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Non-Coding RNA Analysis Using the Rfam Database

Current Protocols in bioinformatics 2018年第1期62卷 e51-e51页

作者： Kalvari, Ioanna Nawrocki, Eric P. Argasinska, Joanna Quinones-Olvera, Natalia Finn, Robert D. Bateman, Alex Petrov, Anton I. European Molecular Biology Laboratory European Bioinformatics Institute Wellcome Genome Campus Hinxton Cambridge United Kingdom National Center for Biotechnology Information National Institutes of Health Department of Health and Human Services Bethesda MD United States Systems Biology Graduate Program Harvard University Cambridge MA United States

Rfam is a database of non-coding RNA families in which each family is represented by a multiple sequence alignment, a consensus secondary structure, and a covariance model. Using a combination of manual and literature-based curation and a custom software pipeline, Rfam converts descriptions of RNA families found in the scientific literature into computational models that can be used to annotate RNAs belonging to those families in any DNA or RNA sequence. Valuable research outputs that are often locked up in figures and supplementary information files are encapsulated in Rfam entries and made accessible through the Rfam Web site. The data produced by Rfam have a broad application, from genome annotation to providing training sets for algorithm development. This article gives an overview of how to search and navigate the Rfam Web site, and how to annotate sequences with RNA families. The Rfam database is freely available at http://***. © 2018 by John Wiley & Sons, Inc. Copyright © 2018 John Wiley & Sons, Inc.

关键词： genome annotation Infernal non-coding RNA Rfam RNA family

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Distinct gut microbiomes in Thai patients with colorectal polyps

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World Journal of Gastroenterology 2024年第27期30卷 3336-3355页

作者： Thoranin Intarajak Ahmad Nuruddin Khoiri Kanthida Kusonmano Weerayuth Kittichotirat Sawannee Sutheeworapong Supapon Cheevadhanarak Wandee Udomchaiprasertkul Chinae Thammarongtham Bioinformatics Unit Chulabhorn Royal AcademyLak Si 10210BangkokThailand Bioinformatics and Systems Biology Program School of Bioresources and Technologyand School of Information TechnologyKing Mongkut’s University of Technology ThonburiBang Khun Thian 10150BangkokThailand Bioinformatics and Systems Biology ProgramSchool of Bioresources and Technologyand School of Information TechnologyKing Mongkut’s University of Technology ThonburiBang Khun Thian 10150BangkokThailand Systems Biology and Bioinformatics Unit Pilot Plant Development and Training InstituteKing Mongkut’s University of Technology ThonburiBang Khun Thian 10150BangkokThailand Molecular Genomic Research Laboratory Chulabhorn Royal AcademyLak Si 10210BangkokThailand National Center for Genetic Engineering and Biotechnology King Mongkut's University of Technology ThonburiBang Khun Thian 10150BangkokThailand School of Bioresources and Technology King Mongkut’s University of Technology ThonburiBank Khun Thian 10150BangkokThailand Fungal Biotechnology Unit Pilot Plant Development and Training InstituteKing Mongkut’s University of Technology ThonburiBang Khun Thian 10150BangkokThailand

BACKGROUND Colorectal polyps that develop via the conventional adenoma-carcinoma sequence[e.g.,tubular adenoma(TA)]often progress to malignancy and are closely associated with changes in the composition of the gut *** is limited research concerning the microbial functions and gut microbiomes associated with colorectal polyps that arise through the serrated polyp pathway,such as hyperplastic polyps(HP).Exploration of microbiome alterations asso-ciated with HP and TA would improve the understanding of mechanisms by which specific microbes and their metabolic pathways contribute to colorectal *** To investigate gut microbiome signatures,microbial associations,and microbial functions in HP and TA *** Full-length 16S rRNA sequencing was used to characterize the gut microbiome in stool samples from control participants without polyps[control group(CT),n=40],patients with HP(n=52),and patients with TA(n=60).Significant differences in gut microbiome composition and functional mechanisms were identified between the CT group and patients with HP or *** techniques in this study included differential abundance analysis,co-occurrence network analysis,and differential pathway *** Colorectal cancer(CRC)-associated bacteria,including Streptococcus gallolyticus(***),Bacteroides fragilis,and Clostridium symbiosum,were identified as characteristic microbial species in TA *** gnavus,associated with dysbiosis and gastrointestinal diseases,was significantly differentially abundant in the HP and TA *** pathway analysis revealed that HP patients exhibited enrichment in the sulfur oxidation pathway exclusively,whereas TA patients showed dominance in pathways related to secondary metabolite biosynthesis(e.g.,mevalonate);*** was a major ***-occurrence network and dynamic network analyses revealed co-occurrence of dysbiosis-associated bacteria in HP patients,wh

