J. Neefjes

W. Zwart, J. Neefjes, P. Baas, 2018, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

HFE crosstalks with the MHC class I antigen presentation pathway Running title: The antigen presentation in HFE C282Y mutant cells

J. Neefjes, J. Cordeiro, M. Sousa, 2016 .

A fluorescent broad-spectrum proteasome inhibitor for labeling proteasomes in vitro and in vivo.

D. Filippov, H. Overkleeft, G. A. van der Marel, 2006, Chemistry & biology.

HFE cross-talks with the MHC class I antigen presentation pathway.

J. Neefjes, J. Cordeiro, S. F. de Almeida, 2005, Blood.

Two Listeria monocytogenes CTL epitopes are processed from the same antigen with different efficiencies.

E. Pamer, J. Neefjes, A. Sijts, 1996, Journal of immunology.

SKIP‐HOPS recruits TBC1D15 for a Rab7‐to‐Arl8b identity switch to control late endosome transport

Rik van der Kant, J. Neefjes, N. Liv, 2020, The EMBO journal.

Intracellular transport and peptide loading of MHC class II molecules: regulation by chaperones and motors

J. Neefjes, R. Wubbolts, 1999, Immunological reviews.

The ins and outs of intracellular peptides and antigen presentation by MHC class I molecules.

J. Neefjes, T. Groothuis, 2005, Current topics in microbiology and immunology.

Application of one-dimensional isoelectric focusing to separate different major histocompatibility complex class I alleles and determine their allelic interactions with transporter associated with antigen processing (TAP).

J. Neefjes, A. Neisig, 2001, Methods in molecular biology.

Interleukin-10 Down-Regulates MHC Class II αβ Peptide Complexes at the Plasma Membrane of Monocytes by Affecting Arrival and Recycling

J. Neefjes, J. Vries, R. D. Malefyt, 1997 .

A catalogue of treatment and technologies for malignant pleural mesothelioma

J. Neefjes, P. Baas, L. Schunselaar, 2016, Expert review of anticancer therapy.

Chaperoning antigen presentation by MHC class II molecules and their role in oncogenesis.

I. Jordens, M. Marsman, J. Neefjes, 2005, Advances in cancer research.

In Vivo and In Vitro Modulation of HLA-DM and HLA-DO Is Induced by B Lymphocyte Activation1

J. Trowsdale, J. Neefjes, M. V. van Ham, 2001, The Journal of Immunology.

CIIV, MIIC and other compartments for MHC class II loading

J. Neefjes, 1999, European journal of immunology.

The journey of Ca2+ through the cell – pulsing through the network of ER membrane contact sites

J. Neefjes, Ilana Berlin, T. Cremer, 2020, Journal of Cell Science.

A CD8+ T cell immune evasion protein specific to Epstein-Barr virus and its close relatives in Old World primates

M. Ressing, J. Neefjes, N. Croft, 2007, The Journal of experimental medicine.

DNA damage independent inhibition of NF-κB transcription by anthracyclines

V. Beneš, J. Neefjes, M. Sattler, 2020, bioRxiv.

Peptide Vaccination with an Anchor‐Replaced CTL Epitope Protects Against Human Papillomavirus Type 16‐Induced Tumors Expressing the Wild‐Type Epitope

M. Feltkamp, J. Drijfhout, W. Kast, 1998, Journal of immunotherapy.

A splice variant of RILP induces lysosomal clustering independent of dynein recruitment.

I. Jordens, M. Marsman, Nuno Rocha, 2006, Biochemical and biophysical research communications.

Splice variant of the Rab 7 effector RILP induces lysosomal clustering without dynein motor recruitment

I. Jordens, M. Marsman, Nuno Rocha, 2006 .

Radiation modulates the peptide repertoire, enhances MHC class I expression, and induces successful antitumor immunotherapy

Kevin Camphausen, Jacques Neefjes, Peter A. van Veelen, 2006 .

Reduced cell surface expression of HLA-C molecules correlates with restricted peptide binding and stable TAP interaction.

C. Melief, J. Neefjes, A. Neisig, 1998, Journal of immunology.

Recycling MHC class I molecules and endosomal peptide loading.

J. Neefjes, J. Calafat, R. V. Van BInnendijk, 1999, Proceedings of the National Academy of Sciences of the United States of America.

Interference with HIV-induced syncytium formation and viral infectivity by inhibitors of trimming glucosidase

H. Ploegh, J. Neefjes, R. Gruters, 1987, Nature.

Uncoupling DNA damage from chromatin damage to detoxify doxorubicin

C. Mummery, J. Neefjes, Junmin Li, 2020, Proceedings of the National Academy of Sciences.

Comprehensive structure-activity-relationship of azaindoles as highly potent FLT3 inhibitors.

H. Overkleeft, A. W. Tuin, G. V. van Westen, 2019, Bioorganic & medicinal chemistry.

LMP1 association with CD63 in endosomes and secretion via exosomes limits constitutive NF‐κB activation

T. Wurdinger, E. Kieff, D. Geerts, 2011, The EMBO journal.

Ultrastructural Imaging of Salmonella–Host Interactions Using Super‐resolution Correlative Light‐Electron Microscopy of Bioorthogonal Pathogens

A. Koster, J. Neefjes, A. Meijer, 2018, Chembiochem : a European journal of chemical biology.

Cross-presentation by intercellular peptide transfer through gap junctions

J. Drijfhout, J. Neefjes, E. Reits, 2005, Nature.

Synergizing radiation therapy and immunotherapy for curing incurable cancers. Opportunities and challenges.

J. Neefjes, C. Guha, J. Gulley, 2008, Oncology.

Feasibility of Primary Tumor Culture Models and Preclinical Prediction Assays for Head and Neck Cancer: A Narrative Review

J. Neefjes, S. Willems, R. Spijker, 2015, Cancers.

Sponge-supported cultures of primary head and neck tumors for an optimized preclinical model

S. Canisius, J. Neefjes, E. Jordanova, 2018, Oncotarget.

Maintaining soluble protein homeostasis between nuclear and cytoplasmic compartments across mitosis.

J. Neefjes, M. Jongsma, Ilana Berlin, 2022, Trends in cell biology.

The SPPL3-defined glycosphingolipid repertoire regulates immune responses by improving HLA class I access

M. Raaben, T. Brummelkamp, J. Neefjes, 2020, bioRxiv.

The EGFR odyssey – from activation to destruction in space and time

J. Neefjes, Ilana Berlin, J. Bakker, 2017, Journal of Cell Science.

Tight Linkage between Translation and MHC Class I Peptide Ligand Generation Implies Specialized Antigen Processing for Defective Ribosomal Products1

J. Yewdell, J. Bennink, J. Neefjes, 2006, The Journal of Immunology.

ER-embedded UBE2J1/RNF26 ubiquitylation complex in spatiotemporal control of the endolysosomal pathway

J. Neefjes, M. Jongsma, Ilana Berlin, 2020, bioRxiv.

Removal and degradation of the free MHC class II beta chain in the endoplasmic reticulum requires proteasomes and is accelerated by BFA.

J. Neefjes, J. Calafat, R. Wubbolts, 1998, Journal of cell science.

The fate of the three subunits of major histocompatibility complex class I molecules

H. Ploegh, J. Neefjes, L. Smit, 1992, European journal of immunology.

Intracellular transport of MHC class II molecules.

H. Ploegh, J. Neefjes, H. Ploegh, 1992, Immunology today.

The biosynthetic pathway of MHC class II but not class I molecules intersects the endocytic route

H. Geuze, J. Neefjes, P. Peters, 1990, Cell.

Mannose receptor‐mediated uptake of antigens strongly enhances HLA class II‐restricted antigen presentation by cultured dendritic cells

J. Drijfhout, T. Ottenhoff, J. Neefjes, 1997, European journal of immunology.

Inhibition of endosomal proteolytic activity by leupeptin blocks surface expression of MHC class II molecules and their conversion to SDS resistance alpha beta heterodimers in endosomes.

