Identifying drug resistance-associated patterns in HIV genotypes. - Niko Beerenwinkel; Barbara Schmidt; Hauke Walter; Rolf Kaiser; Thomas Lengauer; Daniel Hoffmann; Klaus Korn; Joachim Selbig (German Conference on Bioinformatics, 2001)

Geno2pheno: Interpreting Genotypic HIV Drug Resistance Tests. - Niko Beerenwinkel; Barbara Schmidt; Hauke Walter; Rolf Kaiser; Thomas Lengauer; Daniel Hoffmann; Klaus Korn; Joachim Selbig (IEEE Intell. Syst., 2001)

Diversity and complexity of HIV-1 drug resistance: A bioinformatics approach to predicting phenotype from genotype. - Niko Beerenwinkel; Barbara Schmidt; Hauke Walter; Rolf Kaiser; Thomas Lengauer; Daniel Hoffmann; Klaus Korn; Joachim Selbig (Proc. Natl. Acad. Sci. USA, 2002)

Methods for optimizing antiviral combination therapies. - Niko Beerenwinkel; Thomas Lengauer; Martin Däumer; Rolf Kaiser; Hauke Walter; Klaus Korn; Daniel Hoffmann; Joachim Selbig (ISMB (Supplement of Bioinformatics), 2003)

Geno2pheno: estimating phenotypic drug resistance from HIV-1 genotypes. - Niko Beerenwinkel; Martin Däumer; Mark Oette; Klaus Korn; Daniel Hoffmann; Rolf Kaiser; Thomas Lengauer; Joachim Selbig; Hauke Walter (Nucleic Acids Res., 2003)

Learning Mixtures of Localized Rules by Maximizing the Area Under the ROC Curve. - Tobias Sing; Niko Beerenwinkel; Thomas Lengauer (ROCAI, 2004)

Computational analysis of HIV drug resistance data. - Niko Beerenwinkel (2004)

Supervised and Unsupervised Approaches for Analyzing Covariation and Phenotypic Impact of HIV Drug Resistance Mutations. - Tobias Sing; Niko Beerenwinkel; Thomas Lengauer; Valentina Svicher; Francesca Ceccherini-Silberstein; Carlo-Federico Perno (LWA, 2005)

Characterization of Novel HIV Drug Resistance Mutations Using Clustering, Multidimensional Scaling and SVM-Based Feature Ranking. - Tobias Sing; Valentina Svicher; Niko Beerenwinkel; Francesca Ceccherini-Silberstein; Martin Däumer; Rolf Kaiser; Hauke Walter; Klaus Korn; Daniel Hoffmann; Mark Oette; Jürgen K. Rockstroh; Gerd Fätkenheuer; et al. (PKDD, 2005)

Mtreemix: a software package for learning and using mixture models of mutagenetic trees. - Niko Beerenwinkel; Jörg Rahnenführer; Rolf Kaiser; Daniel Hoffmann; Joachim Selbig; Thomas Lengauer (Bioinform., 2005)

Computational methods for the design of effective therapies against drug resistant HIV strains. - Niko Beerenwinkel; Tobias Sing; Thomas Lengauer; Jörg Rahnenführer; Kirsten Roomp; Igor Savenkov; Roman Fischer; Daniel Hoffmann; Joachim Selbig; Klaus Korn; Hauke Walter; Thomas Berg; et al. (Bioinform., 2005)

Estimating cancer survival and clinical outcome based on genetic tumor progression scores. - Jörg Rahnenführer; Niko Beerenwinkel; Wolfgang A. Schulz; Christian Hartmann 006; Andreas von Deimling; Bernd Wullich; Thomas Lengauer (Bioinform., 2005)

ROCR: visualizing classifier performance in R. - Tobias Sing; Oliver Sander; Niko Beerenwinkel; Thomas Lengauer (Bioinform., 2005)

Learning Multiple Evolutionary Pathways from Cross-Sectional Data. - Niko Beerenwinkel; Jörg Rahnenführer; Martin Däumer; Daniel Hoffmann; Rolf Kaiser; Joachim Selbig; Thomas Lengauer (J. Comput. Biol., 2005)

