21 citations · 33 across the 5 of their papers we have counts for
6 papers
Evolutionary Informed Translation from Protein to Nucleic Acid Sequence
Anna Hart, Mohammed El-Kebir, Huimin Zhao +1
The choice of nucleic acid sequence for a given protein strongly impacts function and is species-specific. Current protein-to-nucleic-acid translation models treat sequences in iso…
Multi-State Perfect Phylogeny Mixture Deconvolution and Applications to Cancer Sequencing
Mohammed El-Kebir, Gryte Satas, Layla Oesper +1
The reconstruction of phylogenetic trees from mixed populations has become important in the study of cancer evolution, as sequencing is often performed on bulk tumor tissue contain…
Solving the Maximum-Weight Connected Subgraph Problem to Optimality
Mohammed El-Kebir, Gunnar W. Klau
Given an undirected node-weighted graph, the Maximum-Weight Connected Subgraph problem (MWCS) is to identify a subset of nodes of maximalsum of weights that induce a connected subg…
eXamine: Exploring annotated modules in networks
Kasper Dinkla, Mohammed El-Kebir, Cristina-Iulia Bucur +4
Background: Biological networks have a growing importance for the interpretation of high-throughput omics data. Integrative network analysis makes use of statistical and combinator…
eXamine: a Cytoscape app for exploring annotated modules in networks
Kasper Dinkla, Mohammed El-Kebir, Cristina-Iulia Bucur +4
Background. Biological networks have growing importance for the interpretation of high-throughput "omics" data. Statistical and combinatorial methods allow to obtain mechanistic in…
Lagrangian Relaxation Applied to Sparse Global Network Alignment
Mohammed El-Kebir, Jaap Heringa, Gunnar W. Klau
Data on molecular interactions is increasing at a tremendous pace, while the development of solid methods for analyzing this network data is lagging behind. This holds in particula…