Jack Kuipers - RankMe

41 papers A* 1B 6Journal 30Unranked 4

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Bayesian inference of fitness landscapes via tree-structured branching processes. Bioinform. Xiang Ge Luo, Jack Kuipers, Kevin Rupp, Koichi Takahashi, Niko Beerenwinkel
2025	J	`jnl`	Benchpress : A Versatile Platform for Structure Learning in Causal and Probabilistic Graphical Models. J. Stat. Softw. Felix L. Rios, Giusi Moffa, Jack Kuipers
2025	J	`jnl`	Determining distances and consensus between mutation trees. CoRR Luís Cunha, Jack Kuipers, Thiago Lopes
2025	—	`conf`	Exact discovery is polynomial for certain sparse causal Bayesian networks. CLeaR Felix Leopoldo Rios, Giusi Moffa, Jack Kuipers
2025	—	`conf`	Fair Clustering: A Causal Perspective. CLeaR Fritz M. Bayer, Drago Plecko, Niko Beerenwinkel, Jack Kuipers
2025	J	`jnl`	Scaling Up Bayesian DAG Sampling. CoRR Daniele Nikzad, Alexander Zhilkin, Juha Harviainen, Jack Kuipers, Giusi Moffa, Mikko Koivisto
2025	J	`jnl`	Single-cell copy number calling and event history reconstruction. Bioinform. Jack Kuipers, Mustafa Anil Tuncel, Pedro F. Ferreira, Katharina Jahn, Niko Beerenwinkel
2025	—	`conf`	The interventional Bayesian Gaussian equivalent score for Bayesian causal inference with unknown soft interventions. CLeaR Jack Kuipers, Giusi Moffa
2024	J	`jnl`	Bayesian Causal Inference with Gaussian Process Networks. CoRR Enrico Giudice, Jack Kuipers, Giusi Moffa
2023	A*	`conf`	A Bayesian Take on Gaussian Process Networks. NeurIPS Enrico Giudice, Jack Kuipers, Giusi Moffa
2023	J	`jnl`	A Bayesian Take on Gaussian Process Networks. CoRR Enrico Giudice, Jack Kuipers, Giusi Moffa
2023	J	`jnl`	Bayesian Structure Learning and Sampling of Bayesian Networks with the J. Stat. Softw. Polina Suter, Jack Kuipers, Giusi Moffa, Niko Beerenwinkel
2023	J	`jnl`	Fair Clustering: A Causal Perspective. CoRR Fritz M. Bayer, Drago Plecko, Niko Beerenwinkel, Jack Kuipers
2023	J	`jnl`	The dual PC algorithm and the role of Gaussianity for structure learning of Bayesian networks. Int. J. Approx. Reason. Enrico Giudice, Jack Kuipers, Giusi Moffa
2022	J	`jnl`	Discovering gene regulatory networks of multiple phenotypic groups using dynamic Bayesian networks. Briefings Bioinform. Polina Suter, Jack Kuipers, Niko Beerenwinkel
2022	J	`jnl`	Efficient Sampling and Structure Learning of Bayesian Networks. J. Comput. Graph. Stat. Jack Kuipers, Polina Suter, Giusi Moffa
2022	B	`conf`	Joint Inference of Repeated Evolutionary Trajectories and Patterns of Clonal Exclusivity or Co-occurrence from Tumor Mutation Trees. RECOMB Xiang Ge Luo, Jack Kuipers, Niko Beerenwinkel
2022	B	`conf`	Mapping Single-Cell Transcriptomes to Copy Number Evolutionary Trees. RECOMB Pedro F. Ferreira, Jack Kuipers, Niko Beerenwinkel
2022	J	`jnl`	Multi-omics subtyping of hepatocellular carcinoma patients using a Bayesian network mixture model. PLoS Comput. Biol. Polina Suter, Eva Dazert, Jack Kuipers, Charlotte K. Y. Ng, Tuyana Boldanova, Michael N. Hall, Markus H. Heim, Niko Beerenwinkel
2022	J	`jnl`	Single-cell mutation calling and phylogenetic tree reconstruction with loss and recurrence. Bioinform. Jack Kuipers, Jochen Singer, Niko Beerenwinkel
2022	—	`conf`	The Dual PC Algorithm for Structure Learning. PGM Enrico Giudice, Jack Kuipers, Giusi Moffa