关键词： Gut microbiome Colorectal adenoma Hyperplastic polyp Full-length 16s rRNA Microbial correlation networks Predicted functional mechanisms

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CoreGenes3.5: A webserver for the determination of core genes from sets of viral and small bacterial genomes

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BMC Research Notes 2013年第1期6卷 1-4页

作者： Turner, Dann Reynolds, Darren Seto, Donald Mahadevan, Padmanabhan Centre for Research in Biosciences Faculty of Applied Sciences University of the West of England Bristol BS16 1QY United Kingdom Bioinformatics and Computational Biology Program School of Systems Biology George Mason University Manassas VA 20110 United States Department of Biology University of Tampa Tampa FL 33606 United States

Background: CoreGenes3.5 is a webserver that determines sets of core genes from viral and small bacterial genomes as an automated batch process. Previous versions of CoreGenes have been used to classify bacteriophage genomes and mine data from pathogen genomes. Findings. CoreGenes3.5 accepts as input GenBank accession numbers of genomes and performs iterative BLASTP analyses to output a set of core genes. After completion of the program run, the results can be either displayed in a new window for one pair of reference and query genomes or emailed to the user for multiple pairs of small genomes in tabular format. Conclusions: With the number of genomes sequenced increasing daily and interest in determining phylogenetic relationships, CoreGenes3.5 provides a user-friendly web interface for wet-bench biologists to process multiple small genomes for core gene determinations. CoreGenes3.5 is available at. © 2013 Turner et al.;licensee BioMed Central Ltd.

关键词： Bacteriophage Core genes Data mining Taxonomy Viral genomics

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Peak analysis of cell-free RNA finds recurrently protected narrow regions with clinical potential

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Genome biology 2025年第1期26卷 119页

作者： Pengfei Bao Taiwei Wang Xiaofan Liu Shaozhen Xing Hanjin Ruan Hongli Ma Yuhuan Tao Qing Zhan Efres Belmonte-Reche Lizheng Qin Zhengxue Han Minghui Mao Mengtao Li Zhi John Lu MOE Key Laboratory of Bioinformatics State Key Lab of Green Biomanufacturing Center for Synthetic and Systems Biology School of Life Sciences Tsinghua University Beijing 100084 China. Institute for Precision Medicine Tsinghua University Beijing 100084 China. Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program School of Life Sciences Tsinghua University Beijing China. Department of Rheumatology and Clinical Immunology Chinese Academy of Medical Sciences & Peking Union Medical College Beijing 100730 China. National Clinical Research Center for Dermatologic and Immunologic Diseases (Ministry of Science & Technology) MOE Key Laboratory of Rheumatology and Clinical Immunology State Key Laboratory of Complex Severe and Rare Diseases Peking Union Medical College Hospital Beijing 100730 China. Academy for Advanced Interdisciplinary Studies (AAIS)and Sciences Joint Graduate Program (PTN) Peking University Beijing China. Department of Oral and Maxillofacial & Head and Neck Oncology Beijing Stomatological Hospital Capital Medical University Beijing China. Centre for Genomics and Oncological Research (GENYO) Avenida de La Ilustración 114 Granada 18016 Spain. Department of Biochemistry and Molecular Biology II Faculty of Pharmacy University of Granada Granada Spain. Instituto de Investigación Biosanitaria Ibs.GRANADA Hospital Virgen de Las Nieves Granada Spain. Department of Oral and Maxillofacial & Head and Neck Oncology Beijing Stomatological Hospital Capital Medical University Beijing China. mmh_hover@***. Department of Rheumatology and Clinical Immunology Chinese Academy of Medical Sciences & Peking Union Medical College Beijing 100730 China. mengtao.li@***. National Clinical Research Center for Dermatologic and Immunologic Diseases (Ministry of Science & Technology) MOE Key Laboratory of Rheumatology and Clinical Immunology State Key Laboratory of Complex Severe and Rare Diseases Peking Union Medical College Hospita

