Publications by authors named "Alex Henneman"

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The pan-cancer proteome atlas, a mass spectrometry-based landscape for discovering tumor biology, biomarkers, and therapeutic targets.
Jaco C Knol, Mengge Lyu, Franziska Böttger, Madalena Nunes Monteiro, Thang V Pham, Alex A Henneman

Cancer Cell· July 2025

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CellEKT: A Robust Chemical Proteomics Workflow to Profile Cellular Target Engagement of Kinase Inhibitors.
Joel Rüegger, Berend Gagestein, Antonius P A Janssen, Alexandra Valeanu, Alger Lazo Mori, Alex A Henneman

Mol Cell Proteomics· June 2025

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Non-thermal plasma as promising anti-cancer therapy against bladder cancer by inducing DNA damage and cell cycle arrest.
Jojanneke Stoof, Zakaria Kalmoua, Ana Sobota, Ruud H Brakenhoff, Marijke Stigter, Alex Henneman

Sci Rep· January 2025

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Insight in the (Phospho)proteome of Vascular Smooth Muscle Cells Derived From Patients With Abdominal Aortic Aneurysm Reveals Novel Disease Mechanisms.
Karlijn B Rombouts, Tara A R van Merrienboer, Alex A Henneman, Jaco C Knol, Thang V Pham

Arterioscler Thromb Vasc Biol· October 2024

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Kinase activities in pancreatic ductal adenocarcinoma with prognostic and therapeutic avenues.
Andrea Vallés-Martí, Richard R de Goeij-de Haas, Alex A Henneman, Sander R Piersma, Thang V Pham

Mol Oncol· August 2024

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msproteomics sitereport: reporting DIA-MS phosphoproteomics experiments at site level with ease.
Thang V Pham, Alex A Henneman, Nam X Truong, Connie R Jimenez

Bioinformatics· July 2024

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Inferring kinase activity from phosphoproteomic data: Tool comparison and recent applications.
Sander R Piersma, Andrea Valles-Marti, Frank Rolfs, Thang V Pham, Alex A Henneman

Mass Spectrom Rev· June 2024

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Candidate biomarkers for treatment benefit from sunitinib in patients with advanced renal cell carcinoma using mass spectrometry-based (phospho)proteomics.
Hanneke van der Wijngaart, Robin Beekhof, Jaco C Knol, Alex A Henneman, Richard de Goeij-de Haas

Clin Proteomics· November 2023

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EGFR/IGF1R Signaling Modulates Relaxation in Hypertrophic Cardiomyopathy.
Sila Algül, Maike Schuldt, Emmy Manders, Valentijn Jansen, Saskia Schlossarek, Alex A Henneman

Circ Res· August 2023

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Phosphoproteomics of patient-derived xenografts identifies targets and markers associated with sensitivity and resistance to EGFR blockade in colorectal cancer.
Robin Beekhof, Andrea Bertotti, Franziska Böttger, Valentina Vurchio, Francesca Cottino, Alex A Henneman

Sci Transl Med· August 2023

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Phosphoproteomics guides effective low-dose drug combinations against pancreatic ductal adenocarcinoma.
Andrea Vallés-Martí, Giulia Mantini, Paul Manoukian, Cynthia Waasdorp, Arantza Fariña Sarasqueta, Alex A Henneman

Cell Rep· June 2023

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A transformer architecture for retention time prediction in liquid chromatography mass spectrometry-based proteomics.
Thang V Pham, Vinh V Nguyen, Duong Vu, Alex A Henneman, Robin A Richardson

Proteomics· April 2023

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Phosphoproteomic Analysis of FLCN Inactivation Highlights Differential Kinase Pathways and Regulatory TFEB Phosphoserines.
Iris E Glykofridis, Alex A Henneman, Jesper A Balk, Richard Goeij-de Haas, Denise Westland

Mol Cell Proteomics· September 2022

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Tumor Drug Concentration and Phosphoproteomic Profiles After Two Weeks of Treatment With Sunitinib in Patients with Newly Diagnosed Glioblastoma.
Myra E van Linde, Mariette Labots, Cyrillo G Brahm, Koos E Hovinga, Philip C De Witt Hamer, Alex A Henneman

Clin Cancer Res· April 2022

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Phosphoproteomic profiling of T cell acute lymphoblastic leukemia reveals targetable kinases and combination treatment strategies.
Valentina Cordo', Mariska T Meijer, Rico Hagelaar, Richard R de Goeij-de Haas, Vera M Poort, Alex A Henneman

Nat Commun· February 2022

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Quantitative Phosphoproteomic Analysis Reveals Dendritic Cell- Specific STAT Signaling After α2-3-Linked Sialic Acid Ligand Binding.
Rui-Jún Eveline Li, Aram de Haas, Ernesto Rodríguez, Hakan Kalay, Anouk Zaal, Alex A Henneman

Front Immunol· October 2021

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Retention Time Prediction and Protein Identification.
Alex Henneman, Magnus Palmblad

Methods Mol Biol· October 2020

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Phosphotyrosine-based Phosphoproteomics for Target Identification and Drug Response Prediction in AML Cell Lines.
Carolien van Alphen, Jacqueline Cloos, Robin Beekhof, David G J Cucchi, Sander R Piersma, Alex A Henneman

Mol Cell Proteomics· May 2020

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iq: an R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics.
Thang V Pham, Alex A Henneman, Connie R Jimenez

Bioinformatics· April 2020

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INKA, an integrative data analysis pipeline for phosphoproteomic inference of active kinases.
Robin Beekhof, Carolien van Alphen, Alex A Henneman, Jaco C Knol, Thang V Pham

Mol Syst Biol· May 2019

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INKA, an integrative data analysis pipeline for phosphoproteomic inference of active kinases.
Robin Beekhof, Carolien van Alphen, Alex A Henneman, Jaco C Knol, Thang V Pham

Mol Syst Biol· April 2019

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Proteomic identification of Axc, a novel beta-lactamase with carbapenemase activity in a meropenem-resistant clinical isolate of Achromobacter xylosoxidans.
Frank Fleurbaaij, Alex A Henneman, Jeroen Corver, Cornelis W Knetsch, Wiep Klaas Smits

Sci Rep· May 2018

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Identifying proteins in zebrafish embryos using spectral libraries generated from dissected adult organs and tissues.
Suzanne J van der Plas-Duivesteijn, Yassene Mohammed, Hans Dalebout, Annemarie Meijer, Anouk Botermans, Alex A Henneman

J Proteome Res· March 2014

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Retention time prediction and protein identification.
Alex A Henneman, Magnus Palmblad

Methods Mol Biol· December 2013

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Online spectral library for GC-atmospheric pressure chemical ionization-ToF MS.
Tiziana Pacchiarotta, Rico J E Derks, Elena Hurtado-Fernandez, Pauline van Bezooijen, Alex Henneman

Bioanalysis· June 2013

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