Arevir: A Secure Platform for Designing Personalized Antiretroviral Therapies Against HIV. - Kirsten Roomp; Niko Beerenwinkel; Tobias Sing; Eugen Schülter; Joachim Büch; Saleta Sierra-Aragon; Martin Däumer; Daniel Hoffmann; Rolf Kaiser; Thomas Lengauer; Joachim Selbig (DILS, 2006)

Mutagenetic tree Fisher kernel improves prediction of HIV drug resistance from viral genotype. - Tobias Sing; Niko Beerenwinkel (NIPS, 2006)

Genetic Progression and the Waiting Time to Cancer. - Niko Beerenwinkel; Tibor Antal; David Dingli; Arne Traulsen; Kenneth W. Kinzler; Victor E. Velculescu; Bert Vogelstein; Martin A. Nowak (PLoS Comput. Biol., 2007)

Viral Population Estimation Using Pyrosequencing. - Nicholas Eriksson; Lior Pachter; Yumi Mitsuya; Soo-Yon Rhee; Chunlin Wang; Baback Gharizadeh; Mostafa Ronaghi; Robert W. Shafer; Niko Beerenwinkel (PLoS Comput. Biol., 2008)

Multiple Sequence Alignment System for Pyrosequencing Reads. - Fahad Saeed; Ashfaq A. Khokhar; Osvaldo Zagordi; Niko Beerenwinkel (BICoB, 2009)

Quantifying cancer progression with conjunctive Bayesian networks. - Moritz Gerstung; Michael Baudis; Holger Moch; Niko Beerenwinkel (Bioinform., 2009)

Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction. - Osvaldo Zagordi; Lukas Geyrhofer; Volker Roth 001; Niko Beerenwinkel (J. Comput. Biol., 2010)

ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data. - Osvaldo Zagordi; Arnab Bhattacharya 003; Nicholas Eriksson; Niko Beerenwinkel (BMC Bioinform., 2011)

Evolutionary Games with Affine Fitness Functions: Applications to Cancer. - Moritz Gerstung; Hani Nakhoul; Niko Beerenwinkel (Dyn. Games Appl., 2011)

Efficient sampling for Bayesian inference of conjunctive Bayesian networks. - Thomas Sakoparnig; Niko Beerenwinkel (Bioinform., 2012)

Stability of gene rankings from RNAi screens. - Juliane Siebourg; Gunter Merdes; Benjamin Misselwitz; Wolf-Dietrich Hardt; Niko Beerenwinkel (Bioinform., 2012)

Binding Profiles of Chromatin-Modifying Proteins Are Predictive for Transcriptional Activity and Promoter-Proximal Pausing. - Thomas Sakoparnig; Tobias Kockmann; Renato Paro; Christian Beisel; Niko Beerenwinkel (J. Comput. Biol., 2012)

Probing of viral diversity by global haplotype prediction. - Armin Töpfer; Francesca Di Giallonardo; Karin J. Metzner; Huldrych F. Günthard; Niko Beerenwinkel (ICCABS, 2013)

Probabilistic Inference of Viral Quasispecies Subject to Recombination. - Armin Töpfer; Osvaldo Zagordi; Sandhya Prabhakaran; Volker Roth 001; Eran Halperin; Niko Beerenwinkel (J. Comput. Biol., 2013)

The Individualized Genetic Barrier Predicts Treatment Response in a Large Cohort of HIV-1 Infected Patients. - Niko Beerenwinkel; Hesam Montazeri; Heike Schuhmacher; Patrick Knupfer; Viktor von Wyl; Hansjakob Furrer; Manuel Battegay; Bernard Hirschel; Matthias Cavassini; Pietro Vernazza; Enos Bernasconi; Sabine Yerly; et al. (PLoS Comput. Biol., 2013)

Viral quasispecies assembly from paired-end reads. - Armin Töpfer; Niko Beerenwinkel (ICCABS, 2014)

Exact likelihood computation in Boolean networks with probabilistic time delays, and its application in signal network reconstruction. - Sebastian Dümcke; Johannes Bräuer; Benedict Anchang; Rainer Spang; Niko Beerenwinkel; Achim Tresch (Bioinform., 2014)

Challenges in RNA virus bioinformatics. - Manja Marz; Niko Beerenwinkel; Christian Drosten; Markus Fricke; Dmitrij Frishman; Ivo L. Hofacker; Dieter Hoffmann; Martin Middendorf; Thomas Rattei; Peter F. Stadler; Armin Töpfer (Bioinform., 2014)

