Defining Candidate Imprinted loci in <i>Bos taurus</i> by Minou Bina

“…By displaying my datasets on the UCSC genome browser, one could view peak positions with respect to genomic landmarks. …”
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SNPexp - A web tool for calculating and visualizing correlation between HapMap genotypes and gene expression levels by Franke Andre, Melum Espen, Holm Kristian, Karlsen Tom H

“…Correlation between genotype and transcript expression levels are calculated by performing linear regression and the Wald test as implemented in PLINK and visualized using the UCSC Genome Browser. Validation of SNPexp using previously published eQTLs yielded comparable results.…”
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Upregulated lncRNA Gm2044 inhibits male germ cell development by acting as miR-202 host gene by Meng Liang, Ke Hu, Chaofan He, Jinzhao Zhou, Yaping Liao

“…Using lncRNA microarray of testicular tissue for male infertility and bioinformatics methods, we identified the relatively conserved lncRNA Gm2044 which may play important roles in non-obstructive azoospermia. The UCSC Genome Browser showed that lncRNA Gm2044 is the miR-202 host gene. …”
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iHAP – integrated haplotype analysis pipeline for characterizing the haplotype structure of genes by Lim Yun Ping, Yang Yuchen, Tantoso Erwin, Yeo Boon Huat, Song Chun Meng, Li Kuo-Bin, Rajagopal Gunaretnam

“…In addition to incorporating genotype and haplotype data from the International HapMap Project and gene information from the UCSC Genome Browser Database, iHAP also provides capabilities for inferring haplotype blocks and selecting tag SNPs that are representative of haplotype patterns. …”
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Genome-wide methylation data from R1 (wild-type) and the transgenic Dnmt1Tet/Tet mouse embryonic stem cells overexpressing DNA methyltransferase 1 (DNMT1) by Sonal Saxena, Sumana Choudhury, K. Naga Mohan

“…The data was processed to determine the methylation percentages of target genes and was visualized using the UCSC genome browser. The observed methylation differences were validated by Combined Bisulfite Restriction Analysis (COBRA). …”
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Genome-wide functional element detection using pairwise statistical alignment outperforms multiple genome footprinting techniques. by Satija, R, Hein, J, Lunter, G

“…We tested GRAPeFoot using the human and mouse genomes and compared its performance to a set of phastCons predictions hosted on the UCSC genome browser. Our results demonstrate that despite the use of only two genomes, GRAPeFoot identified constrained elements at rates comparable with phastCons, which analyzed data from 28 vertebrate genomes. …”

arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays by Moreau Yves, Vermeesch Joris, van Vooren Steven, De Paepe Anne, Mortier Geert, Buysse Karen, Michels Evi, Robbrecht Piet, De Preter Katleen, Pattyn Filip, Menten Björn, De Moor Bart, Vermeulen Stefan, Speleman Frank, Vandesompele Jo

“…Data can be exported in a multitude of formats, including BED files to map copy number information on the genome using the Ensembl or UCSC genome browser.</p> <p>Conclusion</p> <p><it>ArrayCGHbase </it>is a web based and platform independent arrayCGH data analysis tool, that allows users to access the analysis suite through the internet or a local intranet after installation on a private server. …”
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The Ruby UCSC API: accessing the UCSC genome database using Ruby by Mishima Hiroyuki, Aerts Jan, Katayama Toshiaki, Bonnal Raoul J P, Yoshiura Koh-ichiro

“…The database offers an excellent web-based graphical user interface (the UCSC genome browser) and several means for programmatic queries. …”
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Conservation analysis and pathogenicity prediction of mutant genes of ectodysplasin a by Fangqi He, Hongfeng Wang, Xiaoyu Zhang, Qingping Gao, Feng Guo, Chang Chen

“…Methods Conservation analysis of the related homologous proteins in 3 unknown EDA gene mutation sites was conducted using the University of California Santa Cruz (UCSC) Genome Browser database. SIFT and PolyPhen-2, the online gene function prediction software, were utilized to predict the pathogenicity of point mutation of c.878 T > G. …”
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SeqAnt: A web service to rapidly identify and annotate DNA sequence variations by Patel Viren, Steinberg Karyn, Horner Vanessa L, Mondal Kajari, Athri Prashanth, Shetty Amol, Caspary Tamara, Cutler David J, Zwick Michael E

“…Annotated variants can be viewed on a web browser, downloaded in a tab-delimited text file, or directly uploaded in a BED format to the UCSC genome browser. To demonstrate the speed of SeqAnt, we annotated a series of publicly available datasets that ranged in size from 37 to 3,439,107 variant sites. …”
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Discovering candidate imprinted genes and imprinting control regions in the human genome by Minou Bina

