Links to previous NAR Papers: 2022 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8728131/ 2021 http://www.ncbi.nlm.nih.gov/pmc/articles/pmc7779060/ 2020 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145642/ 2019 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323953/ 2018 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753355/ 2017 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210591/ 2016 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702902/ 2015 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383971 2014 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964947 2013 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531082 2012 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245018 2011 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3242726 2010 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808870 2006: https://pubmed.ncbi.nlm.nih.gov/16381938/ Historic Outlines of the NAR Paper to generate ideas for future outlines -- The UCSC Genome Browser database: 2022 update Abstract INTRODUCTION BACKGROUND NEW GENOME BROWSER DATA -New assemblies -New and updated clinical data -SARS-CoV-2 data -New public hubs NEW GENOME BROWSER SOFTWARE -Recommended track sets -Updated variant display -SARS-CoV-2 phylogenetics -Enhanced signal display -New font options -Updated multi-region access -Enhanced track hub filters -Track hub settings for conveying more information -Dynamic PCR and BLAT for assembly hubs FUTURE PLANS OUTREACH AND CONTACT INFORMATION SUPPLEMENTARY DATA [updated tracks/tables in previous year] ACKNOWLEDGEMENTS FUNDING REFERENCES -- The UCSC Genome Browser database: 2021 update Abstract INTRODUCTION ANNOTATIONS AND VISUALIZATIONS Improvements for clinical genetics Gene set updates New track and assembly hubs New and updated assemblies SARS-CoV-2 Genome Browser and COVID-19 annotations in Human Browsers Patch sequences and the mitochondrial genome (chrMT) ENCODE registry of candidate cis-regulatory elements (cCREs) Eukaryotic Promoter Database (EPD) Promoters NCBI RefSeq Select & Matched Annotation from NCBI and EMBL-EBI (MANE) Gene expression from GTEx project completion SOFTWARE AND TOOL IMPROVEMENTS *Track visualization improvements Hide empty subtracks Collapse track items Track auto-scale changes *RESTful API changes *New track displays Hi-C display Personal genomics trio display New dbSNP display and JSON format OUTREACH AND CONTACT INFORMATION FUTURE PLANS FUNDING REFERENCES -- UCSC Genome Browser enters 20th year Abstract INTRODUCTION ANNOTATIONS AND VISUALIZATIONS GeneHancer and interact track format improvements TCGA Pan-Cancer data and the new lollipop plot display Tabula Muris and the single-cell browser Human patch sequences ENCODE transcription factor binding site peaks and clusters DGV Gold Standard Variants Genomenon Mastermind Gene set updates Multiple alignments for chicken, Drosophila and Caenorhabditis elegans New public track hubs SOFTWARE AND TOOL IMPROVEMENTS BLAT against all genomes REST API Session Custom-Track backups OUTREACH AND CONTACT INFORMATION FUTURE PLANS SUPPLEMENTARY DATA ACKNOWLEDGEMENTS FUNDING REFERENCES --The UCSC Genome Browser database: 2019 update Abstract INTRODUCTION NEW ASSEMBLIES AND ANNOTATIONS Genomes from more organisms and the CHO cell line Genotype-Tissue expression project New NCBI RefSeq tracks -RefSeq functional elements Ensembl/gencode updates -Cancer gene expression -gnomAD -SNPedia More alignments SOFTWARE IMPROVEMENTS Improved search Track collections New track type - bigNarrowPeak New track type - interact and bigInteract Command line tools OUTREACH AND CONTACT INFORMATION PLANS FOR THE FUTURE SUPPLEMENTARY DATA ACKNOWLEDGEMENTS FUNDING REFERENCES --The UCSC Genome Browser database: 2018 update Abstract INTRODUCTION NEW DATA AND DISPLAYS CRISPR/Cas9 track release Gene Interactions track release RefSeq Genes track update: now with NCBI mappings GTEx Gene Track update: body map selection tool Track hub portal updates TOOL IMPROVEMENTS European public MySQL server with GBiB support Command-line version of the Variant Annotation Integrator GBiC: Genome Browser in the cloud New track type: barChart Human Genome Variation Society (HGVS) term support Track hub portal search improvements Track hub backend upgrades Multi-feature and multi-color highlighting Updated policy for storing BLAT search results OUTREACH AND CONTACT INFORMATION PLANS FOR THE FUTURE SUPPLEMENTARY DATA ACKNOWLEDGEMENTS FUNDING REFERENCES --The UCSC Genome Browser database: 2017 update Abstract INTRODUCTION Genome assemblies -New and updated UCSC-hosted genomes, 2015-2016 Genome browser annotation data tracks -Mapping and sequencing -Genes and gene