#1 - First newsletter! Hypothesis in science, mutation signatures and more.
1 - Mutations and bioinformatics
The discovery of new mutations and how they affect patients has been heavily studied in cancer research, with new tools being developed for biologists to fully explore the mutational landscape. With this, bioinformaticians develop new methods to use the data in clinically relevant setting. The following review goes over the different ways of analysing mutation signatures, its importance and caveats.
Link to read the freely available paper: https://www.nature.com/articles/s41568-021-00377-7.epdf?sharing_token=wD6KXm0JQQvkN_uSvTYR89RgN0jAjWel9jnR3ZoTv0NrKahlU_oE65ZS_RrJsI8a_3B5S0Wp2h-q24tNvu5tj0xVP-Jng_ZClunT_JRkl4ZbMY8xXSq6gyty0odHv1eGCvNb90BjQM2TE5PCFeeUrkQ7sDRiIWtC5wQML7_Iw_Y%3D
2 - The role of hypothesis in science
When we are exploring a new dataset, should we do it without a hypothesis and discover something not known - for us - or should we let the hypothesis guide our exploration? The paper and blogpost below discuss these options giving some interesting thoughts on how we could approach data analysis in light of science.
Link to the paper: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02133-w
Link to the blogpost: https://statmodeling.stat.columbia.edu/2021/07/17/more-on-the-role-of-hypotheses-in-science/
3 - Connected papers: finding similar papers
Ever tried to find similar papers to the one you liked? Connected Papers helps you in this task. Based on a database of ~50000 papers, they can find similar papers based on co-citation and bibliographic coupling.
Link to the website: https://www.connectedpapers.com/
4 - Biology is more theoretical than physics
The paper and twitter thread discuss how biology could be considered more theoretical than physics using some examples. They discuss the importance of mathematical models in some aspects of biology and how they led to new experiments and discoveries.
Link to the paper: https://www.molbiolcell.org/doi/10.1091/mbc.e12-03-0227 Link to the twitter thread: https://twitter.com/ulkar_aghayeva/status/1420931956544622592
5 - Topology and cancer research: new opportunities
Topological data analysis (TDA) is a new field In mathematics that studies the shape of data. Usually algorithms from this area are trying to find topological hidden structures, such as connected components, holes and voids. The paper below is a review listing several results from TDA in cancer research.
Link to the paper: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btab553/6329825?login=true