Thang V. Pham
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View article: Supplementary Figure S7 from Combined Inactivation of MEK and mTOR Can Lead to Synergistic Cell Death in Glioblastoma Models and Associates with NF1 Deficiency and a Mesenchymal Subtype
Supplementary Figure S7 from Combined Inactivation of MEK and mTOR Can Lead to Synergistic Cell Death in Glioblastoma Models and Associates with NF1 Deficiency and a Mesenchymal Subtype Open
Supplementary Figure S7: HRAS over expression in NF1 wildtype or NF1 mutant GB cell lines did not result in stronger synergy in dual mTOR/MEK inhibition.
View article: Supplementary Table S5 from Combined Inactivation of MEK and mTOR Can Lead to Synergistic Cell Death in Glioblastoma Models and Associates with NF1 Deficiency and a Mesenchymal Subtype
Supplementary Table S5 from Combined Inactivation of MEK and mTOR Can Lead to Synergistic Cell Death in Glioblastoma Models and Associates with NF1 Deficiency and a Mesenchymal Subtype Open
Supplementary Table S5 shows phospho STY sites
View article: Supplementary Figure S4 from Combined Inactivation of MEK and mTOR Can Lead to Synergistic Cell Death in Glioblastoma Models and Associates with NF1 Deficiency and a Mesenchymal Subtype
Supplementary Figure S4 from Combined Inactivation of MEK and mTOR Can Lead to Synergistic Cell Death in Glioblastoma Models and Associates with NF1 Deficiency and a Mesenchymal Subtype Open
Supplementary Figure S4: Overview of averaged cell viability (n = 3) of titrated dual RAD001 and Trametinib therapy in primary glioma cell lines.
View article: Polynomial extensions of Raimi's theorem
Polynomial extensions of Raimi's theorem Open
Raimi's theorem guarantees the existence of a partition of $\mathbb{N}$ into two parts with an unavoidable intersection property: for any finite coloring of $\mathbb{N}$, some color class intersects both parts infinitely many times, after …
View article: Cerebrospinal fluid proteomic analysis of long-term antihypertensive treatment with amlodipine and atenolol in hypertensive rats
Cerebrospinal fluid proteomic analysis of long-term antihypertensive treatment with amlodipine and atenolol in hypertensive rats Open
View article: Boosting the speed and accuracy of protein quantification algorithms in mass spectrometry-based proteomics
Boosting the speed and accuracy of protein quantification algorithms in mass spectrometry-based proteomics Open
Current methods for protein level quantification in mass spectrometry-based proteomics do not scale with the increasing number of samples because of limited system memory and algorithmic complexities. Here we propose a new data structure t…
View article: The functional Loomis-Whitney type inequality in the Heisenberg groups and Projection theorems over finite fields
The functional Loomis-Whitney type inequality in the Heisenberg groups and Projection theorems over finite fields Open
We develop a functional Loomis--Whitney framework on the finite Heisenberg groups $\mathbb{H}^n(\mathbb{F}_q)$ and discover connections to the boundedness and orthogonal projection problems. For $n=1$ we determine the sharp region of expon…
View article: Streamlining single-cell spatial transcriptomics for human kidney tissue
Streamlining single-cell spatial transcriptomics for human kidney tissue Open
Single-cell spatial technologies have emerged in recent years, enabling characterization of tissue architecture and organization at unprecedented resolution. However, computational analysis of spatial transcriptomics data remains a bottlen…
View article: Proteome and transcriptome analysis reveals tubulin isotype switching in paclitaxel-treated esophageal cancer
Proteome and transcriptome analysis reveals tubulin isotype switching in paclitaxel-treated esophageal cancer Open
View article: Proteome Differences in Smooth Muscle Cells from Diabetic and Non-Diabetic Abdominal Aortic Aneurysm Patients Reveal Metformin-Induced Mechanisms
Proteome Differences in Smooth Muscle Cells from Diabetic and Non-Diabetic Abdominal Aortic Aneurysm Patients Reveal Metformin-Induced Mechanisms Open
Aims: Surgery remains the only definitive treatment option for abdominal aortic aneurysms (AAA), as no conclusive evidence supports drug effectiveness in preventing AAA growth. Although type 2 diabetes (T2D) is an important cardiovascular …
View article: Streamlining Spatial Transcriptomics for Human Kidney Tissue
