Dr. Jack Kuipers

Additional information

Preprints:

• Exact discovery is polynomial for sparse causal Bayesian networks
  Felix L. Rios, Giusi Moffa and Jack Kuipers
  arXiv:2406.15012
• A new way to evaluate G-Wishart normalising constants via Fourier analysis
  Ching Wong, Giusi Moffa and Jack Kuipers
  arXiv:2404.06803
• Bayesian causal inference with Gaussian process networks
  Enrico Giudice, Jack Kuipers and Giusi Moffa
  arXiv:2402.00623
• Fair clustering: A causal perspective
  Fritz M. Bayer, Drago Plečko, Niko Beerenwinkel and Jack Kuipers
  arXiv:2312.09061
• Network-based clustering unveils interconnected landscapes of genomic and clinical features across myeloid malignancies
  Fritz Bayer, Marco Roncador, Giusi Moffa, Kiyomi Morita, Koichi Takahashi, Niko Beerenwinkel and Jack Kuipers
  bioRxiv:2023.10.25.563992
• DelSIEVE: joint inference of single-nucleotide variants, somatic deletions and cell phylogeny from single-cell DNA sequencing data
  Senbai Kang, Nico Borgsmüller, Monica Valecha, Jack Kuipers, Niko Beerenwinkel, David Posada and Ewa Szczurek
  bioRxiv:2023.09.09.556903
• Uncovering network structure relating academic achievement, motivation, and schooling experience using structure learning of directed acyclic graphs
  Farhan Ali, Siska K. Lim, Giusi Moffa, Jack Kuipers and Rebecca P. Ang
  EdArXiv:3e7za
• Identifying hierarchical cell states and gene signatures with deep exponential families for single-cell transcriptomics
  Pedro F. Ferreira, Jack Kuipers^ and Niko Beerenwinkel^
  bioRxiv:2022.10.15.512383
• The interventional Bayesian Gaussian equivalent score for Bayesian causal inference with unknown soft interventions
  Jack Kuipers and Giusi Moffa
  arXiv:2205.02602
• High-dimensional inference in Bayesian networks
  Fritz M. Bayer, Giusi Moffa, Niko Beerenwinkel and Jack Kuipers
  arXiv:2112.09217
• Mapping single-cell transcriptomes to copy number evolutionary trees
  Pedro F. Ferreira, Jack Kuipers^ and Niko Beerenwinkel^
  RECOMB 2022
  bioRxiv:2021.11.04.467244
• Within-patient genetic diversity of SARS-CoV-2
  Jack Kuipers*, Aashil A Batavia*, Kim Philipp Jablonski*, Fritz Bayer, Nico Borgsmüller, Arthur Dondi, Monica-Andreea Drăgan, Pedro Ferreira, Katharina Jahn, Lisa Lamberti, Martin Pirkl, Susana Posada-Céspedes, Ivan Topolsky, Ina Nissen, Natascha Santacroce, Elodie Burcklen, Tobias Schär, Vincenzo Capece, Christiane Beckmann, Olivier Kobel, Christoph Noppen, Maurice Redondo, Sarah Nadeau, Sophie Seidel, Noemie Santamaria de Souza, Christian Beisel, Tanja Stadler and Niko Beerenwinkel
  bioRxiv:2020.10.12.335919
• Single-cell copy number calling and event history reconstruction
  Jack Kuipers*, Mustafa Anıl Tuncel*, Pedro Ferreira, Katharina Jahn and Niko Beerenwinkel
  bioRxiv:2020.04.28.065755

In press:

• Single-cell landscape of innate and acquired drug resistance in acute myeloid leukemia
  Rebekka Wegmann*, Ximena Bonilla*, Ruben Casanova*, Stéphane Chevrier*, RicardoCoelho*, Cinzia Esposito*, Joanna Ficek-Pascual*, Sandra Goetze*, Gabriele Gut*, Francis Jacob*, Andrea Jacobs*, Jack Kuipers*, Ulrike Lischetti*, Julien Mena*, Emanuela S. Milani*, Michael Prummer*, Jacobo Sarabia del Castillo*, Franziska Singer*, Sujana Sivapatham*, Nora C. Toussaint*, Oliver Vilinovszki*, Mattheus H.E. Wildschut*, Tharshika Thavayogarajah, Disha Malani, Tumor Profiler Consortium, Rudolf Aebersold^, Marina Bacac^, Niko Beerenwinkel^, Christian Beisel^, Bernd Bodenmiller^, Viola Heinzelmann-Schwarz^, Viktor H. Koelzer^, Mitchell P. Levesque^, Holger Moch^, Lucas Pelkmans^, Gunnar Rätsch^, Markus Tolnay^, Andreas Wicki^, Bernd Wollscheid^, Markus G. Manz^, Berend Snijder^, Alexandre P.A. Theocharides^
  Nature Communications, in press
• Benchpress: a scalable and platform-independent workflow for benchmarking structure learning algorithms for graphical models
  Felix L. Rios, Giusi Moffa and Jack Kuipers
  Journal of Statistical Software, in press
  arXiv:2107.03863

Computational Biology (30):

