@article{61ef06f373cd43329fe209ea77ecdccb,
title = "A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice",
abstract = "Systematic mappings of protein interactome networks have provided invaluable functional information for numerous model organisms. Here we develop PCR-mediated Linkage of barcoded Adapters To nucleic acid Elements for sequencing (PLATE-seq) that serves as a general tool to rapidly sequence thousands of DNA elements. We validate its utility by generating the ORFeome for Oryza sativa covering 2,300 genes and constructing a high-quality protein-protein interactome map consisting of 322 interactions between 289 proteins, expanding the known interactions in rice by roughly 50%. Our work paves the way for high-throughput profiling of protein-protein interactions in a wide range of organisms.",
keywords = "Networks, Next-generation sequencing, ORFeome, Protein-protein interaction, Rice",
author = "Wierbowski, {Shayne D.} and Vo, {Tommy V.} and Pascal Falter-Braun and Jobe, {Timothy O.} and Kruse, {Lars H.} and Xiaomu Wei and Jin Liang and Meyer, {Michael J.} and Nurten Akturk and Rivera-Erick, {Christen A.} and Cordero, {Nicolas A.} and Paramo, {Mauricio I.} and Shayhidin, {Elnur E.} and Marta Bertolotti and Tippens, {Nathaniel D.} and Kazi Akther and Rita Sharma and Yuichi Katayose and Kourosh Salehi-Ashtiani and Tong Hao and Ronald, {Pamela C.} and Ecker, {Joseph R.} and Schweitzer, {Peter A.} and Shoshi Kikuchi and Hiroshi Mizuno and Hill, {David E.} and Marc Vidal and Moghe, {Gaurav D.} and McCouch, {Susan R.} and Haiyuan Yu",
note = "Funding Information: ACKNOWLEDGMENTS. This work was supported by grants from the National Science Foundation (NSF #1661380 to H.Y.; NSF #1639075 to H.Y. and S.R.M.; NSF #1444511 to S.R.M.; NSF #0520253 to J.R.E.; NSF #0703905 to M.V., D.E.H., and J.R.E.; and NSF #1237975 to P.C.R.), the National Institute of General Medical Sciences (R01 GM124559 to H.Y.; R01 GM125639 to H.Y.; and R01 GM122968 to P.C.R.), the National Institute of Diabetes and Digestive and Kidney Diseases (R01 DK115398 to H.Y.), the National Institute of Food and Agriculture (2013-67013-21379 to S.R.M.), the Deutsche Forschungsgemeinschaft (Award #411255989 to L.H.K.), the Foundation for Food and Agriculture Research (534683 to P.C.R.), the European Research Council{\textquoteright}s Horizon 2020 Research and Innovation Programme (648420 to P.F.-B.), and the Bio-Oriented Technology Research Advancement Institution (to S.K.). J.R.E. is an Investigator of the Howard Hughes Medical Institute. Positive and negative control clones used for BiFC experiments were generous gifts from Julian I. Schroeder. We thank Horacio Caniza and Alberto Paccanaro for useful discussions about the use and interpretation of semantic similarity scores and in particular Horacio Caniza for assistance and feedback in running the GOssTO software to calculate these semantic similarity scores. Publisher Copyright: {\textcopyright} 2020 National Academy of Sciences. All rights reserved.",
year = "2020",
month = may,
day = "26",
doi = "10.1073/pnas.1918068117",
language = "English (US)",
volume = "117",
journal = "Proceedings of the National Academy of Sciences of the United States of America",
issn = "0027-8424",
publisher = "National Academy of Sciences",
number = "21",
}