Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future

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