ArticleGenome research2009
Shifted Transversal Design smart-pooling for high coverage interactome mapping.
Article in Genome research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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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.
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Who cites it
19 citing papers in PubMed.
- Combinatorial group testing for efficient scaling across biological applications.Nature communications · 2026Article
- When to use one-dimensional, two-dimensional, and Shifted Transversal Design pooling in mycotoxin screening.PloS one · 2020Article
- Development and application of a recombination-based library versus library high- throughput yeast two-hybrid (RLL-Y2H) screening system.Nucleic acids research · 2018Article
- Making the Right Choice: Critical Parameters of the Y2H Systems.Methods in molecular biology (Clifton, N.J.) · 2018Article
- Article
- Evolution of disorder in Mediator complex and its functional relevance.Nucleic acids research · 2016Article
- The DEP domain-containing protein TOE-2 promotes apoptosis in the Q lineage of C. elegans through two distinct mechanisms.Development (Cambridge, England) · 2014Article
- Article
- Bck2 acts through the MADS box protein Mcm1 to activate cell-cycle-regulated genes in budding yeast.PLoS genetics · 2013Article
- SH3 interactome conserves general function over specific form.Molecular systems biology · 2013Article
- Weighted pooling--practical and cost-effective techniques for pooled high-throughput sequencing.Bioinformatics (Oxford, England) · 2012Article
- Article
- Identifying microbial fitness determinants by insertion sequencing using genome-wide transposon mutant libraries.Nature protocols · 2011Article
- Assembling a protein-protein interaction map of the SSU processome from existing datasets.PloS one · 2011Article
- New insights into protein-protein interaction data lead to increased estimates of the S. cerevisiae interactome size.BMC bioinformatics · 2010Article
- poolMC: smart pooling of mRNA samples in microarray experiments.BMC bioinformatics · 2010Article
- Compressed Genotyping.IEEE transactions on information theory · 2010Article
- Combinatorics and next-generation sequencing.Nature biotechnology · 2009Article
- Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
"Smart-pooling," in which test reagents are multiplexed in a highly redundant manner, is a promising strategy for achieving high efficiency, sensitivity, and specificity in systems-level projects. However, previous applications relied on low redundancy designs that do not leverage the full potential of smart-pooling, and more powerful theoretical constructions, such as the Shifted Transversal Design (STD), lack experimental validation. Here we evaluate STD smart-pooling in yeast two-hybrid (Y2H) interactome mapping. We employed two STD designs and two established methods to perform ORFeome-wide Y2H screens with 12 baits. We found that STD pooling achieves similar levels of sensitivity and specificity as one-on-one array-based Y2H, while the costs and workloads are divided by three. The screening-sequencing approach is the most cost- and labor-efficient, yet STD identifies about twofold more interactions. Screening-sequencing remains an appropriate method for quickly producing low-coverage interactomes, while STD pooling appears as the method of choice for obtaining maps with higher coverage.
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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.