Inferring differential subcellular localisation in comparative spatial proteomics using BANDLE
暂无分享,去创建一个
[1] Hee Min Choi,et al. The Polya-Gamma Gibbs sampler for Bayesian logistic regression is uniformly ergodic , 2013 .
[2] Kathryn S. Lilley,et al. Assessing sub-cellular resolution in spatial proteomics experiments , 2019, Current opinion in chemical biology.
[3] G. S. Watson,et al. Smooth regression analysis , 1964 .
[4] J. Alwine,et al. Viral effects on metabolism: changes in glucose and glutamine utilization during human cytomegalovirus infection. , 2011, Trends in microbiology.
[5] S. Jonjić,et al. Cytomegaloviruses Exploit Recycling Rab Proteins in the Sequential Establishment of the Assembly Compartment , 2018, Front. Cell Dev. Biol..
[6] I. Hamachi,et al. Chemical proteomics for subcellular proteome analysis. , 2019, Current opinion in chemical biology.
[7] P. Pellett,et al. Spatial Relationships between Markers for Secretory and Endosomal Machinery in Human Cytomegalovirus-Infected Cells versus Those in Uninfected Cells , 2011, Journal of Virology.
[8] M. Robinson,et al. Characterization of a fourth adaptor-related protein complex. , 1999, Molecular biology of the cell.
[9] S. Gygi,et al. Multiplexed Phosphoproteomic Profiling Using Titanium Dioxide and Immunoaffinity Enrichments Reveals Complementary Phosphorylation Events. , 2017, Journal of proteome research.
[10] J. Cox,et al. Global, quantitative and dynamic mapping of protein subcellular localization , 2016, eLife.
[11] D. Segal,et al. Adaptor protein complex 4 deficiency: a paradigm of childhood-onset hereditary spastic paraplegia caused by defective protein trafficking. , 2020, Human molecular genetics.
[12] Jeffrey E. Lee,et al. The Secret Life of Viral Entry Glycoproteins: Moonlighting in Immune Evasion , 2013, PLoS pathogens.
[13] Xiaojun Ding,et al. Protein kinase WNK3 regulates the neuronal splicing factor Fox-1 , 2012, Proceedings of the National Academy of Sciences.
[14] Rui Paulo. Default priors for Gaussian processes , 2005 .
[15] J. Hirst,et al. Adaptor Protein Complexes AP‐4 and AP‐5: New Players in Endosomal Trafficking and Progressive Spastic Paraplegia , 2013, Traffic.
[16] Oliver M. Crook,et al. A subcellular atlas of Toxoplasma reveals the functional context of the proteome , 2020, bioRxiv.
[17] E. Nadaraya. On Estimating Regression , 1964 .
[18] Raphael Gottardo,et al. Orchestrating high-throughput genomic analysis with Bioconductor , 2015, Nature Methods.
[19] I. Cristea,et al. The life cycle and pathogenesis of human cytomegalovirus infection: lessons from proteomics , 2014, Expert review of proteomics.
[20] Y. Benjamini,et al. Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .
[21] Edward L. Huttlin,et al. Human cytomegalovirus interactome analysis identifies degradation hubs, domain associations and viral protein functions , 2019, eLife.
[22] P. Angel,et al. AP-1 subunits: quarrel and harmony among siblings , 2004, Journal of Cell Science.
[23] Bradley Efron,et al. Large-scale inference , 2010 .
[24] R. Seger,et al. The MAPK cascades: signaling components, nuclear roles and mechanisms of nuclear translocation. , 2011, Biochimica et biophysica acta.
[25] A. Yurochko. Human cytomegalovirus modulation of signal transduction. , 2008, Current topics in microbiology and immunology.
[26] M. Trotter,et al. The effect of organelle discovery upon sub-cellular protein localisation. , 2013, Journal of proteomics.
