ArticleGenome medicine2013
BAIT: Organizing genomes and mapping rearrangements in single cells.
Article in Genome medicine, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
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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.
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Who cites it
22 citing papers in PubMed.
- Strand-seq and the future of personalized genomics.Nature genetics · 2026Review
- High-throughput mapping of spontaneous mitotic crossover and genome instability events with sci-L3-Strand-seq.Nucleic acids research · 2026Article
- Graphasing: phasing diploid genome assembly graphs with single-cell strand sequencing.Genome biology · 2024Article
- Phasing Diploid Genome Assembly Graphs with Single-Cell Strand Sequencing.bioRxiv : the preprint server for biology · 2024Article
- Quantitative and qualitative mutational impact of ionizing radiation on normal cells.Cell genomics · 2024Article
- A non-genetic switch triggers alternative telomere lengthening and cellular immortalization in ATRX deficient cells.Nature communications · 2023Article
- Progress in Methods for Copy Number Variation Profiling.International journal of molecular sciences · 2022Review
- Construction of Whole Genomes from Scaffolds Using Single Cell Strand-Seq Data.International journal of molecular sciences · 2021Article
- Single-cell analysis of structural variations and complex rearrangements with tri-channel processing.Nature biotechnology · 2020Article
- Structural variant identification and characterization.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2020Article
- Structural variation in the sequencing era.Nature reviews. Genetics · 2020Review
- Strand-seq enables reliable separation of long reads by chromosome via expectation maximization.Bioinformatics (Oxford, England) · 2018Article
- BLM helicase suppresses recombination at G-quadruplex motifs in transcribed genes.Nature communications · 2018Article
- Genome-wide mapping of sister chromatid exchange events in single yeast cells using Strand-seq.eLife · 2017Article
- Assembling draft genomes using contiBAIT.Bioinformatics (Oxford, England) · 2017Article
- Single-cell template strand sequencing by Strand-seq enables the characterization of individual homologs.Nature protocols · 2017Article
- Characterizing polymorphic inversions in human genomes by single-cell sequencing.Genome research · 2016Article
- Direct chromosome-length haplotyping by single-cell sequencing.Genome research · 2016Article
- Bromodeoxyuridine does not contribute to sister chromatid exchange events in normal or Bloom syndrome cells.Nucleic acids research · 2016Article
- The developmental potential of iPSCs is greatly influenced by reprogramming factor selection.Cell stem cell · 2014Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Strand-seq is a single-cell sequencing technique to finely map sister chromatid exchanges (SCEs) and other rearrangements. To analyze these data, we introduce BAIT, software which assigns templates and identifies and localizes SCEs. We demonstrate BAIT can refine completed reference assemblies, identifying approximately 21 Mb of incorrectly oriented fragments and placing over half (2.6 Mb) of the orphan fragments in mm10/GRCm38. BAIT also stratifies scaffold-stage assemblies, potentially accelerating the assembling and finishing of reference genomes. BAIT is available at http://sourceforge.net/projects/bait/.
Identifiers
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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.