J. Neefjes, H. Ploegh, 1992, The EMBO journal.

Phosphorylated peptides can be transported by TAP molecules, presented by class I MHC molecules, and recognized by phosphopeptide-specific CTL.

T. Elliott, J. Neefjes, J. Zeuthen, 1999, Journal of immunology.

Antigen Presentation: Visualizing the MHC Class I Peptide-Loading Bottleneck

M. Lamers, J. Neefjes, Ilana Berlin, 2018, Current Biology.

CTLs by Blocking ATP Binding to TAP Cowpox Virus Protein CPXV012 Eludes

Robert, E. Kremmer, M. Ressing, 2014 .

Cowpox Virus Protein CPXV012 Eludes CTLs by Blocking ATP Binding to TAP

E. Kremmer, J. Drijfhout, M. Ressing, 2014, The Journal of Immunology.

Binding and Stable TAP Interaction Molecules Correlates with Restricted Peptide Reduced Cell Surface Expression of HLA-C

C. Melief, J. Neefjes, A. Neisig, 1997 .

Proteasome subunits encoded by the major histocompatibility complex are not essential for antigen presentation

J. Neefjes, H. Spits, F. Momburg, 1992, Nature.

Proteases, proteases and proteases for presentation

J. Neefjes, E. Reits, C. Herberts, 2003, Nature Immunology.

Phosphorylation of surface E‐selectin and the effect of soluble ligand (Sialyl Lewisx) on the half‐life of E‐selectin

J. Neefjes, W. Buurman, W. Buurman, 1993, European journal of immunology.

Predictive algorithm for tamoxifen resistance in breast cancer patients based on PKA-induced phosphorylation of ERα at serine 305 and PAK1

L. Wessels, W. Zwart, L. J. Veer, 2009 .

Assembly and intracellular transport of major histocompatibility complex molecules.

T. Schumacher, H. Ploegh, J. Neefjes, 1991, Current opinion in cell biology.

Dynamics within tetraspanin pairs affect MHC class II expression

J. Neefjes, P. Paul, H. Janssen, 2012, Journal of Cell Science.

Dynamics of proteins within tetraspanin webs in MVBs

J. Neefjes, H. Janssen, L. Janssen, 2011 .

How is the proteasome degraded?

J. Neefjes, F. Leeuwen, V. Menéndez-Benito, 2015 .

Assaying peptide translocation by the peptide transporter TAP.

J. Neefjes, M. Jongsma, 2013, Methods in molecular biology.

The Immunoproteasome Cleans up after Inflammation

J. Neefjes, S. V. Deventer, 2010, Cell.

Antigen presentation by MHC class I and II molecules.

J. Neefjes, 1996, Immunobiology.

Doxorubicin and Aclarubicin: Shuffling Anthracycline Glycans for Improved Anticancer Agents

H. Overkleeft, G. A. van der Marel, J. Neefjes, 2020, Journal of medicinal chemistry.

Specialized Antigen Processing for Defective Class I Peptide Ligand Generation Implies Tight Linkage between Translation and MHC

J. Yewdell, J. Bennink, J. Neefjes, 2006 .

Association with beta 2-microglobulin controls the expression of transfected human class I genes.

H. Ploegh, J. Neefjes, F. Hochstenbach, 1987, Journal of immunology.

Assembly and Intracellular Transport of MHC Molecules

J. Neefjes, H. Ploegh, 1993 .

Non-carrier-mediated uptake of the mannosidase I inhibitor 1-deoxymannojirimycin by K562 erythroleukemic cells.

G. A. van der Marel, H. Ploegh, J. Neefjes, 1989, The Journal of biological chemistry.

Activated pDCs: open to new antigen-presentation possibilities

J. Neefjes, T. Hoorn, 2008, Nature Immunology.

Stable expression of MHC class I heavy chain/HLA‐DO complexes at the plasma membrane

J. Neefjes, M. van Lith, M. V. van Ham, 2003, European journal of immunology.

Body HLA-DM / DO and Class II within the Presentation by Sorting of Recycling Regulation of MHC Class II Antigen

J. Neefjes, D. Verwoerd, J. Calafat, 2001 .

Major histocompatibility complex class II molecules induce the formation of endocytic MIIC-like structures

J. Neefjes, J. Calafat, M. Nijenhuis, 1994, The Journal of cell biology.

Recombination-induced tag exchange to track old and new proteins

H. Ovaa, J. Neefjes, Tibor van Welsem, 2009, Proceedings of the National Academy of Sciences.

B Cell Receptor-Mediated Internalization of Salmonella: A Novel Pathway for Autonomous B Cell Activation and Antibody Production1

J. Neefjes, A. Griekspoor, H. Janssen, 2009, The Journal of Immunology.

Immune escape and spreading of Salmonella after specific B Cell Receptor-mediated uptake 6 B cell activation and induction of acquired immunity through BCR- mediated phagocytosis of Salmonella

J. Neefjes, A. Griekspoor, H. Janssen, 2006 .

Activation and Antibody : A Novel Pathway for Salmonella B Cell Receptor-Mediated Internalization of

J. Neefjes, A. Griekspoor, H. Janssen, 2022 .

Antigen-Specific B Cells Reactivate an Effective Cytotoxic T Cell Response against Phagocytosed Salmonella through Cross-Presentation

J. Neefjes, A. ten Brinke, Y. Souwer, 2010, PloS one.

Influenza virus changes cell-surface glycoproteins including major histocompatibility complex determinants on lymphocytes.

J. Neefjes, F. Rotteveel, C. Lucas, 1989, Human immunology.

Biochemical complexity of serum HLA class I molecules

J. Neefjes, M. Giphart, N. Stam, 2004, Immunogenetics.

An improved biochemical method for the analysis of HLA-class I antigens. Definition of new HLA-class I subtypes.

H. Ploegh, J. Neefjes, G. V. van Seventer, 1986, Human immunology.

Recycling glycoproteins do not return to the cis-Golgi

G. A. van der Marel, H. Ploegh, J. Neefjes, 1988, The Journal of cell biology.

A biochemical characterization of feline MHC products: Unusually high expression of class 11 antigens on peripheral blood lymphocytes

H. Ploegh, J. Neefjes, E. Hensen, 2004, Immunogenetics.

Intracellular interactions of transferrin and its receptor during biosynthesis

H. Ploegh, J. Neefjes, T. Hengeveld, 1990, The Journal of cell biology.

Production and Thermal Exchange of Conditional Peptide‐MHC I Multimers

J. Drijfhout, H. Ovaa, J. Neefjes, 2019, Current protocols in immunology.

Interference with T cell receptor–HLA-DR interactions by Epstein–Barr virus gp42 results in reduced T helper cell recognition

T. Schumacher, M. Schilham, M. Ressing, 2003, Proceedings of the National Academy of Sciences of the United States of America.

N-linked glycan modification on antigen-presenting cells restores an allospecific cytotoxic T cell response

C. Melief, J. Neefjes, C. Boog, 1990, The Journal of experimental medicine.

HLA-DO is a negative modulator of HLA-DM-mediated MHC class II peptide loading

J. Trowsdale, T. Ottenhoff, D. Pappin, 1997, Current Biology.

Mannose receptor mediated uptake of antigens strongly enhances HLA-class II restricted antigen presentation by cultured dendritic cells.

J. Drijfhout, T. Ottenhoff, J. Neefjes, 1997, Advances in experimental medicine and biology.

Statins affect cell-surface expression of major histocompatibility complex class II molecules by disrupting cholesterol-containing microdomains.

