Publications by authors named "Jennifer J Knapp"

3 Publications

  • Page 1 of 1

A Comprehensive, Flexible Collection of SARS-CoV-2 Coding Regions.

G3 (Bethesda) 2020 09 2;10(9):3399-3402. Epub 2020 Sep 2.

Donnelly Centre, University of Toronto, Toronto, Ontario, Canada

The world is facing a global pandemic of COVID-19 caused by the SARS-CoV-2 coronavirus. Here we describe a collection of codon-optimized coding sequences for SARS-CoV-2 cloned into Gateway-compatible entry vectors, which enable rapid transfer into a variety of expression and tagging vectors. The collection is freely available. We hope that widespread availability of this SARS-CoV-2 resource will enable many subsequent molecular studies to better understand the viral life cycle and how to block it.
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http://dx.doi.org/10.1534/g3.120.401554DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7467003PMC
September 2020

A reference map of the human binary protein interactome.

Nature 2020 04 8;580(7803):402-408. Epub 2020 Apr 8.

Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.

Global insights into cellular organization and genome function require comprehensive understanding of the interactome networks that mediate genotype-phenotype relationships. Here we present a human 'all-by-all' reference interactome map of human binary protein interactions, or 'HuRI'. With approximately 53,000 protein-protein interactions, HuRI has approximately four times as many such interactions as there are high-quality curated interactions from small-scale studies. The integration of HuRI with genome, transcriptome and proteome data enables cellular function to be studied within most physiological or pathological cellular contexts. We demonstrate the utility of HuRI in identifying the specific subcellular roles of protein-protein interactions. Inferred tissue-specific networks reveal general principles for the formation of cellular context-specific functions and elucidate potential molecular mechanisms that might underlie tissue-specific phenotypes of Mendelian diseases. HuRI is a systematic proteome-wide reference that links genomic variation to phenotypic outcomes.
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http://dx.doi.org/10.1038/s41586-020-2188-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169983PMC
April 2020

Pooled-matrix protein interaction screens using Barcode Fusion Genetics.

Mol Syst Biol 2016 Apr 22;12(4):863. Epub 2016 Apr 22.

Joint 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.

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.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4848762PMC
http://dx.doi.org/10.15252/msb.20156660DOI Listing
April 2016
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