[27] E. Huttlin,et al. High-Definition Analysis of Host Protein Stability during Human Cytomegalovirus Infection Reveals Antiviral Factors and Viral Evasion Mechanisms , 2018, Cell host & microbe.
[28] Lorenz Wernisch,et al. Clusternomics: Integrative context-dependent clustering for heterogeneous datasets , 2017, bioRxiv.
[29] A. Motley,et al. Clathrin-mediated endocytosis in AP-2–depleted cells , 2003, The Journal of cell biology.
[30] Chad D Williamson,et al. Trafficking of UL37 Proteins into Mitochondrion-Associated Membranes during Permissive Human Cytomegalovirus Infection , 2010, Journal of Virology.
[31] Roger Woodard,et al. Interpolation of Spatial Data: Some Theory for Kriging , 1999, Technometrics.
[32] Emma L. Smith,et al. The Regulation of NF-κB Subunits by Phosphorylation , 2016, Cells.
[33] Thomas Burger,et al. Mass-spectrometry-based spatial proteomics data analysis using pRoloc and pRolocdata , 2014, Bioinform..
[34] M. Robinson. Forty Years of Clathrin‐coated Vesicles , 2015, Traffic.
[35] D. Ledbetter,et al. Adaptor protein complex-4 (AP-4) deficiency causes a novel autosomal recessive cerebral palsy syndrome with microcephaly and intellectual disability , 2010, Journal of Medical Genetics.
[36] P. Lehner,et al. Latency, chromatin remodeling, and reactivation of human cytomegalovirus in the dendritic cells of healthy carriers. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[37] Kathryn S. Lilley,et al. Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics , 2015, bioRxiv.
[38] I. Cristea,et al. A Portrait of the Human Organelle Proteome In Space and Time during Cytomegalovirus Infection. , 2016, Cell systems.
[39] B. Cubelos,et al. Immunohistochemical localization of the amino acid transporter SNAT2 in the rat brain , 2005, Neuroscience.
[40] Morton B. Brown. 400: A Method for Combining Non-Independent, One-Sided Tests of Significance , 1975 .
[41] I. Cristea,et al. Human cytomegalovirus tegument protein pUL83 inhibits IFI16-mediated DNA sensing for immune evasion. , 2013, Cell host & microbe.
[42] Jens Milbradt,et al. Cytomegaloviral proteins pUL50 and pUL53 are associated with the nuclear lamina and interact with cellular protein kinase C. , 2007, The Journal of general virology.
[43] Edward L. Huttlin,et al. Quantitative Temporal Viromics: An Approach to Investigate Host-Pathogen Interaction , 2014, Cell.
[44] T. Shenk,et al. Human Cytomegalovirus pUS24 Is a Virion Protein That Functions Very Early in the Replication Cycle , 2006, Journal of Virology.
[45] S. Copley,et al. An evolutionary perspective on protein moonlighting. , 2014, Biochemical Society transactions.
[46] M. Cannon,et al. Review of cytomegalovirus seroprevalence and demographic characteristics associated with infection , 2010, Reviews in medical virology.
[47] V. Ganapathy,et al. Primary structure, functional characteristics and tissue expression pattern of human ATA2, a subtype of amino acid transport system A. , 2000, Biochimica et biophysica acta.
[48] S. Oliver,et al. The subcellular organisation of Saccharomyces cerevisiae , 2019, Current opinion in chemical biology.
[49] P. Pellett,et al. Three-Dimensional Structure of the Human Cytomegalovirus Cytoplasmic Virion Assembly Complex Includes a Reoriented Secretory Apparatus , 2007, Journal of Virology.
[50] David B. Dunson,et al. Bayesian consensus clustering , 2013, Bioinform..
[51] S. Tooze,et al. Axonal autophagosome maturation defect through failure of ATG9A sorting underpins pathology in AP-4 deficiency syndrome , 2019, Autophagy.
[52] Bailey K. Fosdick,et al. Modern Statistics for Modern Biology , 2020 .
