Yeast Resource Center | Publications
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Publications

Latest YRC Publications

(see all in PubMed)

  1. Santi, L et al. (2018) Secretomic analysis of Beauveria bassiana related to cattle tick, Rhipicephalus microplus, infection. Folia Microbiol. (Praha) :. PubMed PMID:30361880
  2. Ziegler, YS et al. (2018) Proteomic analysis identifies highly expressed plasma membrane proteins for detection and therapeutic targeting of specific breast cancer subtypes. Clin Proteomics 15 :30. PubMed PMID:30250408
  3. Starita, LM et al. (2018) A Multiplex Homology-Directed DNA Repair Assay Reveals the Impact of More Than 1,000 BRCA1 Missense Substitution Variants on Protein Function. Am. J. Hum. Genet. 103 (4):498-508. PubMed PMID:30219179
  4. Wang, Z et al. (2018) Defective RNA polymerase III is negatively regulated by the SUMO-Ubiquitin-Cdc48 pathway. Elife 7 :. PubMed PMID:30192228
  5. Mutlu, B et al. (2018) Regulated nuclear accumulation of a histone methyltransferase times the onset of heterochromatin formation in C. elegans embryos. Sci Adv 4 (8):eaat6224. PubMed PMID:30140741
  6. González, DP et al. (2018) CBD-1 organizes two independent complexes required for eggshell vitelline layer formation and egg activation in C. elegans. Dev. Biol. 442 (2):288-300. PubMed PMID:30120927
  7. Richard, P et al. (2018) NRDE-2, the human homolog of fission yeast Nrl1, prevents DNA damage accumulation in human cells. RNA Biol 15 (7):868-876. PubMed PMID:29902117
  8. Bamberger, C et al. (2018) Deducing the presence of proteins and proteoforms in quantitative proteomics. Nat Commun 9 (1):2320. PubMed PMID:29899466
  9. Burke, JE et al. (2018) Spliceosome Profiling Visualizes Operations of a Dynamic RNP at Nucleotide Resolution. Cell 173 (4):1014-1030.e17. PubMed PMID:29727661
  10. Yates, JR 3rd et al. (2018) Content Is King: Databases Preserve the Collective Information of Science. J Biomol Tech 29 (1):1-3. PubMed PMID:29618955
  11. Xu, Y et al. (2018) A Stem-Loop Structure in Potato Leafroll Virus Open Reading Frame 5 (ORF5) Is Essential for Readthrough Translation of the Coat Protein ORF Stop Codon 700 Bases Upstream. J. Virol. 92 (11):. PubMed PMID:29514911
  12. Helgeson, LA et al. (2018) Human Ska complex and Ndc80 complex interact to form a load-bearing assembly that strengthens kinetochore-microtubule attachments. Proc. Natl. Acad. Sci. U.S.A. 115 (11):2740-2745. PubMed PMID:29487209
  13. Iwasaki, M et al. (2018) Interactome analysis of the lymphocytic choriomeningitis virus nucleoprotein in infected cells reveals ATPase Na+/K+ transporting subunit Alpha 1 and prohibitin as host-cell factors involved in the life cycle of mammarenaviruses. PLoS Pathog. 14 (2):e1006892. PubMed PMID:29462184
  14. Luan, Q et al. (2018) Identification of Wiskott-Aldrich syndrome protein (WASP) binding sites on the branched actin filament nucleator Arp2/3 complex. Proc. Natl. Acad. Sci. U.S.A. 115 (7):E1409-E1418. PubMed PMID:29386393
  15. Tirloni, L et al. (2017) Tick-Host Range Adaptation: Changes in Protein Profiles in Unfed Adult Ixodes scapularis and Amblyomma americanum Saliva Stimulated to Feed on Different Hosts. Front Cell Infect Microbiol 7 :517. PubMed PMID:29312895
  16. Song, Y et al. (2017) Double mimicry evades tRNA synthetase editing by toxic vegetable-sourced non-proteinogenic amino acid. Nat Commun 8 (1):2281. PubMed PMID:29273753
  17. Payea, MJ et al. (2018) Widespread temperature sensitivity and tRNA decay due to mutations in a yeast tRNA. RNA 24 (3):410-422. PubMed PMID:29259051
  18. Hollmann, T et al. (2018) Identification and characterization of proteins in the Amblyomma americanum tick cement cone. Int. J. Parasitol. 48 (3-4):211-224. PubMed PMID:29258831
  19. Oh, CK et al. (2017) S-Nitrosylation of PINK1 Attenuates PINK1/Parkin-Dependent Mitophagy in hiPSC-Based Parkinson's Disease Models. Cell Rep 21 (8):2171-2182. PubMed PMID:29166608