Estimating HIV-1 Fitness Characteristics from Cross-Sectional Genotype Data. - Sathej Gopalakrishnan; Hesam Montazeri; Stephan Menz; Niko Beerenwinkel; Wilhelm Huisinga (PLoS Comput. Biol., 2014)

Modeling Mutual Exclusivity of Cancer Mutations. - Ewa Szczurek; Niko Beerenwinkel (PLoS Comput. Biol., 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)

HIV Haplotype Inference Using a Propagating Dirichlet Process Mixture Model. - Sandhya Prabhakaran; Mélanie Rey; Osvaldo Zagordi; Niko Beerenwinkel; Volker Roth 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

Finding Dense Subgraphs in Relational Graphs. - Vinay Jethava; Niko Beerenwinkel (ECML/PKDD (2), 2015)

ISMB/ECCB 2015. - Yves Moreau; Niko Beerenwinkel (Bioinform., 2015)

Covering Pairs in Directed Acyclic Graphs. - Niko Beerenwinkel; Stefano Beretta 001; Paola Bonizzoni; Riccardo Dondi; Yuri Pirola (Comput. J., 2015)

Identification of Constrained Cancer Driver Genes Based on Mutation Timing. - Thomas Sakoparnig; Patrick Fried; Niko Beerenwinkel (PLoS Comput. Biol., 2015)

NEMix: Single-cell Nested Effects Models for Probabilistic Pathway Stimulation. - Juliane Siebourg-Polster; Daria Mudrak; Mario Emmenlauer; Pauli Rämö; Christoph Dehio; Urs F. Greber; Holger Fröhlich; Niko Beerenwinkel (PLoS Comput. Biol., 2015)

Detecting patterns of co-variation in deep-sequenced virus populations. - Susana Posada-Céspedes; David Seifert; Niko Beerenwinkel (ICCABS, 2016)

pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and Their Dependencies in Tumor Progression. - Simona Cristea; Jack Kuipers; Niko Beerenwinkel (RECOMB, 2016)

Tree Inference for Single-Cell Data. - Katharina Jahn 001; Jack Kuipers; Niko Beerenwinkel (RECOMB, 2016)

TiMEx: a waiting time model for mutually exclusive cancer alterations. - Simona Constantinescu; Ewa Szczurek; Pejman Mohammadi 001; Jörg Rahnenführer; Niko Beerenwinkel (Bioinform., 2016)

BMix: probabilistic modeling of occurring substitutions in PAR-CLIP data. - Monica Golumbeanu; Pejman Mohammadi 001; Niko Beerenwinkel (Bioinform., 2016)

Large-scale inference of conjunctive Bayesian networks. - Hesam Montazeri; Jack Kuipers; Roger D. Kouyos; Jürg Böni; Sabine Yerly; Thomas Klimkait; Vincent Aubert; Huldrych F. Günthard; Niko Beerenwinkel; The Swiss Hiv Cohort Study (Bioinform., 2016)

Linear effects models of signaling pathways from combinatorial perturbation data. - Ewa Szczurek; Niko Beerenwinkel (Bioinform., 2016)

Computational Cancer Biology: An Evolutionary Perspective. - Niko Beerenwinkel; Chris D. Greenman; Jens Lagergren (PLoS Comput. Biol., 2016)

ISMB/ECCB 2017 proceedings. - Niko Beerenwinkel; Yana Bromberg (Bioinform., 2017)

Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers. - Ariane L. Hofmann; Jonas Behr; Jochen Singer; Jack Kuipers; Christian Beisel; Peter Schraml; Holger Moch; Niko Beerenwinkel (BMC Bioinform., 2017)

Addressing the Computational Challenges of Personalized Medicine (Dagstuhl Seminar 17472). - Niko Beerenwinkel; Holger Fröhlich; Susan A. Murphy (Dagstuhl Reports, 2017)

pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and Their Progression Dynamics. - Simona Cristea; Jack Kuipers; Niko Beerenwinkel (J. Comput. Biol., 2017)

