List of works - John Yates

20 Years...2 Decades...10 Bienniums...5 Quadrenniums...4 Lustrums

scientific article published on 14 June 2021

A TRAF-like motif of the inducible costimulator ICOS controls development of germinal center TFH cells via the kinase TBK1.

scientific article published on 02 May 2016

A posttranslational modification code for CFTR maturation is altered in cystic fibrosis

scientific article published on 01 January 2019

Altered network and rescue of human neurons derived from individuals with early-onset genetic epilepsy

scientific article published on 22 April 2021

An SMC-like protein binds and regulates Caenorhabditis elegans condensins.

scientific article

Analysis of the Tropism of SARS-CoV-2 Based on the Host Interactome of the Spike Protein

scientific article published on 8 November 2023

Arg-tRNA synthetase links inflammatory metabolism to RNA splicing and nuclear trafficking via SRRM2

scientific article published in April 2023

Aurora Kinase A proximity interactome reveals centriolar satellites as regulators of its function during primary cilium biogenesis

scientific article published on 6 November 2020

Autism-linked Cullin3 germline haploinsufficiency impacts cytoskeletal dynamics and cortical neurogenesis through RhoA signaling

scientific article published on 16 March 2021

Cancer Conformational Landscape Shapes Tumorigenesis

scientific article published in April 2022

Changes in porcine cauda epididymal fluid proteome by disrupting the HPT axis: Unveiling potential mechanisms of male infertility

scientific article published on 04 August 2020

Cleavage of the SUN-domain protein Mps3 at its N-terminus regulates centrosome disjunction in budding yeast meiosis.

scientific article

ComPIL 2.0: An Updated Comprehensive Metaproteomics Database

scientific article published on 14 January 2019

Comparative Proteomic Analysis of Murine Cutaneous Lesions Induced by Leishmania amazonensis or Leishmania major

scientific article published on 29 May 2019

Comparative membrane proteomics reveals diverse cell regulators concentrated at the nuclear envelope

scientific article published in September 2023

Comparative membrane proteomics reveals diverse cell regulators concentrated at the nuclear envelope

scientific article published on 14 February 2023

Comparison of CRISPR Genomic Tagging for Affinity Purification and Endogenous Immunoprecipitation Coupled with Quantitative Mass Spectrometry To Identify the Dynamic AMPKα2 Interactome

scientific article published on 06 September 2019

Confronting Racism in Chemistry Journals

scientific article published on 19 June 2020

Control of seed dormancy and germination by DOG1-AHG1 PP2C phosphatase complex via binding to heme.

scientific article

Correction to “The Curiosity of the Young”

scientific article published on 22 February 2024

Cortical organoids model early brain development disrupted by 16p11.2 copy number variants in autism

scientific article published on 26 August 2021

Coupling of spliceosome complexity to intron diversity

scientific article published in November 2021

Covalent Protein Painting Reveals Structural Changes in the Proteome in Alzheimer Disease

scientific article published on 2 February 2020

DAF-16/FOXO and HLH-30/TFEB function as combinatorial transcription factors to promote stress resistance and longevity

scientific article published in Nature Communications

DNA replication acts as an error correction mechanism to maintain centromere identity by restricting CENP-A to centromeres

scientific article published on 03 June 2019

DeGlyPHER: An Ultrasensitive Method for the Analysis of Viral Spike -Glycoforms

scientific article published on 12 October 2021

Deducing the presence of proteins and proteoforms in quantitative proteomics.

scientific article published on 13 June 2018

Deep interactome profiling of membrane proteins by co-interacting protein identification technology

scientific article

Differential Precipitation of Proteins: A Simple Protein Fractionation Strategy to Gain Biological Insights with Proteomics

scientific article published in August 2023

Differential processing of HIV envelope glycans on the virus and soluble recombinant trimer

scientific article published in Nature Communications

Double mimicry evades tRNA synthetase editing by toxic vegetable-sourced non-proteinogenic amino acid.

scientific article published on 22 December 2017

EThcD and 213 nm UVPD for Top-Down Analysis of Bovine Seminal Plasma Proteoforms on Electrophoretic and Chromatographic Time Frames

scientific article published on 29 January 2020

Evolving spike-protein -glycosylation in SARS-CoV-2 variants

scientific article published on 18 December 2023

Fimbrin phosphorylation by metaphase Cdk1 regulates actin cable dynamics in budding yeast.

scientific article

Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii

scientific article

Global Analysis of Protein Expression of Inner Ear Hair Cells

scientific article published on 30 December 2016

Global site-specific N-glycosylation analysis of HIV envelope glycoprotein.

