Publications
15660
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Publications

Latest YRC Publications

(see all in PubMed)

  1. Shah, SH et al. (2022) Quantitative BONCAT Allows Identification of Newly Synthesized Proteins after Optic Nerve Injury. J Neurosci 42 (19):4042-4052. PubMed PMID:35396330
  2. Hills, E et al. (2022) Comprehensive Mutational Analysis of the Lasso Peptide Klebsidin. ACS Chem Biol 17 (4):998-1010. PubMed PMID:35315272
  3. Shah, SH et al. (2022) Quantitative transportomics identifies Kif5a as a major regulator of neurodegeneration. Elife 11 :. PubMed PMID:35259089
  4. Plubell, DL et al. (2022) Putting Humpty Dumpty Back Together Again: What Does Protein Quantification Mean in Bottom-Up Proteomics?. J Proteome Res 21 (4):891-898. PubMed PMID:35220718
  5. Stillman, M et al. (2022) Activity dependent dissociation of the Homer1 interactome. Sci Rep 12 (1):3207. PubMed PMID:35217690
  6. Yildirim, Z et al. (2022) Intercepting IRE1 kinase-FMRP signaling prevents atherosclerosis progression. EMBO Mol Med 14 (4):e15344. PubMed PMID:35191199
  7. Riffle, M et al. (2022) Discovery and Visualization of Uncharacterized Drug-Protein Adducts Using Mass Spectrometry. Anal Chem 94 (8):3501-3509. PubMed PMID:35184559
  8. Schiapparelli, LM et al. (2022) Proteomic screen reveals diverse protein transport between connected neurons in the visual system. Cell Rep 38 (4):110287. PubMed PMID:35081342
  9. Zhao, X et al. (2022) The metabolome as a biomarker of aging in Drosophila melanogaster. Aging Cell 21 (2):e13548. PubMed PMID:35019203
  10. Marsh, AN et al. (2022) Skyline Batch: An Intuitive User Interface for Batch Processing with Skyline. J Proteome Res 21 (1):289-294. PubMed PMID:34919405
  11. Cohen, ZR et al. (2022) Prebiotic Membranes and Micelles Do Not Inhibit Peptide Formation During Dehydration. Chembiochem 23 (3):e202100614. PubMed PMID:34881485
  12. Kirkwood, KI et al. (2022) Development and Application of Multidimensional Lipid Libraries to Investigate Lipidomic Dysregulation Related to Smoke Inhalation Injury Severity. J Proteome Res 21 (1):232-242. PubMed PMID:34874736
  13. Bamberger, C et al. (2021) SMG1 and CDK12 Link ΔNp63α Phosphorylation to RNA Surveillance in Keratinocytes. J Proteome Res 20 (12):5347-5358. PubMed PMID:34761935
  14. Baboo, S et al. (2021) DeGlyPHER: An Ultrasensitive Method for the Analysis of Viral Spike N-Glycoforms. Anal Chem 93 (40):13651-13657. PubMed PMID:34597027
  15. Ganguly, A et al. (2021) Clathrin packets move in slow axonal transport and deliver functional payloads to synapses. Neuron 109 (18):2884-2901.e7. PubMed PMID:34534453
  16. Jiang, P et al. (2021) A modified fluctuation assay reveals a natural mutator phenotype that drives mutation spectrum variation within Saccharomyces cerevisiae. Elife 10 :. PubMed PMID:34523420
  17. Woodall, NB et al. (2021) De novo design of tyrosine and serine kinase-driven protein switches. Nat Struct Mol Biol 28 (9):762-770. PubMed PMID:34518698
  18. Zhou, W et al. (2021) Expanding the binding specificity for RNA recognition by a PUF domain. Nat Commun 12 (1):5107. PubMed PMID:34429425
  19. Fondrie, WE et al. (2021) ppx: Programmatic Access to Proteomics Data Repositories. J Proteome Res 20 (9):4621-4624. PubMed PMID:34342226
  20. Lu, YY et al. (2021) DIAmeter: matching peptides to data-independent acquisition mass spectrometry data. Bioinformatics 37 (Suppl_1):i434-i442. PubMed PMID:34252924
  21. Wellington Miranda, S et al. (2021) A covariation analysis reveals elements of selectivity in quorum sensing systems. Elife 10 :. PubMed PMID:34180398
  22. Thomas, EB et al. (2021) Staging Encystation Progression in Giardia lamblia Using Encystation-Specific Vesicle Morphology and Associating Molecular Markers. Front Cell Dev Biol 9 :662945. PubMed PMID:33987184
  23. Brilot, AF et al. (2021) CM1-driven assembly and activation of yeast γ-tubulin small complex underlies microtubule nucleation. Elife 10 :. PubMed PMID:33949948
  24. Mohieldin, AM et al. (2021) Ciliary extracellular vesicles are distinct from the cytosolic extracellular vesicles. J Extracell Vesicles 10 (6):e12086. PubMed PMID:33936569
  25. Ollodart, AR et al. (2021) Multiplexing mutation rate assessment: determining pathogenicity of Msh2 variants in Saccharomyces cerevisiae. Genetics 218 (2):. PubMed PMID:33848333
  26. 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
  27. 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
  28. Bamberger, C et al. (2021) The Host Interactome of Spike Expands the Tropism of SARS-CoV-2. bioRxiv :. PubMed PMID:33619478
  29. Fondrie, WE et al. (2021) mokapot: Fast and Flexible Semisupervised Learning for Peptide Detection. J Proteome Res 20 (4):1966-1971. PubMed PMID:33596079
  30. 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
  31. 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
  32. 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
  33. 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
  34. Shan, CM et al. (2020) The INO80 Complex Regulates Epigenetic Inheritance of Heterochromatin. Cell Rep 33 (13):108561. PubMed PMID:33378674
  35. 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
  36. 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
  37. Yu, H et al. (2021) HSP70 chaperones RNA-free TDP-43 into anisotropic intranuclear liquid spherical shells. Science 371 (6529):. PubMed PMID:33335017
  38. 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
