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Latest YRC Publications

(see all in PubMed)

  1. Fuller, GG et al. (2020) RNA promotes phase separation of glycolysis enzymes into yeast G bodies in hypoxia. Elife 9 :. PubMed PMID:32298230
  2. Chen, Z et al. (2020) De novo design of protein logic gates. Science 368 (6486):78-84. PubMed PMID:32241946
  3. Dorrity, MW et al. (2020) Dimensionality reduction by UMAP to visualize physical and genetic interactions. Nat Commun 11 (1):1537. PubMed PMID:32210240
  4. Kim, TK et al. (2020) Time-resolved proteomic profile of Amblyomma americanum tick saliva during feeding. PLoS Negl Trop Dis 14 (2):e0007758. PubMed PMID:32049966
  5. Pino, LK et al. (2020) Matrix-Matched Calibration Curves for Assessing Analytical Figures of Merit in Quantitative Proteomics. J. Proteome Res. 19 (3):1147-1153. PubMed PMID:32037841
  6. Lazarchuk, P et al. (2020) Mutual Balance of Histone Deacetylases 1 and 2 and the Acetyl Reader ATAD2 Regulates the Level of Acetylation of Histone H4 on Nascent Chromatin of Human Cells. Mol. Cell. Biol. 40 (9):. PubMed PMID:32015101
  7. Adams, KJ et al. (2020) Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics. J. Proteome Res. 19 (4):1447-1458. PubMed PMID:31984744
  8. Gomes, FP et al. (2020) EThcD and 213 nm UVPD for Top-Down Analysis of Bovine Seminal Plasma Proteoforms on Electrophoretic and Chromatographic Time Frames. Anal. Chem. 92 (4):2979-2987. PubMed PMID:31962043
  9. Fernández-Costa, C et al. (2020) Improving Proteomics Data Reproducibility with a Dual-Search Strategy. Anal. Chem. 92 (2):1697-1701. PubMed PMID:31880919
  10. Stein, BD et al. (2019) Quantitative In Vivo Proteomics of Metformin Response in Liver Reveals AMPK-Dependent and -Independent Signaling Networks. Cell Rep 29 (10):3331-3348.e7. PubMed PMID:31801093
  11. Sonntag, T et al. (2019) The KLDpT activation loop motif is critical for MARK kinase activity. PLoS ONE 14 (12):e0225727. PubMed PMID:31794565
  12. Johnson, RS et al. (2020) Assessing Protein Sequence Database Suitability Using De Novo Sequencing. Mol. Cell Proteomics 19 (1):198-208. PubMed PMID:31732549
  13. Jaiswal, D et al. (2020) Function of the MYND Domain and C-Terminal Region in Regulating the Subcellular Localization and Catalytic Activity of the SMYD Family Lysine Methyltransferase Set5. Mol. Cell. Biol. 40 (2):. PubMed PMID:31685550
  14. Wang, J et al. (2019) Biochemical analysis of protein arginylation. Meth. Enzymol. 626 :89-113. PubMed PMID:31606094
  15. Miller, MP et al. (2019) Kinetochore-associated Stu2 promotes chromosome biorientation in vivo. PLoS Genet. 15 (10):e1008423. PubMed PMID:31584935
  16. Lancaster, SM et al. (2019) Fitness benefits of loss of heterozygosity in Saccharomyces hybrids. Genome Res. 29 (10):1685-1692. PubMed PMID:31548357
  17. Read, DF et al. (2019) Predicting gene expression in the human malaria parasite Plasmodium falciparum using histone modification, nucleosome positioning, and 3D localization features. PLoS Comput. Biol. 15 (9):e1007329. PubMed PMID:31509524
  18. Rosa, RL et al. (2019) Proteomics of Rat Lungs Infected by Cryptococcus gattii Reveals a Potential Warburg-like Effect. J. Proteome Res. 18 (11):3885-3895. PubMed PMID:31502459
  19. Schiapparelli, LM et al. (2019) The Retinal Ganglion Cell Transportome Identifies Proteins Transported to Axons and Presynaptic Compartments in the Visual System In Vivo. Cell Rep 28 (7):1935-1947.e5. PubMed PMID:31412257
  20. Gomes, FP et al. (2019) Recent trends of capillary electrophoresis-mass spectrometry in proteomics research. Mass Spectrom Rev 38 (6):445-460. PubMed PMID:31407381
  21. Stein, BD et al. (2019) Comparison of CRISPR Genomic Tagging for Affinity Purification and Endogenous Immunoprecipitation Coupled with Quantitative Mass Spectrometry To Identify the Dynamic AMPKα2 Interactome. J. Proteome Res. 18 (10):3703-3714. PubMed PMID:31398040
  22. Searle, BC et al. (2019) Thesaurus: quantifying phosphopeptide positional isomers. Nat. Methods 16 (8):703-706. PubMed PMID:31363206
  23. Sanchez, JC et al. (2019) Phenotypic and Genotypic Consequences of CRISPR/Cas9 Editing of the Replication Origins in the rDNA of Saccharomyces cerevisiae. Genetics 213 (1):229-249. PubMed PMID:31292210
