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View article: Genome-wide in vivo CRISPR screens identify GATOR1 complex as a tumor suppressor in Myc-driven lymphoma
Genome-wide in vivo CRISPR screens identify GATOR1 complex as a tumor suppressor in Myc-driven lymphoma Open
Identifying tumor suppressor genes is predicted to inform on the development of novel strategies for cancer therapy. To identify new lymphoma driving processes that cooperate with oncogenic MYC, which is abnormally highly expressed in ~70%…
View article: Fibroblast hierarchy dynamics during mammary gland morphogenesis and tumorigenesis
Fibroblast hierarchy dynamics during mammary gland morphogenesis and tumorigenesis Open
Fibroblasts form a major component of the stroma in normal mammary tissue and breast tumors. Here, we have applied longitudinal single-cell transcriptome profiling of >45,000 fibroblasts in the mouse mammary gland across five different dev…
View article: Thioredoxin reductase 3 inhibition sensitizes triple-negative breast cancer cells to EGFR inhibitors
Thioredoxin reductase 3 inhibition sensitizes triple-negative breast cancer cells to EGFR inhibitors Open
Triple-negative breast cancer (TNBC) is an aggressive subtype with poor prognosis and limited treatments. Although 40-70% of TNBC cases overexpress EGFR, anti-EGFR therapies show minimal clinical benefit. This may result from inherent resi…
View article: Supplementary Methods, Figures S1-14 from Dual Targeting of CDK4/6 and BCL2 Pathways Augments Tumor Response in Estrogen Receptor–Positive Breast Cancer
Supplementary Methods, Figures S1-14 from Dual Targeting of CDK4/6 and BCL2 Pathways Augments Tumor Response in Estrogen Receptor–Positive Breast Cancer Open
Supplemental Methods and Figures
View article: Supplementary Methods, Figures S1-14 from Dual Targeting of CDK4/6 and BCL2 Pathways Augments Tumor Response in Estrogen Receptor–Positive Breast Cancer
Supplementary Methods, Figures S1-14 from Dual Targeting of CDK4/6 and BCL2 Pathways Augments Tumor Response in Estrogen Receptor–Positive Breast Cancer Open
Supplemental Methods and Figures
View article: Data from Dual Targeting of CDK4/6 and BCL2 Pathways Augments Tumor Response in Estrogen Receptor–Positive Breast Cancer
Data from Dual Targeting of CDK4/6 and BCL2 Pathways Augments Tumor Response in Estrogen Receptor–Positive Breast Cancer Open
Purpose:Although cyclin-dependent kinase 4 and 6 (CDK4/6) inhibitors significantly extend tumor response in patients with metastatic estrogen receptor–positive (ER+) breast cancer, relapse is almost inevitable. This may, in part…
View article: Table S1 from Dual Targeting of CDK4/6 and BCL2 Pathways Augments Tumor Response in Estrogen Receptor–Positive Breast Cancer
Table S1 from Dual Targeting of CDK4/6 and BCL2 Pathways Augments Tumor Response in Estrogen Receptor–Positive Breast Cancer Open
Differential sgRNA enrichment from CRISPR-Cas9 genome-wide screens
View article: Table S3 from Dual Targeting of CDK4/6 and BCL2 Pathways Augments Tumor Response in Estrogen Receptor–Positive Breast Cancer
Table S3 from Dual Targeting of CDK4/6 and BCL2 Pathways Augments Tumor Response in Estrogen Receptor–Positive Breast Cancer Open
Summary of clinical features for patient derived xenograft and patient derived organoids
View article: Table S1 from Dual Targeting of CDK4/6 and BCL2 Pathways Augments Tumor Response in Estrogen Receptor–Positive Breast Cancer