• Mutation order in acute myeloid leukemia identifies uncommon patterns of evolution and illuminates phenotypic heterogeneity (2024)
  Matthew Schwede*, Katharina Jahn*, Jack Kuipers, Linde Miles, Robert Bowman, Troy Robinson, Ken Furudate, Hidetaka Uryu, Tomoyuki Tanaka, Yuya Sasaki, Asiri Ediriwickrema, Brooks Benard, Andrew Gentles, Ross Levine, Niko Beerenwinkel^, Koichi Takahashi^ and Ravi Majeti^
  Leukemia 38 1501-1510
  Abstract
• Single-cell phylogenies reveal deviations from clock-like, neutral evolution in cancer and healthy tissues (2023)
  Nico Borgsmüller*, Monica Valecha*, Jack Kuipers, Niko Beerenwinkel^ and David Posada^
  Cell Genomics 3 100380
  Abstract   bioRxiv:2022.08.09.503287
• COMPASS: Joint copy number and mutation phylogeny reconstruction from single-cell amplicon sequencing data (2023)
  Etienne Sollier, Jack Kuipers, Koichi Takahashi, Niko Beerenwinkel and Katharina Jahn
  Nature Communications 14 4921
  Abstract   bioRxiv:2022.01.06.475205
• Joint inference of repeated evolutionary trajectories and patterns of clonal exclusivity or co-occurrence from tumor mutation trees (2023)
  Xiang Ge Luo, Jack Kuipers and Niko Beerenwinkel
  RECOMB 2022
  Nature Communications 14 3676
  Abstract   bioRxiv:2021.11.04.467347
• SIEVE: joint inference of single-nucleotide variants and cell phylogeny from single-cell DNA sequencing data (2022)
  Senbai Kang, Nico Borgsmüller, Monica Valecha, Jack Kuipers, Joao Alves, Sonia Prado-López, Débora Chantada, Niko Beerenwinkel, David Posada and Ewa Szczurek
  Genome Biology 23 248
  Abstract   bioRxiv:2022.03.24.485657
• Single-cell mutation calling and phylogenetic tree reconstruction with loss and recurrence (2022)
  Jack Kuipers*, Jochen Singer* and Niko Beerenwinkel
  Bioinformatics 38 4713-4719
  Abstract   bioRxiv:2022.01.28.478229
• Multi-omics subtyping of hepatocellular carcinoma patients using a Bayesian network mixture model (2022)
  Polina Suter, Eva Dazert, Jack Kuipers, Charlotte K.Y. Ng, Tuyana Boldanova, Michael N. Hall, Markus H. Heim and Niko Beerenwinkel
  PLoS Computational Biology 18 e1009767
  Abstract   bioRxiv:2021.12.16.473083
• Discovering gene regulatory networks of multiple phenotypic groups using dynamic Bayesian networks (2022)
  Polina Suter, Jack Kuipers and Niko Beerenwinkel
  Briefings in Bioinformatics 23 bbac219
  Abstract   bioRxiv:2021.12.16.473035
• scAmpi - A versatile pipeline for single-cell RNA-seq analysis from basics to clinics (2022)
  Anne Bertolini*, Michael Prummer*, Mustafa A. Tuncel, Ulrike Menzel, M. Lourdes Rosano-González, Jack Kuipers, Daniel J. Stekhoven, Tumor Profiler Consortium, Niko Beerenwinkel and Franziska Singer
  PLoS Computational Biology 18 e1010097
  Abstract   bioRxiv:2021.03.25.437054
• Statistical tests for intra-tumour clonal co-occurrence and exclusivity (2021)
  Jack Kuipers*, Ariane L. Moore*, Katharina Jahn, Peter Schraml, Feng Wang, Kiyomi Morita, P. Andrew Futreal, Koichi Takahashi, Christian Beisel, Holger Moch and Niko Beerenwinkel
  PLoS Computational Biology 17 e1009036
  Abstract   bioRxiv:2021.05.05.442732
