Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future
出版年份 2015 全文链接
标题
Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future
作者
关键词
Biological data visualization, Network biology, Genomics, Systems biology, Multivariate analysis
出版物
GigaScience
Volume 4, Issue 1, Pages -
出版商
Oxford University Press (OUP)
发表日期
2015-08-25
DOI
10.1186/s13742-015-0077-2
参考文献
相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。- Big biological impacts from big data
- (2017) Mike May SCIENCE
- Family genome browser: visualizing genomes with pedigree information
- (2015) Liran Juan et al. BIOINFORMATICS
- RNASeqBrowser: A genome browser for simultaneous visualization of raw strand specific RNAseq reads and UCSC genome browser custom tracks
- (2015) Jiyuan An et al. BMC GENOMICS
- Vanno: A Visualization-Aided Variant Annotation Tool
- (2015) Po-Jung Huang et al. HUMAN MUTATION
- Protein–protein interaction predictions using text mining methods
- (2015) Nikolas Papanikolaou et al. METHODS
- Orchestrating high-throughput genomic analysis with Bioconductor
- (2015) Wolfgang Huber et al. NATURE METHODS
- GenPlay Multi-Genome, a tool to compare and analyze multiple human genomes in a graphical interface
- (2014) Julien Lajugie et al. BIOINFORMATICS
- BicOverlapper 2.0: visual analysis for gene expression
- (2014) R. Santamaria et al. BIOINFORMATICS
- eRNA: a graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing
- (2014) Tiezheng Yuan et al. BMC GENOMICS
- ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases
- (2014) Li Shen et al. BMC GENOMICS
- Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes
- (2014) Iakes Ezkurdia et al. HUMAN MOLECULAR GENETICS
- The personal genome browser: visualizing functions of genetic variants
- (2014) Liran Juan et al. NUCLEIC ACIDS RESEARCH
- The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification
- (2014) T.B.K. Reddy et al. NUCLEIC ACIDS RESEARCH
- The UCSC Cancer Genomics Browser: update 2015
- (2014) Mary Goldman et al. NUCLEIC ACIDS RESEARCH
- BiNA: A Visual Analytics Tool for Biological Network Data
- (2014) Andreas Gerasch et al. PLoS One
- TraV: A Genome Context Sensitive Transcriptome Browser
- (2014) Sascha Dietrich et al. PLoS One
- DyCoNet: A Gephi Plugin for Community Detection in Dynamic Complex Networks
- (2014) Julie Kauffman et al. PLoS One
- STAR: an integrated solution to management and visualization of sequencing data
- (2013) T. Wang et al. BIOINFORMATICS
- RNAseqViewer: visualization tool for RNA-Seq data
- (2013) Xavier Rogé et al. BIOINFORMATICS
- Pathview: an R/Bioconductor package for pathway-based data integration and visualization
- (2013) Weijun Luo et al. BIOINFORMATICS
- ContigScape: a Cytoscape plugin facilitating microbial genome gap closing
- (2013) Biao Tang et al. BMC GENOMICS
- Visualizing time-related data in biology, a review
- (2013) Maria Secrier et al. BRIEFINGS IN BIOINFORMATICS
- Omix - A Visualization Tool for Metabolic Networks with Highest Usability and Customizability in Focus
- (2013) Peter Droste et al. CHEMIE INGENIEUR TECHNIK
- Variant View: Visualizing Sequence Variants in their Gene Context
- (2013) Joel A. Ferstay et al. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
- Meander: visually exploring the structural variome using space-filling curves
- (2013) G. A. Pavlopoulos et al. NUCLEIC ACIDS RESEARCH
- The genome portal of the Department of Energy Joint Genome Institute: 2014 updates
- (2013) Henrik Nordberg et al. NUCLEIC ACIDS RESEARCH
- PhenoTimer: Software for the Visual Mapping of Time-Resolved Phenotypic Landscapes
- (2013) Maria Secrier et al. PLoS One
- Unraveling genomic variation from next generation sequencing data
- (2013) Georgios A Pavlopoulos et al. BioData Mining
- Scribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web
- (2012) Chase A. Miller et al. BIOINFORMATICS
- CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis
- (2012) Pei Li et al. BIOINFORMATICS
- clusterMaker: a multi-algorithm clustering plugin for Cytoscape
- (2012) John H Morris et al. BMC BIOINFORMATICS
