ArticleGenome research2004
The Atlas genome assembly system.
Article in Genome research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
66 citing papers in PubMed, 193 citations in OpenAlex.
- Phenotypic variability of osteogenesis imperfecta type V caused by an IFITM5 mutation.Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research · 2013Trial
- DNA Methylation Dynamics During Esophageal Epithelial Regeneration Following Repair with Acellular Silk Fibroin Grafts in Rat.Advanced biology · 2023Article
- Beyond Genes: Inclusion of Alternative Splicing and Alternative Polyadenylation to Assess the Genetic Architecture of Predisposition to Voluntary Alcohol Consumption in Brain of the HXB/BXH Recombinant Inbred Rat Panel.Frontiers in genetics · 2022Article
- Genome-to-phenome research in rats: progress and perspectives.International journal of biological sciences · 2021Review
- A linked-read approach to museomics: Higher quality de novo genome assemblies from degraded tissues.Molecular ecology resources · 2020Article
- Targeted viral vector transduction of relaxin-3 neurons in the ratIBRO reports · 2020Article
- Two-step genomic sequence comparison strategy to design Trichoderma strain-specific primers for quantitative PCR.AMB Express · 2019Article
- Histamine Modulates Midbrain Dopamine Neuron Differentiation Through the Regulation of Epigenetic Marks.Frontiers in cellular neuroscience · 2019Article
- Application of Bacillus velezensis NJAU-Z9 Enhanced Plant Growth Associated with Efficient Rhizospheric Colonization Monitored by qPCR with Primers Designed from the Whole Genome Sequence.Current microbiology · 2018Article
- Unsupervised, Statistically Based Systems Biology Approach for Unraveling the Genetics of Complex Traits: A Demonstration with Ethanol Metabolism.Alcoholism, clinical and experimental research · 2018Article
- Sequencing, de novo assembling, and annotating the genome of the endangered Chinese crocodile lizard Shinisaurus crocodilurus.GigaScience · 2017Article
- Genome-wide profiling and differential expression of microRNA in rat pluripotent stem cells.Scientific reports · 2017Article
- Quantification of Azospirillum brasilense FP2 Bacteria in Wheat Roots by Strain-Specific Quantitative PCR.Applied and environmental microbiology · 2015Article
- Do echinoderm genomes measure up?Marine genomics · 2015Review
- A field guide to whole-genome sequencing, assembly and annotation.Evolutionary applications · 2014Review
- Article
- Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication.GigaScience · 2014Article
- Osteogenesis imperfecta without features of type V caused by a mutation in the IFITM5 gene.Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research · 2013Article
- Unraveling genomic variation from next generation sequencing data.BioData mining · 2013Article
- Improving genome assemblies and annotations for nonhuman primates.ILAR journal · 2013Review
6 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
Atlas is a suite of programs developed for assembly of genomes by a "combined approach" that uses DNA sequence reads from both BACs and whole-genome shotgun (WGS) libraries. The BAC clones afford advantages of localized assembly with reduced computational load, and provide a robust method for dealing with repeated sequences. Inclusion of WGS sequences facilitates use of different clone insert sizes and reduces data production costs. A core function of Atlas software is recruitment of WGS sequences into appropriate BACs based on sequence overlaps. Because construction of consensus sequences is from local assembly of these reads, only small (<0.1%) units of the genome are assembled at a time. Once assembled, each BAC is used to derive a genomic layout. This "sequence-based" growth of the genome map has greater precision than with non-sequence-based methods. Use of BACs allows correction of artifacts due to repeats at each stage of the process. This is aided by ancillary data such as BAC fingerprint, other genomic maps, and syntenic relations with other genomes. Atlas was used to assemble a draft DNA sequence of the rat genome; its major components including overlapper and split-scaffold are also being used in pure WGS projects.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.