• Comparing mutational pathways to lopinavir resistance in HIV-1 subtypes B versus C (2021)
  Susana Posada-Céspedes, Gert Van Zyl, Hesam Montazeri, Jack Kuipers, Soo-Yon Rhee, Roger Kouyos, Huldrych F. Günthard and Niko Beerenwinkel
  PLoS Computational Biology 17 e1008363
  Abstract   bioRxiv:2020.09.25.312942
• Spatial distribution of private gene mutations in clear cell renal cell carcinoma (2021)
  Ariane L. Moore*, Aashil A. Batavia*, Jack Kuipers, Jochen Singer, Elodie Burcklen, Peter Schraml, Christian Beisel, Holger Moch and Niko Beerenwinkel
  Cancers, 13 2163
  Abstract   bioRxiv:305623
• The Tumor Profiler Study: Integrated, multi-omic, functional tumor profiling for clinical decision support (2021)
  Anja Irmisch*, Ximena Bonilla*, Stéphane Chevrier*, Kjong-Van Lehmann*, Franziska Singer*, Nora C. Toussaint*, Cinzia Esposito*, Julien Mena*, Emanuela S. Milani*, Ruben Casanova*, Daniel J. Stekhoven*, Rebekka Wegmann*, Francis Jacob*, Bettina Sobottka*, Sandra Goetze*, Jack Kuipers*, Jacobo Sarabia del Castillo*, Michael Prummer, Mustafa A. Tuncel, Ulrike Menzel, Andrea Jacobs, Stefanie Engler, Sujana Sivapatham, Anja L. Frei, Gabriele Gut, Joanna Ficek, Nicola Miglino, Tumor Profiler Consortium, Rudolf Aebersold^, Marina Bacac^, Niko Beerenwinkel^, Christian Beisel^, Bernd Bodenmiller^, Reinhard Dummer^, Viola Heinzelmann-Schwarz^, Viktor H. Koelzer^, Markus G. Manz^, Holger Moch^, Lucas Pelkmans^, Berend Snijder^, Alexandre P.A. Theocharides^, Markus Tolnay^, Andreas Wicki^, Bernd Wollscheid^, Gunnar Rätsch^, Mitchell P. Levesque^
  Cancer Cell 39 288-293
  Abstract   medRxiv:2020.02.13.20017921
• Tracing clonal dynamics reveals that two- and three-dimensional patient-derived cell models capture tumor heterogeneity of clear cell renal cell carcinoma (2021)
  Hella A. Bolck*, Claudia Corrò*, Abdullah Kahraman, Adriana von Teichman, Nora C. Toussaint, Jack Kuipers, Francesca Chiovaro, Viktor H. Koelzer, Chantal Pauli, Wolfgang Moritz, Peter K. Bode, Markus Rechsteiner, Niko Beerenwinkel, Peter Schraml^ and Holger Moch^
  European Urology Focus 7 152-162
  Abstract
• Clonal evolution of Acute Myeloid Leukemia revealed by high-throughput single-cell genomics (2020)
  K. Morita*, F. Wang*, K. Jahn*, T. Hu, T. Tanaka, Y. Sasaki, J. Kuipers, S. Loghavi, S.A. Wang, Y. Yan, K. Furudate, J. Matthews, L. Little, C. Gumbs, J. Zhang, X. Song, E. Thompson, K. Patel, C.E. Bueso-Ramos, C.D. DiNardo, F. Ravandi, E. Jabbour, M. Andreeff, J. Cortes, K. Bhalla, G. Garcia-Manero, H. Kantarjian, M. Konopleva, D. Nakada, N. Navin, N. Beerenwinkel^, P.A. Futreal^ and K. Takahashi^
  Nature Communications 11 5327
  Abstract   bioRxiv:2020.02.07.925743
• Computational model reveals a stochastic mechanism behind germinal center clonal bursts (2020)
  Aurélien Pélissier, Youcef Akrout, Katharina Jahn, Jack Kuipers, Ulf Klein, Niko Beerenwinkel and María Rodríguez Martínez
  Cells 9 1448
  Abstract
• Predicting colorectal cancer risk from adenoma detection via a two-type branching process model (2020)
  Brian M. Lang*, Jack Kuipers*, Benjamin Misselwitz and Niko Beerenwinkel
  PLoS Computational Biology 16 e1007552
