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Authors
Joao A. Paulo

Joao A. Paulo

Harvard University

ORCID: 0000-0002-4291-413X

Biochemistry, Genetics and Molecular BiologyNeuroscience

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 1%percentile

4.7Author DataRank

Indexed papers

2in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 2 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

Top data-sharing exemplar

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

Dual Proteome-scale Networks Reveal Cell-specific Remodeling of the Human Interactome

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.01.19.905109

Top 6%

3.7DataRank

Top 6%121 citations

Raphael J. Bruckner, José Navarrete-Perea, Joe R. Cannon, Kurt Baltier, Fana Gebreab +21 more

Papers

Driven by 188 papers — median percentile 87. Top paper: “EDF1 coordinates cellular responses to ribosome collisions”.

EDF1 coordinates cellular responses to ribosome collisions

eLife(2020)10.7554/elife.58828

N/A

3.9DataRank · unranked

192 citations

Alban Ordureau, Katharina Best, James A. Saba, Boris Zinshteyn, Elayanambi Sundaramoorthy +10 more

Dual Proteome-scale Networks Reveal Cell-specific Remodeling of the Human Interactome

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.01.19.905109

Top 6%

3.7DataRank

Top 6%121 citations

Raphael J. Bruckner, José Navarrete-Perea, Joe R. Cannon, Kurt Baltier, Fana Gebreab +21 more

Mitochondrial fatty acid synthesis coordinates oxidative metabolism in mammalian mitochondria

eLife(2020)10.7554/elife.58041

N/A

2.8DataRank · unranked

142 citations

Ashley Solmonson, Scott Rusin, J. Alan Maschek, Claire Bensard, Sarah Fogarty +14 more

The 22q11.2 region regulates presynaptic gene-products linked to schizophrenia

Nature Communications(2022)10.1038/s41467-022-31436-8

N/A

1.4DataRank · unranked

61 citations

Olli Pietiläinen, Mykyta Artomov, Matthew Tegtmeyer, Vera Valakh, Leevi Lehtonen +40 more

Regulation of protein abundance in genetically diverse mouse populations

Cell Genomics(2021)10.1016/j.xgen.2021.100003

Top 19%

1.1DataRank

Top 19%50 citations

Tian Zhang, Duy T. Pham, Matthew Vincent, Timothy A. Bell, Pablo Hock +8 more

Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenation

eLife(2023)10.7554/elife.90579

N/A

0.781DataRank · unranked

25 citations

Ludger J.E. Goeminne, Alexander Tyshkovskiy, Sirui Zhang, Julie Chen, Joao A. Paulo +6 more

mTMT: An Alternative, Nonisobaric, Tandem Mass Tag Allowing for Precursor-Based Quantification

Analytical Chemistry(2019)10.1021/acs.analchem.9b03162

N/A

0.678DataRank · unranked

12 citations

Steven P. Gygi, Joao A. Paulo

Genetic dissection of the pluripotent proteome through multi-omics data integration

Cell Genomics(2023)10.1016/j.xgen.2023.100283

N/A

0.570DataRank · unranked

18 citations

Duy T. Pham, Tian Zhang, Gregory R. Keele, Daniel A. Skelly, Joao A. Paulo +8 more

The Hao-Fountain syndrome protein USP7 regulates neuronal connectivity in the brain via a novel p53-independent ubiquitin signaling pathway

Cell Reports(2025)10.1016/j.celrep.2025.115231

N/A

0.562DataRank · unranked

10 citations

Cole Ferguson, Dylan C. Mitchell, Isabel Risch, Amanda Titus, Joao A. Paulo +13 more

The age-dependent regulation of pancreatic islet landscape is fueled by a HNF1a-immune signaling loop

Mechanisms of Ageing and Development(2024)10.1016/j.mad.2024.111951

N/A

0.368DataRank · unranked

10 citations

Thomas Aga Legøy, Ulrik Larsen, Lucas Unger, Shadab Abadpour, Joao A. Paulo +4 more

Translation elongation factor 2 depletion by siRNA in mouse liver leads to mTOR-independent translational upregulation of ribosomal protein genes

Scientific Reports(2020)10.1038/s41598-020-72399-4

N/A

0DataRank · unranked

20 citations

Mikhail V. Nesterchuk, Elena M. Smekalova, Joao A. Paulo, Piotr S. Kowalski, Kseniya A. Akulich +8 more

In vivo Environment Swiftly Restricts Human Pancreatic Progenitors Toward Mono-Hormonal Identity via a HNF1A/HNF4A Mechanism

Frontiers in Cell and Developmental Biology(2020)10.3389/fcell.2020.00109

N/A

0DataRank · unranked

24 citations

Andreas Frøslev Mathisen, Zaidon Salim, Heidrun Vethe, Yngvild Bjørlykke, Shadab Abadpour +6 more

Membrane skeleton modulates erythroid proteome remodeling and organelle clearance

Blood(2020)10.1182/blood.2020006673

N/A

0DataRank · unranked

23 citations

Yang Mei, Xu Han, Farida Korobova, Miguel A. Prado, Jing Yang +6 more

Growth media selection alters the proteome profiles of three model microorganisms

Journal of Proteomics(2020)10.1016/j.jprot.2020.104006

N/A

0DataRank · unranked

13 citations

Steven P. Gygi, Joao A. Paulo, José Navarrete-Perea

Facultative protein selenation regulates redox sensitivity, adipose tissue thermogenesis, and obesity

Proceedings of the National Academy of Sciences(2020)10.1073/pnas.2001387117

N/A

0DataRank · unranked

39 citations

Gina Z. Lu, John Szpyt, Marco Mariotti, Ryan Garrity, Joao A. Paulo +9 more

Encapsulation boosts islet-cell signature in differentiating human induced pluripotent stem cells via integrin signalling

Scientific Reports(2020)10.1038/s41598-019-57305-x

N/A

0DataRank · unranked

36 citations

Heidrun Vethe, Shadab Abadpour, Berit L. Strand, Hanne Scholz, Joao A. Paulo +4 more

O-GlcNAc regulates gene expression by controlling detained intron splicing

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.03.27.012781

N/A

0DataRank · unranked

12 citations

George Fei, Joao A. Paulo, Stanislav Bellaousov, Sara E. Martin, Damien Duveau +5 more

DPP9 directly sequesters the NLRP1 C-terminus to repress inflammasome activation

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.08.14.246132

N/A

0DataRank · unranked

6 citations

Humayun Sharif, Andrew R. Griswold, Pietro Fontana, Julian Mintseris, Kevin B. Dagbay +5 more

Mammalian Cell Proliferation Requires Noncatalytic Functions of O-GlcNAc Transferase

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.10.22.351288

N/A

0DataRank · unranked

5 citations

Sarah Potter, Cassandra M. Joiner, George Q. Fei, Behnam Nabet, Matthew Sonnett +5 more

Global proteomics of Ubqln 2-based murine models of ALS

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.02.22.956524

N/A

0DataRank · unranked

2 citations

Miguel A. Prado, Stefanie A.H. de Poot, Joao A. Paulo, Marissa Ashton, Sara L. Domínguez +11 more

Crosstalk between repair pathways elicits Double-Strand Breaks in alkylated DNA: implications for the action of temozolomide

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.21.391326

N/A

0DataRank · unranked

1 citations

Asako Isogawa, Joao A. Paulo, Kazumitsu Onizuka, Tatsuro Takahashi, Ravindra Amunugama +3 more

Co-option of Plasmodium falciparum PP1 for egress from host erythrocytes

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.01.05.890483

N/A

0DataRank · unranked

0 citations

Alexandra Miliu, Joao A. Paulo, Jonathan M. Goldberg, Arianna M. Bonilla, Laurence Berry +10 more

