Christopher A. Maher
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View article: Leveraging sequences missing from the human genome to diagnose cancer
Leveraging sequences missing from the human genome to diagnose cancer Open
Background Cancer diagnosis using cell-free DNA (cfDNA) has the potential to improve treatment and survival but has several technical limitations. Methods In this study, we developed a prediction model based on neomers, DNA sequences 13–17…
View article: Supplementary Figure S8 from Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer
Supplementary Figure S8 from Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer Open
Supplementary Figure S8. Transcription factor analysis in localized prostate cancer versus blood. Log2 fold change of the 20 TFs with most accessible and least accessible binding sites in plasma cell-free DNA (see Fig. 4E, Table S12 and Ta…
View article: Supplementary Figure S3 from Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer
Supplementary Figure S3 from Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer Open
Supplementary Figure S3. Kaplan-Meier analysis of an additional cohort of 27 patients with oligometastatic mCRPC, stratified by AR enhancer amplification status in plasma cell-free DNA. (A) Progression-free survival, (B) radiographic progr…
View article: Supplementary Figure S9 from Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer
Supplementary Figure S9 from Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer Open
Supplementary Figure S9. Cell-free DNA methylation analysis of differentially accessible transcription factor binding sites. The box and whisker plots summarize methylation levels in plasma cfDNA from AR/enhancer altered versus wild-type m…
View article: Supplementary Figure S7 from Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer
Supplementary Figure S7 from Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer Open
Supplementary Figure S7. Distribution of differentially methylated regions in mCRPC plasma cell-free DNA. (A) Distribution of hypomethylated and hypermethylated genic DMRs in pre-treatment plasma cfDNA in AR/enhancer altered lethal mCRPC (…
View article: Supplementary Table S1-S14 from Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer
Supplementary Table S1-S14 from Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer Open
Table S1. Patient characteristics. Table S2. Patients-level clinical treatment and outcome details. Table S3. Mutations detected in patient cell-free DNA by EnhanceAR-Seq. Table S4. Copy number alterations detected in patient cell-free DNA…
View article: Data from Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer
Data from Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer Open
Purpose:Metastatic castration-resistant prostate cancer (mCRPC) resistant to androgen receptor signaling inhibitors (ARSI) is often lethal. Liquid biopsy biomarkers for this deadly form of disease remain under investigation, and underpinni…
View article: Supplementary Figure S2 from Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer
Supplementary Figure S2 from Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer Open
Supplementary Figure S2. Kaplan-Meier analysis based on plasma collected prior to first-line androgen receptor-signaling inhibitor (ARSI) treatment according to (A,B) Androgen receptor (AR) gene body status and (C,D) AR enhancer region sta…
View article: Supplementary Figure S11 from Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer
Supplementary Figure S11 from Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer Open
Supplementary Figure S11. Cell-free DNA methylation levels of the top 10 least stem-like signature genes in plasma. The box and whisker plots summarize the promoter methylation rates for the top 10 least stem-like genes in plasma cfDNA fro…
View article: Supplementary Figure S1 from Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer
Supplementary Figure S1 from Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer Open
Supplementary Figure S1. Genomic landscape of metastatic castration-resistant prostate cancer (mCRPC) samples profiled using EnhanceAR-Seq. EnhanceAR-Seq, Enhancer and neighboring loci of Androgen Receptor Sequencing.
View article: Supplementary Figure S5 from Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer
Supplementary Figure S5 from Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer Open
Supplementary Figure S5. Kaplan-Meier survival analysis based on plasma collected prior to first-line androgen receptor-signaling inhibitor (ARSI) treatment in 63 mCRPC patients according to (A,B) PTEN copy number loss status in cfDNA, (C,…
View article: Supplementary Figure S4 from Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer
Supplementary Figure S4 from Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer Open
Supplementary Figure S4. Summary of alterations in biologically relevant pathways found in pre-ARSI plasma cell-free DNA of 63 metastatic castration-resistant prostate cancer patients. ARSI, androgen receptor-signaling inhibitors.
