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. Berger, S et al. (2025) Computational design of potent and selective binders of BAK and BAX. Sci Adv 11 (36):eadt4170. PubMed PMID:40911686
  2. Liu, X et al. (2025) Proteomic profiling of primary cilia in the developing brain uncovers new regulators of cortical development. bioRxiv :. PubMed PMID:40654709
  3. Xie, Y et al. (2025) Activity-dependent synthesis of Emerin gates neuronal plasticity by regulating proteostasis. Cell Rep 44 (4):115439. PubMed PMID:40208794
  4. Shen, H et al. (2025) De novo design of inducibly assembling multi-component filaments. bioRxiv :. PubMed PMID:40196579
  5. Lavallée-Adam, M et al. (2025) TargetSeeker-MS: A Bayesian Inference Approach for Drug-Target Discovery Using Protein Fractionation Coupled to Mass Spectrometry. J Am Soc Mass Spectrom 36 (4):664-679. PubMed PMID:40067882
  6. Riffle, M et al. (2025) Limelight: An Open, Web-Based Tool for Visualizing, Sharing, and Analyzing Mass Spectrometry Data from DDA Pipelines. J Proteome Res 24 (4):1895-1906. PubMed PMID:40036265
  7. Zhang, J et al. (2025) Proximity based proteomics reveals Git1 as a regulator of Smoothened signaling. bioRxiv :. PubMed PMID:39829937
  8. Kulkarni, SS et al. (2025) The Heterotaxy Gene CCDC11 Is Important for Cytokinesis via RhoA Regulation. Cytoskeleton (Hoboken) 82 (6):360-371. PubMed PMID:39479942
  9. Zelter, A et al. (2024) Detection and Quantification of Drug-Protein Adducts in Human Liver. J Proteome Res 23 (11):5143-5152. PubMed PMID:39442081
  10. Lev-Ram, V et al. (2024) Do Perineuronal Nets Stabilize the Engram of a Synaptic Circuit?. Cells 13 (19):. PubMed PMID:39404392
  11. Tsantilas, KA et al. (2024) A Framework for Quality Control in Quantitative Proteomics. J Proteome Res 23 (10):4392-4408. PubMed PMID:39248652
  12. Vicente, JJ et al. (2024) The kinesin motor Kif9 regulates centriolar satellite positioning and mitotic progression. bioRxiv :. PubMed PMID:38617353
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. Keller, A et al. (2023) Condition-dependent fitness effects of large synthetic chromosome amplifications. bioRxiv :. PubMed PMID:37333112
  19. 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
  20. Witus, SR et al. (2023) BRCA1/BARD1 intrinsically disordered regions facilitate chromatin recruitment and ubiquitylation. EMBO J 42 (15):e113565. PubMed PMID:37305927
  21. 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
  22. Baboo, S et al. (2023) Evolving spike-protein N-glycosylation in SARS-CoV-2 variants. bioRxiv :. PubMed PMID:37214937
  23. 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
  24. 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
  25. 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
  26. Cheng, LC et al. (2023) Comparative membrane proteomics reveals diverse cell regulators concentrated at the nuclear envelope. bioRxiv :. PubMed PMID:36824861
  27. 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
  28. 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
  29. 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
  30. 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
  31. Schiapparelli, LM et al. (2022) Activity-Induced Cortical Glutamatergic Neuron Nascent Proteins. J Neurosci 42 (42):7900-7920. PubMed PMID:36261270
  32. 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
  33. 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
  34. 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
  35. Wicky, BIM et al. (2022) Hallucinating symmetric protein assemblies. Science 378 (6615):56-61. PubMed PMID:36108048
  36. Chen, YS et al. (2022) Rvb1/Rvb2 proteins couple transcription and translation during glucose starvation. Elife 11 :. PubMed PMID:36107469
  37. 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
  38. 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
  39. 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
  40. 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
  41. Jiang, P et al. (2022) A Modified Fluctuation Assay with a CAN1 Reporter in Yeast. Bio Protoc 12 (11):. PubMed PMID:35799910
  42. Peng, D et al. (2022) A male steroid controls female sexual behaviour in the malaria mosquito. Nature 608 (7921):93-97. PubMed PMID:35794471
  43. 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
  44. Macé, K et al. (2022) Cryo-EM structure of a type IV secretion system. Nature 607 (7917):191-196. PubMed PMID:35732732
  45. 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
  46. 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
  47. 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
  48. Santos, MDM et al. (2022) Simple, efficient and thorough shotgun proteomic analysis with PatternLab V. Nat Protoc 17 (7):1553-1578. PubMed PMID:35411045
  49. 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
