Yeast Resource Center | Publications
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Publications

Latest YRC Publications

(see all in PubMed)

  1. Amodei, D et al. (2019) Improving Precursor Selectivity in Data-Independent Acquisition Using Overlapping Windows. J. Am. Soc. Mass Spectrom. :. PubMed PMID:30671891
  2. Correia, SP et al. (2019) The circadian E3 ligase complex SCFFBXL3+CRY targets TLK2. Sci Rep 9 (1):198. PubMed PMID:30655559
  3. Sonntag, T et al. (2019) Mitogenic Signals Stimulate the CREB Coactivator CRTC3 through PP2A Recruitment. iScience 11 :134-145. PubMed PMID:30611118
  4. Bao, K et al. (2019) Anti-silencing factor Epe1 associates with SAGA to regulate transcription within heterochromatin. Genes Dev. 33 (1-2):116-126. PubMed PMID:30573453
  5. Keich, U et al. (2018) Controlling the FDR in imperfect matches to an incomplete database. J Am Stat Assoc 113 (523):973-982. PubMed PMID:30546175
  6. Natividad, LA et al. (2018) From Synapse to Function: A Perspective on the Role of Neuroproteomics in Elucidating Mechanisms of Drug Addiction. Proteomes 6 (4):. PubMed PMID:30544849
  7. Krahmer, J et al. (2019) Time-resolved interaction proteomics of the GIGANTEA protein under diurnal cycles in Arabidopsis. FEBS Lett. 593 (3):319-338. PubMed PMID:30536871
  8. Riffle, M et al. (2019) Proxl (Protein Cross-Linking Database): A Public Server, QC Tools, and Other Major Updates. J. Proteome Res. 18 (2):759-764. PubMed PMID:30525651
  9. Searle, BC et al. (2018) Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry. Nat Commun 9 (1):5128. PubMed PMID:30510204
  10. Kim, YJ et al. (2018) Data-independent acquisition mass spectrometry to quantify protein levels in FFPE tumor biopsies for molecular diagnostics. J. Proteome Res. :. PubMed PMID:30481034
  11. DaRosa, PA et al. (2018) A Bifunctional Role for the UHRF1 UBL Domain in the Control of Hemi-methylated DNA-Dependent Histone Ubiquitylation. Mol. Cell 72 (4):753-765.e6. PubMed PMID:30392931
  12. Beys-da-Silva, WO et al. (2018) Zika Virus Infection of Human Mesenchymal Stem Cells Promotes Differential Expression of Proteins Linked to Several Neurological Diseases. Mol. Neurobiol. :. PubMed PMID:30377986
  13. Santi, L et al. (2018) Secretomic analysis of Beauveria bassiana related to cattle tick, Rhipicephalus microplus, infection. Folia Microbiol. (Praha) :. PubMed PMID:30361880
  14. 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
  15. Lin, A et al. (2018) Combining High-Resolution and Exact Calibration To Boost Statistical Power: A Well-Calibrated Score Function for High-Resolution MS2 Data. J. Proteome Res. 17 (11):3644-3656. PubMed PMID:30221945
  16. 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
  17. Louka, P et al. (2018) Proteins that control the geometry of microtubules at the ends of cilia. J. Cell Biol. 217 (12):4298-4313. PubMed PMID:30217954
  18. Jester, BW et al. (2018) Engineered Biosensors from Dimeric Ligand-Binding Domains. ACS Synth Biol 7 (10):2457-2467. PubMed PMID:30204430
  19. Wang, Z et al. (2018) Defective RNA polymerase III is negatively regulated by the SUMO-Ubiquitin-Cdc48 pathway. Elife 7 :. PubMed PMID:30192228
  20. 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
  21. 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
  22. Diniz, MRV et al. (2018) An overview of Phoneutria nigriventer spider venom using combined transcriptomic and proteomic approaches. PLoS ONE 13 (8):e0200628. PubMed PMID:30067761
  23. Brandsen, BM et al. (2018) A Biosensor Strategy for E. coli Based on Ligand-Dependent Stabilization. ACS Synth Biol 7 (9):1990-1999. PubMed PMID:30064218
  24. McClatchy, DB et al. (2018) Structural Analysis of Hippocampal Kinase Signal Transduction. ACS Chem Neurosci :. PubMed PMID:30053369
  25. MacLean, BX et al. (2018) Using Skyline to Analyze Data-Containing Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry Dimensions. J. Am. Soc. Mass Spectrom. 29 (11):2182-2188. PubMed PMID:30047074
  26. McClatchy, DB et al. (2018) Quantitative temporal analysis of protein dynamics in cardiac remodeling. J. Mol. Cell. Cardiol. 121 :163-172. PubMed PMID:30009778
  27. Ma, Y et al. (2018) Proteomics and pulse azidohomoalanine labeling of newly synthesized proteins: what are the potential applications?. Expert Rev Proteomics 15 (7):545-554. PubMed PMID:30005169
  28. Fong, KK et al. (2018) Novel phosphorylation states of the yeast spindle pole body. Biol Open 7 (10):. PubMed PMID:29903865
  29. 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
  30. Bamberger, C et al. (2018) Deducing the presence of proteins and proteoforms in quantitative proteomics. Nat Commun 9 (1):2320. PubMed PMID:29899466
  31. Nishimura, N et al. (2018) Control of seed dormancy and germination by DOG1-AHG1 PP2C phosphatase complex via binding to heme. Nat Commun 9 (1):2132. PubMed PMID:29875377
  32. Song, C et al. (2018) PML Recruits TET2 to Regulate DNA Modification and Cell Proliferation in Response to Chemotherapeutic Agent. Cancer Res. 78 (10):2475-2489. PubMed PMID:29735542
  33. 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
  34. Tseng, BS et al. (2018) A Biofilm Matrix-Associated Protease Inhibitor Protects Pseudomonas aeruginosa from Proteolytic Attack. MBio 9 (2):. PubMed PMID:29636440
  35. 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
  36. 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
  37. 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
  38. Sharma, V et al. (2018) Panorama Public: A Public Repository for Quantitative Data Sets Processed in Skyline. Mol. Cell Proteomics 17 (6):1239-1244. PubMed PMID:29487113
