NOTE: The YRC shutdown in March 2022. No new collaborations are being accepted.
Publications
15660
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Publications

Latest YRC Publications

(see all in PubMed)

  1. Nguyen, TT et al. (2024) A tick saliva serpin, IxsS17 inhibits host innate immune system proteases and enhances host colonization by Lyme disease agent. PLoS Pathog 20 (2):e1012032. PubMed PMID:38394332
  2. da Silva Vaz Junior, I et al. (2024) Changes in saliva protein profile throughout Rhipicephalus microplus blood feeding. Parasit Vectors 17 (1):36. PubMed PMID:38281054
  3. Martin, R et al. (2024) Template switching between the leading and lagging strands at replication forks generates inverted copy number variants through hairpin-capped extrachromosomal DNA. PLoS Genet 20 (1):e1010850. PubMed PMID:38175823
  4. Cheng, LC et al. (2023) Comparative membrane proteomics reveals diverse cell regulators concentrated at the nuclear envelope. Life Sci Alliance 6 (9):. PubMed PMID:37433644
  5. Song, R et al. (2023) Trans-Golgi protein TVP23B regulates host-microbe interactions via Paneth cell homeostasis and Goblet cell glycosylation. Nat Commun 14 (1):3652. PubMed PMID:37339972
  6. Keller, A et al. (2023) Condition-dependent fitness effects of large synthetic chromosome amplifications. bioRxiv :. PubMed PMID:37333112
  7. Jones, JA et al. (2023) Nuclear translocation of an aminoacyl-tRNA synthetase may mediate a chronic "integrated stress response". Cell Rep 42 (6):112632. PubMed PMID:37314928
  8. Witus, SR et al. (2023) BRCA1/BARD1 intrinsically disordered regions facilitate chromatin recruitment and ubiquitylation. EMBO J 42 (15):e113565. PubMed PMID:37305927
  9. Cui, H et al. (2023) Publisher Correction: Arg-tRNA synthetase links inflammatory metabolism to RNA splicing and nuclear trafficking via SRRM2. Nat Cell Biol 25 (7):1073. PubMed PMID:37237245
  10. Baboo, S et al. (2023) Evolving spike-protein N-glycosylation in SARS-CoV-2 variants. bioRxiv :. PubMed PMID:37214937
  11. Koppes, EA et al. (2023) Insulin secretion deficits in a Prader-Willi syndrome β-cell model are associated with a concerted downregulation of multiple endoplasmic reticulum chaperones. PLoS Genet 19 (4):e1010710. PubMed PMID:37068109
  12. Cui, H et al. (2023) Arg-tRNA synthetase links inflammatory metabolism to RNA splicing and nuclear trafficking via SRRM2. Nat Cell Biol 25 (4):592-603. PubMed PMID:37059883
  13. Baboo, S et al. (2023) DeGlyPHER: Highly sensitive site-specific analysis of N-linked glycans on proteins. Methods Enzymol 682 :137-185. PubMed PMID:36948700
  14. Cheng, LC et al. (2023) Comparative membrane proteomics reveals diverse cell regulators concentrated at the nuclear envelope. bioRxiv :. PubMed PMID:36824861
  15. Grabowsky, ER et al. (2023) Montane Rattlesnakes in México: Venoms of Crotalus tancitarensis and Related Species within the Crotalus intermedius Group. Toxins (Basel) 15 (1):. PubMed PMID:36668891
  16. Hoopmann, MR et al. (2023) Improved Analysis of Cross-Linking Mass Spectrometry Data with Kojak 2.0, Advanced by Integration into the Trans-Proteomic Pipeline. J Proteome Res 22 (2):647-655. PubMed PMID:36629399
  17. Martinez, TF et al. (2023) Profiling mouse brown and white adipocytes to identify metabolically relevant small ORFs and functional microproteins. Cell Metab 35 (1):166-183.e11. PubMed PMID:36599300
  18. Mulenga, A et al. (2022) Identification and characterization of proteins that form the inner core Ixodes scapularis tick attachment cement layer. Sci Rep 12 (1):21300. PubMed PMID:36494396
  19. Schiapparelli, LM et al. (2022) Activity-Induced Cortical Glutamatergic Neuron Nascent Proteins. J Neurosci 42 (42):7900-7920. PubMed PMID:36261270
  20. Bamberger, C et al. (2022) Nvp63 and nvPIWIL1 Suppress Retrotransposon Activation in the Sea Anemone Nematostella vectensis. J Proteome Res 21 (11):2586-2595. PubMed PMID:36195974
  21. Oh, CK et al. (2023) Targeted protein S-nitrosylation of ACE2 inhibits SARS-CoV-2 infection. Nat Chem Biol 19 (3):275-283. PubMed PMID:36175661
  22. Basisty, N et al. (2023) TurnoveR: A Skyline External Tool for Analysis of Protein Turnover in Metabolic Labeling Studies. J Proteome Res 22 (2):311-322. PubMed PMID:36165806
