PhD

PhD Project: RNA Sequencing-based Tools for Breast Cancer Diagnostics
My PhD work in developing RNA sequencing-based diagnostic tools for breast cancer.
PhD Project: RNA Sequencing-based Tools for Breast Cancer Diagnostics
The mutational landscape of the SCAN-B real-world primary breast cancer transcriptome
Breast cancer is a disease of genomic alterations, of which the panorama of somatic mutations and how these relate to subtypes and …
Christian Brueffer, Sergii Gladchuk, Christof Winter, Johan Vallon-Christersson, Cecilia Hegardt, Jari Häkkinen, Anthony M. George, Yilun Chen, Anna Ehinger, Christer Larsson, Niklas Loman, Martin Malmberg, Lisa Rydén, Åke Borg, Lao H. Saal
DOI PDF bioRxiv Preprint Code Dataset Press Release PhD Project
The mutational landscape of the SCAN-B real-world primary breast cancer transcriptome
Defining the Mutational Landscape of 3,217 Primary Breast Cancer Transcriptomes through large-scale RNA-seq within the Sweden Cancerome Analysis Network: Breast Project (SCAN-B; NCT03430492)
May 29, 2020 08:00 — 11:00 ASCO Annual Meeting 2020 McCormick Place, Chicago, IL, USA
PhD Project MutationExplorer Project
Defining the mutational landscape of 3,217 primary breast cancer transcriptomes through large-scale RNA-seq within the Sweden Cancerome Analysis Network: Breast Project (SCAN-B; NCT03430492).
Background
Breast cancer is a disease of genomic alterations, of which the complete panorama of somatic mutations and how these relate …
Christian Brueffer, Sergii Gladchuk, Christof Winter, Johan Vallon-Christersson, Cecilia Hegardt, Jari Häkkinen, Anthony M George, Yilun Chen, Anna Ehinger, Christer Larsson, Niklas Loman, Martin Malmberg, Lisa Rydén, Åke Borg, Lao H. Saal
DOI
Defining the mutational landscape of 3,217 primary breast cancer transcriptomes through large-scale RNA-seq within the Sweden Cancerome Analysis Network: Breast Project (SCAN-B; NCT03430492).
SCAN-B MutationExplorer
A web-based application for exploring tumor somatic mutations.
SCAN-B MutationExplorer
Defining the Mutational Landscape of the Primary Breast Cancer Transcriptome through large-scale RNA-seq in the SCAN-B Project
Nov 4, 2019 10:45 — 11:05 Swedish Cancer Research Meeting 2019 Folkets Hus, Umeå, Sweden
PhD Project MutationExplorer Project
Towards Better Breast Cancer Diagnostics: Large-scale Profiling of Tumor Transcriptomes
May 23, 2019 09:10 — 09:35 RSG-Sweden Bioinformatics in Diseases Symposium Ekologihuset, Lund, Sweden
PhD Project MutationExplorer Project
RNA-seq-Based Classifiers for Prediction of the Five Conventional Breast Cancer Biomarkers in the Population-Based Multicenter SCAN-B Study
May 7, 2018 16:15 — 16:30 Keystone Symposium on Precision Medicine in Cancer Clarion Hotel Sign, Stockholm, Sweden
PhD Project
Clinical Value of RNA Sequencing-Based Classifiers for Prediction of the Five Conventional Breast Cancer Biomarkers: A Report From the Population-Based Multicenter Sweden Cancerome Analysis Network–Breast Initiative
Purpose
In early breast cancer (BC), five conventional biomarkers—estrogen receptor (ER), progesterone receptor (PgR), human epidermal …
Christian Brueffer, Johan Vallon-Christersson, Dorthe Grabau, Anna Ehinger, Jari Häkkinen, Cecilia Hegardt, Janne Malina, Yilun Chen, Pär-Ola Bendahl, Jonas Manjer, Martin Malmberg, Christer Larsson, Niklas Loman, Lisa Rydén, Åke Borg, Lao H. Saal
DOI PDF Dataset PhD Project
Clinical Value of RNA Sequencing-Based Classifiers for Prediction of the Five Conventional Breast Cancer Biomarkers: A Report From the Population-Based Multicenter Sweden Cancerome Analysis Network–Breast Initiative
TopHat-Recondition: A post-processor for TopHat unmapped reads
Background
TopHat is a popular spliced junction mapper for RNA sequencing data, and writes files in the BAM format – the binary version …
Christian Brueffer, Lao H. Saal
DOI PDF bioRxiv Preprint Code PhD Project
TopHat-Recondition: A post-processor for TopHat unmapped reads