Jack Kuipers

Publication Activity (10 Years)

Years Active: 2014-2024
Publications (10 Years): 31

Top Topics

Bayesian Networks

Joint Inference

Conditional Independence

Top Venues

PLoS Comput. Biol.

Publications

Enrico Giudice, Jack Kuipers, Giusi Moffa
Bayesian Causal Inference with Gaussian Process Networks. CoRR (2024)
Fritz M. Bayer, Drago Plecko, Niko Beerenwinkel, Jack Kuipers
Fair Clustering: A Causal Perspective. CoRR (2023)
Polina Suter, Jack Kuipers, Giusi Moffa, Niko Beerenwinkel
Package BiDAG. J. Stat. Softw. 105 (9) (2023)
Enrico Giudice, Jack Kuipers, Giusi Moffa
The dual PC algorithm and the role of Gaussianity for structure learning of Bayesian networks. Int. J. Approx. Reason. 161 (2023)
Enrico Giudice, Jack Kuipers, Giusi Moffa
A Bayesian Take on Gaussian Process Networks. CoRR (2023)
Enrico Giudice, Jack Kuipers, Giusi Moffa
A Bayesian Take on Gaussian Process Networks. NeurIPS (2023)
Polina Suter, Eva Dazert, Jack Kuipers, Charlotte K. Y. Ng, Tuyana Boldanova, Michael N. Hall, Markus H. Heim, Niko Beerenwinkel
Multi-omics subtyping of hepatocellular carcinoma patients using a Bayesian network mixture model. PLoS Comput. Biol. 18 (9) (2022)
Jack Kuipers, Polina Suter, Giusi Moffa
Efficient Sampling and Structure Learning of Bayesian Networks. J. Comput. Graph. Stat. 31 (3) (2022)
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
scAmpi - A versatile pipeline for single-cell RNA-seq analysis from basics to clinics. PLoS Comput. Biol. 18 (6) (2022)
Xiang Ge Luo, Jack Kuipers, Niko Beerenwinkel
Joint Inference of Repeated Evolutionary Trajectories and Patterns of Clonal Exclusivity or Co-occurrence from Tumor Mutation Trees. RECOMB (2022)
Jack Kuipers, Jochen Singer, Niko Beerenwinkel
Single-cell mutation calling and phylogenetic tree reconstruction with loss and recurrence. Bioinform. 38 (20) (2022)
Pedro F. Ferreira, Jack Kuipers, Niko Beerenwinkel
Mapping Single-Cell Transcriptomes to Copy Number Evolutionary Trees. RECOMB (2022)
Enrico Giudice, Jack Kuipers, Giusi Moffa
The Dual PC Algorithm for Structure Learning. PGM (2022)
Polina Suter, Jack Kuipers, Niko Beerenwinkel
Discovering gene regulatory networks of multiple phenotypic groups using dynamic Bayesian networks. Briefings Bioinform. 23 (4) (2022)
Fritz M. Bayer, Giusi Moffa, Niko Beerenwinkel, Jack Kuipers
Marginalization in Bayesian Networks: Integrating Exact and Approximate Inference. CoRR (2021)
Jack Kuipers, Ariane L. Moore, Katharina Jahn, Peter Schraml, Feng Wang, Kiyomi Morita, P. Andrew Futreal, Koichi Takahashi, Christian Beisel, Holger Moch, Niko Beerenwinkel
Statistical tests for intra-tumour clonal co-occurrence and exclusivity. PLoS Comput. Biol. 17 (12) (2021)
Susana Posada-Céspedes, Gert van Zyl, Hesam Montazeri, Jack Kuipers, Soo-Yon Rhee, Roger D. Kouyos, Huldrych F. Günthard, Niko Beerenwinkel
Comparing mutational pathways to lopinavir resistance in HIV-1 subtypes B versus C. PLoS Comput. Biol. 17 (9) (2021)
Felix L. Rios, Giusi Moffa, Jack Kuipers
Benchpress: a scalable and platform-independent workflow for benchmarking structure learning algorithms for graphical models. CoRR (2021)
Enrico Giudice, Jack Kuipers, Giusi Moffa
The Dual PC Algorithm for Structure Learning. CoRR (2021)
Xiang Ge Luo, Giusi Moffa, Jack Kuipers
Learning Bayesian Networks from Ordinal Data. J. Mach. Learn. Res. 22 (2021)
Brian Lang, Jack Kuipers, Benjamin Misselwitz, Niko Beerenwinkel
Predicting colorectal cancer risk from adenoma detection via a two-type branching process model. PLoS Comput. Biol. 16 (2) (2020)
Jack Kuipers, Polina Suter, Giusi Moffa
Efficient Structure Learning and Sampling of Bayesian Networks. CoRR (2018)
Sumana Srivatsa, Jack Kuipers, Fabian Schmich, Simone Eicher, Mario Emmenlauer, Christoph Dehio, Niko Beerenwinkel
Improved pathway reconstruction from RNA interference screens by exploiting off-target effects. Bioinform. 34 (13) (2018)
Jochen Singer, Jack Kuipers, Katharina Jahn, Niko Beerenwinkel
SCIΦ: Single-Cell Mutation Identification via Phylogenetic Inference. RECOMB (2018)
Salem Malikic, Katharina Jahn, Jack Kuipers, Süleyman Cenk Sahinalp, Niko Beerenwinkel
Integrative Inference of Subclonal Tumour Evolution from Single-Cell and Bulk Sequencing Data. RECOMB (2018)
Claus Kadelka, Yuan Li, Jack Kuipers, John O. Adeyeye, Reinhard C. Laubenbacher
Multistate nested canalizing functions and their networks. Theor. Comput. Sci. 675 (2017)
Simona Cristea, Jack Kuipers, Niko Beerenwinkel
pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and Their Progression Dynamics. J. Comput. Biol. 24 (6) (2017)
Ariane L. Hofmann, Jonas Behr, Jochen Singer, Jack Kuipers, Christian Beisel, Peter Schraml, Holger Moch, Niko Beerenwinkel
Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers. BMC Bioinform. 18 (1) (2017)
Katharina Jahn, Jack Kuipers, Niko Beerenwinkel
Tree Inference for Single-Cell Data. RECOMB (2016)
Simona Cristea, Jack Kuipers, Niko Beerenwinkel
pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and Their Dependencies in Tumor Progression. RECOMB (2016)
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
Large-scale inference of conjunctive Bayesian networks. Bioinform. 32 (17) (2016)
Jack Kuipers, Giusi Moffa
Uniform random generation of large acyclic digraphs. Stat. Comput. 25 (2) (2015)
Giusi Moffa, Jack Kuipers
Sequential Monte Carlo EM for multivariate probit models. Comput. Stat. Data Anal. 72 (2014)