Nucleic Acids Research, 2003, Vol. 31, No. 1 51-54
© 2003 Oxford University Press
The UCSC Genome Browser Database
Genome Bioinformatics Group, The University of California Santa Cruz (UCSC), School of Engineering, 1156 High Street, Santa Cruz, CA 95064-1077, USA
*To whom correspondence should be addressed. Email: donnak{at}soe.ucsc.edu
Received August 15, 2002; Revised and Accepted October 27, 2002
ABSTRACT
The University of California Santa Cruz (UCSC) Genome Browser Database is an up to date source for genome sequence data integrated with a large collection of related annotations. The database is optimized to support fast interactive performance with the web-based UCSC Genome Browser, a tool built on top of the database for rapid visualization and querying of the data at many levels. The annotations for a given genome are displayed in the browser as a series of tracks aligned with the genomic sequence. Sequence data and annotations may also be viewed in a text-based tabular format or downloaded as tab-delimited flat files. The Genome Browser Database, browsing tools and downloadable data files can all be found on the UCSC Genome Bioinformatics website (http://genome.ucsc.edu), which also contains links to documentation and related technical information.
INTRODUCTION
As the amount of genomic sequence in the public databases grows, annotation has become a critical element in data analysis and interpretation. The UCSC Genome Brower Database (http://genome.ucsc.edu) provides access to current and archived genome assemblies of selected organisms. One of the distinctive features of the database is the large collection of annotation data that accompanies each assembly. The annotations include mRNA and expressed sequence tag (EST) alignments, gene predictions, cross-species homologies, high-level maps, single nucleotide polymorphisms (SNPs) and many other types of data.
The vast size of vertebrate genome data sets presents challenges in efficient data storage and retrieval. In addition, the burgeoning number of versions of a particular genome demands a process that can rapidly integrate new data and annotations into the database while implementing creative solutions for maintaining and enhancing views of the data. Through software algorithmic refinements and optimizations to both the database and hardware, the UCSC Genome Browser viewer maintains the same interactive response time on the large Homo sapiens and Mus musculus genomes that its predecessor had on the much smaller Caenorhabditis elegans genome.
The Genome Browser Database—originally designed to support the Human Genome Project (1)—is readily extensible to accommodate the increasing number of genomic sequences in the public domain. Early assemblies of the human genome in the database were produced at UCSC from public data. Since the December 2001 freeze, the assemblies have been obtained directly from the National Center for Biotechnology Information (NCBI). A mouse genome based on data from the Mouse Sequencing Consortium was added early in 2002, with assemblies provided by the Mouse Genome Sequencing Consortium. The Genome Browser Database will support several additional genomes by 2003.
DATABASE ORGANIZATION
Sequence and annotation data for each genome assembly are stored in a MySQL relational database, which is quite efficient at retrieving data from indexed files. The database is loaded in large batches and is used primarily as a read-only database. To improve performance, each of the Genome Browser web servers has a copy of the database on its local disk.
The Genome Browser Database contains both positional tables with data based on genomic start–stop coordinates and non-positional tables with data independent of position. The coordinates in positional tables are defined using half-open zero-based ranges, i.e. the first 100 bases of a chromosome are represented as 0,100, while the next 100 bases are represented as 100,200 and so on. Half-open coordinates allow the length of a feature to be obtained by simply subtracting the start from the end and tend to minimize +/-1 errors during software development.
With such a large data set, care must be taken in the database organization to ensure good interactive performance in the Genome Browser, which creates each line of its graphical annotation image by querying the corresponding table in the database. The database is optimized to support the browser's range-based queries, with additional optimizations to accommodate the varying sizes of the positional tables in the database.
For smaller tables, it is often sufficient to create a few critical indices and do some initial presorting of the data before loading the database. For example, in the cpgIsland table, indices are created on chrom,chromStart and chrom,chromEnd. Presorting the data by chrom,chromStart significantly improves performance, particularly in tables where the indices are small enough to fit into RAM, thus reducing the number of disk seeks needed to load the data from the table into the Genome Browser.
Larger tables, such as the EST alignment table, require more complex schemes to keep interactive performance at an acceptable level. This is accomplished by first dividing up the data by chromosome into separate tables (e.g. chrN_est), which eliminates the need to index the chromosome field and increases the likelihood that the indices will fit into RAM. To further improve performance on large chromosome tables, a binning scheme suggested by Lincoln Stein and Richard Durbin has been implemented (2).
In addition to these tables, the database includes several non-positional tables that contain auxiliary data related to the mRNA sequences, e.g. DNA sequence, organism, or author. This information supplements the details pages for individual features in the graphical browser, but is not used in the display.