J. Neefjes, T. Groothuis, H. Kuipers, 2005, Human immunology.

An analysis of class I antigens of man and other species by one-dimensional IEF and immunoblotting

H. Ploegh, J. Neefjes, C. Beckers, 2004, Immunogenetics.

Assembled Pre-B Cell Receptor Complexes Are Retained in the Endoplasmic Reticulum by a Mechanism That Is Not Selective for the Pseudo-light Chain*

J. Neefjes, J. Borst, E. de Vries, 1996, The Journal of Biological Chemistry.

Specific immune responses restored by alteration in carbohydrate chains of surface molecules on antigen‐presenting cells

C. Melief, H. Ploegh, J. Neefjes, 1989, European journal of immunology.

Peptide Binding and Intracellular Transport of MHC Molecules

J. Neefjes, 1993 .

Major histocompatibility complex class II compartments in human B lymphoblastoid cells are distinct from early endosomes

H. Ploegh, J. Neefjes, P. Peters, 1995, The Journal of experimental medicine.

HLA class I and II molecules present influenza virus antigens with different kinetics

F. Miedema, J. Neefjes, R. V. van Lier, 1992, European journal of immunology.

ER contact sites direct late endosome transport

J. Neefjes, M. Jongsma, Ilana Berlin, 2015, BioEssays : news and reviews in molecular, cellular and developmental biology.

Modulation of TAP-dependent antigen compartmentalization during human monocyte-to-DC differentiation.

F. Klawonn, R. Tampé, J. Neefjes, 2019, Blood advances.

Expanding the peptidome for immunotherapy.

J. Neefjes, 2015, Blood.

Mobile late endosomes modulate peripheral endoplasmic reticulum network architecture

J. Neefjes, R. Wijdeven, Birol Cabukusta, 2021, EMBO reports.

Ras (proto)oncogene induces N‐linked carbohydrate modification: temporal relationship with induction of invasive potential.

J. Neefjes, A. Hall, J. Bolscher, 1988, The EMBO journal.

Aberrant MHC class II antigen presentation is linked to expansion of the activated T cell compartment in B-CLL

C. Meijer, J. Neefjes, G. Ossenkoppele, 2011 .

USP32 regulates late endosomal transport and recycling through deubiquitylation of Rab7

H. Ovaa, J. Neefjes, E. Bos, 2019, Nature Communications.

Neuronal ceroid lipofuscinosis protein CLN3 interacts with motor proteins and modifies location of late endosomal compartments

J. Neefjes, V. Olkkonen, A. Jalanko, 2012, Cellular and Molecular Life Sciences.

Cholesterol sensor ORP1L contacts the ER protein VAP to control Rab7–RILP–p150Glued and late endosome positioning

W. Zwart, Rik van der Kant, Nuno Rocha, 2009, The Journal of cell biology.

Cholesterol sensor ORP1L organizes late endosomal contacts with the ER protein VAP that controls Rab7-RILP-p150 Glued and late endosomal positioning

W. Zwart, Nuno Rocha, J. Neefjes, 2009 .

HLA-DM and MHC class II molecules co-distribute with peptidase-containing lysosomal subcompartments.

J. Trowsdale, J. Neefjes, M. Fernandez-Borja, 1996, International immunology.

Targeting major histocompatibility complex class II molecules to the cell surface by invariant chain allows antigen presentation upon recycling

J. Neefjes, J. Calafat, M. de Haas, 1994, European journal of immunology.

Bovine herpesvirus 1 interferes with TAP-dependent peptide transport and intracellular trafficking of MHC class I molecules in human cells

M. Ressing, J. Neefjes, K. Bieńkowska-Szewczyk, 2003, Archives of Virology.

The UL41-encoded virion host shutoff (vhs) protein and vhs-independent mechanisms are responsible for down-regulation of MHC class I molecules by bovine herpesvirus 1.

M. Ressing, J. Neefjes, D. Koppers-Lalic, 2001, The Journal of general virology.

Segregation of MHC class II molecules from MHC class I molecules in the Golgi complex for transport to lysosomal compartments

H. Geuze, H. Ploegh, J. Neefjes, 1991, Nature.

Studying MHC class II transport in dendritic cells.

J. Neefjes, P. Paul, 2013, Methods in molecular biology.

Multivesicular body morphogenesis requires phosphatidyl-inositol 3-kinase activity

J. Neefjes, N. Divecha, J. Calafat, 1999, Current Biology.

MHC class II molecules: transport pathways for antigen presentation.

J. Neefjes, R. Wubbolts, M. Fernandez-Bona, 1997, Trends in cell biology.

Allele-specific down-regulation of MHC class I antigens in Burkitt lymphoma lines.

G. Klein, H. Ploegh, J. Neefjes, 1989, Cellular immunology.

The labyrinth unfolds: architectural rearrangements of the endolysosomal system in antigen-presenting cells.

J. Neefjes, M. Jongsma, Ilana Berlin, 2019, Current opinion in immunology.

An ER-Associated Pathway Defines Endosomal Architecture for Controlled Cargo Transport

J. Neefjes, R. Spaapen, M. Jongsma, 2016, Cell.

analysis of genes involved in MHC class II antigen presentation

J. Neefjes, 2015 .

Determining Protein Transport to the Plasma Membrane

J. Neefjes, 2000, Current protocols in cell biology.

Synthesis of the Antibiotic 1,5-dideoxy-1,5-imino-d-mannitol

H. Ploegh, J. Neefjes, J. H. Boom, 1988 .

PKA Phosphorylation redirects Estrogen Receptor to promoters of a unique gene set to induce tamoxifen resistance

W. Zwart, S. Canisius, J. Neefjes, 2012 .

Moving and positioning the endolysosomal system.

J. Bonifacino, J. Neefjes, 2017, Current opinion in cell biology.

Empty MHC class I molecules come out in the cold

Hidde L. Ploegh, Klas Kärre, Hans-Gustaf Ljunggren, 1990, Nature.

Visualizing the action of steroid hormone receptors in living cells

W. Zwart, J. Neefjes, R. Michalides, 2007, Nuclear receptor signaling.

Lectin‐induced retardation of subcellular organelles during preparative density gradient electrophoresis: Selective purification of plasma membranes

J. Neefjes, D. Verwoerd, A. Tulp, 1999, Electrophoresis.

Connect the Immune System: Roles of Gap Junctions in Antigen Presentation and T Cell Activation

J. Neefjes, B. Pang, 2013 .

Coupled for Cross-Presentation in Tumor Immunotherapy

J. Neefjes, B. Pang, Baoxu Pang, 2010, Science Translational Medicine.

Gap Junction Communication between Autologous Endothelial and Tumor Cells Induce Cross-Recognition and Elimination by Specific CTL1

J. Neefjes, C. Robert, T. Tursz, 2009, Journal of Immunology.

Specific CTL Induce Cross-Recognition and Elimination by Autologous Endothelial and Tumor Cells Gap Junction Communication between

J. Neefjes, C. Robert, T. Tursz, 2009 .

MHC class II compartments and the kinetics of antigen presentation in activated mouse spleen dendritic cells.

W. Kast, C. Melief, J. Neefjes, 1995, Journal of immunology.

Antigen processing and recognition Editorial overview

J. Neefjes, C. Harding, 2005 .

IL-24 The small GTPase Rab7 and its effector protein RILP regulate lysosomal transport

I. Jordens, M. Marsman, J. Neefjes, 2003 .

Exploring genome-wide datasets of MHC class II antigen presentation.

J. Neefjes, P. Paul, J. Bakker, 2013, Molecular immunology.

Synthetic (N,N-Dimethyl)doxorubicin Glycosyl Diastereomers to Dissect Modes of Action of Anthracycline Anticancer Drugs

H. Overkleeft, G. A. van der Marel, J. Neefjes, 2021, The Journal of organic chemistry.

Human VAPome Analysis Reveals MOSPD1 and MOSPD3 as Membrane Contact Site Proteins Interacting with FFAT-Related FFNT Motifs.