2022	J	`jnl`	scAmpi - A versatile pipeline for single-cell RNA-seq analysis from basics to clinics. PLoS Comput. Biol. 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
2021	J	`jnl`	Benchpress: a scalable and platform-independent workflow for benchmarking structure learning algorithms for graphical models. CoRR Felix L. Rios, Giusi Moffa, Jack Kuipers
2021	J	`jnl`	Comparing mutational pathways to lopinavir resistance in HIV-1 subtypes B versus C. PLoS Comput. Biol. Susana Posada-Céspedes, Gert van Zyl, Hesam Montazeri, Jack Kuipers, Soo-Yon Rhee, Roger D. Kouyos, Huldrych F. Günthard, Niko Beerenwinkel
2021	J	`jnl`	Learning Bayesian Networks from Ordinal Data. J. Mach. Learn. Res. Xiang Ge Luo, Giusi Moffa, Jack Kuipers
2021	J	`jnl`	Marginalization in Bayesian Networks: Integrating Exact and Approximate Inference. CoRR Fritz M. Bayer, Giusi Moffa, Niko Beerenwinkel, Jack Kuipers
2021	J	`jnl`	Statistical tests for intra-tumour clonal co-occurrence and exclusivity. PLoS Comput. Biol. Jack Kuipers, Ariane L. Moore, Katharina Jahn, Peter Schraml, Feng Wang, Kiyomi Morita, P. Andrew Futreal, Koichi Takahashi, Christian Beisel, Holger Moch, Niko Beerenwinkel
2021	J	`jnl`	The Dual PC Algorithm for Structure Learning. CoRR Enrico Giudice, Jack Kuipers, Giusi Moffa
2020	J	`jnl`	Predicting colorectal cancer risk from adenoma detection via a two-type branching process model. PLoS Comput. Biol. Brian Lang, Jack Kuipers, Benjamin Misselwitz, Niko Beerenwinkel
2018	J	`jnl`	Efficient Structure Learning and Sampling of Bayesian Networks. CoRR Jack Kuipers, Polina Suter, Giusi Moffa
2018	J	`jnl`	Improved pathway reconstruction from RNA interference screens by exploiting off-target effects. Bioinform. Sumana Srivatsa, Jack Kuipers, Fabian Schmich, Simone Eicher, Mario Emmenlauer, Christoph Dehio, Niko Beerenwinkel
2018	B	`conf`	Integrative Inference of Subclonal Tumour Evolution from Single-Cell and Bulk Sequencing Data. RECOMB Salem Malikic, Katharina Jahn, Jack Kuipers, Süleyman Cenk Sahinalp, Niko Beerenwinkel
2018	B	`conf`	SCIΦ: Single-Cell Mutation Identification via Phylogenetic Inference. RECOMB Jochen Singer, Jack Kuipers, Katharina Jahn, Niko Beerenwinkel
2017	J	`jnl`	Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers. BMC Bioinform. Ariane L. Hofmann, Jonas Behr, Jochen Singer, Jack Kuipers, Christian Beisel, Peter Schraml, Holger Moch, Niko Beerenwinkel
2017	J	`jnl`	Multistate nested canalizing functions and their networks. Theor. Comput. Sci. Claus Kadelka, Yuan Li, Jack Kuipers, John O. Adeyeye, Reinhard C. Laubenbacher
2017	J	`jnl`	pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and Their Progression Dynamics. J. Comput. Biol. Simona Cristea, Jack Kuipers, Niko Beerenwinkel
2016	J	`jnl`	Large-scale inference of conjunctive Bayesian networks. Bioinform. 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
2016	B	`conf`	Tree Inference for Single-Cell Data. RECOMB Katharina Jahn, Jack Kuipers, Niko Beerenwinkel
2016	B	`conf`	pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and Their Dependencies in Tumor Progression. RECOMB Simona Cristea, Jack Kuipers, Niko Beerenwinkel
2015	J	`jnl`	Uniform random generation of large acyclic digraphs. Stat. Comput. Jack Kuipers, Giusi Moffa
2014	J	`jnl`	Sequential Monte Carlo EM for multivariate probit models. Comput. Stat. Data Anal. Giusi Moffa, Jack Kuipers