Yeast Resource Center | Publications
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Publications

Latest YRC Publications

(see all in PubMed)

  1. Zimmerman, SG et al. (2017) Proteomics Analysis Identifies Orthologs of Human Chitinase-Like Proteins as Inducers of Tube-Morphogenesis Defects in Drosophila. Genetics :. PMID:28404605
  2. Conkar, D et al. (2017) The centriolar satellite protein CCDC66 interacts with CEP290 and functions in cilium formation and trafficking. J. Cell. Sci. 130 (8):1450-1462. PMID:28235840
  3. Matthews, ML et al. (2017) Chemoproteomic profiling and discovery of protein electrophiles in human cells. Nat Chem 9 (3):234-243. PMID:28221344
  4. Thakar, S et al. (2017) Evidence for opposing roles of Celsr3 and Vangl2 in glutamatergic synapse formation. Proc. Natl. Acad. Sci. U.S.A. 114 (4):E610-E618. PMID:28057866
  5. Hickox, AE et al. (2017) Global Analysis of Protein Expression of Inner Ear Hair Cells. J. Neurosci. 37 (5):1320-1339. PMID:28039372
  6. Luhtala, N et al. (2017) Secreted Glioblastoma Nanovesicles Contain Intracellular Signaling Proteins and Active Ras Incorporated in a Farnesylation-dependent Manner. J. Biol. Chem. 292 (2):611-628. PMID:27909058
  7. Pankow, S et al. (2016) Deep interactome profiling of membrane proteins by co-interacting protein identification technology. Nat Protoc 11 (12):2515-2528. PMID:27854364
  8. Timmins-Schiffman, E et al. (2017) Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns. ISME J 11 (2):309-314. PMID:27824341
  9. Berger, S et al. (2016) Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer. Elife 5 :. PMID:27805565
  10. Mita, P et al. (2016) URI Regulates KAP1 Phosphorylation and Transcriptional Repression via PP2A Phosphatase in Prostate Cancer Cells. J. Biol. Chem. 291 (49):25516-25528. PMID:27780869
  11. Bereman, MS et al. (2016) An Automated Pipeline to Monitor System Performance in Liquid Chromatography-Tandem Mass Spectrometry Proteomic Experiments. J. Proteome Res. 15 (12):4763-4769. PMID:27700092
  12. Shan, CM et al. (2016) A histone H3K9M mutation traps histone methyltransferase Clr4 to prevent heterochromatin spreading. Elife 5 :. PMID:27648579
  13. The, M et al. (2016) Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0. J. Am. Soc. Mass Spectrom. 27 (11):1719-1727. PMID:27572102
  14. Chatterjee, S et al. (2016) A comprehensive and scalable database search system for metaproteomics. BMC Genomics 17 (1):642. PMID:27528457
  15. Halloran, JT et al. (2016) Dynamic Bayesian Network for Accurate Detection of Peptides from Tandem Mass Spectra. J. Proteome Res. 15 (8):2749-59. PMID:27397138
  16. May, DH et al. (2016) An Alignment-Free "Metapeptide" Strategy for Metaproteomic Characterization of Microbiome Samples Using Shotgun Metagenomic Sequencing. J. Proteome Res. 15 (8):2697-705. PMID:27396978
  17. Gamble, CE et al. (2016) Adjacent Codons Act in Concert to Modulate Translation Efficiency in Yeast. Cell 166 (3):679-90. PMID:27374328
  18. Hsia, Y et al. (2016) Design of a hyperstable 60-subunit protein dodecahedron. [corrected]. Nature 535 (7610):136-9. PMID:27309817
  19. Riffle, M et al. (2016) ProXL (Protein Cross-Linking Database): A Platform for Analysis, Visualization, and Sharing of Protein Cross-Linking Mass Spectrometry Data. J. Proteome Res. 15 (8):2863-70. PMID:27302480
  20. Zhao, X et al. (2016) Circadian Amplitude Regulation via FBXW7-Targeted REV-ERBα Degradation. Cell 165 (7):1644-57. PMID:27238018
