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Computational Analysis of DNA and RNA Sequencing Data Obtained from Liquid Biopsies.

Marass F, Castro-Giner F, Szczerba BM, Jahn K, Kuipers J, Aceto N, Beerenwinkel N.

Recent Results Cancer Res. 2020;215:347-368. doi: 10.1007/978-3-030-26439-0_18.


Tracing Clonal Dynamics Reveals that Two- and Three-dimensional Patient-derived Cell Models Capture Tumor Heterogeneity of Clear Cell Renal Cell Carcinoma.

Bolck HA, Corrò C, Kahraman A, von Teichman A, Toussaint NC, Kuipers J, Chiovaro F, Koelzer VH, Pauli C, Moritz W, Bode PK, Rechsteiner M, Beerenwinkel N, Schraml P, Moch H.

Eur Urol Focus. 2019 Jun 29. pii: S2405-4569(19)30164-6. doi: 10.1016/j.euf.2019.06.009. [Epub ahead of print]


Integrative inference of subclonal tumour evolution from single-cell and bulk sequencing data.

Malikic S, Jahn K, Kuipers J, Sahinalp SC, Beerenwinkel N.

Nat Commun. 2019 Jun 21;10(1):2750. doi: 10.1038/s41467-019-10737-5.


The Prevalence of Intradialytic Hypotension in Patients on Conventional Hemodialysis: A Systematic Review with Meta-Analysis.

Kuipers J, Verboom LM, Ipema KJR, Paans W, Krijnen WP, Gaillard CAJM, Westerhuis R, Franssen CFM.

Am J Nephrol. 2019;49(6):497-506. doi: 10.1159/000500877. Epub 2019 May 24. Review.


Association between quality of life and various aspects of intradialytic hypotension including patient-reported intradialytic symptom score.

Kuipers J, Oosterhuis JK, Paans W, Krijnen WP, Gaillard CAJM, Westerhuis R, Franssen CFM.

BMC Nephrol. 2019 May 14;20(1):164. doi: 10.1186/s12882-019-1366-2.


Evaluation of simulated driving in comparison to laboratory-based tests to assess the pharmacodynamics of alprazolam and alcohol.

Huizinga CR, Zuiker RG, de Kam ML, Ziagkos D, Kuipers J, Mejia Y, van Gerven JM, Cohen AF.

J Psychopharmacol. 2019 Jul;33(7):791-800. doi: 10.1177/0269881119836198. Epub 2019 Mar 26.


Effect of microchannel structure and fluid properties on non-inertial particle migration.

Maitri RV, De S, Koesen SP, Wyss HM, van der Schaaf J, Kuipers JAM, Padding JT, Peters EAJF.

Soft Matter. 2019 Mar 20;15(12):2648-2656. doi: 10.1039/c8sm02348d.


netprioR: a probabilistic model for integrative hit prioritisation of genetic screens.

Schmich F, Kuipers J, Merdes G, Beerenwinkel N.

Stat Appl Genet Mol Biol. 2019 Mar 6;18(3). pii: /j/sagmb.2019.18.issue-3/sagmb-2018-0033/sagmb-2018-0033.xml. doi: 10.1515/sagmb-2018-0033.


Exosomes derived from monocytes and from endothelial cells mediate monocyte and endothelial cell activation under high d-glucose conditions.

Sáez T, de Vos P, Kuipers J, Sobrevia L, Faas MM.

Immunobiology. 2019 Mar;224(2):325-333. doi: 10.1016/j.imbio.2019.02.004. Epub 2019 Feb 22.


Changes in cerebral oxygenation and cerebral blood flow during hemodialysis - A simultaneous near-infrared spectroscopy and positron emission tomography study.

Polinder-Bos HA, Elting JWJ, Aries MJ, García DV, Willemsen AT, van Laar PJ, Kuipers J, Krijnen WP, Slart RH, Luurtsema G, Westerhuis R, Gansevoort RT, Gaillard CA, Franssen CF.

J Cereb Blood Flow Metab. 2018 Dec 12:271678X18818652. doi: 10.1177/0271678X18818652. [Epub ahead of print]


Single-cell mutation identification via phylogenetic inference.

Singer J, Kuipers J, Jahn K, Beerenwinkel N.

Nat Commun. 2018 Dec 4;9(1):5144. doi: 10.1038/s41467-018-07627-7.


Direct Numerical Simulation of Reactive Fluid-Particle Systems Using an Immersed Boundary Method.

Lu J, Tan MD, Peters EAJF, Kuipers JAM.

Ind Eng Chem Res. 2018 Nov 14;57(45):15565-15578. doi: 10.1021/acs.iecr.8b03158. Epub 2018 Oct 19.


