200 citations · 485 across the 11 of their papers we have counts for
11 papers
Genomic reproducibility in the bioinformatics era
Pelin Icer Baykal, Paweł P. Łabaj, Florian Markowetz +4
In biomedical research, validation of a new scientific discovery is tied to the reproducibility of its experimental results. However, in genomics, the definition and implementation…
A phylogenetic latent feature model for clonal deconvolution
Francesco Marass, Florent Mouliere, Ke Yuan +2
Tumours develop in an evolutionary process, in which the accumulation of mutations produces subpopulations of cells with distinct mutational profiles, called clones. This process l…
SANTA: quantifying the functional content of molecular networks
Alex J. Cornish, Florian Markowetz
Linking networks of molecular interactions to cellular functions and phenotypes is a key goal in systems biology. Here, we adapt concepts of spatial statistics to assess the functi…
Estimating cellular pathways from an ensemble of heterogeneous data sources
Alexander Franks, Florian Markowetz, Edoardo Airoldi
Building better models of cellular pathways is one of the major challenges of systems biology and functional genomics. There is a need for methods to build on established expert kn…
Reconstructing evolving signalling networks by hidden Markov nested effects models
Xin Wang, Ke Yuan, Christoph Hellmayr +2
Inferring time-varying networks is important to understand the development and evolution of interactions over time. However, the vast majority of currently used models assume direc…
Phylogenetic quantification of intra-tumour heterogeneity
Roland F Schwarz, Anne Trinh, Botond Sipos +3
Background: Intra-tumour heterogeneity (ITH) is the result of ongoing evolutionary change within each cancer. The expansion of genetically distinct sub-clonal populations may expla…
Evolutionary distances in the twilight zone -- a rational kernel approach
Roland F. Schwarz, William Fletcher, Frank Förster +4
Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing s…
Mapping Dynamic Histone Acetylation Patterns to Gene Expression in Nanog-depleted Murine Embryonic Stem Cells
Florian Markowetz, Klaas W Mulder, Edoardo M Airoldi +2
Embryonic stem cells (ESC) have the potential to self-renew indefinitely and to differentiate into any of the three germ layers. The molecular mechanisms for self-renewal, maintena…
A sparse regulatory network of copy-number driven expression reveals putative breast cancer oncogenes
Yinyin Yuan, Christina Curtis, Carlos Caldas +1
The influence of DNA cis-regulatory elements on a gene's expression has been intensively studied. However, little is known about expressions driven by trans-acting DNA hotspots. DN…
How to understand the cell by breaking it: network analysis of gene perturbation screens
Florian Markowetz
Modern high-throughput gene perturbation screens are key technologies at the forefront of genetic research. Combined with rich phenotypic descriptors they enable researchers to obs…
Structure Learning in Nested Effects Models
Achim Tresch, Florian Markowetz
Nested Effects Models (NEMs) are a class of graphical models introduced to analyze the results of gene perturbation screens. NEMs explore noisy subset relations between the high-di…