J. Neefjes, P. V. van Veelen, Ilana Berlin, 2020, Cell reports.

Rab 7 and Rab 27 a control two motor protein activities competing in melanosomal transport

I. Jordens, W. Westbroek, M. Marsman, 2006 .

A conditionally immortalized dendritic cell line which differentiates in contact with T cells or T cell‐derived cytokines

B. Stockinger, J. Neefjes, A. Volkmann, 1996, European journal of immunology.

TBC1D5 controls the GTPase cycle of Rab7b

J. Neefjes, J. P. Morth, O. Bakke, 2018, Journal of Cell Science.

Association of Checkpoint Inhibitor-Induced Toxic Effects With Shared Cancer and Tissue Antigens in Non-Small Cell Lung Cancer.

D. Speiser, B. Ludewig, J. Neefjes, 2019, JAMA Oncology.

Ubiquitination by the Membrane-associated RING-CH-8 (MARCH-8) Ligase Controls Steady-state Cell Surface Expression of Tumor Necrosis Factor-related Apoptosis Inducing Ligand (TRAIL) Receptor 1*

J. Neefjes, J. Borst, E. de Vries, 2013, The Journal of Biological Chemistry.

Ubiquitination by MARCH-8 controls TRAIL-R1

J. Neefjes, E. D. Vries, J. Borst, 2013 .

Reciprocal chemical genetics for swift lead and target identification.

A. W. Tuin, J. Neefjes, C. Kuijl, 2008, Molecular bioSystems.

The AF-1 and hinge region of the human Estrogen Receptor cooperate in the quantitative response to estradiol and tamoxifen

W. Zwart, J. Neefjes, R. Michalides, 2009 .

Gap junction-mediated intercellular communication in the immune system.

J. Neefjes, J. Neijssen, B. Pang, 2007, Progress in biophysics and molecular biology.

Mechanisms of lysosomal positioning and movement

J. Neefjes, Birol Cabukusta, 2018, Traffic.

Leucine Aminopeptidase Is Not Essential for Trimming Peptides in the Cytosol or Generating Epitopes for MHC Class I Antigen Presentation1

K. Rock, A. Murphy, G. Yancopoulos, 2005, The Journal of Immunology.

Varicellovirus UL49.5 Proteins Differentially Affect the Function of the Transporter Associated with Antigen Processing, TAP

R. Tampé, J. Koch, M. Ressing, 2008, PLoS pathogens.

Varicelloviruses avoid T cell recognition by UL49.5-mediated inactivation of the transporter associated with antigen processing.

R. Tampé, J. Koch, M. Ressing, 2005, Proceedings of the National Academy of Sciences of the United States of America.

E-selectin and intercellular adhesion molecule-1 are released by activated human endothelial cells in vitro.

J. Neefjes, W. Buurman, J. Leeuwenberg, 1992, Immunology.

Salmonella Manipulation of Host Signaling Pathways Provokes Cellular Transformation Associated with Gallbladder Carcinoma.

A. Broeks, J. Neefjes, R. Spaapen, 2015, Cell host & microbe.

The Rab7 effector protein RILP controls lysosomal transport by inducing the recruitment of dynein-dynactin motors

Jacques Neefjes, Hans Janssen, I. Jordens, 2001, Current Biology.

Variations in MHC Class II Antigen Processing and Presentation in Health and Disease.

E. Unanue, J. Neefjes, V. Turk, 2016, Annual review of immunology.

The ER-embedded UBE2J1/RNF26 ubiquitylation complex exerts spatiotemporal control over the endolysosomal pathway.

J. Neefjes, M. Jongsma, Ilana Berlin, 2021, Cell reports.

Cholesterol-binding molecules MLN64 and ORP1L mark distinct late endosomes with transporters ABCA3 and NPC1[S]

Rik van der Kant, J. Neefjes, L. Janssen, 2013, Journal of Lipid Research.

A Genome-wide Multidimensional RNAi Screen Reveals Pathways Controlling MHC Class II Antigen Presentation

P. Cresswell, D. Egan, R. Beijersbergen, 2011, Cell.

Costimulatory ligand CD70 is delivered to the immunological synapse by shared intracellular trafficking with MHC class II molecules

Anna M. Keller, M. Marsman, J. Neefjes, 2007, Proceedings of the National Academy of Sciences.

Spatial separation of HLA-DM/HLA-DR interactions within MIIC and phagosome-induced immune escape.

W. Zwart, M. Marsman, J. Neefjes, 2005, Immunity.

Tamoxifen resistance by a conformational arrest of the estrogen receptor alpha after PKA activation in breast cancer.

A. Floore, J. Neefjes, R. Michalides, 2004, Cancer cell.

New insights into the activities and toxicities of the old anticancer drug doxorubicin

J. Neefjes, Xiaohang Qiao, Sabina Y. van der Zanden, 2020, The FEBS journal.

Distribution and Elimination of the Glycosidase Inhibitors 1-Deoxymannojirimycin and N-Methyl-1-Deoxynojirimycin in the Rat in Vivo

H. Ploegh, J. Neefjes, D. Meijer, 1992, Pharmaceutical Research.

Immunoproteasomes and immunotherapy-a smoking gun for lung cancer?

J. Neefjes, Menno Spits, 2016, Journal of thoracic disease.

Glutaminyl cyclase is an enzymatic modifier of the CD47- SIRPα axis and target for cancer immunotherapy

T. Schumacher, M. Raaben, T. Brummelkamp, 2019, Nature Medicine.

Radiation modulates the peptide repertoire, enhances MHC class I expression, and induces successful antitumor immunotherapy

K. Camphausen, J. Schlom, J. Neefjes, 2006, The Journal of experimental medicine.

Protein glycosylation.

J. Neefjes, H. Ploegh, 1990, Current opinion in cell biology.

High resolution density gradient electrophoresis of cellular organelles

J. Neefjes, D. Verwoerd, M. Fernandez-Borja, 1996, Electrophoresis.

Genome-Wide Identification and Characterization of Novel Factors Conferring Resistance to Topoisomerase II Poisons in Cancer.

L. Wessels, T. Brummelkamp, J. Neefjes, 2015, Cancer research.

High‐resolution density gradient electrophoresis of proteins and subcellular organelles

J. Neefjes, D. Verwoerd, A. Benham, 1997, Electrophoresis.

Accumulation of HLA-DM, a regulator of antigen presentation, in MHC class II compartments.

J. Trowsdale, J. Neefjes, H. Geuze, 1994, Science.

Opposing motor activities of dynein and kinesin determine retention and transport of MHC class II-containing compartments.

C. Echeverri, R. Vallee, I. Jordens, 1999, Journal of cell science.

Electromigration for separations of protein complexes.

J. Neefjes, A Tulp, D Verwoerd, 1999, Journal of chromatography. B, Biomedical sciences and applications.

High‐resolution density gradient electrophoresis of subcellular organelles and proteins under nondenaturing conditions

J. Neefjes, D. Verwoerd, M. Fernandez-Borja, 1998, Electrophoresis.

Direct vesicular transport of MHC class II molecules from lysosomal structures to the cell surface

J. Neefjes, J. Calafat, R. Wubbolts, 1996, The Journal of cell biology.

The hinge region of the human estrogen receptor determines functional synergy between AF-1 and AF-2 in the quantitative response to estradiol and tamoxifen

W. Zwart, J. Neefjes, R. Michalides, 2010, Journal of Cell Science.

Quantifying exosome secretion from single cells reveals a modulatory role for GPCR signaling

J. Neefjes, M. Verhage, R. Toonen, 2018, The Journal of cell biology.

The major substrates for TAP in vivo are derived from newly synthesized proteins

J. Neefjes, E. Reits, J. C. Vos, 2000, Nature.

MED12 Controls the Response to Multiple Cancer Drugs through Regulation of TGF-β Receptor Signaling

R. Bernards, T. Knijnenburg, L. Wessels, 2012, Cell.

Neuronal ceroid lipofuscinosis protein CLN3 interacts with motor proteins and modifies location of late endosomal compartments

J. Neefjes, V. Olkkonen, A. Jalanko, 2012, Cellular and Molecular Life Sciences.

Stop or Go? Endosome Positioning in the Establishment of Compartment Architecture, Dynamics, and Function.

