Explanipedia

Plasma proteomic profiles of patients during oral anti‐coagulant treatment with vitamin K antagonists Open

Eleonora Camilleri, Bart J.M. van Vlijmen, Mettine H.A. Bos, Manfred Wuhrer, David R. Goodlett , et al. · 2025

The Neurolipid Atlas: a lipidomics resource for neurodegenerative diseases Open

Femke M. Feringa, Sascha Koppes-den Hertog, Li-Chiao Wang, Rico J. E. Derks, Iris Kruijff , et al. · 2025

Lipid alterations in the brain have been implicated in many neurodegenerative diseases. To facilitate comparative lipidomic research across brain diseases, we establish a data common named the Neurolipid Atlas that we prepopulated with iso…

Corrigendum to “Quantitative protein mass spectrometry for multiplex measurement of coagulation and fibrinolytic proteins towards clinical application: What, why and how?”, [Thromb. Res. 241 (2024) 109090] Open

Eleonora Camilleri, Mirjam Kruijt, Paul L. den Exter, Suzanne C. Cannegieter, Nienke van Rein , et al. · 2025

Quantitative targeted proteomics for occult cancer screening in patients with unprovoked venous thromboembolism: results from the prospective PLATO-VTE study Open

Noori A.M. Guman, Noémie Kraaijpoel, Frits I. Mulder, Marc Carrier, Luis Jara‐Palomares , et al. · 2025

Intra-Host Evolution During Relapsing Parvovirus B19 Infection in Immunocompromised Patients Open

Anne Russcher, Yassene Mohammed, Margriet E. M. Kraakman, Xavier Chow, Şahin Kök , et al. · 2025

Background: Parvovirus B19 (B19V) can cause severe relapsing episodes of pure red cell aplasia in immunocompromised individuals, which are commonly treated with intravenous immunoglobulins (IVIGs). Few data are available on B19V intra-host…

Privacy-preserving multicenter differential protein abundance analysis with FedProt Open

Yuliya Burankova, Miriam Abele, Mohammad Bakhtiari, Christine von Toerne, Teresa K. Barth , et al. · 2025

Quantitative mass spectrometry has revolutionized proteomics by enabling simultaneous quantification of thousands of proteins. Pooling patient-derived data from multiple institutions enhances statistical power but raises serious privacy co…

Privacy-preserving multicenter differential protein abundance analysis with FedProt Open

Yuliya Burankova, Miriam Abele, Mohammad Bakhtiari, Christine von Törne, Teresa K. Barth , et al. · 2025

Quantitative mass spectrometry has revolutionized proteomics by enabling simultaneous quantification of thousands of proteins. Pooling patient-derived data from multiple institutions enhances statistical power but raises serious privacy co…

Reducing Impulse Noise in Images Using an Improved Formula Conjugate Gradient Method Open

Basim A. Hassan, Yassene Mohammed · 2025

The conjugate formula's significance is frequently emphasised by conjugate gradient approaches. In this paper, a novel conjugate coefficient for the conjugate gradient technique is introduced using a quadratic model and conjugacy condition…

Non-invasive identification of steatohepatitis in patients with MASLD using a sterol and lipidomic signature Open

Ratna Budhi Pebriana, Ting Chen, Rico J. E. Derks, Niek Blomberg, Aldo Grefhorst , et al. · 2025

The accumulation of cholesterol and other lipids leading to hepatic lipotoxicity drives the progression of metabolic dysfunction-associated steatotic liver (MASL) to metabolic dysfunction-associated steatohepatitis (MASH), the advanced pro…

SysQuan: Repurposing SILAC Mice for the Cost-Effective Absolute Quantitation of the Human Proteome Open

Yassene Mohammed, Vincent R. Richard, M. Immanuel Reyes Madlangsakay, Ying Lao, Victor Spicer , et al. · 2025

Relative quantitation, used by most mass spectrometry-based proteomics laboratories to determine protein fold-changes, requires samples being processed and analyzed together for best comparability through minimizing batch differences. This…

Ovarian metastasis from lobular breast carcinoma: A case report with review of literature Open

