The DOI matches its Crossref record; 41 of the 41 references it cites were found in a registry or an index.
The Human Genome Browser at UCSC
Open accessAbstract
As vertebrate genome sequences near completion and research refocuses to their analysis, the issue of effective genome annotation display becomes critical. A mature web tool for rapid and reliable display of any requested portion of the genome at any scale, together with several dozen aligned annotation tracks, is provided at http://genome.ucsc.edu . This browser displays assembly contigs and gaps, mRNA and expressed sequence tag alignments, multiple gene predictions, cross-species homologies, single nucleotide polymorphisms, sequence-tagged sites, radiation hybrid data, transposon repeats, and more as a stack of coregistered tracks. Text and sequence-based searches provide quick and precise access to any region of specific interest. Secondary links from individual features lead to sequence details and supplementary off-site databases. One-half of the annotation tracks are computed at the University of California, Santa Cruz from publicly available sequence data; collaborators worldwide provide the rest. Users can stably add their own custom tracks to the browser for educational or research purposes. The conceptual and technical framework of the browser, its underlying MYSQL database, and overall use are described. The web site currently serves over 50,000 pages per day to over 3000 different users.
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“To identify specific genes with reduced H3K9me2 levels, we performed H3K9me2-based ChIP-sequencing (ChIP-seq) in biological duplicate (Fig. 4a, http://genome.ucsc.edu30), and validated significantly H3K9me2 depleted genes with quantitative PCR (qPCR) (Fig. 4b).”
From Tau promotes neurodegeneration through global chromatin relaxation (2014) · cites this paper as [30]
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“we have observed that the genomic region distal to the HSA2 fusion site maps well to the near-telomeric region of chimpanzee chromosome 2B, and thus the corresponding UBCS statistics has high values (Fig. 1).”
From Revised time estimation of the ancestral human chromosome 2 fusion (2022) · cites this paper as [29]
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In the citing paper
“Hematologic phenotypes of a balanced mix of male and female mice for all models were examined at more than 7 weeks of age to avoid inter-individual variation42.”
From Genetic dissection of the α-globin super-enhancer in vivo (2016) · cites this paper as [42]
Experimental — accuracy not yet measuredIn the citing paper
“Examples include the Human Genome Browser at UCSC (119), the STRBase (120) maintained by the National Institute of Standards and Technology (NIST, Maryland, US) or the Tandem Repeats Database (TRDB; (121)).”
From Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases (2019) · cites this paper as [119]
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Citations
Cites
Initial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216
Tandem repeats finder: a program to analyze DNA sequences
Benson, G. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.2.573 · Cited by 9,374
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480
Self-citationInternational System for Human Cytogenetic Nomenclature
National Cancer Institute (2020) · Definitions · doi:10.32388/78qroa · Cited by 6,831
Genome Sequence of the Nematode C. elegans : A Platform for Investigating Biology
Berg, J. (1998) · Science · doi:10.1126/science.282.5396.2012 · Cited by 4,458
Prediction of complete gene structures in human genomic DNA
Burge, C., & Karlin, S. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.0951 · Cited by 4,211
A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms
The International SNP Map Working Group, Laboratories:, C. S. H., Sachidanandam, R., Weissman, D., Schmidt, S. C., Kakol, J. M., Stein, L. D., National Center for Biotechnology Information:, Marth, G., Sherry, S., et al. (2001) · Nature · doi:10.1038/35057149 · Cited by 2,977
A comprehensive genetic map of the human genome based on 5,264 microsatellites
Dib, C., Fauré, S., Fizames, C., Samson, D. S., Drouot, N., Alain Vignal, A., Millasseau, P., Marc, S., Kazan, J., Seboun, E., et al. (1996) · Nature · doi:10.1038/380152a0 · Cited by 2,927
The DNA sequence of human chromosome 22
Dunham, I., Hunt, A. R., Collins, J. E., Bruskiewich, R., Beare, D. M., Clamp, M. E., Smink, L. J., Ainscough, R., Almeida, J. P., Babbage, A., et al. (1999) · Nature · doi:10.1038/990031 · Cited by 1,147
SGD: Saccharomyces Genome Database
Cherry, J. M. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.1.73 · Cited by 1,145
Cited by
Sorted by citations
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895
BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
Liao, Y., Smyth, G. K., & Shi, W. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btt656 · Cited by 27,219
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
Li, B., & Dewey, C. N. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-323 · Cited by 22,179
Metadata
- Authors
- Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., & Haussler, A. D.
- Affiliations
- Howard Hughes Medical Institute (US)
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2002-05-16
- Volume
- 12
- Issue
- 6
- Pages
- 996-1006
- ISSN
- 1088-9051 (ISSN-L)
- 1549-5469
- PMC
- PMC186604
- OpenAlex
- W2128016314
- Cited by
- 10,400
- References
- 41
- Citations by year
- 2026: 174 · 2025: 366 · 2024: 686 · 2023: 771 · 2022: 765 · 2021: 828 · 2020: 714 · 2019: 677 · 2018: 594 · 2017: 526 · 2016: 530 · 2015: 522 · 2014: 461 · 2013: 449 · 2012: 362
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- Genome Research (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- U.S. Department of Energy (FG0399ER62849)
- National Human Genome Research Institute (P41HG002371, 1P41 HG 02371-01)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genetics, Bioinformatics, and Biomedical Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- UCSC Genome Browser, expressed sequence tags, gene prediction, cross-species homology, single nucleotide polymorphisms, sequence-tagged sites, MySQL
- MeSH terms
- California, Database Management Systems, Genes, Humans, RNA, Messenger, Sequence Homology, Nucleic Acid, Software, Universities, Gene Expression, Genome, Human, Databases, Genetic
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