  Abstract
• Integrative inference of subclonal tumour evolution from single-cell and bulk sequencing data (2019)
  Salem Malikic*, Katharina Jahn*, Jack Kuipers*, Cenk Sahinalp^ and Niko Beerenwinkel^
  RECOMB 2018
  Nature Communications 10 2750
  Abstract   bioRxiv:234914
• netprioR: A probabilistic model for integrative hit prioritisation of genetic screens (2019)
  Fabian Schmich, Jack Kuipers, Gunter Merdes and Niko Beerenwinkel
  Statistical Applications in Genetics and Molecular Biology 18 20180033
  Abstract
• Single-cell mutation identification via phylogenetic inference (2018)
  Jochen Singer*, Jack Kuipers*, Katharina Jahn and Niko Beerenwinkel
  RECOMB 2018
  Nature Communications 9 5144
  Abstract   bioRxiv:290908
• Mutational interactions define novel cancer subgroups (2018)
  Jack Kuipers^, Thomas Thurnherr, Giusi Moffa, Polina Suter, Jonas Behr, Ryan Goosen, Gerhard Christofori, Niko Beerenwinkel^
  Nature Communications 9 4353
  Abstract   bioRxiv:187260
• Improved pathway reconstruction from RNA interference screens by exploiting off-target effects (2018)
  Sumana Srivatsa, Jack Kuipers, Fabian Schmich, Simone Eicher, Mario Emmenlauer, Christoph Dehio, Niko Beerenwinkel
  ISMB 2018
  Bioinformatics 34 i519–i527
  Abstract   bioRxiv:258319
• Single-cell sequencing data reveal widespread recurrence and loss of mutational hits in the life histories of tumors (2017)
  Jack Kuipers*, Katharina Jahn*, Benjamin J Raphael and Niko Beerenwinkel
  Genome Research 27 1885-1894
  Abstract   bioRxiv:094722
• The influence of canalization on the robustness of Boolean networks (2017)
  Claus Kadelka, Jack Kuipers and Reinhard Laubenbacher
  Physica D 353-354 39-47
  Abstract   arXiv:1607.04474   bioRxiv:064089
• Multistate nested canalizing functions and their networks (2017)
  Claus Kadelka, Yuan Li, Jack Kuipers, John O. Adeyeye and Reinhard Laubenbacher
  Theoretical Computer Science 675 1-14
  Abstract   arXiv:1411.4067
• Advances in understanding tumour evolution through single-cell sequencing (2017)
  Jack Kuipers*, Katharina Jahn* and Niko Beerenwinkel
  BBA Reviews on Cancer 1867 127-138
  Abstract
• pathTiMEx: Joint inference of mutually exclusive cancer pathways and their dependencies in tumor progression (2017)
  Simona Cristea, Jack Kuipers and Niko Beerenwinkel
  RECOMB 2016, Research in Computational Molecular Biology, 65-82 Abstract
  Journal of Computational Biology 24 603-615
  Abstract
• Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers (2017)
  Ariane Hofmann*, Jonas Behr*, Jochen Singer, Jack Kuipers, Christian Beisel, Peter Schraml, Holger Moch and Niko Beerenwinkel
  BMC Bioinformatics 18 8
  Abstract
• Large-scale inference of conjunctive Bayesian networks (2016)
  Hesam Montazeri, Jack Kuipers, Roger Kouyos, Jürg Böni, Sabine Yerly, Thomas Klimkait, Vincent Aubert, Huldrych F Günthard and Niko Beerenwinkel
  ECCB 2016
  Bioinformatics 32 i727-i735
  Abstract
• Tree inference for single-cell data (2016)
  Katharina Jahn*, Jack Kuipers* and Niko Beerenwinkel
  RECOMB 2016
  Genome Biology 17 86
  Abstract   bioRxiv:047795