  39. Nakamura, T et al. (2021) Noncanonical transnitrosylation network contributes to synapse loss in Alzheimer's disease. Science 371 (6526):. PubMed PMID:33273062
  40. 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
  41. 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
  42. McClatchy, DB et al. (2020) Quantitative analysis of global protein stability rates in tissues. Sci Rep 10 (1):15983. PubMed PMID:32994440
  43. 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
  44. 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
  45. Remes, PM et al. (2020) Highly Multiplex Targeted Proteomics Enabled by Real-Time Chromatographic Alignment. Anal Chem 92 (17):11809-11817. PubMed PMID:32867497
  46. 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
  47. 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
  48. 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
  49. 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
  50. 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
  51. 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
  52. 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
  53. 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
  54. Fuller, GG et al. (2020) RNA promotes phase separation of glycolysis enzymes into yeast G bodies in hypoxia. Elife 9 :. PubMed PMID:32298230
  55. Chen, Z et al. (2020) De novo design of protein logic gates. Science 368 (6486):78-84. PubMed PMID:32241946
  56. 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
  57. Dorrity, MW et al. (2020) Dimensionality reduction by UMAP to visualize physical and genetic interactions. Nat Commun 11 (1):1537. PubMed PMID:32210240
  58. 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
  59. 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
  60. 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
  61. 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
  62. 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
  63. 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
  64. 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
  65. Fernández-Costa, C et al. (2020) Improving Proteomics Data Reproducibility with a Dual-Search Strategy. Anal Chem 92 (2):1697-1701. PubMed PMID:31880919
  66. 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
  67. Sonntag, T et al. (2019) The KLDpT activation loop motif is critical for MARK kinase activity. PLoS One 14 (12):e0225727. PubMed PMID:31794565
  68. da Silva, BS et al. (2019) Integrative proteomics and pharmacogenomics analysis of methylphenidate treatment response. Transl Psychiatry 9 (1):308. PubMed PMID:31740662
  69. 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
  70. 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
  71. Wang, J et al. (2019) Biochemical analysis of protein arginylation. Methods Enzymol 626 :89-113. PubMed PMID:31606094
  72. Miller, MP et al. (2019) Kinetochore-associated Stu2 promotes chromosome biorientation in vivo. PLoS Genet 15 (10):e1008423. PubMed PMID:31584935
  73. Lancaster, SM et al. (2019) Fitness benefits of loss of heterozygosity in Saccharomyces hybrids. Genome Res 29 (10):1685-1692. PubMed PMID:31548357
  74. 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
  75. 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
  76. 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
  77. 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
  78. 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
  79. Searle, BC et al. (2019) Thesaurus: quantifying phosphopeptide positional isomers. Nat Methods 16 (8):703-706. PubMed PMID:31363206
  80. 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
  81. 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
  82. Alonso, AM et al. (2019) Exploring protein myristoylation in Toxoplasma gondii. Exp Parasitol 203 :8-18. PubMed PMID:31150653
  83. 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
  84. 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
  85. 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
  86. Santos, MDM et al. (2019) A quantitation module for isotope-labeled peptides integrated into PatternLab for proteomics. J Proteomics 202 :103371. PubMed PMID:31034900
  87. 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
  88. Yates, JR 3rd et al. (2019) Recent technical advances in proteomics. F1000Res 8 :. PubMed PMID:30997033
  89. 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
  90. Dorrity, MW et al. (2019) High-throughput identification of dominant negative polypeptides in yeast. Nat Methods 16 (5):413-416. PubMed PMID:30962621
  91. 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
  92. 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
  93. 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
  94. Correia, SP et al. (2019) The circadian E3 ligase complex SCFFBXL3+CRY targets TLK2. Sci Rep 9 (1):198. PubMed PMID:30655559
  95. Sonntag, T et al. (2019) Mitogenic Signals Stimulate the CREB Coactivator CRTC3 through PP2A Recruitment. iScience 11 :134-145. PubMed PMID:30611118
  96. Pankow, S et al. (2019) A posttranslational modification code for CFTR maturation is altered in cystic fibrosis. Sci Signal 12 (562):. PubMed PMID:30600261
  97. 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
  98. 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
  99. 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
  100. 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