Yeast Resource Center | Publications
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Publications

Latest YRC Publications

(see all in PubMed)

  1. Shan, CM et al. (2016) A histone H3K9M mutation traps histone methyltransferase Clr4 to prevent heterochromatin spreading. Elife 5 :. PMID:27648579
  2. 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
  3. Chatterjee, S et al. (2016) A comprehensive and scalable database search system for metaproteomics. BMC Genomics 17 (1):642. PMID:27528457
  4. 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
  5. 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
  6. Gamble, CE et al. (2016) Adjacent Codons Act in Concert to Modulate Translation Efficiency in Yeast. Cell 166 (3):679-90. PMID:27374328
  7. Hsia, Y et al. (2016) Design of a hyperstable 60-subunit protein icosahedron. Nature 535 (7610):136-9. PMID:27309817
  8. 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
  9. Zhao, X et al. (2016) Circadian Amplitude Regulation via FBXW7-Targeted REV-ERBα Degradation. Cell 165 (7):1644-57. PMID:27238018
  10. 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
  11. Homer, CM et al. (2016) Intracellular Action of a Secreted Peptide Required for Fungal Virulence. Cell Host Microbe 19 (6):849-64. PMID:27212659
  12. 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
  13. 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
  14. 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
  15. Ma, J et al. (2016) Improved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides. Anal. Chem. 88 (7):3967-75. PMID:27010111
  16. 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
  17. 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
  18. 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
  19. Rich, MS et al. (2016) Comprehensive Analysis of the SUL1 Promoter of Saccharomyces cerevisiae. Genetics 203 (1):191-202. PMID:26936925
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. Feng, J et al. (2015) A general strategy to construct small molecule biosensors in eukaryotes. Elife 4 :. PMID:26714111
  27. Taylor, ND et al. (2016) Engineering an allosteric transcription factor to respond to new ligands. Nat. Methods 13 (2):177-83. PMID:26689263
  28. 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
  29. 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
  30. 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
  31. Pankow, S et al. (2015) ∆F508 CFTR interactome remodelling promotes rescue of cystic fibrosis. Nature 528 (7583):510-6. PMID:26618866
  32. 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
  33. 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
  34. Sun, S et al. (2015) IRE1α is an endogenous substrate of endoplasmic-reticulum-associated degradation. Nat. Cell Biol. 17 (12):1546-55. PMID:26551274
  35. 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
  36. 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
  37. He, L et al. (2015) Extracting Accurate Precursor Information for Tandem Mass Spectra by RawConverter. Anal. Chem. 87 (22):11361-7. PMID:26499134
  38. Payen, C et al. (2016) Experimental Evolution and Resequencing Analysis of Yeast. Methods Mol. Biol. 1361 :361-74. PMID:26483032
  39. 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
  40. 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
  41. Callaci, S et al. (2015) Phosphoregulation of the C. elegans cadherin-catenin complex. Biochem. J. 472 (3):339-52. PMID:26443865
  42. 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
  43. Kersten, RD et al. (2015) Mechanism-Based Post-Translational Modification and Inactivation in Terpene Synthases. ACS Chem. Biol. 10 (11):2501-11. PMID:26378620
  44. 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
  45. 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
  46. 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
  47. Savas, JN et al. (2015) The Sorting Receptor SorCS1 Regulates Trafficking of Neurexin and AMPA Receptors. Neuron 87 (4):764-80. PMID:26291160
  48. 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
  49. 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
  50. 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
  51. 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
  52. 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
  53. 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
  54. 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
  55. 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
  56. Xu, T et al. (2015) ProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity. J Proteomics 129 :16-24. PMID:26171723
  57. Yimit, A et al. (2015) Genetic Regulation of Dna2 Localization During the DNA Damage Response. G3 (Bethesda) 5 (9):1937-44. PMID:26163422
  58. 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