scientific article published on 28 March 2017

Global site-specific analysis of glycoprotein N-glycan processing.

scientific article published on 3 May 2018

HSP70 chaperones RNA-free TDP-43 into anisotropic intranuclear liquid spherical shells

scientific article published on 17 December 2020

Hexokinase 3 enhances myeloid cell survival via non-glycolytic functions

scientific article published on 11 May 2022

Hsc70 chaperone activity is required for the cytosolic slow axonal transport of synapsin.

scientific article published on 30 May 2017

IRE1α is an endogenous substrate of endoplasmic-reticulum-associated degradation

scientific article

Identification of Microprotein-Protein Interactions via APEX Tagging

scientific article

Identification of Open Stomata1-Interacting Proteins Reveals Interactions with Sucrose Non-fermenting1-Related Protein Kinases2 and with Type 2A Protein Phosphatases That Function in Abscisic Acid Responses.

scientific article published on 14 July 2015

Identification of in vivo CFTR conformations during biogenesis and upon misfolding by covalent protein painting (CPP)

scientific article published on 3 March 2021

Identification of novel targets for miR-29a using miRNA proteomics

scientific article published in 2012

Impact of the identification strategy on the reproducibility of DDA and DIA results

scientific article published on 08 June 2020

Improving Proteomics Data Reproducibility with a Dual-Search Strategy

scientific article published on 09 January 2020

Increased proteomic complexity in Drosophila hybrids during development.

scientific article published on 7 February 2018

Innovation's Mean Free Path

scientific article published on 24 March 2017

Innovation: Risk-Takers and Visionaries

scientific article published on 23 May 2019

Innovation: Structural Proteomics Goes Global

article

Innovations in Proteomics: The Drive to Single Cells

scientific article published on 19 July 2018

Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0.

scientific article

Integrating DIA Single-Cell Proteomics Data with the DiagnoMass Proteomic Hub for Biological Insights

scientific article published on 11 September 2024

Integrative proteomics and pharmacogenomics analysis of methylphenidate treatment response

scientific article published on 18 November 2019

Interactome analysis illustrates diverse gene regulatory processes associated with LIN28A in human iPS cell-derived neural progenitor cells

scientific article published on 23 October 2021

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.

scientific article published on 20 February 2018

Interlaboratory Study for Characterizing Monoclonal Antibodies by Top-Down and Middle-Down Mass Spectrometry

scientific article published on 19 August 2020

Intracellular amyloid toxicity induces oxytosis/ferroptosis regulated cell death

scientific article published on 06 October 2020

Intrinsic mesoscale properties of a Polycomb protein underpin heterochromatin fidelity

scientific article published on 22 May 2023

Ist1 regulates ESCRT-III assembly and function during multivesicular endosome biogenesis in Caenorhabditis elegans embryos.

scientific article published on 13 November 2017

Label-Free Proteomic Analysis Reveals Parasite-Specific Protein Alterations in Macrophages Following Leishmania amazonensis, Leishmania major, or Leishmania infantum Infection

scientific article published on 23 April 2019

MIEF1 Microprotein Regulates Mitochondrial Translation

scientific article published on 14 September 2018

Mechanistic Determinants of Slow Axonal Transport and Presynaptic Targeting of Clathrin Packets

scientific article published on 20 February 2020

Metabolic Reprogramming of Klebsiella pneumoniae Exposed to Serum and Its Potential Implications in Host Immune System Evasion and Resistance

scientific article published on 3 October 2024

Mitotic R-loops direct Aurora B kinase to maintain centromeric cohesion

scientific article published on 15 January 2021

National Cancer Institute Think-Tank Meeting Report on Proteomic Cartography and Biomarkers at the Single-Cell Level: Interrogation of Premalignant Lesions

scientific article published on 02 April 2020

Native top-down proteomics reveals EGFR-ERα signaling crosstalk in breast cancer cells dissociates NUTF2 dimers to modulate ERα signaling and cell growth

scientific article published on 24 July 2023

Next Generation Proteomic Pipeline for Chromosome-Based Proteomic Research Using NeXtProt and GENCODE Databases.

scientific article published in October 2017

Noncanonical transnitrosylation network contributes to synapse loss in Alzheimer's disease

scientific article published on 03 December 2020

Nvp63 and nvPIWIL1 Suppress Retrotransposon Activation in the Sea Anemone Nematostella vectensis

scientific article published on 4 October 2022

O-GlcNAcase targets pyruvate kinase M2 to regulate tumor growth

scientific article published on 09 September 2019

PACOM: A Versatile Tool for Integrating, Filtering, Visualizing, and Comparing Multiple Large Mass Spectrometry Proteomics Data Sets.