Supramolecular Packing and Macroscopic Alignment Controls Actuation Speed in Macroscopic Strings of Molecular Motor Amphiphiles.

Leung FK, van den Enk T, Kajitani T, Chen J, Stuart MCA, Kuipers J, Fukushima T, Feringa BL.

J Am Chem Soc. 2018 Dec 19;140(50):17724-17733. doi: 10.1021/jacs.8b10778. Epub 2018 Dec 4.


Effect of Dentin Matrix Components on the Mineralization of Human Mesenchymal Stromal Cells.

Petridis X, Beems BP, Tomson PL, Scheven B, Giepmans BNG, Kuipers J, van der Sluis LWM, Harmsen MC.

Tissue Eng Part A. 2019 Aug;25(15-16):1104-1115. doi: 10.1089/ten.TEA.2018.0192. Epub 2018 Dec 28.


Mutational interactions define novel cancer subgroups.

Kuipers J, Thurnherr T, Moffa G, Suter P, Behr J, Goosen R, Christofori G, Beerenwinkel N.

Nat Commun. 2018 Oct 19;9(1):4353. doi: 10.1038/s41467-018-06867-x.


Deactivation Kinetics of Solid Acid Catalyst with Laterally Interacting Protons.

Sengar A, van Santen RA, Steur E, Kuipers JAM, Padding J.

ACS Catal. 2018 Oct 5;8(10):9016-9033. doi: 10.1021/acscatal.8b01511. Epub 2018 Aug 16.


Human adipose tissue-derived stromal cells act as functional pericytes in mice and suppress high-glucose-induced proinflammatory activation of bovine retinal endothelial cells.

Hajmousa G, Przybyt E, Pfister F, Paredes-Juarez GA, Moganti K, Busch S, Kuipers J, Klaassen I, van Luyn MJA, Krenning G, Hammes HP, Harmsen MC.

Diabetologia. 2018 Nov;61(11):2371-2385. doi: 10.1007/s00125-018-4713-0. Epub 2018 Aug 27.


Effect of plasma sodium concentration on blood pressure regulators during hemodialysis: a randomized crossover study.

Ettema EM, Kuipers J, van Faassen M, Groen H, van Roon AM, Lefrandt JD, Westerhuis R, Kema IP, van Goor H, Gansevoort RT, Gaillard CAJM, Franssen CFM.

BMC Nephrol. 2018 Aug 22;19(1):214. doi: 10.1186/s12882-018-0997-z.


[S2e guideline: treatment of rheumatoid arthritis with disease-modifying drugs].

Fiehn C, Holle J, Iking-Konert C, Leipe J, Weseloh C, Frerix M, Alten R, Behrens F, Baerwald C, Braun J, Burkhardt H, Burmester G, Detert J, Gaubitz M, Gause A, Gromnica-Ihle E, Kellner H, Krause A, Kuipers J, Lorenz HM, Müller-Ladner U, Nothacker M, Nüsslein H, Rubbert-Roth A, Schneider M, Schulze-Koops H, Seitz S, Sitter H, Specker C, Tony HP, Wassenberg S, Wollenhaupt J, Krüger K.

Z Rheumatol. 2018 Aug;77(Suppl 2):35-53. doi: 10.1007/s00393-018-0481-y. Review. German.


Improved pathway reconstruction from RNA interference screens by exploiting off-target effects.

Srivatsa S, Kuipers J, Schmich F, Eicher S, Emmenlauer M, Dehio C, Beerenwinkel N.

Bioinformatics. 2018 Jul 1;34(13):i519-i527. doi: 10.1093/bioinformatics/bty240.


Fetoplacental endothelial exosomes modulate high d-glucose-induced endothelial dysfunction.

Sáez T, de Vos P, Kuipers J, Sobrevia L, Faas MM.

Placenta. 2018 Jun;66:26-35. doi: 10.1016/j.placenta.2018.04.010. Epub 2018 Apr 21.


Links between psychotic and neurotic symptoms in the general population: an analysis of longitudinal British National Survey data using Directed Acyclic Graphs.

Kuipers J, Moffa G, Kuipers E, Freeman D, Bebbington P.

Psychol Med. 2019 Feb;49(3):388-395. doi: 10.1017/S0033291718000879. Epub 2018 May 29.


Abstract images and words can convey the same meaning.

Kuipers JR, Jones MW, Thierry G.

Sci Rep. 2018 May 8;8(1):7190. doi: 10.1038/s41598-018-25441-5.


Episodic traces and statistical regularities: Paired associate learning in typical and dyslexic readers.

Jones MW, Kuipers JR, Nugent S, Miley A, Oppenheim G.