Dual proteome-scale networks reveal cell-specific remodeling of the human interactome

Cell(2021)10.1016/j.cell.2021.04.011

N/A

0DataRank · unranked

1006 citations

Raphael J. Bruckner, José Navarrete-Perea, Joe R. Cannon, Kurt Baltier, Fana Gebreab +23 more

Proteome-wide mapping of short-lived proteins in human cells

Molecular Cell(2021)10.1016/j.molcel.2021.09.015

N/A

0DataRank · unranked

179 citations

Zhenying Cai, Laura Pontano Vaites, Ning Shen, Dylan C. Mitchell, Edward L. Huttlin +4 more

Quantitative proteomics reveals the selectivity of ubiquitin-binding autophagy receptors in the turnover of damaged lysosomes by lysophagy

eLife(2021)10.7554/elife.72328

N/A

0DataRank · unranked

170 citations

Sharan Swarup, Melissa Hoyer, Joao A. Paulo, J. Wade Harper, Vinay V. Eapen

Temporal proteomics during neurogenesis reveals large-scale proteome and organelle remodeling via selective autophagy

Molecular Cell(2021)10.1016/j.molcel.2021.10.001

N/A

0DataRank · unranked

104 citations

Felix Kraus, Jiuchun Zhang, Heeseon An, Sookhee Park, Tim Ahfeldt +3 more

Translocation of polyubiquitinated protein substrates by the hexameric Cdc48 ATPase

Molecular Cell(2021)10.1016/j.molcel.2021.11.033

N/A

0DataRank · unranked

81 citations

Hao Li, Daniele Peterle, Joao A. Paulo, Scott B. Ficarro, Thomas E. Wales +5 more

Mechanism of p38 MAPK–induced EGFR endocytosis and its crosstalk with ligand-induced pathways

The Journal of Cell Biology(2021)10.1083/jcb.202102005

N/A

0DataRank · unranked

38 citations

Tian Zhang, Joao A. Paulo, Steven P. Gygi, Simon C. Watkins, Hiroaki Sakurai +2 more

Targeting oncoproteins with a positive selection assay for protein degraders

Science Advances(2021)10.1126/sciadv.abd6263

N/A

0DataRank · unranked

47 citations

Leslie Duplaquet, Benjamin L. Lampson, Adam C. Wang, Amin H. Sabet, Mette Ishoey +21 more

Structures of chaperone-associated assembly intermediates reveal coordinated mechanisms of proteasome biogenesis

Nature Structural & Molecular Biology(2021)10.1038/s41594-021-00583-9

N/A

0DataRank · unranked

46 citations

Richard M. Walsh, Shaun Rawson, Mandeep Kaur, Meera K. Bhanu, Geng Tian +8 more

ORF10–Cullin-2–ZYG11B complex is not required for SARS-CoV-2 infection

Proceedings of the National Academy of Sciences(2021)10.1073/pnas.2023157118

N/A

0DataRank · unranked

36 citations

Callie J. Donahue, Laura Pontano Vaites, Jie Li, Gergely Róna, Colin O’Leary +11 more

Rapid toxin sequestration modifies poison frog physiology

Journal of Experimental Biology(2021)10.1242/jeb.230342

N/A

0DataRank · unranked

34 citations

Jeremy D. O’Connell, Joao A. Paulo, Sunia A. Trauger, Steven P. Gygi, Andrew W. Murray +1 more

A composite DNA element that functions as a maintainer required for epigenetic inheritance of heterochromatin

Molecular Cell(2021)10.1016/j.molcel.2021.07.017

N/A

0DataRank · unranked

31 citations

Joao A. Paulo, Xue Li, Haining Zhou, Juntao Yu, Steven P. Gygi +2 more

Crosstalk between repair pathways elicits double-strand breaks in alkylated DNA and implications for the action of temozolomide

eLife(2021)10.7554/elife.69544

N/A

0DataRank · unranked

25 citations

Asako Isogawa, Joao A. Paulo, Kazumitsu Onizuka, Tatsuro Takahashi, Ravindra Amunugama +3 more

Maternal Iron Deficiency Modulates Placental Transcriptome and Proteome in Mid-Gestation of Mouse Pregnancy

Journal of Nutrition(2021)10.1093/jn/nxab005

N/A

0DataRank · unranked

23 citations

Miguel A. Prado, Liang Sun, Shira Rockowitz, Piotr Sliz, Joao A. Paulo +3 more

Development of a colorimetric α-ketoglutarate detection assay for prolyl hydroxylase domain (PHD) proteins

Journal of Biological Chemistry(2021)10.1016/j.jbc.2021.100397

N/A

0DataRank · unranked

18 citations

Alison E. Ringel, William Yuan, Joao A. Paulo, Haejin Yoon, Mark A. Currie +2 more

Immune Checkpoint Blockade Augments Changes Within Oncolytic Virus-induced Cancer MHC-I Peptidome, Creating Novel Antitumor CD8 T Cell Reactivities

Molecular & Cellular Proteomics(2021)10.1016/j.mcpro.2021.100182

N/A

0DataRank · unranked

8 citations

Prathyusha Konda, J. Patrick Murphy, Joao A. Paulo, Steven P. Gygi, Shashi Gujar +1 more

Strain-Specific Peptide (SSP) Interference Reference Sample: A Genetically Encoded Quality Control for Isobaric Tagging Strategies

Analytical Chemistry(2021)10.1021/acs.analchem.0c05483

N/A

0DataRank · unranked

13 citations

Gregory R. Keele, Gary A. Churchill, Steven P. Gygi, Joao A. Paulo, Tian Zhang

Temporal proteomic changes induced by nicotine in human cells: A quantitative proteomics approach

Journal of Proteomics(2021)10.1016/j.jprot.2021.104244

N/A

0DataRank · unranked

6 citations

Steven P. Gygi, Joao A. Paulo, José Navarrete-Perea

Dual DNA and protein tagging of open chromatin unveils dynamics of epigenomic landscapes in leukemia

Nature Methods(2021)10.1038/s41592-021-01077-8

N/A

0DataRank · unranked

9 citations

Joao A. Paulo, Ryan R. Posey, Vera Mugoni, Nikki R. Kong, Giulia Cheloni +7 more

Super Heavy TMTpro Labeling Reagent: An Alternative and Higher-Charge-State-Amenable Stable-Isotope-Labeled TMTpro Variant

Journal of Proteome Research(2021)10.1021/acs.jproteome.0c01056

N/A

0DataRank · unranked

4 citations

Qing Yu, Ryan Bomgarden, John Rogers, J. Wade Harper, Steven P. Gygi +2 more

The fission yeast FLCN/FNIP complex augments TORC1 repression or activation in response to amino acid (AA) availability

iScience(2021)10.1016/j.isci.2021.103338

N/A

0DataRank · unranked

3 citations

Shalini Sharma, Joao A. Paulo, Alexander O. D. Gulka, Andras Boeszoermenyi, Jingyu Zhang +8 more

Chronically Elevated Exogenous Glucose Elicits Antipodal Effects on the Proteome Signature of Differentiating Human iPSC-Derived Pancreatic Progenitors

International Journal of Molecular Sciences(2021)10.3390/ijms22073698

N/A

0DataRank · unranked

4 citations

Thomas Aga Legøy, Andreas Frøslev Mathisen, Shadab Abadpour, Joao A. Paulo, Hanne Scholz +3 more

