Visualizing genomes: techniques and challenges

[1]  Cathy Riemer,et al.  MultiPipMaker: A Comparative Alignment Server for Multiple DNA Sequences , 2010, Current protocols in bioinformatics.

[2]  Heinrich Magnus Manske,et al.  LookSeq: a browser-based viewer for deep sequencing data. , 2009, Genome research.

[3]  Paul Medvedev,et al.  Computational methods for discovering structural variation with next-generation sequencing , 2009, Nature Methods.

[4]  Inanç Birol,et al.  ABySS-Explorer: Visualizing Genome Sequence Assemblies , 2009, IEEE Transactions on Visualization and Computer Graphics.

[5]  Tamara Munzner,et al.  MizBee: A Multiscale Synteny Browser , 2009, IEEE Transactions on Visualization and Computer Graphics.

[6]  Paul Flicek,et al.  Sense from sequence reads: methods for alignment and assembly , 2009, Nature Methods.

[7]  A. Gnirke,et al.  ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads , 2009, Genome Biology.

[8]  Steven J. M. Jones,et al.  Circos: an information aesthetic for comparative genomics. , 2009, Genome research.

[9]  Ann E. Loraine,et al.  The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets , 2009, Bioinform..

[10]  Lincoln Stein,et al.  CMap 1.01: a comparative mapping application for the Internet , 2009, Bioinform..

[11]  Mihai Pop,et al.  Genome assembly reborn: recent computational challenges , 2009, Briefings Bioinform..

[12]  L. Stein,et al.  JBrowse: a next-generation genome browser. , 2009, Genome research.

[13]  Hui Guo,et al.  MapView: visualization of short reads alignment on a desktop computer , 2009, Bioinform..

[14]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[15]  Thomas M. Keane,et al.  Next-generation sequencing of vertebrate experimental organisms , 2009, Mammalian Genome.

[16]  Ting Wang,et al.  The UCSC Cancer Genomics Browser , 2009, Nature Methods.

[17]  M. Freeling,et al.  Conserved noncoding sequences (CNSs) in higher plants. , 2009, Current opinion in plant biology.

[18]  Inna Dubchak,et al.  Multiple whole-genome alignments without a reference organism. , 2009, Genome research.

[19]  Simon Anders,et al.  Visualisation of genomic data with the Hilbert curve , 2009 .

[20]  M. Cline,et al.  Understanding genome browsing , 2009, Nature Biotechnology.

[21]  Masaru Tomita,et al.  Genome Projector: zoomable genome map with multiple views , 2009, BMC Bioinformatics.

[22]  Haibao Tang,et al.  Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups Papaya, Poplar, and Grape: CoGe with Rosids1[W] , 2008, Plant Physiology.

[23]  Matthew Berriman,et al.  Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database , 2008, Bioinform..

[24]  Yuji Nagata,et al.  GenomeMatcher: A graphical user interface for DNA sequence comparison , 2008, BMC Bioinformatics.

[25]  E. Mardis.  Next-generation DNA sequencing methods. , 2008, Annual review of genomics and human genetics.

[26]  Gabor T. Marth,et al.  EagleView: a genome assembly viewer for next-generation sequencing technologies. , 2008, Genome research.

[27]  S. Nelson,et al.  Resolving Individuals Contributing Trace Amounts of DNA to Highly Complex Mixtures Using High-Density SNP Genotyping Microarrays , 2008, PLoS genetics.

[28]  R. Lister,et al.  Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis , 2008, Cell.

[29]  David Hernández,et al.  De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. , 2008, Genome research.

[30]  E. Birney,et al.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

[31]  Hwan-Gue Cho,et al.  A Scaffold Analysis Tool Using Mate-Pair Information in Genome Sequencing , 2008, Journal of biomedicine & biotechnology.

[32]  Mark J. P. Chaisson,et al.  Short read fragment assembly of bacterial genomes. , 2008, Genome research.

[33]  Daniel J. Blankenberg,et al.  28-way vertebrate alignment and conservation track in the UCSC Genome Browser. , 2007, Genome research.

[34]  Melanie A. Huntley,et al.  Evolution of genes and genomes on the Drosophila phylogeny , 2007, Nature.

[35]  Michal J. Okoniewski,et al.  X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis , 2007, Nucleic Acids Res..

[36]  Nicholas H. Putnam,et al.  Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization , 2007, Science.

[37]  Daniel H. Huson,et al.  BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btm153 Genome analysis OSLay: optimal syntenic layout of unfinished assemblies , 2022 .

[38]  William Stafford Noble,et al.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project , 2007, Nature.

[39]  Ben Shneiderman,et al.  Hawkeye: an interactive visual analytics tool for genome assemblies , 2007, Genome Biology.

[40]  Amit U. Sinha,et al.  Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms , 2007, BMC Bioinformatics.

[41]  Eileen Kraemer,et al.  SynView: a GBrowse-compatible approach to visualizing comparative genome data , 2006, Bioinform..

[42]  Jill P. Mesirov,et al.  Combo: a whole genome comparative browser , 2006, Bioinform..

[43]  David J. Reiss,et al.  The Gaggle: An open-source software system for integrating bioinformatics software and data sources , 2006, BMC Bioinformatics.

[44]  T. Furey,et al.  Comparison of human (and other) genome browsers , 2006, Human Genomics.

[45]  Shyam Prabhakar,et al.  Close sequence comparisons are sufficient to identify human cis-regulatory elements. , 2005, Genome research.

