ArticleMolecular systems biology2016
Pooled-matrix protein interaction screens using Barcode Fusion Genetics.
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Article in Molecular systems biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
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79 citing papers in PubMed.
- Mutational landscape and molecular bases of echinocandin resistance in Saccharomyces cerevisiae.Genetics · 2026Article
- Predicting antifolate resistance in the unculturable fungal pathogen Pneumocystis jirovecii.PLoS genetics · 2026Article
- Experimental assessment of AI-based interactome mapping.Nature communications · 2026Article
- BOGO: A Proteome-Wide Gene Overexpression Platform for Discovering Rational Cancer Combination Therapies.bioRxiv : the preprint server for biology · 2025Article
- Barcode sequencing: a robust, platform-agnostic method for massively parallel cell-based screens.G3 (Bethesda, Md.) · 2025Article
- Long-read sequencing to detect full-length protein-protein interactions.Scientific reports · 2025Article
- Spatially resolved subcellular protein-protein interactomics in drug-perturbed lung-cancer cultures and tissues.Nature biomedical engineering · 2025Article
- NGPINT V3: a containerized orchestration Python software for discovery of next-generation protein-protein interactions.Bioinformatics (Oxford, England) · 2025Article
- ThemSphere · 2025Article
- Decoding Plant-Pathogen Interactions: A Comprehensive Exploration of Effector-Plant Transcription Factor Dynamics.Molecular plant pathology · 2025Review
- Pooled PPIseq: Screening the SARS-CoV-2 and human interface with a scalable multiplexed protein-protein interaction assay platform.PloS one · 2025Article
- A comprehensive two-hybrid analysis to explore themSystems · 2024Article
- Massively parallel measurement of protein-protein interactions by sequencing using MP3-seq.Nature chemical biology · 2024Article
- Review
- Bidirectional linkage of DNA barcodes for the multiplexed mapping of higher-order protein interactions in cells.Nature biomedical engineering · 2024Article
- Powdery mildew effectors AVRMolecular plant pathology · 2024Article
- Deep mutational scanning of Pneumocystis jirovecii dihydrofolate reductase reveals allosteric mechanism of resistance to an antifolate.PLoS genetics · 2024Article
- Compensatory mutations potentiate constructive neutral evolution by gene duplication.bioRxiv : the preprint server for biology · 2024Article
- From beer to breadboards: yeast as a force for biological innovation.Genome biology · 2024Review
- An Overview of the Deubiquitinase USP53: A Promising Diagnostic Marker and Therapeutic Target.Current protein & peptide science · 2024Review
19 more citing papers are in PubMed but not listed here.
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Authors and funding
33 authors.
Nozomu YachieDonnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada Synthetic Biology Division, Research Center for Advanced Science and Technology The University of Tokyo, Tokyo, Japan Institute for Advanced Bioscience, Keio University, Tsuruoka, Yamagata, Japan PRESTO, Japan Science and Technology Agency (JST), Tokyo, Japan yachie@synbiol.rcast.u-tokyo.ac.jp fritz.roth@utoronto.ca.
Evangelia PetsalakiDonnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada.
Joseph C MellorDonnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada.
Jochen WeileDonnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
Yves JacobDépartement de Virologie, Unité de Génétique Moléculaire des Virus à ARN Institut Pasteur, Paris, France.
Marta VerbyDonnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada.
Sedide B OzturkDonnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada.
Siyang LiDonnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada.
Atina G CoteDonnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada.
Roberto MoscaJoint IRB-BSC Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain.
Jennifer J KnappDonnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada.
Minjeong KoDonnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada.
Analyn YuDonnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada.
Marinella GebbiaDonnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada.
Nidhi SahniCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA.
Song YiCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA.
Tanya TyagiDonnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada.
Dayag SheykhkarimliDonnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
Jonathan F RothDonnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
Cassandra WongDonnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada.
Louai MusaDonnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada.
Jamie SniderDonnelly Centre, University of Toronto, Toronto, ON, Canada.
Yi-Chun LiuDonnelly Centre, University of Toronto, Toronto, ON, Canada.
Haiyuan YuWeill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA.
Pascal BraunCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA Department of Plant Systems Biology, Technische Universität München Wissenschaftszentrum Weihenstephan, Freising, Germany.
Igor StagljarDonnelly Centre, University of Toronto, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
Tong HaoCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA.
Michael A CalderwoodCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0001-6475-1418
Laurence PelletierLunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
Patrick AloyJoint IRB-BSC Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
David E HillCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0001-5192-0921
Marc VidalCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0003-3391-5410
Frederick P RothDonnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Canadian Institute for Advanced Research, Toronto, ON, Canada Department of Computer Science, University of Toronto, Toronto, Ontario, Canada yachie@synbiol.rcast.u-tokyo.ac.jp fritz.roth@utoronto.ca.
Funding
Genomic Analysis of Network Perturbations in Human DiseaseP50HG004233 · NHGRI · DANA-FARBER CANCER INST · PI VIDAL, MARC · 2007 to 2017
$31.6MThe C. elegans Interactome ProjectR01HG001715 · NHGRI · MASSACHUSETTS GENERAL HOSPITAL · PI HILL, DAVID E., ROTH, FREDERICK P · 1998 to 2010
$16.5MMapping the first half of the REFERENCE human binary protein interactomeU01HG001715 · NHGRI · DANA-FARBER CANCER INST · PI HILL, DAVID E., ROTH, FREDERICK P · 2012 to 2014
$5.4MResource ProjectU41HG001715 · NHGRI · DANA-FARBER CANCER INST · PI HILL, DAVID E. · 2015 to 2017
$4.7MTowards a comprehensive protein interactome network in Schizosaccharomyces pombeR01GM097358 · NIGMS · CORNELL UNIVERSITY · PI YU, HAIYUAN · 2012 to 2016
$1.7MTechnology for large-scale genetic interaction discovery in S. cerevisiaeR21HG004756 · NHGRI · HARVARD MEDICAL SCHOOL · PI ROTH, FREDERICK P · 2008 to 2009
$466kCIHR MOP-123468CIHR MOP-130507NHGRI NIH HHS HG001715NHGRI NIH HHS HG004233NHGRI NIH HHS P50 HG004233NHGRI NIH HHS R01 HG001715NHGRI NIH HHS U01 HG001715NHGRI NIH HHS U41 HG001715
Abstract
High-throughput binary protein interaction mapping is continuing to extend our understanding of cellular function and disease mechanisms. However, we remain one or two orders of magnitude away from a complete interaction map for humans and other major model organisms. Completion will require screening at substantially larger scales with many complementary assays, requiring further efficiency gains in proteome-scale interaction mapping. Here, we report Barcode Fusion Genetics-Yeast Two-Hybrid (BFG-Y2H), by which a full matrix of protein pairs can be screened in a single multiplexed strain pool. BFG-Y2H uses Cre recombination to fuse DNA barcodes from distinct plasmids, generating chimeric protein-pair barcodes that can be quantified via next-generation sequencing. We applied BFG-Y2H to four different matrices ranging in scale from ~25 K to 2.5 M protein pairs. The results show that BFG-Y2H increases the efficiency of protein matrix screening, with quality that is on par with state-of-the-art Y2H methods.
Indexed as
CentrosomeChromosomes, HumanGene LibraryHigh-Throughput Nucleotide SequencingHumansProtein BindingProtein Interaction MappingProteomeSaccharomyces cerevisiaeTwo-Hybrid System TechniquesProteomeDNA barcodeinteractomenext‐generation sequencingprotein interactionyeast two‐hybrid
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