Thomas Fleischer
YOU?
Author Swipe
View article: Integrative pan-cancer analysis reveals a common architecture of dysregulated transcriptional networks characterized by loss of enhancer methylation
Integrative pan-cancer analysis reveals a common architecture of dysregulated transcriptional networks characterized by loss of enhancer methylation Open
Aberrant DNA methylation contributes to gene expression deregulation in cancer. However, these alterations’ precise regulatory role and clinical implications are still not fully understood. In this study, we performed expression-methylatio…
View article: Explainable multi-omics deep clustering model reveals an important role of DNA methylation in pancreatic ductal adenocarcinoma
Explainable multi-omics deep clustering model reveals an important role of DNA methylation in pancreatic ductal adenocarcinoma Open
Patients with pancreatic ductal adenocarcinoma (PDAC) have the lowest survival rate among all cancer patients in Europe. Since western societies have the highest incidence of pancreatic cancer, it has been projected that PDAC will soon bec…
View article: An integrated omics approach highlights how epigenetic events can explain and predict response to neoadjuvant chemotherapy and bevacizumab in breast cancer
An integrated omics approach highlights how epigenetic events can explain and predict response to neoadjuvant chemotherapy and bevacizumab in breast cancer Open
Treatment with the anti‐angiogenic drug bevacizumab in addition to chemotherapy has shown efficacy for breast cancer in some clinical trials, but better biomarkers are needed to optimally select patients for treatment. Here, we present an …
View article: Multi‐omics analysis reveals epigenetically regulated processes and patient classification in lung adenocarcinoma
Multi‐omics analysis reveals epigenetically regulated processes and patient classification in lung adenocarcinoma Open
Aberrant DNA methylation is a hallmark of many cancer types. Despite our knowledge of epigenetic and transcriptomic alterations in lung adenocarcinoma (LUAD), we lack robust multi‐modal molecular classifications for patient stratification.…
View article: Integrative pan-cancer analysis reveals a common architecture of dysregulated transcriptional networks characterized by loss of enhancer methylation
Integrative pan-cancer analysis reveals a common architecture of dysregulated transcriptional networks characterized by loss of enhancer methylation Open
Aberrant DNA methylation contributes to gene expression deregulation in cancer. However, these alterations’ precise regulatory role and clinical implications are still not fully understood. In this study, we performed expression-methylatio…
View article: MRI Assessment of Changes in Tumor Vascularization during Neoadjuvant Anti-Angiogenic Treatment in Locally Advanced Breast Cancer Patients
MRI Assessment of Changes in Tumor Vascularization during Neoadjuvant Anti-Angiogenic Treatment in Locally Advanced Breast Cancer Patients Open
Anti-VEGF (vascular endothelial growth factor) treatment improves response rates, but not progression-free or overall survival in advanced breast cancer. It has been suggested that subgroups of patients may benefit from this treatment; how…
View article: Explainable Machine Learning Reveals the Role of the Breast Tumor Microenvironment in Neoadjuvant Chemotherapy Outcome
Explainable Machine Learning Reveals the Role of the Breast Tumor Microenvironment in Neoadjuvant Chemotherapy Outcome Open
Recent advancements in single-cell RNA sequencing (scRNA-seq) have enabled the identification of phenotypic diversity within breast tumor tissues. However, the contribution of these cell phenotypes to tumor biology and treatment response h…