BACKGROUND:Cell-free RNAs (cfRNAs) can be detected in biofluids and have emerged as valuable disease biomarkers. Accurate identification of the fragmented cfRNA signals, especially those originating from pathological cells, is crucial for understanding their biological functions and clinical value. However, many challenges still need to be addressed for their application, including developing specific analysis methods and translating cfRNA fragments with biological support into clinical applications. RESULTS:We present cfPeak, a novel method combining statistics and machine learning models to detect the fragmented cfRNA signals effectively. When test in real and artificial cfRNA sequencing (cfRNA-seq) data, cfPeak shows an improved performance compared with other applicable methods. We reveal that narrow cfRNA peaks preferentially overlap with protein binding sites, vesicle-sorting sites, structural sites, and novel small non-coding RNAs (sncRNAs). When applied in clinical cohorts, cfPeak identified cfRNA peaks in patients' plasma that enable cancer detection and are informative of cancer types and metastasis. CONCLUSIONS:Our study fills the gap in the current small cfRNA-seq analysis at fragment-scale and builds a bridge to the scientific discovery in cfRNA fragmentomics. We demonstrate the significance of finding low abundant tissue-derived signals in small cfRNA and prove the feasibility for application in liquid biopsy.

关键词： Cell-free RNA CfRNA fragment Liquid biopsy biomarker Noninvasive cancer detection Peak calling SncRNA Tissue-of-origin

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Designing metabolic engineering strategies with genome-scale metabolic flux modeling

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Advances in Genomics and Genetics 2015年 5卷 93页

作者： Yen, Jiun Y Tanniche, Imen Fisher, Amanda K Gillaspy, Glenda E Bevan, David R Senger, Ryan S Department of Biological Systems Engineering Virginia Tech Department of Biochemistry Virginia Tech Genomics Bioinformatics and Computational Biology Interdisciplinary Program Virginia Tech

New in silico tools that make use of genome-scale metabolic flux modeling are improving the design of metabolic engineering strategies. This review highlights the latest developments in this area, explains the interface between these in silico tools and the experimental implementation tools of metabolic engineers, and provides a way forward so that in silico predictions can better mimic reality and more experimental methods can be considered in simulation studies. The several methodologies for solving genome-scale models (eg, flux balance analysis [FBA], parsimonious FBA, flux variability analysis, and minimization of metabolic adjustment) all have unique advantages and applications. There are two basic approaches to designing metabolic engineering strategies in silico, and both have demonstrated success in the literature. The first involves: 1) making a genetic manipulation in a model; 2) testing for improved performance through simulation; and 3) iterating the process. The second approach has been used in more recently designed in silico tools and involves: 1) comparing metabolic flux profiles of a wild-type and ideally engineered state and 2) designing engineering strategies based on the differences in these flux profiles. Improvements in genome-scale modeling are anticipated in areas such as the inclusion of all relevant cellular machinery, the ability to understand and anticipate the results of combinatorial enrichment experiments, and constructing dynamic and flexible biomass equations that can respond to environmental and genetic manipulations.