CMOST: an open-source framework for the microsimulation of colorectal cancer screening strategies. - Meher K. Prakash; Brian Lang; Henriette Heinrich; Piero V. Valli; Peter Bauerfeind; Amnon Sonnenberg; Niko Beerenwinkel; Benjamin Misselwitz (BMC Medical Informatics Decis. Mak., 2017)

Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb. - Remo Monti; Iros Barozzi; Marco Osterwalder; Elizabeth Lee; Momoe Kato; Tyler H. Garvin; Ingrid Plajzer-Frick; Catherine S. Pickle; Jennifer A. Akiyama; Veena Afzal; Niko Beerenwinkel; Diane E. Dickel; et al. (PLoS Comput. Biol., 2017)

Inferring modulators of genetic interactions with epistatic nested effects models. - Martin Pirkl; Madeline Diekmann; Marlies van der Wees; Niko Beerenwinkel; Holger Fröhlich; Florian Markowetz (PLoS Comput. Biol., 2017)

Integrative Inference of Subclonal Tumour Evolution from Single-Cell and Bulk Sequencing Data. - Salem Malikic; Katharina Jahn 001; Jack Kuipers; Süleyman Cenk Sahinalp; Niko Beerenwinkel (RECOMB, 2018)

ModulOmics: Integrating Multi-Omics Data to Identify Cancer Driver Modules. - Dana Silverbush; Simona Cristea; Gali Yanovich; Tamar Geiger; Niko Beerenwinkel; Roded Sharan (RECOMB, 2018)

SCIΦ: Single-Cell Mutation Identification via Phylogenetic Inference. - Jochen Singer; Jack Kuipers; Katharina Jahn 001; Niko Beerenwinkel (RECOMB, 2018)

Network-based integration of multi-omics data for prioritizing cancer genes. - Christos Dimitrakopoulos; Sravanth Kumar Hindupur; Luca Häfliger; Jonas Behr; Hesam Montazeri; Michael N. Hall; Niko Beerenwinkel (Bioinform., 2018)

Single cell network analysis with a mixture of Nested Effects Models. - Martin Pirkl; Niko Beerenwinkel (Bioinform., 2018)

NGS-pipe: a flexible, easily extendable and highly configurable framework for NGS analysis. - Jochen Singer; Hans-Joachim Ruscheweyh; Ariane L. Hofmann; Thomas Thurnherr; Franziska Singer; Nora C. Toussaint; Charlotte K. Y. Ng; Salvatore Piscuoglio; Christian Beisel; Gerhard Christofori; Reinhard Dummer; Michael N. Hall; et al. (Bioinform., 2018)

Improved pathway reconstruction from RNA interference screens by exploiting off-target effects. - Sumana Srivatsa; Jack Kuipers; Fabian Schmich; Simone Eicher; Mario Emmenlauer; Christoph Dehio; Niko Beerenwinkel (Bioinform., 2018)

Ensemble outlier detection and gene selection in triple-negative breast cancer data. - Marta B. Lopes; André Veríssimo; Eunice Carrasquinha; Sandra Casimiro; Niko Beerenwinkel; Susana Vinga (BMC Bioinform., 2018)

SwissMTB: establishing comprehensive molecular cancer diagnostics in Swiss clinics. - Franziska Singer; Anja Irmisch; Nora C. Toussaint; Linda Grob; Jochen Singer; Thomas Thurnherr; Niko Beerenwinkel; Mitchell P. Levesque; Reinhard Dummer; Luca Quagliata; Sacha I. Rothschild; Andreas Wicki; et al. (BMC Medical Informatics Decis. Mak., 2018)

Bioinformatics for precision oncology. - Jochen Singer; Anja Irmisch; Hans-Joachim Ruscheweyh; Franziska Singer; Nora C. Toussaint; Mitchell P. Levesque; Daniel J. Stekhoven; Niko Beerenwinkel (Briefings Bioinform., 2019)

Inferring signalling dynamics by integrating interventional with observational data. - Mathias Cardner; Nathalie Meyer-Schaller; Gerhard Christofori; Niko Beerenwinkel (Bioinform., 2019)

Estimating the predictability of cancer evolution. - Sayed-Rzgar Hosseini; Ramón Díaz-Uriarte; Florian Markowetz; Niko Beerenwinkel (Bioinform., 2019)

