Unbiased and Error-Detecting Combinatorial Pooling Experiments with Balanced Constant-Weight Gray Codes for Consecutive Positives Detection

He, Guanchen, Kovaleva, Vasilisa A, Barton, Carl, Thomas, Paul G, Pogorelyy, Mikhail V, Meyer, Hannah V, Huang, Qin (November 2025) Unbiased and Error-Detecting Combinatorial Pooling Experiments with Balanced Constant-Weight Gray Codes for Consecutive Positives Detection. Bioinformatics. btaf611. ISSN 1367-4803

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Abstract

MOTIVATION: Combinatorial pooling schemes have enabled the measurement of thousands of experiments in a small number of reactions. This efficiency is achieved by distributing the items to be measured across multiple reaction units called pools. However, current methods for the design of pooling schemes do not adequately address the need for balanced item distribution across pools, a property particularly important for biological applications. RESULTS: Here, we introduce balanced constant-weight Gray codes for detecting consecutive positives (DCP-CWGCs) for the efficient construction of combinatorial pooling schemes. Balanced DCP-CWGCs ensure uniform item distribution across pools, allow for the identification of consecutive positive items such as overlapping biological sequences, and enable error detection by ensuring a constant number of tests on each item and pair of consecutive items. For the efficient construction of balanced DCP-CWGCs, we have released an open-source python package codePUB, with implementations of the two core algorithms: a branch-and-bound algorithm (BBA) and a recursive combination with BBA (rcBBA). Simulations using codePUB show that our algorithms can construct long, balanced DCP-CWGCs that allow for error detection in tractable runtime. AVAILABILITY AND IMPLEMENTATION: The source code of codePUB is available at https://github.com/meyer-lab-cshl/codepub, with detailed documentation at https://codepub.readthedocs.io/.

Item Type:	Paper
Subjects:	bioinformatics bioinformatics > computational biology
CSHL Authors:	Meyer, Hannah V. Kovaleva, Vasilisa
Communities:	CSHL Cancer Center Program > Cancer Genetics and Genomics Program CSHL labs > Meyer Lab School of Biological Sciences > Publications
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	14 November 2025
Date Deposited:	02 Dec 2025 16:15
Last Modified:	02 Dec 2025 16:15
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/42023

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