Jacques Neefjes, J. Neefjes, M. Jongsma, 2017, Trends in cell biology.

Small regulators, major consequences – Ca2+ and cholesterol at the endosome–ER interface

Rik van der Kant, J. Neefjes, 2014, Journal of Cell Science.

Stuck in traffic: an emerging theme in diseases of the nervous system

J. Neefjes, R. Kant, 2014, Trends in Neurosciences.

Late endosomal transport and tethering are coupled processes controlled by RILP and the cholesterol sensor ORP1L

J. Carette, T. Brummelkamp, Rik van der Kant, 2013, Journal of Cell Science.

Cholesterol sensor ORP 1 L organizes late endosomal contacts with the ER protein VAP that controls Rab 7-RILP-p 150 Glued and late endosomal positioning Submitted

W. Zwart, Nuno Rocha, J. Neefjes, 2009 .

Activation of endosomal dynein motors by stepwise assembly of Rab7–RILP–p150Glued, ORP1L, and the receptor βlll spectrin

W. Zwart, I. Jordens, Nuno Rocha, 2007, The Journal of cell biology.

Dynein-mediated vesicle transport controls intracellular Salmonella replication.

I. Jordens, M. Marsman, J. Neefjes, 2004, Molecular biology of the cell.

TAP Peptide Transporters and Antigen Presentation

J. Neefjes, F. Momburg, G. Hämmerling, 1996 .

Routes to manipulate MHC class II antigen presentation.

J. Neefjes, M. Jongsma, P. Paul, 2011, Current opinion in immunology.

Bacterial infections and cancer

J. Neefjes, D. V. van Elsland, Daphne M. van Elsland, 2018, EMBO reports.

A peptide's perspective on antigen presentation to the immune system.

H. Ovaa, J. Neefjes, 2013, Nature chemical biology.

Increased colon cancer risk after severe Salmonella infection

J. Neefjes, W. van Pelt, L. Mughini-Gras, 2018, PloS one.

Association of BMI1 with Polycomb Bodies Is Dynamic and Requires PRC2/EZH2 and the Maintenance DNA Methyltransferase DNMT1

P. Taghavi, J. Neefjes, C. Kuijl, 2005, Molecular and Cellular Biology.

MHC class II molecules on the move for successful antigen presentation

Jacques Neefjes, Nuno Rocha, J. Neefjes, 2008, The EMBO journal.

Homeostasis of soluble proteins and the proteasome post nuclear envelope reformation in mitosis

L. M. Voortman, H. Ovaa, J. Neefjes, 2019, Journal of Cell Science.

The Curative Outcome of Radioimmunotherapy in a Mouse Breast Cancer Model Relies on mTOR Signaling

J. Neefjes, R. Johnstone, M. Verheij, 2014, Radiation research.

Identification of a novel ATM inhibitor with cancer cell specific radiosensitization activity

H. Ovaa, J. Neefjes, P. Halonen, 2017, Oncotarget.

Cholesterol and ORP1L-mediated ER contact sites control autophagosome transport and fusion with the endocytic pathway

J. Neefjes, K. Jalink, H. Janssen, 2016, Nature Communications.

Characterization of the Mammalian CORVET and HOPS Complexes and Their Modular Restructuring for Endosome Specificity*

Rik van der Kant, J. Neefjes, J. Klumperman, 2015, The Journal of Biological Chemistry.

Multiple sclerosis-associated CLEC16A controls HLA class II expression via late endosome biogenesis.

J. Neefjes, R. Hintzen, J. Laman, 2015, Brain : a journal of neurology.

Serine-305 Phosphorylation Modulates Estrogen Receptor Alpha Binding to a Coregulator Peptide Array, with Potential Application in Predicting Responses to Tamoxifen

J. Martens, R. Houtman, J. Neefjes, 2012, Molecular Cancer Therapeutics.

Membrane topology and dimerization of the two subunits of the transporter associated with antigen processing reveal a three-domain structure.

J. Neefjes, F. Momburg, J. C. Vos, 1999, Journal of immunology.

Selective and ATP-dependent translocation of peptides by the MHC-encoded transporter.

J. Neefjes, F. Momburg, G. Hämmerling, 1993, Science.

Recent and new targets for small molecule anti-cancer agents.

H. Ovaa, J. Neefjes, C. Kuijl, 2009, Drug discovery today. Technologies.

Biochemical evidence that the DLA-B locus codes for a class II determinant expressed on all canine peripheral blood lymphocytes.

J. Neefjes, H. Grosse-wilde, I. Doxiadis, 1989, Experimental and clinical immunogenetics.

A FRET profile of modifications in Estrogen Receptor α associated with resistance to anti-estrogens Submitted 10

W. Zwart, J. Neefjes, R. Michalides, 2006 .

Towards an understanding of C9orf82 protein/CAAP1 function

I. Huijbers, J. Neefjes, Ji-Ying Song, 2019, PloS one.

A Role for Estrogen Receptor Phosphorylation in the Resistance to Tamoxifen

J. Neefjes, R. Michalides, R. de Leeuw, 2011, International journal of breast cancer.

Antigen degradation or presentation by MHC class I molecules via classical and non-classical pathways.

J. Neefjes, M. Grommé, 2002, Molecular immunology.

Ubiquitin crosstalk connecting cellular processes

J. Neefjes, N. Dantuma, F. Salomons, 2006, Cell Division.

The Journal of Cell Biology

J. Neefjes, M. Pardue, N. Dantuma, 2002 .

Comprehensive Pharmacogenomic Profiling of Malignant Pleural Mesothelioma Identifies a Subgroup Sensitive to FGFR Inhibition

A. Berns, U. McDermott, F. Iorio, 2017, Clinical Cancer Research.

Chemical biology of antigen presentation by MHC molecules.

H. Ovaa, J. Neefjes, S. V. van Kasteren, 2014, Current opinion in immunology.

Complement is a central mediator of radiotherapy-induced tumor-specific immunity and clinical response.

M. Okoniewski, R. Dummer, M. van den Broek, 2015, Immunity.

Opportunities for Small Molecules in Cancer Immunotherapy.

H. Ovaa, J. Neefjes, J. Borst, 2020, Trends in immunology.

Presentation of Cytosolic Glycosylated Peptides by Human Class I Major Histocompatibility Complex Molecules in Vivo

T. Elliott, J. Neefjes, J. Zeuthen, 1999, The Journal of experimental medicine.

Chemical and genetic control of IFNγ‐induced MHCII expression

J. Neefjes, R. Hintzen, P. J. van den Elsen, 2018, EMBO reports.

Collateral damage: insights into bacterial mechanisms that predispose host cells to cancer

B. Nadel, D. Raoult, J. Neefjes, 2017, Nature Reviews Microbiology.

LIVE-IMAGING OF MVB-PM FUSION

J. Neefjes, M. Verhage, R. Toonen, 2022 .

Modulation of the Major Histocompatibility Complex Class II–Associated Peptide Repertoire by Human Histocompatibility Leukocyte Antigen (Hla)-Do

Jacques Neefjes, John Trowsdale, J. Trowsdale, 2000, The Journal of experimental medicine.