- Arena3D: visualizing time-driven phenotypic differences in biological systems
- (2012) Maria Secrier et al. BMC BIOINFORMATICS
- ABrowse - a customizable next-generation genome browser framework
- (2012) Lei Kong et al. BMC BIOINFORMATICS
- Bio.Phylo: A unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython
- (2012) Eric Talevich et al. BMC BIOINFORMATICS
- A brief introduction to web-based genome browsers
- (2012) J. Wang et al. BRIEFINGS IN BIOINFORMATICS
- BamView: visualizing and interpretation of next-generation sequencing read alignments
- (2012) T. Carver et al. BRIEFINGS IN BIOINFORMATICS
- Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
- (2012) H. Thorvaldsdottir et al. BRIEFINGS IN BIOINFORMATICS
- Structural and dynamical analysis of biological networks
- (2012) Cecilia Klein et al. Briefings in Functional Genomics
- MuSiC: Identifying mutational significance in cancer genomes
- (2012) N. D. Dees et al. GENOME RESEARCH
- A comparison of cataloged variation between International HapMap Consortium and 1000 Genomes Project data
- (2012) Carrie C Buchanan et al. JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
- A travel guide to Cytoscape plugins
- (2012) Rintaro Saito et al. NATURE METHODS
- EvolView, an online tool for visualizing, annotating and managing phylogenetic trees
- (2012) Huangkai Zhang et al. NUCLEIC ACIDS RESEARCH
- T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks
- (2012) A. Boc et al. NUCLEIC ACIDS RESEARCH
- PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees
- (2012) Huaiyu Mi et al. NUCLEIC ACIDS RESEARCH
- The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data: Figure 1.
- (2012) Ethan Cerami et al. Cancer Discovery
- ggbio: an R package for extending the grammar of graphics for genomic data
- (2012) Tengfei Yin et al. GENOME BIOLOGY
- TVNViewer: An interactive visualization tool for exploring networks that change over time or space
- (2011) R. E. Curtis et al. BIOINFORMATICS
- GenPlay, a multipurpose genome analyzer and browser
- (2011) Julien Lajugie et al. BIOINFORMATICS
- SVA: software for annotating and visualizing sequenced human genomes
- (2011) Dongliang Ge et al. BIOINFORMATICS
- TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data
- (2011) Yan W. Asmann et al. BIOINFORMATICS
- BiologicalNetworks - tools enabling the integration of multi-scale data for the host-pathogen studies
- (2011) Sergey Kozhenkov et al. BMC Systems Biology
- Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies
- (2011) M. C. Schatz et al. BRIEFINGS IN BIOINFORMATICS
- Hive plots--rational approach to visualizing networks
- (2011) M. Krzywinski et al. BRIEFINGS IN BIOINFORMATICS
- Analyzing Protein-Protein Interaction Networks with Web Tools
- (2011) Charalampos N. Moschopoulos et al. Current Bioinformatics
- PileLineGUI: a desktop environment for handling genome position files in next-generation sequencing studies
- (2011) H. Lopez-Fernandez et al. NUCLEIC ACIDS RESEARCH
- Phytozome: a comparative platform for green plant genomics
- (2011) David M. Goodstein et al. NUCLEIC ACIDS RESEARCH
- GenomeView: a next-generation genome browser
- (2011) T. Abeel et al. NUCLEIC ACIDS RESEARCH
- inGAP-sv: a novel scheme to identify and visualize structural variation from paired end mapping data
- (2011) Ji Qi et al. NUCLEIC ACIDS RESEARCH
- iPath2.0: interactive pathway explorer
- (2011) Takuji Yamada et al. NUCLEIC ACIDS RESEARCH
- The Genome Portal of the Department of Energy Joint Genome Institute
- (2011) I. V. Grigoriev et al. NUCLEIC ACIDS RESEARCH
- Ensembl 2012
- (2011) P. Flicek et al. NUCLEIC ACIDS RESEARCH
- Gitools: Analysis and Visualisation of Genomic Data Using Interactive Heat-Maps
- (2011) Christian Perez-Llamas et al. PLoS One
- Using graph theory to analyze biological networks
- (2011) Georgios A Pavlopoulos et al. BioData Mining
- The GMOD Drupal Bioinformatic Server Framework
- (2010) A. Papanicolaou et al. BIOINFORMATICS
- CellPublisher: a web platform for the intuitive visualization and sharing of metabolic, signalling and regulatory pathways: Fig. 1.