  50. Hills, E et al. (2022) Comprehensive Mutational Analysis of the Lasso Peptide Klebsidin. ACS Chem Biol 17 (4):998-1010. PubMed PMID:35315272
  51. Shah, SH et al. (2022) Quantitative transportomics identifies Kif5a as a major regulator of neurodegeneration. Elife 11 :. PubMed PMID:35259089
  52. 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
  53. Stillman, M et al. (2022) Activity dependent dissociation of the Homer1 interactome. Sci Rep 12 (1):3207. PubMed PMID:35217690
  54. Yildirim, Z et al. (2022) Intercepting IRE1 kinase-FMRP signaling prevents atherosclerosis progression. EMBO Mol Med 14 (4):e15344. PubMed PMID:35191199
  55. 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
  56. 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
  57. Zhao, X et al. (2022) The metabolome as a biomarker of aging in Drosophila melanogaster. Aging Cell 21 (2):e13548. PubMed PMID:35019203
  58. 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
  59. Cohen, ZR et al. (2022) Prebiotic Membranes and Micelles Do Not Inhibit Peptide Formation During Dehydration. Chembiochem 23 (3):e202100614. PubMed PMID:34881485
  60. 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
  61. 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
  62. 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
  63. 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
  64. 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
  65. 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
  66. Zhou, W et al. (2021) Expanding the binding specificity for RNA recognition by a PUF domain. Nat Commun 12 (1):5107. PubMed PMID:34429425
  67. Fondrie, WE et al. (2021) ppx: Programmatic Access to Proteomics Data Repositories. J Proteome Res 20 (9):4621-4624. PubMed PMID:34342226
  68. Lu, YY et al. (2021) DIAmeter: matching peptides to data-independent acquisition mass spectrometry data. Bioinformatics 37 (Suppl_1):i434-i442. PubMed PMID:34252924
  69. Wellington Miranda, S et al. (2021) A covariation analysis reveals elements of selectivity in quorum sensing systems. Elife 10 :. PubMed PMID:34180398
  70. 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
  71. Brilot, AF et al. (2021) CM1-driven assembly and activation of yeast γ-tubulin small complex underlies microtubule nucleation. Elife 10 :. PubMed PMID:33949948
  72. Mohieldin, AM et al. (2021) Ciliary extracellular vesicles are distinct from the cytosolic extracellular vesicles. J Extracell Vesicles 10 (6):e12086. PubMed PMID:33936569
  73. Ollodart, AR et al. (2021) Multiplexing mutation rate assessment: determining pathogenicity of Msh2 variants in Saccharomyces cerevisiae. Genetics 218 (2):. PubMed PMID:33848333
  74. 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
  75. 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
  76. Bamberger, C et al. (2021) The Host Interactome of Spike Expands the Tropism of SARS-CoV-2. bioRxiv :. PubMed PMID:33619478
  77. Fondrie, WE et al. (2021) mokapot: Fast and Flexible Semisupervised Learning for Peptide Detection. J Proteome Res 20 (4):1966-1971. PubMed PMID:33596079
  78. 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
  79. 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
  80. 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
  81. 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
  82. Shan, CM et al. (2020) The INO80 Complex Regulates Epigenetic Inheritance of Heterochromatin. Cell Rep 33 (13):108561. PubMed PMID:33378674
  83. 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
  84. 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
  85. Yu, H et al. (2021) HSP70 chaperones RNA-free TDP-43 into anisotropic intranuclear liquid spherical shells. Science 371 (6529):. PubMed PMID:33335017
  86. 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
  87. Nakamura, T et al. (2021) Noncanonical transnitrosylation network contributes to synapse loss in Alzheimer's disease. Science 371 (6526):. PubMed PMID:33273062
  88. 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
  89. 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
  90. McClatchy, DB et al. (2020) Quantitative analysis of global protein stability rates in tissues. Sci Rep 10 (1):15983. PubMed PMID:32994440
  91. 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
  92. 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
  93. Remes, PM et al. (2020) Highly Multiplex Targeted Proteomics Enabled by Real-Time Chromatographic Alignment. Anal Chem 92 (17):11809-11817. PubMed PMID:32867497
  94. 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
  95. 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
  96. 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
  97. 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
  98. 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
  99. 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
  100. 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