  20. Frankel, EB et al. (2017) Ist1 regulates ESCRT-III assembly and function during multivesicular endosome biogenesis in Caenorhabditis elegans embryos. Nat Commun 8 (1):1439. PubMed PMID:29129923
  21. Ju Lee, H et al. (2017) A post-transcriptional program coordinated by CSDE1 prevents intrinsic neural differentiation of human embryonic stem cells. Nat Commun 8 (1):1456. PubMed PMID:29129916
  22. Andeen, NK et al. (2018) DnaJ Homolog Subfamily B Member 9 Is a Putative Autoantigen in Fibrillary GN. J. Am. Soc. Nephrol. 29 (1):231-239. PubMed PMID:29097624
  23. Cuperus, JT et al. (2017) Deep learning of the regulatory grammar of yeast 5' untranslated regions from 500,000 random sequences. Genome Res. 27 (12):2015-2024. PubMed PMID:29097404
  24. Basisty, NB et al. (2018) Stable Isotope Labeling Reveals Novel Insights Into Ubiquitin-Mediated Protein Aggregation With Age, Calorie Restriction, and Rapamycin Treatment. J. Gerontol. A Biol. Sci. Med. Sci. 73 (5):561-570. PubMed PMID:28958078
  25. Wang, J et al. (2017) Protein arginylation targets alpha synuclein, facilitates normal brain health, and prevents neurodegeneration. Sci Rep 7 (1):11323. PubMed PMID:28900170
  26. Smukowski Heil, C et al. (2018) Identification of a novel interspecific hybrid yeast from a metagenomic spontaneously inoculated beer sample using Hi-C. Yeast 35 (1):71-84. PubMed PMID:28892574
  27. Moody, JD et al. (2017) First critical repressive H3K27me3 marks in embryonic stem cells identified using designed protein inhibitor. Proc. Natl. Acad. Sci. U.S.A. 114 (38):10125-10130. PubMed PMID:28864533
  28. Subramanian, K et al. (2017) Quantitative Analysis of the Proteome Response to the Histone Deacetylase Inhibitor (HDACi) Vorinostat in Niemann-Pick Type C1 disease. Mol. Cell Proteomics 16 (11):1938-1957. PubMed PMID:28860124
  29. Hanna, MG 4th et al. (2017) TFG facilitates outer coat disassembly on COPII transport carriers to promote tethering and fusion with ER-Golgi intermediate compartments. Proc. Natl. Acad. Sci. U.S.A. 114 (37):E7707-E7716. PubMed PMID:28851831
  30. Widjaja, CE et al. (2017) Proteasome activity regulates CD8+ T lymphocyte metabolism and fate specification. J. Clin. Invest. 127 (10):3609-3623. PubMed PMID:28846070
  31. Rosenberger, G et al. (2017) Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses. Nat. Methods 14 (9):921-927. PubMed PMID:28825704
  32. DeBlasio, SL et al. (2017) Evaluation of a Bead-Free Coimmunoprecipitation Technique for Identification of Virus-Host Protein Interactions Using High-Resolution Mass Spectrometry. J Biomol Tech 28 (3):111-121. PubMed PMID:28785175
  33. Ting, YS et al. (2017) PECAN: library-free peptide detection for data-independent acquisition tandem mass spectrometry data. Nat. Methods 14 (9):903-908. PubMed PMID:28783153
  34. Jin, M et al. (2017) Glycolytic Enzymes Coalesce in G Bodies under Hypoxic Stress. Cell Rep 20 (4):895-908. PubMed PMID:28746874
  35. Mu, R et al. (2017) CKS Proteins Promote Checkpoint Recovery by Stimulating Phosphorylation of Treslin. Mol. Cell. Biol. 37 (20):. PubMed PMID:28739856
  36. Ogami, K et al. (2017) An Mtr4/ZFC3H1 complex facilitates turnover of unstable nuclear RNAs to prevent their cytoplasmic transport and global translational repression. Genes Dev. 31 (12):1257-1271. PubMed PMID:28733371
  37. Goulding, SP et al. (2017) A mass spectrometry-based proteomic analysis of Homer2-interacting proteins in the mouse brain. J Proteomics 166 :127-137. PubMed PMID:28728878
  38. Pino, LK et al. (2017) The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics. Mass Spectrom Rev :. PubMed PMID:28691345
  39. Sakano, H et al. (2017) Proteomic analyses of nucleus laminaris identified candidate targets of the fragile X mental retardation protein. J. Comp. Neurol. 525 (15):3341-3359. PubMed PMID:28685837
  40. Noble, WS et al. (2017) Response to "Mass spectrometrists should search for all peptides, but assess only the ones they care about". Nat. Methods 14 (7):644. PubMed PMID:28661496