[53] Michael Boeckh,et al. The impact of cytomegalovirus serostatus of donor and recipient before hematopoietic stem cell transplantation in the era of antiviral prophylaxis and preemptive therapy. , 2004, Blood.
[54] O. Frings,et al. SubCellBarCode: Proteome-wide Mapping of Protein Localization and Relocalization. , 2019, Molecular cell.
[55] J. Alwine. The Human Cytomegalovirus Assembly Compartment: A Masterpiece of Viral Manipulation of Cellular Processes That Facilitates Assembly and Egress , 2012, PLoS pathogens.
[56] Victor De Oliveira,et al. Objective Bayesian analysis of spatial data with measurement error , 2007 .
[57] Haavard Rue,et al. Constructing Priors that Penalize the Complexity of Gaussian Random Fields , 2015, Journal of the American Statistical Association.
[58] A. McKenna,et al. Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data , 2017, bioRxiv.
[59] James G. Scott,et al. Bayesian Inference for Logistic Models Using Pólya–Gamma Latent Variables , 2012, 1205.0310.
[60] Kathryn S. Lilley,et al. MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation , 2012, Bioinform..
[61] Laurent Gatto,et al. A Bioconductor workflow for the Bayesian analysis of spatial proteomics , 2019, F1000Research.
[62] T. Compton,et al. Virus entry and innate immune activation. , 2008, Current topics in microbiology and immunology.
[63] J. Bonifacino,et al. Altered distribution of ATG9A and accumulation of axonal aggregates in neurons from a mouse model of AP-4 deficiency syndrome , 2018, PLoS genetics.
[64] Oliver M. Crook,et al. Combining LOPIT with differential ultracentrifugation for high-resolution spatial proteomics , 2019, Nature Communications.
[65] Carl E. Rasmussen,et al. Gaussian processes for machine learning , 2005, Adaptive computation and machine learning.
[66] Casper F Winsnes,et al. Deep learning is combined with massive-scale citizen science to improve large-scale image classification , 2018, Nature Biotechnology.
[67] J. Shabanowitz,et al. Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae , 2002, Nature Biotechnology.
[68] Oliver M Crook,et al. Moving Profiling Spatial Proteomics Beyond Discrete Classification , 2020, Proteomics.
[69] Daniel J. Wilson,et al. The harmonic mean p-value for combining dependent tests , 2019, Proceedings of the National Academy of Sciences.
[70] P. Green,et al. On Bayesian Analysis of Mixtures with an Unknown Number of Components (with discussion) , 1997 .
[71] Sylvia Richardson,et al. Markov Chain Monte Carlo in Practice , 1997 .
[72] Toby J Gibson,et al. Cell regulation: determined to signal discrete cooperation. , 2009, Trends in biochemical sciences.
[73] Laurent Gatto,et al. Using hyperLOPIT to perform high-resolution mapping of the spatial proteome , 2017, Nature Protocols.
[74] V. Dall’Asta,et al. SNAT2 silencing prevents the osmotic induction of transport system A and hinders cell recovery from hypertonic stress , 2005, FEBS letters.
[75] N. Krogan,et al. Cullin E3 Ligases and Their Rewiring by Viral Factors , 2014, Biomolecules.
[76] T. L. Archuleta,et al. AP-4 vesicles contribute to spatial control of autophagy via RUSC-dependent peripheral delivery of ATG9A , 2018, Nature Communications.
[77] K. Tanaka,et al. Microtubule Network Facilitates Nuclear Targeting of Human Cytomegalovirus Capsid , 2003, Journal of Virology.
[78] I. Cristea,et al. Diverse mechanisms evolved by DNA viruses to inhibit early host defenses , 2016, Critical reviews in biochemistry and molecular biology.
[79] Scott W. Linderman,et al. Dependent Multinomial Models Made Easy: Stick-Breaking with the Polya-gamma Augmentation , 2015, NIPS.