Book chapters (2):

• Computational analysis of DNA and RNA sequencing data obtained from liquid biopsies (2020)
  Francesco Marass*, Francesc Castro-Giner*, Barbara M Szczerba, Katharina Jahn, Jack Kuipers, Nicola Aceto^ and Niko Beerenwinkel^
  In Tumor Liquid Biopsies, 347-368; Recent Results in Cancer Research 215; Springer, Cham
  Abstract
• Phylogeny-guided single-cell mutation calling (2019)
  Jochen Singer, Katherina Jahn, Jack Kuipers and Niko Beerenwinkel
  In Computational Systems Biology Approaches in Cancer Research; Recent Results in Cancer Research; CRC Press
  Abstract

Consortium papers (6):

• Detection of isoforms and genomic alterations by high-throughput full-length single-cell RNA sequencing in ovarian cancer (2023)
  Arthur Dondi*, Ulrike Lischetti*, Francis Jacob, Franziska Singer, Nico Borgsmüller, Ricardo Coelho, Tumor Profiler Consortium, Viola Heinzelmann-Schwarz, Christian Beisel^ and Niko Beerenwinkel^
  Nature Communications 14 7780
  Abstract
• ROS induction targets persister cancer cells with low metabolic activity in NRAS-mutated melanoma (2023)
  Ossia M Eichhoff, Corinne I Stoffel, Jan Käsler, Luzia Briker, Patrick Turko, Gergely Karsai, Nina Zila, Verena Paulitschke, Phil F Cheng, Alexander Leitner, Andrea Bileck, Nicola Zamboni, Anja Irmisch, Zsolt Balazs, Aizhan Tastanova, Susana Pascoal, Pål Johansen, Rebekka Wegmann, Julien Mena, Alaa Othman, Vasanthi S Viswanathan, Judith Wenzina, Andrea Aloia, Annalisa Saltari, Andreas Dzung, TuPro Consortium, Michael Krauthammer, Stuart L Schreiber, Thorsten Hornemann, Martin Distel, Berend Snijder, Reinhard Dummer, Mitchell P Levesque
  Cancer Research 83 1128-1146
  Abstract
• scROSHI: robust supervised hierarchical identification of single cells (2023)
  Michael Prummer, Anne Bertolini, Lars Bosshard, Florian Barkmann, Josephine Yates, Valentina Boeva, Tumor Profiler Consortium, Daniel Stekhoven, Franziska Singer
  NAR Genomics and Bioinformatics 5 lqad058
  Abstract
• Establishing standardized immune phenotyping of metastatic melanoma by digital pathology (2021)
  Bettina Sobottka, Marta Nowak, Anja Laura Frei, Martina Haberecker, Samuel Merki, Tumor Profiler Consortium, Mitchell P. Levesque, Reinhard Dummer, Holger Moch and Viktor H. Koelzer
  Laboratory Investigation 101 1561–1570
  Abstract
• SCIM: universal single-cell matching with unpaired feature sets (2020)
  Stefan G. Stark*, Joanna Ficek*, Francesco Locatello, Ximena Bonilla, Stéphane Chevrier, Franziska Singer, Tumor Profiler Consortium, Gunnar Rätsch^, Kjong-Van Lehmann^
  Bioinformatics 36 i919–i927
  Abstract   bioRxiv:2020.06.11.146845
• CATALYST: An R-based reproducible and user-friendly preprocessing pipeline for CyTOF data (2020)
  Helena L. Crowell*, Stéphane Chevrier*, Andrea Jacobs, Sujana Sivapatham, Tumor Profiler Consortium, Bernd Bodenmiller*, Mark D. Robinson*
  F1000Research 9 1263
  Abstract