PyBDA: a command line tool for automated analysis of big biological data sets. - Simon Dirmeier; Mario Emmenlauer; Christoph Dehio; Niko Beerenwinkel (BMC Bioinform., 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)

Bayesian Non-parametric Clustering of Single-Cell Mutation Profiles. - Nico Borgsmüller; José Bonet 001; Francesco Marass; Abel Gonzalez-Perez; Núria López-Bigas; Niko Beerenwinkel (RECOMB, 2020)

BnpC: Bayesian non-parametric clustering of single-cell mutation profiles. - Nico Borgsmüller; José Bonet 001; Francesco Marass; Abel Gonzalez-Perez; Núria López-Bigas; Niko Beerenwinkel (Bioinform., 2020)

Host factor prioritization for pan-viral genetic perturbation screens using random intercept models and network propagation. - Simon Dirmeier; Christopher Dächert; Martijn van Hemert; Ali Tas; Natacha S. Ogando; Frank J. M. van Kuppeveld; Ralf Bartenschlager; Lars Kaderali; Marco Binder; Niko Beerenwinkel (PLoS Comput. Biol., 2020)

Predicting colorectal cancer risk from adenoma detection via a two-type branching process model. - Brian Lang; Jack Kuipers; Benjamin Misselwitz; Niko Beerenwinkel (PLoS Comput. Biol., 2020)

A mathematical model of the metastatic bottleneck predicts patient outcome and response to cancer treatment. - Ewa Szczurek; Tyll Krüger; Barbara Klink; Niko Beerenwinkel (PLoS Comput. Biol., 2020)

The Bourque distances for mutation trees of cancers. - Katharina Jahn 001; Niko Beerenwinkel; Louxin Zhang (Algorithms Mol. Biol., 2021)

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. - Franziska Hufsky; Kevin Lamkiewicz; Alexandre Almeida; Abdel Aouacheria; Cecilia N. Arighi; Alex Bateman; Jan Baumbach; Niko Beerenwinkel; Christian Brandt; Marco Cacciabue; Sara Chuguransky; Oliver Drechsel; et al. (Briefings Bioinform., 2021)

Inferring perturbation profiles of cancer samples. - Martin Pirkl; Niko Beerenwinkel (Bioinform., 2021)

V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data. - Susana Posada-Céspedes; David Seifert; Ivan Topolsky; Kim Philipp Jablonski; Karin J. Metzner; Niko Beerenwinkel (Bioinform., 2021)

Marginalization in Bayesian Networks: Integrating Exact and Approximate Inference. - Fritz M. Bayer; Giusi Moffa; Niko Beerenwinkel; Jack Kuipers (CoRR, 2021)

Statistical tests for intra-tumour clonal co-occurrence and exclusivity. - Jack Kuipers; Ariane L. Moore; Katharina Jahn 001; Peter Schraml; Feng Wang; Kiyomi Morita; P. Andrew Futreal; Koichi Takahashi; Christian Beisel; Holger Moch; Niko Beerenwinkel (PLoS Comput. Biol., 2021)

Drug-induced resistance evolution necessitates less aggressive treatment. - Teemu Kuosmanen; Johannes Cairns; Robert Noble; Niko Beerenwinkel; Tommi Mononen; Ville Mustonen (PLoS Comput. Biol., 2021)

Comparing mutational pathways to lopinavir resistance in HIV-1 subtypes B versus C. - Susana Posada-Céspedes; Gert van Zyl; Hesam Montazeri; Jack Kuipers; Soo-Yon Rhee; Roger D. Kouyos; Huldrych F. Günthard; Niko Beerenwinkel (PLoS Comput. Biol., 2021)

Reproducibility of Bioinformatics Tools. - Pelin Icer Baykal; Niko Beerenwinkel; Serghei Mangul (IPDPS Workshops, 2022)

Mapping Single-Cell Transcriptomes to Copy Number Evolutionary Trees. - Pedro F. Ferreira; Jack Kuipers; Niko Beerenwinkel (RECOMB, 2022)

Joint Inference of Repeated Evolutionary Trajectories and Patterns of Clonal Exclusivity or Co-occurrence from Tumor Mutation Trees. - Xiang Ge Luo; Jack Kuipers; Niko Beerenwinkel (RECOMB, 2022)

