g., gene set enrichment analysis, represent one class of important bio- informatical resources for mining patterns in biomedical datasets. However, tools for inferring patterns and rules of a list of drugs are limited. In this study, we developed a web-based tool, DrugPattern, for drug set enrichment analysis. We first collected and curated 7019 drug sets, including indications, adverse reactions, targets, pathways, etc. from public databases. For a list of interested drugs, DrugPat- tern then evaluates the significance of the enrichment of these drugs in each of the 7019 drug sets. To validate DrugPattern, we employed it for the prediction of the effects of oxidized low-density lipoprotein （oxLDL）, a factor expected to be deleterious. We predicted that oxLDL has beneficial effects on some diseases, most of which were supported by evidence in the literature. Because DrugPattern predicted the potential beneficial effects of oxLDL in type 2 diabetes （T2D）, animal experiments were then performed to further verify this prediction. As a result, the experimental evidences validated the DrugPattern prediction that oxLDL indeed has beneficial effects on T2D in the case of energy restriction. These data confirmed the prediction accuracy of our approach and revealed unexpected protective roles for oxLDL in various diseases. This study provides a tool to infer patterns and rules in biomedical datasets based on drug set enrichment analysis.

关键词： Enrichment analysis Drug Data mining oxLDL Type 2 diabetes

来源：评论

学校读者我要写书评

暂无评论

TISSUES 2.0: an integrative web resource on mammalian tissue expression (vol 2018, 2018)

引用

DATABASE-THE JOUrnaL OF BIOLOGICAL DATABASES AND CURATION 2018年第2018期2018卷 1-N.PAG页

作者： Palasca, Oana Santos, Alberto Stolte, Christian Gorodkin, Jan Jensen, Lars Juhl Novo Nordisk Foundation Center for Protein Research Faculty of Health and Medical Sciences University of Copenhagen Copenhagen DenmarkCenter for non-coding RNA in Technology and Health Faculty of Health and Medical Sciences University of Copenhagen Copenhagen DenmarkDepartment of Veterinary and Animal Sciences Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark Novo Nordisk Foundation Center for Protein Research Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark New York Genome Center New York NY USA Center for non-coding RNA in Technology and Health Faculty of Health and Medical Sciences University of Copenhagen Copenhagen DenmarkDepartment of Veterinary and Animal Sciences Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark Correspondence may also be addressed to Jan Gorodkin. Email: gorodkin@rth.dk Novo Nordisk Foundation Center for Protein Research Faculty of Health and Medical Sciences University of Copenhagen Copenhagen DenmarkCenter for non-coding RNA in Technology and Health Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark Corresponding author: Tel: +45 35325025 Email: lars.juhl.jensen@cpr.ku.dk

Physiological and molecular similarities between organisms make it possible to translate findings from simpler experimental systems—model organisms—into more complex ones, such as human. This translation facilitates the understanding of biological processes under normal or disease conditions. Researchers aiming to identify the similarities and differences between organisms at the molecular level need resources collecting multi-organism tissue expression data. We have developed a database of gene-tissue associations in human, mouse, rat and pig by integrating multiple sources of evidence: transcriptomics covering all four species and proteomics (human only), manually curated and mined from the scientific literature. Through a scoring scheme, these associations are made comparable across all sources of evidence and across organisms. Furthermore, the scoring produces a confidence score assigned to each of the associations. The TISSUES database (version 2.0) is publicly accessible through a user-friendly web interface and as part of the STRING app for Cytoscape. In addition, we analyzed the agreement between datasets, across and within organisms, and identified that the agreement is mainly affected by the quality of the datasets rather than by the technologies used or organisms *** URL: http://***/

关键词： DATABASES TRANSCRIPTOMES PROTEOMICS

来源：评论

学校读者我要写书评

暂无评论

Discovering and Evaluating Organizational Knowledge from Textual Data: Application to Crisis Management

SSRN

引用

SSRN 2023年

作者： Grissa, Dhouha Andonoff, Eric Hanachi, Chihab Center for non-coding RNA in Technology and Health Department of Veterinary and Animal Science University of Copenhagen Frederiksberg C1870 Denmark Université Toulouse - Capitole IRIT 2 rue du Doyen Gabriel Marty Toulouse31042 France

Crisis management effectiveness relies mainly on the quality of the distributed human organization deployed for saving lives, limiting damage and reducing risks. Organizations set up in this context are not always predefined and static;they could evolve and new forms could emerge since actors, such as volunteers or NGO, could join dynamically to collaborate. To improve crisis resolution effectiveness, it is first important to understand, analyze and evaluate such dynamic organizations in order to adjust crisis management plans and ease coordination among actors. Giving a textual experience feedback from past crisis, the objective of this paper is to discover the organizational structure deployed in the considered crisis and then evaluate it according to a set of criteria. For that purpose, we combine in a coherent framework text and association rule mining for pattern discovery and annotation, and multi-agent system models and techniques for formally building and evaluating organizational structures. We present the OSminer algorithm that discovers association rules based on relevant textual patterns and then builds an organizational structure including three main relations between actors: power, control and coordination. A real-life case study, a flood crisis hitting the south west of France, serves as a basis for testing/experimenting our solution. The organizational structure, discovered in this case study, has 24 actors. Its evaluation indicates its efficiency, but shows that it is neither robust nor flexible. Our findings highlight the potential of our approach to discover and evaluate organizational structures from a text recording interactions between stakeholders in a crisis context. © 2023, The Authors. All rights reserved.

关键词： Association rules

来源：评论

学校读者我要写书评

暂无评论

Targeting non-coding rnas to overcome cancer therapy resistance

引用

Signal Transduction and Targeted Therapy 2022年第5期7卷 1447-1466页

作者： BaoQing Chen Mihnea P.Dragomir Chen Yang Qiaoqiao Li David Horst George A.Calin Department of Radiation Oncology State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineSun Yat-sen University Cancer CenterGuangzhouGuangdong 510060China Institute of Pathology Charité-Universitätsmedizin Berlincorporate member of Freie Universität BerlinHumboldt-Universität zu Berlin and Berlin Institute of HealthBerlin 10117Germany Berlin Institute of Health Anna-Louisa-Karsch-Straße 210178 BerlinGermany German Cancer Consortium(DKTK) Partner Site BerlinGerman Cancer Research Center(DKFZ)69210 HeidelbergGermany Department of Translational Molecular Pathology The University of Texas MD Anderson Cancer CenterHoustonTX 77030USA Center for RNA Interference and Non-Coding RNAs The University of Texas MD Anderson Cancer CenterHoustonTX 77030USA

It is now well known that non-coding rnas(ncrnas),rather than protein-coding transcripts,are the preponderant rna ***,particularly micrornas(mirnas),long non-coding rnas(lncrnas),and circular rnas(circrnas),are widely appreciated as pervasive regulators of multiple cancer hallmarks such as proliferation,apoptosis,invasion,metastasis,and genomic *** recent discoveries in cancer therapy,resistance to chemotherapy,radiotherapy,targeted therapy.

关键词： chemotherapy metastasis rnas

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：