  59. Fuhs, SR et al. (2015) Monoclonal 1- and 3-Phosphohistidine Antibodies: New Tools to Study Histidine Phosphorylation. Cell 162 (1):198-210. PMID:26140597
  60. Cajigas, I et al. (2015) Evf2 lncRNA/BRG1/DLX1 interactions reveal RNA-dependent inhibition of chromatin remodeling. Development 142 (15):2641-52. PMID:26138476
  61. 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
  62. Noble, WS et al. (2015) Mass spectrometrists should search only for peptides they care about. Nat. Methods 12 (7):605-8. PMID:26125591
  63. Eng, JK et al. (2015) A deeper look into Comet--implementation and features. J. Am. Soc. Mass Spectrom. 26 (11):1865-74. PMID:26115965
  64. Tirloni, L et al. (2015) Saliva from nymph and adult females of Haemaphysalis longicornis: a proteomic study. Parasit Vectors 8 :338. PMID:26104117
  65. 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
  66. Kertesz-Farkas, A et al. (2015) Tandem Mass Spectrum Identification via Cascaded Search. J. Proteome Res. 14 (8):3027-38. PMID:26084232
  67. 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
  68. Egertson, JD et al. (2015) Multiplexed peptide analysis using data-independent acquisition and Skyline. Nat Protoc 10 (6):887-903. PMID:25996789
  69. 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
  70. 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
  71. 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
  72. 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
  73. 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
  74. 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
  75. Starita, LM et al. (2015) Massively Parallel Functional Analysis of BRCA1 RING Domain Variants. Genetics 200 (2):413-22. PMID:25823446
  76. Hoopmann, MR et al. (2015) Kojak: efficient analysis of chemically cross-linked protein complexes. J. Proteome Res. 14 (5):2190-8. PMID:25812159
  77. Papp, SJ et al. (2015) DNA damage shifts circadian clock time via Hausp-dependent Cry1 stabilization. Elife 4 :. PMID:25756610
  78. 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
  79. Khakhina, S et al. (2015) Control of Plasma Membrane Permeability by ABC Transporters. Eukaryotic Cell 14 (5):442-53. PMID:25724885
  80. 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
  81. 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
  82. Tsai, HY et al. (2015) A ribonuclease coordinates siRNA amplification and mRNA cleavage during RNAi. Cell 160 (3):407-19. PMID:25635455
  83. Peng, Y et al. (2015) Casein kinase 1 promotes initiation of clathrin-mediated endocytosis. Dev. Cell 32 (2):231-40. PMID:25625208
  84. 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
  85. 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
  86. Kitzman, JO et al. (2015) Massively parallel single-amino-acid mutagenesis. Nat. Methods 12 (3):203-6, 4 p following 206. PMID:25559584
  87. 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
  88. 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
  89. 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
  90. Keich, U et al. (2015) On the importance of well-calibrated scores for identifying shotgun proteomics spectra. J. Proteome Res. 14 (2):1147-60. PMID:25482958
  91. Song, YH et al. (2014) Distinct roles of FKF1, Gigantea, and Zeitlupe proteins in the regulation of Constans stability in Arabidopsis photoperiodic flowering. Proc. Natl. Acad. Sci. U.S.A. 111 (49):17672-7. PMID:25422419
  92. Magdeldin, S et al. (2015) Behavioral and proteomic analysis of stress response in zebrafish (Danio rerio). J. Proteome Res. 14 (2):943-52. PMID:25398274
  93. Han, X et al. (2014) In-line separation by capillary electrophoresis prior to analysis by top-down mass spectrometry enables sensitive characterization of protein complexes. J. Proteome Res. 13 (12):6078-86. PMID:25382489
  94. Choi, MS et al. (2014) Transnitrosylation from DJ-1 to PTEN attenuates neuronal cell death in parkinson's disease models. J. Neurosci. 34 (45):15123-31. PMID:25378175
  95. Han, X et al. (2014) Sheathless capillary electrophoresis-tandem mass spectrometry for top-down characterization of Pyrococcus furiosus proteins on a proteome scale. Anal. Chem. 86 (22):11006-12. PMID:25346219
  96. Rauniyar, N et al. (2014) Isobaric labeling-based relative quantification in shotgun proteomics. J. Proteome Res. 13 (12):5293-309. PMID:25337643
  97. Marsillach, J et al. (2014) Human valacyclovir hydrolase/biphenyl hydrolase-like protein is a highly efficient homocysteine thiolactonase. PLoS ONE 9 (10):e110054. PMID:25333274
  98. Kim, TY et al. (2015) Substrate trapping proteomics reveals targets of the βTrCP2/FBXW11 ubiquitin ligase. Mol. Cell. Biol. 35 (1):167-81. PMID:25332235
  99. Baird, NA et al. (2014) HSF-1-mediated cytoskeletal integrity determines thermotolerance and life span. Science 346 (6207):360-3. PMID:25324391
  100. Chen, Y et al. (2014) A gene-specific role for the Ssu72 RNAPII CTD phosphatase in HIV-1 Tat transactivation. Genes Dev. 28 (20):2261-75. PMID:25319827