关键词： genome-scale modeling flux balance analysis flux variability analysis minimization of metabolic adjustment metabolic bottleneck pathway optimization

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Meeting report on RECOMB 2013 （the 17th Annual International Conference on Research in Computational Molecular biology）

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Frontiers of Electrical and Electronic Engineering in China 2013年第2期8卷 175-181页

作者： Xuegong Zhang Fengzhu Sun MOE Key Laboratory of Bioinformatics and Bioinformatics Division/Center for Synthetic and Systems Biology TNLIST and Department of Automation Tsinghua University Beijing 100084 China Molecular and Computational Biology Program University of Southern California Los Angeles CA 90089 USA

RECOMB 2013 was successfully held in Tsinghua University, Beijing, China on April 7-10, 2013, hosted by the bioinformatics Division and Center for Synthetic and systems biology, Tsinghua National Laboratory for Information Science and Technology （TNLIST）. A total of about 500 professionals from both academia and industry from 29 countries and regions attended the conference and its RECOMB-Seq satellite workshop after the main conference.

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Pitfalls of restriction enzyme analysis in identifying, characterizing,typing, and naming viral pathogens in the era of whole genome data, as illustrated by HAdV type 55

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Virologica Sinica 2016年第5期31卷 448-453页

作者： Qiwei Zhang Shoaleh Dehghan Donald Seto Biosafety Level-3 Laboratory School of Public HealthSouthern Medical University(Guangdong Provincial Key Laboratory of Tropical Disease Research) Chemistry Department American University Bioinformatics and Computational Biology Program School of Systems BiologyGeorge Mason University

Restriction endonuclease analysis(REA),or restriction fragment length polymorphism(RFLP),was useful for identifying and determining the relatedness and putative identities of microbial strains(Tang et al.,1997)and for... 详细信息

关键词： and naming viral pathogens in the era of whole genome data DLL QS characterizing,typing Pitfalls of restriction enzyme analysis in identifying REA type

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Bibliome Mining Platform and Application for Building Metabolic Interaction Network

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Procedia Computer Science 2012年 11卷 55-62页

作者： P. Patumcharoenpol J. Chan A. Meechai B. Shen W. Vongsangnak Center for Systems Biology Soochow University No. 1. Shizi Street Suzhou 215006 China Bioinformatics and Systems Biology Program School of Information Technology Department of Chemical Engineering and Biological Engineering Program King Mongkut's University of Technology Thonburi Bangkok Thailand

Bibliome mining is a powerful technique for large-scale information extraction from textual data and connecting between biological entities as well as functional hypotheses. Currently, most bibliome mining is used for some specific studies involving genes and proteins; however, much less efforts have been focused on metabolites. In addition to application works, the focus has been on proving the concepts and algorithms, but very few reports on development of applicable text mining platform. In this study, we aimed to develop a bibliome mining platform that could be used to perform basic text mining tasks and further be used for building metabolic interaction networks. We developed a platform with the evaluated tools and subsequently tested its functions for extraction of interactions between biomolecules (e.g. genes, enzymes, proteins and metabolites) in yeast Saccharomyces cerevisiae . The results were then manually curated afterwards using KEGG LIGAND and public yeast database. Of the collected 11 text mining tools, we selected 3 suitable tools, namely ABNER, OpenNLP and LingPipe for further implementing the bibliome mining platform. In summary, a prototype of a bibliome mining platform was successfully developed and may further be used for building metabolic interaction network of S. cerevisiae . This study can be used as a basic framework for further improvement as well as extension of relevant text mining tasks and broad applications.

关键词： bibliome mining biomolecules metabolic interaction network Saccharomyces cerevisiae text mining

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A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH (Jan, 10.1038/s41587-022-01568-9, 2023)

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NATURE BIOTECHNOLOGY 2023年第7期41卷 1027-1027页

作者： Jia, Bojing Blair Jussila, Adam Kern, Colin Zhu, Quan Ren, Bing Bioinformatics and Systems Biology Graduate Program University of California San Diego La Jolla CA USA Medical Scientist Training Program University of California San Diego La Jolla CA USA Department of Cellular and Molecular Medicine Center for Epigenomics University of California San Diego La Jolla CA USA Ludwig Institute for Cancer Research La Jolla CA USA Institute of Genomic Medicine Moores Cancer Center School of Medicine University of California San Diego La Jolla CA USA