[80] J. Cox,et al. A Mass Spectrometry-Based Approach for Mapping Protein Subcellular Localization Reveals the Spatial Proteome of Mouse Primary Neurons , 2017, Cell reports.
[81] J. Bonifacino,et al. AP-4 mediates export of ATG9A from the trans-Golgi network to promote autophagosome formation , 2017, Proceedings of the National Academy of Sciences.
[82] L. Gatto,et al. A draft map of the mouse pluripotent stem cell spatial proteome , 2016, Nature Communications.
[83] L. L. Bailey,et al. Quantifying climate sensitivity and climate-driven change in North American amphibian communities , 2018, Nature Communications.
[84] A. Hoischen,et al. TMEM199 Deficiency Is a Disorder of Golgi Homeostasis Characterized by Elevated Aminotransferases, Alkaline Phosphatase, and Cholesterol and Abnormal Glycosylation. , 2016, American journal of human genetics.
[85] F. Conti,et al. Localization of the Na+-coupled neutral amino acid transporter 2 in the cerebral cortex , 2006, Neuroscience.
[86] Kathryn S Lilley,et al. Mapping organelle proteins and protein complexes in Drosophila melanogaster. , 2009, Journal of proteome research.
[87] Zoubin Ghahramani,et al. Bayesian correlated clustering to integrate multiple datasets , 2012, Bioinform..
[88] Domènec Farré,et al. A Prominent Role of the Human Cytomegalovirus UL8 Glycoprotein in Restraining Proinflammatory Cytokine Production by Myeloid Cells at Late Times during Infection , 2018, Journal of Virology.
[89] David B. Dunson,et al. Bayesian Data Analysis , 2010 .
[90] Van Der Vaart,et al. Adaptive Bayesian estimation using a Gaussian random field with inverse Gamma bandwidth , 2009, 0908.3556.
[91] Cécile Viboud,et al. Deploying digital health data to optimize influenza surveillance at national and local scales , 2018, PLoS Comput. Biol..
[92] H. Rue,et al. An explicit link between Gaussian fields and Gaussian Markov random fields: the stochastic partial differential equation approach , 2011 .
[93] Marco Y. Hein,et al. Decoding Human Cytomegalovirus , 2012, Science.
[94] Pamela A. Silver,et al. Nuclear transport and cancer: from mechanism to intervention , 2004, Nature Reviews Cancer.
[95] R. Kalejta,et al. Proteasome-dependent, ubiquitin-independent degradation of Daxx by the viral pp71 protein in human cytomegalovirus-infected cells. , 2007, Virology.
[96] M. von Zastrow,et al. Subcellular localization of MC4R with ADCY3 at neuronal primary cilia underlies a common pathway for genetic predisposition to obesity , 2017, Nature Genetics.
[97] Steven P. Miller,et al. Defining the clinical, molecular and imaging spectrum of adaptor protein complex 4-associated hereditary spastic paraplegia. , 2020, Brain : a journal of neurology.
[98] M. Debruyne,et al. Minimum covariance determinant , 2010 .
[99] B. Chait,et al. Human Cytomegalovirus pUL83 Stimulates Activity of the Viral Immediate-Early Promoter through Its Interaction with the Cellular IFI16 Protein , 2010, Journal of Virology.
[100] L. Gatto,et al. Proteome Mapping of a Cyanobacterium Reveals Distinct Compartment Organization and Cell-Dispersed Metabolism , 2019, Plant Physiology.
[101] E. Yang,et al. Human Cytomegalovirus Primase UL70 Specifically Interacts with Cellular Factor Snapin , 2011, Journal of Virology.
[102] P. Walther,et al. Human cytomegalovirus-induced reduction of extracellular matrix proteins in vascular smooth muscle cell cultures: a pathomechanism in vasculopathies? , 2006, The Journal of general virology.