  21. Lyon, AS et al. (2016) Higher-order oligomerization of Spc110p drives γ-tubulin ring complex assembly. Mol. Biol. Cell 27 (14):2245-58. PMID:27226487
  22. Homer, CM et al. (2016) Intracellular Action of a Secreted Peptide Required for Fungal Virulence. Cell Host Microbe 19 (6):849-64. PMID:27212659
  23. Pedros, C et al. (2016) A TRAF-like motif of the inducible costimulator ICOS controls development of germinal center TFH cells via the kinase TBK1. Nat. Immunol. 17 (7):825-33. PMID:27135603
  24. Shrestha, E et al. (2016) Poly(ADP-ribose) Polymerase 1 Represses Liver X Receptor-mediated ABCA1 Expression and Cholesterol Efflux in Macrophages. J. Biol. Chem. 291 (21):11172-84. PMID:27026705
  25. Lavallée-Adam, M et al. (2016) Using PSEA-Quant for Protein Set Enrichment Analysis of Quantitative Mass Spectrometry-Based Proteomics. Curr Protoc Bioinformatics 53 :13.28.1-16. PMID:27010334
  26. Ma, J et al. (2016) Improved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides. Anal. Chem. 88 (7):3967-75. PMID:27010111
  27. Wang, J et al. (2016) The proper connection between shelterin components is required for telomeric heterochromatin assembly. Genes Dev. 30 (7):827-39. PMID:26988418
  28. Greenberg, CH et al. (2016) Structure of γ-tubulin small complex based on a cryo-EM map, chemical cross-links, and a remotely related structure. J. Struct. Biol. 194 (3):303-10. PMID:26968363
  29. Yonashiro, R et al. (2016) The Rqc2/Tae2 subunit of the ribosome-associated quality control (RQC) complex marks ribosome-stalled nascent polypeptide chains for aggregation. Elife 5 :e11794. PMID:26943317
  30. Rich, MS et al. (2016) Comprehensive Analysis of the SUL1 Promoter of Saccharomyces cerevisiae. Genetics 203 (1):191-202. PMID:26936925
  31. Zich, J et al. (2016) Mps1Mph1 Kinase Phosphorylates Mad3 to Inhibit Cdc20Slp1-APC/C and Maintain Spindle Checkpoint Arrests. PLoS Genet. 12 (2):e1005834. PMID:26882497
  32. Savas, JN et al. (2016) Proteomic Analysis of Protein Turnover by Metabolic Whole Rodent Pulse-Chase Isotopic Labeling and Shotgun Mass Spectrometry Analysis. Methods Mol. Biol. 1410 :293-304. PMID:26867752
  33. Bollinger, JG et al. (2016) Selecting Optimal Peptides for Targeted Proteomic Experiments in Human Plasma Using In Vitro Synthesized Proteins as Analytical Standards. Methods Mol. Biol. 1410 :207-21. PMID:26867746
  34. Hoggard, T et al. (2016) High Throughput Analyses of Budding Yeast ARSs Reveal New DNA Elements Capable of Conferring Centromere-Independent Plasmid Propagation. G3 (Bethesda) 6 (4):993-1012. PMID:26865697
  35. Borges, MH et al. (2016) Venomous extract protein profile of Brazilian tarantula Grammostola iheringi: searching for potential biotechnological applications. J Proteomics 136 :35-47. PMID:26828374
  36. Kim, TK et al. (2016) Ixodes scapularis Tick Saliva Proteins Sequentially Secreted Every 24 h during Blood Feeding. PLoS Negl Trop Dis 10 (1):e0004323. PMID:26751078
  37. Feng, J et al. (2015) A general strategy to construct small molecule biosensors in eukaryotes. Elife 4 :. PMID:26714111
  38. Taylor, ND et al. (2016) Engineering an allosteric transcription factor to respond to new ligands. Nat. Methods 13 (2):177-83. PMID:26689263
  39. Alessi, AF et al. (2015) Casein kinase II promotes target silencing by miRISC through direct phosphorylation of the DEAD-box RNA helicase CGH-1. Proc. Natl. Acad. Sci. U.S.A. 112 (52):E7213-22. PMID:26669440
  40. Buffon, G et al. (2016) Physiological and Molecular Alterations Promoted by Schizotetranychus oryzae Mite Infestation in Rice Leaves. J. Proteome Res. 15 (2):431-46. PMID:26667653
