Alexander Schönhuth

According to our database, Alexander Schönhuth authored at least 59 papers between 2002 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2023

Predicting the prevalence of complex genetic diseases from individual genotype profiles using capsule networks.

Xiao Luo, Xiongbin Kang, Alexander Schönhuth

Nat. Mac. Intell., February, 2023

2022

Deep variational graph autoencoders for novel host-directed therapy options against COVID-19.

Sumanta Ray, Snehalika Lall, Anirban Mukhopadhyay, Sanghamitra Bandyopadhyay, Alexander Schönhuth

Artif. Intell. Medicine, 2022

2021

OGRE: Overlap Graph-based metagenomic Read clustEring.

Marleen Balvert, Xiao Luo, Ernestina Hauptfeld, Alexander Schönhuth, Bas E. Dutilh

Bioinform., 2021

2020

Strain-Aware Assembly of Genomes from Mixed Samples Using Flow Variation Graphs.

Jasmijn A. Baaijens, Leen Stougie, Alexander Schönhuth

Proceedings of the Research in Computational Molecular Biology, 2020

2019

12 Grand Challenges in Single-Cell Data Science.

David Laehnemann, Johannes Köster, Ewa Szczurek, Davis J. McCarthy, Stephanie C. Hicks, Mark D. Robinson, Catalina A. Vallejos, Niko Beerenwinkel, Kieran R. Campbell, Ahmed Mahfouz, Luca Pinello, Pavel Skums, Alexandros Stamatakis, Camille Stephan-Otto Attolini, Samuel Aparicio, Jasmijn A. Baaijens, Marleen Balvert, Buys de Barbanson, Antonio Cappuccio, Giacomo Corleone, Bas E. Dutilh, Maria Florescu, Victor Guryev, Rens Holmer, Katharina Jahn, Thamar Jessurun Lobo, Emma M. Keizer, Indu Khatri, Szymon M. Kielbasa, Jan O. Korbel, Alexey M. Kozlov, Tzu-Hao Kuo, Boudewijn P. F. Lelieveldt, Ion I. Mandoiu, John C. Marioni, Tobias Marschall, Felix Mölder, Amir Niknejad, Lukasz Raczkowski, Marcel J. T. Reinders, Jeroen de Ridder, Antoine-Emmanuel Saliba, Antonios Somarakis, Oliver Stegle, Fabian J. Theis, Huan Yang, Alex Zelikovsky, Alice C. McHardy, Benjamin J. Raphael, Sohrab P. Shah, Alexander Schönhuth

PeerJ Prepr., 2019

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

Alexander Schönhuth, Leen Stougie

ERCIM News, 2019

Artificial Intelligence: Understanding Diseases that People Cannot Understand?

Marleen Balvert, Alexander Schönhuth

ERCIM News, 2019

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

Marleen Balvert, Georgios Patoulidis, Andrew Patti, Timo M. Deist, Christine Eyler, Bas E. Dutilh, Alexander Schönhuth, David Craft

CoRR, 2019

Automatic discovery of 100-miRNA signature for cancer classification using ensemble feature selection.

Alejandro Lopez Rincon, Marlet Martínez-Archundia, Gustavo U. Martinez-Ruiz, Alexander Schönhuth, Alberto Paolo Tonda

BMC Bioinform., 2019

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

Bojian Yin, Marleen Balvert, Rick A. A. van der Spek, Bas E. Dutilh, Sander M. Bohté, Jan Veldink, Alexander Schönhuth

Bioinform., 2019

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

Jasmijn A. Baaijens, Alexander Schönhuth

Bioinform., 2019

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

Jasmijn A. Baaijens, Bastiaan Van der Roest, Johannes Köster, Leen Stougie, Alexander Schönhuth

Bioinform., 2019

2018

An image representation based convolutional network for DNA classification.

Bojian Yin, Marleen Balvert, Davide Zambrano, Alexander Schönhuth, Sander M. Bohté

Proceedings of the 6th International Conference on Learning Representations, 2018

Metagenomic read clustering based on overlap graphs.

Marleen Balvert, Alexander Schönhuth, Bas E. Dutilh

Proceedings of the 8th IEEE International Conference on Computational Advances in Bio and Medical Sciences, 2018

Dualities in Tree Representations.

Rayan Chikhi, Alexander Schönhuth

Proceedings of the Annual Symposium on Combinatorial Pattern Matching, 2018

2017

Genotyping inversions and tandem duplications.