Cognition. 2018 Aug;177:214-225. doi: 10.1016/j.cognition.2018.04.010. Epub 2018 Apr 27.


Nonspherical particles in a pseudo-2D fluidized bed: Experimental study.

Mahajan VV, Padding JT, Nijssen TMJ, Buist KA, Kuipers JAM.

AIChE J. 2018 May;64(5):1573-1590. doi: 10.1002/aic.16078. Epub 2018 Feb 6.


Adherence and health literacy as related to outcome of patients treated for rheumatoid arthritis : Analyses of a large-scale observational study.

Kuipers JG, Koller M, Zeman F, Müller K, Rüffer JU.

Z Rheumatol. 2019 Feb;78(1):74-81. doi: 10.1007/s00393-018-0449-y.


Direct Numerical Simulation of Fluid Flow and Mass Transfer in Particle Clusters.

Lu J, Peters EAJF, Kuipers JAM.

Ind Eng Chem Res. 2018 Apr 4;57(13):4664-4679. doi: 10.1021/acs.iecr.8b00268. Epub 2018 Mar 15.


Deregulation of secondary metabolism in a histone deacetylase mutant of Penicillium chrysogenum.

Guzman-Chavez F, Salo O, Samol M, Ries M, Kuipers J, Bovenberg RAL, Vreeken RJ, Driessen AJM.

Microbiologyopen. 2018 Oct;7(5):e00598. doi: 10.1002/mbo3.598. Epub 2018 Mar 24.


There's no place like OM: Vesicular sorting and secretion of the peptidylarginine deiminase of Porphyromonas gingivalis.

Gabarrini G, Palma Medina LM, Stobernack T, Prins RC, du Teil Espina M, Kuipers J, Chlebowicz MA, Rossen JWA, van Winkelhoff AJ, van Dijl JM.

Virulence. 2018 Jan 1;9(1):456-464. doi: 10.1080/21505594.2017.1421827.


Hemodialysis Induces an Acute Decline in Cerebral Blood Flow in Elderly Patients.

Polinder-Bos HA, García DV, Kuipers J, Elting JWJ, Aries MJH, Krijnen WP, Groen H, Willemsen ATM, van Laar PJ, Strijkert F, Luurtsema G, Slart RHJA, Westerhuis R, Gansevoort RT, Gaillard CAJM, Franssen CFM.

J Am Soc Nephrol. 2018 Apr;29(4):1317-1325. doi: 10.1681/ASN.2017101088. Epub 2018 Mar 1. Erratum in: J Am Soc Nephrol. 2018 Aug;29(8):2256.


Iron deficiency impairs contractility of human cardiomyocytes through decreased mitochondrial function.

Hoes MF, Grote Beverborg N, Kijlstra JD, Kuipers J, Swinkels DW, Giepmans BNG, Rodenburg RJ, van Veldhuisen DJ, de Boer RA, van der Meer P.

Eur J Heart Fail. 2018 May;20(5):910-919. doi: 10.1002/ejhf.1154. Epub 2018 Feb 27.


A novel flatworm-specific gene implicated in reproduction in Macrostomum lignano.

Grudniewska M, Mouton S, Grelling M, Wolters AHG, Kuipers J, Giepmans BNG, Berezikov E.

Sci Rep. 2018 Feb 16;8(1):3192. doi: 10.1038/s41598-018-21107-4.


A small protein probe for correlated microscopy of endogenous proteins.

de Beer MA, Kuipers J, van Bergen En Henegouwen PMP, Giepmans BNG.

Histochem Cell Biol. 2018 Mar;149(3):261-268. doi: 10.1007/s00418-018-1632-6. Epub 2018 Jan 11.


Magnetic particle tracking for nonspherical particles in a cylindrical fluidized bed.

Buist KA, Jayaprakash P, Kuipers JAM, Deen NG, Padding JT.

AIChE J. 2017 Dec;63(12):5335-5342. doi: 10.1002/aic.15854. Epub 2017 Jul 18.


Viscoelastic flow past mono- and bidisperse random arrays of cylinders: flow resistance, topology and normal stress distribution.

De S, Kuipers JAM, Peters EAJF, Padding JT.

Soft Matter. 2017 Dec 13;13(48):9138-9146. doi: 10.1039/c7sm01818e.


Effect of Superficial Gas Velocity on the Solid Temperature Distribution in Gas Fluidized Beds with Heat Production.

Banaei M, Jegers J, van Sint Annaland M, Kuipers JAM, Deen NG.

Ind Eng Chem Res. 2017 Aug 2;56(30):8729-8737. doi: 10.1021/acs.iecr.7b00338. Epub 2017 Jul 11.


Effect of isolated ultrafiltration and isovolemic dialysis on myocardial perfusion and left ventricular function assessed with 13N-NH3 positron emission tomography and echocardiography.