Table S1 from Dual Targeting of CDK4/6 and BCL2 Pathways Augments Tumor Response in Estrogen Receptor–Positive Breast Cancer Open
Differential sgRNA enrichment from CRISPR-Cas9 genome-wide screens
View article: Table S4 from Dual Targeting of CDK4/6 and BCL2 Pathways Augments Tumor Response in Estrogen Receptor–Positive Breast Cancer
Table S4 from Dual Targeting of CDK4/6 and BCL2 Pathways Augments Tumor Response in Estrogen Receptor–Positive Breast Cancer Open
Targeted gene sequencing of patient derived organoids
View article: Table S2 from Dual Targeting of CDK4/6 and BCL2 Pathways Augments Tumor Response in Estrogen Receptor–Positive Breast Cancer
Table S2 from Dual Targeting of CDK4/6 and BCL2 Pathways Augments Tumor Response in Estrogen Receptor–Positive Breast Cancer Open
Differential gene enrichment from CRISPR-Cas9 genome-wide screens
View article: Table S2 from Dual Targeting of CDK4/6 and BCL2 Pathways Augments Tumor Response in Estrogen Receptor–Positive Breast Cancer
Table S2 from Dual Targeting of CDK4/6 and BCL2 Pathways Augments Tumor Response in Estrogen Receptor–Positive Breast Cancer Open
Differential gene enrichment from CRISPR-Cas9 genome-wide screens
View article: Data from Dual Targeting of CDK4/6 and BCL2 Pathways Augments Tumor Response in Estrogen Receptor–Positive Breast Cancer
Data from Dual Targeting of CDK4/6 and BCL2 Pathways Augments Tumor Response in Estrogen Receptor–Positive Breast Cancer Open
Purpose:Although cyclin-dependent kinase 4 and 6 (CDK4/6) inhibitors significantly extend tumor response in patients with metastatic estrogen receptor–positive (ER+) breast cancer, relapse is almost inevitable. This may, in part…
View article: Table S3 from Dual Targeting of CDK4/6 and BCL2 Pathways Augments Tumor Response in Estrogen Receptor–Positive Breast Cancer
Table S3 from Dual Targeting of CDK4/6 and BCL2 Pathways Augments Tumor Response in Estrogen Receptor–Positive Breast Cancer Open
Summary of clinical features for patient derived xenograft and patient derived organoids
View article: Table S4 from Dual Targeting of CDK4/6 and BCL2 Pathways Augments Tumor Response in Estrogen Receptor–Positive Breast Cancer
Table S4 from Dual Targeting of CDK4/6 and BCL2 Pathways Augments Tumor Response in Estrogen Receptor–Positive Breast Cancer Open
Targeted gene sequencing of patient derived organoids
View article: Author Correction: Generation of a CRISPR activation mouse that enables modelling of aggressive lymphoma and interrogation of venetoclax resistance
Author Correction: Generation of a CRISPR activation mouse that enables modelling of aggressive lymphoma and interrogation of venetoclax resistance Open
View article: Generation of a CRISPR activation mouse that enables modelling of aggressive lymphoma and interrogation of venetoclax resistance
Generation of a CRISPR activation mouse that enables modelling of aggressive lymphoma and interrogation of venetoclax resistance Open
View article: Genome-wide<i>in vivo</i>CRISPR screens identify GATOR1 as a potent tumor suppressor in MYC-driven lymphomagenesis
Genome-wide<i>in vivo</i>CRISPR screens identify GATOR1 as a potent tumor suppressor in MYC-driven lymphomagenesis Open
Identifying tumor suppressor genes is predicted to inform on the development of novel strategies for cancer therapy. To identify new lymphoma driving processes that cooperate with oncogenic MYC (which is abnormally highly expressed in ∼70%…
View article: A novel CRISPR activation mouse enables modelling of aggressive lymphoma and interrogation of venetoclax resistance.