RNAmetasome network for macromolecule biogenesis in human cells

Communications Biology(2021)10.1038/s42003-021-02928-y

N/A

0DataRank · unranked

4 citations

Joao A. Paulo, Shiro Iuchi

Protein profiling in the habenula after chronic (–)‐menthol exposure in mice

Journal of Neurochemistry(2021)10.1111/jnc.15495

N/A

0DataRank · unranked

2 citations

Stephanie M. Huard, Joao A. Paulo, Jonathan H Wang, Sheri McKinney, Michael J. Marks +3 more

Transcriptomic and proteomic retinal pigment epithelium signatures of age-related macular degeneration

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.08.19.457044

N/A

0DataRank · unranked

9 citations

Maciej Daniszewski, Grace E. Lidgerwood, Helena H. Liang, Damián Hernández, Mehdi Mirzaei +25 more

Translocation of polyubiquitinated protein substrates by the hexameric Cdc48 ATPase

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.10.21.465358

N/A

0DataRank · unranked

7 citations

Hao Li, Daniele Peterle, Joao A. Paulo, Scott B. Ficarro, Thomas E. Wales +5 more

Quantitative proteomics reveals the selectivity of ubiquitin-binding autophagy receptors in the turnover of damaged lysosomes by lysophagy

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.07.19.452535

N/A

0DataRank · unranked

4 citations

Sharan Swarup, Melissa Hoyer, Joao A. Paulo, J. Wade Harper, Vinay V. Eapen

Regulation of GTPase function by autophosphorylation

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.06.23.449327

N/A

0DataRank · unranked

3 citations

Hyuk‐Soo Seo, Elizabeth M. Terrell, Fenneke KleinJan, Teklab Gebregiworgis, Geneviève M. C. Gasmi-Seabrook +13 more

The p97-UBXD8 complex modulates ER-Mitochondria contact sites by modulating membrane lipid saturation and composition

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.12.08.471763

N/A

0DataRank · unranked

3 citations

Joao A. Paulo, Yuecheng Xi, Ian Kline, Jiang Zhu, Christoph S. Clemen +5 more

TXNRD3 supports male fertility via the redox control of spermatogenesis

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.12.29.474493

N/A

0DataRank · unranked

2 citations

Anton A. Turanov, Marco Mariotti, Jae Yeon Hwang, Huafeng Wang, Sang‐Goo Lee +6 more

Deficiency of the frontotemporal dementia gene GRN results in gangliosidosis

Nature Communications(2022)10.1038/s41467-022-33500-9

N/A

0DataRank · unranked

101 citations

Sharan Swarup, Yohannes A. Ambaw, Pedro Carpio Malia, Ruth C. Richards, Alexander W. Fischer +14 more

A peroxisomal ubiquitin ligase complex forms a retrotranslocation channel

Nature(2022)10.1038/s41586-022-04903-x

N/A

0DataRank · unranked

65 citations

Xudong Wu, Satchal K. Erramilli, Joao A. Paulo, Paweł P. Knejski, Steven P. Gygi +3 more

Spatial snapshots of amyloid precursor protein intramembrane processing via early endosome proteomics

Nature Communications(2022)10.1038/s41467-022-33881-x

N/A

0DataRank · unranked

58 citations

Frances V Hundley, Qing Yu, Katherine A. Overmyer, Dain R. Brademan, Lia R. Serrano +7 more

Pathogenesis of Cardiomyopathy Caused by Variants in ALPK3 , an Essential Pseudokinase in the Cardiomyocyte Nucleus and Sarcomere

Circulation(2022)10.1161/circulationaha.122.059688

N/A

0DataRank · unranked

50 citations

Hiroko Wakimoto, Joao A. Paulo, Qi Zhang, Daniel Reichart, Christopher N. Toepfer +9 more

Time-resolved proximity labeling of protein networks associated with ligand-activated EGFR

Cell Reports(2022)10.1016/j.celrep.2022.110950

N/A

0DataRank · unranked

40 citations

Tian Zhang, Sachin Surve, Joao A. Paulo, Callen T. Wallace, Simon C. Watkins +3 more

Architecture of the outbred brown fat proteome defines regulators of metabolic physiology

Cell(2022)10.1016/j.cell.2022.10.003

N/A

0DataRank · unranked

39 citations

Luiz H. M. Bozi, Yizhi Sun, Christopher L. Riley, Vivek M. Philip, Mandy Chen +41 more

Liver RBFOX2 regulates cholesterol homeostasis via Scarb1 alternative splicing in mice

Nature Metabolism(2022)10.1038/s42255-022-00681-y

N/A

0DataRank · unranked

39 citations

Sijia Yu, Natalia Artigas, Miguel A. Prado, Nejc Haberman, Yi-Fang Wang +17 more

Selenoprotein TXNRD3 supports male fertility via the redox regulation of spermatogenesis

Journal of Biological Chemistry(2022)10.1016/j.jbc.2022.102183

N/A

0DataRank · unranked

38 citations

Anton A. Turanov, Marco Mariotti, Jae Yeon Hwang, Huafeng Wang, Sang‐Goo Lee +6 more

MCL-1 is a master regulator of cancer dependency on fatty acid oxidation

Cell Reports(2022)10.1016/j.celrep.2022.111445

N/A

0DataRank · unranked

34 citations

Utsarga Adhikary, Dong Wook Choi, Erika P. Portero, Joao A. Paulo, Pruthvi Gowda +6 more

Rixosomal RNA degradation contributes to silencing of Polycomb target genes

Nature(2022)10.1038/s41586-022-04598-0

N/A

0DataRank · unranked

37 citations

Chad B. Stein, Tiasha A. Shafiq, Gergana Shipkovenska, Marian Kalocsay, Joao A. Paulo +6 more

Disrupting the DREAM complex enables proliferation of adult human pancreatic β cells

Journal of Clinical Investigation(2022)10.1172/jci157086

N/A

0DataRank · unranked

37 citations

Esra Karaköse, Carmen Argmann, Huan Wang, Metodi Balev, Rachel Brody +13 more

Concurrent inhibition of CDK2 adds to the anti-tumour activity of CDK4/6 inhibition in GIST

British Journal of Cancer(2022)10.1038/s41416-022-01990-5

N/A

0DataRank · unranked

27 citations

Matthew L. Hemming, Meijun Z. Lundberg, Matthew Serrata, Isabel Goldaracena, Ninning Liu +17 more

Proximity labeling for investigating protein-protein interactions

Methods in cell biology(2022)10.1016/bs.mcb.2021.12.006

N/A

0DataRank · unranked

21 citations

Joao A. Paulo, Steven P. Gygi, Howard A. Rockman, Conrad T. Pfeiffer

Regulation of GTPase function by autophosphorylation

Molecular Cell(2022)10.1016/j.molcel.2022.02.011

N/A

0DataRank · unranked

21 citations

Hyuk‐Soo Seo, Elizabeth M. Terrell, Moonhee Yang, Fenneke KleinJan, Teklab Gebregiworgis +15 more

Enzymatic analysis of WWP2 E3 ubiquitin ligase using protein microarrays identifies autophagy-related substrates

Journal of Biological Chemistry(2022)10.1016/j.jbc.2022.101854

N/A

0DataRank · unranked

18 citations

Claire Y Chiang, Zan Chen, Sara Nathan, Gabriel D. D’Agostino, Joao A. Paulo +5 more

Fe3+-NTA magnetic beads as an alternative to spin column-based phosphopeptide enrichment

Journal of Proteomics(2022)10.1016/j.jprot.2022.104561

N/A

0DataRank · unranked

16 citations

Valentina Rossio, Sanjukta Guha Thakurta, Amarjeet Flora, Leigh Foster, Ryan Bomgarden +3 more

