ProClust: improved clustering of protein sequences with an extended graph-based approach. - P. Pipenbacher; Alexander Schliep; Sebastian Schneckener; Alexander Schönhuth; Dietmar Schomburg; Rainer Schrader (ECCB, 2002)

Using hidden Markov models to analyze gene expression time course data. - Alexander Schliep; Alexander Schönhuth; Christine Steinhoff (ISMB (Supplement of Bioinformatics), 2003)

Robust inference of groups in gene expression time-courses using mixtures of HMMs. - Alexander Schliep; Christine Steinhoff; Alexander Schönhuth (ISMB/ECCB (Supplement of Bioinformatics), 2004)

Note on Negative Probabilities and Observable Processes. - Ulrich Faigle; Alexander Schönhuth (Algorithms for Optimization with Incomplete Information, 2005)

The Graphical Query Language: a tool for analysis of gene expression time-courses. - Ivan G. Costa; Alexander Schönhuth; Alexander Schliep (Bioinform., 2005)

A fractional programming approach to efficient DNA melting temperature calculation. - Markus Leber; Lars Kaderali; Alexander Schönhuth; Rainer Schrader (Bioinform., 2005)

Analyzing Gene Expression Time-Courses. - Alexander Schliep; Ivan G. Costa; Christine Steinhoff; Alexander Schönhuth (IEEE ACM Trans. Comput. Biol. Bioinform., 2005)

Quantum Predictor Models. - Ulrich Faigle; Alexander Schönhuth (Electron. Notes Discret. Math., 2006)

Asymptotic Mean Stationarity of Sources With Finite Evolution Dimension. - Ulrich Faigle; Alexander Schönhuth (IEEE Trans. Inf. Theory, 2007)

The Relation between Indel Length and Functional Divergence: A Formal Study. - Raheleh Salari; Alexander Schönhuth; Fereydoun Hormozdiari; Artem Cherkasov; Süleyman Cenk Sahinalp (WABI, 2008)

On analytic properties of entropy rate of discrete random sources - Alexander Schönhuth (CoRR, 2008)

The ergodic decomposition of asymptotically mean stationary random sources - Alexander Schönhuth (CoRR, 2008)

A simple and efficient solution of the identifiability problem for hidden Markov sources - Alexander Schönhuth (CoRR, 2008)

Dense Graphlet Statistics of Protein Interaction and Random Networks. - Recep Colak; Fereydoun Hormozdiari; Flavia Moser; Alexander Schönhuth; J. Holman; Martin Ester; Süleyman Cenk Sahinalp (Pacific Symposium on Biocomputing, 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 (WABI, 2009)

Constrained mixture estimation for analysis and robust classification of clinical time series. - Ivan G. Costa; Alexander Schönhuth; Christoph Hafemeister; Alexander Schliep (Bioinform., 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)

On analytic properties of entropy rate. - Alexander Schönhuth (IEEE Trans. Inf. Theory, 2009)

Characterization of ergodic hidden Markov sources. - Alexander Schönhuth; Herbert Jaeger (IEEE Trans. Inf. Theory, 2009)

Pair HMM Based Gap Statistics for Re-evaluation of Indels in Alignments with Affine Gap Penalties. - Alexander Schönhuth; Raheleh Salari; Süleyman Cenk Sahinalp (WABI, 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)

Discrete Quantum Markov Chains - Ulrich Faigle; Alexander Schönhuth (CoRR, 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)

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)

Representations of Power Series over Word Algebras. - Ulrich Faigle; Alexander Schönhuth (CTW, 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)

Efficient Tests for Equivalence of Hidden Markov Processes and Quantum Random Walks. - Ulrich Faigle; Alexander Schönhuth (IEEE Trans. Inf. Theory, 2011)

Mirroring co-evolving trees in the light of their topologies. - Iman Hajirasouliha; Alexander Schönhuth; David de Juan; Alfonso Valencia; Süleyman Cenk Sahinalp (Bioinform., 2012)

CLEVER: clique-enumerating variant finder. - Tobias Marschall; Ivan G. Costa; Stefan Canzar; Markus Bauer 001; Gunnar W. Klau; Alexander Schliep; Alexander Schönhuth (Bioinform., 2012)

Observation and evolution of finite-dimensional Markov systems. - Ulrich Faigle; Alexander Schönhuth (CTW, 2013)

MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels. - Tobias Marschall; Iman Hajirasouliha; Alexander Schönhuth (Bioinform., 2013)

Discovering motifs that induce sequencing errors. - Manuel Allhoff; Alexander Schönhuth; Marcel Martin; Ivan G. Costa; Sven Rahmann; Tobias Marschall (BMC Bioinform., 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)

WhatsHap: Haplotype Assembly for Future-Generation Sequencing Reads. - Murray Patterson; Tobias Marschall; Nadia Pisanti; Leo van Iersel; Leen Stougie; Gunnar W. Klau; Alexander Schönhuth (RECOMB, 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)

Repeat- and error-aware comparison of deletions. - Roland Wittler; Tobias Marschall; Alexander Schönhuth; Veli Mäkinen (Bioinform., 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 027 (Datenbank-Spektrum, 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)

Next generation cluster editing. - Thomas Bellitto; Tobias Marschall; Alexander Schönhuth; Gunnar W. Klau (PeerJ Prepr., 2015)

Snowball: strain aware gene assembly of metagenomes. - I. Gregor; Alexander Schönhuth; Alice Carolyn McHardy (Bioinform., 2016)

On Hidden States in Quantum Random Walks. - Ulrich Faigle; Alexander Schönhuth (CoRR, 2016)

Eliminating Blind Spots in Genetic Variant Discovery. - Alexander Schönhuth; Tobias Marschall (ERCIM News, 2016)

A probabilistic model to recover individual genomes from metagenomes. - Johannes Dröge; Alexander Schönhuth; Alice Carolyn McHardy (PeerJ Prepr., 2016)

Genotyping inversions and tandem duplications. - Jana Ebler; Alexander Schönhuth; Tobias Marschall (Bioinform., 2017)

Dualities in Tree Representations. - Rayan Chikhi; Alexander Schönhuth (CPM, 2018)

Metagenomic read clustering based on overlap graphs. - Marleen Balvert; Alexander Schönhuth; Bas E. Dutilh (ICCABS, 2018)

An image representation based convolutional network for DNA classification. - Bojian Yin; Marleen Balvert; Davide Zambrano; Alexander Schönhuth; Sander M. Bohté (ICLR (Poster), 2018)

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)

Overlap graph-based generation of haplotigs for diploids and polyploids. - Jasmijn A. Baaijens; Alexander Schönhuth (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)

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)

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)

Artificial Intelligence: Understanding Diseases that People Cannot Understand? - Marleen Balvert; Alexander Schönhuth (ERCIM News, 2019)

The Genetic Diversity of Viruses on a Graphical Map: Discovery of Resistant and Virulent Strains. - Alexander Schönhuth; Leen Stougie (ERCIM News, 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; et al. (PeerJ Prepr., 2019)

Strain-Aware Assembly of Genomes from Mixed Samples Using Flow Variation Graphs. - Jasmijn A. Baaijens; Leen Stougie; Alexander Schönhuth (RECOMB, 2020)

OGRE: Overlap Graph-based metagenomic Read clustEring. - Marleen Balvert; Xiao Luo; Ernestina Hauptfeld; Alexander Schönhuth; Bas E. Dutilh (Bioinform., 2021)

Deep variational graph autoencoders for novel host-directed therapy options against COVID-19. - Sumanta Ray; Snehalika Lall; Anirban Mukhopadhyay 001; Sanghamitra Bandyopadhyay; Alexander Schönhuth (Artif. Intell. Medicine, 2022)

Predicting the prevalence of complex genetic diseases from individual genotype profiles using capsule networks. - Xiao Luo; Xiongbin Kang; Alexander Schönhuth (Nat. Mac. Intell., 2023)

Generating Synthetic Genotypes using Diffusion Models. - Philip Kenneweg; Raghuram Dandinasivara; Xiao Luo; Barbara Hammer; Alexander Schönhuth (CoRR, 2024)

DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs. - Ali Ghaffaari; Alexander Schönhuth; Tobias Marschall (WABI, 2025)

Genetic features for drug responses in cancer - Investigating an ensemble-feature-selection approach. - Johannes Schlüter; Alexander Schönhuth (Comput. Biol. Medicine, 2025)

From data chaos to precision medicine. - Alexander Schönhuth (Nat. Mac. Intell., 2025)