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Journal Articles
- 2023
[j18]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: 108975 (2023)- [j17]Polina Suter, Jack Kuipers, Giusi Moffa, Niko Beerenwinkel:
Bayesian Structure Learning and Sampling of Bayesian Networks with the R Package BiDAG. J. Stat. Softw. 105(9) (2023) - 2022
- [j16]Polina Suter, Jack Kuipers, Niko Beerenwinkel:
Discovering gene regulatory networks of multiple phenotypic groups using dynamic Bayesian networks. Briefings Bioinform. 23(4) (2022) - [j15]Jack Kuipers, Jochen Singer, Niko Beerenwinkel:
Single-cell mutation calling and phylogenetic tree reconstruction with loss and recurrence. Bioinform. 38(20): 4713-4719 (2022) - [j14]Jack Kuipers, Polina Suter, Giusi Moffa:
Efficient Sampling and Structure Learning of Bayesian Networks. J. Comput. Graph. Stat. 31(3): 639-650 (2022) - [j13]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) - [j12]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): 1009767 (2022) - 2021
- [j11]Xiang Ge Luo, Giusi Moffa, Jack Kuipers:
Learning Bayesian Networks from Ordinal Data. J. Mach. Learn. Res. 22: 266:1-266:44 (2021) - [j10]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) - [j9]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) - 2020
- [j8]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) - 2018
- [j7]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): i519-i527 (2018) - 2017
- [j6]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): 8:1-8:15 (2017) - [j5]Simona Cristea, Jack Kuipers, Niko Beerenwinkel:
pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and Their Progression Dynamics. J. Comput. Biol. 24(6): 603-615 (2017) - [j4]Claus Kadelka, Yuan Li, Jack Kuipers, John O. Adeyeye, Reinhard C. Laubenbacher:
Multistate nested canalizing functions and their networks. Theor. Comput. Sci. 675: 1-14 (2017) - 2016
- [j3]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): 727-735 (2016) - 2015
- [j2]Jack Kuipers, Giusi Moffa:
Uniform random generation of large acyclic digraphs. Stat. Comput. 25(2): 227-242 (2015) - 2014
- [j1]Giusi Moffa, Jack Kuipers:
Sequential Monte Carlo EM for multivariate probit models. Comput. Stat. Data Anal. 72: 252-272 (2014)
Conference and Workshop Papers
- 2023
- [c8]Enrico Giudice, Jack Kuipers, Giusi Moffa:
A Bayesian Take on Gaussian Process Networks. NeurIPS 2023 - 2022
- [c7]Enrico Giudice, Jack Kuipers, Giusi Moffa:
The Dual PC Algorithm for Structure Learning. PGM 2022: 301-312 - [c6]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: 304-305 - [c5]Pedro F. Ferreira, Jack Kuipers, Niko Beerenwinkel:
Mapping Single-Cell Transcriptomes to Copy Number Evolutionary Trees. RECOMB 2022: 380-381 - 2018
- [c4]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: 269-270 - [c3]Jochen Singer, Jack Kuipers, Katharina Jahn, Niko Beerenwinkel:
SCIΦ: Single-Cell Mutation Identification via Phylogenetic Inference. RECOMB 2018: 285-286 - 2016
- [c2]Simona Cristea, Jack Kuipers, Niko Beerenwinkel:
pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and Their Dependencies in Tumor Progression. RECOMB 2016: 65-82 - [c1]Katharina Jahn, Jack Kuipers, Niko Beerenwinkel:
Tree Inference for Single-Cell Data. RECOMB 2016: 252
Informal and Other Publications
- 2024
- [i7]Enrico Giudice, Jack Kuipers, Giusi Moffa:
Bayesian Causal Inference with Gaussian Process Networks. CoRR abs/2402.00623 (2024) - 2023
- [i6]Enrico Giudice, Jack Kuipers, Giusi Moffa:
A Bayesian Take on Gaussian Process Networks. CoRR abs/2306.11380 (2023) - [i5]Fritz M. Bayer, Drago Plecko, Niko Beerenwinkel, Jack Kuipers:
Fair Clustering: A Causal Perspective. CoRR abs/2312.09061 (2023) - 2021
- [i4]Felix L. Rios, Giusi Moffa, Jack Kuipers:
Benchpress: a scalable and platform-independent workflow for benchmarking structure learning algorithms for graphical models. CoRR abs/2107.03863 (2021) - [i3]Enrico Giudice, Jack Kuipers, Giusi Moffa:
The Dual PC Algorithm for Structure Learning. CoRR abs/2112.09036 (2021) - [i2]Fritz M. Bayer, Giusi Moffa, Niko Beerenwinkel, Jack Kuipers:
Marginalization in Bayesian Networks: Integrating Exact and Approximate Inference. CoRR abs/2112.09217 (2021) - 2018
- [i1]Jack Kuipers, Polina Suter, Giusi Moffa:
Efficient Structure Learning and Sampling of Bayesian Networks. CoRR abs/1803.07859 (2018)
Coauthor Index
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