Isobaric labeling: Expanding the breadth, accuracy, depth, and diversity of sample multiplexing

PROTEOMICS(2022)10.1002/pmic.202200328

N/A

0DataRank · unranked

9 citations

Joao A. Paulo

Integrated changes in thermal stability and proteome abundance during altered nutrient states in Escherichia coli and human cells

PROTEOMICS(2022)10.1002/pmic.202100254

N/A

0DataRank · unranked

6 citations

Beau Blackmore, Ronnie Du, Olivier Philips, Joao A. Paulo, J. Patrick Murphy +1 more

Identification of Deubiquitinase Substrates in Xenopus Egg Extract

Methods in molecular biology(2022)10.1007/978-1-0716-2803-4_13

N/A

0DataRank · unranked

1 citations

Joao A. Paulo, Randall W. King, Valentina Rossio

Multi-omics analysis identifies drivers of protein phosphorylation

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.06.03.494740

N/A

0DataRank · unranked

7 citations

Gregory R. Keele, Isabela Gerdes Gyuricza, Matthew Vincent, Catherine Brunton, Timothy A. Bell +9 more

PARK15/FBXO7 is dispensable for PINK1/Parkin mitophagy in iNeurons and HeLa cell systems

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.11.02.514817

N/A

0DataRank · unranked

4 citations

Ellen A. Goodall, Ian R. Smith, Yizhi Jiang, Julia C. Paoli, Frank Adolf +5 more

Quantitative mapping of autophagic cargo during nutrient stress reveals YIPF3-YIPF4 as membrane receptors for Golgiphagy

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.12.06.519342

N/A

0DataRank · unranked

4 citations

Sharan Swarup, Ian R. Smith, Julia C. Paoli, Joao A. Paulo, J. Wade Harper +1 more

Time-resolved proximity labeling of protein networks associated with ligand-activated EGFR

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.01.07.475389

N/A

0DataRank · unranked

3 citations

Tian Zhang, Joao A. Paulo, Callen T. Wallace, Simon C. Watkins, Steven P. Gygi +2 more

The relaxin receptor RXFP1 signals through a mechanism of autoinhibition

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.01.22.477343

N/A

0DataRank · unranked

3 citations

Shaun Rawson, James Osei‐Owusu, Kelly P. Brock, Xinyue Liu, Joao A. Paulo +6 more

Early Endosome Capture Proteomics and its Application to Amyloid Precursor Protein Intramembrane Processing by β and γ-Secretases

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.03.31.486371

N/A

0DataRank · unranked

0 citations

Qing Yu, Frances V Hundley, Katherine A. Overmyer, Lia R. Serrano, Joao A. Paulo +6 more

Retinal Pathological Features and Proteome Signatures of Alzheimer’s

Research Square(2022)10.21203/rs.3.rs-2152218/v1

N/A

0DataRank · unranked

0 citations

Altan Rentsendorj, Nazanin Mirzaei, Giovanna C. Regis, Julia Sheyn, Haoshen Shi +21 more

UBXN1 maintains ER proteostasis and represses UPR activation by modulating translation independently of the p97 ATPase

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.12.16.520763

N/A

0DataRank · unranked

0 citations

Rakesh Ganji, Sirisha Mukkavalli, Joao A. Paulo, Steve P. Gygi, Malavika Raman +1 more

Retinal pathological features and proteome signatures of Alzheimer’s disease

Acta Neuropathologica(2023)10.1007/s00401-023-02548-2

N/A

0DataRank · unranked

159 citations

Altan Rentsendorj, Nazanin Mirzaei, Giovanna C. Regis, Julia Sheyn, Haoshen Shi +21 more

A disordered region controls cBAF activity via condensation and partner recruitment

Cell(2023)10.1016/j.cell.2023.08.032

N/A

0DataRank · unranked

157 citations

Amy R. Strom, Joao A. Paulo, Clayton K. Collings, Kiersten M. Ruff, Min Kyung Shinn +11 more

The p97-UBXD8 complex regulates ER-Mitochondria contact sites by altering membrane lipid saturation and composition

Nature Communications(2023)10.1038/s41467-023-36298-2

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46 citations

Joao A. Paulo, Yuecheng Xi, Ian Kline, Jiang Zhu, Christoph S. Clemen +5 more

Accelerating multiplexed profiling of protein-ligand interactions: High-throughput plate-based reactive cysteine profiling with minimal input

Cell chemical biology(2023)10.1016/j.chembiol.2023.11.015

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0DataRank · unranked

46 citations

Rebecca L. Whitehouse, S L Dawson, Lu Zhang, Jeffrey G. Martin, Douglas S. Johnson +4 more

PARK15/FBXO7 is dispensable for PINK1/Parkin mitophagy in iNeurons and HeLa cell systems

EMBO Reports(2023)10.15252/embr.202256399

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0DataRank · unranked

35 citations

Ellen A. Goodall, Ian R. Smith, Yizhi Jiang, Julia C. Paoli, Frank Adolf +5 more

Rapid recruitment and IFN-I–mediated activation of monocytes dictate focal radiotherapy efficacy

Science Immunology(2023)10.1126/sciimmunol.add7446

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0DataRank · unranked

33 citations

Derek R. Clements, Sanjana Saravanan, Rebeca Arroyo Hornero, Anja Lüdtke, Beau Blackmore +14 more

The relaxin receptor RXFP1 signals through a mechanism of autoinhibition

Nature Chemical Biology(2023)10.1038/s41589-023-01321-6

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0DataRank · unranked

28 citations

Shaun Rawson, James Osei‐Owusu, Kelly P. Brock, Xinyue Liu, Joao A. Paulo +6 more

Sample multiplexing-based targeted pathway proteomics with real-time analytics reveals the impact of genetic variation on protein expression

Nature Communications(2023)10.1038/s41467-023-36269-7

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0DataRank · unranked

35 citations

Xinyue Liu, Mark P. Keller, José Navarrete-Perea, Tian Zhang, Sipei Fu +14 more

Multi-omics analysis identifies drivers of protein phosphorylation

Genome biology(2023)10.1186/s13059-023-02892-2

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0DataRank · unranked

23 citations

Gregory R. Keele, Isabela Gerdes Gyuricza, Matthew Vincent, Catherine Brunton, Timothy A. Bell +9 more

A conserved membrane curvature-generating protein is crucial for autophagosome formation in fission yeast

Nature Communications(2023)10.1038/s41467-023-40530-4

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22 citations

Yoko Shibata, Joao A. Paulo, Steven P. Gygi, Tom A. Rapoport, Ning Wang

USP2 inhibition prevents infection with ACE2-dependent coronaviruses in vitro and is protective against SARS-CoV-2 in mice

Science Translational Medicine(2023)10.1126/scitranslmed.adh7668

N/A

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19 citations

Lei Bai, Jiazhen Dong, Xiaoping Hu, Jingchao Wang, Joao A. Paulo +22 more

Hypoxia induced responses are reflected in the stromal proteome of breast cancer

Nature Communications(2023)10.1038/s41467-023-39287-7

N/A

0DataRank · unranked

16 citations

Kenneth Finne, Even Birkeland, Vandana Ardawatia, Ingeborg Winge, Sura Aziz +7 more

Targeting MCL-1 triggers DNA damage and an anti-proliferative response independent from apoptosis induction

Cell Reports(2023)10.1016/j.celrep.2023.113176

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15 citations

Joao A. Paulo, Marina Godes, Shrabasti Roychoudhury, Michelle S. Prew, Yael Ben‐Nun +7 more

Spin column-based peptide fractionation alternatives for streamlined tandem mass tag (SL-TMT) sample processing