View article: Supplementary Figure legends from DNA Methylation Status of Key Cell-Cycle Regulators Such as <i>CDKNA2</i>/p16 and <i>CCNA1</i> Correlates with Treatment Response to Doxorubicin and 5-Fluorouracil in Locally Advanced Breast Tumors
Supplementary Figure legends from DNA Methylation Status of Key Cell-Cycle Regulators Such as <i>CDKNA2</i>/p16 and <i>CCNA1</i> Correlates with Treatment Response to Doxorubicin and 5-Fluorouracil in Locally Advanced Breast Tumors Open
Supplementary Figure legends. supplementary data
View article: Supplementary Table 1-6 from DNA Methylation Status of Key Cell-Cycle Regulators Such as <i>CDKNA2</i>/p16 and <i>CCNA1</i> Correlates with Treatment Response to Doxorubicin and 5-Fluorouracil in Locally Advanced Breast Tumors
Supplementary Table 1-6 from DNA Methylation Status of Key Cell-Cycle Regulators Such as <i>CDKNA2</i>/p16 and <i>CCNA1</i> Correlates with Treatment Response to Doxorubicin and 5-Fluorouracil in Locally Advanced Breast Tumors Open
Supplementary Table 1-6. Supplementary Table 1: Differentially methylated genes and functions of the genes before/after treatment with doxorubicin and FUMI Supplementary Table 2: Ingenuity Pathway analysis Supplementary Table 3: List and f…
View article: Supplementary Text from Toward Personalized Computer Simulation of Breast Cancer Treatment: A Multiscale Pharmacokinetic and Pharmacodynamic Model Informed by Multitype Patient Data
Supplementary Text from Toward Personalized Computer Simulation of Breast Cancer Treatment: A Multiscale Pharmacokinetic and Pharmacodynamic Model Informed by Multitype Patient Data Open
Supplementary text to the main article detailing mathematical model, model initialisation and parametrisation, computational details and overview of clinical data .
View article: Data from DNA Methylation Status of Key Cell-Cycle Regulators Such as <i>CDKNA2</i>/p16 and <i>CCNA1</i> Correlates with Treatment Response to Doxorubicin and 5-Fluorouracil in Locally Advanced Breast Tumors
Data from DNA Methylation Status of Key Cell-Cycle Regulators Such as <i>CDKNA2</i>/p16 and <i>CCNA1</i> Correlates with Treatment Response to Doxorubicin and 5-Fluorouracil in Locally Advanced Breast Tumors Open
Purpose: To explore alterations in gene promoter methylation as a potential cause of acquired drug resistance to doxorubicin or combined treatment with 5-fluorouracil and mitomycin C in human breast cancers.Experimental Design: Paired tumo…
View article: Data from The Longitudinal Transcriptional Response to Neoadjuvant Chemotherapy with and without Bevacizumab in Breast Cancer
Data from The Longitudinal Transcriptional Response to Neoadjuvant Chemotherapy with and without Bevacizumab in Breast Cancer Open
Purpose: Chemotherapy-induced alterations to gene expression are due to transcriptional reprogramming of tumor cells or subclonal adaptations to treatment. The effect on whole-transcriptome mRNA expression was investigated in a randomized …
View article: Figure S1, Figure S2 from The Longitudinal Transcriptional Response to Neoadjuvant Chemotherapy with and without Bevacizumab in Breast Cancer
Figure S1, Figure S2 from The Longitudinal Transcriptional Response to Neoadjuvant Chemotherapy with and without Bevacizumab in Breast Cancer Open
Supplementary figures as referred to in the manuscript
View article: Supplementary Table 1-6 from DNA Methylation Status of Key Cell-Cycle Regulators Such as <i>CDKNA2</i>/p16 and <i>CCNA1</i> Correlates with Treatment Response to Doxorubicin and 5-Fluorouracil in Locally Advanced Breast Tumors
Supplementary Table 1-6 from DNA Methylation Status of Key Cell-Cycle Regulators Such as <i>CDKNA2</i>/p16 and <i>CCNA1</i> Correlates with Treatment Response to Doxorubicin and 5-Fluorouracil in Locally Advanced Breast Tumors Open
Supplementary Table 1-6. Supplementary Table 1: Differentially methylated genes and functions of the genes before/after treatment with doxorubicin and FUMI Supplementary Table 2: Ingenuity Pathway analysis Supplementary Table 3: List and f…
