Direct link to our Youtube channel: ITN CONTRA.
Interviews
- Jeffrey Townsend. Jeffrey Townsend’s Top Ten Advice for LifeSci PhD Students.
Final CONTRA conference, Andermatt 2022
- Sarah Aitken. Re-running cancer evolution in vivo to disentangle DNA damage and repair.
- Jose Bonet Giner. Direct detection of different sources of DNA damage through Nanopore sequencing.
- Nico Borgsmüller. Single-cell DNA-seq data reveals deviations from clock-like evolution in cancerous and healthy tissue.
- Yeman Brhane Hagos. Deep learning to decipher the multispectral immune landscape of follicular lymphoma.
- Mandi Chen. Detecting DNA Base Modifications on Nanopore Sequencing Data.
- Fabian Crespo. Estimation of growth rate and age of somatic clones from single-cell DNA-seq data.
- Aedin Culhane. Dimension Reduction & integration of single cell data.
- Arthur Dondi. Single-cell transcript isoform sequencing for precision oncology.
- Senbai Kang. SIEVE: joint inference of single-nucleotide variants and cell phylogeny from single-cell DNA sequencing data.
- Hanna Kranas. Genomic segments with different UV DNA damage repair dynamics.
- Núria López-Bigas. Studying the mutagenic and cancer promotion effect of chemotherapies.
- Magda Markowska. CONET: Copy number event tree model of evolutionary tumor history for single-cell data.
- Mathilde Meyenberg. Obesity Associated Cancers – A DNA Repair Perspective.
- Hrvoje Misetic. Identification and impact of clonal and subclonal driver alterations during cancer progression at single-patient resolution.
- Mohammadreza Mohaghegh Neyshaboouri. ToMExO: Simultaneous inference of mutual exclusivity and progression patterns among oncogenes.
- David Posada. Tumor phylogeography and phylodynamics from single-cells.
- María Rodrígues Martínez. AI-driven approaches for cancer personalized medicine.
- Monica Valecha. Benchmarking single-cell DNA somatic variant callers.
Spatial Models of Tumours, London (virtual event) 2020
- Binzhi Qian. The role of macrophages in cancer metastasis and therapy resistance.
- Marcel Gehrung. Early disease detection and the art of asking clinical questions.
- María Rodríguez Martínez. DEPICTION: extracting insight from deep learning models in computational biology.
- Robert Noble. Spatial models for forecasting tumour growth and survival.
- Stephanie Ling. Integrated Imaging and Analysis to understand the biological complexity of tissues.
Cancer Biology and Treatment, Cambridge 2019
- Peter Bankhead. QuPath: Open source bioimage analysis (not just) for pathology.
- Daniel Hübschmann. Homologous recombination, BRCAness and the TOP-ART trial.
- Ultan McDermott. Cancer Pharmacogenomics.
- Jacob Scott. Controlling disease evolution: models and experiments to understand timescales, trajectories and outcomes.
- Giovanni Tonon. From targeted therapies to cancer evolution: a new paradigm to tackle cancer resistance.
Models of Evolution Workshop, Barcelona 2019
Lectures
- Mar Albà. De novo proteins in evolution and disease.
- Niko Beerenwinkel. The intra-tumor phylogeny problem.
- Francesca Ciccarelli. Systems biology to study cancer evolution.
- Holger Heyn. Single Cell Genomics: From Sample to Cell Atlas.
- Núria López-Bigas. Understanding mutational processes to understand genome evolution.
- David Posada. Inferring phylogenies from tumor NGS data.
- Ricard Solé. The evolutionary dynamics of cancer.
Tutorial
- Andrew Roth. Part 1: Introduction to probabilistic modelling
- Andrew Roth. Part 2: Inferring clonal population structure from SNV data
- Andrew Roth. Part 3: Copy number variation
- Andrew Roth. Part 4: Phylogenetics
- Andrew Roth. Part 5: Advanced inference methods
Handling Single Cell Data Workshop, Warsaw 2018
Lectures
- Michaela Asp. Spatial Transcriptomics : Bridging histology and RNA sequencing.
- Alexandra Chloé‐Villani. Unraveling new insights into human immune system landscape one cell at the time.
- Anna Cuomo. Genetic analysis of differentiating cells using single-cell RNA-seq.
- Aleksandra Deczkowska. The power of ONE: Immunology in the age of single cell genomics.
- Peter Kharchenko. Transcriptional Dynamics with Single-Cell Data.
- Aleksandra Kolodziejczyk. Single cell RNA sequencing technologies.
- Jan Korbel. Single cell & big data approaches to understanding genome variation in normal individuals & disease.
- Jonas Maaskola. Charting Tissue Expression Anatomy by Spatial Transcriptome Deconvolution.
- Alexander Schoenhuth. Discovering somatic variants in single cells.
Tutorial
The CONTRA ESR students were given a practical tutorial in handling single-cell data. We recorded the presentations given by the tutors.
- Anna Cuomo & Ximena Ibarra. Part 1: DNA sequencing and experimental design.
- Anna Cuomo & Ximena Ibarra. Part 2: Next‐generation sequencing data processing.
- Anna Cuomo & Ximena Ibarra. Part 3: Bulk and single‐cell RNA‐seq experiments and batch correction methods.
- Anna Cuomo & Ximena Ibarra. Part 4: Single-cell RNA-seq data analysis – QC and technical variance.
- Anna Cuomo & Ximena Ibarra. Part 5: Single-cell RNA-seq data analysis – clustering and dimensionality reduction.
- Anna Cuomo & Ximena Ibarra. Part 6: Single-cell RNA-seq data analysis – differential expression and dynamic processes.
Downloads: Course materials. Schedule. Slides.
ITN-CONTRA Kickoff, Bertinoro 2018
- Valentina Boeva. Discovery of two states of neuroblastoma cells via the analysis of super-enhancer landscape.
- Brian Cleary. Understanding biological systems with compressive statements.
- Carlo Maley. Evolutionary Approaches to the Big Questions in Cancer.
- Florian Markowetz. A continuum of genomes.
- Nicholas McGranahan. Lung Cancer Evolution and Immune Escape.
- Quaid Morris. Making sense of the “noise” in cancer data.
- Ben Raphael. Inferring Cellular Migrations in Metastatic Cancers.
- Johannes Reiter. Evolutionary dynamics of cancer initiation and metastases.
- Russell Schwartz. Reconstructing tumor evolution and progression in structurally variant cancer cells.
- Sohrab Shah. Determinants of cancer evolution.
- Ewa Szczurek. Introduction to probabilistic graphical models part 1.
- Ewa Szczurek. Introduction to probabilistic graphical models part 2.
- Jeffrey Townsend. Effect sizes of somatic mutations.
- Bartłomiej Wacław. Intra-tumour heterogeneity – implications for treatment.
- David Wedge. Cancer evolution: Copy number and metastatis.
- Benjamin Werner. Population genetics of intratumour heterogeneity.