Journal of Proteomics(2023)10.1016/j.jprot.2023.104839

N/A

0DataRank · unranked

14 citations

Valentina Rossio, Joao A. Paulo, Xinyue Liu

Enhancing Proteome Coverage by Using Strong Anion-Exchange in Tandem with Basic-pH Reversed-Phase Chromatography for Sample Multiplexing-Based Proteomics

Journal of Proteome Research(2023)10.1021/acs.jproteome.3c00492

N/A

0DataRank · unranked

12 citations

Xinyue Liu, Valentina Rossio, S L Dawson, Steven P. Gygi, Joao A. Paulo +1 more

Differences in syncytia formation by SARS-CoV-2 variants modify host chromatin accessibility and cellular senescence via TP53

Cell Reports(2023)10.1016/j.celrep.2023.113478

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0DataRank · unranked

12 citations

Bridget L. Menasché, Maria Mavrikaki, Madison M. Uyemura, Su Min Hong, Nina Kozlova +13 more

Enriching Cysteine-Containing Peptides Using a Sulfhydryl-Reactive Alkylating Reagent with a Phosphonic Acid Group and Immobilized Metal Affinity Chromatography

Journal of Proteome Research(2023)10.1021/acs.jproteome.2c00806

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11 citations

Valentina Rossio, Steven P. Gygi, Joao A. Paulo, Xinyue Liu

Quantitative proteomics and RNA-sequencing of mouse liver endothelial cells identify novel regulators of BMP6 by iron

iScience(2023)10.1016/j.isci.2023.108555

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11 citations

Chia‐Yu Wang, Yang Xu, Sydney Phillips, Joao A. Paulo, Beata Małachowska +5 more

SENP3 and USP7 regulate Polycomb-rixosome interactions and silencing functions

Cell Reports(2023)10.1016/j.celrep.2023.112339

N/A

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10 citations

Wenzhi Feng, Juntao Yu, Tiasha A. Shafiq, Joao A. Paulo, Jiuchun Zhang +4 more

Global proteomics reveals insulin abundance as a marker of human islet homeostasis alterations

Acta Physiologica(2023)10.1111/apha.14037

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10 citations

Shadab Abadpour, Thomas Aga Legøy, Joao A. Paulo, Luiza Ghila, Hanne Scholz +2 more

Quantitative proteomics defines mechanisms of antiviral defence and cell death during modified vaccinia Ankara infection

Nature Communications(2023)10.1038/s41467-023-43299-8

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0DataRank · unranked

10 citations

Joanne Kite, Marisa Oliveira, Hanqi Li, Ying Di, Maria H. Christensen +8 more

Comparison of the Proteomes and Phosphoproteomes of S. cerevisiae Cells Harvested with Different Strategies

Proteomes(2023)10.3390/proteomes11040028

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9 citations

Joao A. Paulo, Valentina Rossio

After virus exposure, early bystander naïve CD8 T cell activation relies on NAD+ salvage metabolism

Frontiers in Immunology(2023)10.3389/fimmu.2022.1047661

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0DataRank · unranked

6 citations

Barry E. Kennedy, J. Patrick Murphy, Prathyusha Konda, Michael Giacomantonio, Tatjana Brauer-Chapin +10 more

Proteome-Wide Profiling Using Sample Multiplexing of a Human Cell Line Treated with Cannabidiol (CBD) and Tetrahydrocannabinol (THC)

Proteomes(2023)10.3390/proteomes11040036

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0DataRank · unranked

6 citations

Vivek Gupta, Xinyue Liu, Valentina Rossio, Mehdi Mirzaei, Jennifer L. Cornish +3 more

Adapting an Isobaric Tag-Labeled Yeast Peptide Standard to Develop Targeted Proteomics Assays

Journal of Proteome Research(2023)10.1021/acs.jproteome.3c00493

N/A

0DataRank · unranked

5 citations

E. Schmid, Ryan Bomgarden, Jae Hyuk Choi, Steven P. Gygi, Qing Yu +2 more

Proteome‐wide abundance profiling of yeast deletion strains for GET pathway members using sample multiplexing

PROTEOMICS(2023)10.1002/pmic.202300303

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4 citations

Xinyue Liu, Benjamin P. Levi, Joao A. Paulo, Joel S. Gygi

Identification of Proteins Specifically Assembled on a Stem-Loop Composed of a CAG Triplet Repeat

DNA(2023)10.3390/dna3020009

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0DataRank · unranked

1 citations

Asako Isogawa, Joao A. Paulo, Shingo Fujii, Robert P. Fuchs

Synaptic Activity Causes Minute-scale Changes in BAF Complex Composition and Function

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.13.562244

N/A

0DataRank · unranked

5 citations

Wendy Wenderski, Joao A. Paulo, Sung Hyun Kim, Katharina Roepke, Christine Ellis +3 more

Combinatorial selective ER-phagy remodels the ER during neurogenesis

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.06.26.546565

N/A

0DataRank · unranked

4 citations

Cristina Capitanio, Ian R. Smith, Julia C. Paoli, Anna Bieber, Yizhi Jiang +7 more

Differences in syncytia formation by SARS-CoV-2 variants modify host chromatin accessibility and cellular senescence via TP53

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.08.31.555625

N/A

0DataRank · unranked

3 citations

Bridget L. Menasché, Maria Mavrikaki, Madison M. Uyemura, Su Min Hong, Nina Kozlova +13 more

Substrate identification and specificity profiling of deubiquitylases against endogenously-generated ubiquitin-protein conjugates

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.12.20.572581

N/A

0DataRank · unranked

3 citations

Joao A. Paulo, Xinyue Liu, Steven P. Gygi, Randall W. King, Valentina Rossio

Global and single-cell proteomics view of the co-evolution between neural progenitors and breast cancer cells in a co-culture model

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.03.539050

N/A

0DataRank · unranked

2 citations

Manuel Carrasco, Kenneth Finne, Ingeborg Winge, Cecilie Askeland, Jarle B. Arnes +6 more

ALS-related p97 R155H mutation disrupts lysophagy in iPSC-derived motor neurons

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.06.21.545956

N/A

0DataRank · unranked

2 citations

Michelle A. Johnson, Pantelis Antonoudiou, Jamie Maguire, Joao A. Paulo, Steve P. Gygi +3 more

Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenation

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.06.30.546730

N/A

0DataRank · unranked

2 citations

Ludger J.E. Goeminne, Alexander Tyshkovskiy, Sirui Zhang, Julie Y. Chen, Joao A. Paulo +6 more

Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenation

(2023)10.7554/elife.90579.1

N/A

0DataRank · unranked

2 citations

Ludger J.E. Goeminne, Alexander Tyshkovskiy, Sirui Zhang, Joao A. Paulo, Kerry A. Pierce +5 more

The Hao-Fountain syndrome protein USP7 regulates neuronal connectivity in the brain via a novel p53-independent ubiquitin signaling pathway

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.24.563880

N/A

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2 citations

Cole Ferguson, Dylan C. Mitchell, Amanda Titus, Joao A. Paulo, Andrew Hwang +9 more

Cell growth and nutrient availability control the mitotic exit signaling network in budding yeast

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.08.04.552008

N/A

0DataRank · unranked

0 citations

Beth E. Prichard, Robert A. Sommer, Ricardo Leitão, Christopher J. Sarabia, Semin Hazir +4 more

UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER

Nature(2024)10.1038/s41586-024-07073-0

N/A

0DataRank · unranked

54 citations

Ivan Penchev, Samantha C. Gumbin, Francesco Scavone, Magda Wąchalska, Joao A. Paulo +8 more

