Miranda D. Stobbe
A5006687544- Cancer Genomics and Diagnostics
- Bioinformatics and Genomic Networks
- Genomics and Phylogenetic Studies
- Microbial Metabolic Engineering and Bioproduction
- Genomics and Chromatin Dynamics
- Genetic factors in colorectal cancer
- Evolution and Genetic Dynamics
- Genetics, Bioinformatics, and Biomedical Research
- RNA modifications and cancer
- Cancer-related molecular mechanisms research
- Chromosomal and Genetic Variations
- Nutrition, Genetics, and Disease
- Epigenetics and DNA Methylation
- Metabolomics and Mass Spectrometry Studies
- Genomics and Rare Diseases
- Genomic variations and chromosomal abnormalities
- Cancer, Hypoxia, and Metabolism
- RNA Research and Splicing
- Mitochondrial Function and Pathology
- Scientific Computing and Data Management
- Telomeres, Telomerase, and Senescence
- Biofuel production and bioconversion
- Lung Cancer Treatments and Mutations
- Gene expression and cancer classification
- DNA Repair Mechanisms
Universitat Pompeu Fabra
2017-2023
Centre for Genomic Regulation
2017-2022
University of Amsterdam
2011-2015
Amsterdam UMC Location University of Amsterdam
2011-2015
Netherlands Bioinformatics Centre
2013-2014
Abstract In cancer, the primary tumour’s organ of origin and histopathology are strongest determinants its clinical behaviour, but in 3% cases a patient presents with metastatic tumour no obvious primary. Here, as part ICGC/TCGA Pan-Cancer Analysis Whole Genomes (PCAWG) Consortium , we train deep learning classifier to predict cancer type based on patterns somatic passenger mutations detected whole genome sequencing (WGS) 2606 tumours representing 24 common types produced by PCAWG...
Abstract Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, most cancers outside the sex organs. Efforts to link these clinical specific molecular features focused on somatic mutations within coding regions genome. Here we report a pan-cancer analysis whole genomes 1983 tumours 28 subtypes as part ICGC/TCGA Pan-Cancer Analysis Whole Genomes (PCAWG) Consortium. We both confirm results exome studies, also uncover previously undescribed...
Multiple pathway databases are available that describe the human metabolic network and have proven their usefulness in many applications, ranging from analysis interpretation of high-throughput data to use as a reference repository. However, so far various networks described by these not been systematically compared contrasted, nor has extent which they differ quantified. For researcher using for particular analyses metabolism, it is crucial know differences content underlying causes....
The sheer size of the human genome makes it improbable that identical somatic mutations at exact same position are observed in multiple tumours solely by chance. scarcity cancer driver also precludes positive selection as sole explanation. Therefore, recurrent may be highly informative characteristics mutational processes. To explore potential, we use recurrence a starting point to cluster >2,500 whole genomes pan-cancer cohort. We describe each with 13 recurrence-based and 29 general...
To collect the ever-increasing yet scattered knowledge on metabolism, multiple pathway databases like Kyoto Encyclopedia of Genes and Genomes have been created. A complete accurate description metabolic network for human other organisms is essential to foster new biological discoveries. Previous research has shown, however, that level agreement among surprisingly low. We investigated whether lack consensus can be explained by an inaccurate representation described in scientific literature....
Abstract Background The metabolic network of H. sapiens and many other organisms is described in multiple pathway databases. level agreement between these descriptions, however, has proven to be low. We can use different descriptions our advantage by identifying conflicting information combining their knowledge into a single, more accurate, complete description. This task is, far from trivial. Results introduce the concept Consensus Conflict Cards (C 2 Cards) provide concise overviews what...
When meeting someone for the first time—whether another PhD student, or Founding Editor-in-chief of PLOS Computational Biology—nothing breaks ice like eating pancakes having drinks together. A social atmosphere provides a relaxed, informal environment where people can connect, share ideas, and form collaborations. Being able to build network thrive in is crucial successful scientific career. This article highlights importance bringing together who speak same language an setting. Using...
Abstract Bringing together cancer genomes from different projects increases power and allows the investigation of pan-cancer, molecular mechanisms. However, working with whole sequenced over several years in sequencing centres requires a framework to compare quality these sequences. We used Pan-Cancer Analysis Whole Genomes cohort as test case construct such framework. This contains 2832 donors 18 centres. developed non-redundant set five control (QC) measurements establish star rating...
Abstract Working with cancer whole genomes sequenced over a period of many years in different sequencing centres requires validated framework to compare the quality these sequences. The Pan-Cancer Analysis Whole Genomes (PCAWG) International Cancer Genome Consortium (ICGC), project cohort 2800 donors provided us challenge assessing genome A non-redundant set five control (QC) measurements were assembled and used establish star rating system. These QC measures reflect known differences...
Sharing results, techniques, and challenges is paramount to advance our understanding of any field science. In the scientific community this exchange ideas mainly made possible through national international conferences. Scientists have opportunity showcase their work, receive feedback, improve presentation skills. However, conferences can be large intimidating for young researchers. addition, many more prestigious conferences, very high number submissions low selection rate are major...