Primates and mouse NumtS in the UCSC Genome Browser by Calabrese Francesco Maria, Simone Domenico, Attimonelli Marcella

“…NumtS retrieval through the UCSC Genome Browser, in the species examined, is now feasible at a glance.…”

GenArk: towards a million UCSC genome browsers by Hiram Clawson, Brian T. Lee, Brian J. Raney, Galt P. Barber, Jonathan Casper, Mark Diekhans, Clay Fischer, Jairo Navarro Gonzalez, Angie S. Hinrichs, Christopher M. Lee, Luis R. Nassar, Gerardo Perez, Brittney Wick, Daniel Schmelter, Matthew L. Speir, Joel Armstrong, Ann S. Zweig, Robert M. Kuhn, Bogdan M. Kirilenko, Michael Hiller, David Haussler, W. James Kent, Maximilian Haeussler

“…We create Genome Archive (GenArk) collection of UCSC Genome Browsers from NCBI assemblies. Built on our established track hub system, this enables fast visualization of annotations. …”
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MakeHub: Fully Automated Generation of UCSC Genome Browser Assembly Hubs by Katharina Jasmin Hoff

“…Visualizing resulting annotation is a crucial step of quality control. The UCSC Genome Browser is a powerful and popular genome visualization tool. …”
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Visualization enhancement of bioinformatics software for genetic recombination via UCSC genome browser by Wong, Ryan Wei Jiat

“…In short, the enhancement of LDsplit, using UCSC Genome browser, will bring about momentous breakthrough in research. …”
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LncRNA-Associated Genetic Etiologies Are Shared between Type 2 Diabetes and Cancers in the UAE Population by Roberta Giordo, Rida Gulsha, Sarah Kalla, George A. Calin, Leonard Lipovich

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GenomeGems: evaluation of genetic variability from deep sequencing data by Ben-Zvi Sharon, Givati Adi, Shomron Noam

“…The tool allows the user to compare and visualize SNPs from multiple experiments and to easily load SNP data onto the UCSC Genome browser for further detailed information.</p>…”
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PhenCode: connecting ENCODE data with mutations and phenotype. by Giardine, B, Riemer, C, Hefferon, T, Thomas, D, Hsu, F, Zielenski, J, Sang, Y, Elnitski, L, Cutting, G, Trumbower, H, Kern, A, Kuhn, R, Patrinos, G, Hughes, J, Higgs, D, Chui, D, Scriver, C, Phommarinh, M, Patnaik, S, Blumenfeld, O, Gottlieb, B, Vihinen, M, Väliaho, J, Kent, J, Miller, W

“…Users can find interesting mutations in the UCSC Genome Browser (in a new Locus Variants track) and follow links back to the LSDBs for more detailed information. …”

Visualization and sharing of genomics data via a cloud based system by Chen, Guohao

“…External web applications like UCSC Genome Browser and Integrated Genome Browser (IGB) were also introduced to enhanced users’ experience in performing data analysis. …”
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Comparison of human (and other) genome browsers by Furey Terrence S

“…This review describes the basic functionality of genome browsers and compares three of them: the University of California Santa Cruz (UCSC) Genome Browser, the Ensembl Genome Browser and the NCBI MapViewer.…”
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Imaging Intron Evolution by Maria Antonietta Panaro, Rosa Calvello, Daniela Valeria Miniero, Vincenzo Mitolo, Antonia Cianciulli

“…Intron evolution may be readily imaged through the combined use of the “dot plot” function of the NCBI BLAST, aligning two sequences at a time, and the Vertebrate “Multiz” alignment and conservation tool of the UCSC Genome Browser. With the NCBI BLAST, an ideal alignment of two highly conserved sequences generates a diagonal straight line in the plot from the lower left corner to the upper right corner. …”
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Evolution of gene regulation of pluripotency - the case for wiki tracks at genome browsers by Struckmann Stephan, Fuellen Georg

“…</p> <p>Results</p> <p>We demonstrate the power of integrative bioinformatics by including curated transcription factor binding site information into the UCSC genome browser, using wiki and custom tracks, which enable easy publication of annotation data. …”
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Finding and verifying enhancers for endothelial-expressed genes by Neal, A, Rodriguez-Caro, H, De Val, S

“…Here we describe how to use publicly available datasets displayed on the UCSC Genome Browser to identify putative endothelial enhancers for mammalian genes. …”

Along the Bos taurus genome, uncover candidate imprinting control regions by Phillip Wyss, Carol Song, Minou Bina

“…Furthermore, the UCSC genome browser offers tools to produce enlarged views: to uncover the genes in the vicinity of candidate ICRs and thus discover potential imprinted genes for experimental validations.…”
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How accurately is ncRNA aligned within whole-genome multiple alignments? by Ruzzo Walter L, Wang Adrienne X, Tompa Martin

“…We inspect the MULTIZ 17-vertebrate alignment from the UCSC Genome Browser for all the human sequences in the Rfam seed alignments. …”
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Bioinformatic Evaluation of Features on Cis-regulatory Elements at 6q25.1 by N Sreekar, Smeeta Shrestha

“…Here, we review and report the different regulatory features present on ER with the objective to delineate potential mechanisms which may contribute to development of resistance. The UCSC Genome Browser, data mining, and bioinformatics tools were used to review enhancers, transcription factors (TFs), histone marks, long non-coding RNAs (lncRNAs), and variants residing in the non-coding region of the ER gene. …”
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wigExplorer, a BioJS component to visualise wig data [version 3; referees: 1 approved, 2 approved with reservations, 1 not approved] by Anil S. Thanki, Rafael C. Jimenez, Gemy G. Kaithakottil, Manuel Corpas, Robert P. Davey

“…Wig files are extensively used by genome browsers such as the UCSC Genome Browser. wigExplorer follows the BioJS standard specification, requiring a simple configuration and installation. wigExplorer provides an easy way to navigate the visible region of the canvas and allows interaction with other components via predefined events. …”
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GENCODE 2021

“…Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org.</jats:p>…”
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Segtor: rapid annotation of genomic coordinates and single nucleotide variations using segment trees. by Gabriel Renaud, Pedro Neves, Edson Luiz Folador, Carlos Gil Ferreira, Fabio Passetti

“…Our system currently can be made to work with any species available on the UCSC Genome Browser. Segtor is a suitable tool for groups, especially those with limited access to programmers or with interest to analyze large amounts of individual genomes, who wish to determine the relative position of very large sets of mapped reads and subsequently annotate observed mutations between the reads and the reference. …”
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GENCODE 2021 by Boix, Carles

“…Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org.</jats:p>…”
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ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines [v2; ref status: indexed, http://f1000r.es/5mq] by Michael T. Wolfinger, Jörg Fallmann, Florian Eggenhofer, Fabian Amman

“…Moreover, ViennaNGS provides software components for identification and characterization of splice junctions from RNA-seq data, parsing and condensing sequence motif data, automated construction of Assembly and Track Hubs for the UCSC genome browser, as well as wrapper routines for a set of commonly used NGS command line tools.…”
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