A trimeric Rab7 GEF controls NPC1-dependent lysosomal cholesterol export

P. Lehner, J. Neefjes, J. Luzio, 2019, Nature Communications.

Spatiotemporal analysis of organelle and macromolecular complex inheritance

J. Neefjes, F. van Leeuwen, V. Menéndez-Benito, 2012, Proceedings of the National Academy of Sciences.

Translocation of long peptides by transporters associated with antigen processing (TAP)

J. Neefjes, F. Momburg, G. Hämmerling, 1996, European journal of immunology.

Interleukin-10 down-regulates MHC class II alphabeta peptide complexes at the plasma membrane of monocytes by affecting arrival and recycling.

R. de Waal Malefyt, J. Neefjes, J. D. de Vries, 1997, Immunity.

Translocation of PKCθ in T cells is mediated by a nonconventional, PI3-K– and Vav-dependent pathway, but does not absolutely require phospholipase C

Jacques Neefjes, Robert T. Abraham, Amnon Altman, 2002, The Journal of cell biology.

Modulation of DNA Repair and the Epigenetic Landscape by Selective Histone Eviction: a Novel Mechanism of Doxorubicin Anti-cancer Activity

W. Zwart, H. Ovaa, J. Neefjes, 2013 .

Resistance to antiestrogen arzoxifene is mediated by overexpression of cyclin D1.

W. Zwart, J. Neefjes, Z. D. Sharp, 2009, Molecular endocrinology.

Old drugs, novel ways out: Drug resistance toward cytotoxic chemotherapeutics.

Y. Assaraf, J. Neefjes, R. Wijdeven, 2016, Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy.

Profiling proteasome activity in tissue with fluorescent probes.

H. Ovaa, J. Neefjes, J. Borst, 2007, Molecular pharmaceutics.

The proteasome‐specific inhibitor lactacystin blocks presentation of cytotoxic T lymphocyte epitopes in human and murine cells

J. Neefjes, V. Cerundolo, K. Gould, 1997, European journal of immunology.

Restriction of self‐antigen presentation to cytolytic T lymphocytes by mouse peptide pumps

J. Neefjes, F. Lemonnier, T. Rose, 1995, European journal of immunology.

Peptide selection by MHC class I molecules

Hidde L. Ploegh, T. Schumacher, W. Kast, 1991, Nature.

Direct binding of peptide to empty MHC class I molecules on intact cells and in vitro

Hidde L. Ploegh, Marie-Thérèse Heemels, T. Schumacher, 1990, Cell.

The Murine Cytomegalovirus pp89 Immunodominant H-2Ld Epitope Is Generated and Translocated into the Endoplasmic Reticulum as an 11-Mer Precursor Peptide1

P. Kloetzel, J. Neefjes, P. Henklein, 2001, The Journal of Immunology.

Precursor Peptide Endoplasmic Reticulum as an 11-Mer Generated and Translocated into the Epitope IsdImmunodominant H-2 L The Murine Cytomegalovirus pp 89

P. Kloetzel, J. Neefjes, P. Henklein, 2001 .

Point mutations in the α2 domain of HLA-A2.1 define a functionally relevant interaction with TAP

T. Elliott, J. Neefjes, Jonathan W. Lewis, 1996, Current Biology.

Allele-specific differences in the interaction of MHC class I molecules with transporters associated with antigen processing.

C. Melief, J. Neefjes, R. Wubbolts, 1996, Journal of immunology.

Analysis of the fine specificity of rat, mouse and human TAP peptide transporters

R. Obst, J. Neefjes, F. Momburg, 1995, European journal of immunology.

Peptide size selection by the major histocompatibility complex-encoded peptide transporter

J. Neefjes, F. Momburg, G. Hämmerling, 1994, The Journal of experimental medicine.

Folding and assembly of major histocompatibility complex class I heterodimers in the endoplasmic reticulum of intact cells precedes the binding of peptide

J. Neefjes, F. Momburg, G. Hämmerling, 1993, The Journal of experimental medicine.

Abrogation of CTL Epitope Processing by Single Amino Acid Substitution Flanking the C-Terminal Proteasome Cleavage Site1

P M Kloetzel, P. Kloetzel, C. Melief, 2000, The Journal of Immunology.

C-Terminal Proteasome Cleavage Site Single Amino Acid Substitution Flanking the Abrogation of CTL Epitope Processing by

P. Kloetzel, C. Melief, J. Neefjes, 2000 .

Major differences in transporter associated with antigen presentation (TAP)-dependent translocation of MHC class I-presentable peptides and the effect of flanking sequences.

M. Feltkamp, W. Kast, C. Melief, 1995, Journal of immunology.

Peptide selection by MHC-encoded TAP transporters.

J. Neefjes, F. Momburg, G. Hämmerling, 1994, Current opinion in immunology.

Dynamics of proteasome distribution in living cells

J. Trowsdale, J. Neefjes, B. Plougastel, 1997, The EMBO journal.

A single residue exchange within a viral CTL epitope alters proteasome-mediated degradation resulting in lack of antigen presentation.

P M Kloetzel, P. Kloetzel, C. Melief, 1996, Immunity.

B Cell Receptor-Mediated Internalization of Salmonella: A Novel Pathway for Autonomous B Cell Activation and Antibody Production

J. Neefjes, A. Griekspoor, H. Janssen, 2009 .

Antigen processing by nardilysin and thimet oligopeptidase generates cytotoxic T cell epitopes

P. Kloetzel, L. Hersh, A. Prat, 2011, Nature Immunology.

How does TAP pump peptides? insights from DNA repair and traffic ATPases.

J. Neefjes, A. Griekspoor, E. Reits, 2000, Immunology today.

Three-Domain Structure with Antigen Processing Reveal a Two Subunits of the Transporter Associated Membrane Topology and Dimerization of the Neefjes

J. Neefjes, F. Momburg, J. C. Vos, 1999 .

The rational design of TAP inhibitors using peptide substrate modifications and peptidomimetics

J. Neefjes, R. Liskamp, F. Momburg, 1997, European journal of immunology.

On the move: organelle dynamics during mitosis.

J. Neefjes, M. Jongsma, Ilana Berlin, 2015, Trends in cell biology.

Overexpression of the ABC transporter TAP in multidrug-resistant human cancer cell lines.

J. Neefjes, M. Flens, M. Izquierdo, 1996, British Journal of Cancer.

The many roads to cross-presentation

J. Neefjes, T. Groothuis, 2005, The Journal of experimental medicine.

N-terminal acetylation and replicative age affect proteasome localization and cell fitness during aging

J. Neefjes, F. van Leeuwen, V. Menéndez-Benito, 2015, Journal of Cell Science.

Recombination-Induced Tag Exchange (RITE) Cassette Series to Monitor Protein Dynamics in Saccharomyces cerevisiae

J. Neefjes, Tibor van Welsem, F. van Leeuwen, 2013, G3: Genes, Genomes, Genetics.

Trimming of TAP-translocated peptides in the endoplasmic reticulum and in the cytosol during recycling

J. Neefjes, F. Momburg, G. Hämmerling, 1994, The Journal of experimental medicine.

Multidrug resistance-associated protein 9 (ABCC12) is present in mouse and boar sperm.

T. Ishikawa, I. van der Heijden, P. Borst, 2007, The Biochemical journal.

Invariant chain regulates endosomal fusion and maturation through an interaction with the SNARE Vti1b

J. Neefjes, O. Bakke, L. Janssen, 2020, Journal of Cell Science.

Invariant chain regulates endosomal fusion and maturation through the SNARE Vti1b

J. Neefjes, O. Bakke, L. Janssen, 2019, bioRxiv.

Creating molecules that modulate immune responses

H. Ovaa, J. Neefjes, S. V. van Kasteren, 2018, Nature Reviews Chemistry.

Hierarchy of Epstein-Barr virus-specific cytotoxic T-cell responses in individuals carrying different subtypes of an HLA allele: implications for epitope-based antiviral vaccines

J. Neefjes, S. L. Silins, S. Burrows, 1997, Journal of virology.

MHC class I alleles and their exploration of the antigen‐processing machinery

J. Neefjes, A. Griekspoor, J. Neijssen, 2005, Immunological reviews.

Identification of a novel ATM inhibitor with cancer cell specific radiosensitization activity

H. Ovaa, J. Neefjes, P. Halonen, 2017, Oncotarget.

Ubiquitin-Based Probes Prepared by Total Synthesis To Profile the Activity of Deubiquitinating Enzymes

B. Rodenko, H. Ovaa, J. Neefjes, 2012, Chembiochem : a European journal of chemical biology.

monoubiquitylation of histone H 2 A DNA damage triggers nucleotide excision repair-dependent data

Wim, J. Neefjes, A. Houtsmuller, 2006 .

