Predicting Parkinson disease related genes based on PyFeat and gradient boosted decision tree by Marwa Helmy, Eman Eldaydamony, Nagham Mekky, Mohammed Elmogy, Hassan Soliman

“…First, we preprocessed the genes into DNA FASTA sequences from the University of California Santa Cruz (UCSC) genome browser and removed the redundancies. Second, we extracted some significant features of DNA FASTA sequences using the PyFeat method with the AdaBoost as feature selection. …”
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Supporting data for characterization of non-coding RNAs associated with the Neuronal growth regulator 1 (NEGR1) adhesion protein by Prameet Kaur, Jun Rong Tan, Dwi Setyowati Karolina, Sugunavathi Sepramaniam, Arunmozhiarasi Armugam, Tsun-Hon Peter Wong, Kandiah Jeyaseelan

“…This data article contains detailed bioinformatics analysis of genetic signatures at the Negr1 gene locus retrieved from the UCSC genome browser. This approach could be adopted to identify putative regulatory non-coding RNAs in other tissues and diseases. …”
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Schistosoma mansoni Egg, Adult Male and Female Comparative Gene Expression Analysis and Identification of Novel Genes by RNA-Seq. by Letícia Anderson, Murilo S Amaral, Felipe Beckedorff, Lucas F Silva, Bianca Dazzani, Katia C Oliveira, Giulliana T Almeida, Monete R Gomes, David S Pires, João C Setubal, Ricardo DeMarco, Sergio Verjovski-Almeida

“…Importantly, all data have been consolidated into a UCSC Genome Browser search- and download-tool (http://schistosoma.usp.br/). …”
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Activation of <i>ABCC</i> Genes by Cisplatin Depends on the CoREST Occurrence at Their Promoters in A549 and MDA-MB-231 Cell Lines by Maciej Sobczak, Magdalena Strachowska, Karolina Gronkowska, Agnieszka Robaszkiewicz

“…Analysis of data for A549 cells deposited in UCSC Genome Browser provided evidence on the negative interdependence between the occurrence of the CoREST complex at the gene promoters and the overexpression of <i>ABCC</i> genes in cisplatin-resistant lung cancer cells. …”
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G-OnRamp: Generating genome browsers to facilitate undergraduate-driven collaborative genome annotation. by Luke Sargent, Yating Liu, Wilson Leung, Nathan T Mortimer, David Lopatto, Jeremy Goecks, Sarah C R Elgin

“…To address the technical barriers to creating genome browsers, the Genomics Education Partnership (GEP; https://gep.wustl.edu/) has partnered with the Galaxy Project (https://galaxyproject.org) to develop G-OnRamp (http://g-onramp.org), a web-based platform for creating UCSC Genome Browser Assembly Hubs and JBrowse genome browsers. …”
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Snat: a SNP annotation tool for bovine by integrating various sources of genomic information by Liu Jian-Feng, Fu Weixuan, Zhou Bin, Jiang Li, Jiang Jicai, Zhang Qin

“…</p> <p>Results</p> <p>With Snat, various sources of genomic information are integrated and retrieved from several leading online databases, including SNP information from dbSNP, gene information from Entrez Gene, protein features from UniProt, linkage information from AnimalQTLdb, conserved elements from UCSC Genome Browser Database and gene functions from Gene Ontology (GO), KEGG PATHWAY and Online Mendelian Inheritance in Animals (OMIA). …”
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CNV Workshop: an integrated platform for high-throughput copy number variation discovery and clinical diagnostics by Rappaport Eric F, Xie Hongbo M, Wenocur Adam, D'arcy Monica, O'Hara Ryan, Murphy Kevin, Perin Juan C, Gai Xiaowu, Shaikh Tamim H, White Peter S

“…Results are easily queried, sorted, filtered, and visualized via a web-based presentation layer that includes a GBrowse-based graphical representation of CNV content and relevant public data, integration with the UCSC Genome Browser, and tabular displays of genomic attributes for each CNV.…”
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CASCAD: a database of annotated candidate single nucleotide polymorphisms associated with expressed sequences by Cuppen Edwin, Berezikov Eugene, Guryev Victor

“…Although there are enormous amounts of SNPs for a wide variety of organisms submitted to NCBI dbSNP and annotated in most genome assembly viewers like Ensembl and the UCSC Genome Browser, these platforms do not easily allow for extensive annotation and incorporation of experimental data supporting the polymorphism. …”
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gb4gv: a genome browser for geminivirus by Eric S. Ho, Catherine M. Newsom-Stewart, Lysa Diarra, Caroline S. McCauley

“…Besides genomic content, our website provides visualization capability inherited from UCSC Genome Browser. Discussion With the genomic information readily accessible, we hope that our database will inspire researchers in gaining a better understanding of the incredible degree of diversity of these viruses, and of the complex relationships within and between the different genera in the Geminiviridae. …”
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Comparison of gene coverage of mouse oligonucleotide microarray platforms by Medrano Juan F, Verdugo Ricardo A

“…In order to make consistent comparisons between platforms, probes in each microarray were annotated with an Entrez Gene id and the chromosomal position for each gene was obtained from the UCSC Genome Browser Database. Gene coverage was estimated as the percentage of Entrez Genes with a unique position in the UCSC Genome database that is tested by a given microarray platform.…”
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Genome-wide prediction, display and refinement of binding sites with information theory-based models by Leeder J Steven, Vyhlidal Carrie A, Gadiraju Sashidhar, Rogan Peter K

