Evolution of the highly networked deubiquitinating enzymes USP4, USP15, and USP11

Structure and Catalytic Regulatory Function of Ubiquitin Specific Protease 11 N-Terminal and Ubiquitin-like Domains

(2014) Stephen Harper et al.   BIOCHEMISTRY

Correlations between predicted protein disorder and post-translational modifications in plants

(2014) Atsushi Kurotani et al.   BIOINFORMATICS

Alternative splicing in osteoclasts and Paget’s disease of bone

(2014) Roscoe Klinck et al.   BMC Medical Genetics

The U4/U6 Recycling Factor SART3 Has Histone Chaperone Activity and Associates with USP15 to Regulate H2B Deubiquitination

(2014) Lindsey Long et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

USP11 regulates p53 stability by deubiquitinating p53

(2014) Jia-ying Ke et al.   Journal of Zhejiang University-SCIENCE B

Elephant shark genome provides unique insights into gnathostome evolution

(2014) Byrappa Venkatesh et al.   NATURE

USP15 stabilizes MDM2 to mediate cancer-cell survival and inhibit antitumor T cell responses

(2014) Qiang Zou et al.   NATURE IMMUNOLOGY

The Ubiquitin-Specific Protease USP15 Promotes RIG-I-Mediated Antiviral Signaling by Deubiquitylating TRIM25

(2014) E.-K. Pauli et al.   Science Signaling

The DUSP–Ubl domain of USP4 enhances its catalytic efficiency by promoting ubiquitin exchange

(2014) Marcello Clerici et al.   Nature Communications

Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes

(2014) Shengfeng Huang et al.   Nature Communications

Ultradeep Human Phosphoproteome Reveals a Distinct Regulatory Nature of Tyr and Ser/Thr-Based Signaling

(2014) Kirti Sharma et al.   Cell Reports

USP15 targets ALK3/BMPR1A for deubiquitylation to enhance bone morphogenetic protein signalling

(2014) L. Herhaus et al.   Open Biology

Detecting Functional Divergence after Gene Duplication through Evolutionary Changes in Posttranslational Regulatory Sequences

(2014) Alex N. Nguyen Ba et al.   PLoS Computational Biology

Deubiquitylating Enzymes and DNA Damage Response Pathways

(2013) Xavier Jacq et al.   CELL BIOCHEMISTRY AND BIOPHYSICS

Ubiquitin-specific protease 4 promotes TNF-α-induced apoptosis by deubiquitination of RIP1 in head and neck squamous cell carcinoma

(2013) Xiaozhi Hou et al.   FEBS LETTERS

An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome

(2013) Yangyang Bian et al.   Journal of Proteomics

USP4 Positively Regulates RIG-I-Mediated Antiviral Response through Deubiquitination and Stabilization of RIG-I

(2013) L. Wang et al.   JOURNAL OF VIROLOGY

Systems-wide Analysis of K-Ras, Cdc42, and PAK4 Signaling by Quantitative Phosphoproteomics

(2013) Florian Gnad et al.   MOLECULAR & CELLULAR PROTEOMICS

DAMBE5: A Comprehensive Software Package for Data Analysis in Molecular Biology and Evolution

(2013) Xuhua Xia   MOLECULAR BIOLOGY AND EVOLUTION

Regulation of protein–protein binding by coupling between phosphorylation and intrinsic disorder: analysis of human protein complexes

(2013) Hafumi Nishi et al.   Molecular BioSystems

USP15 Negatively Regulates Nrf2 through Deubiquitination of Keap1

(2013) Nicole F. Villeneuve et al.   MOLECULAR CELL

Somatic cells regulate maternal mRNA translation and developmental competence of mouse oocytes

(2013) Jing Chen et al.   NATURE CELL BIOLOGY

Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution

(2013) Jeramiah J Smith et al.   NATURE GENETICS

Deubiquitylases From Genes to Organism

(2013) Michael J. Clague et al.   PHYSIOLOGICAL REVIEWS

Evidence for at least six Hox clusters in the Japanese lamprey (Lethenteron japonicum)

(2013) T. K. Mehta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Roles of Whole-Genome and Small-Scale Duplications in the Functional Specialization of Saccharomyces cerevisiae Genes

(2013) Mario A. Fares et al.   PLoS Genetics

Differential expression of GDF9, TGFB1, TGFB2 and TGFB3 in porcine oocytes isolated from follicles of different size before and after culturein vitro

(2012) Marta Jackowska et al.   ACTA VETERINARIA HUNGARICA

The ubiquitin specific protease-4 (USP4) interacts with the S9/Rpn6 subunit of the proteasome

(2012) Bin Zhao et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Posttranslational regulation of self-renewal capacity: insights from proteome and phosphoproteome analyses of stem cell leukemia

(2012) M. Trost et al.   BLOOD

Direct and Indirect Control of Mitogen-activated Protein Kinase Pathway-associated Components, BRAP/IMP E3 Ubiquitin Ligase and CRAF/RAF1 Kinase, by the Deubiquitylating Enzyme USP15