Jana Ebler, Alexander Schönhuth, Tobias Marschall

Bioinform., 2017

2016

A probabilistic model to recover individual genomes from metagenomes.

Johannes Dröge, Alexander Schönhuth, Alice Carolyn McHardy

PeerJ Prepr., 2016

Eliminating Blind Spots in Genetic Variant Discovery.

Alexander Schönhuth, Tobias Marschall

ERCIM News, 2016

On Hidden States in Quantum Random Walks.

Ulrich Faigle, Alexander Schönhuth

CoRR, 2016

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

I. Gregor, Alexander Schönhuth, Alice Carolyn McHardy

Bioinform., 2016

2015

Next generation cluster editing.

Thomas Bellitto, Tobias Marschall, Alexander Schönhuth, Gunnar W. Klau

PeerJ Prepr., 2015

WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads.

Murray Patterson, Tobias Marschall, Nadia Pisanti, Leo van Iersel, Leen Stougie, Gunnar W. Klau, Alexander Schönhuth

J. Comput. Biol., 2015

Genome sequence analysis with MonetDB - A case study on Ebola virus diversity.

Robin Cijvat, Stefan Manegold, Martin L. Kersten, Gunnar W. Klau, Alexander Schönhuth, Tobias Marschall, Ying Zhang

Datenbank-Spektrum, 2015

Repeat- and error-aware comparison of deletions.

Roland Wittler, Tobias Marschall, Alexander Schönhuth, Veli Mäkinen

Bioinform., 2015

2014

Viral Quasispecies Assembly via Maximal Clique Enumeration.

Armin Töpfer, Tobias Marschall, Rowena A. Bull, Fabio Luciani, Alexander Schönhuth, Niko Beerenwinkel

PLoS Comput. Biol., 2014

WhatsHap: Haplotype Assembly for Future-Generation Sequencing Reads.

Murray Patterson, Tobias Marschall, Nadia Pisanti, Leo van Iersel, Leen Stougie, Gunnar W. Klau, Alexander Schönhuth

Proceedings of the Research in Computational Molecular Biology, 2014

2013

Mapping proteins in the presence of paralogs using units of coevolution.

Mohammed El-Kebir, Tobias Marschall, Inken Wohlers, Murray Patterson, Jaap Heringa, Alexander Schönhuth, Gunnar W. Klau

BMC Bioinform., 2013

Discovering motifs that induce sequencing errors.

Manuel Allhoff, Alexander Schönhuth, Marcel Martin, Ivan G. Costa, Sven Rahmann, Tobias Marschall

BMC Bioinform., 2013

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

Tobias Marschall, Iman Hajirasouliha, Alexander Schönhuth

Bioinform., 2013

Observation and evolution of finite-dimensional Markov systems.

Ulrich Faigle, Alexander Schönhuth

Proceedings of the 12th Cologne-Twente Workshop on Graphs and Combinatorial Optimization, 2013

2012

CLEVER: clique-enumerating variant finder.

Tobias Marschall, Ivan G. Costa, Stefan Canzar, Markus Bauer, Gunnar W. Klau, Alexander Schliep, Alexander Schönhuth

Bioinform., 2012

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

Iman Hajirasouliha, Alexander Schönhuth, David de Juan, Alfonso Valencia, Süleyman Cenk Sahinalp

Bioinform., 2012

2011

Efficient Tests for Equivalence of Hidden Markov Processes and Quantum Random Walks.

Ulrich Faigle, Alexander Schönhuth

IEEE Trans. Inf. Theory, 2011

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

Christoph Hafemeister, Ivan G. Costa, Alexander Schönhuth, Alexander Schliep

Bioinform., 2011

Representations of Power Series over Word Algebras.

Ulrich Faigle, Alexander Schönhuth

Proceedings of the 10th Cologne-Twente Workshop on graphs and combinatorial optimization. Extended Abstracts, 2011

2010

MetMap Enables Genome-Scale Methyltyping for Determining Methylation States in Populations.

Meromit Singer, Dario Boffelli, Joseph Dhahbi, Alexander Schönhuth, Gary P. Schroth, David I. K. Martin, Lior Pachter

PLoS Comput. Biol., 2010

Towards Improved Assessment of Functional Similarity in Large-Scale Screens: A Study on Indel Length.

