Alexander Schönhuth

71 papers B 4C 7Misc 1Journal 53Unranked 6
YearRankTypeTitle / Venue / Authors
2025 C conf
DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs.
WABI
Ali Ghaffaari, Alexander Schönhuth, Tobias Marschall
2025 J jnl
From data chaos to precision medicine.
Nat. Mac. Intell.
Alexander Schönhuth
2025 J jnl
Generating synthetic genotypes using diffusion models.
Bioinform.
Philip Kenneweg, Raghuram Dandinasivara, Xiao Luo, Barbara Hammer, Alexander Schönhuth
2025 J jnl
Genetic features for drug responses in cancer - Investigating an ensemble-feature-selection approach.
Comput. Biol. Medicine
Johannes Schlüter, Alexander Schönhuth
2024 J jnl
Computing linkage disequilibrium aware genome embeddings using autoencoders.
Bioinform.
Gizem Tas, Timo Westerdijk, Eric O. Postma, Project MinE ALS GWAS Consortium, Jan H. Veldink, Alexander Schönhuth, Marleen Balvert
2024 J jnl
Generating Synthetic Genotypes using Diffusion Models.
CoRR
Philip Kenneweg, Raghuram Dandinasivara, Xiao Luo, Barbara Hammer, Alexander Schönhuth
2023 J jnl
Predicting the prevalence of complex genetic diseases from individual genotype profiles using capsule networks.
Nat. Mac. Intell.
Xiao Luo, Xiongbin Kang, Alexander Schönhuth
2022 J jnl
Deep variational graph autoencoders for novel host-directed therapy options against COVID-19.
Artif. Intell. Medicine
Sumanta Ray, Snehalika Lall, Anirban Mukhopadhyay, Sanghamitra Bandyopadhyay, Alexander Schönhuth
2021 J jnl
OGRE: Overlap Graph-based metagenomic Read clustEring.
Bioinform.
Marleen Balvert, Xiao Luo, Ernestina Hauptfeld, Alexander Schönhuth, Bas E. Dutilh
2020 B conf
Strain-Aware Assembly of Genomes from Mixed Samples Using Flow Variation Graphs.
RECOMB
Jasmijn A. Baaijens, Leen Stougie, Alexander Schönhuth
2019 J jnl
12 Grand Challenges in Single-Cell Data Science.
PeerJ Prepr.
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
2019 J jnl
A Drug Recommendation System (Dr.S) for cancer cell lines.
CoRR
Marleen Balvert, Georgios Patoulidis, Andrew Patti, Timo M. Deist, Christine Eyler, Bas E. Dutilh, Alexander Schönhuth, David Craft
2019 J jnl
Artificial Intelligence: Understanding Diseases that People Cannot Understand?
ERCIM News
Marleen Balvert, Alexander Schönhuth
2019 J jnl
Automatic discovery of 100-miRNA signature for cancer classification using ensemble feature selection.
BMC Bioinform.
Alejandro Lopez Rincon, Marlet Martínez-Archundia, Gustavo U. Martinez-Ruiz, Alexander Schönhuth, Alberto Paolo Tonda
2019 J jnl
Full-length de novo viral quasispecies assembly through variation graph construction.
Bioinform.
Jasmijn A. Baaijens, Bastiaan Van der Roest, Johannes Köster, Leen Stougie, Alexander Schönhuth
2019 J jnl
Overlap graph-based generation of haplotigs for diploids and polyploids.
Bioinform.
Jasmijn A. Baaijens, Alexander Schönhuth
2019 J jnl
The Genetic Diversity of Viruses on a Graphical Map: Discovery of Resistant and Virulent Strains.
ERCIM News
Alexander Schönhuth, Leen Stougie
2019 J jnl
Using the structure of genome data in the design of deep neural networks for predicting amyotrophic lateral sclerosis from genotype.
Bioinform.
Bojian Yin, Marleen Balvert, Rick A. A. van der Spek, Bas E. Dutilh, Sander M. Bohté, Jan Veldink, Alexander Schönhuth
2018 — conf
An image representation based convolutional network for DNA classification.
ICLR (Poster)
Bojian Yin, Marleen Balvert, Davide Zambrano, Alexander Schönhuth, Sander M. Bohté
2018 J jnl
An image representation based convolutional network for DNA classification.
CoRR
Bojian Yin, Marleen Balvert, Davide Zambrano, Alexander Schönhuth, Sander M. Bohté
2018 B conf
Dualities in Tree Representations.
CPM
Rayan Chikhi, Alexander Schönhuth
2018 J jnl
Dualities in Tree Representations.
CoRR
Rayan Chikhi, Alexander Schönhuth
2018 — conf
Metagenomic read clustering based on overlap graphs.
ICCABS
Marleen Balvert, Alexander Schönhuth, Bas E. Dutilh
2017 J jnl
A probabilistic model to recover individual genomes from metagenomes.
PeerJ Comput. Sci.