- (2010) Lope A. Flórez et al. BIOINFORMATICS
- Savant: genome browser for high-throughput sequencing data
- (2010) M. Fiume et al. BIOINFORMATICS
- MetPA: a web-based metabolomics tool for pathway analysis and visualization
- (2010) J. Xia et al. BIOINFORMATICS
- Arcadia: a visualization tool for metabolic pathways
- (2010) Alice C. Villéger et al. BIOINFORMATICS
- geWorkbench: an open source platform for integrative genomics
- (2010) Aris Floratos et al. BIOINFORMATICS
- Cytoscape 2.8: new features for data integration and network visualization
- (2010) M. E. Smoot et al. BIOINFORMATICS
- rSW-seq: Algorithm for detection of copy number alterations in deep sequencing data
- (2010) Tae-Min Kim et al. BMC BIOINFORMATICS
- Biana: a software framework for compiling biological interactions and analyzing networks
- (2010) Javier Garcia-Garcia et al. BMC BIOINFORMATICS
- ETE: a python Environment for Tree Exploration
- (2010) Jaime Huerta-Cepas et al. BMC BIOINFORMATICS
- TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses
- (2010) Ben C Stöver et al. BMC BIOINFORMATICS
- Computational approaches for detecting protein complexes from protein interaction networks: a survey
- (2010) Xiaoli Li et al. BMC GENOMICS
- A survey of sequence alignment algorithms for next-generation sequencing
- (2010) H. Li et al. BRIEFINGS IN BIOINFORMATICS
- A Max-Flow-Based Approach to the Identification of Protein Complexes Using Protein Interaction and Microarray Data
- (2010) Jianxing Feng et al. IEEE-ACM Transactions on Computational Biology and Bioinformatics
- A map of human genome variation from population-scale sequencing
- (2010) Richard M. Durbin et al. NATURE
- Visualizing biological data—now and in the future
- (2010) Seán I O'Donoghue et al. NATURE METHODS
- Visualizing genomes: techniques and challenges
- (2010) Cydney B Nielsen et al. NATURE METHODS
- Visualization of multiple alignments, phylogenies and gene family evolution
- (2010) James B Procter et al. NATURE METHODS
- Visualization of omics data for systems biology
- (2010) Nils Gehlenborg et al. NATURE METHODS
- Network medicine: a network-based approach to human disease
- (2010) Albert-László Barabási et al. NATURE REVIEWS GENETICS
- MagicViewer: integrated solution for next-generation sequencing data visualization and genetic variation detection and annotation
- (2010) H. Hou et al. NUCLEIC ACIDS RESEARCH
- ZOOM Lite: next-generation sequencing data mapping and visualization software
- (2010) Z. Zhang et al. NUCLEIC ACIDS RESEARCH
- SEWAL: an open-source platform for next-generation sequence analysis and visualization
- (2010) J. N. Pitt et al. NUCLEIC ACIDS RESEARCH
- TreeVector: Scalable, Interactive, Phylogenetic Trees for the Web
- (2010) Ralph Pethica et al. PLoS One
- jsPhyloSVG: A Javascript Library for Visualizing Interactive and Vector-Based Phylogenetic Trees on the Web
- (2010) Samuel A. Smits et al. PLoS One
- Seevolution: visualizing chromosome evolution
- (2009) A. Esteban-Marcos et al. BIOINFORMATICS
- Illoura™: a software tool for analysis, visualization and semantic querying of cellular and other spatial biological data
- (2009) Tim McComb et al. BIOINFORMATICS
- Treevolution: visual analysis of phylogenetic trees
- (2009) R. Santamaria et al. BIOINFORMATICS
- UTGB toolkit for personalized genome browsers
- (2009) T. L. Saito et al. BIOINFORMATICS
- jClust: a clustering and visualization toolbox
- (2009) G. A. Pavlopoulos et al. BIOINFORMATICS
- Caleydo: connecting pathways and gene expression
- (2009) Marc Streit et al. BIOINFORMATICS