  41. Carvalho, PC et al. (2016) Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0. Nat Protoc 11 (1):102-17. PMID:26658470
  42. Pankow, S et al. (2015) ∆F508 CFTR interactome remodelling promotes rescue of cystic fibrosis. Nature 528 (7583):510-6. PMID:26618866
  43. Zelter, A et al. (2015) The molecular architecture of the Dam1 kinetochore complex is defined by cross-linking based structural modelling. Nat Commun 6 :8673. PMID:26560693
  44. Kawahara, R et al. (2016) A targeted proteomic strategy for the measurement of oral cancer candidate biomarkers in human saliva. Proteomics 16 (1):159-73. PMID:26552850
  45. Sun, S et al. (2015) IRE1α is an endogenous substrate of endoplasmic-reticulum-associated degradation. Nat. Cell Biol. 17 (12):1546-55. PMID:26551274
  46. Young, DL et al. (2015) The role of functional data in interpreting the effects of genetic variation. Mol. Biol. Cell 26 (22):3904-8. PMID:26543197
  47. Silva, E et al. (2016) Ccdc11 is a novel centriolar satellite protein essential for ciliogenesis and establishment of left-right asymmetry. Mol. Biol. Cell 27 (1):48-63. PMID:26538025
  48. He, L et al. (2015) Extracting Accurate Precursor Information for Tandem Mass Spectra by RawConverter. Anal. Chem. 87 (22):11361-7. PMID:26499134
  49. Payen, C et al. (2016) Experimental Evolution and Resequencing Analysis of Yeast. Methods Mol. Biol. 1361 :361-74. PMID:26483032
  50. D'Amico, D et al. (2015) Non-canonical Hedgehog/AMPK-Mediated Control of Polyamine Metabolism Supports Neuronal and Medulloblastoma Cell Growth. Dev. Cell 35 (1):21-35. PMID:26460945
  51. McClatchy, DB et al. (2015) Pulsed Azidohomoalanine Labeling in Mammals (PALM) Detects Changes in Liver-Specific LKB1 Knockout Mice. J. Proteome Res. 14 (11):4815-22. PMID:26445171
  52. Callaci, S et al. (2015) Phosphoregulation of the C. elegans cadherin-catenin complex. Biochem. J. 472 (3):339-52. PMID:26443865
  53. Kudalkar, EM et al. (2015) Regulation of outer kinetochore Ndc80 complex-based microtubule attachments by the central kinetochore Mis12/MIND complex. Proc. Natl. Acad. Sci. U.S.A. 112 (41):E5583-9. PMID:26430240
  54. Kersten, RD et al. (2015) Mechanism-Based Post-Translational Modification and Inactivation in Terpene Synthases. ACS Chem. Biol. 10 (11):2501-11. PMID:26378620
  55. Xia, HG et al. (2015) Degradation of HK2 by chaperone-mediated autophagy promotes metabolic catastrophe and cell death. J. Cell Biol. 210 (5):705-16. PMID:26323688
  56. Tang, B et al. (2015) Fmr1 deficiency promotes age-dependent alterations in the cortical synaptic proteome. Proc. Natl. Acad. Sci. U.S.A. 112 (34):E4697-706. PMID:26307763
  57. Bustos, F et al. (2015) NEDD4 Regulates PAX7 Levels Promoting Activation of the Differentiation Program in Skeletal Muscle Precursors. Stem Cells 33 (10):3138-51. PMID:26304770
  58. Savas, JN et al. (2015) The Sorting Receptor SorCS1 Regulates Trafficking of Neurexin and AMPA Receptors. Neuron 87 (4):764-80. PMID:26291160
  59. Yates, JR 3rd et al. (2015) Pivotal role of computers and software in mass spectrometry - SEQUEST and 20 years of tandem MS database searching. J. Am. Soc. Mass Spectrom. 26 (11):1804-13. PMID:26286455
  60. Dumesic, PA et al. (2015) Noncanoncial signal recognition particle RNAs in a major eukaryotic phylum revealed by purification of SRP from the human pathogen Cryptococcus neoformans. Nucleic Acids Res. 43 (18):9017-27. PMID:26275773