Johannes Dröge, Alexander Schönhuth, Alice C. McHardy
2017 J jnl
Genotyping inversions and tandem duplications.
Bioinform.
Jana Ebler, Alexander Schönhuth, Tobias Marschall
2016 J jnl
A probabilistic model to recover individual genomes from metagenomes.
PeerJ Prepr.
Johannes Dröge, Alexander Schönhuth, Alice Carolyn McHardy
2016 J jnl
Eliminating Blind Spots in Genetic Variant Discovery.
ERCIM News
Alexander Schönhuth, Tobias Marschall
2016 J jnl
On Hidden States in Quantum Random Walks.
CoRR
Ulrich Faigle, Alexander Schönhuth
2015 J jnl
Genome sequence analysis with MonetDB - A case study on Ebola virus diversity.
Datenbank-Spektrum
Robin Cijvat, Stefan Manegold, Martin L. Kersten, Gunnar W. Klau, Alexander Schönhuth, Tobias Marschall, Ying Zhang
2015 — conf
Genome sequence analysis with monetdb: a case study on ebola virus diversity.
BTW Workshops
Robin Cijvat, Stefan Manegold, Martin L. Kersten, Gunnar W. Klau, Alexander Schönhuth, Tobias Marschall, Ying Zhang
2015 J jnl
Next generation cluster editing.
PeerJ Prepr.
Thomas Bellitto, Tobias Marschall, Alexander Schönhuth, Gunnar W. Klau
2015 J jnl
Repeat- and error-aware comparison of deletions.
Bioinform.
Roland Wittler, Tobias Marschall, Alexander Schönhuth, Veli Mäkinen
2015 J jnl
WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads.
J. Comput. Biol.
Murray Patterson, Tobias Marschall, Nadia Pisanti, Leo van Iersel, Leen Stougie, Gunnar W. Klau, Alexander Schönhuth
2014 B conf
Viral Quasispecies Assembly via Maximal Clique Enumeration.
RECOMB
Armin Töpfer, Tobias Marschall, Rowena A. Bull, Fabio Luciani, Alexander Schönhuth, Niko Beerenwinkel
2014 J jnl
Viral Quasispecies Assembly via Maximal Clique Enumeration.
PLoS Comput. Biol.
Armin Töpfer, Tobias Marschall, Rowena A. Bull, Fabio Luciani, Alexander Schönhuth, Niko Beerenwinkel
2014 B conf
WhatsHap: Haplotype Assembly for Future-Generation Sequencing Reads.
RECOMB
Murray Patterson, Tobias Marschall, Nadia Pisanti, Leo van Iersel, Leen Stougie, Gunnar W. Klau, Alexander Schönhuth
2013 J jnl
Discovering motifs that induce sequencing errors.
BMC Bioinform.
Manuel Allhoff, Alexander Schönhuth, Marcel Martin, Ivan G. Costa, Sven Rahmann, Tobias Marschall
2013 J jnl
MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels.
Bioinform.
Tobias Marschall, Iman Hajirasouliha, Alexander Schönhuth
2013 J jnl
Mapping proteins in the presence of paralogs using units of coevolution.
BMC Bioinform.
Mohammed El-Kebir, Tobias Marschall, Inken Wohlers, Murray Patterson, Jaap Heringa, Alexander Schönhuth, Gunnar W. Klau
2013 J jnl
Next Generation Cluster Editing.
CoRR
Thomas Bellitto, Tobias Marschall, Alexander Schönhuth, Gunnar W. Klau
2013 C conf
Observation and evolution of finite-dimensional Markov systems.
CTW
Ulrich Faigle, Alexander Schönhuth
2012 J jnl
CLEVER: clique-enumerating variant finder.
Bioinform.
Tobias Marschall, Ivan G. Costa, Stefan Canzar, Markus Bauer, Gunnar W. Klau, Alexander Schliep, Alexander Schönhuth
2012 J jnl
Mirroring co-evolving trees in the light of their topologies.
Bioinform.
Iman Hajirasouliha, Alexander Schönhuth, David de Juan, Alfonso Valencia, Süleyman Cenk Sahinalp
2011 J jnl
Classifying short gene expression time-courses with Bayesian estimation of piecewise constant functions.
Bioinform.
Christoph Hafemeister, Ivan G. Costa, Alexander Schönhuth, Alexander Schliep
2011 J jnl
Efficient Tests for Equivalence of Hidden Markov Processes and Quantum Random Walks.
IEEE Trans. Inf. Theory
Ulrich Faigle, Alexander Schönhuth
2011 J jnl
Mirroring co-evolving trees in the light of their topologies
CoRR
Iman Hajirasouliha, Alexander Schönhuth, David de Juan, Alfonso Valencia, Süleyman Cenk Sahinalp
2011 C conf
Representations of Power Series over Word Algebras.
CTW
Ulrich Faigle, Alexander Schönhuth
2010 J jnl
Discrete Quantum Markov Chains
CoRR
Ulrich Faigle, Alexander Schönhuth
2010 J jnl
Inferring cancer subnetwork markers using density-constrained biclustering.