  24. Martínez-Bartolomé, S et al. (2019) Proteomics INTegrator (PINT): An Online Tool To Store, Query, and Visualize Large Proteomics Experiment Results. J. Proteome Res. 18 (8):2999-3008. PubMed PMID:31260318
  25. Alonso, AM et al. (2019) Exploring protein myristoylation in Toxoplasma gondii. Exp. Parasitol. 203 :8-18. PubMed PMID:31150653
  26. Cheng, LC et al. (2019) Identification of new transmembrane proteins concentrated at the nuclear envelope using organellar proteomics of mesenchymal cells. Nucleus 10 (1):126-143. PubMed PMID:31142202
  27. Negrão, F et al. (2019) Comparative Proteomic Analysis of Murine Cutaneous Lesions Induced by Leishmania amazonensis or Leishmania major. ACS Infect Dis 5 (8):1295-1305. PubMed PMID:31094195
  28. Burke, JE et al. (2019) A Non-Dicer RNase III and Four Other Novel Factors Required for RNAi-Mediated Transposon Suppression in the Human Pathogenic Yeast Cryptococcus neoformans. G3 (Bethesda) 9 (7):2235-2244. PubMed PMID:31092606
  29. Santos, MDM et al. (2019) A quantitation module for isotope-labeled peptides integrated into PatternLab for proteomics. J Proteomics 202 :103371. PubMed PMID:31034900
  30. Kachaev, ZM et al. (2019) Paip2 cooperates with Cbp80 at an active promoter and participates in RNA Polymerase II phosphorylation in Drosophila. FEBS Lett. 593 (10):1102-1112. PubMed PMID:31001806
  31. Yates, JR 3rd et al. (2019) Recent technical advances in proteomics. F1000Res 8 :. PubMed PMID:30997033
  32. Negrão, F et al. (2019) Label-Free Proteomic Analysis Reveals Parasite-Specific Protein Alterations in Macrophages Following Leishmania amazonensis, Leishmania major, or Leishmania infantum Infection. ACS Infect Dis 5 (6):851-862. PubMed PMID:30978002
  33. Dorrity, MW et al. (2019) High-throughput identification of dominant negative polypeptides in yeast. Nat. Methods 16 (5):413-416. PubMed PMID:30962621
  34. Xavier, MA et al. (2019) Tick Gené's organ engagement in lipid metabolism revealed by a combined transcriptomic and proteomic approach. Ticks Tick Borne Dis 10 (4):787-797. PubMed PMID:30904537
  35. Kim, JJ et al. (2019) Proteomic analyses reveal misregulation of LIN28 expression and delayed timing of glial differentiation in human iPS cells with MECP2 loss-of-function. PLoS ONE 14 (2):e0212553. PubMed PMID:30789962
  36. Amodei, D et al. (2019) Improving Precursor Selectivity in Data-Independent Acquisition Using Overlapping Windows. J. Am. Soc. Mass Spectrom. 30 (4):669-684. PubMed PMID:30671891
  37. Correia, SP et al. (2019) The circadian E3 ligase complex SCFFBXL3+CRY targets TLK2. Sci Rep 9 (1):198. PubMed PMID:30655559
  38. Sonntag, T et al. (2019) Mitogenic Signals Stimulate the CREB Coactivator CRTC3 through PP2A Recruitment. iScience 11 :134-145. PubMed PMID:30611118
  39. Pankow, S et al. (2019) A posttranslational modification code for CFTR maturation is altered in cystic fibrosis. Sci Signal 12 (562):. PubMed PMID:30600261
  40. 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
  41. Keich, U et al. (2019) Averaging Strategy To Reduce Variability in Target-Decoy Estimates of False Discovery Rate. J. Proteome Res. 18 (2):585-593. PubMed PMID:30560673
  42. 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
  43. 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
  44. 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
  45. Park, SKR et al. (2019) ComPIL 2.0: An Updated Comprehensive Metaproteomics Database. J. Proteome Res. 18 (2):616-622. PubMed PMID:30525664
  46. 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
  47. 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
  48. Kim, YJ et al. (2019) Data-Independent Acquisition Mass Spectrometry To Quantify Protein Levels in FFPE Tumor Biopsies for Molecular Diagnostics. J. Proteome Res. 18 (1):426-435. PubMed PMID:30481034
  49. 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
  50. Beys-da-Silva, WO et al. (2019) Zika Virus Infection of Human Mesenchymal Stem Cells Promotes Differential Expression of Proteins Linked to Several Neurological Diseases. Mol. Neurobiol. 56 (7):4708-4717. PubMed PMID:30377986
  51. Hu, A et al. (2019) Joint Precursor Elution Profile Inference via Regression for Peptide Detection in Data-Independent Acquisition Mass Spectra. J. Proteome Res. 18 (1):86-94. PubMed PMID:30362768