“…Individual binding sites are displayed either as high-resolution sequence walkers or in low-resolution custom tracks in the UCSC genome browser. For large datasets, we applied a data reduction strategy that limited displays of binding sites exceeding a threshold information content to specific chromosomal regions within or adjacent to genes. …”
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Identifying Susceptibility Loci for Cutaneous Squamous Cell Carcinoma Using a Fast Sequence Kernel Association Test by Manyan Huang, Chen Lyu, Xin Li, Xin Li, Abrar A. Qureshi, Jiali Han, Jiali Han, Ming Li

“…The study included 1,710 cSCC cases and 24,304 cancer-free controls from the Nurses’ Health Study, the Nurses’ Health Study II and the Health Professionals Follow-up Study. We used UCSC Genome Browser to define gene units as candidate loci, and further evaluated the association between all variants within each gene unit and disease outcome. …”
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ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data by Pagès Hervé, Lawson Nathan D, Gazin Claude, Zhu Lihua J, Lin Simon M, Lapointe David S, Green Michael R

“…A number of algorithms have been developed in parallel that allow identification of binding sites from ChIP-seq or ChIP-chip datasets and subsequent visualization in the University of California Santa Cruz (UCSC) Genome Browser as custom annotation tracks. However, summarizing these tracks can be a daunting task, particularly if there are a large number of binding sites or the binding sites are distributed widely across the genome.…”
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Association of DSC3 mRNA down-regulation in prostate cancer with promoter hypermethylation and poor prognosis. by Jincheng Pan, Yu Chen, Chengqiang Mo, Daohu Wang, Junxing Chen, Xiaopeng Mao, Shengjie Guo, Jintao Zhuang, Shaopeng Qiu

“…Epigenetic status of DSC3 gene promoter in PCa was investigated by uploading three dataset (ENCODE Infinium 450K array data and two methylation sequencing) in UCSC genome browser. While pyrosequencing analysis measured promoter DNA methylation, Q-PCR estimates were obtained for DSC3 transcript re-expression after 5-Aza-deoxycytidine (5-Aza) treatment. …”
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miRdSNP: a database of disease-associated SNPs and microRNA target sites on 3'UTRs of human genes by Bruno Andrew E, Li Li, Kalabus James L, Pan Yuzhuo, Yu Aiming, Hu Zihua

“…The integration of dSNPs with the UCSC Genome browser is also supported.</p> <p>Conclusion</p> <p>miRdSNP provides a comprehensive data source of dSNPs and robust tools for exploring their distance from miRNA target sites on the 3'UTRs of human genes. miRdSNP enables researchers to further explore the molecular mechanism of gene dysregulation for dSNPs at posttranscriptional level. miRdSNP is freely available on the web at <url>http://mirdsnp.ccr.buffalo.edu</url>.…”
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Hyperglycemia-induced oxidative stress and epigenetic regulation of ET-1 gene in endothelial cells by Dalal Nasser Binjawhar, Alaa T. Alhazmi, Wejdan Nasser Bin Jawhar, Walaa MohammedSaeed, Sher Zaman Safi

“…Computational analysis were performed using UCSC genome browser and eukaryotic promoter database (EPD). …”
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Splicing Express: a software suite for alternative splicing analysis using next-generation sequencing data by Jose E. Kroll, Jihoon Kim, Lucila Ohno-Machado, Sandro J. de Souza

“…Splicing Express performs automatic annotation of transcriptome data (GTF files) using gene coordinates available from the UCSC genome browser and allows the analysis of data from all available species. …”
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TassDB2 - A comprehensive database of subtle alternative splicing events by Hampe Jochen, Rosenstiel Philip, Huse Klaus, Szafranski Karol, Friedel Swetlana, Gausmann Ulrike, Jahn Niels, Lenser Thorsten, Sinha Rileen, Schuster Stefan, Hiller Michael, Backofen Rolf, Platzer Matthias

“…Links are provided to the UCSC genome browser and other external resources.</p> <p>Conclusion</p> <p>TassDB2, available via <url>http://www.tassdb.info</url>, provides comprehensive resources for researchers interested in both targeted experimental studies and large-scale bioinformatics analyses of short distance tandem splice sites.…”
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Evolutionary origin of germline pathogenic variants in human DNA mismatch repair genes by Huijun Lei, Jiaheng Li, Bojin Zhao, Si Hoi Kou, Fengxia Xiao, Tianhui Chen, San Ming Wang

“…The genomes of 100 vertebrates were collected from the UCSC genome browser and ancient human sequencing data were obtained through comprehensive data mining. …”
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Annotation of suprachromosomal families reveals uncommon types of alpha satellite organization in pericentromeric regions of hg38 human genome assembly by V.A. Shepelev, L.I. Uralsky, A.A. Alexandrov, Y.B. Yurov, E.I. Rogaev, I.A. Alexandrov

“…We used the PERCON program previously described by us to annotate various suprachromosomal families (SFs) of AS in the hg38 assembly and presented the results of our primary analysis as an easy-to-read track for the UCSC Genome Browser. The monomeric classes, characteristic of the five known SFs, were color-coded, which allowed quick visual assessment of AS composition in whole multi-megabase centromeres down to each individual AS monomer. …”
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