What is smart-pooling?

Smart-pooling (AKA combinatorial group testing) is an experimental methodology susceptible of increasing efficiency, accuracy and coverage in high-throughput screening projects. It consists in assaying well-chosen pools of probes, such that each probe is present in several pools, hence tested several times. The goal is to construct the pools so that the positive probes can usually be identified from the pattern of positive pools, despite the occurrence of false positives and false negatives.

For a more detailed introduction to smart-pooling, have a look at my smart-pooling papers and references therein, especially the Nature Methods 2006 N&V and the introductory section of my BMC Bioinformatics 2006 paper.

The Shifted Transversal Design

This is the name of my smart-pooling design, see my BMC Bioinformatics 2006 paper.

It's very flexible: if you are considering doing some smart-pooling experiments, there's almosty certainly an STD design perfectly adapted to your experimental setup/constraints (maximum pool size, expected fraction of positives, false positive and false negative error rates).

It out-performs every design I've looked at, both from a combinatorial point of view (satisfying the "guarantee requirement", see paper for details) and from a real-life perspective (through simulations, unpublished observations).

If you want to understand the STD construction better, you may find the slides of my DIMACS 2006 talk useful, especially page 10. I think that figure really helps, too bad I didn't think of it in time for the BMC paper.

If you wish to experiment with STD but don't want to bother coding it, download my interpool package. It includes a program (ipoolSTD) for generating any STD design (in a convenient text-file format).

Interpool: Interpreting smart-pooling results

This is the name of the algorithm and software that I developed for interpreting the results of a smart-pooling experiment, see my Bioinformatics 2008 paper.

It's useful both before any experimental work, for performing simulations in order to choose a good design; and later on, when you are actually screening your pools, for interpreting the results.

Interpool is an exact algorithm, i.e. it always find the optimal solution, yet it's (usually) very fast.

The software package is freely available under the GNU GPL. Download latest version! Or browse older releases.

Note that a version is also available in the Supplemental Data file that accompanies my Genome Research 2009 paper. It is almost identical to interpool-080121.tar.gz, with just a few customizations for the paper. See the Publications section below for details and downloading.

If you have any questions, comments, suggestions, or bugs to report: please email me, with "interpool" in the subject.

Publications, talks and posters.

Papers - pdf files are usually provided on my publications page.

Xin X, Boone C, Thierry-Mieg N.
Mapping interactomes with high coverage and efficiency using the shifted transversal design.
Methods Mol Biol. 2012;812:147-59.

Xin X^*, Rual JF, Hirozane-Kishikawa T, Hill DE, Vidal M⁺, Boone C⁺, Thierry-Mieg N^+* (*: contributed equally; +: corresponding authors).
Shifted Transversal Design smart-pooling for high coverage interactome mapping.
Genome Res. 2009 Jul;19(7):1262-9. Epub 2009 May 15.
I am providing here the Supplemental Data file in tar.bz2 format: this archive's content is identical to the Suppl Data zip file available on the Genome Research website, but it may download faster as it is much smaller (2.7Mb vs 8Mb).

Schliep A, Shokrollahi A, Thierry-Mieg N (editors).
Dagstuhl Seminar 08301 Report: Group Testing in the Life Sciences.
Dagstuhl Seminar Proceedings, July 2008, Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany.
Seminar homepage.

Thierry-Mieg N, Bailly G.
Interpool: interpreting smart-pooling results.
Bioinformatics. 2008 Mar 1; 24(5):696-703.

Thierry-Mieg N.
Pooling in systems biology becomes smart.
Nat Methods. 2006 Mar; 3(3):161-2.

Thierry-Mieg N.
A new pooling strategy for high-throughput screening: the Shifted Transversal Design.
BMC Bioinformatics. 2006 Jan 19; 7:28. Open-access!

Talks and posters.

Thierry-Mieg N.
Combinatorial group testing with the Shifted Transversal Design, applications to biology.
Talk, Nagoya University, Department of Computer Science and Mathematical Informatics Seminar (host: Masakazu Jimbo), July 2012, Nagoya, Japan.

Thierry-Mieg N.
Mapping protein-protein interactions with the Shifted Transversal Design.
Talk, the second Institute of Mathematical Statistics - Asia Pacific Rim Meeting (IMS-APRM2012), TCP12, July 2012, Tsukuba, Japan.

Thierry-Mieg N.
Shifted Transversal Design smart-­pooling for high­-throughput biology.
Talk, IMA Workshop on Group Testing Designs, Algorithms, and Applications to Biology, Feb 2012, Minneapolis, USA.
Slides and video of my talk.

Thierry-Mieg N.
Smart Pooling: increasing accuracy, coverage and efficiency in high-throughput screening.
Talk, Ontario Institute for Cancer Research (host: Francis Ouellette), Sept 2008, Toronto, Canada.

Thierry-Mieg N.
Smart Pooling: increasing accuracy, coverage and efficiency in high-throughput screening.
Talk, UofT Department of Molecular Genetics Guest Speaker Series, Sept 2008, Toronto, Canada.

Xin X*, Thierry-Mieg N*, Rual JF, Hirozane-Kishikawa T, Hill D, Vidal M, Boone C (*: contributed equally).
Smart-pooling for proteome-scale interactome mapping using the Shifted Transversal Design.
Talk, 2008 CSHL/WT Network Biology Meeting, Aug 2008, Hinxton, UK.

Thierry-Mieg N.
Smart-pooling.
Talk, Dagstuhl Seminar: Group Testing in the Life Sciences, Jul 2008, Dagstuhl, Germany.

X Xin*, N Thierry-Mieg*, D Hill, M Vidal, C Boone (*: contributed equally).
Smart-pooling for proteome-scale interactome mapping using the Shifted Transversal Design (STD).
Poster, 2008 Yeast Genetics and Molecular Biology Meeting, Jul 2008, Toronto, Canada.

Thierry-Mieg N.
Smart-pooling: increasing accuracy, coverage and efficiency in high-throughput screening.
Talk, MAGMA Seminar, June 2008, Marseille, France.

Thierry-Mieg N.
Smart-pooling for interactome mapping.
Talk, Towards Systems Biology workshop, Oct 2007, Grenoble, France. slides.

Thierry-Mieg N, Rual JF, Hirozane-Kishikawa T, Hill D, Vidal M.
Smart pooling for sensitive and specific interactome mapping: a pilot experiment.
Poster, 2007 CSHL/WT Interactome Networks Meeting, Aug 2007, Hinxton, UK.

Thierry-Mieg N.
A new smart-pooling strategy for high-throughput screening: the Shifted Transversal Design.
Talk, DIMACS Workshop on Combinatorial Group Testing, May 2006, Rutgers U., New Jersey. slides.

Thierry-Mieg N.
A new pooling strategy for high-throughput screening: The Shuffled Transversal Design.
Flash talk and poster, JOBIM 2005, Lyon, France. pdf.

Thierry-Mieg N.
Smart-pooling for the interactome: better, faster, cheaper!
Poster, ORFeome Meeting 2004, Boston.

Thierry-Mieg N, Trilling L, Roch JL.
A novel pooling design for protein-protein interaction mapping.
Poster, European Conference on Computational Biology (ECCB) 2003, Paris, France. pdf.

last modified 20/07/2012