Publications
15660
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Publications

Latest YRC Publications

(see all in PubMed)

  1. Brilot, AF et al. (2021) CM1-driven assembly and activation of yeast γ-tubulin small complex underlies microtubule nucleation. Elife 10 :. PubMed PMID:33949948
  2. Pirie, E et al. (2021) S-nitrosylated TDP-43 triggers aggregation, cell-to-cell spread, and neurotoxicity in hiPSCs and in vivo models of ALS/FTD. Proc Natl Acad Sci U S A 118 (11):. PubMed PMID:33692125
  3. Kim, TK et al. (2021) Borrelia burgdorferi infection modifies protein content in saliva of Ixodes scapularis nymphs. BMC Genomics 22 (1):152. PubMed PMID:33663385
  4. Bamberger, C et al. (2021) The Host Interactome of Spike Expands the Tropism of SARS-CoV-2. bioRxiv :. PubMed PMID:33619478
  5. Fondrie, WE et al. (2021) mokapot: Fast and Flexible Semisupervised Learning for Peptide Detection. J Proteome Res 20 (4):1966-1971. PubMed PMID:33596079
  6. Choi, CP et al. (2021) SNPC-1.3 is a sex-specific transcription factor that drives male piRNA expression in C. elegans. Elife 10 :. PubMed PMID:33587037
  7. Schipper, S et al. (2021) Identification of sulfenylation patterns in trophozoite stage Plasmodium falciparum using a non-dimedone based probe. Mol Biochem Parasitol 242 :111362. PubMed PMID:33513391
  8. Patra, KP et al. (2020) A Hetero-Multimeric Chitinase-Containing Plasmodium falciparum and Plasmodium gallinaceum Ookinete-Secreted Protein Complex Involved in Mosquito Midgut Invasion. Front Cell Infect Microbiol 10 :615343. PubMed PMID:33489941
  9. Lu, S et al. (2021) The SARS-CoV-2 nucleocapsid phosphoprotein forms mutually exclusive condensates with RNA and the membrane-associated M protein. Nat Commun 12 (1):502. PubMed PMID:33479198
  10. Shan, CM et al. (2020) The INO80 Complex Regulates Epigenetic Inheritance of Heterochromatin. Cell Rep 33 (13):108561. PubMed PMID:33378674
  11. Chaves, DA et al. (2021) The RNA phosphatase PIR-1 regulates endogenous small RNA pathways in C. elegans. Mol Cell 81 (3):546-557.e5. PubMed PMID:33378643
  12. Cui, H et al. (2021) Regulation of ex-translational activities is the primary function of the multi-tRNA synthetase complex. Nucleic Acids Res 49 (7):3603-3616. PubMed PMID:33341895
  13. Yu, H et al. (2021) HSP70 chaperones RNA-free TDP-43 into anisotropic intranuclear liquid spherical shells. Science 371 (6529):. PubMed PMID:33335017
  14. Tran, JR et al. (2021) An APEX2 proximity ligation method for mapping interactions with the nuclear lamina. J Cell Biol 220 (1):. PubMed PMID:33306092
  15. Nakamura, T et al. (2021) Noncanonical transnitrosylation network contributes to synapse loss in Alzheimer's disease. Science 371 (6526):. PubMed PMID:33273062
  16. Ma, Y et al. (2021) Temporal Quantitative Profiling of Newly Synthesized Proteins during Aβ Accumulation. J Proteome Res 20 (1):763-775. PubMed PMID:33147027
  17. Berndsen, ZT et al. (2020) Visualization of the HIV-1 Env glycan shield across scales. Proc Natl Acad Sci U S A 117 (45):28014-28025. PubMed PMID:33093196
  18. McClatchy, DB et al. (2020) Quantitative analysis of global protein stability rates in tissues. Sci Rep 10 (1):15983. PubMed PMID:32994440
  19. Gomes, FP et al. (2020) Protein signatures of seminal plasma from bulls with contrasting frozen-thawed sperm viability. Sci Rep 10 (1):14661. PubMed PMID:32887897
  20. Chen, H et al. (2020) Loss of MAGEL2 in Prader-Willi syndrome leads to decreased secretory granule and neuropeptide production. JCI Insight 5 (17):. PubMed PMID:32879135
  21. Remes, PM et al. (2020) Highly Multiplex Targeted Proteomics Enabled by Real-Time Chromatographic Alignment. Anal Chem 92 (17):11809-11817. PubMed PMID:32867497
  22. Giadone, RM et al. (2020) Expression of Amyloidogenic Transthyretin Drives Hepatic Proteostasis Remodeling in an Induced Pluripotent Stem Cell Model of Systemic Amyloid Disease. Stem Cell Reports 15 (2):515-528. PubMed PMID:32735824
  23. Terhorst, A et al. (2020) The environmental stress response causes ribosome loss in aneuploid yeast cells. Proc Natl Acad Sci U S A 117 (29):17031-17040. PubMed PMID:32632008