- Visualization of genomic data with the Hilbert curve
- (2009) S. Anders BIOINFORMATICS
- MapView: visualization of short reads alignment on a desktop computer
- (2009) H. Bao et al. BIOINFORMATICS
- Tablet--next generation sequence assembly visualization
- (2009) I. Milne et al. BIOINFORMATICS
- The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets
- (2009) J. W. Nicol et al. BIOINFORMATICS
- The Sequence Alignment/Map format and SAMtools
- (2009) H. Li et al. BIOINFORMATICS
- CMap 1.01: a comparative mapping application for the Internet
- (2009) K. Youens-Clark et al. BIOINFORMATICS
- Genome Projector: zoomable genome map with multiple views
- (2009) Kazuharu Arakawa et al. BMC BIOINFORMATICS
- Graphle: Interactive exploration of large, dense graphs
- (2009) Curtis Huttenhower et al. BMC BIOINFORMATICS
- GIBA: a clustering tool for detecting protein complexes
- (2009) Charalampos N Moschopoulos et al. BMC BIOINFORMATICS
- CNV-seq, a new method to detect copy number variation using high-throughput sequencing
- (2009) Chao Xie et al. BMC BIOINFORMATICS
- PhyloExplorer: a web server to validate, explore and query phylogenetic trees
- (2009) Vincent Ranwez et al. BMC EVOLUTIONARY BIOLOGY
- Next generation tools for the annotation of human SNPs
- (2009) Rachel Karchin BRIEFINGS IN BIOINFORMATICS
- LookSeq: A browser-based viewer for deep sequencing data
- (2009) H. M. Manske et al. GENOME RESEARCH
- JBrowse: A next-generation genome browser
- (2009) M. E. Skinner et al. GENOME RESEARCH
- Circos: An information aesthetic for comparative genomics
- (2009) M. Krzywinski et al. GENOME RESEARCH
- ABySS-Explorer: Visualizing Genome Sequence Assemblies
- (2009) C.B. Nielsen et al. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
- MizBee: A Multiscale Synteny Browser
- (2009) M. Meyer et al. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
- Visual Exploration of Three-Dimensional Gene Expression Using Physical Views and Linked Abstract Views
- (2009) G.H. Weber et al. IEEE-ACM Transactions on Computational Biology and Bioinformatics
- The UCSC Cancer Genomics Browser
- (2009) Jingchun Zhu et al. NATURE METHODS
- Computational methods for discovering structural variation with next-generation sequencing
- (2009) Paul Medvedev et al. NATURE METHODS
- Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
- (2009) Da Wei Huang et al. Nature Protocols
- Network visualization and analysis of gene expression data using BioLayout Express3D
- (2009) Athanasios Theocharidis et al. Nature Protocols
- Sequencing technologies — the next generation
- (2009) Michael L. Metzker NATURE REVIEWS GENETICS
- STITCH 2: an interaction network database for small molecules and proteins
- (2009) Michael Kuhn et al. NUCLEIC ACIDS RESEARCH
- VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology
- (2009) Zhenjun Hu et al. NUCLEIC ACIDS RESEARCH
- SNOW, a web-based tool for the statistical analysis of protein–protein interaction networks
- (2009) Pablo Minguez et al. NUCLEIC ACIDS RESEARCH
- Pathway Projector: Web-Based Zoomable Pathway Browser Using KEGG Atlas and Google Maps API
- (2009) Nobuaki Kono et al. PLoS One
- PhyloWidget: web-based visualizations for the tree of life
- (2008) G. E. Jordan et al. BIOINFORMATICS
- ProCope--protein complex prediction and evaluation
- (2008) J. Krumsiek et al. BIOINFORMATICS
- BicOverlapper: A tool for bicluster visualization
- (2008) R. Santamaria et al. BIOINFORMATICS
- NetworkBLAST: comparative analysis of protein networks
- (2008) M. Kalaev et al. BIOINFORMATICS
- Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database