Yassene Mohammed, Zuhair D. Hammood, Abdulwahid M. Salih, Hadeel A. Yasseen, Soran H. Tahir , et al. · 2025

Author Correction: Neuronal polyunsaturated fatty acids are protective in ALS/FTD Open

Ashling Giblin, Alexander J. Cammack, Niek Blomberg, Sharifah Anoar, Alla Mikheenko , et al. · 2025

Neuronal polyunsaturated fatty acids are protective in ALS/FTD Open

Ashling Giblin, Alexander J. Cammack, Niek Blomberg, Sharifah Anoar, Alla Mikheenko , et al. · 2025

Here we report a conserved transcriptomic signature of reduced fatty acid and lipid metabolism gene expression in a Drosophila model of C9orf72 repeat expansion, the most common genetic cause of amyotrophic lateral sclerosis and frontotemp…

iSODA: A Comprehensive Tool for Integrative Omics Data Analysis in Single- and Multi-Omics Experiments Open

Damien Olivier‐Jimenez, Rico J. E. Derks, Oscar Harari, Carlos Cruchaga, Muhammad Ali , et al. · 2025

Thanks to the plummeting costs of continuously evolving omics analytical platforms, research centers collect multiomics data more routinely. They are, however, confronted with the lack of a versatile software solution to harmoniously analy…

SysQuan: repurposing SILAC mice for the affordable absolute quantitation of the human proteome Open

Yassene Mohammed, Vincent R. Richard, M. Immanuel Reyes Madlangsakay, Ying Lao, Victor Spicer , et al. · 2024

Relative quantitation, used by most MS-based proteomics laboratories to determine protein fold-changes , requires samples being processed and analyzed together for best comparability through minimizing batch differences. This limits the ad…

iSODA: A Comprehensive Tool for Integrative Omics Data Analysis in Single- and Multi-Omics Experiments Open

Damien Olivier‐Jimenez, Rico J. E. Derks, Oscar Harari, Carlos Cruchaga, Muhammad Ali , et al. · 2024

Omics technologies including genomics, proteomics, metabolomics, and lipidomics allow profound insights into health and disease. Thanks to plummeting costs of continuously evolving omics analytical platforms, research centers collect multi…

The Neurolipid Atlas: a lipidomics resource for neurodegenerative diseases uncovers cholesterol as a regulator of astrocyte reactivity impaired by ApoE4 Open

Femke M. Feringa, Sascha J. Koppes-den Hertog, Lian Wang, Rico J. E. Derks, Iris Kruijff , et al. · 2024

Lipid changes in the brain have been implicated in many neurodegenerative diseases including Alzheimer’s Disease (AD), Parkinson’s disease and Amyotrophic Lateral Sclerosis. To facilitate comparative lipidomic research across brain-disease…

Establishing Personalized Blood Protein Reference Ranges Using Noninvasive Microsampling and Targeted Proteomics: Implications for Antidoping Strategies Open

Vincent R. Richard, Georgia Mitsa, Azad Eshghi, Daria Chaplygina, Yassene Mohammed , et al. · 2024

To prevent doping practices in sports, the World Anti-Doping Agency implemented the Athlete Biological Passport (ABP) program, monitoring biological variables over time to indirectly reveal the effects of doping rather than detect the dopi…

Neuronal polyunsaturated fatty acids are protective in FTD/ALS Open

Ashling Giblin, AJ Cammack, N. Blomberg, Alla Mikheenko, Mireia Carcolé , et al. · 2024

We report a conserved transcriptomic signature of reduced fatty acid and lipid metabolism gene expression in human post-mortem ALS spinal cord and a Drosophila model of the most common genetic cause of FTD/ALS, a repeat expansion in C9orf7…

Spatially and temporally resolved metabolome of the human oral cavity Open

Alessio Ciurli, Yassene Mohammed, Christine Ammon, Rico J. E. Derks, Damien Olivier‐Jimenez , et al. · 2024

Multiple reaction monitoring assays for large-scale quantitation of proteins from 20 mouse organs and tissues Open

Sarah Michaud, Helena Pětrošová, Nicholas J. Sinclair, Andrea L Kinnear, Angela Jackson , et al. · 2024