Alexander Schönhuth, Raheleh Salari, Fereydoun Hormozdiari, Artem Cherkasov, Süleyman Cenk Sahinalp

J. Comput. Biol., 2010

Discrete Quantum Markov Chains

Ulrich Faigle, Alexander Schönhuth

CoRR, 2010

Inferring cancer subnetwork markers using density-constrained biclustering.

Phuong Dao, Recep Colak, Raheleh Salari, Flavia Moser, Elai Davicioni, Alexander Schönhuth, Martin Ester

Bioinform., 2010

Pair HMM Based Gap Statistics for Re-evaluation of Indels in Alignments with Affine Gap Penalties.

Alexander Schönhuth, Raheleh Salari, Süleyman Cenk Sahinalp

Proceedings of the Algorithms in Bioinformatics, 10th International Workshop, 2010

2009

Characterization of ergodic hidden Markov sources.

Alexander Schönhuth, Herbert Jaeger

IEEE Trans. Inf. Theory, 2009

On analytic properties of entropy rate.

Alexander Schönhuth

IEEE Trans. Inf. Theory, 2009

The Effect of Insertions and Deletions on Wirings in Protein-Protein Interaction Networks: A Large-Scale Study.

Fereydoun Hormozdiari, Raheleh Salari, Michael Hsing, Alexander Schönhuth, Simon K. Chan, Süleyman Cenk Sahinalp, Artem Cherkasov

J. Comput. Biol., 2009

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

Ivan G. Costa, Alexander Schönhuth, Christoph Hafemeister, Alexander Schliep

Bioinform., 2009

Quantifying Systemic Evolutionary Changes by Color Coding Confidence-Scored PPI Networks.

Phuong Dao, Alexander Schönhuth, Fereydoun Hormozdiari, Iman Hajirasouliha, Süleyman Cenk Sahinalp, Martin Ester

Proceedings of the Algorithms in Bioinformatics, 9th International Workshop, 2009

Dense Graphlet Statistics of Protein Interaction and Random Networks.

Recep Colak, Fereydoun Hormozdiari, Flavia Moser, Alexander Schönhuth, J. Holman, Martin Ester, Süleyman Cenk Sahinalp

Proceedings of the Biocomputing 2009: Proceedings of the Pacific Symposium, 2009

2008

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

Alexander Schönhuth

CoRR, 2008

The ergodic decomposition of asymptotically mean stationary random sources

Alexander Schönhuth

CoRR, 2008

On analytic properties of entropy rate of discrete random sources

Alexander Schönhuth

CoRR, 2008

The Relation between Indel Length and Functional Divergence: A Formal Study.

Raheleh Salari, Alexander Schönhuth, Fereydoun Hormozdiari, Artem Cherkasov, Süleyman Cenk Sahinalp

Proceedings of the Algorithms in Bioinformatics, 8th International Workshop, 2008

2007

Asymptotic Mean Stationarity of Sources With Finite Evolution Dimension.

Ulrich Faigle, Alexander Schönhuth

IEEE Trans. Inf. Theory, 2007

2006

Quantum Predictor Models.

Ulrich Faigle, Alexander Schönhuth

Electron. Notes Discret. Math., 2006

2005

Analyzing Gene Expression Time-Courses.

Alexander Schliep, Ivan G. Costa, Christine Steinhoff, Alexander Schönhuth

IEEE ACM Trans. Comput. Biol. Bioinform., 2005

A fractional programming approach to efficient DNA melting temperature calculation.

Markus Leber, Lars Kaderali, Alexander Schönhuth, Rainer Schrader

Bioinform., 2005

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

Ivan G. Costa, Alexander Schönhuth, Alexander Schliep

Bioinform., 2005

Note on Negative Probabilities and Observable Processes.

Ulrich Faigle, Alexander Schönhuth

Proceedings of the Algorithms for Optimization with Incomplete Information, 2005

2004

Robust inference of groups in gene expression time-courses using mixtures of HMMs.

Alexander Schliep, Christine Steinhoff, Alexander Schönhuth

Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004

2003

Using hidden Markov models to analyze gene expression time course data.

Alexander Schliep, Alexander Schönhuth, Christine Steinhoff

Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology, June 29, 2003

2002

ProClust: improved clustering of protein sequences with an extended graph-based approach.

P. Pipenbacher, Alexander Schliep, Sebastian Schneckener, Alexander Schönhuth, Dietmar Schomburg, Rainer Schrader

Proceedings of the European Conference on Computational Biology (ECCB 2002), 2002