scientific article published on 20 March 2018

PASS-DIA: A Data-Independent Acquisition Approach for Discovery Studies

scientific article published on 20 October 2020

PTPN22 phosphorylation acts as a molecular rheostat for the inhibition of TCR signaling

scientific article published on 17 March 2020

Phenotypic and functional variation in venom and venom resistance of two sympatric rattlesnakes and their prey

scientific article published in 2021

Phosphotyrosine-dependent interaction between the kinases PKCθ and Zap70 promotes proximal TCR signaling

scientific article published on 16 April 2019

Profiling of Protein O-GlcNAcylation in Murine CD8+ Effector- and Memory-like T Cells.

scientific article published on 10 November 2017

Protein Footprinting via Covalent Protein Painting Reveals Structural Changes of the Proteome in Alzheimer's Disease

scientific article published on 7 May 2021

Protein arginylation targets alpha synuclein, facilitates normal brain health, and prevents neurodegeneration

scientific article published on 12 September 2017

Proteomic Analysis of Peripheral Blood Mononuclear Cells after a High-Fat, High-Carbohydrate Meal with Orange Juice.

scientific article

Proteomics INTegrator (PINT): An Online Tool To Store, Query, and Visualize Large Proteomics Experiment Results

scientific article published on 01 July 2019

Proteomics and pulse azidohomoalanine labeling of newly synthesized proteins: what are the potential applications?

scientific article published on 23 July 2018

Proteomics of Communities: Metaproteomics

scientific article published on 01 May 2019

Proteomics of Rat Lungs Infected by Cryptococcus gattii Reveals a Potential Warburg-like Effect

scientific article published on 26 September 2019

Publisher Correction: Arg-tRNA synthetase links inflammatory metabolism to RNA splicing and nuclear trafficking via SRRM2

scientific article published on 26 May 2023

Publisher Correction: Double mimicry evades tRNA synthetase editing by toxic vegetable-sourced non-proteinogenic amino acid

scientific article published on 13 March 2018

Quantitative analysis of newly synthesized proteins

scientific article published on 01 August 2018

Quantitative transportomics identifies Kif5a as a major regulator of neurodegeneration

scientific article published on 08 March 2022

RNA promotes phase separation of glycolysis enzymes into yeast G bodies in hypoxia

scientific article published on 16 April 2020

Recent technical advances in proteomics

scientific article published on 29 March 2019

Regulated nuclear accumulation of a histone methyltransferase times the onset of heterochromatin formation in embryos

scientific article published on 22 August 2018

Rising Stars in Proteomics and Metabolomics

scientific article published on 14 January 2021

Rvb1/Rvb2 proteins couple transcription and translation during glucose starvation

scientific article published on 15 September 2022

SHMT2 and the BRCC36/BRISC deubiquitinase regulate HIV-1 Tat K63-ubiquitylation and destruction by autophagy.

scientific article published on 23 May 2018

SMG1 and CDK12 Link ΔNp63α Phosphorylation to RNA Surveillance in Keratinocytes

scientific article published on 3 December 2021

Shared and Distinctive Neighborhoods of Emerin and Lamin B Receptor Revealed by Proximity Labeling and Quantitative Proteomics

scientific article published on 2 September 2022

Shared and distinctive neighborhoods of emerin and LBR revealed by proximity labeling and quantitative proteomics

scientific article published on 11 May 2022

Structural Analysis of Hippocampal Kinase Signal Transduction

scientific article published on 13 August 2018

Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate

scientific article published on 06 August 2020

Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate

scientific article published on 20 October 2020

TDP-43 and HSP70 phase separate into anisotropic, intranuclear liquid spherical annuli

scientific article published on 29 March 2020

Tandem Mass Tag Proteomic Analysis of in Vitro and in Vivo Models of Cutaneous Leishmaniasis Reveals Parasite-Specific and Nonspecific Modulation of Proteins in the Host

scientific article published on 24 October 2019

TargetSeeker-MS: A computational method for drug target discovery using protein separation coupled to mass spectrometry

Targeted Searches for Novel Peptides in Big Mass Spectrometry Data Sets

scientific article published on 25 December 2017

Temporal Quantitative Profiling of Newly Synthesized Proteins during Aβ Accumulation

scientific article published on 04 November 2020

The Curiosity of the Young

scientific article published on 5 January 2024

The Host Interactome of Spike Expands the Tropism of SARS-CoV-2

scientific article published on 16 February 2021

The Journey is the Reward, a Taoist Proverb, John B. Fenn Award for Distinguished Contribution in Mass Spectrometry Lecture

scientific article published on 27 April 2020

The SARS-CoV-2 nucleocapsid phosphoprotein forms mutually exclusive condensates with RNA and the membrane-associated M protein

scholarly article by Shan Lu published in January 2021

The circadian E3 ligase complex SCF targets TLK2

scientific article published in Scientific Reports

The human naive B cell repertoire contains distinct subclasses for a germline-targeting HIV-1 vaccine immunogen

article

The interactome of 2-Cys peroxiredoxins in Plasmodium falciparum.