View article: Supplementary Figure 1 from DNA Methylation Status of Key Cell-Cycle Regulators Such as <i>CDKNA2</i>/p16 and <i>CCNA1</i> Correlates with Treatment Response to Doxorubicin and 5-Fluorouracil in Locally Advanced Breast Tumors
Supplementary Figure 1 from DNA Methylation Status of Key Cell-Cycle Regulators Such as <i>CDKNA2</i>/p16 and <i>CCNA1</i> Correlates with Treatment Response to Doxorubicin and 5-Fluorouracil in Locally Advanced Breast Tumors Open
Supplementary Figure 1. Canonical pathway:Communication between Innate and Adaptive Immune Cells
View article: Supplementary Figure 2 from DNA Methylation Status of Key Cell-Cycle Regulators Such as <i>CDKNA2</i>/p16 and <i>CCNA1</i> Correlates with Treatment Response to Doxorubicin and 5-Fluorouracil in Locally Advanced Breast Tumors
Supplementary Figure 2 from DNA Methylation Status of Key Cell-Cycle Regulators Such as <i>CDKNA2</i>/p16 and <i>CCNA1</i> Correlates with Treatment Response to Doxorubicin and 5-Fluorouracil in Locally Advanced Breast Tumors Open
Supplementary Figure 2. Canonical pathway:Gαi Signalling
View article: Supplementary Figure 1 from DNA Methylation Status of Key Cell-Cycle Regulators Such as <i>CDKNA2</i>/p16 and <i>CCNA1</i> Correlates with Treatment Response to Doxorubicin and 5-Fluorouracil in Locally Advanced Breast Tumors
Supplementary Figure 1 from DNA Methylation Status of Key Cell-Cycle Regulators Such as <i>CDKNA2</i>/p16 and <i>CCNA1</i> Correlates with Treatment Response to Doxorubicin and 5-Fluorouracil in Locally Advanced Breast Tumors Open
Supplementary Figure 1. Canonical pathway:Communication between Innate and Adaptive Immune Cells
View article: Supplementary Text from Toward Personalized Computer Simulation of Breast Cancer Treatment: A Multiscale Pharmacokinetic and Pharmacodynamic Model Informed by Multitype Patient Data
Supplementary Text from Toward Personalized Computer Simulation of Breast Cancer Treatment: A Multiscale Pharmacokinetic and Pharmacodynamic Model Informed by Multitype Patient Data Open
Supplementary text to the main article detailing mathematical model, model initialisation and parametrisation, computational details and overview of clinical data .
View article: Supplementary Tables from The Longitudinal Transcriptional Response to Neoadjuvant Chemotherapy with and without Bevacizumab in Breast Cancer
Supplementary Tables from The Longitudinal Transcriptional Response to Neoadjuvant Chemotherapy with and without Bevacizumab in Breast Cancer Open
Table S1: Genes significantly differentially expressed in samples with pathological complete response compared to those without in the Combination arm. Table S2: DAVID analysis of 720 differentially expressed genes in tumors that achieved …
View article: Data from Toward Personalized Computer Simulation of Breast Cancer Treatment: A Multiscale Pharmacokinetic and Pharmacodynamic Model Informed by Multitype Patient Data
Data from Toward Personalized Computer Simulation of Breast Cancer Treatment: A Multiscale Pharmacokinetic and Pharmacodynamic Model Informed by Multitype Patient Data Open
The usefulness of mechanistic models to disentangle complex multiscale cancer processes, such as treatment response, has been widely acknowledged. However, a major barrier for multiscale models to predict treatment outcomes in individual p…
View article: Data from DNA Methylation Status of Key Cell-Cycle Regulators Such as <i>CDKNA2</i>/p16 and <i>CCNA1</i> Correlates with Treatment Response to Doxorubicin and 5-Fluorouracil in Locally Advanced Breast Tumors
Data from DNA Methylation Status of Key Cell-Cycle Regulators Such as <i>CDKNA2</i>/p16 and <i>CCNA1</i> Correlates with Treatment Response to Doxorubicin and 5-Fluorouracil in Locally Advanced Breast Tumors Open