Streamlining Spatial Transcriptomics for Human Kidney Tissue Open
Single-cell spatial technologies have emerged in recent years, enabling tissue architecture and organization characterization at unprecedented resolution. However, computational analysis of spatial transcriptomics data is often a bottlenec…
View article: KIAA1199: A Novel Regulator of Chemoresistance in Human Cancer Cells
KIAA1199: A Novel Regulator of Chemoresistance in Human Cancer Cells Open
KIAA1199 (also known as CEMIP or HYBID), an archived gene listed in the Human Unidentified Gene-Encoded (HUGE) database, has been implicated in tumor progression and metastasis in a wide range of cancers, including breast, cervical, cholan…
View article: The innate immune receptor NLRX1 is a novel required modulator for mPTP opening: implications for cardioprotection
The innate immune receptor NLRX1 is a novel required modulator for mPTP opening: implications for cardioprotection Open
View article: HOOK2 downregulation compromises the tumorigenic and stemness properties of ovarian cancer cells by increasing endoplasmic reticulum stress
HOOK2 downregulation compromises the tumorigenic and stemness properties of ovarian cancer cells by increasing endoplasmic reticulum stress Open
Ovarian cancer stands out as one of the tumors with a high mortality rate in women. Therefore, the search for new therapeutic targets is essential to enhance patient prognosis. There is evidence suggesting that Hook2, an adaptor protein in…
View article: The pan-cancer proteome atlas, a mass spectrometry-based landscape for discovering tumor biology, biomarkers, and therapeutic targets
The pan-cancer proteome atlas, a mass spectrometry-based landscape for discovering tumor biology, biomarkers, and therapeutic targets Open
Most cancer proteomics studies to date have focused on a single cancer type. We report The Pan-Cancer Proteome Atlas (TPCPA) based on data-independent acquisition mass spectrometry, to better understand cancer biology and identify therapeu…
View article: Non-thermal plasma as promising anti-cancer therapy against bladder cancer by inducing DNA damage and cell cycle arrest
Non-thermal plasma as promising anti-cancer therapy against bladder cancer by inducing DNA damage and cell cycle arrest Open
View article: NUAK1 regulates contraction in vascular smooth muscle cells derived from abdominal aortic aneurysm patients
NUAK1 regulates contraction in vascular smooth muscle cells derived from abdominal aortic aneurysm patients Open
Aim Abdominal aortic aneurysms (AAA) are defined as a dilatation of the aortic wall. Impaired contractile ability of vascular smooth muscle cells (vSMC) is a hallmark of AAA. This study investigates the underlying mechanism of altered in v…
View article: Discovery of dementia type specific biomarkers with untargeted CSF proteomics
Discovery of dementia type specific biomarkers with untargeted CSF proteomics Open
Background Different pathologies can cause dementia, including Alzheimer’s disease (AD), dementia with Lewy bodies (DLB) and frontotemporal dementia. Understanding the biological mechanisms underlying these diseases is important in order t…
View article: AAMP and MTSS1 Are Novel Negative Regulators of Endothelial Barrier Function Identified in a Proteomics Screen
AAMP and MTSS1 Are Novel Negative Regulators of Endothelial Barrier Function Identified in a Proteomics Screen Open
Cell–cell adhesion in endothelial monolayers is tightly controlled and crucial for vascular integrity. Recently, we reported on the importance of fast protein turnover for maintenance of endothelial barrier function. Specifically, continuo…
View article: IGF1R signaling induces epithelial-mesenchymal plasticity via ITGAV in cutaneous carcinoma
IGF1R signaling induces epithelial-mesenchymal plasticity via ITGAV in cutaneous carcinoma Open
View article: msproteomics sitereport: reporting DIA-MS phosphoproteomics experiments at site level with ease
msproteomics sitereport: reporting DIA-MS phosphoproteomics experiments at site level with ease Open
Summary Identification and quantification of phosphorylation sites are essential for biological interpretation of a phosphoproteomics experiment. For data independent acquisition mass spectrometry-based (DIA-MS) phosphoproteomics, extracti…
View article: Integrating Clinical Phenotype With Multiomics Analyses of Human Cardiac Tissue Unveils Divergent Metabolic Remodeling in Genotype-Positive and Genotype-Negative Patients With Hypertrophic Cardiomyopathy