“…Since the datafiles are available for download and display at the UCSC genome browser, it is possible to examine the plots in the context of Single nucleotide polymorphisms (SNPs) to design experiments to discover novel ICRs and imprinted genes in the human genome.…”
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MicroRNA and Hemophilia-A Disease: Bioinformatics Prediction and Experimental Analysis by Halimeh Rezaei, Majid Motovali-Bashi, Seyed Javad Mowla

“…The ability to express new microRNAs in F8 locus was studied through reliable bioinformatics databases such as SSCProfiler, RNA fold, miREval, miR-FIND, UCSC genome browser and miRBase. Then, expression and processing of the predicted microRNAs were examined based on bioinformatics methods, in the HEK293 cell lines. …”
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Integrating diverse datasets improves developmental enhancer prediction. by Genevieve D Erwin, Nir Oksenberg, Rebecca M Truty, Dennis Kostka, Karl K Murphy, Nadav Ahituv, Katherine S Pollard, John A Capra

“…Our genome-wide developmental enhancer predictions are freely available as a UCSC Genome Browser track, which we hope will enable researchers to further investigate questions in developmental biology.…”
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SEARCH FOR ARE REGULATORY SEQUENCES IN GENES of MASTER REGULATORS OF autophagy and LYSOSOMAL BIOGENESIS TFEB AND TFE3 by A. V. Chechushkov, E. B. Menshchikova

“…ARE-like sequences were labeled in the UCSC genome browser for analysis of evolutionary conservation, colocalization with various functional DNA and chromatin modifications, as well as with other regulatory elements. …”
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Integrating multiple genome annotation databases improves the interpretation of microarray gene expression data by Kennedy Breandan, Glaviano Antonino, Jeffery Ian B, McLoughlin Sarah, Yin Jun, Higgins Desmond G

“…</p> <p>Results</p> <p>Transcript data from the RefSeq, GenBank and Ensembl databases were downloaded from the UCSC genome browser, and integrated to generate a combined zebrafish genome annotation. …”
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Tissue-specific classification of alternatively spliced human exons by Rothman, Craig Jeremy

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Role of ACE2 Gene Expression in Renin Angiotensin System and Its Importance in Covid-19: In Silico Approach by Sevgi Kalkanli Tas, Duygu Kirkik, Mehmet Emirhan Işik, Nevin Kalkanli, Aylin Seher Uzunoglu, Merve Saide Uzunoglu, Derya Altunkanat, Jalal Mohammed Mohammed Alragabi, Alpaslan Tanoglu

“…Then, DISEASES resource, FitSNPs, UniProt, BioXpress, IGV Browser, Ensembl Genome Browser, and UCSC Genome Browser were used to predict the ACE2 gene-related diseases and expression profile in human normal and cancer tissues. …”
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In silico analysis of genomic variables associated to HPV16 integration sites by Nicole Díaz-Moreno

“…Propósito: Identificar in silico, las regiones moleculares del genoma donde ocurren los eventos de integración del VPH Métodos: Realizamos un estudio bioinformático basado en una búsqueda sistemática en Medline a través de PubMed, Embase y Lilacs desde el inicio hasta abril de 2019. Utilizamos el UCSC Genome Browser Home (https://genome.ucsc.edu) para evaluar el entorno genético. …”
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MicroRNA-Mediated Regulation of ITGB3 and CHL1 Is Implicated in SSRI Action by Keren Oved, Luba Farberov, Avial Gilam, Ifat Israel, Danielle Haguel, David Gurwitz, Noam Shomron

“…Our earlier genome-wide studies indicated that two genes encoding for cell adhesion proteins, close homolog of L1 (CHL1) and integrin beta-3 (ITGB3), and microRNAs, miR-151a-3p and miR-221/222, are implicated in the variable sensitivity and response of human lymphoblastoid cell lines (LCL) from unrelated individuals to SSRI drugs.Methods: The microRNAs miR-221, miR-222, and miR-151-a-3p, along with their target gene binding sites, were explored in silico using miRBase, TargetScan, microRNAviewer, and the UCSC Genome Browser. Luciferase reporter assays were conducted for demonstrating the direct functional regulation of ITGB3 and CHL1 expression by miR-221/222 and miR-151a-3p, respectively. …”
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A new measurement of sequence conservation by Li Xiaoman, Hu Haiyan, Cai Xiaohui

“…We also found that 72% of the mouse homologous regions identified based on the new measurement are more similar to the human functional sequences than the aligned mouse sequences from the UCSC genome browser. We further compared BLAST and discontiguous MegaBLAST with our method. …”
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