28 citations · 48 across the 12 of their papers we have counts for
15 papers
CancerZigZag: Iterative Seed-Anchored Diffusion for Generative Modeling of Single-Cell State Transitions
Johannes Schlüter, Alexander Schönhuth
Single-cell cancer datasets are predominantly cross-sectional and rarely provide paired or longitudinal observations linking individual healthy-like cells to tumor-associated state…
Retracing the Process of Translation: Proteome-wide mapping of stable transcriptomic predictors of protein abundance in cancer cell lines
Johannes Schlüter, Alexander Schönhuth
Understanding the relationship between gene expression and protein abundance is central to molecular and systems biology. While gene expression reflects transcriptional activity, p…
A Drug Recommendation System (Dr.S) for cancer cell lines
Marleen Balvert, Georgios Patoulidis, Andrew Patti +5
Personalizing drug prescriptions in cancer care based on genomic information requires associating genomic markers with treatment effects. This is an unsolved challenge requiring ge…
An image representation based convolutional network for DNA classification
Bojian Yin, Marleen Balvert, Davide Zambrano +2
The folding structure of the DNA molecule combined with helper molecules, also referred to as the chromatin, is highly relevant for the functional properties of DNA. The chromatin…
On Hidden States in Quantum Random Walks
Ulrich Faigle, Alexander Schönhuth
It was recently pointed out that identifiability of quantum random walks and hidden Markov processes underlie the same principles. This analogy immediately raises questions on the…
Snowball: Strain aware gene assembly of Metagenomes
I. Gregor, A. Schönhuth, A. C. McHardy
Gene assembly is an important step in functional analysis of shotgun metagenomic data. Nonetheless, strain aware assembly remains a challenging task, as current assembly tools ofte…
Next Generation Cluster Editing
Thomas Bellitto, Tobias Marschall, Alexander Schönhuth +1
This work aims at improving the quality of structural variant prediction from the mapped reads of a sequenced genome. We suggest a new model based on cluster editing in weighted gr…
CLEVER: Clique-Enumerating Variant Finder
Tobias Marschall, Ivan Costa, Stefan Canzar +4
Next-generation sequencing techniques have facilitated a large scale analysis of human genetic variation. Despite the advances in sequencing speeds, the computational discovery of…
Mirroring co-evolving trees in the light of their topologies
Iman Hajirasouliha, Alexander Schönhuth, David Juan +2
Determining the interaction partners among protein/domain families poses hard computational problems, in particular in the presence of paralogous proteins. Available approaches aim…
Generic identification of binary-valued hidden Markov processes
Alexander Schönhuth
The generic identification problem is to decide whether a stochastic process is a hidden Markov process and if yes to infer its parameters for all but a subset of parametri…
A Markovian Model for Joint Observations, Bell's Inequality and Hidden States
Ulrich Faigle, Alexander Schönhuth
While the standard approach to quantum systems studies length preserving linear transformations of wave functions, the Markov picture focuses on trace preserving operators on the s…
Pair HMM based gap statistics for re-evaluation of indels in alignments with affine gap penalties: Extended Version
Alexander Schönhuth, Raheleh Salari, S. Cenk Sahinalp
Although computationally aligning sequence is a crucial step in the vast majority of comparative genomics studies our understanding of alignment biases still needs to be improved.…
Efficient tests for equivalence of hidden Markov processes and quantum random walks
Ulrich Faigle, Alexander Schönhuth
While two hidden Markov process (HMP) resp. quantum random walk (QRW) parametrizations can differ from one another, the stochastic processes arising from them can be equivalent. He…
The ergodic decomposition of asymptotically mean stationary random sources
Alexander Schoenhuth
It is demonstrated how to represent asymptotically mean stationary (AMS) random sources with values in standard spaces as mixtures of ergodic AMS sources. This an extension of the…
On analytic properties of entropy rate
Alexander Schönhuth
Entropy rate is a real valued functional on the space of discrete random sources which lacks a closed formula even for subclasses of sources which have intuitive parameterizations.…