ArticleBioinformatics advances2024
Quantifying orthogonal barcodes for sequence census assays.
Article in Bioinformatics advances, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 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
7 citing papers in PubMed.
- Single-nucleus multiome sequencing identifies candidate regulators of mouse gastric epithelial homeostasis.bioRxiv : the preprint server for biology · 2026Article
- Mapping cis- and trans-regulatory target genes of human-specific deletions.Nature communications · 2025Article
- Article
- Scalable design of orthogonal DNA barcode libraries.Nature computational science · 2024Article
- kallisto, bustools, and kb-python for quantifying bulk, single-cell, and single-nucleus RNA-seq.bioRxiv : the preprint server for biology · 2024Article
- Universal preprocessing of single-cell genomics data.bioRxiv : the preprint server for biology · 2023Article
- Mutations from patients with IPEX ported to mice reveal different patterns of FoxP3 and Treg dysfunction.Cell reports · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Summary: Barcode-based sequence census assays utilize custom or random oligonucloetide sequences to label various biological features, such as cell-surface proteins or CRISPR perturbations. These assays all rely on barcode quantification, a task that is complicated by barcode design and technical noise. We introduce a modular approach to quantifying barcodes that achieves speed and memory improvements over existing tools. We also introduce a set of quality control metrics, and accompanying tool, for validating barcode designs. Availability and implementation: https://github.com/pachterlab/kb_python, https://github.com/pachterlab/qcbc.
Identifiers
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.