scientific article published on 19 September 2019

The pseudokinase CaMKv is required for the activity-dependent maintenance of dendritic spines.

scientific article

Twelve Rules for Science (Yates Lab Version)

scientific article published on 07 February 2020

Update to Our Reader, Reviewer, and Author Communities-April 2020

scientific article published on 22 April 2020

Update to Our Reader, Reviewer, and Author Communities-April 2020

scientific article published on 23 April 2020

Vaccine priming of rare HIV broadly neutralizing antibody precursors in nonhuman primates

scientific article published in 2024

Venom Composition in a Phenotypically Variable Pit Viper ( Trimeresurus insularis) across the Lesser Sunda Archipelago

scientific article published on 17 April 2019

Visualization of the HIV-1 Env Glycan Shield Across Scales

scientific article published on 12 November 2019

Visualization of the HIV-1 Env glycan shield across scales

scientific article published on 22 October 2020

Want to Publish in JPR ? This Is What You Need to Know!

scientific article published on 14 November 2022

Where Are They Now...?

scientific article published on 6 August 2021

Wiskott-Aldrich syndrome protein forms nuclear condensates and regulates alternative splicing

scientific article published on 25 June 2022

“To Infinity...and beyond”: Looking Past Model Systems

scientific article published in 2020

List of works by John Yates

20 Years...2 Decades...10 Bienniums...5 Quadrenniums...4 Lustrums

A TRAF-like motif of the inducible costimulator ICOS controls development of germinal center TFH cells via the kinase TBK1.

A posttranslational modification code for CFTR maturation is altered in cystic fibrosis

Altered network and rescue of human neurons derived from individuals with early-onset genetic epilepsy

An SMC-like protein binds and regulates Caenorhabditis elegans condensins.

Analysis of the Tropism of SARS-CoV-2 Based on the Host Interactome of the Spike Protein

Arg-tRNA synthetase links inflammatory metabolism to RNA splicing and nuclear trafficking via SRRM2

Aurora Kinase A proximity interactome reveals centriolar satellites as regulators of its function during primary cilium biogenesis

Autism-linked Cullin3 germline haploinsufficiency impacts cytoskeletal dynamics and cortical neurogenesis through RhoA signaling

Cancer Conformational Landscape Shapes Tumorigenesis

Changes in porcine cauda epididymal fluid proteome by disrupting the HPT axis: Unveiling potential mechanisms of male infertility

Cleavage of the SUN-domain protein Mps3 at its N-terminus regulates centrosome disjunction in budding yeast meiosis.

ComPIL 2.0: An Updated Comprehensive Metaproteomics Database

Comparative Proteomic Analysis of Murine Cutaneous Lesions Induced by Leishmania amazonensis or Leishmania major

Comparative membrane proteomics reveals diverse cell regulators concentrated at the nuclear envelope

Comparative membrane proteomics reveals diverse cell regulators concentrated at the nuclear envelope

Comparison of CRISPR Genomic Tagging for Affinity Purification and Endogenous Immunoprecipitation Coupled with Quantitative Mass Spectrometry To Identify the Dynamic AMPKα2 Interactome

Confronting Racism in Chemistry Journals

Control of seed dormancy and germination by DOG1-AHG1 PP2C phosphatase complex via binding to heme.

Correction to “The Curiosity of the Young”

Cortical organoids model early brain development disrupted by 16p11.2 copy number variants in autism

Coupling of spliceosome complexity to intron diversity

Covalent Protein Painting Reveals Structural Changes in the Proteome in Alzheimer Disease

DAF-16/FOXO and HLH-30/TFEB function as combinatorial transcription factors to promote stress resistance and longevity

DNA replication acts as an error correction mechanism to maintain centromere identity by restricting CENP-A to centromeres

DeGlyPHER: An Ultrasensitive Method for the Analysis of Viral Spike -Glycoforms

Deducing the presence of proteins and proteoforms in quantitative proteomics.

Deep interactome profiling of membrane proteins by co-interacting protein identification technology

Differential Precipitation of Proteins: A Simple Protein Fractionation Strategy to Gain Biological Insights with Proteomics

Differential processing of HIV envelope glycans on the virus and soluble recombinant trimer

Double mimicry evades tRNA synthetase editing by toxic vegetable-sourced non-proteinogenic amino acid.