A replisome-associated histone H3-H4 chaperone required for epigenetic inheritance

Cell(2024)10.1016/j.cell.2024.07.006

N/A

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48 citations

Yujie Zhang, Yimeng Fang, Joao A. Paulo, Dadmehr Yaghoubi, Xu Hua +8 more

Achieving a 35-Plex Tandem Mass Tag Reagent Set through Deuterium Incorporation

Journal of Proteome Research(2024)10.1021/acs.jproteome.4c00668

N/A

0DataRank · unranked

46 citations

Dustin C. Frost, Karsten Kuhn, Myungsun Shin, Rebecca L. Whitehouse, Ting-Yu Wei +7 more

USP7-Based Deubiquitinase-Targeting Chimeras Stabilize AMPK

Journal of the American Chemical Society(2024)10.1021/jacs.4c02373

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29 citations

Xiaoping Hu, Kaixiu Luo, Yan Xiong, Li Chen, Zhen Wang +11 more

Principles of paralog-specific targeted protein degradation engaging the C-degron E3 KLHDC2

Nature Communications(2024)10.1038/s41467-024-52966-3

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0DataRank · unranked

26 citations

Suresh Dharuman, Elizabeth C. Griffith, Sergio C. Chai, Jarrid Ronnebaum, Moeko T. King +17 more

Endo-IP and lyso-IP toolkit for endolysosomal profiling of human-induced neurons

Proceedings of the National Academy of Sciences(2024)10.1073/pnas.2419079121

N/A

0DataRank · unranked

22 citations

Miguel A. Gonzalez‐Lozano, Lena M. Gottschalk, Aslan N. K. Cook, Jiuchun Zhang, Joao A. Paulo +2 more

Structural basis for C-degron selectivity across KLHDCX family E3 ubiquitin ligases

Nature Communications(2024)10.1038/s41467-024-54126-z

N/A

0DataRank · unranked

13 citations

Sagar Chittori, Nicholas Purser, Moeko T. King, Samuel Maiwald, Kelly Churion +9 more

ALS-related p97 R155H mutation disrupts lysophagy in iPSC-derived motor neurons

Stem Cell Reports(2024)10.1016/j.stemcr.2024.01.002

N/A

0DataRank · unranked

17 citations

Michelle A. Johnson, Pantelis Antonoudiou, Jamie Maguire, Joao A. Paulo, Steve P. Gygi +3 more

RNA quality control factors nucleate Clr4/SUV39H and trigger constitutive heterochromatin assembly

Cell(2024)10.1016/j.cell.2024.04.042

N/A

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17 citations

Richard Joh, M. Perez, Joao A. Paulo, Christina M. Palmieri, Jingyu Zhang +5 more

Structural basis of respiratory complex adaptation to cold temperatures

Cell(2024)10.1016/j.cell.2024.09.029

N/A

0DataRank · unranked

15 citations

Pedro Latorre‐Muro, Amina Djurabekova, Oleksii Zdorevskyi, Christopher F. Bennett, Nils Burger +8 more

Specificity profiling of deubiquitylases against endogenously generated ubiquitin-protein conjugates

Cell chemical biology(2024)10.1016/j.chembiol.2024.05.001

N/A

0DataRank · unranked

14 citations

Joao A. Paulo, Xinyue Liu, Steven P. Gygi, Randall W. King, Valentina Rossio

Phosphorylation patterns in the AT1R C-terminal tail specify distinct downstream signaling pathways

Science Signaling(2024)10.1126/scisignal.adk5736

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13 citations

Conrad T. Pfeiffer, Xue Jiang, Joao A. Paulo, Steven P. Gygi, Uyen Pham +10 more

Dissecting OGT’s TPR domain to identify determinants of cellular function

Proceedings of the National Academy of Sciences(2024)10.1073/pnas.2401729121

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12 citations

Bettine E. Gibbs, Forrest A. Hammel, Cassandra M. Joiner, Joao A. Paulo, John Janetzko +5 more

Global and single-cell proteomics view of the co-evolution between neural progenitors and breast cancer cells in a co-culture model

EBioMedicine(2024)10.1016/j.ebiom.2024.105325

N/A

0DataRank · unranked

12 citations

Manuel Carrasco, Kenneth Finne, Vandana Ardawatia, Ingeborg Winge, Cecilie Askeland +7 more

Matrisome proteomics reveals novel mediators of muscle remodeling with aerobic exercise training

Matrix Biology Plus(2024)10.1016/j.mbplus.2024.100159

N/A

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6 citations

Eileen M. Cooney, Tara MacDonald, Joao A. Paulo, Hui Pan, Jonathan M. Dreyfuss +2 more

Profiling Proteins and Phosphorylation Sites During T Cell Activation Using an Integrated Thermal Shift Assay

Molecular & Cellular Proteomics(2024)10.1016/j.mcpro.2024.100801

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0DataRank · unranked

5 citations

Edward L. Huttlin, Emily M. Huntsman, Tomer M. Yaron-Barir, Jared L. Johnson, Kiran Kurmi +6 more

Enhanced Sample Multiplexing-Based Targeted Proteomics with Intelligent Data Acquisition

Journal of the American Society for Mass Spectrometry(2024)10.1021/jasms.4c00234

N/A

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4 citations

Joao A. Paulo, Steven P. Gygi, Qing Yu, Ka Yang

UBXN1 maintains ER proteostasis and represses UPR activation by modulating translation

EMBO Reports(2024)10.1038/s44319-023-00027-z

N/A

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10 citations

Rakesh Ganji, Sirisha Mukkavalli, Joao A. Paulo, Steve P. Gygi, Malavika Raman +1 more

Huntingtin contains an ubiquitin-binding domain and regulates lysosomal targeting of mitochondrial and RNA-binding proteins

Proceedings of the National Academy of Sciences(2024)10.1073/pnas.2319091121

N/A

0DataRank · unranked

9 citations

Vinay V. Eapen, Ryan G. Lim, Clinton Yu, Lisa Salazar, Nicolette R. McClure +16 more

Systematic analysis of nonprogrammed frameshift suppression in E. coli via translational tiling proteomics

Proceedings of the National Academy of Sciences(2024)10.1073/pnas.2317453121

N/A

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6 citations

Joao A. Paulo, Hankum Park, Kemardo Henry, Eleanor Fleming, Zoë A. Feder +3 more

Biallelic USP14 variants cause a syndromic neurodevelopmental disorder

Genetics in Medicine(2024)10.1016/j.gim.2024.101120

N/A

0DataRank · unranked

2 citations

Xénia Latypova, Ka Ying Sharon Hung, Miguel A. Prado, Byung‐Hoon Lee, Sophie Möller +19 more

Cell growth and nutrient availability control the mitotic exit signaling network in budding yeast

The Journal of Cell Biology(2024)10.1083/jcb.202305008

N/A

0DataRank · unranked

7 citations

Beth E. Prichard, Robert A. Sommer, Ricardo Leitão, Christopher J. Sarabia, Semin Hazir +4 more

Pleiotropic tumor suppressive functions of PTEN missense mutations during gliomagenesis

iScience(2024)10.1016/j.isci.2024.111278

N/A

0DataRank · unranked

4 citations

Joao A. Paulo, Victoria A. Appleman, Tomer M. Yaron, Jared L. Johnson, Alan T. Yeo +7 more

Carrier-Guided Proteome Analysis in a High Protein Background: An Improved Approach to Host Cell Protein Identification

Journal of Proteome Research(2024)10.1021/acs.jproteome.4c00158

N/A

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2 citations

Niloofar Seifihesar, Mukhayyo Sultonova, Beau Blackmore, Joao A. Paulo, Matthew Harty +2 more

