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Genome Research, ISSN 1088-9051, 09/2009, Volume 19, Issue 9, pp. 1630 - 1638
Journal Article
Current Protocols in Bioinformatics, ISSN 1934-3396, 2009, Volume Chapter 1, Issue 28, p. 1.4.26
Journal Article
by Sun, C and Hu, ZQ and Zheng, TQ and Lu, KC and Zhao, Y and Wang, WS and Shi, JX and Wang, CC and Lu, JY and Zhang, DB and Li, ZK and Wei, CC
NUCLEIC ACIDS RESEARCH, ISSN 0305-1048, 01/2017, Volume 45, Issue 2, pp. 597 - 605
A pan-genome is the union of the gene sets of all the individuals of a clade or a species and it provides a new dimension of genome complexity with the... 
PROJECT | DATABASE | ALIGNMENT | BIOCHEMISTRY & MOLECULAR BIOLOGY | UCSC | MAP | TOOL
Journal Article
PeerJ, ISSN 2167-8359, 2017, Volume 2017, Issue 4, pp. e3165 - e3165
Journal Article
PEERJ, ISSN 2167-8359, 04/2017, Volume 5
Background. Geminiviruses (family Geminiviridae);are prevalent plant viruses that imperil agriculture globally, causing serious damage to the livelihood of... 
UCSC Genome Browser | GEMINIVIRUS DNA-REPLICATION | Mastrevirus | CHINA | MULTIDISCIPLINARY SCIENCES | Begomovirus | BINDING PROTEIN | IDENTIFICATION | Curtovirus | ORGANIZATION | Alphasatellite | ALIGNMENT | Betasatellite | Geminivirus | Geminiviridae | LEAF CURL DISEASE | VIRUSES
Journal Article
Nucleic Acids Research, ISSN 0305-1048, 07/2014, Volume 42, Issue 1, pp. W192 - W197
Advances in high-throughput sequencing technologies have brought us into the individual genome era. Projects such as the 1000 Genomes Project have led the... 
DATABASE | FORMAT | WEB | BIOCHEMISTRY & MOLECULAR BIOLOGY | UCSC | SEQUENCING DATA | PROGRAM | Genetic Variation | Computer Graphics | Genomics | Humans | Software | Internet | Genome, Human | Index Medicus
Journal Article
Nucleic Acids Research, ISSN 0305-1048, 07/2012, Volume 40, Issue 1, pp. W615 - W621
High-throughput sequencing (HTS) technologies are providing an unprecedented capacity for data generation, and there is a corresponding need for efficient data... 
SEQUENCING DATA | UCSC | BIOCHEMISTRY & MOLECULAR BIOLOGY | Computer Graphics | High-Throughput Nucleotide Sequencing | Polymorphism, Single Nucleotide | Software | Internet | Genomics - methods | Population - genetics | INDEL Mutation | Index Medicus | Stand Alone Programs
Journal Article
Current protocols in bioinformatics, 12/2009, Volume Chapter 1, p. Unit1.4
The University of California Santa Cruz (UCSC) Genome Browser is a popular Web-based tool for quickly displaying a requested portion of a genome at any scale,... 
User-Computer Interface | Information Storage and Retrieval - methods | Chromosome Mapping - methods | Database Management Systems | Databases, Genetic | Software | California | Internet | Sequence Analysis, DNA - methods
Journal Article
Methods in Molecular Biology, ISSN 1064-3745, 01/2007, Volume 395, pp. 17 - 34
Comparative analysis of DNA sequence from multiple species can provide insights into the function and evolutionary processes that shape genomes. The University... 
Comparative genomics | Cross-species alignments | UCSC genome browser | Orthology | Evolutionary conservation | UCSC table browser | Databases, Genetic | User-Computer Interface | Animals | Genomics | Humans | Evolution, Molecular | Index Medicus
Conference Proceeding
Nucleic Acids Research, ISSN 0305-1048, 01/2017, Volume 45, Issue 1, pp. D635 - D642
Journal Article
RNA, ISSN 1355-8382, 11/2014, Volume 20, Issue 11, pp. 1666 - 1670
Recently, several laboratories have reported thousands of circular RNAs (circRNAs) in animals. Numerous circRNAs are highly stable and have specific... 
Database | Gene expression | Circular RNA | database | TRANSCRIPTOME | circular RNA | BIOCHEMISTRY & MOLECULAR BIOLOGY | UCSC | gene expression | GENOME BROWSER | User-Computer Interface | Animals | Sequence Analysis, RNA | RNA | Humans | Databases, Genetic | Internet | Index Medicus | Bioinformatics
Journal Article
Haematologica, ISSN 0390-6078, 07/2018, Volume 103, Issue 8, pp. e341 - e344
Journal Article
Nucleic Acids Research, ISSN 0305-1048, 01/2018, Volume 46, Issue D1, pp. D267 - D275
Abstract With this latest release of ReMap (http://remap.cisreg.eu), we present a unique collection of regulatory regions in human, as a result of a... 