Integrating Clinical Phenotype With Multiomics Analyses of Human Cardiac Tissue Unveils Divergent Metabolic Remodeling in Genotype-Positive and Genotype-Negative Patients With Hypertrophic Cardiomyopathy Open
BACKGROUND: Hypertrophic cardiomyopathy (HCM) is caused by sarcomere gene mutations (genotype-positive HCM) in ≈50% of patients and occurs in the absence of mutations (genotype-negative HCM) in the other half of patients. We explored how a…
View article: Protein homeostasis maintained by HOOK1 levels promotes the tumorigenic and stemness properties of ovarian cancer cells through reticulum stress and autophagy
Protein homeostasis maintained by HOOK1 levels promotes the tumorigenic and stemness properties of ovarian cancer cells through reticulum stress and autophagy Open
View article: VRK1 Regulates Sensitivity to Oxidative Stress by Altering Histone Epigenetic Modifications and the Nuclear Phosphoproteome in Tumor Cells
VRK1 Regulates Sensitivity to Oxidative Stress by Altering Histone Epigenetic Modifications and the Nuclear Phosphoproteome in Tumor Cells Open
The chromatin organization and its dynamic remodeling determine its accessibility and sensitivity to DNA damage oxidative stress, the main source of endogenous DNA damage. We studied the role of the VRK1 chromatin kinase in the response to…
View article: Kinase activities in pancreatic ductal adenocarcinoma with prognostic and therapeutic avenues
Kinase activities in pancreatic ductal adenocarcinoma with prognostic and therapeutic avenues Open
Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease with a limited number of known driver mutations but considerable cancer cell heterogeneity. Phosphoproteomics provides a direct read‐out of aberrant signaling and the resulta…
View article: Reviewer #2 (Public Review): Large pan-cancer cell screen coupled to (phospho-)proteomics underscores high-dose vitamin C as a potent anti-cancer agent
Reviewer #2 (Public Review): Large pan-cancer cell screen coupled to (phospho-)proteomics underscores high-dose vitamin C as a potent anti-cancer agent Open
Increasing preclinical and clinical evidence has positioned high-dose vitamin C as a promising anti-cancer treatment that merits more clinical attention. Multiple cytotoxicity mechanisms have been described, including pro-oxidant effects. …
View article: Large pan-cancer cell screen coupled to (phospho-)proteomics underscores high-dose vitamin C as a potent anti-cancer agent
Large pan-cancer cell screen coupled to (phospho-)proteomics underscores high-dose vitamin C as a potent anti-cancer agent Open
Increasing preclinical and clinical evidence has positioned high-dose vitamin C as a promising anti-cancer treatment that merits more clinical attention. Multiple cytotoxicity mechanisms have been described, including pro-oxidant effects. …
View article: Reviewer #3 (Public Review): Large pan-cancer cell screen coupled to (phospho-)proteomics underscores high-dose vitamin C as a potent anti-cancer agent
Reviewer #3 (Public Review): Large pan-cancer cell screen coupled to (phospho-)proteomics underscores high-dose vitamin C as a potent anti-cancer agent Open
Increasing preclinical and clinical evidence has positioned high-dose vitamin C as a promising anti-cancer treatment that merits more clinical attention. Multiple cytotoxicity mechanisms have been described, including pro-oxidant effects. …
View article: Author Response: Large pan-cancer cell screen coupled to (phospho-)proteomics underscores high-dose vitamin C as a potent anti-cancer agent
Author Response: Large pan-cancer cell screen coupled to (phospho-)proteomics underscores high-dose vitamin C as a potent anti-cancer agent Open
Increasing preclinical and clinical evidence has positioned high-dose vitamin C as a promising anti-cancer treatment that merits more clinical attention. Multiple cytotoxicity mechanisms have been described, including pro-oxidant effects. …
View article: Large pan-cancer cell screen coupled to (phospho-)proteomics underscores high-dose vitamin C as a potent anti-cancer agent
Large pan-cancer cell screen coupled to (phospho-)proteomics underscores high-dose vitamin C as a potent anti-cancer agent Open
Increasing preclinical and clinical evidence has positioned high-dose vitamin C as a promising anti-cancer treatment that merits more clinical attention. Multiple cytotoxicity mechanisms have been described, including pro-oxidant effects. …