Recharacterization of RSL3 reveals that the selenoproteome is a druggable target in colorectal cancer

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.03.29.587381

N/A

0DataRank · unranked

11 citations

Liang Zhao, Sofia Dziechciarz, Myungsun Shin, Sumeet Solanki, Andrii Balia +18 more

Spatiotemporal proteomic profiling of cellular responses to NLRP3 agonists

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.04.19.590338

N/A

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9 citations

Priya Veeraraghavan, Joao A. Paulo, J. Wade Harper, Louis Hollingsworth

BRD4-mediated epigenetic regulation of endoplasmic reticulum-mitochondria contact sites is governed by the mitochondrial complex III

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.02.02.578646

N/A

0DataRank · unranked

5 citations

Drew Stark, Pankaj Jadhav, Theophilus Nguyen, Benjamin Halligan, Nicholas J. Rossiter +25 more

Multi-omic Analysis of Human B-cell Activation Reveals a Key Lysosomal BCAT1 Role in mTOR Hyperactivation by B-cell receptor and TLR9

Research Square(2024)10.21203/rs.3.rs-4413958/v1

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0DataRank · unranked

2 citations

Matthew Lim, Hardik Shah, Joao A. Paulo, Yuchen Zhang, Haopeng Yang +18 more

Endo-IP and Lyso-IP Toolkit for Endolysosomal Profiling of Human Induced Neurons

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.09.24.614704

N/A

0DataRank · unranked

1 citations

Miguel A. Gonzalez‐Lozano, Lena M. Gottschalk, Aslan N. K. Cook, Jiuchun Zhang, Joao A. Paulo +2 more

Reviewer #2 (Public Review): Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenation

(2024)10.7554/elife.90579.2.sa0

N/A

0DataRank · unranked

0 citations

Ludger J.E. Goeminne, Alexander Tyshkovskiy, Sirui Zhang, Julie Chen, Joao A. Paulo +6 more

Global cellular proteo-lipidomic profiling of diverse lysosomal storage disease mutants using nMOST

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.03.26.586828

N/A

0DataRank · unranked

0 citations

Yuchen He, Sharan Swarup, Katherine A. Overmyer, Yizhi Jiang, Johann Brenner +15 more

Paradoxical mitotic exit induced by a small molecule inhibitor of APC/CCdc20

UNC Libraries(2024)10.17615/sjqr-7680

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0 citations

Joao A. Paulo, Randall W. King, Katharine L. Sackton, Masaya Yamaguchi, Katherine V. Richeson +4 more

Comparative Proteome-Wide Abundance Profiling of Yeast Strains Deleted for Cdc48 Adaptors

Proteomes(2024)10.3390/proteomes12040031

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0 citations

Joao A. Paulo, Valentina Rossio

Proteome Profiling of S. cerevisiae Strains Lacking the Ubiquitin-Conjugating Enzymes Ubc4 and Ubc5 During Exponential Growth and After Heat Shock Treatment

Microorganisms(2024)10.3390/microorganisms12112235

N/A

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0 citations

Xinyue Liu, Joao A. Paulo, Valentina Rossio

Isobaric Tagging and Data Independent Acquisition as Complementary Strategies for Proteome Profiling on an Orbitrap Astral Mass Spectrometer

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.12.17.628765

N/A

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0 citations

S L Dawson, Steven P. Gygi, Joao A. Paulo, Xinyue Liu

Ergothioneine controls mitochondrial function and exercise performance via direct activation of MPST

Cell Metabolism(2025)10.1016/j.cmet.2025.01.024

N/A

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45 citations

Melanie J. Mittenbühler, Yizhi Sun, Jonathan G. Van Vranken, Sebastian Schindler, Abhilash Jayaraj +23 more

GUK1 activation is a metabolic liability in lung cancer

Cell(2025)10.1016/j.cell.2025.01.024

N/A

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16 citations

Kiran Kurmi, Yutong Dai, Ishita Dhiman, Shakchhi Joshi, Brandon M. Gassaway +21 more

Isobaric Tagging and Data Independent Acquisition as Complementary Strategies for Proteome Profiling on an Orbitrap Astral Mass Spectrometer

Journal of Proteome Research(2025)10.1021/acs.jproteome.4c01107

N/A

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11 citations

S L Dawson, Steven P. Gygi, Joao A. Paulo, Xinyue Liu

TMT-Based Multiplexed (Chemo)Proteomics on the Orbitrap Astral Mass Spectrometer

Molecular & Cellular Proteomics(2025)10.1016/j.mcpro.2025.100968

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11 citations

Ka Yang, S. Li, Martin Zeller, Graeme C. McAlister, Hamish Stewart +7 more

CRISPR screens and quantitative proteomics reveal remodeling of the aryl hydrocarbon receptor–driven proteome through PARP7 activity

Proceedings of the National Academy of Sciences(2025)10.1073/pnas.2424985122

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8 citations

Joao A. Paulo, Christina B. Schroeter, Melanie Lad, Abigail Shurr, Chara Mastrokalou +9 more

Expanding the landscape of aging via orbitrap astral mass spectrometry and tandem mass tag integration

Nature Communications(2025)10.1038/s41467-025-60022-x

N/A

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7 citations

Yue Dou, Seth P. Kodikara, Erin D. Jeffery, Dina L. Bai, Erik Hultenius +6 more

CEBPA repression by MECOM blocks differentiation to drive aggressive leukemias

Blood(2025)10.1182/blood.2025028954

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6 citations

Mateusz Antoszewski, Sander Lambo, Michael C. Gundry, Riccardo Piussi, Lara Wahlster +19 more

Heterogeneity of Extracellular Vesicles and Non‐Vesicular Nanoparticles in Glioblastoma

Journal of Extracellular Vesicles(2025)10.1002/jev2.70168

N/A

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6 citations

Joao A. Paulo, Piyan Zhang, Xinyue Liu, Alya Nguyen, Yuanhua Cheng +14 more

Synaptic activity causes minute-scale changes in BAF complex composition and function

Molecular Cell(2025)10.1016/j.molcel.2025.05.017

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5 citations

Sabin A. Nettles, Wendy Wenderski, Joao A. Paulo, Sam H. Kim, Kyra C Roepke +5 more

The p97 ATPase and its adaptor UBXD8 maintain peroxisome pools by preventing pexophagy

The Journal of Cell Biology(2025)10.1083/jcb.202409024

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5 citations

Suganthan Amirthagunanathan, Rakesh Ganji, Joao A. Paulo, Brittany A. Ahlstedt, Ly Nguyen +3 more

Shifted assembly and function of mSWI/SNF family subcomplexes underlie targetable dependencies in dedifferentiated endometrial carcinomas

Nature Genetics(2025)10.1038/s41588-025-02333-9

N/A

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2 citations

Grace Xu, Alexander W. Ying, Bengul Gokbayrak, Ajinkya Patil, Joao A. Paulo +14 more

Cardiac adaptation to endurance exercise training requires suppression of GDF15 via PGC-1α

Nature Cardiovascular Research(2025)10.1038/s44161-025-00712-3

N/A

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5 citations

Haobo Li, Tevis Vitale, James Rhee, Saketh Challa, Claire Castro +31 more

Deazaguanylation is a nucleobase-protein conjugation required for type IV CBASS immunity

Science(2025)10.1126/science.adx6053

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4 citations

Patrick Pfaff, Joao A. Paulo, Steven P. Gygi, Kevan M. Shokat, Philip J. Kranzusch +1 more