EThcD and 213 nm UVPD for Top-Down Analysis of Bovine Seminal Plasma Proteoforms on Electrophoretic and Chromatographic Time Frames

Evolving spike-protein -glycosylation in SARS-CoV-2 variants

Fimbrin phosphorylation by metaphase Cdk1 regulates actin cable dynamics in budding yeast.

Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii

Global Analysis of Protein Expression of Inner Ear Hair Cells

Global site-specific N-glycosylation analysis of HIV envelope glycoprotein.

Global site-specific analysis of glycoprotein N-glycan processing.

HSP70 chaperones RNA-free TDP-43 into anisotropic intranuclear liquid spherical shells

Hexokinase 3 enhances myeloid cell survival via non-glycolytic functions

Hsc70 chaperone activity is required for the cytosolic slow axonal transport of synapsin.

IRE1α is an endogenous substrate of endoplasmic-reticulum-associated degradation

Identification of Microprotein-Protein Interactions via APEX Tagging

Identification of Open Stomata1-Interacting Proteins Reveals Interactions with Sucrose Non-fermenting1-Related Protein Kinases2 and with Type 2A Protein Phosphatases That Function in Abscisic Acid Responses.

Identification of in vivo CFTR conformations during biogenesis and upon misfolding by covalent protein painting (CPP)

Identification of novel targets for miR-29a using miRNA proteomics

Impact of the identification strategy on the reproducibility of DDA and DIA results

Improving Proteomics Data Reproducibility with a Dual-Search Strategy

Increased proteomic complexity in Drosophila hybrids during development.

Innovation's Mean Free Path

Innovation: Risk-Takers and Visionaries

Innovation: Structural Proteomics Goes Global

Innovations in Proteomics: The Drive to Single Cells

Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0.

Integrating DIA Single-Cell Proteomics Data with the DiagnoMass Proteomic Hub for Biological Insights

Integrative proteomics and pharmacogenomics analysis of methylphenidate treatment response

Interactome analysis illustrates diverse gene regulatory processes associated with LIN28A in human iPS cell-derived neural progenitor cells

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.

Interlaboratory Study for Characterizing Monoclonal Antibodies by Top-Down and Middle-Down Mass Spectrometry

Intracellular amyloid toxicity induces oxytosis/ferroptosis regulated cell death

Intrinsic mesoscale properties of a Polycomb protein underpin heterochromatin fidelity

Ist1 regulates ESCRT-III assembly and function during multivesicular endosome biogenesis in Caenorhabditis elegans embryos.

Label-Free Proteomic Analysis Reveals Parasite-Specific Protein Alterations in Macrophages Following Leishmania amazonensis, Leishmania major, or Leishmania infantum Infection

MIEF1 Microprotein Regulates Mitochondrial Translation

Mechanistic Determinants of Slow Axonal Transport and Presynaptic Targeting of Clathrin Packets

Metabolic Reprogramming of Klebsiella pneumoniae Exposed to Serum and Its Potential Implications in Host Immune System Evasion and Resistance

Mitotic R-loops direct Aurora B kinase to maintain centromeric cohesion

National Cancer Institute Think-Tank Meeting Report on Proteomic Cartography and Biomarkers at the Single-Cell Level: Interrogation of Premalignant Lesions

Native top-down proteomics reveals EGFR-ERα signaling crosstalk in breast cancer cells dissociates NUTF2 dimers to modulate ERα signaling and cell growth

Next Generation Proteomic Pipeline for Chromosome-Based Proteomic Research Using NeXtProt and GENCODE Databases.

Noncanonical transnitrosylation network contributes to synapse loss in Alzheimer's disease

Nvp63 and nvPIWIL1 Suppress Retrotransposon Activation in the Sea Anemone Nematostella vectensis

O-GlcNAcase targets pyruvate kinase M2 to regulate tumor growth

PACOM: A Versatile Tool for Integrating, Filtering, Visualizing, and Comparing Multiple Large Mass Spectrometry Proteomics Data Sets.

PASS-DIA: A Data-Independent Acquisition Approach for Discovery Studies

PTPN22 phosphorylation acts as a molecular rheostat for the inhibition of TCR signaling

Phenotypic and functional variation in venom and venom resistance of two sympatric rattlesnakes and their prey

Phosphotyrosine-dependent interaction between the kinases PKCθ and Zap70 promotes proximal TCR signaling

Profiling of Protein O-GlcNAcylation in Murine CD8+ Effector- and Memory-like T Cells.