Next-generation large-scale binary protein interaction network for Drosophila melanogaster
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István A. Kovács | Benjamin W. Booth | Atina G. Coté | N. Perrimon | J. Bader | M. Vidal | M. Calderwood | Yanhui Hu | I. Lemmens | J. Tavernier | Yifang Liu | Katja Luck | Kerstin Spirohn | Carl Pollis | Sadie Schlabach | Dae-Kyum Kim | Dawit Balcha | S. Celniker | K. Wan | Jennifer J. Knapp | S. Mohr | Donghui Yang-Zhou | Bridget Teeking | Steffi de Rouck | Roujia Li | D. Markey | Dayag Sheykhkarimli | R. Binari | Hong-Wen Tang | Jonathan Rodiger | K. Y. Goh | F. Roth | Yue Gao | Wen Xing Lee | Cathleen Li | Mian Li | H. Lim | Sudharshan Rangarajan | Tong Hao | Wenting Bian | Yun A Shen | D. Hill | Alice Desbuleux
[1] István A. Kovács,et al. Binary interactome models of inner- versus outer-complexome organisation , 2022, bioRxiv.
[2] Daniel A. Sutton,et al. Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly , 2022, Science.
[3] P. D’Avino,et al. Identification of GOLPH3 Partners in Drosophila Unveils Potential Novel Roles in Tumorigenesis and Neural Disorders , 2021, Cells.
[4] Antonia P. Sagona,et al. Selective autophagy controls innate immune response through a TAK1/TAB2/SH3PX1 axis. , 2021, Cell reports.
[5] Phani Garapati,et al. FlyBase: updates to the Drosophila melanogaster knowledge base , 2020, Nucleic Acids Res..
[6] Hongjie Li. Single‐cell RNA sequencing in Drosophila: Technologies and applications , 2020, Wiley interdisciplinary reviews. Developmental biology.
[7] Patrick Aloy,et al. A reference map of the human binary protein interactome , 2020, Nature.
[8] N. Perrimon,et al. A cell atlas of the adult Drosophila midgut , 2020, Proceedings of the National Academy of Sciences.
[9] T. Lamark,et al. Selective Autophagy: ATG8 Family Proteins, LIR Motifs and Cargo Receptors. , 2020, Journal of molecular biology.
[10] M. Darino,et al. Systematic Y2H Screening Reveals Extensive Effector-Complex Formation , 2019, Front. Plant Sci..
[11] N. Perrimon,et al. Drosophila melanogaster: a simple system for understanding complexity , 2019, Disease Models & Mechanisms.
[12] Hafiz M.N. Iqbal,et al. A Comprehensive Review of Autophagy and Its Various Roles in Infectious, Non-Infectious, and Lifestyle Diseases: Current Knowledge and Prospects for Disease Prevention, Novel Drug Design, and Therapy , 2019, Cells.
[13] Stephen S. Gisselbrecht,et al. A Comprehensive Drosophila melanogaster Transcription Factor Interactome , 2019, Cell reports.
[14] Soon Gang Choi,et al. Maximizing binary interactome mapping with a minimal number of assays , 2019, Nature Communications.
[15] Kara Dolinski,et al. The BioGRID interaction database: 2019 update , 2018, Nucleic Acids Res..
[16] Giulia Antonazzo,et al. FlyBase 2.0: the next generation , 2018, Nucleic Acids Res..
[17] N. Perrimon,et al. A cell atlas of the adult Drosophila midgut , 2018, bioRxiv.
[18] N. Perrimon,et al. The TORC1-Regulated CPA Complex Rewires an RNA Processing Network to Drive Autophagy and Metabolic Reprogramming. , 2018, Cell metabolism.
[19] S. Mohr. First in Fly: Drosophila Research and Biological Discovery , 2018, Science.
[20] Albert-László Barabási,et al. Network-based prediction of protein interactions , 2018, Nature Communications.
[21] M. Boutros,et al. RNA Interference (RNAi) Screening in Drosophila , 2018, Genetics.
[22] Mark Gerstein,et al. The ModERN Resource: Genome-Wide Binding Profiles for Hundreds of Drosophila and Caenorhabditis elegans Transcription Factors , 2017, Genetics.