Purpose: To explore alterations in gene promoter methylation as a potential cause of acquired drug resistance to doxorubicin or combined treatment with 5-fluorouracil and mitomycin C in human breast cancers.Experimental Design: Paired tumo…
View article: Figure S1, Figure S2 from The Longitudinal Transcriptional Response to Neoadjuvant Chemotherapy with and without Bevacizumab in Breast Cancer
Figure S1, Figure S2 from The Longitudinal Transcriptional Response to Neoadjuvant Chemotherapy with and without Bevacizumab in Breast Cancer Open
Supplementary figures as referred to in the manuscript
View article: Supplementary Figure legends from DNA Methylation Status of Key Cell-Cycle Regulators Such as <i>CDKNA2</i>/p16 and <i>CCNA1</i> Correlates with Treatment Response to Doxorubicin and 5-Fluorouracil in Locally Advanced Breast Tumors
Supplementary Figure legends from DNA Methylation Status of Key Cell-Cycle Regulators Such as <i>CDKNA2</i>/p16 and <i>CCNA1</i> Correlates with Treatment Response to Doxorubicin and 5-Fluorouracil in Locally Advanced Breast Tumors Open
Supplementary Figure legends. supplementary data
View article: Supplementary Tables from The Longitudinal Transcriptional Response to Neoadjuvant Chemotherapy with and without Bevacizumab in Breast Cancer
Supplementary Tables from The Longitudinal Transcriptional Response to Neoadjuvant Chemotherapy with and without Bevacizumab in Breast Cancer Open
Table S1: Genes significantly differentially expressed in samples with pathological complete response compared to those without in the Combination arm. Table S2: DAVID analysis of 720 differentially expressed genes in tumors that achieved …
View article: Data from Toward Personalized Computer Simulation of Breast Cancer Treatment: A Multiscale Pharmacokinetic and Pharmacodynamic Model Informed by Multitype Patient Data
Data from Toward Personalized Computer Simulation of Breast Cancer Treatment: A Multiscale Pharmacokinetic and Pharmacodynamic Model Informed by Multitype Patient Data Open
The usefulness of mechanistic models to disentangle complex multiscale cancer processes, such as treatment response, has been widely acknowledged. However, a major barrier for multiscale models to predict treatment outcomes in individual p…
View article: Data from The Longitudinal Transcriptional Response to Neoadjuvant Chemotherapy with and without Bevacizumab in Breast Cancer
Data from The Longitudinal Transcriptional Response to Neoadjuvant Chemotherapy with and without Bevacizumab in Breast Cancer Open
Purpose: Chemotherapy-induced alterations to gene expression are due to transcriptional reprogramming of tumor cells or subclonal adaptations to treatment. The effect on whole-transcriptome mRNA expression was investigated in a randomized …
View article: Supplementary Figure 2 from DNA Methylation Status of Key Cell-Cycle Regulators Such as <i>CDKNA2</i>/p16 and <i>CCNA1</i> Correlates with Treatment Response to Doxorubicin and 5-Fluorouracil in Locally Advanced Breast Tumors
Supplementary Figure 2 from DNA Methylation Status of Key Cell-Cycle Regulators Such as <i>CDKNA2</i>/p16 and <i>CCNA1</i> Correlates with Treatment Response to Doxorubicin and 5-Fluorouracil in Locally Advanced Breast Tumors Open
Supplementary Figure 2. Canonical pathway:Gαi Signalling
View article: ABCB1 Amplicon Contains Cyclic AMP Response Element-Driven TRIP6 Gene in Taxane-Resistant MCF-7 Breast Cancer Sublines
ABCB1 Amplicon Contains Cyclic AMP Response Element-Driven TRIP6 Gene in Taxane-Resistant MCF-7 Breast Cancer Sublines Open
A limited number of studies are devoted to regulating TRIP6 expression in cancer. Hence, we aimed to unveil the regulation of TRIP6 expression in MCF-7 breast cancer cells (with high TRIP6 expression) and taxane-resistant MCF-7 sublines (m…