VISUALIZATION | DATABASE | BIOCHEMISTRY & MOLECULAR BIOLOGY | UCSC GENOME BROWSER | Life Sciences | Quantitative Methods | Database Issue
Journal Article
Nucleic Acids Research, ISSN 0305-1048, 01/2018, Volume 46, Issue D1, pp. D794 - D801
Abstract The Encyclopedia of DNA Elements (ENCODE) Data Coordinating Center has developed the ENCODE Portal database and website as the source for the data and... 
ANTIBODIES | FUNCTIONAL ELEMENTS | PROJECT | INTEGRATIVE ANALYSIS | BIOCHEMISTRY & MOLECULAR BIOLOGY | MODENCODE | IDENTIFICATION | UCSC GENOME BROWSER | Database Issue
Journal Article
Virus Research, ISSN 0168-1702, 06/2019, Volume 266, pp. 43 - 47
In 1936, John Joseph Bittner identified mouse mammary tumor virus (MMTV), a milk transmitted beta retrovirus, a form of single-stranded positive-sense RNA... 
Breast cancer | The UCSC Genome Browser | Mouse mammary tumor virus | The Cancer Genome Atlas | VIRUS | VIROLOGY | BIOMARKER | CANCER
Journal Article
Bioinformatics, ISSN 1367-4803, 07/2010, Volume 26, Issue 17, pp. 2204 - 2207
Big Wig and Big Bed files are compressed binary indexed files containing data at several resolutions that allow the high-performance display of next-generation... 
UCSC | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | GENOME BROWSER | Data Mining | Computational Biology - methods | Software | Internet | Genomics - methods | Data Compression | Index Medicus | Applications Note
Journal Article
Bioinformatics, ISSN 1367-4803, 03/2011, Volume 27, Issue 5, pp. 718 - 719
Tabix is the first generic tool that indexes position sorted files in TAB-delimited formats such as GFF, BED, PSL, SAM and SQL export, and quickly retrieves... 
UCSC | DATABASE | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | GENOME BROWSER | Computational Biology - methods | Algorithms | Information Storage and Retrieval - methods | Software | Genome | Genomics - methods | Sequence Analysis, DNA - methods | Index Medicus | Applications Note
Journal Article
by Myers, Richard M and Stamatoyannopoulos, John and Snyder, Michael and Dunham, Ian and Hardison, Ross C and Bernstein, Bradley E and Gingeras, Thomas R and Kent, W. James and Birney, Ewan and Wold, Barbara and Crawford, Gregory E and Epstein, Charles B and Shoresh, Noam and Ernst, Jason and Mikkelsen, Tarjei S and Kheradpour, Pouya and Zhang, Xiaolan and Wang, Li and Issner, Robbyn and Coyne, Michael J and Durham, Timothy and Ku, Manching and Truong, Thanh and Ward, Lucas D and Altshuler, Robert C and Lin, Michael F and Kellis, Manolis and Davis, Carrie A and Kapranov, Philipp and Dobin, Alexander and Zaleski, Christopher and Schlesinger, Felix and Batut, Philippe and Chakrabortty, Sudipto and Jha, Sonali and Lin, Wei and Drenkow, Jorg and Wang, Huaien and Bell, Kim and Bell, Ian and Gao, Hui and Dumais, Erica and Dumais, Jacqueline and Antonarakis, Stylianos E and Ucla, Catherine and Borel, Christelle and Guigo, Roderic and Djebali, Sarah and Lagarde, Julien and Kingswood, Colin and Ribeca, Paolo and Sammeth, Micha and Alioto, Tyler and Merkel, Angelika and Tilgner, Hagen and Carninci, Piero and Hayashizaki, Yoshihide and Lassmann, Timo and Takahashi, Hazuki and Abdelhamid, Rehab F and Hannon, Gregory and Fejes, Katalin-Toth and Preall, Jonathan and Gordon, Assaf and Sotirova, Vihra and Reymond, Alexandre and Howald, Cedric and Graison, Emilie Aït Yahya and Chrast, Jacqueline and Ruan, Yijun and Ruan, Xiaoan and Shahab, Atif and Poh, Wan Ting and Wei, Chia-Lin and Furey, Terrence S and Boyle, Alan P and Sheffield, Nathan C and Song, Lingyun and Shibata, Yoichiro and Vales, Teresa and Winter, Deborah and Zhang, Zhancheng and London, Darin and Wang, Tianyuan and Keefe, Damian and Iyer, Vishwanath R and Lee, Bum-Kyu and McDaniell, Ryan M and Liu, Zheng and Battenhouse, Anna and Bhinge, Akshay A and Lieb, Jason D and Grasfeder, Linda L and Showers, Kimberly A and Giresi, Paul G and Kim, Seul K. C and Shestak, Christopher and Pauli, Florencia and Reddy, Timothy E and Gertz, Jason and ... and ENCODE Project Consortium and The ENCODE Project Consortium
PLoS Biology, ISSN 1544-9173, 04/2011, Volume 9, Issue 4, pp. e1001046 - e1001046
Journal Article