Eight years after its intial release we are more than proud to announce that the MEDICC2 algorithm and paper for inferring cancer evolution from somatic copy-number alterations is now published online at Genome Biology.
MEDICC2 is the leading algorithm for phylogenetic reconstruction from and quantification of chromosomal instability. It is based on an efficient finite-state transducer framework which, together with integrated parallelisations, allows accurate phylogentic inference even for single-cell data with thousands of cells.
MEDICC2 not only outperforms the original implementation in speed by orders of magnitude, but also, as the first and only algorithm in the field, allows the accurate detection of clonal and subclonal whole-genome doubling events.
The Schwarzlab is welcoming several new members to our group at our site in Cologne at the ICCB!
Daniel Schütte is a clinician scientist who is interested in molecular biomarkers and cancer early detection and prevention and already joined some months ago.
Felix Schifferdecker and Selina Wächter are two MD students who will be writing their dissertation in the lab in parallel to their MD coursework and clinical pratice over the next years. Felix will be working on simulating chromosomal aberrations in cancer evolution and Selina will be investigating methods for detecting selection in cancer phylogenies.
Finally, we would like to welcome Teodora Bucaciuc, who has joined the lab as a research associate, developing pipelines for copy-number analysis and investigating the co-evolution of genomic and epignomic alterations in cancer. Welcome all, great to have you on board!
We are incredibly thrilled that Julia Markowski successfully defended her PhD on October 21, 2022 at the Berlin Institute for Molecular Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association.
Her PhD thesis is titled "Inferring haplotype-specific chromatin conformation using Genome Architecture Mapping" and she will receive her PhD from the Humboldt University Berlin in the near future.
After completing her Masters degree in Bioinformatics at the Max-Planck-Institute for Molecular Genetics and the University of Potsdam, Julia joined our lab in May 2017 on a MDC PhD Fellowship. She was subsequently supported by the DFG priority programme SPP2202 "Chromatin Architecture in Health and Disease".
She is now moving to Boston as a postdoctoral fellow in the Park Lab at Harvard Medical School and we wish her all the best for the future!