  41. Bhagavatula, G et al. (2017) A Massively Parallel Fluorescence Assay to Characterize the Effects of Synonymous Mutations on TP53 Expression. Mol. Cancer Res. 15 (10):1301-1307. PubMed PMID:28652265
  42. Chu, Q et al. (2017) Identification of Microprotein-Protein Interactions via APEX Tagging. Biochemistry 56 (26):3299-3306. PubMed PMID:28589727
  43. Ganguly, A et al. (2017) Hsc70 chaperone activity is required for the cytosolic slow axonal transport of synapsin. J. Cell Biol. 216 (7):2059-2074. PubMed PMID:28559423
  44. Kim, S et al. (2017) The dynamic three-dimensional organization of the diploid yeast genome. Elife 6 :. PubMed PMID:28537556
  45. French, ME et al. (2017) Mechanism of ubiquitin chain synthesis employed by a HECT domain ubiquitin ligase. J. Biol. Chem. 292 (25):10398-10413. PubMed PMID:28461335
  46. Hope, EA et al. (2017) Experimental Evolution Reveals Favored Adaptive Routes to Cell Aggregation in Yeast. Genetics 206 (2):1153-1167. PubMed PMID:28450459
  47. Ma, Y et al. (2017) HILAQ: A Novel Strategy for Newly Synthesized Protein Quantification. J. Proteome Res. 16 (6):2213-2220. PubMed PMID:28437088
  48. Callens, C et al. (2017) A multiplex culture system for the long-term growth of fission yeast cells. Yeast 34 (8):343-355. PubMed PMID:28426144
  49. Zimmerman, SG et al. (2017) Proteomics Analysis Identifies Orthologs of Human Chitinase-Like Proteins as Inducers of Tube Morphogenesis Defects in Drosophila melanogaster. Genetics 206 (2):973-984. PubMed PMID:28404605
  50. Cao, L et al. (2017) Global site-specific N-glycosylation analysis of HIV envelope glycoprotein. Nat Commun 8 :14954. PubMed PMID:28348411
  51. Chao, LF et al. (2017) An SMC-like protein binds and regulates Caenorhabditis elegans condensins. PLoS Genet. 13 (3):e1006614. PubMed PMID:28301465
  52. May, DH et al. (2017) Param-Medic: A Tool for Improving MS/MS Database Search Yield by Optimizing Parameter Settings. J. Proteome Res. 16 (4):1817-1824. PubMed PMID:28263070
  53. 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. PubMed PMID:28235840
  54. Matthews, ML et al. (2017) Chemoproteomic profiling and discovery of protein electrophiles in human cells. Nat Chem 9 (3):234-243. PubMed PMID:28221344
  55. Spencer, SE et al. (2017) Automated Trapping Column Exchanger for High-Throughput Nanoflow Liquid Chromatography. Anal. Chem. 89 (4):2383-2389. PubMed PMID:28192907
  56. Kim, JO et al. (2017) The Ndc80 complex bridges two Dam1 complex rings. Elife 6 :. PubMed PMID:28191870
  57. 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. PubMed PMID:28057866
  58. Hickox, AE et al. (2017) Global Analysis of Protein Expression of Inner Ear Hair Cells. J. Neurosci. 37 (5):1320-1339. PubMed PMID:28039372
  59. 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. PubMed PMID:27909058
  60. Pankow, S et al. (2016) Deep interactome profiling of membrane proteins by co-interacting protein identification technology. Nat Protoc 11 (12):2515-2528. PubMed PMID:27854364
  61. 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. PubMed PMID:27824341
  62. Hsia, Y et al. (2016) Corrigendum: Design of a hyperstable 60-subunit protein icosahedron. Nature 540 (7631):150. PubMed PMID:27760110
  63. Berger, S et al. (2016) Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer. Elife 5 :. PubMed PMID:27805565
  64. 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. PubMed PMID:27780869
  65. 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. PubMed PMID:27700092
  66. Shan, CM et al. (2016) A histone H3K9M mutation traps histone methyltransferase Clr4 to prevent heterochromatin spreading. Elife 5 :. PubMed PMID:27648579
  67. 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. PubMed PMID:27572102
  68. Chatterjee, S et al. (2016) A comprehensive and scalable database search system for metaproteomics. BMC Genomics 17 (1):642. PubMed PMID:27528457
  69. Koizumi, H et al. (2017) DCLK1 phosphorylates the microtubule-associated protein MAP7D1 to promote axon elongation in cortical neurons. Dev Neurobiol 77 (4):493-510. PubMed PMID:27503845