  24. Alghanem, B et al. (2020) Proteomics Profiling of KAIMRC1 in Comparison to MDA-MB231 and MCF-7. Int J Mol Sci 21 (12):. PubMed PMID:32570693
  25. Fernández-Costa, C et al. (2020) Impact of the Identification Strategy on the Reproducibility of the DDA and DIA Results. J Proteome Res 19 (8):3153-3161. PubMed PMID:32510229
  26. Freund, EC et al. (2020) Unbiased Identification of trans Regulators of ADAR and A-to-I RNA Editing. Cell Rep 31 (7):107656. PubMed PMID:32433965
  27. Erijman, A et al. (2020) A High-Throughput Screen for Transcription Activation Domains Reveals Their Sequence Features and Permits Prediction by Deep Learning. Mol Cell 78 (5):890-902.e6. PubMed PMID:32416068
  28. Pino, LK et al. (2020) Acquiring and Analyzing Data Independent Acquisition Proteomics Experiments without Spectrum Libraries. Mol Cell Proteomics 19 (7):1088-1103. PubMed PMID:32312845
  29. Thompson, AJ et al. (2020) Human Influenza Virus Hemagglutinins Contain Conserved Oligomannose N-Linked Glycans Allowing Potent Neutralization by Lectins. Cell Host Microbe 27 (5):725-735.e5. PubMed PMID:32298658
  30. Fuller, GG et al. (2020) RNA promotes phase separation of glycolysis enzymes into yeast G bodies in hypoxia. Elife 9 :. PubMed PMID:32298230
  31. Chen, Z et al. (2020) De novo design of protein logic gates. Science 368 (6486):78-84. PubMed PMID:32241946
  32. Andrews, B et al. (2020) Distinct patterns of mutational sensitivity for λ resistance and maltodextrin transport in Escherichia coli LamB. Microb Genom 6 (4):. PubMed PMID:32238226
  33. Dorrity, MW et al. (2020) Dimensionality reduction by UMAP to visualize physical and genetic interactions. Nat Commun 11 (1):1537. PubMed PMID:32210240
  34. Yang, S et al. (2020) PTPN22 phosphorylation acts as a molecular rheostat for the inhibition of TCR signaling. Sci Signal 13 (623):. PubMed PMID:32184287
  35. Federation, AJ et al. (2020) Highly Parallel Quantification and Compartment Localization of Transcription Factors and Nuclear Proteins. Cell Rep 30 (8):2463-2471.e5. PubMed PMID:32101728
  36. 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
  37. 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
  38. Fondrie, WE et al. (2020) Machine Learning Strategy That Leverages Large Data sets to Boost Statistical Power in Small-Scale Experiments. J Proteome Res 19 (3):1267-1274. PubMed PMID:32009418
  39. 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
  40. Catania, S et al. (2020) Evolutionary Persistence of DNA Methylation for Millions of Years after Ancient Loss of a De Novo Methyltransferase. Cell 180 (2):263-277.e20. PubMed PMID:31955845
  41. Fernández-Costa, C et al. (2020) Improving Proteomics Data Reproducibility with a Dual-Search Strategy. Anal Chem 92 (2):1697-1701. PubMed PMID:31880919
  42. 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
  43. Sonntag, T et al. (2019) The KLDpT activation loop motif is critical for MARK kinase activity. PLoS One 14 (12):e0225727. PubMed PMID:31794565
  44. da Silva, BS et al. (2019) Integrative proteomics and pharmacogenomics analysis of methylphenidate treatment response. Transl Psychiatry 9 (1):308. PubMed PMID:31740662
  45. Deutsch, EW et al. (2020) The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics. Nucleic Acids Res 48 (D1):D1145-D1152. PubMed PMID:31686107
  46. 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
  47. Wang, J et al. (2019) Biochemical analysis of protein arginylation. Methods Enzymol 626 :89-113. PubMed PMID:31606094
  48. Miller, MP et al. (2019) Kinetochore-associated Stu2 promotes chromosome biorientation in vivo. PLoS Genet 15 (10):e1008423. PubMed PMID:31584935
  49. Lancaster, SM et al. (2019) Fitness benefits of loss of heterozygosity in Saccharomyces hybrids. Genome Res 29 (10):1685-1692. PubMed PMID:31548357
  50. 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
  51. 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
  52. 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
  53. 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