Computational Statistics (15):

• A Bayesian take on Gaussian process networks (2023)
  Enrico Giudice, Jack Kuipers and Giusi Moffa
  NeurIPS 36 56602-56514
  Abstract   arXiv:2306.11380
• Sexual abuse and psychotic phenomena: a Directed Acyclic Graph analysis of affective symptoms using English national psychiatric survey data (2023)
  G. Moffa, J. Kuipers, E. Kuipers, S. McManus and P. Bebbington
  Psychological Medicine 38 7817-7826
  Abstract
• The dual PC algorithm and the role of Gaussianity for structure learning of Bayesian networks (2023)
  Enrico Giudice, Jack Kuipers and Giusi Moffa
  IJAR 161 108975
  Abstract   arXiv:2112.09036
• Bayesian structure learning and sampling of Bayesian networks with the R package BiDAG (2023)
  Polina Suter, Jack Kuipers, Giusi Moffa and Niko Beerenwinkel
  Journal of Statistical Software 105 i09
  Abstract   arXiv:2105.00488
• Longitudinal symptomatic interactions in long-standing schizophrenia: a novel five-point analysis based on directed acyclic graphs (2023)
  G. Moffa*, J. Kuipers*, G. Carrà, C. Crocamo, E. Kuipers, M. Angermeyer, T. Brugha, M. Toumi and P. Bebbington
  Psychological Medicine 53 1371-1378
  Abstract
• The dual PC algorithm for structure learning (2022)
  Enrico Giudice, Jack Kuipers and Giusi Moffa
  PGM 2022, best student paper award
  PMLR 186 301-312
  Abstract
• Efficient sampling and structure learning of Bayesian networks (2022)
  Jack Kuipers, Polina Suter and Giusi Moffa
  Journal of Computational and Graphical Statistics 31 639-650
  Abstract   arXiv:1803.07859
• The variance of causal effect estimators for binary v-structures (2022)
  Jack Kuipers and Giusi Moffa
  Journal of Causal Inference 10 90-105
  Abstract   arXiv:2004.09181
• Learning Bayesian networks from ordinal data (2021)
  Xiang Ge Luo, Giusi Moffa and Jack Kuipers
  Journal of Machine Learning Research, 22 1-44
  Abstract   arXiv:2010.15808
• Links between psychotic and neurotic symptoms in the general population: An analysis of longitudinal British National Survey data using Directed Acyclic Graphs (2019)
  J. Kuipers*, G. Moffa*, E. Kuipers, D. Freeman and P. Bebbington
  Psychological Medicine 49 388-395
  Abstract
• Using directed acyclic graphs in epidemiological research in psychosis: An analysis of the role of bullying in psychosis (2017)
  G. Moffa*, G. Catone*, J. Kuipers, E. Kuipers, D. Freeman, S. Marwaha, B. Lennox, M. Broome and P. Bebbington
  Schizophrenia Bulletin 43 1273-1279
  Abstract
• Partition MCMC for inference on acyclic digraphs (2017)
  Jack Kuipers and Giusi Moffa
  J. Am. Stat. Assoc. 112 282-299
  Abstract   arXiv:1504.05006
• Uniform random generation of large acyclic digraphs (2015)
  Jack Kuipers and Giusi Moffa
  Stats. & Comp. 25 227-242
  Abstract   arXiv:1202.6590
• Addendum on the scoring of Gaussian directed acyclic graphical models (2014)
  Jack Kuipers, Giusi Moffa and David Heckerman
  Ann. Stats. 42 1689-1691
  Abstract   arXiv:1402.6863
• Sequential Monte Carlo EM for multivariate probit models (2014)
  Giusi Moffa and Jack Kuipers
  Comp. Stats. & Data An. 72 252-272
  Abstract   arXiv:1107.2205