  52. Santi, L et al. (2019) Secretomic analysis of Beauveria bassiana related to cattle tick, Rhipicephalus microplus, infection. Folia Microbiol. (Praha) 64 (3):361-372. PubMed PMID:30361880
  53. Pino, LK et al. (2018) Calibration Using a Single-Point External Reference Material Harmonizes Quantitative Mass Spectrometry Proteomics Data between Platforms and Laboratories. Anal. Chem. 90 (21):13112-13117. PubMed PMID:30350613
  54. Pankow, S et al. (2019) Understanding molecular mechanisms of disease through spatial proteomics. Curr Opin Chem Biol 48 :19-25. PubMed PMID:30308467
  55. 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
  56. 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
  57. 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
  58. 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
  59. Rathore, A et al. (2018) MIEF1 Microprotein Regulates Mitochondrial Translation. Biochemistry 57 (38):5564-5575. PubMed PMID:30215512
  60. Jester, BW et al. (2018) Engineered Biosensors from Dimeric Ligand-Binding Domains. ACS Synth Biol 7 (10):2457-2467. PubMed PMID:30204430
  61. Wang, Z et al. (2018) Defective RNA polymerase III is negatively regulated by the SUMO-Ubiquitin-Cdc48 pathway. Elife 7 :. PubMed PMID:30192228
  62. 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
  63. 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
  64. 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
  65. 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
  66. McClatchy, DB et al. (2018) Structural Analysis of Hippocampal Kinase Signal Transduction. ACS Chem Neurosci 9 (12):3072-3085. PubMed PMID:30053369
  67. 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
  68. McClatchy, DB et al. (2018) Quantitative temporal analysis of protein dynamics in cardiac remodeling. J. Mol. Cell. Cardiol. 121 :163-172. PubMed PMID:30009778
  69. 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
  70. Fong, KK et al. (2018) Novel phosphorylation states of the yeast spindle pole body. Biol Open 7 (10):. PubMed PMID:29903865
  71. 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
  72. Bamberger, C et al. (2018) Deducing the presence of proteins and proteoforms in quantitative proteomics. Nat Commun 9 (1):2320. PubMed PMID:29899466
  73. 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
  74. 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
  75. 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
  76. Cao, L et al. (2018) Global site-specific analysis of glycoprotein N-glycan processing. Nat Protoc 13 (6):1196-1212. PubMed PMID:29725121
  77. Tseng, BS et al. (2018) A Biofilm Matrix-Associated Protease Inhibitor Protects Pseudomonas aeruginosa from Proteolytic Attack. mBio 9 (2):. PubMed PMID:29636440
  78. 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
  79. 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
  80. 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
  81. 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
  82. 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
  83. Bamberger, C et al. (2018) Increased proteomic complexity in Drosophila hybrids during development. Sci Adv 4 (2):eaao3424. PubMed PMID:29441361
  84. 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
  85. 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
  86. 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
  87. 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
  88. 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
  89. 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
  90. 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
  91. 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
  92. 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
  93. 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
  94. 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
  95. 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
  96. 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
  97. 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
  98. 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
  99. 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
  100. 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