Jack Kuipers

According to our database, Jack Kuipers authored at least 31 papers between 2014 and 2024.

Collaborative distances:

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

2024

Bayesian Causal Inference with Gaussian Process Networks.

Enrico Giudice, Jack Kuipers, Giusi Moffa

CoRR, 2024

2023

The dual PC algorithm and the role of Gaussianity for structure learning of Bayesian networks.

Enrico Giudice, Jack Kuipers, Giusi Moffa

Int. J. Approx. Reason., October, 2023

Bayesian Structure Learning and Sampling of Bayesian Networks with the <i>R</i> Package BiDAG.

Polina Suter, Jack Kuipers, Giusi Moffa, Niko Beerenwinkel

J. Stat. Softw., 2023

Fair Clustering: A Causal Perspective.

Fritz M. Bayer, Drago Plecko, Niko Beerenwinkel, Jack Kuipers

CoRR, 2023

A Bayesian Take on Gaussian Process Networks.

Enrico Giudice, Jack Kuipers, Giusi Moffa

Proceedings of the Advances in Neural Information Processing Systems 36: Annual Conference on Neural Information Processing Systems 2023, 2023

2022

Single-cell mutation calling and phylogenetic tree reconstruction with loss and recurrence.

Jack Kuipers, Jochen Singer, Niko Beerenwinkel

Bioinform., October, 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., September, 2022

Efficient Sampling and Structure Learning of Bayesian Networks.

Jack Kuipers, Polina Suter, Giusi Moffa

J. Comput. Graph. Stat., July, 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

Discovering gene regulatory networks of multiple phenotypic groups using dynamic Bayesian networks.

Polina Suter, Jack Kuipers, Niko Beerenwinkel

Briefings Bioinform., 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

Proceedings of the Research in Computational Molecular Biology, 2022

Mapping Single-Cell Transcriptomes to Copy Number Evolutionary Trees.

Pedro F. Ferreira, Jack Kuipers, Niko Beerenwinkel

Proceedings of the Research in Computational Molecular Biology, 2022

The Dual PC Algorithm for Structure Learning.

Enrico Giudice, Jack Kuipers, Giusi Moffa

Proceedings of the International Conference on Probabilistic Graphical Models, 2022

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

Statistical tests for intra-tumour clonal co-occurrence and exclusivity.

Jack Kuipers, Ariane L. Moore, Katharina Jahn, Peter Schraml, Feng Wang, Kiyomi Morita, P. Andrew Futreal, Koichi Takahashi, Christian Beisel, Holger Moch, Niko Beerenwinkel

PLoS Comput. Biol., 2021

Learning Bayesian Networks from Ordinal Data.

Xiang Ge Luo, Giusi Moffa, Jack Kuipers

J. Mach. Learn. Res., 2021

Marginalization in Bayesian Networks: Integrating Exact and Approximate Inference.

Fritz M. Bayer, Giusi Moffa, Niko Beerenwinkel, Jack Kuipers

CoRR, 2021

Benchpress: a scalable and platform-independent workflow for benchmarking structure learning algorithms for graphical models.

Felix L. Rios, Giusi Moffa, Jack Kuipers

CoRR, 2021

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

2018

Efficient Structure Learning and Sampling of Bayesian Networks.

Jack Kuipers, Polina Suter, Giusi Moffa

CoRR, 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

SCIΦ: Single-Cell Mutation Identification via Phylogenetic Inference.

Jochen Singer, Jack Kuipers, Katharina Jahn, Niko Beerenwinkel

Proceedings of the Research in Computational Molecular Biology, 2018

Integrative Inference of Subclonal Tumour Evolution from Single-Cell and Bulk Sequencing Data.

Salem Malikic, Katharina Jahn, Jack Kuipers, Süleyman Cenk Sahinalp, Niko Beerenwinkel

Proceedings of the Research in Computational Molecular Biology, 2018

2017

Multistate nested canalizing functions and their networks.

Claus Kadelka, Yuan Li, Jack Kuipers, John O. Adeyeye, Reinhard C. Laubenbacher

Theor. Comput. Sci., 2017

pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and Their Progression Dynamics.

Simona Cristea, Jack Kuipers, Niko Beerenwinkel

J. Comput. Biol., 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

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

Tree Inference for Single-Cell Data.

Katharina Jahn, Jack Kuipers, Niko Beerenwinkel

Proceedings of the Research in Computational Molecular Biology - 20th Annual Conference, 2016

pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and Their Dependencies in Tumor Progression.

Simona Cristea, Jack Kuipers, Niko Beerenwinkel

Proceedings of the Research in Computational Molecular Biology - 20th Annual Conference, 2016

2015

Uniform random generation of large acyclic digraphs.

Jack Kuipers, Giusi Moffa

Stat. Comput., 2015

2014

Sequential Monte Carlo EM for multivariate probit models.

Giusi Moffa, Jack Kuipers

Comput. Stat. Data Anal., 2014