The document http://genome.ucsc.edu/goldenPath/gbdDescriptions.html contains a detailed description of the tables in the database.
To facilitate the programmatic interaction between the database and the graphical browser, UCSC uses the autoSql program written by Jim Kent (3). This program takes a data definition as input and creates a C structure, a SQL create statement and various C functions for data loading and memory management.
ANNOTATIONS
The Genome Browser Database provides dozens of aligned annotations for each genome assembly. Approximately half of the annotations are computed at UCSC and the remainder are contributed by external research scientists.
UCSC generates several annotations based on mRNA alignments. The mRNA and EST sequences are extracted from GenBank, and are aligned against the genome using the BLAST-like Alignment Tool (BLAT), a fast sequence alignment tool developed by Jim Kent (4). The data is filtered based on percentage identity and near best in genome to select only those alignments that best match the sequence. The spliced EST annotation is computed from the filtered data by analyzing the EST alignments for evidence of splicing.
The database contains a large collection of gene prediction annotations. The RefSeq Genes annotation is computed at UCSC from RefSeq mRNAs that have been aligned against the genome using BLAT and then filtered. The protein-coding portion of the mRNA is mapped to the genome and blocks separated by gaps of 5 or fewer bases are merged into exons. Gene prediction annotations contributed by external sources include Ensembl (5), Fgenesh++ (6), Genie (7), Acembly (contributed by Danielle and Jean Thierry-Mieg and Vahan Simonyan), and Genscan (8).
Several cross-species homology annotations are computed by UCSC and its collaborators, including BLAT and BLASTZ alignments of human and mouse genomes against the target genome, mRNA and EST alignments from other species, and synteny annotations. In cross-species annotations, RepeatMasker (9) and Tandem Repeats Finder (10) are first applied to the target genome to mask repetitive elements before the alignments are generated.
The database includes several high-level map annotations. Some examples of these include the Chromosome Bands annotation that approximates the locations of Giemsa-stained chromosomes bands at an 800-band resolution, the Sequence-Tagged Site (STS) Markers annotation showing the positions of several markers—many of which were used in constructing genome-wide genetic and physical maps—and the Fluorescent In Situ Hybridization (FISH) Clones annotation showing the location of FISH-mapped BAC clones from the BAC Resource consortium (11) on the genome.
Custom annotations are an important research feature supported by UCSC. Space constraints and confidentiality restrictions exclude many interesting annotations from the public version of the Genome Browser Database. The Genome Browser's custom annotation track feature allows individuals to upload formatted personal data for temporary display on the machine where the data resides. The custom annotation track is viewable only by users on that machine or via a custom URL that the users provide to other collaborators, thus making it an ideal mechanism for displaying and sharing private data. The document http://genome.ucsc.edu/customTrack.html contains complete information for constructing and uploading a custom annotation track.
VIEWING AND DOWNLOADING DATA
The UCSC Genome Bioinformatics website provides both graphical and text-based views of the sequence data and annotations.
The Genome Browser—accessed via the Genome Browser link on the home page—is a rapid interactive interface to the data at varying levels of detail. In response to a user's query, the Genome Browser displays a set of annotations tracks corresponding to the assembly and range dictated by the query and configured based on user preferences. Alternatively, the BLAT search tool can be used to quickly search for homologous regions to a DNA or protein sequence, which can then be displayed in the browser. The user can navigate through the assembly and zoom the image in or out using navigation buttons. A set of track controls allows the user to display each annotation in single line (dense) or expanded (full) mode or hide the track completely. Some tracks have filters to fine-tune the data displayed. Individual entries within a track have associated details pages that provide information about the annotation, related links to outside sites and database, and in some cases links to the genomic, mRNA and protein sequence.
At the chromosome level (Fig. 1), the Genome Browser display provides an overview of the coverage and completeness for the region. At a zoomed in level (Fig. 2), the display can focus on a specific area of research interest, for example the examination of alternative splicing patterns of a gene. Most annotation tracks are displayed in a horizontal linear fashion, with the exception of a few ‘wiggle’ tracks that plot the feature's scores on a vertical axis.
|
|
The Genome Browser menu bar provides access to the BLAT search tool, the DNA sequence underlying the features in the annotation tracks graphic, a coordinate conversion tool for locating the position of a feature in a different release of a genome, and user documentation. The menu bar also contains direct links to the complementary annotation in the Ensembl Genome Browser and NCBI's Entrez MapView.
The Table Browser—accessed through the Tables link on the UCSC Genome Bioinformatics home page—furnishes an alternative text-based view of the data. This tool provides access to both positional and non-positional tables, and offers an enhanced level of query support that includes free-form SQL queries and restrictions based on field values. Output can be filtered to restrict which fields and lines are returned, and may be organized into one of several formats, including a simple tab-delimited file that can be loaded into a spreadsheet or database and then processed to produce the data format suitable for a custom annotation track.