  61. Sanders, SS et al. (2015) Curation of the Mammalian Palmitoylome Indicates a Pivotal Role for Palmitoylation in Diseases and Disorders of the Nervous System and Cancers. PLoS Comput. Biol. 11 (8):e1004405. PMID:26275289
  62. Das, M et al. (2015) Phosphorylation-dependent inhibition of Cdc42 GEF Gef1 by 14-3-3 protein Rad24 spatially regulates Cdc42 GTPase activity and oscillatory dynamics during cell morphogenesis. Mol. Biol. Cell 26 (19):3520-34. PMID:26246599
  63. Ting, YS et al. (2015) Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data. Mol. Cell Proteomics 14 (9):2301-7. PMID:26217018
  64. Zhang, Y et al. (2015) ProteinInferencer: Confident protein identification and multiple experiment comparison for large scale proteomics projects. J Proteomics 129 :25-32. PMID:26196237
  65. López-Malo, M et al. (2015) Evolutionary engineering of a wine yeast strain revealed a key role of inositol and mannoprotein metabolism during low-temperature fermentation. BMC Genomics 16 :537. PMID:26194190
  66. Waadt, R et al. (2015) Identification of Open Stomata1-Interacting Proteins Reveals Interactions with Sucrose Non-fermenting1-Related Protein Kinases2 and with Type 2A Protein Phosphatases That Function in Abscisic Acid Responses. Plant Physiol. 169 (1):760-79. PMID:26175513
  67. Xu, T et al. (2015) ProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity. J Proteomics 129 :16-24. PMID:26171723
  68. Yimit, A et al. (2015) Genetic Regulation of Dna2 Localization During the DNA Damage Response. G3 (Bethesda) 5 (9):1937-44. PMID:26163422
  69. Thiffault, I et al. (2015) Recessive mutations in POLR1C cause a leukodystrophy by impairing biogenesis of RNA polymerase III. Nat Commun 6 :7623. PMID:26151409
  70. Fuhs, SR et al. (2015) Monoclonal 1- and 3-Phosphohistidine Antibodies: New Tools to Study Histidine Phosphorylation. Cell 162 (1):198-210. PMID:26140597
  71. Cajigas, I et al. (2015) Evf2 lncRNA/BRG1/DLX1 interactions reveal RNA-dependent inhibition of chromatin remodeling. Development 142 (15):2641-52. PMID:26138476
  72. Riffle, M et al. (2015) Visualization and dissemination of multidimensional proteomics data comparing protein abundance during Caenorhabditis elegans development. J. Am. Soc. Mass Spectrom. 26 (11):1827-36. PMID:26133526
  73. Noble, WS et al. (2015) Mass spectrometrists should search only for peptides they care about. Nat. Methods 12 (7):605-8. PMID:26125591
  74. Eng, JK et al. (2015) A deeper look into Comet--implementation and features. J. Am. Soc. Mass Spectrom. 26 (11):1865-74. PMID:26115965
  75. Tirloni, L et al. (2015) Saliva from nymph and adult females of Haemaphysalis longicornis: a proteomic study. Parasit Vectors 8 :338. PMID:26104117
  76. Searle, BC et al. (2015) Using Data Independent Acquisition (DIA) to Model High-responding Peptides for Targeted Proteomics Experiments. Mol. Cell Proteomics 14 (9):2331-40. PMID:26100116
  77. Kertesz-Farkas, A et al. (2015) Tandem Mass Spectrum Identification via Cascaded Search. J. Proteome Res. 14 (8):3027-38. PMID:26084232
  78. Lavallée-Adam, M et al. (2015) From raw data to biological discoveries: a computational analysis pipeline for mass spectrometry-based proteomics. J. Am. Soc. Mass Spectrom. 26 (11):1820-6. PMID:26002791
  79. Egertson, JD et al. (2015) Multiplexed peptide analysis using data-independent acquisition and Skyline. Nat Protoc 10 (6):887-903. PMID:25996789
