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View article: CINner: Modeling and simulation of chromosomal instability in cancer at single-cell resolution
CINner: Modeling and simulation of chromosomal instability in cancer at single-cell resolution Open
Cancer development is characterized by chromosomal instability, manifesting in frequent occurrences of different genomic alteration mechanisms ranging in extent and impact. Mathematical modeling can help evaluate the role of each mutationa…
Birth and death processes in phylogenetics and population genetics Open
This review focuses on linear birth-and-death processes (LBDPs), describing the basic properties of the population-size process and the underlying ancestral trees that record how the evolving species (or individuals or cells) are related. …
View article: Consortium Author List from Cancer Research in the Age of Spatial Omics: Lessons from IMAXT
Consortium Author List from Cancer Research in the Age of Spatial Omics: Lessons from IMAXT Open
IMAXT Consortium Author List
View article: Data from Cancer Research in the Age of Spatial Omics: Lessons from IMAXT
Data from Cancer Research in the Age of Spatial Omics: Lessons from IMAXT Open
Summary:The Imaging and Molecular Annotation of Xenografts and Tumors Cancer Grand Challenges team was set up with the objective of developing the “next generation” of pathology and cancer research by using a combination of single-cell and…
View article: Consortium Author List from Cancer Research in the Age of Spatial Omics: Lessons from IMAXT
Consortium Author List from Cancer Research in the Age of Spatial Omics: Lessons from IMAXT Open
IMAXT Consortium Author List
Cancer Research in the Age of Spatial Omics: Lessons from IMAXT Open
Summary: The Imaging and Molecular Annotation of Xenografts and Tumors Cancer Grand Challenges team was set up with the objective of developing the “next generation” of pathology and cancer research by using a combination of single-cell an…
Supplementary Table S4 from Single-cell RNA sequencing unifies developmental programs of Esophageal and Gastric Intestinal Metaplasia. Open
This table contains results of pairwise differential expression analysis between E-GM and gastric tissues and Atrophic gastritis and gastric tissue.
Supplementary Table S3 from Single-cell RNA sequencing unifies developmental programs of Esophageal and Gastric Intestinal Metaplasia. Open
This table contains marker genes identified in the pairwise comparison of clusters defined as columnar cells.
Supplementary Figures from Single-cell RNA sequencing unifies developmental programs of Esophageal and Gastric Intestinal Metaplasia. Open
This file captions for supplementary tables and supplementary figures S1-S28 together with their legends
Supplementary Figures from Single-cell RNA sequencing unifies developmental programs of Esophageal and Gastric Intestinal Metaplasia. Open
This file captions for supplementary tables and supplementary figures S1-S28 together with their legends
Supplementary Table S1 from Single-cell RNA sequencing unifies developmental programs of Esophageal and Gastric Intestinal Metaplasia. Open
This file contains details of individual samples (including clinical data) used in the sutdy
Supplementary Table S6 from Single-cell RNA sequencing unifies developmental programs of Esophageal and Gastric Intestinal Metaplasia. Open
This table contains marker genes identified in the pairwise comparison of clusters identified in fibroblast population
Supplementary Table S5 from Single-cell RNA sequencing unifies developmental programs of Esophageal and Gastric Intestinal Metaplasia. Open
This table contains details of mutations identified in WGS of E-GM samples.
Supplementary Table S3 from Single-cell RNA sequencing unifies developmental programs of Esophageal and Gastric Intestinal Metaplasia. Open
This table contains marker genes identified in the pairwise comparison of clusters defined as columnar cells.
Supplementary Table S4 from Single-cell RNA sequencing unifies developmental programs of Esophageal and Gastric Intestinal Metaplasia. Open
This table contains results of pairwise differential expression analysis between E-GM and gastric tissues and Atrophic gastritis and gastric tissue.
Supplementary Table S2 from Single-cell RNA sequencing unifies developmental programs of Esophageal and Gastric Intestinal Metaplasia. Open
This table contains marker genes identified in each cluster of cells.
Supplementary Table S1 from Single-cell RNA sequencing unifies developmental programs of Esophageal and Gastric Intestinal Metaplasia. Open
This file contains details of individual samples (including clinical data) used in the sutdy
Supplementary Table S5 from Single-cell RNA sequencing unifies developmental programs of Esophageal and Gastric Intestinal Metaplasia. Open
This table contains details of mutations identified in WGS of E-GM samples.
Supplementary Table S6 from Single-cell RNA sequencing unifies developmental programs of Esophageal and Gastric Intestinal Metaplasia. Open
This table contains marker genes identified in the pairwise comparison of clusters identified in fibroblast population
Supplementary Table S2 from Single-cell RNA sequencing unifies developmental programs of Esophageal and Gastric Intestinal Metaplasia. Open
This table contains marker genes identified in each cluster of cells.
View article: Ongoing genome doubling promotes evolvability and immune dysregulation in ovarian cancer
Ongoing genome doubling promotes evolvability and immune dysregulation in ovarian cancer Open
Whole-genome doubling (WGD) is a critical driver of tumor development and is linked to drug resistance and metastasis in solid malignancies. Here, we demonstrate that WGD is an ongoing mutational process in tumor evolution. Using single-ce…
Approximate Bayesian Computation sequential Monte Carlo via random forests Open
Approximate Bayesian Computation (ABC) is a popular inference method when likelihoods are hard to come by. Practical bottlenecks of ABC applications include selecting statistics that summarize the data without losing too much information o…
Supplementary Table S2 from Single-Cell RNA Sequencing Unifies Developmental Programs of Esophageal and Gastric Intestinal Metaplasia Open
This table contains marker genes identified in each cluster of cells.
Data from Single-Cell RNA Sequencing Unifies Developmental Programs of Esophageal and Gastric Intestinal Metaplasia Open
Intestinal metaplasia in the esophagus (Barrett's esophagus IM, or BE-IM) and stomach (GIM) are considered precursors for esophageal and gastric adenocarcinoma, respectively. We hypothesize that BE-IM and GIM follow parallel developmental …
Supplementary Table S3 from Single-Cell RNA Sequencing Unifies Developmental Programs of Esophageal and Gastric Intestinal Metaplasia Open
This table contains marker genes identified in the pairwise comparison of clusters defined as columnar cells.
Supplementary Table S3 from Single-Cell RNA Sequencing Unifies Developmental Programs of Esophageal and Gastric Intestinal Metaplasia Open
This table contains marker genes identified in the pairwise comparison of clusters defined as columnar cells.
Supplementary Table S4 from Single-Cell RNA Sequencing Unifies Developmental Programs of Esophageal and Gastric Intestinal Metaplasia Open
This table contains results of pairwise differential expression analysis between E-GM and gastric tissues and Atrophic gastritis and gastric tissue.