The Downloads link on the UCSC Genome Bioinformatics home page offers a convenient interface for downloading current and archived sequence and annotation data. Data can also be downloaded via ftp at ftp://genome.cse.ucsc.edu/goldenPath/. Zipped data for each genome assembly is organized into three folders. BigZips contains the sequence data, which is packaged by chromosome and by contig. Files ending in suffix .fa contain the sequence in Fasta format for the contig layout. Files with suffix .agp contain an index that shows how the corresponding .fa file is built, with each line representing an actual sequence record or a gap. The Chromosomes folder contains the assembled sequence in Fasta format divided up by chromosome. The Database folder contains the genome annotation database tables in tab-delimited format.
A large portion of the Genome Browser Database is accessible using the Distributed Annotation Service (DAS) protocol (12). The UCSC DAS server is located at http://genome.ucsc.edu/cgi-bin/das. To accommodate the large size of some of the annotation tables, it is best to enable compression on DAS clients when accessing the UCSC DAS server.
In addition to the browsing tools, the UCSC Genome Bioinformatics home page provides links to the BLAT alignment tool, user and technical documentation, the Genome Browser mirror sites and archives, and acknowledgements to the many people who have contributed to the Genome Browser Database.
FUTURE DIRECTIONS
In the coming years, UCSC plans to add several new genomes to the Genome Browser Database, in addition to updating currently supported genomes as new assemblies become available. Enhanced searching capabilities will improve the query interface to the database. We will continue to incorporate annotations from the research community into our public Genome Browser, as well as support private access to custom annotation tracks created by users.
CONTACTING US
The mailing list genome{at}cse.ucsc.edu provides a forum for announcements of new releases and features, questions and discussion about the Genome Browser Database. Users may subscribe to this list at http://www.cse.ucsc.edu/mailman/listinfo/genome. To report problems accessing the website, servers, or mirror sites, or for correspondence inappropriate for the public forum, send email to genome-www{at}cse.ucsc.edu.
ACKNOWLEDGEMENTS
The UCSC Genome Browser Database project is funded by grants from the National Human Genome Research Institute (NHGRI) and the Howard Hughes Medical Institute (HHMI). We would also like to thank the many collaborators who have contributed annotation data to our project, as well as our users for their feedback and support.
REFERENCES
- International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860–921.[CrossRef][Medline]
- Kent,W.J., Sugnet,C.W., Furey,T.S., Roskin,K.M., Pringle,T.H., Zahler,A.M. and Haussler,D. (2002) The Human Genome Browser at UCSC. Genome Res., 12, 996–1006.
[Abstract/Free Full Text] - Kent,W.J. and Brumbaugh,H. (2002) autoSql and autoXml: Code Generators from the Genome Project. Linux J., 99, 68–77.
- Kent,W.J. (2002) BLAT—the BLAST-like alignment tool. Genome Res., 12, 656–664.
[Abstract/Free Full Text] - Hubbard,T., Barker,D., Birney,E., Cameron,G., Chen,Y., Clark,L., Cox,T., Cuff,J., Curwen,V., Down,T., Durbin,R., Eyras,E., Gilbert,J., Hammond,M., Huminiecki,L., Kasprzyk,A., Lehvaslaiho,H., Lijnzaad,P., Melsopp,C., Mongin,E., Pettett,R., Pocock,M., Potter,S., Rust,A., Schmidt,E., Searle,S., Slater,G., Smith,J., Spooner,W., Stabenau,A., Stalker,J., Stupka,E., Ureta-Vidal,A., Vastrik,I. and Clamp,M. (2002) The Ensembl genome database project. Nucleic Acids Res., 30, 38–41.
[Abstract/Free Full Text] - Salamov,A.A. and Solovyev,V.V. (2000) Ab initio gene finding in Drosophila genomic DNA. Genome Res., 10, 516–522.
[Abstract/Free Full Text] - Kulp,D., Haussler,D., Reese,M.G. and Eeckman,F.H. (1996) A generalized hidden Markov model for the recognition of human genes in DNA. Ismb, 4, 134–142.
- Burge,C. and Karlin,S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol., 268, 78–94.[CrossRef][Web of Science][Medline]
- Smit,A.F. (1999) Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr. Opin. Genet. Dev., 9, 657–663.[CrossRef][Web of Science][Medline]
- Benson,G. (1999) Tandem repeats finder: A program to analyze DNA sequences. Nucleic Acids Res., 27, 12–17.
