GenBank: update

By Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, David L. Wheeler. Nucleic Acids Res., 2004

510 citations recorded by the source corpus.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/f63521eb2e6275d55b93db385df442b4662548f2

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Citations in the corpus

Oocyte generation in adult mammalian ovaries by putative germ cells in bone marrow and peripheral blood. (2005, unknown): “For example, expression of Mvh, Dazl, Stella, and Fragilis has been identified in mouse BM (http:// genome.ucsc.edu; Benson et al., 2004; Su et al., 2004), and STELLA expression has been identified in human BM (http://genome.ucsc.edu; GenBank Accession Number CV414052 from Dias Neto et al. [2000]).”
GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses (2005, methodology): “The web software programs have been extensively used— currently >21 000 nucleotide sequence and 329 000 protein sequence records in GenBank (4) contain references to the GeneMark programs.”
The EMBL Nucleotide Sequence Database (2004, methodology): “This database is the European part of an international collaboration with DDBJ (Japan) (2) and GenBank (USA) (3) (INSDC, International Nucleotide Sequence Database Collaboration).”
WindowMasker: window-based masker for sequenced genomes (2006, methodology): “Another direction for further investigation is whether either the combinatorial or the library-based approach to masking can be extended from inputs of single genomes to species-heterogeneous databases such as GenBank's non-redundant (nr) database?”
FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization (2006, background): “The function report on a SNP contains seven sections on the SNP’s functional effects, namely (i) genomic information, presents the nearby sequence, the alleles and the allele frequency among different ethnic groups; (ii) functional effects summary, presents the risk assessment; (iii) transcription r”
FunGene: the functional gene pipeline and repository (2013, background): “The FunGene Repository (FGR; http://fungene . cme . msu . edu/) is designed to help researchers explore publicly available sequences harvested from GenBank (Benson et al., 2004) and assigned to a speciﬁc collection of gene families.”
MRS: a fast and compact retrieval system for biological data (2005, background): “Data banks, such as EMBL (2) or GenBank (3), have reached such a size that only large institutes like those 44 that host SRS can afford to keep these data on-line.”
The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics (2008, methodology): “Daily update releases from GenBank form the bulk of sequence additions to the database (8) are complemented by weekly PDB releases (13).”
Principles of Gene Manipulation and Genomics (2006, background): “In 1982 there were enough DNA sequences to justify the establishment of the first nucleotide sequence database, GenBank (Benson et al. 2004).”
VFDB: a reference database for bacterial virulence factors (2004, methodology): “We then used Perl scripts to extract positions and sequences of these VFs from the GenBank (10) ﬁles.”
Convergence of Acquired Mutations and Alternative Splicing of CD19 Enables Resistance to CART-19 Immunotherapy (2015, background): “Alternatively Spliced CD19 mRNA Variants Accumulate in Post–CART-19 Relapses The SIB Genes Track (16) implemented in the UCSC Genome Browser postulates the existence of CD19 mRNA isoforms skipping exons 2 and 5 to 6 (Fig.”
Ancient DNA derived from alkenone‐biosynthesizing haptophytes and other algae in Holocene sediments from the Black Sea (2006, unknown): “[ 21 ] Sequence data were compiled using ARB software [ Ludwig et al. , 2004] and aligned with complete length sequences of closest relatives obtained from the GenBank database [ Benson et al. , 2004] using the ARB FastAligner utility.”
NONCODE: an integrated knowledge database of non-coding RNAs (2004, methodology): “GenBank entries were the major source of data, and the PubMed database was used as the starting point for the data collection (31).”