Daniel Skubleny
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View article: Evaluation of a Gene Expression-Based Machine Learning Classifier to Discriminate Normal from Cancer Gastric Organoids
Evaluation of a Gene Expression-Based Machine Learning Classifier to Discriminate Normal from Cancer Gastric Organoids Open
Three-dimensional cell model systems such as tumour organoids allow for in vitro modelling of self-organized tissue with functional and histologic similarity to in vivo tissue. However, there is a need for standard protocols and techniques…
View article: A 107 Gene Nanostring Assay Effectively Translates the Cancer Genome Atlas, and Tumour Microenvironment Gastric Cancer Molecular Classification to a Patient‐Derived Organoid Model
A 107 Gene Nanostring Assay Effectively Translates the Cancer Genome Atlas, and Tumour Microenvironment Gastric Cancer Molecular Classification to a Patient‐Derived Organoid Model Open
There is a need to improve the translation of gastric cancer molecular classification schemes, such as those proposed by the Cancer Genome Atlas (TCGA) and Tumour Microenvironment score (TME), to clinical specimens and three‐dimensional or…
View article: Supplementary Data 1 from The Tumor Immune Microenvironment Drives Survival Outcomes and Therapeutic Response in an Integrated Molecular Analysis of Gastric Adenocarcinoma
Supplementary Data 1 from The Tumor Immune Microenvironment Drives Survival Outcomes and Therapeutic Response in an Integrated Molecular Analysis of Gastric Adenocarcinoma Open
Supplemental Methods and Figures
View article: Data from The Tumor Immune Microenvironment Drives Survival Outcomes and Therapeutic Response in an Integrated Molecular Analysis of Gastric Adenocarcinoma
Data from The Tumor Immune Microenvironment Drives Survival Outcomes and Therapeutic Response in an Integrated Molecular Analysis of Gastric Adenocarcinoma Open
Purpose:We performed an integrated analysis of molecular classification systems proposed by The Cancer Genome Atlas (TCGA), the Asian Cancer Research Group (ACRG), and the tumor microenvironment (TME) score to identify which classification…
View article: Supplementary Data 1 from Learning Individual Survival Models from PanCancer Whole Transcriptome Data
Supplementary Data 1 from Learning Individual Survival Models from PanCancer Whole Transcriptome Data Open
Supplementary
View article: Supplementary Data 1 from Learning Individual Survival Models from PanCancer Whole Transcriptome Data
Supplementary Data 1 from Learning Individual Survival Models from PanCancer Whole Transcriptome Data Open
Supplementary
View article: Data from Learning Individual Survival Models from PanCancer Whole Transcriptome Data
Data from Learning Individual Survival Models from PanCancer Whole Transcriptome Data Open
Purpose: Personalized medicine attempts to predict survival time for each patient, based on their individual tumour molecular profile. We investigate whether our survival learner in combination with a dimension reduction method can produce…
View article: Feature-specific quantile normalization and feature-specific mean–variance normalization deliver robust bi-directional classification and feature selection performance between microarray and RNAseq data
Feature-specific quantile normalization and feature-specific mean–variance normalization deliver robust bi-directional classification and feature selection performance between microarray and RNAseq data Open
Background Cross-platform normalization seeks to minimize technological bias between microarray and RNAseq whole-transcriptome data. Incorporating multiple gene expression platforms permits external validation of experimental findings, and…
View article: Individual Survival Distributions Generated by Multi-Task Logistic Regression Yield a New Perspective on Molecular and Clinical Prognostic Factors in Gastric Adenocarcinoma
Individual Survival Distributions Generated by Multi-Task Logistic Regression Yield a New Perspective on Molecular and Clinical Prognostic Factors in Gastric Adenocarcinoma Open
Recent advances in our understanding of gastric cancer biology have prompted a shift towards more personalized therapy. However, results are based on population-based survival analyses, which evaluate the average survival effects of entire…
View article: Supplementary Data 1 from Learning Individual Survival Models from PanCancer Whole Transcriptome Data
Supplementary Data 1 from Learning Individual Survival Models from PanCancer Whole Transcriptome Data Open
Supplementary
View article: Data from Learning Individual Survival Models from PanCancer Whole Transcriptome Data
Data from Learning Individual Survival Models from PanCancer Whole Transcriptome Data Open
Purpose:Personalized medicine attempts to predict survival time for each patient, based on their individual tumor molecular profile. We investigate whether our survival learner in combination with a dimension reduction method can produce u…
View article: Data from Learning Individual Survival Models from PanCancer Whole Transcriptome Data
Data from Learning Individual Survival Models from PanCancer Whole Transcriptome Data Open
Purpose:Personalized medicine attempts to predict survival time for each patient, based on their individual tumor molecular profile. We investigate whether our survival learner in combination with a dimension reduction method can produce u…
View article: Supplementary Data 1 from Learning Individual Survival Models from PanCancer Whole Transcriptome Data
Supplementary Data 1 from Learning Individual Survival Models from PanCancer Whole Transcriptome Data Open
Supplementary
View article: A prospective Canadian gastroesophageal cancer database: What have we learned?
