Alexander Schönhuth

According to our database1, Alexander Schönhuth authored at least 56 papers between 2002 and 2020.

Collaborative distances:



In proceedings 
PhD thesis 




Strain-Aware Assembly of Genomes from Mixed Samples Using Flow Variation Graphs.
Proceedings of the Research in Computational Molecular Biology, 2020

12 Grand Challenges in Single-Cell Data Science.
PeerJ Prepr., 2019

The Genetic Diversity of Viruses on a Graphical Map: Discovery of Resistant and Virulent Strains.
ERCIM News, 2019

Artificial Intelligence: Understanding Diseases that People Cannot Understand?
ERCIM News, 2019

A Drug Recommendation System (Dr.S) for cancer cell lines.
CoRR, 2019

Automatic discovery of 100-miRNA signature for cancer classification using ensemble feature selection.
BMC Bioinform., 2019

Using the structure of genome data in the design of deep neural networks for predicting amyotrophic lateral sclerosis from genotype.
Bioinform., 2019

Overlap graph-based generation of haplotigs for diploids and polyploids.
Bioinform., 2019

Full-length de novo viral quasispecies assembly through variation graph construction.
Bioinform., 2019

An image representation based convolutional network for DNA classification.
Proceedings of the 6th International Conference on Learning Representations, 2018

Metagenomic read clustering based on overlap graphs.
Proceedings of the 8th IEEE International Conference on Computational Advances in Bio and Medical Sciences, 2018

Dualities in Tree Representations.
Proceedings of the Annual Symposium on Combinatorial Pattern Matching, 2018

A probabilistic model to recover individual genomes from metagenomes.
PeerJ Comput. Sci., 2017

Genotyping inversions and tandem duplications.
Bioinform., 2017

Eliminating Blind Spots in Genetic Variant Discovery.
ERCIM News, 2016

On Hidden States in Quantum Random Walks.
CoRR, 2016

<i>Snowball</i>: strain aware gene assembly of metagenomes.
Bioinform., 2016

Next generation cluster editing.
PeerJ Prepr., 2015

WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads.
J. Comput. Biol., 2015

Genome sequence analysis with MonetDB - A case study on Ebola virus diversity.
Datenbank-Spektrum, 2015

Repeat- and error-aware comparison of deletions.
Bioinform., 2015

Viral Quasispecies Assembly via Maximal Clique Enumeration.
PLoS Comput. Biol., 2014

WhatsHap: Haplotype Assembly for Future-Generation Sequencing Reads.
Proceedings of the Research in Computational Molecular Biology, 2014

Mapping proteins in the presence of paralogs using units of coevolution.
BMC Bioinform., 2013

Discovering motifs that induce sequencing errors.
BMC Bioinform., 2013

MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels.
Bioinform., 2013

Observation and evolution of finite-dimensional Markov systems.
Proceedings of the 12th Cologne-Twente Workshop on Graphs and Combinatorial Optimization, 2013

CLEVER: clique-enumerating variant finder.
Bioinform., 2012

Mirroring co-evolving trees in the light of their topologies.
Bioinform., 2012

Efficient Tests for Equivalence of Hidden Markov Processes and Quantum Random Walks.
IEEE Trans. Inf. Theory, 2011

Classifying short gene expression time-courses with Bayesian estimation of piecewise constant functions.
Bioinform., 2011

Representations of Power Series over Word Algebras.
Proceedings of the 10th Cologne-Twente Workshop on graphs and combinatorial optimization. Extended Abstracts, 2011

MetMap Enables Genome-Scale Methyltyping for Determining Methylation States in Populations.
PLoS Comput. Biol., 2010

Towards Improved Assessment of Functional Similarity in Large-Scale Screens: A Study on Indel Length.
J. Comput. Biol., 2010

Discrete Quantum Markov Chains
CoRR, 2010

Inferring cancer subnetwork markers using density-constrained biclustering.
Bioinform., 2010

Pair HMM Based Gap Statistics for Re-evaluation of Indels in Alignments with Affine Gap Penalties.
Proceedings of the Algorithms in Bioinformatics, 10th International Workshop, 2010

Characterization of ergodic hidden Markov sources.
IEEE Trans. Inf. Theory, 2009

On analytic properties of entropy rate.
IEEE Trans. Inf. Theory, 2009

The Effect of Insertions and Deletions on Wirings in Protein-Protein Interaction Networks: A Large-Scale Study.
J. Comput. Biol., 2009

Constrained mixture estimation for analysis and robust classification of clinical time series.
Bioinform., 2009

Quantifying Systemic Evolutionary Changes by Color Coding Confidence-Scored PPI Networks.
Proceedings of the Algorithms in Bioinformatics, 9th International Workshop, 2009

Dense Graphlet Statistics of Protein Interaction and Random Networks.
Proceedings of the Biocomputing 2009: Proceedings of the Pacific Symposium, 2009

A simple and efficient solution of the identifiability problem for hidden Markov sources
CoRR, 2008

The ergodic decomposition of asymptotically mean stationary random sources
CoRR, 2008

On analytic properties of entropy rate of discrete random sources
CoRR, 2008

The Relation between Indel Length and Functional Divergence: A Formal Study.
Proceedings of the Algorithms in Bioinformatics, 8th International Workshop, 2008

Asymptotic Mean Stationarity of Sources With Finite Evolution Dimension.
IEEE Trans. Inf. Theory, 2007

Quantum Predictor Models.
Electron. Notes Discret. Math., 2006

Analyzing Gene Expression Time-Courses.
IEEE ACM Trans. Comput. Biol. Bioinform., 2005

A fractional programming approach to efficient DNA melting temperature calculation.
Bioinform., 2005

The Graphical Query Language: a tool for analysis of gene expression time-courses.
Bioinform., 2005

Note on Negative Probabilities and Observable Processes.
Proceedings of the Algorithms for Optimization with Incomplete Information, 2005

Robust inference of groups in gene expression time-courses using mixtures of HMMs.
Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004

Using hidden Markov models to analyze gene expression time course data.
Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology, June 29, 2003

ProClust: improved clustering of protein sequences with an extended graph-based approach.
Proceedings of the European Conference on Computational Biology (ECCB 2002), 2002