predictions -GENCODE genes -UCSC genes Phenotype and literature Expression Regulation Comparative genomics Variation -New dbSNP Build 146 and Build 147 -New phase 3 data of the 1000 Genomes Project Home and gateway pages Visualizing genomes: genome browser tracks display New multi-region display feature New density graph feature New keyboard shortcuts New browser menu options New features in gene description page New sessions gallery and public sessions Table-based browsing and querying -Related database tables in the data integrator -Updated dbNSFP data in hgVai Custom tracks, track hubs, assembly hubs and public hubs -Custom tracks -Track hubs Public UCSC-reviewed track and assembly hubs --New track and assembly public hubs hosted by UCSC, 2015-2016 Alternative UCSC genome browsers: GBiB, mirrors Public MySQL server access Utilities and source code Support, training and documentation FUTURE PLANS CONTACT US SUPPLEMENTARY DATA ACKNOWLEDGEMENTS FUNDING REFERENCES --The UCSC Genome Browser database: 2016 update Abstract INTRODUCTION OVERVIEW OF THE BROWSER Visualizing and navigating data Incorporating user-generated data Genome browser tools NEW AND UPDATED DATA IN THE GENOME BROWSER New and updated genome assemblies -New and updated genome browsers New and updated genomic annotations -New and updated annotation tracks in the Genome Browser New track and assembly data hubs Gene sets -UCSC genes -GENCODE genes -Augustus genes Phenotype and variation Gene expression ENCODE regulatory data Comparative genomics NEW SOFTWARE FEATURES IN THE GENOME BROWSER Data integrator Enhancements to data hubs -BLAT your genomes -More robust gene prediction display -Use your data hubs across genome browsers -Clinical variants beacon Improvements to the browser display -Exon-number display -Display data on both strands Expanded training and workshop program FUTURE PLANS CONTACT US FUNDING REFERENCES --The UCSC Genome Browser database: 2015 update Abstract INTRODUCTION KEY FEATURES OF THE BROWSER Display and navigation User data in the browser Other tools NEW DATA IN THE GENOME BROWSER New genome assemblies -Human genome -Rat genome -Ebola virus genome -Other species -New genome browsers New and updated genome annotation New annotation tracks in the Genome Browser Public track hubs in the Genome Browser Public assembly hubs in the Genome Browser Gene sets -UCSC genes -GENCODE genes -Ensembl genes Phenotype, literature and variation Gene expression and regulatory elements -Transcriptome -Epigenome and transcriptional regulation Comparative genomics Other -Dog genome -Zebrafish genome NEW SOFTWARE FEATURES IN THE GENOME BROWSER General display enhancements Stacked "wiggle" display Region highlighting Specific annotation display enhancements Transcription factor motifs Hierarchical alignment format RepeatMasker-nested elements Locating data of interest Data Integration Comparative assembly hubs Software distribution -Genome browser in a box (GBiB) FUTURE PLANS Expanding the hg38 human genome browser Gene sets, expression and pathways Software CREATING A GENOME BROWSER CONTACTING US FUNDING REFERENCES --The UCSC Genome Browser database: 2014 update Abstract INTRODUCTION GENOME BROWSER DATA SETS New genome assemblies New and updated annotations Gene annotations Variation data Comparative alignments ENCODE data Publications data Denisova data GENOME BROWSER SOFTWARE UPDATES Track and assembly data hubs Variant annotation integrator Gene haplotype alleles Updates to Browser display and navigation User training and mirror support FUTURE PLANS CONTACTING US FUNDING ACKNOWLEDGEMENTS REFERENCES --The UCSC Genome Browser database: extensions and updates 2013 Abstract INTRODUCTION LOCAL DATASETS New genome assemblies New and updated annotations SOFTWARE IMPROVEMENTS FUTURE DIRECTIONS CONTACTING US FUNDING ACKNOWLEDGEMENTS REFERENCES --The UCSC Genome Browser database: extensions and updates 2011 [2012] Abstract INTRODUCTION LOCAL DATA SETS New genome assemblies New and updated annotations DECENTRALIZED DATA Extending the browser with track data hubs NEW USABILITY FEATURES FUTURE DIRECTIONS FUNDING ACKNOWLEDGEMENTS REFERENCES --The UCSC Genome Browser database: update 2011 Abstract INTRODUCTION NEW FEATURES Gene search Drag-reorder BigBed/BigWig and BAM file support Display enhancements Table Browser support for external software NEW DATA Neandertal data portal Phenotype and disease association data Human RNA editing New assemblies New tracks in other organisms Updates to existing tracks and assemblies FUTURE DIRECTIONS CONTACTING US FUNDING ACKNOWLEDGEMENTS REFERENCES --The UCSC Genome Browser database: update 2010 Abstract INTRODUCTION NEW DATA New assemblies Regular