  39. 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
  40. 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
  41. 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
  42. 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
  43. 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
  44. 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
  45. Henderson, CM et al. (2018) Skyline Performs as Well as Vendor Software in the Quantitative Analysis of Serum 25-Hydroxy Vitamin D and Vitamin D Binding Globulin. Clin. Chem. 64 (2):408-410. PubMed PMID:29203474
  46. 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
  47. 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
  48. 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
  49. Lopez Aguilar, A et al. (2017) Profiling of Protein O-GlcNAcylation in Murine CD8+ Effector- and Memory-like T Cells. ACS Chem. Biol. 12 (12):3031-3038. PubMed PMID:29125738
  50. 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
  51. 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
  52. 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
  53. 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
  54. 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
  55. 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
  56. 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
  57. 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
  58. 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
  59. 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
  60. 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
  61. 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
  62. Jin, M et al. (2017) Glycolytic Enzymes Coalesce in G Bodies under Hypoxic Stress. Cell Rep 20 (4):895-908. PubMed PMID:28746874
  63. Mu, R et al. (2017) CKS Proteins Promote Checkpoint Recovery by Stimulating Phosphorylation of Treslin. Mol. Cell. Biol. 37 (20):. PubMed PMID:28739856
  64. 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
  65. 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
  66. Pino, LK et al. (2017) The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics. Mass Spectrom Rev :. PubMed PMID:28691345
  67. 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
  68. 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
  69. 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
  70. Chu, Q et al. (2017) Identification of Microprotein-Protein Interactions via APEX Tagging. Biochemistry 56 (26):3299-3306. PubMed PMID:28589727
  71. 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
  72. Kim, S et al. (2017) The dynamic three-dimensional organization of the diploid yeast genome. Elife 6 :. PubMed PMID:28537556
  73. 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
  74. Hope, EA et al. (2017) Experimental Evolution Reveals Favored Adaptive Routes to Cell Aggregation in Yeast. Genetics 206 (2):1153-1167. PubMed PMID:28450459
  75. Ma, Y et al. (2017) HILAQ: A Novel Strategy for Newly Synthesized Protein Quantification. J. Proteome Res. 16 (6):2213-2220. PubMed PMID:28437088
  76. 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
  77. 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
  78. Cao, L et al. (2017) Global site-specific N-glycosylation analysis of HIV envelope glycoprotein. Nat Commun 8 :14954. PubMed PMID:28348411
  79. Chao, LF et al. (2017) An SMC-like protein binds and regulates Caenorhabditis elegans condensins. PLoS Genet. 13 (3):e1006614. PubMed PMID:28301465
  80. Bickhart, DM et al. (2017) Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome. Nat. Genet. 49 (4):643-650. PubMed PMID:28263316
  81. 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
  82. 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
  83. Matthews, ML et al. (2017) Chemoproteomic profiling and discovery of protein electrophiles in human cells. Nat Chem 9 (3):234-243. PubMed PMID:28221344
  84. Spencer, SE et al. (2017) Automated Trapping Column Exchanger for High-Throughput Nanoflow Liquid Chromatography. Anal. Chem. 89 (4):2383-2389. PubMed PMID:28192907
  85. Kim, JO et al. (2017) The Ndc80 complex bridges two Dam1 complex rings. Elife 6 :. PubMed PMID:28191870
  86. 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
  87. Hickox, AE et al. (2017) Global Analysis of Protein Expression of Inner Ear Hair Cells. J. Neurosci. 37 (5):1320-1339. PubMed PMID:28039372
  88. 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
  89. 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
  90. 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
  91. Hsia, Y et al. (2016) Corrigendum: Design of a hyperstable 60-subunit protein icosahedron. Nature 540 (7631):150. PubMed PMID:27760110
  92. Berger, S et al. (2016) Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer. Elife 5 :. PubMed PMID:27805565
  93. 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
  94. 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
  95. Shan, CM et al. (2016) A histone H3K9M mutation traps histone methyltransferase Clr4 to prevent heterochromatin spreading. Elife 5 :. PubMed PMID:27648579
  96. 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
  97. Chatterjee, S et al. (2016) A comprehensive and scalable database search system for metaproteomics. BMC Genomics 17 (1):642. PubMed PMID:27528457
  98. 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
  99. 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
  100. 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