Discovering gene regulatory networks of multiple phenotypic groups using dynamic Bayesian networks. - Polina Suter; Jack Kuipers; Niko Beerenwinkel (Briefings Bioinform., 2022)

Identifying cancer pathway dysregulations using differential causal effects. - Kim Philipp Jablonski; Martin Pirkl; Domagoj Cevid; Peter Bühlmann; Niko Beerenwinkel (Bioinform., 2022)

scAmpi - A versatile pipeline for single-cell RNA-seq analysis from basics to clinics. - Anne Bertolini; Michael Prummer; Mustafa Anil Tuncel; Ulrike Menzel; María Lourdes Rosano-González; Jack Kuipers; Daniel J. Stekhoven; Tumor Profiler Consortium; Niko Beerenwinkel; Franziska Singer (PLoS Comput. Biol., 2022)

Multi-omics subtyping of hepatocellular carcinoma patients using a Bayesian network mixture model. - Polina Suter; Eva Dazert; Jack Kuipers; Charlotte K. Y. Ng; Tuyana Boldanova; Michael N. Hall; Markus H. Heim; Niko Beerenwinkel (PLoS Comput. Biol., 2022)

Single-cell mutation calling and phylogenetic tree reconstruction with loss and recurrence. - Jack Kuipers; Jochen Singer; Niko Beerenwinkel (Bioinform., 2022)

Beyond Normal: On the Evaluation of Mutual Information Estimators. - Pawel Czyz; Frederic Grabowski; Julia E. Vogt; Niko Beerenwinkel; Alexander Marx 001 (NeurIPS, 2023)

The Mixtures and the Neural Critics: On the Pointwise Mutual Information Profiles of Fine Distributions. - Pawel Czyz; Frederic Grabowski; Julia E. Vogt; Niko Beerenwinkel; Alexander Marx 001 (CoRR, 2023)

Bayesian Structure Learning and Sampling of Bayesian Networks with the R Package BiDAG. - Polina Suter; Jack Kuipers; Giusi Moffa; Niko Beerenwinkel (J. Stat. Softw., 2023)

Coherent pathway enrichment estimation by modeling inter-pathway dependencies using regularized regression. - Kim Philipp Jablonski; Niko Beerenwinkel (Bioinform., 2023)

Predicting tumour content of liquid biopsies from cell-free DNA. - Mathias Cardner; Francesco Marass; Erika Gedvilaite; Julie L. Yang; Dana W. Y. Tsui; Niko Beerenwinkel (BMC Bioinform., 2023)

Overcoming Observation Bias for Cancer Progression Modeling. - Rudolf Schill; Maren Klever; Andreas Lösch; Y. Linda Hu; Stefan Vocht; Kevin Rupp; Lars Grasedyck; Rainer Spang; Niko Beerenwinkel (RECOMB, 2024)

Oncotree2vec - a method for embedding and clustering of tumor mutation trees. - Monica-Andreea Baciu-Dragan; Niko Beerenwinkel (Bioinform., 2024)

Modeling metastatic progression from cross-sectional cancer genomics data. - Kevin Rupp; Andreas Lösch; Y. Linda Hu; Chenxi Nie; Rudolf Schill; Maren Klever; Simon Pfahler; Lars Grasedyck; Tilo Wettig; Niko Beerenwinkel; Rainer Spang (Bioinform., 2024)

Correcting for Observation Bias in Cancer Progression Modeling. - Rudolf Schill; Maren Klever; Andreas Lösch; Y. Linda Hu; Stefan Vocht; Kevin Rupp; Lars Grasedyck; Rainer Spang; Niko Beerenwinkel (J. Comput. Biol., 2024)

Fair Clustering: A Causal Perspective. - Fritz M. Bayer; Drago Plecko; Niko Beerenwinkel; Jack Kuipers (CLeaR, 2025)

On the Properties and Estimation of Pointwise Mutual Information Profiles. - Pawel Czyz; Frederic Grabowski; Julia E. Vogt; Niko Beerenwinkel; Alexander Marx 001 (Trans. Mach. Learn. Res., 2025)

HIVMedQA: Benchmarking large language models for HIV medical decision support. - Gonzalo Cardenal-Antolin; Jacques Fellay; Bashkim Jaha; Roger D. Kouyos; Niko Beerenwinkel; Diane Duroux (CoRR, 2025)