[23] Yanhui Hu,et al. Molecular Interaction Search Tool (MIST): an integrated resource for mining gene and protein interaction data , 2017, Nucleic Acids Res..
[24] Almagro Armenteros. DeepLoc: prediction of protein subcellular localization using deep learning , 2017, Bioinform..
[25] Michael F. Wangler,et al. Model Organisms Facilitate Rare Disease Diagnosis and Therapeutic Research , 2017, Genetics.
[26] David Bilder,et al. Taking Stock of the Drosophila Research Ecosystem , 2017, Genetics.
[27] J. Yates,et al. The GAGA factor regulatory network: Identification of GAGA factor associated proteins , 2017, PloS one.
[28] Adam P. Rosebrock,et al. A global genetic interaction network maps a wiring diagram of cellular function , 2016, Science.
[29] N. Perrimon,et al. An Integrative Analysis of the InR/PI3K/Akt Network Identifies the Dynamic Response to Insulin Signaling. , 2016, Cell reports.
[30] V. Promponas,et al. iLIR database: A web resource for LIR motif-containing proteins in eukaryotes , 2016, Autophagy.
[31] Fidel Ramírez,et al. deepTools2: a next generation web server for deep-sequencing data analysis , 2016, Nucleic Acids Res..
[32] Anastasia Baryshnikova,et al. Systematic Functional Annotation and Visualization of Biological Networks , 2016, bioRxiv.
[33] Yanhui Hu,et al. GLAD: an Online Database of Gene List Annotation for Drosophila , 2015, Journal of genomics.
[34] Bridget E. Begg,et al. A Proteome-Scale Map of the Human Interactome Network , 2014, Cell.
[35] Alissa M. Resch,et al. DNA copy number evolution in Drosophila cell lines , 2014, Genome Biology.
[36] James B. Brown,et al. Comparative validation of the D. melanogaster modENCODE transcriptome annotation , 2014, Genome research.
[37] M. Carazzolle,et al. IIS – Integrated Interactome System: A Web-Based Platform for the Annotation, Analysis and Visualization of Protein-Metabolite-Gene-Drug Interactions by Integrating a Variety of Data Sources and Tools , 2014, PloS one.
[38] T. P. Neufeld,et al. Assays to monitor autophagy in Drosophila. , 2014, Methods.
[39] R. Finley,et al. Integrating the interactome and the transcriptome of Drosophila , 2014, BMC Bioinformatics.
[40] James B. Brown,et al. Diversity and dynamics of the Drosophila transcriptome , 2014, Nature.
[41] P. Georgiev,et al. Chromatin insulators and long‐distance interactions in Drosophila , 2014, FEBS letters.
[42] Rafael C. Jimenez,et al. The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases , 2013, Nucleic Acids Res..
[43] N. Perrimon,et al. The Hippo Signaling Pathway Interactome , 2013, Science.
[44] N. Perrimon,et al. Protein Complex–Based Analysis Framework for High-Throughput Data Sets , 2013, Science Signaling.
[45] R. Obar,et al. Drosophila Protein interaction Map (DPiM) , 2012, Fly.
[46] B. Faircloth,et al. Primer3—new capabilities and interfaces , 2012, Nucleic acids research.
[47] Rahul C. Deo,et al. Interpreting cancer genomes using systematic host perturbations by tumour virus proteins , 2012, Nature.
[48] Steven L Salzberg,et al. Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.
[49] Rafael C. Jimenez,et al. The IntAct molecular interaction database in 2012 , 2011, Nucleic Acids Res..
[50] Julian Mintseris,et al. A Protein Complex Network of Drosophila melanogaster , 2011, Cell.
[51] Bonnie Berger,et al. An integrative approach to ortholog prediction for disease-focused and other functional studies , 2011, BMC Bioinformatics.
[52] Dongmei Liu,et al. A protein network-guided screen for cell cycle regulators in Drosophila , 2011, BMC Systems Biology.
[53] Angela N. Brooks,et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE , 2011 .
[54] Sangwei Lu,et al. Yeast Two Hybrid Analyses Reveal Novel Binary Interactions between Human Cytomegalovirus-Encoded Virion Proteins , 2011, PloS one.
[55] Li Yang,et al. The transcriptional diversity of 25 Drosophila cell lines. , 2011, Genome research.