Multiplexed fluorescence in situ hybridization (FISH) is a widely used approach for analyzing three-dimensional genome organization, but it is challenging to derive chromosomal conformations from noisy fluorescence signals, and tracing chromatin is not straightforward. Here we report a spatial genome aligner that parses true chromatin signal from noise by aligning signals to a DNA polymer model. Using genomic distances separating imaged loci, our aligner estimates spatial distances expected to separate loci on a polymer in three-dimensional space. Our aligner then evaluates the physical probability observed signals belonging to these loci are connected, thereby tracing chromatin structures. We demonstrate that this spatial genome aligner can efficiently model chromosome architectures from DNA FISH data across multiple scales and be used to predict chromosome ploidies de novo in interphase cells. Reprocessing of previous whole-genome chromosome tracing data with this method indicates the spatial aggregation of sister chromatids in S/G2 phase cells in asynchronous mouse embryonic stem cells and provides evidence for extranumerary chromosomes that remain tightly paired in postmitotic neurons of the adult mouse cortex.

关键词： Gene regulation Image processing

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Construction and Characterization of a Novel Recombinant Attenuated and Replication-Deficient Candidate Human Adenovirus Type 3 Vaccine:"Adenovirus Vaccine Within an Adenovirus Vector"

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Virologica Sinica 2021年第3期36卷 354-364页

作者： Yuqian Yan Shuping Jing Liqiang Feng Jing Zhang Zhiwei Zeng Min Li Shan Zhao Junxian Ou Wendong Lan Wenyi Guan Xiaowei Wu Jianguo Wu Donald Seto Qiwei Zhang Guangdong Provincial Key Laboratory of Tropical Disease Research School of Public HealthSouthern Medical UniversityGuangzhou 510515China Microbiological Laboratory Zhuhai Center for Disease Control and PreventionZhuhai 519000China Guangzhou Institutes of Biomedicine and Health Chinese Academy of SciencesGuangzhou 510530China Guangdong Provincial Key Laboratory of Virology Institute of Medical MicrobiologyJinan UniversityGuangzhou 510632China Bioinformatics and Computational Biology Program School of Systems BiologyGeorge Mason UniversityManassasVA 20110USA

Human adenoviruses(HAd Vs)are highly contagious and result in large number of acute respiratory disease(ARD)cases with severe morbidity and *** adenovirus type 3(HAd V-3)is the most common type that causes ARD outbreaks in Asia,Europe,and the ***,there is currently no vaccine approved for its general *** hexon protein contains the main neutralizing epitopes,provoking strong and lasting *** this study,a novel recombinant and attenuated adenovirus vaccine candidate against HAd V-3 was constructed based on a commercially-available replication-defective HAd V-5 gene therapy and vaccine *** entire HAd V-3 hexon gene was integrated into the E1 region of the vector by homologous recombination using a bacterial *** resultant recombinants expressing the HAd V-3 hexon protein were rescued in AD293 cells,identified and characterized by RT-PCR,Western blots,indirect immunofluorescence,and electron *** potential vaccine candidate had a similar replicative efficacy as the wild-type HAd V-3 ***,and importantly,the vaccine strain had been rendered replication-defective and was incapable of replication in A549 cells after more than twentygeneration passages in AD293 *** represents a significant safety *** mice immunized both intranasally and intramuscularly by this vaccine candidate raised significant neutralizing antibodies against HAd ***,this recombinant,attenuated,and safe adenovirus vaccine is a promising HAd V-3 vaccine *** strategy of using a clinically approved and replication-defective HAd V-5 vector provides a novel approach to develop universal adenovirus vaccine candidates against all the other types of adenoviruses causing ARDs and perhaps other adenovirus-associated diseases.

关键词： Adenovirus vaccine Human adenovirus type 3(HAdV-3) Replication-deficient adenovirus vector Immunity in BALB/c mice Recombination

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