[103] A. Ballabio,et al. The complex relationship between TFEB transcription factor phosphorylation and subcellular localization , 2018, The EMBO journal.
[104] Laurent Gatto,et al. A semi-supervised Bayesian approach for simultaneous protein sub-cellular localisation assignment and novelty detection , 2020, PLoS computational biology.
[105] I. Cristea,et al. A Targeted Spatial-Temporal Proteomics Approach Implicates Multiple Cellular Trafficking Pathways in Human Cytomegalovirus Virion Maturation* , 2009, Molecular & Cellular Proteomics.
[106] Margaret S Robinson,et al. Role of the AP-5 adaptor protein complex in late endosome-to-Golgi retrieval , 2018, PLoS biology.
[107] 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..
[108] J. Berger,et al. Objective Bayesian Analysis of Spatially Correlated Data , 2001 .
[109] T. Stamminger,et al. Intracellular Trafficking of the Human Cytomegalovirus-Encoded 7-trans-Membrane Protein Homologs pUS27 and pUL78 during Viral Infection: A Comparative Analysis , 2014, Viruses.
[110] I. Rigoutsos,et al. Reevaluation of human cytomegalovirus coding potential , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[111] J. Kost,et al. Combining dependent P-values , 2002 .
[112] F. Roland,et al. Global CO2 emissions from dry inland waters share common drivers across ecosystems , 2020, Nature Communications.
[113] Guinevere L. Grice,et al. The vacuolar-ATPase complex and assembly factors, TMEM199 and CCDC115, control HIF1α prolyl hydroxylation by regulating cellular iron levels , 2017, eLife.
[114] Constance J Jeffery,et al. Moonlighting proteins--an update. , 2009, Molecular bioSystems.
[115] R. Kalejta. Functions of human cytomegalovirus tegument proteins prior to immediate early gene expression. , 2008, Current topics in microbiology and immunology.
[116] M. Gstaiger,et al. Open Reading Frame UL26 of Human Cytomegalovirus Encodes a Novel Tegument Protein That Contains a Strong Transcriptional Activation Domain , 2002, Journal of Virology.
[117] Juan Antonio Vizcaíno,et al. Organelle proteomics experimental designs and analysis , 2010, Proteomics.
[118] Jean YH Yang,et al. Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.
[119] D. Lie,et al. Phosphorylation Modulates the Subcellular Localization of SOX11 , 2018, Front. Mol. Neurosci..
[120] M. Vihinen,et al. Prediction of disease-related mutations affecting protein localization , 2009, BMC Genomics.
[121] Laurent Gatto,et al. A Foundation for Reliable Spatial Proteomics Data Analysis* , 2014, Molecular & Cellular Proteomics.
[122] J. Bonifacino,et al. Association of the AP-3 adaptor complex with clathrin. , 1998, Science.
[123] T. Shenk,et al. Human Cytomegalovirus UL28 and UL29 Open Reading Frames Encode a Spliced mRNA and Stimulate Accumulation of Immediate-Early RNAs , 2009, Journal of Virology.
[124] W. Gibson,et al. Structure and formation of the cytomegalovirus virion. , 2008, Current topics in microbiology and immunology.
[125] David B. Dunson,et al. Bayesian learning of joint distributions of objects , 2013, AISTATS.
[126] I. Cristea,et al. Orchestration of protein acetylation as a toggle for cellular defense and virus replication , 2018, Nature Communications.
[127] J. Alwine,et al. Role of the Endoplasmic Reticulum Chaperone BiP, SUN Domain Proteins, and Dynein in Altering Nuclear Morphology during Human Cytomegalovirus Infection , 2010, Journal of Virology.
[128] E. Zandi,et al. AP-1 function and regulation. , 1997, Current opinion in cell biology.
[129] F. White,et al. Phosphoproteomic analysis of rat liver by high capacity IMAC and LC-MS/MS. , 2006, Journal of proteome research.