NGPINT: A Next-generation protein-protein interaction software
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Roger P. Wise | Sagnik Banerjee | Valeria Velásquez-Zapata | J. Mitch Elmore | Gregory Fuerst | R. Wise | Sagnik Banerjee | G. Fuerst | J. Elmore | Valeria Velásquez-Zapata | J. M. Elmore
[1] Bernhard Suter,et al. Next-Generation Sequencing for Binary Protein–Protein Interactions , 2015, Front. Genet..
[2] Pascal Braun,et al. History of protein–protein interactions: From egg‐white to complex networks , 2012, Proteomics.
[3] Jae-Seong Yang,et al. rec-YnH enables simultaneous many-by-many detection of direct protein–protein and protein–RNA interactions , 2018, Nature Communications.
[4] A. Barabasi,et al. A disease module in the interactome explains disease heterogeneity, drug response and captures novel pathways and genes in asthma. , 2015, Human molecular genetics.
[5] J. Turkson,et al. Discovery of JSI-124 (cucurbitacin I), a selective Janus kinase/signal transducer and activator of transcription 3 signaling pathway inhibitor with potent antitumor activity against human and murine cancer cells in mice. , 2003, Cancer research.
[6] F. Kaye,et al. Identification of cellular proteins that can interact specifically with the T/ElA-binding region of the retinoblastoma gene product , 1991, Cell.
[7] Darrell Desveaux,et al. Quantitative Interactor Screening with next-generation Sequencing (QIS-Seq) identifies Arabidopsis thaliana MLO2 as a target of the Pseudomonas syringae type III effector HopZ2 , 2012, BMC Genomics.
[8] Julie M. Sahalie,et al. Supplementary Figure and Table Legends , 2022 .
[9] Damian Szklarczyk,et al. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets , 2018, Nucleic Acids Res..
[10] S. Fields,et al. Protein-protein interactions: methods for detection and analysis , 1995, Microbiological reviews.
[11] D. Inzé,et al. NINJA connects the co-repressor TOPLESS to jasmonate signalling , 2010, Nature.
[12] M. Kabbage,et al. An inhibitor of apoptosis (SfIAP) interacts with SQUAMOSA promoter‐binding protein (SBP) transcription factors that exhibit pro‐cell death characteristics , 2018, bioRxiv.
[13] V. S. Rao,et al. Protein-Protein Interaction Detection: Methods and Analysis , 2014, International journal of proteomics.
[14] Klaus Schulten,et al. Regulation of the protein-conducting channel by a bound ribosome. , 2009, Structure.
[15] A. Galarneau,et al. β-Lactamase protein fragment complementation assays as in vivo and in vitro sensors of protein–protein interactions , 2002, Nature Biotechnology.
[16] S. Fields,et al. The yeast two-hybrid assay: still finding connections after 25 years , 2014, Nature Methods.
[17] Roger P. Wise,et al. Y2H-SCORES: A statistical framework to infer protein-protein interactions from next-generation yeast-two-hybrid sequence data , 2020 .
[18] A. Barabasi,et al. An empirical framework for binary interactome mapping , 2008, Nature Methods.
[19] Nicolas Servant,et al. A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis , 2013, Briefings Bioinform..
[20] Patrick Breheny,et al. DEEPN as an Approach for Batch Processing of Yeast 2-Hybrid Interactions. , 2016, Cell reports.
[21] Jonathan D. G. Jones,et al. Evidence for Network Evolution in an Arabidopsis Interactome Map , 2011, Science.
[22] T. Zal,et al. Using live FRET imaging to reveal early protein-protein interactions during T cell activation. , 2004, Current opinion in immunology.
[23] CHEN CHEN,et al. Construction and analysis of protein-protein interaction networks based on proteomics data of prostate cancer , 2016, International journal of molecular medicine.
[24] Rob Patro,et al. Salmon provides fast and bias-aware quantification of transcript expression , 2017, Nature Methods.
[25] G. Patterson,et al. Photoswitching FRET to monitor protein–protein interactions , 2018, Proceedings of the National Academy of Sciences.
[26] Kara Dolinski,et al. The BioGRID interaction database: 2019 update , 2018, Nucleic Acids Res..
[27] Kai Li,et al. A DnaJ protein that interacts with soybean mosaic virus coat protein serves as a key susceptibility factor for viral infection. , 2020, Virus research.
[28] Sara Linse,et al. Methods for the detection and analysis of protein–protein interactions , 2007, Proteomics.
[29] W. Huber,et al. which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets , 2011 .
[30] Takayuki Tohge,et al. A protein–protein interaction network linking the energy-sensor kinase SnRK1 to multiple signaling pathways in Arabidopsis thaliana , 2016 .
[31] Thomas R. Gingeras,et al. STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..
[32] Ulrich Stelzl,et al. A Y2H-seq approach defines the human protein methyltransferase interactome , 2013, Nature Methods.
[33] Günter Mayer,et al. Systematic evaluation of error rates and causes in short samples in next-generation sequencing , 2018, Scientific Reports.
[34] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[35] Joseph R. Ecker,et al. CrY2H-seq: a massively-multiplexed assay for deep coverage interactome mapping , 2017, Nature Methods.
[36] D. Hasselquist,et al. No evidence that carotenoid pigments boost either immune or antioxidant defenses in a songbird , 2018, Nature Communications.
[37] M. Vidal,et al. High-throughput yeast two-hybrid assays for large-scale protein interaction mapping. , 2001, Methods.
[38] Alyssa C. Frazee,et al. Polyester: Simulating RNA-Seq Datasets With Differential Transcript Expression , 2014, bioRxiv.
[39] W. Huber,et al. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.
[40] Martin Vingron,et al. IntAct: an open source molecular interaction database , 2004, Nucleic Acids Res..
[41] Mi Zhou,et al. Current Experimental Methods for Characterizing Protein–Protein Interactions , 2016, ChemMedChem.
[42] Alain Goossens,et al. A user-friendly platform for yeast two-hybrid library screening using next generation sequencing , 2018, PloS one.
[43] A. Vinayagam,et al. A Directed Protein Interaction Network for Investigating Intracellular Signal Transduction , 2011, Science Signaling.
[44] Bridget E. Begg,et al. A Proteome-Scale Map of the Human Interactome Network , 2014, Cell.
[45] David R. Kelley,et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks , 2012, Nature Protocols.
[46] C. Thermes,et al. Ten years of next-generation sequencing technology. , 2014, Trends in genetics : TIG.
[47] S. Michnick,et al. A highly sensitive protein-protein interaction assay based on Gaussia luciferase , 2006, Nature Methods.
[48] Salvador Ventura,et al. Protein complementation assays: Approaches for the in vivo analysis of protein interactions , 2009, FEBS letters.
[49] Michael I. Love,et al. Differential analysis of count data – the DESeq2 package , 2013 .
[50] David E Hill,et al. next-generation sequencing to generate interactome datasets , 2011 .
[51] Haiyuan Yu,et al. Three-dimensional reconstruction of protein networks provides insight into human genetic disease , 2012, Nature Biotechnology.