A prospective Canadian gastroesophageal cancer database: What have we learned? Open
Many of the patients with GEA in this study presented with advanced disease, and only 61% were offered curative-intent surgery. A prospective multicentre national GEA database is now being established.
View article: Learning Individual Survival Models from PanCancer Whole Transcriptome Data
Learning Individual Survival Models from PanCancer Whole Transcriptome Data Open
Purpose: Personalized medicine attempts to predict survival time for each patient, based on their individual tumor molecular profile. We investigate whether our survival learner in combination with a dimension reduction method can produce …
View article: Increased CD4/CD8 Lymphocyte ratio predicts favourable neoadjuvant treatment response in gastric cancer: A prospective pilot study
Increased CD4/CD8 Lymphocyte ratio predicts favourable neoadjuvant treatment response in gastric cancer: A prospective pilot study Open
We demonstrate that an elevated CD4+/CD8+ Ratio is a promising IHC-based biomarker to predict favourable treatment response to FLOT neoadjuvant chemotherapy in locally advanced gastric cancer.
View article: Murine and Human Gastric Tissue Establishes Organoids after 48 Hours of Cold Ischemia Time during Shipment
Murine and Human Gastric Tissue Establishes Organoids after 48 Hours of Cold Ischemia Time during Shipment Open
An inadequate supply of fresh tissue is a major limitation of three-dimensional patient-derived gastric organoid research. We propose that tissue procurement for organoid culture could be increased by developing a cold storage shipment pro…
View article: Editorial: pancreatic resection in the era of laparoscopy: state of art—a systematic review
Editorial: pancreatic resection in the era of laparoscopy: state of art—a systematic review Open
We appreciate the invitation to comment on the article “ Pancreatic Resection in the era of laparoscopy: State of Art. A systematic review ” published in the International Journal of Surgery (1).
View article: Normothermic Ex Vivo Machine Perfusion for Liver Grafts Recovered from Donors after Circulatory Death: A Systematic Review and Meta-Analysis
Normothermic Ex Vivo Machine Perfusion for Liver Grafts Recovered from Donors after Circulatory Death: A Systematic Review and Meta-Analysis Open
As a result of donation after circulatory death liver grafts’ poor tolerance to cold storage, there has been increasing research interest in normothermic machine perfusion. This study aims to systematically review the current literature co…
View article: 2017 Canadian Surgery Forum Abstracts
2017 Canadian Surgery Forum Abstracts Open
# 01: Iron deficiency in bariatric surgery patients — a single-centre experience over 5 years {#article-title-2} As the prevalence and severity of obesity have increased in Canada, so too has the demand for bariatric surgery. The objective…
View article: Endoscopy services and training: a national survey of general surgeons
Endoscopy services and training: a national survey of general surgeons Open
Endoscopy is considered integral to academic and community general surgeons' practices; however, the adequacy of training seems to be questioned. Postgraduate training in endoscopy needs to be formalized and standardized, with a greater em…