A novel CRISPR activation mouse enables modelling of aggressive lymphoma and interrogation of venetoclax resistance. Open
CRISPR technologies have advanced cancer modelling in mice, but CRISPR activation (CRISPRa) methods have not been thoroughly exploited in this context. Here we establish a CRISPRa mouse (dCas9a-SAMKI/+) for inducing gene express…
View article: Targeting triple-negative breast cancers with the Smac-mimetic birinapant
Targeting triple-negative breast cancers with the Smac-mimetic birinapant Open
Smac mimetics target inhibitor of apoptosis (IAP) proteins, thereby suppressing their function to facilitate tumor cell death. Here we have evaluated the efficacy of the preclinical Smac-mimetic compound A and the clinical lead birinapant …
View article: Peer Review #2 of "qtQDA: quantile transformed quadratic discriminant analysis for high-dimensional RNA-seq data (v0.1)"
Peer Review #2 of "qtQDA: quantile transformed quadratic discriminant analysis for high-dimensional RNA-seq data (v0.1)" Open
Classification on the basis of gene expression data derived from RNA-seq promises to become an important part of modern medicine.We propose a new classification method based on a model where the data is marginally negative binomial but dep…
View article: Peer Review #2 of "qtQDA: quantile transformed quadratic discriminant analysis for high-dimensional RNA-seq data (v0.2)"
Peer Review #2 of "qtQDA: quantile transformed quadratic discriminant analysis for high-dimensional RNA-seq data (v0.2)" Open
Classification on the basis of gene expression data derived from RNA-seq promises to become an important part of modern medicine.We propose a new classification method based on a model where the data is marginally negative binomial but dep…
View article: qtQDA: quantile transformed quadratic discriminant analysis for high-dimensional RNA-seq data
qtQDA: quantile transformed quadratic discriminant analysis for high-dimensional RNA-seq data Open
Classification on the basis of gene expression data derived from RNA-seq promises to become an important part of modern medicine. We propose a new classification method based on a model where the data is marginally negative binomial but de…
View article: Peer Review #1 of "qtQDA: quantile transformed quadratic discriminant analysis for high-dimensional RNA-seq data (v0.1)"
Peer Review #1 of "qtQDA: quantile transformed quadratic discriminant analysis for high-dimensional RNA-seq data (v0.1)" Open
Classification on the basis of gene expression data derived from RNA-seq promises to become an important part of modern medicine.We propose a new classification method based on a model where the data is marginally negative binomial but dep…
View article: Peer Review #1 of "qtQDA: quantile transformed quadratic discriminant analysis for high-dimensional RNA-seq data (v0.2)"
Peer Review #1 of "qtQDA: quantile transformed quadratic discriminant analysis for high-dimensional RNA-seq data (v0.2)" Open
Classification on the basis of gene expression data derived from RNA-seq promises to become an important part of modern medicine.We propose a new classification method based on a model where the data is marginally negative binomial but dep…
View article: A new local covariance matrix estimation for the classification of gene expression profiles in RNA-Seq data
A new local covariance matrix estimation for the classification of gene expression profiles in RNA-Seq data Open
Background and Objective Recent developments in the next-generation sequencing (NGS) based on RNA-sequencing (RNA-Seq) allow researchers to measure the expression levels of thousands of genes for multiple samples simultaneously. In order t…
View article: qtQDA: quantile transformed quadratic discriminant analysis for high-dimensional RNA-seq data
qtQDA: quantile transformed quadratic discriminant analysis for high-dimensional RNA-seq data Open
Classification on the basis of gene expression data derived from RNA-seq promises to become an important part of modern medicine. We propose a new classification method based on a model where the data is marginally negative binomial but de…
View article: FRY: a fast approximation to ROAST gene set test with mean aggregated set statistics
FRY: a fast approximation to ROAST gene set test with mean aggregated set statistics Open
View article: statmod: Probability Calculations for the Inverse Gaussian Distribution
statmod: Probability Calculations for the Inverse Gaussian Distribution Open
The inverse Gaussian distribution (IGD) is a well known and often used probability distribution for which fully reliable numerical algorithms have not been available. Our aim in this article is to develop software for this distribution for…