Mathematical Physics (29):

• Effect of a tunnel barrier on time delay statistics (2023)
  Marcel Novaes and Jack Kuipers
  Phys. Rev. E 108 034201
  Abstract   arXiv:2302.09030
• Universal S-matrix correlations for complex scattering of many-body wavepackets: theory, simulation and experiment (2021)
  Andreas Bereczuk, Barbara Dietz, Jiongning Che, Jack Kuipers, Juan-Diego Urbina and Klaus Richter
  Phys. Rev. E 103 052209
  Abstract   arXiv:2010.07409
• From many-particle interference to correlation spectroscopy (2016)
  Mattia Walschaers, Jack Kuipers and Andreas Buchleitner
  Phys. Rev. A 94 020104(R)
  Abstract   arXiv:1604.00649
• Multiparticle correlations in mesoscopic scattering: Boson sampling, birthday paradox, and Hong-Ou-Mandel profiles (2016)
  Juan-Diego Urbina, Jack Kuipers, Sho Matsumoto, Quirin Hummel and Klaus Richter
  Phys. Rev. Lett. 116 100401
  Abstract   arXiv:1409.1558
• Statistical benchmark for BosonSampling (2016)
  Mattia Walschaers, Jack Kuipers, Juan-Diego Urbina, Klaus Mayer, Malte C Tichy, Klaus Richter and Andreas Buchleitner
  New J. Phys. 18 032001
  Abstract   arXiv:1410.8547
• Efficient semiclassical approach for time delays (2014)
  Jack Kuipers, Dmitry V. Savin and Martin Sieber
  New J. Phys. 16 123018
  Abstract   arXiv:1409.1532
• Quantum graphs whose spectra mimic the zeros of the Riemann zeta function (2014)
  Jack Kuipers, Quirin Hummel and Klaus Richter
  Phys. Rev. Lett. 112 070406
  Abstract   arXiv:1307.6055
• Combinatorial theory of the semiclassical evaluation of transport moments II: Algorithmic approach for moment generating functions (2013)
  Gregory Berkolaiko* and Jack Kuipers*
  J. Math. Phys. 54 123505
  Abstract   arXiv:1307.3280
• Combinatorial theory of the semiclassical evaluation of transport moments I: Equivalence with the random matrix approach (2013)
  Gregory Berkolaiko* and Jack Kuipers*
  J. Math. Phys. 54 112103
  Abstract   arXiv:1305.4875
• Transport moments and Andreev billiards with tunnel barriers (2013)
  Jack Kuipers and Klaus Richter
  J. Phys. A 46 055101
  Abstract   arXiv:1210.7948
• Universality in chaotic quantum transport: The concordance between random matrix and semiclassical theories (2012)
  Gregory Berkolaiko* and Jack Kuipers*
  Phys. Rev. E 85 045201(R)
  Abstract   arXiv:1111.4906
• Conductance fluctuations in chaotic systems with tunnel barriers (2012)
  Daniel Waltner, Jack Kuipers, Philippe Jacquod and Klaus Richter
  Phys. Rev. B 85 024302
  Abstract   arXiv:1108.5091
• Transport moments beyond the leading order (2011)
  Gregory Berkolaiko* and Jack Kuipers*
  New J. Phys.13 063020
  Abstract   arXiv:1012.3526
• Conductance and thermopower of ballistic Andreev cavities (2011)
  Thomas Engl, Jack Kuipers and Klaus Richter
  Phys. Rev. B 83 205414
  Abstract   arXiv:1012.3385
• The density of states of chaotic Andreev billiards (2011)
  Jack Kuipers, Thomas Engl, Gregory Berkolaiko, Cyril Petitjean, Daniel Waltner and Klaus Richter
  Phys. Rev. B 83 195316
  Abstract   arXiv:1004.1327
• Ehrenfest-time dependence of counting statistics for chaotic ballistic systems (2011)
  Daniel Waltner, Jack Kuipers and Klaus Richter
  Phys. Rev. B 83 195315
  Abstract   arXiv:1007.1595
• Weak localization in mesoscopic hole transport: Berry phases and classical correlations (2011)
  Viktor Krueckl, Michael Wimmer, Inanc Adagideli, Jack Kuipers and Klaus Richter
  Phys. Rev. Lett. 106 146801
  Abstract   arXiv:1009.5571
• Ehrenfest-time dependence of quantum transport corrections and spectral statistics (2010)
  Daniel Waltner and Jack Kuipers
  Phys. Rev. E 82 066205
  Abstract   arXiv:1006.0142
• Quantum corrections to fidelity decay in chaotic systems (2010)
  Boris Gutkin, Daniel Waltner, Martha Gutiérrez, Jack Kuipers and Klaus Richter
  Phys. Rev. E 81 036222
  Abstract   arXiv:0911.0823
• Moments of the Wigner delay times (2010)
  Gregory Berkolaiko* and Jack Kuipers*
  J. Phys. A 43 035101
  Abstract   arXiv:0910.0060
• Semiclassical gaps in the density of states of chaotic Andreev billiards (2010)
  Jack Kuipers, Daniel Waltner, Cyril Petitjean, Gregory Berkolaiko and Klaus Richter
  Phys. Rev. Lett. 104 027001
  Abstract   arXiv:0907.2660
• Semiclassics for chaotic systems with tunnel barriers (2009)
  Jack Kuipers
  J. Phys. A 42 425101
  Abstract   arXiv:0906.1964
• Semiclassical approach to the ac-conductance of chaotic cavities (2009)
  Cyril Petitjean, Daniel Waltner, Jack Kuipers, Inanc Adagideli and Klaus Richter
  Phys. Rev. B 80 115310
  Abstract   arXiv:0906.1791
• The semiclassical continuity equation for open chaotic systems (2009)
  Jack Kuipers, Daniel Waltner, Martha Gutiérrez and Klaus Richter
  Nonlinearity 22 1946-1964
  Abstract   arXiv:0811.2164
• Semiclassical theory for decay and fragmentation processes in chaotic quantum systems (2009)
  Martha Gutiérrez, Daniel Waltner, Jack Kuipers and Klaus Richter
  Phys. Rev. E 79 046212
  Abstract   arXiv:0811.1884
• The semiclassical relation between open trajectories and periodic orbits for the Wigner time delay (2008)
  Jack Kuipers and Martin Sieber
  Phys. Rev. E 77 046219
  Abstract   arXiv:0711.4537
• Semiclassical expansion of parametric correlations functions of the quantum time delay (2007)
  Jack Kuipers and Martin Sieber
  Nonlinearity 20 909-926
  Abstract   arXiv:nlin/0608059
• Semiclassical universality of parametric spectral correlations (2007)
  Jack Kuipers and Martin Sieber
  J. Phys. A 40 935-948
  Abstract   arXiv:nlin/0608008
• Nucleated dwarf elliptical galaxies in the Virgo cluster (2005)
  N.I. Grant*, J.A. Kuipers* and S. Phillipps
  MNRAS 363 1019-1030
  Abstract