Assa S, Kuipers J, Ettema E, Gaillard CAJM, Krijnen WP, Hummel YM, Voors AA, van Melle JP, Westerhuis R, Willemsen A, Slart RHJA, Franssen CFM.

Am J Physiol Renal Physiol. 2018 Mar 1;314(3):F445-F452. doi: 10.1152/ajprenal.00368.2017. Epub 2017 Nov 8.


Single-cell sequencing data reveal widespread recurrence and loss of mutational hits in the life histories of tumors.

Kuipers J, Jahn K, Raphael BJ, Beerenwinkel N.

Genome Res. 2017 Nov;27(11):1885-1894. doi: 10.1101/gr.220707.117. Epub 2017 Oct 13.


Particle-based modeling of heterogeneous chemical kinetics including mass transfer.

Sengar A, Kuipers JAM, van Santen RA, Padding JT.

Phys Rev E. 2017 Aug;96(2-1):022115. doi: 10.1103/PhysRevE.96.022115. Epub 2017 Aug 8.


Viscoelastic effects on residual oil distribution in flows through pillared microchannels.

De S, Krishnan P, van der Schaaf J, Kuipers JAM, Peters EAJF, Padding JT.

J Colloid Interface Sci. 2018 Jan 15;510:262-271. doi: 10.1016/j.jcis.2017.09.069. Epub 2017 Sep 20.


Computational Fluid Dynamics-Discrete Element Method (CFD-DEM) Study of Mass-Transfer Mechanisms in Riser Flow.

Carlos Varas ÁE, Peters EAJF, Kuipers JAM.

Ind Eng Chem Res. 2017 May 17;56(19):5558-5572. doi: 10.1021/acs.iecr.7b00366. Epub 2017 Apr 26.


Using Directed Acyclic Graphs in Epidemiological Research in Psychosis: An Analysis of the Role of Bullying in Psychosis.

Moffa G, Catone G, Kuipers J, Kuipers E, Freeman D, Marwaha S, Lennox BR, Broome MR, Bebbington P.

Schizophr Bull. 2017 Oct 21;43(6):1273-1279. doi: 10.1093/schbul/sbx013.


Guanine quadruplex structures localize to heterochromatin.

Hoffmann RF, Moshkin YM, Mouton S, Grzeschik NA, Kalicharan RD, Kuipers J, Wolters AHG, Nishida K, Romashchenko AV, Postberg J, Lipps H, Berezikov E, Sibon OCM, Giepmans BNG, Lansdorp PM.

Nucleic Acids Res. 2017 Jun 2;45(10):6253. doi: 10.1093/nar/gkx301. No abstract available.


Multi-color electron microscopy by element-guided identification of cells, organelles and molecules.

Scotuzzi M, Kuipers J, Wensveen DI, de Boer P, Hagen KC, Hoogenboom JP, Giepmans BN.

Sci Rep. 2017 Apr 7;7:45970. doi: 10.1038/srep45970.


Word meaning acquisition is reflected in brain potentials of isolated words.

Kuipers JR, Uminski A, Green Z, Hughes D, Aglietti T.

Sci Rep. 2017 Mar 3;7:43341. doi: 10.1038/srep43341.


Advances in understanding tumour evolution through single-cell sequencing.

Kuipers J, Jahn K, Beerenwinkel N.

Biochim Biophys Acta Rev Cancer. 2017 Apr;1867(2):127-138. doi: 10.1016/j.bbcan.2017.02.001. Epub 2017 Feb 11. Review.


Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers.

Hofmann AL, Behr J, Singer J, Kuipers J, Beisel C, Schraml P, Moch H, Beerenwinkel N.

BMC Bioinformatics. 2017 Jan 3;18(1):8. doi: 10.1186/s12859-016-1417-7.


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

Cristea S, Kuipers J, Beerenwinkel N.

J Comput Biol. 2017 Jun;24(6):603-615. doi: 10.1089/cmb.2016.0171. Epub 2016 Dec 12.


Causes and Consequences of Interdialytic weight gain.

Ipema KJ, Kuipers J, Westerhuis R, Gaillard CA, van der Schans CP, Krijnen WP, Franssen CF.

Kidney Blood Press Res. 2016;41(5):710-720. Epub 2016 Oct 14.


Large-scale inference of conjunctive Bayesian networks.

Montazeri H, Kuipers J, Kouyos R, Böni J, Yerly S, Klimkait T, Aubert V, Günthard HF, Beerenwinkel N; Swiss HIV Cohort Study.

Bioinformatics. 2016 Sep 1;32(17):i727-i735. doi: 10.1093/bioinformatics/btw459.


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