[46]  Christina A. Cuomo,et al.  Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae , 2005, Nature.

[47]  Daniel J. Blankenberg,et al.  Galaxy: a platform for interactive large-scale genome analysis. , 2005, Genome research.

[48]  Paramvir S. Dehal,et al.  A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database , 2006, BMC Bioinformatics.

[49]  D. Haussler,et al.  Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. , 2005, Genome research.

[50]  David S. Wishart,et al.  Circular genome visualization and exploration using CGView , 2005, Bioinform..

[51]  Steven Salzberg,et al.  DAGchainer: a tool for mining segmental genome duplications and synteny , 2004, Bioinform..

[52]  James Ostell,et al.  The Genome Assembly Archive: A New Public Resource , 2004, PLoS biology.

[53]  Lior Pachter,et al.  VISTA: computational tools for comparative genomics , 2004, Nucleic Acids Res..

[54]  F. Blattner,et al.  Mauve: multiple alignment of conserved genomic sequence with rearrangements. , 2004, Genome research.

[55]  Antony V. Cox,et al.  The Ensembl Web site: mechanics of a genome browser. , 2004, Genome research.

[56]  D. Haussler,et al.  Aligning multiple genomic sequences with the threaded blockset aligner. , 2004, Genome research.

[57]  Bernd Hamann,et al.  Phylo-VISTA: interactive visualization of multiple DNA sequence alignments , 2004, Bioinform..

[58]  S. Salzberg,et al.  Versatile and open software for comparing large genomes , 2004, Genome Biology.

[59]  D. Haussler,et al.  Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[60]  E. Birney,et al.  Comparative genomics: genome-wide analysis in metazoan eukaryotes , 2003, Nature Reviews Genetics.

[61]  E. Birney,et al.  Apollo: a sequence annotation editor , 2002, Genome Biology.

[62]  Colin N. Dewey,et al.  Initial sequencing and comparative analysis of the mouse genome. , 2002 .

[63]  S. Lewis,et al.  The generic genome browser: a building block for a model organism system database. , 2002, Genome research.

[64]  Parvaneh Saeedi,et al.  A physical map of the mouse genome , 2002, Nature.

[65]  Tom H. Pringle,et al.  The human genome browser at UCSC. , 2002, Genome research.

[66]  C. Desmarais,et al.  Automated finishing with autofinish. , 2001, Genome research.

[67]  E. Birney,et al.  Mining the draft human genome , 2001, Nature.

[68]  Lior Pachter,et al.  VISTA : visualizing global DNA sequence alignments of arbitrary length , 2000, Bioinform..

[69]  Andrew Smith.  Genome sequence of the nematode C-elegans: A platform for investigating biology , 1998 .

[70]  P. Green,et al.  Consed: a graphical tool for sequence finishing. , 1998, Genome research.

[71]  P. Green,et al.  Base-calling of automated sequencer traces using phred. I. Accuracy assessment. , 1998, Genome research.

[72]  P Green,et al.  Base-calling of automated sequencer traces using phred. II. Error probabilities. , 1998, Genome research.

[73]  J. D. Parsons,et al.  Miropeats: graphical DNA sequence comparisons , 1995, Comput. Appl. Biosci..

[74]  R. Staden,et al.  A sequence assembly and editing program for efficient management of large projects. , 1991, Nucleic acids research.

[75]  Amy E. Hawkins,et al.  Comprehensive genomic characterization defines human glioblastoma genes and core pathways , 2022 .

[76]  Jonathan Crabtree,et al.  Sybil: methods and software for multiple genome comparison and visualization. , 2007, Methods in molecular biology.

[77]  Inna Dubchak,et al.  Comparative analysis and visualization of genomic sequences using VISTA browser and associated computational tools. , 2007, Methods in molecular biology.

[78]  Colin N. Dewey,et al.  Aligning multiple whole genomes with Mercator and MAVID. , 2007, Methods in molecular biology.

[79]  Volker Brendel,et al.  Visualization of syntenic relationships with SynBrowse. , 2007, Methods in molecular biology.

[80]  David Haussler,et al.  Comparative genomic analysis using the UCSC genome browser. , 2007, Methods in molecular biology.

[81]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology , 2003, Nucleic Acids Res..

[82]  D. Haussler,et al.  Human-mouse alignments with BLASTZ. , 2003, Genome research.

[83]  Mouse Genome Sequencing Consortium.  Initial sequencing and comparative analysis of the mouse genome , 2002, Nature.

[84]  D R Bentley,et al.  Long-range comparison of human and mouse SCL loci: localized regions of sensitivity to restriction endonucleases correspond precisely with peaks of conserved noncoding sequences. , 2001, Genome research.

[85]  International Human Genome Sequencing Consortium.  Initial sequencing and analysis of the human genome , 2001, Nature.

[86]  T G Burland,et al.  DNASTAR's Lasergene sequence analysis software. , 2000, Methods in molecular biology.

[87]  J. Berg.  Genome sequence of the nematode C. elegans: a platform for investigating biology. , 1998, Science.

[88]  J. Bonfield,et al.  A new DNA sequence assembly program. , 1995, Nucleic acids research.

[89]  R. Durbin,et al.  ACeDB and macace. , 1995, Methods in cell biology.

[90]  Chuong B. Do,et al.  Glocal alignment : finding rearrangements during alignment , 2003 .