Cutting Edge: HLA-B27 Acquires Many N-Terminal Dibasic Peptides: Coupling Cytosolic Peptide Stability to Antigen Presentation1

J. Drijfhout, J. Neefjes, E. Reits, 2006, The Journal of Immunology.

PresentationCytosolic Peptide Stability to Antigen N-Terminal Dibasic Peptides: Coupling Cutting Edge: HLA-B27 Acquires Many

J. Drijfhout, J. Neefjes, E. Reits, 2006 .

A brief report on combination chemotherapy and anti-programmed death (ligand) 1 treatment in small-cell lung cancer: Did we choose the optimal chemotherapy backbone?

J. Aerts, J. Neefjes, J. Mankor, 2020, European journal of cancer.

The invariant chain transports TNF family member CD70 to MHC class II compartments in dendritic cells

Anna M. Keller, W. Zwart, J. Neefjes, 2010, Journal of Cell Science.

Puromycin-Sensitive Aminopeptidase Limits MHC Class I Presentation in Dendritic Cells but Does Not Affect CD8 T Cell Responses during Viral Infections1

K. Rock, A. Murphy, G. Yancopoulos, 2008, The Journal of Immunology.

during Viral Infections but Does Not Affect CD8 T Cell Responses MHC Class I Presentation in Dendritic Cells Puromycin-Sensitive Aminopeptidase Limits

K. Rock, A. Murphy, G. Yancopoulos, 2008 .

Detection of aberrant transcription of major histocompatibility complex class II antigen presentation genes in chronic lymphocytic leukaemia identifies HLA‐DOA mRNA as a prognostic factor for survival

C. Meijer, J. Neefjes, G. Ossenkoppele, 2009, British journal of haematology.

Detection of aberrant transcription of MHC class II antigen presentation genes in chronic lymphocytic leukemia identifies HLA-DOA mRNA as a prognostic factor for survival

C. Meijer, J. Neefjes, G. Ossenkoppele, 2009 .

Chemical Profiling of Primary Mesothelioma Cultures Defines Subtypes with Different Expression Profiles and Clinical Responses

W. Zwart, J. Neefjes, P. Baas, 2017, Clinical Cancer Research.

Phosphorylation of the oestrogen receptor α at serine 305 and prediction of tamoxifen resistance in breast cancer

M. Hauptmann, M. Kok, J. Wesseling, 2009, The Journal of pathology.

RhoB regulates endosome transport by promoting actin assembly on endosomal membranes through Dia1

J. Neefjes, P. Hordijk, D. Verwoerd, 2005, Journal of Cell Science.

Absence of preferential homologous H/L chain association in hybrid hybridomas.

W. de Lau, J. Neefjes, B. Bast, 1991, Journal of immunology.

How chemistry supports cell biology: the chemical toolbox at your service.

H. Ovaa, J. Neefjes, R. Wijdeven, 2014, Trends in cell biology.

Direct Antigen Presentation and Gap Junction Mediated Cross-Presentation during Apoptosis1

J. Neefjes, J. Neijssen, H. Janssen, 2009, The Journal of Immunology.

On Terminal Alkynes That Can React with Active-Site Cysteine Nucleophiles in Proteases

A. Scholten, A. Heck, H. Ovaa, 2013, Journal of the American Chemical Society.

TAP‐translocated peptides specifically bind proteins in the endoplasmic reticulum, including gp96, protein disulfide isomerase and calreticulin

J. Neefjes, P. Spee, 1997, European journal of immunology.

The assembly of H2‐Kb class I molecules translated in vitro requires oxidized glutathione and peptide

H. Ploegh, J. Neefjes, M. Bijlmakers, 1993, European journal of immunology.

Export of antigenic peptides from the endoplasmic reticulum intersects with retrograde protein translocation through the Sec61p channel.

J. Neefjes, F. Momburg, G. Hämmerling, 2000, Immunity.

A major role for TPPII in trimming proteasomal degradation products for MHC class I antigen presentation.

Jacques Neefjes, J. Drijfhout, J. Neefjes, 2004, Immunity.

Allelic differences in the relationship between proteasome activity and MHC class I peptide loading.

J. Neefjes, A. Benham, M. Grommé, 1998, Journal of immunology.

Erratum: Selective and ATP-Dependent Translocation of Peptides by the MHC-Encoded Peptide Transporter

J. Neefjes, F. Momburg, Peter J. Haemmerling, 1994, Science.

A flexible MHC class I multimer loading system for large-scale detection of antigen-specific T cells

H. Ovaa, J. Neefjes, J. Falkenburg, 2018, The Journal of experimental medicine.

Definition of Proteasomal Peptide Splicing Rules for High-Efficiency Spliced Peptide Presentation by MHC Class I Molecules

T. Schumacher, B. Rodenko, H. Ovaa, 2015, The Journal of Immunology.

Presentation by MHC Class I Molecules Rules for High-Efficiency Spliced Peptide Definition of Proteasomal Peptide Splicing

T. Schumacher, B. Rodenko, H. Ovaa, 2015 .

The effect of anchor residue modifications on the stability of major histocompatibility complex class I‐peptide interactions

H. Ploegh, J. Neefjes, John Dierx And, 1993, European journal of immunology.

Cross-Presentation of Glycoprotein 96–Associated Antigens on Major Histocompatibility Complex Class I Molecules Requires Receptor-Mediated Endocytosis

H. Rammensee, P. Ricciardi-Castagnoli, H. Schild, 2000, The Journal of experimental medicine.

Early events in the assembly of major histocompatibility complex class II heterotrimers from their free subunits

J. Neefjes, M. Nijenhuis, 1994, European journal of immunology.

Cell biology of antigen presentation.

J. Neefjes, F. Momburg, 1993, Current opinion in immunology.

The first step of peptide selection in antigen presentation by MHC class I molecules

Jacques Neefjes, Anastassis Perrakis, Robbie P Joosten, 2015, Proceedings of the National Academy of Sciences.

Chemical profiling of the genome with anti-cancer drugs defines target specificities.

L. Wessels, J. Neefjes, Xiaohang Qiao, 2015, Nature chemical biology.

Accurate intracellular localization of HLA‐DM requires correct spacing of a cytoplasmic YTPL targeting motif relative to the transmembrane domain

J. Neefjes, J. Calafat, H. Janssen, 1999, European journal of immunology.

Synthesis and assembly of MHC-peptide complexes.

J. Neefjes, A. Benham, A. Tulp, 1995, Immunology today.

Immuno-waste exposure and further management

J. Neefjes, R. Spaapen, 2012, Nature Immunology.

Rab Proteins, Connecting Transport and Vesicle Fusion

I. Jordens, M. Marsman, J. Neefjes, 2005, Traffic.

Drug Discovery Maps, a Machine Learning Model That Visualizes and Predicts Kinome–Inhibitor Interaction Landscapes

Gerard J P van Westen, Antonius P A Janssen, Sebastian H Grimm, 2018, J. Chem. Inf. Model..

A cascading activity-based probe sequentially targets E1-E2-E3 ubiquitin enzymes.