[56] Stephen Guest,et al. DroID 2011: a comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila , 2010, Nucleic Acids Res..
[57] A. Teleman,et al. dDOR Is an EcR Coactivator that Forms a Feed-Forward Loop Connecting Insulin and Ecdysone Signaling , 2010, Current Biology.
[58] C. Bakal,et al. Genomic screening with RNAi: results and challenges. , 2010, Annual review of biochemistry.
[59] S. Gygi,et al. Network organization of the human autophagy system , 2010, Nature.
[60] C. Glass,et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.
[61] Christopher D. Brown,et al. A Comprehensive Map of Insulator Elements for the Drosophila Genome , 2010, PLoS genetics.
[62] T. P. Neufeld,et al. A Genetic Screen in Drosophila Reveals Novel Cytoprotective Functions of the Autophagy-Lysosome Pathway , 2009, PloS one.
[63] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[64] M. Vidal,et al. Literature-curated protein interaction datasets , 2009, Nature Methods.
[65] A. Barabasi,et al. An empirical framework for binary interactome mapping , 2008, Nature Methods.
[66] Julie M. Sahalie,et al. An experimentally derived confidence score for binary protein-protein interactions , 2008, Nature Methods.
[67] Guozhen Liu,et al. DroID: the Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions , 2008, BMC Genomics.
[68] A. Barabasi,et al. High-Quality Binary Protein Interaction Map of the Yeast Interactome Network , 2008, Science.
[69] Clifford A. Meyer,et al. Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.
[70] Sheila M. Thomas,et al. Genetic interactions between Drosophila melanogaster Atg1 and paxillin reveal a role for paxillin in autophagosome formation , 2008, Autophagy.
[71] T. P. Neufeld,et al. Direct Induction of Autophagy by Atg1 Inhibits Cell Growth and Induces Apoptotic Cell Death , 2007, Current Biology.
[72] R. Chanet,et al. Protein interaction mapping: a Drosophila case study. , 2005, Genome research.
[73] Bernardo A Mangiola,et al. A Drosophila protein-interaction map centered on cell-cycle regulators , 2004, Genome Biology.
[74] James R. Knight,et al. A Protein Interaction Map of Drosophila melanogaster , 2003, Science.
[75] P. Shannon,et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.
[76] E. Myers,et al. Finishing a whole-genome shotgun: Release 3 of the Drosophila melanogaster euchromatic genome sequence , 2002, Genome Biology.
[77] G. Rubin,et al. A Drosophila full-length cDNA resource , 2002, Genome Biology.
[78] Daniel St Johnston,et al. The art and design of genetic screens: Drosophila melanogaster , 2002, Nature Reviews Genetics.
[79] Jan Tavernier,et al. Design and application of a cytokine-receptor-based interaction trap , 2001, Nature Cell Biology.
[80] Stephen M. Mount,et al. The genome sequence of Drosophila melanogaster. , 2000, Science.
[81] P. Schedl,et al. The Zw5 protein, a component of the scs chromatin domain boundary, is able to block enhancer-promoter interaction. , 1999, Genes & development.
[82] Kieran McGovern,et al. First to Fly , 1995 .
[83] J. Mattick,et al. 'Touchdown' PCR to circumvent spurious priming during gene amplification. , 1991, Nucleic acids research.
[84] Ole Winther,et al. DeepLoc: prediction of protein subcellular localization using deep learning , 2017, Bioinform..
[85] I. Lemmens,et al. MAPPIT, a mammalian two-hybrid method for in-cell detection of protein-protein interactions. , 2015, Methods in molecular biology.
[86] E. Baehrecke,et al. Autophagy and cell death in the fly. , 2014, Methods in enzymology.
[87] R. Obar,et al. Drosophila Protein interaction Map (DPiM): A paradigm for metazoan protein complex interactions , 2012 .
[88] S. Celniker,et al. Development of expression-ready constructs for generation of proteomic libraries. , 2011, Methods in molecular biology.
[89] Nektarios Tavernarakis,et al. Autophagy and cell death in model organisms , 2009, Cell Death and Differentiation.
[90] Keun-Joon Park,et al. Nucleic Acids Research Advance Access published May 21, 2007 WoLF PSORT: protein localization predictor , 2007 .
[91] K. Nakai,et al. PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. , 1999, Trends in biochemical sciences.