Proteomic Evolution from Acute to Post-COVID-19 Conditions Open

Yassene Mohammed, Karen C. Tran, Chris Carlsten, Christopher J. Ryerson, Alyson W. Wong , et al. · 2023

Many COVID-19 survivors have post-COVID-19 conditions, and females are at a higher risk. We sought to determine (1) how protein levels change from acute to post-COVID-19 conditions, (2) whether females have a plasma protein signature diffe…

Multiomics of iPSC‐derived ApoE3‐ and ApoE4 astrocytes and microglia uncovers cell type specific dysregulation of immunometabolism Open

Rik van der Kant, Niek Blomberg, Lena Erlebach, Femke M. Feringa, Jorin Heijneman , et al. · 2023

Background ApoE4 is the major genetic risk factor for Alzheimer’s disease and the main lipid transporter in brain. How ApoE4 drives AD pathogenesis, and how this is related to changes in lipid metabolism, is not well understood. This lack …

Multi‐omic profiling of isogenic ApoE3/3 and ApoE4/4 iPSC‐derived astrocytes uncovers altered lipid metabolism and mitochondrial function of ApoE4 astrocytes Open

Sascha Koppes, Femke M. Feringa, Aiko Robert, Iris Daphne Kruijff, Damien Olivier‐Jimenez , et al. · 2023

Background As the main genetic risk factor for AD, glial ApoE4 has been implicated in a number of early disease relevant processes, such as lipid dyshomeostasis, mitochondrial dysfunction and altered immune function. This ApoE4 glial pheno…

AD risk variants in APOE differentially affect lipid metabolism in iPSC derived neurons, astrocytes and microglia Open

Femke M. Feringa, Amir Abou Elmagd, Iris Daphne Kruijff, Jorin Heijneman, Sascha Koppes , et al. · 2023

Background Despite the clear function of APOE as a lipid carrier it is still unclear how Alzheimer’s disease (AD) risk variants of APOE affect the lipidome of individual human brain cell types. In addition, while APOE is crucial for transp…

Fatty acid desaturation and lipoxygenase pathways support trained immunity Open

Anaísa V. Ferreira, Juan Carlos Alarcon-Barrera, Jorge Domínguez‐Andrés, Özlem Bulut, Gizem Kılıç , et al. · 2023

OC 46.2 Plasma Protein Signature by Targeted Mass Spectrometry Allows Prediction of Venous Thromboembolism in Colorectal Cancer Patients with 90% Sensitivity Open

Jeroen T. Buijs, Nick van Es, R.J.S. Anijs, Floris T.M. Bosch, Bas van Vlijmen , et al. · 2023

Conclusion(s):A transformer-based NLP model was derived and applied successfully to accurately identify patients with cancer-associated VTE.The loss of performance compared to detection of VTE regardless of association with cancer was not …

OC 46.1 Absolute Quantitative Proteomics for Occult Cancer Screening in Patient with Unprovoked Venous Thromboembolism: Results from the Prospective PLATO-VTE Study Open

N. Guman, Noémie Kraaijpoel, Frits I. Mulder, Marc Carrier, L. Jara-Palomares , et al. · 2023

Background: Coagulopathy with associated bleeding and venous thromboembolism (VTE) is a major cause of early morbidity and mortality in patients with acute leukemia.However, the mechanisms leading to bleeding and VTE have not been fully el…

PB0120 Plasma Profiling of Patients on Vitamin K Antagonists Treatment: A Targeted Quantitative Proteomic Approach Open

E. Camilleri, Bas van Vlijmen, Manfred Wuhrer, Suzanne C. Cannegieter, Nienke van Rein , et al. · 2023

may be used as adjuncts to clinical VTE risk assessment.

Cellular Validation of a Chemically Improved Inhibitor Identifies Monoubiquitination on OTUB2 Open

Gan Jin, J. de Vries, Jimmy J.L.L. Akkermans, Yassene Mohammed, Rayman T.N. Tjokrodirijo , et al. · 2023

Ubiquitin thioesterase OTUB2, a cysteine protease from the ovarian tumor (OTU) deubiquitinase superfamily, is often overexpressed during tumor progression and metastasis. Development of OTUB2 inhibitors is therefore believed to be therapeu…

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