H. Ovaa, J. Neefjes, J. Pruneda, 2016, Nature chemical biology.

JCB_200811005 1209..1226

W. Zwart, Nuno Rocha, J. Neefjes, 2009 .

The Molecular Mechanism of Cholesterol Control of Late Endosomal Transport by Dynein Motors

Wilbert, Nuno Rocha, J. Neefjes, 2008 .

Rac and Rab GTPases dual effector Nischarin regulates vesicle maturation to facilitate survival of intracellular bacteria

R. Scheller, J. Neefjes, H. Janssen, 2013, The EMBO journal.

Loss of the GPI‐anchor in B‐lymphoblastic leukemia by epigenetic downregulation of PIGH expression

J. Neefjes, M. Griffioen, Xiaohang Qiao, 2018, American journal of hematology.

USP32 regulates late endosomal transport and recycling through deubiquitylation of Rab7

H. Ovaa, J. Neefjes, E. Bos, 2019, Nature Communications.

Head–head/tail–tail relative orientation of the pore-forming domains of the heterodimeric ABC transporter TAP

Jacques Neefjes, J. Neefjes, E. Reits, 2000, Current Biology.

How to target MHC class II into the MIIC compartment.

J. Neefjes, M. Garstka, 2013, Molecular immunology.

Generating Epitopes for MHC Class I Trimming Peptides in the Cytosol or Leucine Aminopeptidase Is Not Essential for Yancopoulos

K. Rock, A. Murphy, G. Yancopoulos, 2005 .

Proteasome activity limits the assembly of MHC class I molecules after IFN-gamma stimulation.

J. Neefjes, A. Benham, 1997, Journal of immunology.

Classiﬁ cation of anti-estrogens according to intramolecular FRET effects on phospho-mutants of ERα

W. Zwart, J. Neefjes, R. Michalides, 2009 .

Classification of anti-estrogens according to intramolecular FRET effects on phospho-mutants of estrogen receptor α

W. Zwart, J. Neefjes, R. Michalides, 2007, Molecular Cancer Therapeutics.

New insight into the everlasting host-pathogen arms race

J. Neefjes, C. Kuijl, 2009, Nature Immunology.

Coronin is involved in uptake of Mycobacterium bovis BCG in human macrophages but not in phagosome maintenance

T. Ottenhoff, J. Neefjes, T. Ottenhoff, 2001, Cellular microbiology.

Selective Infection of Antigen-Specific B Lymphocytes by Salmonella Mediates Bacterial Survival and Systemic Spreading of Infection

Jacques Neefjes, Hans Janssen, S. Marieke van Ham, 2012, PloS one.

Association between Salmonella infection and colon cancer: a nationwide registry-based cohort study

J. Neefjes, M. Frisch, E. Franz, 2021, Epidemiology and Infection.

Integrating Chemical and Genetic Silencing Strategies To Identify Host Kinase-Phosphatase Inhibitor Networks That Control Bacterial Infection

H. Ovaa, J. Neefjes, J. den Hertog, 2013, ACS chemical biology.

Photo-crosslinking of clinically relevant kinases using H89-derived photo-affinity probes.

H. Overkleeft, G. A. van der Marel, A. W. Tuin, 2016, Molecular bioSystems.

EFIS is welcoming Immunologists to build even more bridges in Amsterdam

J. Neefjes, E. Reits, C. Helbig, 2018, European journal of immunology.

Total Chemical Synthesis of SUMO and SUMO‐Based Probes for Profiling the Activity of SUMO‐Specific Proteases

H. Ovaa, J. Neefjes, Ilana Berlin, 2018, Angewandte Chemie.

Glutaminyl cyclase is an enzymatic modifier of the CD47- SIRPα axis and a target for cancer immunotherapy

T. Schumacher, M. Raaben, T. Brummelkamp, 2019, Nature Medicine.

Herpes viral proteins manipulating the peptide transporter TAP.

J. Neefjes, A. Griekspoor, E. Reits, 2002, Current topics in microbiology and immunology.

Visualizing the action of steroid hormone receptors in living cells

W. Zwart, J. Neefjes, R. Michalides, 2007, Nuclear receptor signaling.

The Complex Route to MHC Class I-Peptide Complexes

T. Elliott, J. Neefjes, 2006, Cell.

Presenting antigen presentation in living cells using biophysical techniques.

W. Zwart, J. Neefjes, A. Griekspoor, 2005, Current Opinion in Microbiology.

Mechanical Forces Used for Cell Fractionation Can Create Hybrid Membrane Vesicles

J. Neefjes, H. Janssen, Izhar Salomon, 2010, International journal of biological sciences.

Varicellovirus UL49.5-encoded TAP inhibitors: one family, one target, but diverse mechanisms

M. Ressing, J. Neefjes, N. Osterrieder, 2007 .

Novel polymorphisms in HLA-DOA and HLA-DOB in B-cell malignancies

J. Neefjes, M. van Lith, M. V. van Ham, 2002, Immunogenetics.

[The 2004 Nobel Prize in Chemistry for the discovery of ubiquitin-mediated protein degradation].

J. Neefjes, N. Dantuma, T. Groothuis, 2004, Nederlands tijdschrift voor geneeskunde.

Recombination-induced tag exchange to track old and new proteins

H. Ovaa, J. Neefjes, Tibor van Welsem, 2009, Proceedings of the National Academy of Sciences.

CIIV, MIIC and other compartments for MHC class II loading

J. Neefjes, 1999, European journal of immunology.

Correction: Quantifying exosome secretion from single cells reveals a modulatory role for GPCR signaling

J. Neefjes, M. Verhage, R. Toonen, 2018, Journal of Cell Biology.

Identification of novel peptide binding proteins in the endoplasmic reticulum: ERp72, calnexin, and grp170.

J. Neefjes, J. Subjeck, P. Spee, 1999, Biochemistry.

Immunoproteasome Inhibitor–Doxorubicin Conjugates Target Multiple Myeloma Cells and Release Doxorubicin upon Low-Dose Photon Irradiation

H. Overkleeft, J. Neefjes, S. V. van Kasteren, 2020, Journal of the American Chemical Society.

Characterization of the Mammalian CORVET and HOPS Complexes and Their Modular Restructuring for Endosome Specificity*

Rik van der Kant, J. Neefjes, J. Klumperman, 2015, The Journal of Biological Chemistry.

Autophagy in MHC class II presentation: sampling from within.

Jacques Neefjes, J. Neefjes, V. Menéndez-Benito, 2007, Immunity.

The hinge region of the human estrogen receptor determines functional synergy between AF-1 and AF-2 in the quantitative response to estradiol and tamoxifen

W. Zwart, J. Neefjes, R. Michalides, 2010, Journal of Cell Science.

Activation of endosomal dynein motors by stepwise assembly of Rab7–RILP–p150Glued, ORP1L, and the receptor βlll spectrin

W. Zwart, Nuno Rocha, J. Neefjes, 2007, The Journal of cell biology.

Predictive clustering relates gene annotations to phenotype properties extracted from images

S. Džeroski, D. Kocev, B. Ženko, 2010 .

A dynamic ubiquitin equilibrium couples proteasomal activity to chromatin remodeling

J. Neefjes, N. Dantuma, F. Salomons, 2006, The Journal of cell biology.

A CD8+ T cell immune evasion protein specific to Epstein-Barr virus and its close relatives in Old World primates

M. Ressing, J. Neefjes, N. Croft, 2007, The Journal of experimental medicine.

Modulation of TAP-dependent antigen compartmentalization during human monocyte-to-DC differentiation.

F. Klawonn, R. Tampé, J. Neefjes, 2019, Blood Advances.

Multiple sclerosis-associated CLEC16A controls HLA class II expression via late endosome biogenesis.

J. Neefjes, R. Hintzen, J. Laman, 2015, Brain : a journal of neurology.