View article: Supplementary Figure S6 from Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer
Supplementary Figure S6 from Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer Open
Supplementary Figure S6. Kaplan–Meier survival analysis of the 43-patient mCRPC cohort that also underwent genome-wide EM-seq, according to (A,B) AR/enhancer alteration status and (C,D) median-split ichorCNA-based median tumor fraction. p …
View article: Supplementary Figure S10 from Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer
Supplementary Figure S10 from Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer Open
Supplementary Figure S10. Cell-free DNA methylation levels of the top 10 most stem-like signature genes in plasma. The box and whisker plots summarize promoter methylation rates for the top 10 most stem-like signature genes in plasma cfDNA…
View article: Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer
Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer Open
Purpose: Metastatic castration-resistant prostate cancer (mCRPC) resistant to androgen receptor signaling inhibitors (ARSI) is often lethal. Liquid biopsy biomarkers for this deadly form of disease remain under investigation, and underpinn…
View article: Single cell-transcriptomic analysis informs the lncRNA landscape in metastatic castration resistant prostate cancer
Single cell-transcriptomic analysis informs the lncRNA landscape in metastatic castration resistant prostate cancer Open
Metastatic castration-resistant prostate cancer (mCRPC) is a lethal form of prostate cancer. Although long-noncoding RNAs (lncRNAs) have been implicated in mCRPC, past studies have relied on bulk sequencing methods with low depth and lack …
View article: Genomic and epigenomic analysis of plasma cell-free DNA identifies stemness features associated with worse survival in<i>AR</i>-altered lethal prostate cancer
Genomic and epigenomic analysis of plasma cell-free DNA identifies stemness features associated with worse survival in<i>AR</i>-altered lethal prostate cancer Open
Summary Metastatic castration-resistant prostate cancer (mCRPC) resistant to androgen receptor (AR)-targeted agents is often lethal. Unfortunately, biomarkers for this deadly disease remain under investigation, and underpinning mechanisms …
View article: Single-cell transcriptomics reveals long noncoding RNAs associated with tumor biology and the microenvironment in pancreatic cancer
Single-cell transcriptomics reveals long noncoding RNAs associated with tumor biology and the microenvironment in pancreatic cancer Open
Pancreatic ductal adenocarcinoma (PDAC) is highly heterogeneous and lethal. Long noncoding RNAs (lncRNAs) are an important class of genes regulating tumorigenesis and progression. Prior bulk transcriptomic studies in PDAC have revealed the…
View article: INTEGRATE-Circ and INTEGRATE-Vis: unbiased detection and visualization of fusion-derived circular RNA
INTEGRATE-Circ and INTEGRATE-Vis: unbiased detection and visualization of fusion-derived circular RNA Open
Motivation Backsplicing of RNA results in circularized rather than linear transcripts, known as circular RNA (circRNA). A recently discovered and poorly understood subset of circRNAs that are composed of multiple genes, termed fusion-deriv…
View article: PACT: a pipeline for analysis of circulating tumor DNA
PACT: a pipeline for analysis of circulating tumor DNA Open
Motivation Detection of genomic alterations in circulating tumor DNA (ctDNA) is currently used for active clinical monitoring of cancer progression and treatment response. While methods for analysis of small mutations are more developed, s…
View article: Genetic characterization of primary and metastatic high-grade serous ovarian cancer tumors reveals distinct features associated with survival
Genetic characterization of primary and metastatic high-grade serous ovarian cancer tumors reveals distinct features associated with survival Open
High-grade serous ovarian cancer (HGSC) is the most lethal histotype of ovarian cancer and the majority of cases present with metastasis and late-stage disease. Over the last few decades, the overall survival for patients has not significa…
View article: Large, Nested Variant of Urothelial Carcinoma Is Enriched with Activating Mutations in Fibroblast Growth Factor Receptor-3 among Other Targetable Mutations
Large, Nested Variant of Urothelial Carcinoma Is Enriched with Activating Mutations in Fibroblast Growth Factor Receptor-3 among Other Targetable Mutations Open
The large, nested variant of urothelial carcinoma (LNVUC) is characterized by bland histomorphology mimicking that of benign von Brunn nests. In the current study, we aimed to investigate the Fibroblast Growth Factor Receptor-3 (FGFR-3) ac…
View article: The Sorghum bicolor genome and the diversification of grasses.
The Sorghum bicolor genome and the diversification of grasses. Open
Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the approximately 730-megabase Sorghum bicolor (L.) Moench genome, placing approximately 98% of genes in …
View article: Supplementary Methods from Targeted Therapy to β3 Integrin Reduces Chemoresistance in Breast Cancer Bone Metastases
Supplementary Methods from Targeted Therapy to β3 Integrin Reduces Chemoresistance in Breast Cancer Bone Metastases Open
Additional details for methods and materials.
View article: Supplementary Figure S4 from Targeted Therapy to β3 Integrin Reduces Chemoresistance in Breast Cancer Bone Metastases
Supplementary Figure S4 from Targeted Therapy to β3 Integrin Reduces Chemoresistance in Breast Cancer Bone Metastases Open
TEM quantitation of average area per mitochondrion and GO Biological Process GSEA in 4T1 cells.
View article: Supplementary Figure S2 from Targeted Therapy to β3 Integrin Reduces Chemoresistance in Breast Cancer Bone Metastases
Supplementary Figure S2 from Targeted Therapy to β3 Integrin Reduces Chemoresistance in Breast Cancer Bone Metastases Open
Validation of Itgb3 CRISPR knockout in 4T1 and PyMT-BO1 cells and assessment of docetaxel sensitivity in vitro and in vivo.
View article: Supplementary Data from Pan-Cancer Analysis Reveals Recurrent <i>BCAR4</i> Gene Fusions across Solid Tumors
Supplementary Data from Pan-Cancer Analysis Reveals Recurrent <i>BCAR4</i> Gene Fusions across Solid Tumors Open
Supplementary Data from Pan-Cancer Analysis Reveals Recurrent BCAR4 Gene Fusions across Solid Tumors