A triple-action PROTAC for wild-type p53 cancer therapy

Cell Reports Medicine(2025)10.1016/j.xcrm.2025.102467

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2 citations

Utsarga Adhikary, J. Michael Schmidt, Marina Godes, Bethany Tesar, Christina M. Camara +11 more

Decoding spliceosome inhibition: Isobaric tag-based proteomic profiling of pladienolide B treated human cell lines

Journal of Proteomics(2025)10.1016/j.jprot.2025.105565

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1 citations

Karina Martínez-Pérez, Sanjukta Guha Thakurta, Benjamin P. Levi, Joao A. Paulo, Xcanda Ixchel Herrera Lopez

ALS-related p97 R155H mutation disrupts lysophagy in iPSC-derived motor neurons

Stem Cell Reports(2025)10.1016/j.stemcr.2025.102478

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3 citations

Michelle A. Johnson, Pantelis Antonoudiou, Jamie Maguire, Joao A. Paulo, Steve P. Gygi +3 more

Comprehensive Analysis of the Proteome of S. cerevisiae Wild-Type and pdr5Δ Cells in Response to Bisphenol A (BPA) Exposure

Microorganisms(2025)10.3390/microorganisms13010114

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1 citations

Joao A. Paulo, Valentina Rossio

The network response to Egf is tissue-specific

iScience(2025)10.1016/j.isci.2025.112146

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1 citations

Joao A. Paulo, Deborah L. Burkhart, Ian R. Smith, Ryan L. Collins, J. Wade Harper +3 more

Muscle-specific increased expression of JAG1 improves the skeletal muscle phenotype in dystrophin-deficient mice

Proceedings of the National Academy of Sciences(2025)10.1073/pnas.2506437122

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1 citations

Matthias Lambert, Tracy Zhang, James R. Conner, Joao A. Paulo, Sheldon Furtado Oliveira +7 more

Single-cell and clonal analysis of AL amyloidosis plasma cells and their bone marrow microenvironment

Blood(2025)10.1182/blood.2024024719

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2 citations

Maria Moscvin, Matteo Da Vià, Francesca Lazzaroni, Alice Nevone, Sam Sadigh +20 more

Evaluating Protein Extraction Techniques for Elucidating Proteomic Changes in Yeast Deletion Strains

Proteomes(2025)10.3390/proteomes13030028

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1 citations

Joao A. Paulo, Valentina Rossio

Cell-surface proteomic profiling identifies CD72 as a regulator of microglial tiling

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.06.02.657480

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1 citations

Mohit Rastogi, Micah X. Williams, Samuel Zhang, Sophia Shi, Steven R. Shuken +19 more

A SWI/SNF-specific Ig-like domain, SWIFT, is a transcription factor binding platform

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.08.01.667725

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1 citations

Kaylyn E. Williamson, Alexander W. Ying, Aasha M. Turner, Ruidong Jiang, Shaunak Raval +16 more

A human lysosomal storage disorder toolkit for decoding proteome landscapes in cortical and dopaminergic-like induced neurons

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.10.08.681047

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1 citations

Yuchen He, Yizhi Jiang, D. Li, Yohannes A Ambaw, Federico M. Gasparoli +7 more

Integral Synthesis and Clearance Analysis via DIA (ISDia) Reveals Coordinated Protein Dynamics Regulation during Endoplasmic Reticulum Stress

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.07.23.666381

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0DataRank · unranked

0 citations

Danny Qiu, Vivien Li, Gregory R. Keele, Wenpeng Liu, Jie Yang +4 more

AuxB interacts directly with GpsB and PknB to coordinate cell envelope processes that contribute to intrinsic antibiotic resistance in Staphylococcus aureus

mBio(2025)10.1128/mbio.01858-25

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0DataRank · unranked

0 citations

Youngseon Park, Ace George Santiago, Wanassa Beroual, Isabella A. Sobolewski, Wonsik Lee +3 more

Comparative Proteomic Profiling of Human Cell Lines Using Capillary and Micro‐Pillar Array Columns

PROTEOMICS(2025)10.1002/pmic.70052

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0 citations

Joao A. Paulo, Christina B. Schroeter

Endocrine-disrupting chemical exposure during differentiation alters the proliferation–maturation balance in stem-cell islets

Toxicological Sciences(2025)10.1093/toxsci/kfaf163

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0 citations

Lucas Unger, Joao A. Paulo, Luiza Ghila, Thomas Aga Legøy, June H Gudmestad

Altered Molecular Regulation of TUG Is a Central Feature of Insulin-Resistant Human Adipose Tissue

Diabetes(2025)10.2337/db25-0488

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0DataRank · unranked

0 citations

Kasper W. ter Horst, Daeun Sung, Aldo Jongejan, Aaron L. Slusher, Brandon M. Gassaway +10 more

Selective Alanine Transporter Utilization Creates a Targetable Metabolic Niche in Pancreatic Cancer

Cancer Discovery(2020)10.1158/2159-8290.cd-19-0959

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0DataRank · unranked

178 citations

Caroline R. Amendola, Kate E.R. Hollinshead, Qijia Yu, Keisuke Yamamoto, Joel Encarnación-Rosado +13 more

A Quantitative Tissue-Specific Landscape of Protein Redox Regulation during Aging

Cell(2020)10.1016/j.cell.2020.02.012

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420 citations

Mark P. Jedrychowski, Devin K. Schweppe, Edward L. Huttlin, Qing Yu, David E. Heppner +15 more

pH-Gated Succinate Secretion Regulates Muscle Remodeling in Response to Exercise

Cell(2020)10.1016/j.cell.2020.08.039

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0DataRank · unranked

276 citations

Luiz H. M. Bozi, Omar Yaghi, Evanna L. Mills, Haopeng Xiao, Hilary E. Nicholson +15 more

Global Landscape and Dynamics of Parkin and USP30-Dependent Ubiquitylomes in iNeurons during Mitophagic Signaling

Molecular Cell(2020)10.1016/j.molcel.2019.11.013

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225 citations

Joao A. Paulo, Jiuchun Zhang, Heeseon An, Kirby N. Swatek, Joe R. Cannon +4 more

O-GlcNAc regulates gene expression by controlling detained intron splicing

Nucleic Acids Research(2020)10.1093/nar/gkaa263

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123 citations

George Fei, Joao A. Paulo, Stanislav Bellaousov, Sara E. Martin, Damien Duveau +5 more

Selection of Heating Temperatures Improves the Sensitivity of the Proteome Integral Solubility Alteration Assay

Journal of Proteome Research(2020)10.1021/acs.jproteome.0c00063

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62 citations

Jonathan G. Van Vranken, Joao A. Paulo, Edward L. Huttlin, Steven P. Gygi, Jiaming Li

Pathogenic Pathways in Early-Onset Autosomal Recessive Parkinson's Disease Discovered Using Isogenic Human Dopaminergic Neurons

Stem Cell Reports(2020)10.1016/j.stemcr.2019.12.005

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63 citations

Alban Ordureau, Christina Bell, Lily Sarrafha, Chicheng Sun, Silvia Piccinotti +9 more

Co-option of Plasmodium falciparum PP1 for egress from host erythrocytes

Nature Communications(2020)10.1038/s41467-020-17306-1

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59 citations

Alexandra Miliu, Joao A. Paulo, Jonathan M. Goldberg, Arianna M. Bonilla, Laurence Berry +10 more

High-Resolution In Vivo Identification of miRNA Targets by Halo-Enhanced Ago2 Pull-Down

Molecular Cell(2020)10.1016/j.molcel.2020.05.009

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0DataRank · unranked

54 citations

Yuri Pritykin, Carla P. Concepcion, Yuheng Lu, Gaspare La Rocca, Minsi Zhang +14 more