  23. Wicky, BIM et al. (2022) Hallucinating symmetric protein assemblies. Science 378 (6615):56-61. PubMed PMID:36108048
  24. Chen, YS et al. (2022) Rvb1/Rvb2 proteins couple transcription and translation during glucose starvation. Elife 11 :. PubMed PMID:36107469
  25. Lu, S et al. (2022) Heat-shock chaperone HSPB1 regulates cytoplasmic TDP-43 phase separation and liquid-to-gel transition. Nat Cell Biol 24 (9):1378-1393. PubMed PMID:36075972
  26. Cheng, LC et al. (2022) Shared and Distinctive Neighborhoods of Emerin and Lamin B Receptor Revealed by Proximity Labeling and Quantitative Proteomics. J Proteome Res 21 (9):2197-2210. PubMed PMID:35972904
  27. Huynh, HH et al. (2022) A Targeted Liquid Chromatography-Tandem Mass Spectrometry Method for Simultaneous Quantification of Peptides from the Carboxyl-terminal Region of Type III Procollagen, Biomarkers of Collagen Turnover. Clin Chem 68 (10):1281-1291. PubMed PMID:35906802
  28. Kirkwood, KI et al. (2022) Utilizing Skyline to analyze lipidomics data containing liquid chromatography, ion mobility spectrometry and mass spectrometry dimensions. Nat Protoc 17 (11):2415-2430. PubMed PMID:35831612
  29. Peng, D et al. (2022) A male steroid controls female sexual behaviour in the malaria mosquito. Nature 608 (7921):93-97. PubMed PMID:35794471
  30. Savinov, A et al. (2022) Mapping functional regions of essential bacterial proteins with dominant-negative protein fragments. Proc Natl Acad Sci U S A 119 (26):e2200124119. PubMed PMID:35749361
  31. Macé, K et al. (2022) Cryo-EM structure of a type IV secretion system. Nature 607 (7917):191-196. PubMed PMID:35732732
  32. Reiter, KH et al. (2022) Cullin-independent recognition of HHARI substrates by a dynamic RBR catalytic domain. Structure 30 (9):1269-1284.e6. PubMed PMID:35716664
  33. Heil, LR et al. (2022) Building Spectral Libraries from Narrow-Window Data-Independent Acquisition Mass Spectrometry Data. J Proteome Res 21 (6):1382-1391. PubMed PMID:35549345
  34. Phipps, WS et al. (2022) Tandem Mass Spectrometry-Based Amyloid Typing Using Manual Microdissection and Open-Source Data Processing. Am J Clin Pathol 157 (5):748-757. PubMed PMID:35512256
  35. Santos, MDM et al. (2022) Simple, efficient and thorough shotgun proteomic analysis with PatternLab V. Nat Protoc 17 (7):1553-1578. PubMed PMID:35411045
  36. 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
  37. Hills, E et al. (2022) Comprehensive Mutational Analysis of the Lasso Peptide Klebsidin. ACS Chem Biol 17 (4):998-1010. PubMed PMID:35315272
  38. Shah, SH et al. (2022) Quantitative transportomics identifies Kif5a as a major regulator of neurodegeneration. Elife 11 :. PubMed PMID:35259089
  39. 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
  40. Stillman, M et al. (2022) Activity dependent dissociation of the Homer1 interactome. Sci Rep 12 (1):3207. PubMed PMID:35217690
  41. Yildirim, Z et al. (2022) Intercepting IRE1 kinase-FMRP signaling prevents atherosclerosis progression. EMBO Mol Med 14 (4):e15344. PubMed PMID:35191199
  42. 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
  43. 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
  44. Zhao, X et al. (2022) The metabolome as a biomarker of aging in Drosophila melanogaster. Aging Cell 21 (2):e13548. PubMed PMID:35019203
  45. 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
  46. Cohen, ZR et al. (2022) Prebiotic Membranes and Micelles Do Not Inhibit Peptide Formation During Dehydration. Chembiochem 23 (3):e202100614. PubMed PMID:34881485
  47. 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
  48. 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
  49. 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
  50. 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
  51. 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
  52. 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
  53. Zhou, W et al. (2021) Expanding the binding specificity for RNA recognition by a PUF domain. Nat Commun 12 (1):5107. PubMed PMID:34429425
  54. Fondrie, WE et al. (2021) ppx: Programmatic Access to Proteomics Data Repositories. J Proteome Res 20 (9):4621-4624. PubMed PMID:34342226
  55. Lu, YY et al. (2021) DIAmeter: matching peptides to data-independent acquisition mass spectrometry data. Bioinformatics 37 (Suppl_1):i434-i442. PubMed PMID:34252924