  70. Halloran, JT et al. (2016) Dynamic Bayesian Network for Accurate Detection of Peptides from Tandem Mass Spectra. J. Proteome Res. 15 (8):2749-59. PubMed PMID:27397138
  71. 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. PubMed PMID:27396978
  72. Gamble, CE et al. (2016) Adjacent Codons Act in Concert to Modulate Translation Efficiency in Yeast. Cell 166 (3):679-690. PubMed PMID:27374328
  73. Hsia, Y et al. (2016) Design of a hyperstable 60-subunit protein dodecahedron. [corrected]. Nature 535 (7610):136-9. PubMed PMID:27309817
  74. Wang, S et al. (2016) Faster and more accurate graphical model identification of tandem mass spectra using trellises. Bioinformatics 32 (12):i322-i331. PubMed PMID:27307634
  75. 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. PubMed PMID:27302480
  76. Zhao, X et al. (2016) Circadian Amplitude Regulation via FBXW7-Targeted REV-ERBα Degradation. Cell 165 (7):1644-1657. PubMed PMID:27238018
  77. Lyon, AS et al. (2016) Higher-order oligomerization of Spc110p drives γ-tubulin ring complex assembly. Mol. Biol. Cell 27 (14):2245-58. PubMed PMID:27226487
  78. Armbruster, CR et al. (2016) Staphylococcus aureus Protein A Mediates Interspecies Interactions at the Cell Surface of Pseudomonas aeruginosa. MBio 7 (3):. PubMed PMID:27222468
  79. Homer, CM et al. (2016) Intracellular Action of a Secreted Peptide Required for Fungal Virulence. Cell Host Microbe 19 (6):849-64. PubMed PMID:27212659
  80. Topalidou, I et al. (2016) The EARP Complex and Its Interactor EIPR-1 Are Required for Cargo Sorting to Dense-Core Vesicles. PLoS Genet. 12 (5):e1006074. PubMed PMID:27191843
  81. 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. PubMed PMID:27135603
  82. Basisty, N et al. (2016) Mitochondrial-targeted catalase is good for the old mouse proteome, but not for the young: 'reverse' antagonistic pleiotropy?. Aging Cell 15 (4):634-45. PubMed PMID:27061426
  83. 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. PubMed PMID:27026705
  84. 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. PubMed PMID:27010334
  85. Ma, J et al. (2016) Improved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides. Anal. Chem. 88 (7):3967-75. PubMed PMID:27010111
  86. Janke, R et al. (2016) Nonsense-mediated decay regulates key components of homologous recombination. Nucleic Acids Res. 44 (11):5218-30. PubMed PMID:27001511
  87. Wang, J et al. (2016) The proper connection between shelterin components is required for telomeric heterochromatin assembly. Genes Dev. 30 (7):827-39. PubMed PMID:26988418
  88. 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. PubMed PMID:26968363
  89. 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. PubMed PMID:26943317
  90. Rich, MS et al. (2016) Comprehensive Analysis of the SUL1 Promoter of Saccharomyces cerevisiae. Genetics 203 (1):191-202. PubMed PMID:26936925
  91. Zich, J et al. (2016) Mps1Mph1 Kinase Phosphorylates Mad3 to Inhibit Cdc20Slp1-APC/C and Maintain Spindle Checkpoint Arrests. PLoS Genet. 12 (2):e1005834. PubMed PMID:26882497
  92. 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. PubMed PMID:26867752
  93. 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. PubMed PMID:26867746
  94. 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. PubMed PMID:26865697
  95. Borges, MH et al. (2016) Venomous extract protein profile of Brazilian tarantula Grammostola iheringi: searching for potential biotechnological applications. J Proteomics 136 :35-47. PubMed PMID:26828374
  96. 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. PubMed PMID:26751078
  97. Feng, J et al. (2015) A general strategy to construct small molecule biosensors in eukaryotes. Elife 4 :. PubMed PMID:26714111
  98. Taylor, ND et al. (2016) Engineering an allosteric transcription factor to respond to new ligands. Nat. Methods 13 (2):177-83. PubMed PMID:26689263
  99. 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. PubMed PMID:26669440
  100. 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. PubMed PMID:26667653