  54. 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
  55. Searle, BC et al. (2019) Thesaurus: quantifying phosphopeptide positional isomers. Nat Methods 16 (8):703-706. PubMed PMID:31363206
  56. 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
  57. 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
  58. Alonso, AM et al. (2019) Exploring protein myristoylation in Toxoplasma gondii. Exp Parasitol 203 :8-18. PubMed PMID:31150653
  59. 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
  60. 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
  61. 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
  62. Santos, MDM et al. (2019) A quantitation module for isotope-labeled peptides integrated into PatternLab for proteomics. J Proteomics 202 :103371. PubMed PMID:31034900
  63. 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
  64. Yates, JR 3rd et al. (2019) Recent technical advances in proteomics. F1000Res 8 :. PubMed PMID:30997033
  65. 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
  66. Dorrity, MW et al. (2019) High-throughput identification of dominant negative polypeptides in yeast. Nat Methods 16 (5):413-416. PubMed PMID:30962621
  67. 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
  68. 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
  69. 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
  70. Correia, SP et al. (2019) The circadian E3 ligase complex SCFFBXL3+CRY targets TLK2. Sci Rep 9 (1):198. PubMed PMID:30655559
  71. Sonntag, T et al. (2019) Mitogenic Signals Stimulate the CREB Coactivator CRTC3 through PP2A Recruitment. iScience 11 :134-145. PubMed PMID:30611118
  72. Pankow, S et al. (2019) A posttranslational modification code for CFTR maturation is altered in cystic fibrosis. Sci Signal 12 (562):. PubMed PMID:30600261
  73. 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
  74. Gabere, MN et al. (2019) Response to comments on 'Empirical comparison of web-based antimicrobial peptide prediction tools'. Bioinformatics 35 (15):2695-2696. PubMed PMID:30561528
  75. 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
  76. 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
  77. 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
  78. 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
  79. Park, SKR et al. (2019) ComPIL 2.0: An Updated Comprehensive Metaproteomics Database. J Proteome Res 18 (2):616-622. PubMed PMID:30525664
  80. 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
  81. 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
  82. 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
  83. 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
  84. 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
  85. 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
  86. 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
  87. 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
  88. Pankow, S et al. (2019) Understanding molecular mechanisms of disease through spatial proteomics. Curr Opin Chem Biol 48 :19-25. PubMed PMID:30308467
  89. 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
  90. 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
  91. 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
  92. 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
  93. Rathore, A et al. (2018) MIEF1 Microprotein Regulates Mitochondrial Translation. Biochemistry 57 (38):5564-5575. PubMed PMID:30215512
  94. Jester, BW et al. (2018) Engineered Biosensors from Dimeric Ligand-Binding Domains. ACS Synth Biol 7 (10):2457-2467. PubMed PMID:30204430
  95. Wang, Z et al. (2018) Defective RNA polymerase III is negatively regulated by the SUMO-Ubiquitin-Cdc48 pathway. Elife 7 :. PubMed PMID:30192228
  96. 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
  97. 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
  98. 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
  99. 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
  100. McClatchy, DB et al. (2018) Structural Analysis of Hippocampal Kinase Signal Transduction. ACS Chem Neurosci 9 (12):3072-3085. PubMed PMID:30053369