  56. Wellington Miranda, S et al. (2021) A covariation analysis reveals elements of selectivity in quorum sensing systems. Elife 10 :. PubMed PMID:34180398
  57. 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
  58. Brilot, AF et al. (2021) CM1-driven assembly and activation of yeast γ-tubulin small complex underlies microtubule nucleation. Elife 10 :. PubMed PMID:33949948
  59. Mohieldin, AM et al. (2021) Ciliary extracellular vesicles are distinct from the cytosolic extracellular vesicles. J Extracell Vesicles 10 (6):e12086. PubMed PMID:33936569
  60. Ollodart, AR et al. (2021) Multiplexing mutation rate assessment: determining pathogenicity of Msh2 variants in Saccharomyces cerevisiae. Genetics 218 (2):. PubMed PMID:33848333
  61. 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
  62. 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
  63. Bamberger, C et al. (2021) The Host Interactome of Spike Expands the Tropism of SARS-CoV-2. bioRxiv :. PubMed PMID:33619478
  64. Fondrie, WE et al. (2021) mokapot: Fast and Flexible Semisupervised Learning for Peptide Detection. J Proteome Res 20 (4):1966-1971. PubMed PMID:33596079
  65. 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
  66. 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
  67. 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
  68. 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
  69. Shan, CM et al. (2020) The INO80 Complex Regulates Epigenetic Inheritance of Heterochromatin. Cell Rep 33 (13):108561. PubMed PMID:33378674
  70. 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
  71. 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
  72. Yu, H et al. (2021) HSP70 chaperones RNA-free TDP-43 into anisotropic intranuclear liquid spherical shells. Science 371 (6529):. PubMed PMID:33335017
  73. 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
  74. Nakamura, T et al. (2021) Noncanonical transnitrosylation network contributes to synapse loss in Alzheimer's disease. Science 371 (6526):. PubMed PMID:33273062
  75. 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
  76. 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
  77. McClatchy, DB et al. (2020) Quantitative analysis of global protein stability rates in tissues. Sci Rep 10 (1):15983. PubMed PMID:32994440
  78. 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
  79. 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
  80. Remes, PM et al. (2020) Highly Multiplex Targeted Proteomics Enabled by Real-Time Chromatographic Alignment. Anal Chem 92 (17):11809-11817. PubMed PMID:32867497
  81. Mohieldin, AM et al. (2020) Proteomic Identification Reveals the Role of Ciliary Extracellular-Like Vesicle in Cardiovascular Function. Adv Sci (Weinh) 7 (16):1903140. PubMed PMID:32832346
  82. 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
  83. 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
  84. 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
  85. 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
  86. 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
  87. 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
  88. Kim, TK et al. (2020) Amblyomma americanum serpin 41 (AAS41) inhibits inflammation by targeting chymase and chymotrypsin. Int J Biol Macromol 156 :1007-1021. PubMed PMID:32320803
  89. 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
  90. 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
  91. Fuller, GG et al. (2020) RNA promotes phase separation of glycolysis enzymes into yeast G bodies in hypoxia. Elife 9 :. PubMed PMID:32298230
  92. Chen, Z et al. (2020) De novo design of protein logic gates. Science 368 (6486):78-84. PubMed PMID:32241946
  93. 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
  94. Dorrity, MW et al. (2020) Dimensionality reduction by UMAP to visualize physical and genetic interactions. Nat Commun 11 (1):1537. PubMed PMID:32210240
  95. 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
  96. 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
  97. 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
  98. 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
  99. 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
  100. 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