updates to existing tracks New annotation tracks 44-species vertebrate alignment and conservation OMIM genes Variation Expression NEW FEATURES Drag-and-zoom Annotating the genome using the Wiki track Custom tracks for large datasets Bridging genomic variation and protein structure In silico PCR for transcribed sequences CDS FASTA alignments Improved track configuration Performance enhancements FUTURE DIRECTIONS CONTACTING US FUNDING ACKNOWLEDGEMENTS REFERENCES --The UCSC Genome Browser database: update 2009 Abstract INTRODUCTION NEW DATA New assemblies New annotations New UCSC Genes Variation Transmap New Gene Sorter columns NEW DISPLAY FEATURES Custom tracks enhancements Future directions FUNDING ACKNOWLEDGEMENTS REFERENCES --The UCSC Genome Browser database: update 2008 Abstract INTRODUCTION DATA ACQUISITION AND METHODS New data UCSC Genes-the next generation of Known Genes 28-Species conservation Variation and disease Mapping, gene prediction, regulation and expression data Mammalian Gene Collection ENCODE VisiGene and Gene Sorter data sets NEW FEATURES Viewing genome-wide data with Genome Graphs Genomewiki Saving and sharing Genome Browser sessions Managing custom tracks New display options FUTURE DIRECTIONS ACKNOWLEDGEMENTS REFERENCES --The UCSC Genome Browser database: update 2007 Abstract INTRODUCTION NEW DATA New assemblies Human genome browsers Known genes MAMMALIAN GENE COLLECTION Conservation tracks Simple Nucleotide Polymorphism (SNP) tracks HapMap and other variation tracks New track types: regulatory potential, gene trap VISIGENE Mirror sites NEW FEATURES Custom track enhancements phyloGif hgConvert New display features FUTURE DIRECTIONS Acknowledgments REFERENCES --The UCSC Genome Browser Database: update 2006 Abstract INTRODUCTION NEW DATA AND DATA TYPES Additional species supported Genome-wide multi-species alignments and conservation scores UCSC Known Genes Additions to the Proteome Browser Cross-species protein alignments ENCODE pages and tracks Other new gene annotations New expression data New variation data NEW VISUALIZATION FEATURES Beyond the box: 'wiggle' tracks display continuous-valued data Conservation: juxtaposed multi-species alignments and conservation scores Chromosome ideogram New dynamically computed tracks Enhancements to user custom track support New display modes New labeling options in gene annotations, mRNA and Base Position tracks New PostScript or PDF image generation Tracks organized by type Track configuration page Composite tracks NEW TABLE BROWSER INTERFACE AND FUNCTIONALITY NEW TOOLS PROCESS AND INFRASTRUCTURE IMPROVEMENTS FUTURE DIRECTIONS CONTACTING US Acknowledgments REFERENCES --The UCSC Proteome Browser (2005) (Author: Fan, not really just the Browser) ( Nucleic Acids Res 2005 Jan 1;33(Database issue):D454-8. doi: 10.1093/nar/gki100.) Abstract INTRODUCTION DATABASE ORGANIZATION DOWNLOADING DATA PROTEIN BROWSER TRACKS PROTEIN PROPERTY HISTOGRAMS LINKS TO OTHER PROTEIN RESOURCES FUTURE DIRECTIONS CONTACTING US ACKNOWLEDGEMENTS REFERENCES --The UCSC Table Browser data retrieval tool (2004) ( Not the whole site, Nucleic Acids Res. 2004 Jan 1;32(Database issue):D493-6.) Abstract INTRODUCTION BASIC DATA QUERIES ADVANCED QUERIES Output format configuration Filtering Multiple table comparisons Retrieving subregions of features FUTURE DIRECTIONS CONTACTING US ACKNOWLEDGEMENTS REFERENCES --The UCSC Genome Browser database. (2003) (Nucleic Acids Res. 2003 Jan 1;31(1):51-4.) Abstract INTRODUCTION DATABASE ORGANIZATION ANNOTATIONS VIEWING AND DOWNLOADING DATA FUTURE DIRECTIONS CONTACTING US ACKNOWLEDGEMENTS REFERENCES --The UCSC Genome Browser. (2002 -updated March 2007) (Curr Protoc Bioinformatics. 2002;Chapter 1:Unit 1.4.) Abstract INTRODUCTION Basic Protocol: Using the UCSC Genome Browser Navigate to the Genome Browser window to a specific genomic position Browse and configure the annotation tracks display Examine the underlying data and download the sequence and annotation data tables Convert coordinates in the displayed range to a different assembly using the Convert, LiftOver, or BLAT tools Support Protocol 1: Creating a Custom Annotation Track Support Protocol 2: Using the UCSC Table Browser Set up a simple Table Browser query Explore advanced query options Guidelines for Understanding Results Commentary Background Information History and development of the UCSC browser How are various annotation tracks determined? Critical Parameters and Troubleshooting Troubleshooting custom annotation track problems Suggestions for Further Analysis The Gene Sorter The VisiGene image browser The Proteome Browser The in silico PCR utility Additional resources for Genome Browser information Acknowledgments