(2012) Sebastian D. Hayes et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Toward a Comprehensive Characterization of a Human Cancer Cell Phosphoproteome

(2012) Houjiang Zhou et al.   JOURNAL OF PROTEOME RESEARCH

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Insights into bilaterian evolution from three spiralian genomes

(2012) Oleg Simakov et al.   NATURE

Ubiquitin removal in the TGF-β pathway

(2012) Kamna Aggarwal et al.   NATURE CELL BIOLOGY

USP4 is regulated by AKT phosphorylation and directly deubiquitylates TGF-β type I receptor

(2012) Long Zhang et al.   NATURE CELL BIOLOGY

USP15 stabilizes TGF-β receptor I and promotes oncogenesis through the activation of TGF-β signaling in glioblastoma

(2012) Pieter J A Eichhorn et al.   NATURE MEDICINE

InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation

(2012) Karin Breuer et al.   NUCLEIC ACIDS RESEARCH

GenBank

(2012) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues

(2012) Alicia Lundby et al.   Nature Communications

USP11 augments TGF  signalling by deubiquitylating ALK5

(2012) M. A. Al-Salihi et al.   Open Biology

Ubiquitin-specific protease 4 (USP4) targets TRAF2 and TRAF6 for deubiquitination and inhibits TNFα-induced cancer cell migration

(2011) Ning Xiao et al.   BIOCHEMICAL JOURNAL

Structure of the USP15 N-Terminal Domains: A β-Hairpin Mediates Close Association between the DUSP and UBL Domains

(2011) Stephen Harper et al.   BIOCHEMISTRY

USP4 targets TAK1 to downregulate TNFα-induced NF-κB activation

(2011) Y-H Fan et al.   CELL DEATH AND DIFFERENTIATION

USP4 inhibits p53 through deubiquitinating and stabilizing ARF-BP1

(2011) Xinna Zhang et al.   EMBO JOURNAL

Structural variability of the ubiquitin specific protease DUSP-UBL double domains

(2011) Paul R. Elliott et al.   FEBS LETTERS

Proteomic and phosphoproteomic comparison of human ES and iPS cells

(2011) Douglas H Phanstiel et al.   NATURE METHODS

The spatial and temporal organization of ubiquitin networks

(2011) Caroline Grabbe et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse

(2011) P. V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

Phosphoproteomic Analysis Identifies Grb10 as an mTORC1 Substrate That Negatively Regulates Insulin Signaling

(2011) Y. Yu et al.   SCIENCE

G q and Phospholipase C- : Turn On, Turn Off, and Do It Fast

(2011) E. M. Ross   Science Signaling

A Tissue-Specific Atlas of Mouse Protein Phosphorylation and Expression

(2010) Edward L. Huttlin et al.   CELL

Ubiquitin-specific proteases 7 and 11 modulate Polycomb regulation of the INK4a tumour suppressor

(2010) Goedele N Maertens et al.   EMBO JOURNAL

The Prp19 complex and the Usp4Sart3 deubiquitinating enzyme control reversible ubiquitination at the spliceosome

(2010) E. J. Song et al.   GENES & DEVELOPMENT

Quantitative Phosphoproteomics Dissection of Seven-transmembrane Receptor Signaling Using Full and Biased Agonists

(2010) Gitte L. Christensen et al.   MOLECULAR & CELLULAR PROTEOMICS

Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis

(2010) J. V. Olsen et al.   Science Signaling

Lys-N and Trypsin Cover Complementary Parts of the Phosphoproteome in a Refined SCX-Based Approach

(2009) Sharon Gauci et al.   ANALYTICAL CHEMISTRY

Defining the Human Deubiquitinating Enzyme Interaction Landscape

(2009) Mathew E. Sowa et al.   CELL

Phosphorylation Dynamics during Early Differentiation of Human Embryonic Stem Cells

(2009) Dennis Van Hoof et al.   Cell Stem Cell

USP11 negatively regulates TNFα-induced NF-κB activation by targeting on IκBα

(2009) Wenjing Sun et al.   CELLULAR SIGNALLING

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

The ubiquitin specific protease 4 (USP4) is a new player in the Wnt signalling pathway

(2009) Bin Zhao et al.   JOURNAL OF CELLULAR AND MOLECULAR MEDICINE

The COP9 Signalosome Mediates β-Catenin Degradation by Deneddylation and Blocks Adenomatous Polyposis coli Destruction via USP15

(2009) Xiaohua Huang et al.   JOURNAL OF MOLECULAR BIOLOGY

Regulating highly dynamic unstructured proteins and their coding mRNAs

(2009) Buyong Ma et al.   GENOME BIOLOGY

Solid Tumor Proteome and Phosphoproteome Analysis by High Resolution Mass Spectrometry

(2008) Sara Zanivan et al.   JOURNAL OF PROTEOME RESEARCH

A quantitative atlas of mitotic phosphorylation

(2008) N. Dephoure et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Value of Nonmodel Genomes and an Example Using SynMap Within CoGe to Dissect the Hexaploidy that Predates the Rosids

(2008) Eric Lyons et al.   Tropical Plant Biology