[Abstract/Free Full Text] - Cheung,V.G., Nowak,N., Jang,W., Kirsch,I.R., Zhao,S., Chen,X.N., Furey,T.S., Kim,U.J., Kuo,W.L. and Livier,M. (2001) Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature, 409, 953–958.[CrossRef][Medline]
- Dowell,R.D., Jokerst,R.M., Day,A., Eddy,S.R. and Stein,L. (2001) The Distributed Annotation System. BMC Bioinformatics, 2, 7.[CrossRef][Medline]
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  G. Altarescu, T. Eldar-Geva, I. Varshower, B. Brooks, E. Z. Haran, E. J. Margalioth, E. Levy-Lahad, and P. Renbaum Real-time reverse linkage using polar body analysis for preimplantation genetic diagnosis in female carriers of de novo mutations Hum. Reprod., December 1, 2009; 24(12): 3225 - 3229. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. Rhead, D. Karolchik, R. M. Kuhn, A. S. Hinrichs, A. S. Zweig, P. A. Fujita, M. Diekhans, K. E. Smith, K. R. Rosenbloom, B. J. Raney, et al. The UCSC genome browser database: update 2010 Nucleic Acids Res., November 11, 2009; (2009) gkp939v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. C. Boutros, K. A. Bielefeld, R. Pohjanvirta, and P. A. Harper Dioxin-Dependent and Dioxin-Independent Gene Batteries: Comparison of Liver and Kidney in AHR-Null Mice Toxicol. Sci., November 1, 2009; 112(1): 245 - 256. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. J. Dupuy, L. M. Rogers, J. Kim, K. Nannapaneni, T. K. Starr, P. Liu, D. A. Largaespada, T. E. Scheetz, N. A. Jenkins, and N. G. Copeland A Modified Sleeping Beauty Transposon System That Can Be Used to Model a Wide Variety of Human Cancers in Mice Cancer Res., October 15, 2009; 69(20): 8150 - 8156. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Audit, L. Zaghloul, C. Vaillant, G. Chevereau, Y. d'Aubenton-Carafa, C. Thermes, and A. Arneodo Open chromatin encoded in DNA sequence is the signature of 'master' replication origins in human cells Nucleic Acids Res., October 1, 2009; 37(18): 6064 - 6075. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. A. Sharov and M. S.H. Ko Exhaustive Search for Over-represented DNA Sequence Motifs with CisFinder DNA Res, October 1, 2009; 16(5): 261 - 273. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. A. Shanely, K. A. Zwetsloot, T. E. Childs, S. J. Lees, R. W. Tsika, and F. W. Booth IGF-I activates the mouse type IIb myosin heavy chain gene Am J Physiol Cell Physiol, October 1, 2009; 297(4): C1019 - C1027. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. J. de Smith, C. Purmann, R. G. Walters, R. J. Ellis, S. E. Holder, M. M. Van Haelst, A. F. Brady, U. L. Fairbrother, M. Dattani, J. M. Keogh, et al. A deletion of the HBII-85 class of small nucleolar RNAs (snoRNAs) is associated with hyperphagia, obesity and hypogonadism Hum. Mol. Genet., September 1, 2009; 18(17): 3257 - 3265. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Nakken, T. Rognes, and E. Hovig The disruptive positions in human G-quadruplex motifs are less polymorphic and more conserved than their neutral counterparts Nucleic Acids Res., September 1, 2009; 37(17): 5749 - 5756. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. A. Raker, A. A. Mironov, M. S. Gelfand, and D. D. Pervouchine Modulation of alternative splicing by long-range RNA structures in Drosophila Nucleic Acids Res., August 1, 2009; 37(14): 4533 - 4544. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. Takezaki and M. Nei Genomic Drift and Evolution of Microsatellite DNAs in Human Populations Mol. Biol. Evol., August 1, 2009; 26(8): 1835 - 1840. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. A. Novick, H. Basta, M. Floumanhaft, M. A. McClure, and S. Boissinot The Evolutionary Dynamics of Autonomous Non-LTR Retrotransposons in the Lizard Anolis Carolinensis Shows More Similarity to Fish Than Mammals Mol. Biol. Evol., August 1, 2009; 26(8): 1811 - 1822. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. Lee, N. Harris, M. Gibson, R. Chetty, and S. Lewis Apollo: a community resource for genome annotation editing Bioinformatics, July 15, 2009; 25(14): 1836 - 1837. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Fang, C.-T. Ting, C.-R. Lee, K.-H. Chu, C.-C. Wang, and S.-C. Tsaur Molecular Evolution and Functional Diversification of Fatty Acid Desaturases after Recurrent Gene Duplication in Drosophila Mol. Biol. Evol., July 1, 2009; 26(7): 1447 - 1456. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 V. L. Bauer DuMont, N. D. Singh, M. H. Wright, and C. F. Aquadro Locus-Specific Decoupling of Base Composition Evolution at Synonymous Sites and Introns along the Drosophila melanogaster and Drosophila sechellia Lineages Gen Biol Evol, June 22, 2009; 2009(0): 67 - 74. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Podicheti, R. Gollapudi, and Q. Dong WebGBrowse--a web server for GBrowse Bioinformatics, June 15, 2009; 25(12): 1550 - 1551. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Ikeda, K. Tojo, Y. Inada, Y. Takada, M. Sakamoto, M. Lam, W. C Claycomb, and N. Tajima Regulation of urocortin I and its related peptide urocortin II by inflammatory and oxidative stresses in HL-1 cardiomyocytes J. Mol. Endocrinol., June 1, 2009; 42(6): 479 - 489. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Y. Tolstorukov, P. V. Kharchenko, J. A. Goldman, R. E. Kingston, and P. J. Park Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes Genome Res., June 1, 2009; 19(6): 967 - 977. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. C. Hannibal, E. K. Ruzzo, L. R. Miller, B. Betz, J. G. Buchan, D. M. Knutzen, K. Barnett, M. L. Landsverk, A. Brice, E. LeGuern, et al. SEPT9 gene sequencing analysis reveals recurrent mutations in hereditary neuralgic amyotrophy Neurology, May 19, 2009; 72(20): 1755 - 1759. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. E. Calvo, D. J. Pagliarini, and V. K. Mootha Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans PNAS, May 5, 2009; 106(18): 7507 - 7512. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 X. Hu, H. M. Stern, L. Ge, C. O'Brien, L. Haydu, C. D. Honchell, P. M. Haverty, B. A. Peters, T. D. Wu, L. C. Amler, et al. Genetic Alterations and Oncogenic Pathways Associated with Breast Cancer Subtypes Mol. Cancer Res., April 1, 2009; 7(4): 511 - 522. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Alizadeh, L. Z. Hong, C. B. Kaelin, T. Raudsepp, H. Manuel, and G. S. Barsh Genetics of Sex-linked yellow in the Syrian Hamster Genetics, April 1, 2009; 181(4): 1427 - 1436. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Necsulea, C. Guillet, J.-C. Cadoret, M.-N. Prioleau, and L. Duret The Relationship between DNA Replication and Human Genome Organization Mol. Biol. Evol., April 1, 2009; 26(4): 729 - 741. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Taher and I. Ovcharenko Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements Bioinformatics, March 1, 2009; 25(5): 578 - 584. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Matsumura, Z. Huang, T. Baba, P. S. Lee, J. C. Barnett, S. Mori, J. T. Chang, W.-L. Kuo, A. H. Gusberg, R. S. Whitaker, et al. Yin Yang 1 Modulates Taxane Response in Epithelial Ovarian Cancer Mol. Cancer Res., February 1, 2009; 7(2): 210 - 220. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Chen, T. Ara, and D. Gautheret Using Alu Elements as Polyadenylation Sites: A Case of Retroposon Exaptation Mol. Biol. Evol., February 1, 2009; 26(2): 327 - 334. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Xie, P. Rigor, and P. Baldi MotifMap: a human genome-wide map of candidate regulatory motif sites Bioinformatics, January 15, 2009; 25(2): 167 - 174. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. M. Kuhn, D. Karolchik, A. S. Zweig, T. Wang, K. E. Smith, K. R. Rosenbloom, B. Rhead, B. J. Raney, A. Pohl, M. Pheasant, et al. The UCSC Genome Browser Database: update 2009 Nucleic Acids Res., January 1, 2009; 37(suppl_1): D755 - D761. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Axelrod, Y. Lin, P. C. Ng, T. B. Stockwell, J. Crabtree, J. Huang, E. Kirkness, R. L. Strausberg, M. E. Frazier, J. C. Venter, et al. The HuRef Browser: a web resource for individual human genomics Nucleic Acids Res., January 1, 2009; 37(suppl_1): D1018 - D1024. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Li, M. T. Lovci, Y.-S. Kwon, M. G. Rosenfeld, X.-D. Fu, and G. W. Yeo Determination of tag density required for digital transcriptome analysis: Application to an androgen-sensitive prostate cancer model PNAS, December 23, 2008; 105(51): 20179 - 20184. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Ponzielli, P. C. Boutros, S. Katz, A. Stojanova, A. P. Hanley, F. Khosravi, C. Bros, I. Jurisica, and L. Z. Penn Optimization of experimental design parameters for high-throughput chromatin immunoprecipitation studies Nucleic Acids Res., December 1, 2008; 36(21): e144 - e144. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Rossi, O. N. Demidov, C. W. Anderson, E. Appella, and S. J. Mazur Induction of PPM1D following DNA-damaging treatments through a conserved p53 response element coincides with a shift in the use of transcription initiation sites Nucleic Acids Res., December 1, 2008; 36(22): 7168 - 7180. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. H. Perry, F. Yang, T. Marques-Bonet, C. Murphy, T. Fitzgerald, A. S. Lee, C. Hyland, A. C. Stone, M. E. Hurles, C. Tyler-Smith, et al. Copy number variation and evolution in humans and chimpanzees Genome Res., November 1, 2008; 18(11): 1698 - 1710. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. M. Kehoe, M. Oka, K. E. Hankowski, N. Reichert, S. Garcia, J. R. McCarrey, S. Gaubatz, and N. Terada A Conserved E2F6-Binding Element in Murine Meiosis-Specific Gene Promoters Biol Reprod, November 1, 2008; 79(5): 921 - 930. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. E. Babiarz, J. G. Ruby, Y. Wang, D. P. Bartel, and R. Blelloch Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs Genes & Dev., October 15, 2008; 22(20): 2773 - 2785. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. P. Bracken, P. A. Gregory, N. Kolesnikoff, A. G. Bert, J. Wang, M. F. Shannon, and G. J. Goodall A Double-Negative Feedback Loop between ZEB1-SIP1 and the microRNA-200 Family Regulates Epithelial-Mesenchymal Transition Cancer Res., October 1, 2008; 68(19): 7846 - 7854. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. M. Li, J. Wakefield, and S. Self A transdimensional Bayesian model for pattern recognition in DNA sequences Biostat., October 1, 2008; 9(4): 668 - 685. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. L. Organ, R. G. Moreno, and S. V. Edwards Three tiers of genome evolution in reptiles Integr. Comp. Biol., October 1, 2008; 48(4): 494 - 504. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. Baele, Y. Van de Peer, and S. Vansteelandt A Model-Based Approach to Study Nearest-Neighbor Influences Reveals Complex Substitution Patterns in Non-coding Sequences Syst Biol, October 1, 2008; 57(5): 675 - 692. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. K. Holloway, D. J. Begun, A. Siepel, and K. S. Pollard Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster Genome Res., October 1, 2008; 18(10): 1592 - 1601. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. J. Forman, A. Legesse-Miller, and H. A. Coller A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence PNAS, September 30, 2008; 105(39): 14879 - 14884. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. R. Kalari, T. L. Casavant, and T. E. Scheetz A knowledge-based approach to predict intragenic deletions or duplications Bioinformatics, September 15, 2008; 24(18): 1975 - 1979. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J.-T. Li, Y. Zhang, L. Kong, Q.-R. Liu, and L. Wei Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation Nucleic Acids Res., September 1, 2008; 36(15): 4833 - 4844. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. S.M. Smalley, M. Lioni, M. D. Palma, M. Xiao, B. Desai, S. Egyhazi, J. Hansson, H. Wu, A. J. King, P. Van Belle, et al. Increased cyclin D1 expression can mediate BRAF inhibitor resistance in BRAF V600E-mutated melanomas Mol. Cancer Ther., September 1, 2008; 7(9): 2876 - 2883. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Q. Zhou, G. Zhang, Y. Zhang, S. Xu, R. Zhao, Z. Zhan, X. Li, Y. Ding, S. Yang, and W. Wang On the origin of new genes in Drosophila Genome Res., September 1, 2008; 18(9): 1446 - 1455. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Zhang and B. Su MicroRNA regulation and the variability of human cortical gene expression Nucleic Acids Res., August 1, 2008; 36(14): 4621 - 4628. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. S. Kim, T. Matsuda, and C. L. Cepko A Core Paired-Type and POU Homeodomain-Containing Transcription Factor Program Drives Retinal Bipolar Cell Gene Expression J. Neurosci., July 30, 2008; 28(31): 7748 - 7764. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. B. Conley, J. Piriyapongsa, and I. K. Jordan Retroviral promoters in the human genome Bioinformatics, July 15, 2008; 24(14): 1563 - 1567. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. T. Sullivan, C. B. Morehouse, NISC Comparative Sequencing Program, and J. W. Thomas Uprobe 2008: an online resource for universal overgo hybridization-based probe retrieval and design Nucleic Acids Res., July 1, 2008; 36(suppl_2): W149 - W153. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Kirkham, S. J. Nixon, M. T. Howes, L. Abi-Rached, D. E. Wakeham, M. Hanzal-Bayer, C. Ferguson, M. M. Hill, M. Fernandez-Rojo, D. A. Brown, et al. Evolutionary analysis and molecular dissection of caveola biogenesis J. Cell Sci., June 15, 2008; 121(12): 2075 - 2086. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 V. Cappelletti, M. Gariboldi, L. De Cecco, S. Toffanin, J. F Reid, L. Lusa, E. Bajetta, L. Celio, M. Greco, A. Fabbri, et al. Patterns and changes in gene expression following neo-adjuvant anti-estrogen treatment in estrogen receptor-positive breast cancer Endocr. Relat. Cancer, June 1, 2008; 15(2): 439 - 449. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Okada, C. Tashiro, K. Numata, K. Watanabe, H. Nakaoka, N. Yamamoto, K. Okubo, R. Ikeda, R. Saito, A. Kanai, et al. Comparative expression analysis uncovers novel features of endogenous antisense transcription Hum. Mol. Genet., June 1, 2008; 17(11): 1631 - 1640. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. A. Glazov, P. A. Cottee, W. C. Barris, R. J. Moore, B. P. Dalrymple, and M. L. Tizard A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach Genome Res., June 1, 2008; 18(6): 957 - 964. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Verma-Gaur, S. N. Rao, T. Taya, and P. Sadhale Genomewide Recruitment Analysis of Rpb4, a Subunit of Polymerase II in Saccharomyces cerevisiae, Reveals Its Involvement in Transcription Elongation Eukaryot. Cell, June 1, 2008; 7(6): 1009 - 1018. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Liang, Y.-S. Lin, and W.-H. Li Fast Evolution of Core Promoters in Primate Genomes Mol. Biol. Evol., June 1, 2008; 25(6): 1239 - 1244. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. A. Glazov, S. McWilliam, W. C. Barris, and B. P. Dalrymple Origin, Evolution, and Biological Role of miRNA Cluster in DLK-DIO3 Genomic Region in Placental Mammals Mol. Biol. Evol., May 1, 2008; 25(5): 939 - 948. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. C. Hodge, B. J. Quade, M. A. Rubin, E. A. Stewart, P. Dal Cin, and C. C. Morton Molecular and Cytogenetic Characterization of Plexiform Leiomyomata Provide Further Evidence for Genetic Heterogeneity Underlying Uterine Fibroids Am. J. Pathol., May 1, 2008; 172(5): 1403 - 1410. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Cohen, M. Shmoish, L. Levi, U. Cheruti, B. Levavi-Sivan, and E. Lubzens Alterations in Micro-Ribonucleic Acid Expression Profiles Reveal a Novel Pathway for Estrogen Regulation Endocrinology, April 1, 2008; 149(4): 1687 - 1696. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Shriner, T. M. Baye, M. A. Padilla, S. Zhang, L. K. Vaughan, and A. E. Loraine Commonality of functional annotation: a method for prioritization of candidate genes from genome-wide linkage studies Nucleic Acids Res., March 27, 2008; 36(4): e26 - e26. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Bethke, E. Webb, A. Murray, M. Schoemaker, C. Johansen, H. C. Christensen, K. Muir, P. McKinney, S. Hepworth, P. Dimitropoulou, et al. Comprehensive analysis of the role of DNA repair gene polymorphisms on risk of glioma Hum. Mol. Genet., March 15, 2008; 17(6): 800 - 805. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Ansong, S. O. Purvine, J. N. Adkins, M. S. Lipton, and R. D. Smith Proteogenomics: needs and roles to be filled by proteomics in genome annotation Brief Funct Genomic Proteomic, March 10, 2008; (2008) eln010v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Camp, A. De Jaco, L. Zhang, M. Marquez, B. De La Torre, and P. Taylor Acetylcholinesterase Expression in Muscle Is Specifically Controlled by a Promoter-Selective Enhancesome in the First Intron J. Neurosci., March 5, 2008; 28(10): 2459 - 2470. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Sinha, A. S. Adler, Y. Field, H. Y. Chang, and E. Segal Systematic functional characterization of cis-regulatory motifs in human core promoters Genome Res., March 1, 2008; 18(3): 477 - 488. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Astanehe, D. Arenillas, W. W. Wasserman, P. C. K. Leung, S. E. Dunn, B. R. Davies, G. B. Mills, and N. Auersperg Mechanisms underlying p53 regulation of PIK3CA transcription in ovarian surface epithelium and in ovarian cancer J. Cell Sci., March 1, 2008; 121(5): 664 - 674. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. Bethke, A. Murray, E. Webb, M. Schoemaker, K. Muir, P. McKinney, S. Hepworth, P. Dimitropoulou, A. Lophatananon, M. Feychting, et al. Comprehensive Analysis of DNA Repair Gene Variants and Risk of Meningioma J Natl Cancer Inst, February 20, 2008; 100(4): 270 - 276. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Zhao, T. Gu, H. C. Rice, K. L. McAdams, K. M. Roark, K. Lawson, S. A. Gauthier, K. L. Reagan, and R. S. Hewes A Drosophila Gain-of-Function Screen for Candidate Genes Involved in Steroid-Dependent Neuroendocrine Cell Remodeling Genetics, February 1, 2008; 178(2): 883 - 901. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. S. Hughes, C. O. Buckley, and D. E. Neafsey Complex Selection on Intron Size in Cryptococcus neoformans Mol. Biol. Evol., February 1, 2008; 25(2): 247 - 253. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. G. Jegga, A. Inga, D. Menendez, B. J. Aronow, and M. A. Resnick Functional evolution of the p53 regulatory network through its target response elements PNAS, January 22, 2008; 105(3): 944 - 949. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. Bourdeau, J. Deschenes, D. Laperriere, M. Aid, J. H. White, and S. Mader Mechanisms of primary and secondary estrogen target gene regulation in breast cancer cells Nucleic Acids Res., January 17, 2008; 36(1): 76 - 93. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Bao, M. Zhou, and Y. Cui CTCFBSDB: a CTCF-binding site database for characterization of vertebrate genomic insulators Nucleic Acids Res., January 11, 2008; 36(suppl_1): D83 - D87. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Singh, A. Olowoyeye, P. H. Baenziger, J. Dantzer, M. G. Kann, P. Radivojac, R. Heiland, and S. D. Mooney MutDB: update on development of tools for the biochemical analysis of genetic variation Nucleic Acids Res., January 11, 2008; 36(suppl_1): D815 - D819. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. C. Frith, E. Valen, A. Krogh, Y. Hayashizaki, P. Carninci, and A. Sandelin A code for transcription initiation in mammalian genomes Genome Res., January 1, 2008; 18(1): 1 - 12. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Abrusan, H.-J. Krambeck, T. Junier, J. Giordano, and P. E. Warburton Biased Distributions and Decay of Long Interspersed Nuclear Elements in the Chicken Genome Genetics, January 1, 2008; 178(1): 573 - 581. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. J. de Smith, A. Tsalenko, N. Sampas, A. Scheffer, N. A. Yamada, P. Tsang, A. Ben-Dor, Z. Yakhini, R. J. Ellis, L. Bruhn, et al. Array CGH analysis of copy number variation identifies 1284 new genes variant in healthy white males: implications for association studies of complex diseases Hum. Mol. Genet., December 1, 2007; 16(23): 2783 - 2794. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Ro, R. Song, C. Park, H. Zheng, K. M. Sanders, and W. Yan Cloning and expression profiling of small RNAs expressed in the mouse ovary RNA, December 1, 2007; 13(12): 2366 - 2380. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. J. Martin, H. Chen, X. Liao, H. Allayee, D. M. Shih, G. S. Lee, D. N. Hovland Jr, W. A. Robbins, K. Carnes, R. A. Hess, et al. FK506, a Calcineurin Inhibitor, Prevents Cadmium-Induced Testicular Toxicity in Mice Toxicol. Sci., December 1, 2007; 100(2): 474 - 485. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. G. Ruby, A. Stark, W. K. Johnston, M. Kellis, D. P. Bartel, and E. C. Lai Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs Genome Res., December 1, 2007; 17(12): 1850 - 1864. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. P. Luedi, F. S. Dietrich, J. R. Weidman, J. M. Bosko, R. L. Jirtle, and A. J. Hartemink Computational and experimental identification of novel human imprinted genes Genome Res., December 1, 2007; 17(12): 1723 - 1730. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. A. Huntley and A. G. Clark Evolutionary Analysis of Amino Acid Repeats across the Genomes of 12 Drosophila Species Mol. Biol. Evol., December 1, 2007; 24(12): 2598 - 2609. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Coulombe-Huntington and J. Majewski Intron Loss and Gain in Drosophila Mol. Biol. Evol., December 1, 2007; 24(12): 2842 - 2850. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Caspi, B. Williams, J. Kim-Cohen, I. W. Craig, B. J. Milne, R. Poulton, L. C. Schalkwyk, A. Taylor, H. Werts, and T. E. Moffitt Moderation of breastfeeding effects on the IQ by genetic variation in fatty acid metabolism PNAS, November 20, 2007; 104(47): 18860 - 18865. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Xiao, Z. Wang, M. Jang, and C. B. Burge Coevolutionary networks of splicing cis-regulatory elements PNAS, November 20, 2007; 104(47): 18583 - 18588. [Abstract] [Full Text] [PDF]
|
|
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||