- (2008) Tim Carver et al. BIOINFORMATICS
- DNAPlotter: circular and linear interactive genome visualization
- (2008) T. Carver et al. BIOINFORMATICS
- Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing
- (2008) Ryan D. Morin et al. BIOTECHNIQUES
- PSAT: A web tool to compare genomic neighborhoods of multiple prokaryotic genomes
- (2008) Christine Fong et al. BMC BIOINFORMATICS
- GenomeMatcher: A graphical user interface for DNA sequence comparison
- (2008) Yoshiyuki Ohtsubo et al. BMC BIOINFORMATICS
- Presenting and exploring biological pathways with PathVisio
- (2008) Martijn P van Iersel et al. BMC BIOINFORMATICS
- Arena3D: visualization of biological networks in 3D
- (2008) Georgios A Pavlopoulos et al. BMC Systems Biology
- Visualizing Genome Expression and Regulatory Network Dynamics in Genomic and Metabolic Context
- (2008) M. A. Westenberg et al. COMPUTER GRAPHICS FORUM
- EagleView: A genome assembly viewer for next-generation sequencing technologies
- (2008) W. Huang et al. GENOME RESEARCH
- DHPC: A new tool to express genome structural features
- (2008) Xuegong Deng et al. GENOMICS
- Mutational Derivatives of PhiC31 Integrase With Increased Efficiency and Specificity
- (2008) Annahita Keravala et al. MOLECULAR THERAPY
- The future of biocuration
- (2008) Doug Howe et al. NATURE
- Integrated network analysis platform for protein-protein interactions
- (2008) Jianmin Wu et al. NATURE METHODS
- High-resolution mapping of copy-number alterations with massively parallel sequencing
- (2008) Derek Y Chiang et al. NATURE METHODS
- Network Analysis Tools: from biological networks to clusters and pathways
- (2008) Sylvain Brohée et al. Nature Protocols
- RNA-Seq: a revolutionary tool for transcriptomics
- (2008) Zhong Wang et al. NATURE REVIEWS GENETICS
- Hubba: hub objects analyzer—a framework of interactome hubs identification for network biology
- (2008) Chung-Yen Lin et al. NUCLEIC ACIDS RESEARCH
- The HuRef Browser: a web resource for individual human genomics
- (2008) Nelson Axelrod et al. NUCLEIC ACIDS RESEARCH
- GraphWeb: mining heterogeneous biological networks for gene modules with functional significance
- (2008) J. Reimand et al. NUCLEIC ACIDS RESEARCH
- KEGG Atlas mapping for global analysis of metabolic pathways
- (2008) S. Okuda et al. NUCLEIC ACIDS RESEARCH
- NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways
- (2008) S. Brohee et al. NUCLEIC ACIDS RESEARCH
- Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
- (2008) Da Wei Huang et al. NUCLEIC ACIDS RESEARCH
- The CGView Server: a comparative genomics tool for circular genomes
- (2008) J. R. Grant et al. NUCLEIC ACIDS RESEARCH
- Reactome knowledgebase of human biological pathways and processes
- (2008) L. Matthews et al. NUCLEIC ACIDS RESEARCH
- Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups Papaya, Poplar, and Grape: CoGe with Rosids
- (2008) E. Lyons et al. PLANT PHYSIOLOGY
- CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks
- (2008) A. Funahashi et al. PROCEEDINGS OF THE IEEE
- iPath: interactive exploration of biochemical pathways and networks
- (2008) Ivica Letunic et al. TRENDS IN BIOCHEMICAL SCIENCES
- WikiPathways: Pathway Editing for the People
- (2008) Alexander R Pico et al. PLOS BIOLOGY
- A survey of visualization tools for biological network analysis
- (2008) Georgios A Pavlopoulos et al. BioData Mining
Create your own webinar
Interested in hosting your own webinar? Check the schedule and propose your idea to the Peeref Content Team.
Create NowBecome a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get Started