  80. Rardin, MJ et al. (2015) MS1 Peptide Ion Intensity Chromatograms in MS2 (SWATH) Data Independent Acquisitions. Improving Post Acquisition Analysis of Proteomic Experiments. Mol. Cell Proteomics 14 (9):2405-19. PMID:25987414
  81. Peng, Y et al. (2015) Interaction of CK1δ with γTuSC ensures proper microtubule assembly and spindle positioning. Mol. Biol. Cell 26 (13):2505-18. PMID:25971801
  82. Varoquaux, N et al. (2015) Accurate identification of centromere locations in yeast genomes using Hi-C. Nucleic Acids Res. 43 (11):5331-9. PMID:25940625
  83. Jaschob, D et al. (2015) Mason: a JavaScript web site widget for visualizing and comparing annotated features in nucleotide or protein sequences. BMC Res Notes 8 :70. PMID:25884379
  84. Rauniyar, N et al. (2015) Quantitative Proteomics of Human Fibroblasts with I1061T Mutation in Niemann-Pick C1 (NPC1) Protein Provides Insights into the Disease Pathogenesis. Mol. Cell Proteomics 14 (7):1734-49. PMID:25873482
  85. McClatchy, DB et al. (2016) Global quantitative analysis of phosphorylation underlying phencyclidine signaling and sensorimotor gating in the prefrontal cortex. Mol. Psychiatry 21 (2):205-15. PMID:25869802
  86. Starita, LM et al. (2015) Massively Parallel Functional Analysis of BRCA1 RING Domain Variants. Genetics 200 (2):413-22. PMID:25823446
  87. Hoopmann, MR et al. (2015) Kojak: efficient analysis of chemically cross-linked protein complexes. J. Proteome Res. 14 (5):2190-8. PMID:25812159
  88. Papp, SJ et al. (2015) DNA damage shifts circadian clock time via Hausp-dependent Cry1 stabilization. Elife 4 :. PMID:25756610
  89. Cuperus, JT et al. (2015) A tetO Toolkit To Alter Expression of Genes in Saccharomyces cerevisiae. ACS Synth Biol 4 (7):842-52. PMID:25742460
  90. Khakhina, S et al. (2015) Control of Plasma Membrane Permeability by ABC Transporters. Eukaryotic Cell 14 (5):442-53. PMID:25724885
  91. Melamed, D et al. (2015) Combining natural sequence variation with high throughput mutational data to reveal protein interaction sites. PLoS Genet. 11 (2):e1004918. PMID:25671604
  92. Becker, E et al. (2015) Integrated RNA- and protein profiling of fermentation and respiration in diploid budding yeast provides insight into nutrient control of cell growth and development. J Proteomics 119 :30-44. PMID:25662576
  93. Tsai, HY et al. (2015) A ribonuclease coordinates siRNA amplification and mRNA cleavage during RNAi. Cell 160 (3):407-19. PMID:25635455
  94. Peng, Y et al. (2015) Casein kinase 1 promotes initiation of clathrin-mediated endocytosis. Dev. Cell 32 (2):231-40. PMID:25625208
  95. Schuh, AL et al. (2015) The VPS-20 subunit of the endosomal sorting complex ESCRT-III exhibits an open conformation in the absence of upstream activation. Biochem. J. 466 (3):625-37. PMID:25588614
  96. Hart, JR et al. (2015) The butterfly effect in cancer: a single base mutation can remodel the cell. Proc. Natl. Acad. Sci. U.S.A. 112 (4):1131-6. PMID:25583473
  97. Kitzman, JO et al. (2015) Massively parallel single-amino-acid mutagenesis. Nat. Methods 12 (3):203-6, 4 p following 206. PMID:25559584
  98. Dumesic, PA et al. (2015) Product binding enforces the genomic specificity of a yeast polycomb repressive complex. Cell 160 (1-2):204-18. PMID:25533783
  99. Xiao, H et al. (2015) The Pallbearer E3 ligase promotes actin remodeling via RAC in efferocytosis by degrading the ribosomal protein S6. Dev. Cell 32 (1):19-30. PMID:25533207
  100. Aguirre, A et al. (2014) In vivo activation of a conserved microRNA program induces mammalian heart regeneration. Cell Stem Cell 15 (5):589-604. PMID:25517466