Bioinform.
Phuong Dao, Recep Colak, Raheleh Salari, Flavia Moser, Elai Davicioni, Alexander Schönhuth, Martin Ester
2010 J jnl
MetMap Enables Genome-Scale Methyltyping for Determining Methylation States in Populations.
PLoS Comput. Biol.
Meromit Singer, Dario Boffelli, Joseph Dhahbi, Alexander Schönhuth, Gary P. Schroth, David I. K. Martin, Lior Pachter
2010 C conf
Pair HMM Based Gap Statistics for Re-evaluation of Indels in Alignments with Affine Gap Penalties.
WABI
Alexander Schönhuth, Raheleh Salari, Süleyman Cenk Sahinalp
2010 J jnl
Towards Improved Assessment of Functional Similarity in Large-Scale Screens: A Study on Indel Length.
J. Comput. Biol.
Alexander Schönhuth, Raheleh Salari, Fereydoun Hormozdiari, Artem Cherkasov, Süleyman Cenk Sahinalp
2009 J jnl
Characterization of ergodic hidden Markov sources.
IEEE Trans. Inf. Theory
Alexander Schönhuth, Herbert Jaeger
2009 J jnl
Constrained mixture estimation for analysis and robust classification of clinical time series.
Bioinform.
Ivan G. Costa, Alexander Schönhuth, Christoph Hafemeister, Alexander Schliep
2009 Misc conf
Dense Graphlet Statistics of Protein Interaction and Random Networks.
Pacific Symposium on Biocomputing
Recep Colak, Fereydoun Hormozdiari, Flavia Moser, Alexander Schönhuth, J. Holman, Martin Ester, Süleyman Cenk Sahinalp
2009 J jnl
On analytic properties of entropy rate.
IEEE Trans. Inf. Theory
Alexander Schönhuth
2009 C conf
Quantifying Systemic Evolutionary Changes by Color Coding Confidence-Scored PPI Networks.
WABI
Phuong Dao, Alexander Schönhuth, Fereydoun Hormozdiari, Iman Hajirasouliha, Süleyman Cenk Sahinalp, Martin Ester
2009 J jnl
The Effect of Insertions and Deletions on Wirings in Protein-Protein Interaction Networks: A Large-Scale Study.
J. Comput. Biol.
Fereydoun Hormozdiari, Raheleh Salari, Michael Hsing, Alexander Schönhuth, Simon K. Chan, Süleyman Cenk Sahinalp, Artem Cherkasov
2008 J jnl
A simple and efficient solution of the identifiability problem for hidden Markov sources
CoRR
Alexander Schönhuth
2008 J jnl
On analytic properties of entropy rate of discrete random sources
CoRR
Alexander Schönhuth
2008 C conf
The Relation between Indel Length and Functional Divergence: A Formal Study.
WABI
Raheleh Salari, Alexander Schönhuth, Fereydoun Hormozdiari, Artem Cherkasov, Süleyman Cenk Sahinalp
2008 J jnl
The ergodic decomposition of asymptotically mean stationary random sources
CoRR
Alexander Schönhuth
2007 J jnl
Asymptotic Mean Stationarity of Sources With Finite Evolution Dimension.
IEEE Trans. Inf. Theory
Ulrich Faigle, Alexander Schönhuth
2006 J jnl
Quantum Predictor Models.
Electron. Notes Discret. Math.
Ulrich Faigle, Alexander Schönhuth
2005 J jnl
A fractional programming approach to efficient DNA melting temperature calculation.
Bioinform.
Markus Leber, Lars Kaderali, Alexander Schönhuth, Rainer Schrader
2005 J jnl
Analyzing Gene Expression Time-Courses.
IEEE ACM Trans. Comput. Biol. Bioinform.
Alexander Schliep, Ivan G. Costa, Christine Steinhoff, Alexander Schönhuth
2005 — conf
Note on Negative Probabilities and Observable Processes.
Algorithms for Optimization with Incomplete Information
Ulrich Faigle, Alexander Schönhuth
2005 J jnl
The Graphical Query Language: a tool for analysis of gene expression time-courses.
Bioinform.
Ivan G. Costa, Alexander Schönhuth, Alexander Schliep
2004 — conf
Robust inference of groups in gene expression time-courses using mixtures of HMMs.
ISMB/ECCB (Supplement of Bioinformatics)
Alexander Schliep, Christine Steinhoff, Alexander Schönhuth
2003 — conf
Using hidden Markov models to analyze gene expression time course data.
ISMB (Supplement of Bioinformatics)
Alexander Schliep, Alexander Schönhuth, Christine Steinhoff
2002 C conf
ProClust: improved clustering of protein sequences with an extended graph-based approach.
ECCB
P. Pipenbacher, Alexander Schliep, Sebastian Schneckener, Alexander Schönhuth, Dietmar Schomburg, Rainer Schrader