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ArticlesPeer ReviewedFull Text
Transcriptomic and metabolomic data integration
Author / Creator:Cavill, Rachel ; Jennen, Danyel ; Kleinjans, Jos ; Briedé, Jacob Jan
Publisher:England
Journal title:Briefings in bioinformatics, 2016-09, Vol.17 (5), p.891-901
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Validation of polymorphic Gompertzian model of cancer through in vitro and in vivo data
Author / Creator:Soboleva, Arina ; Kaznatcheev, Artem ; Cavill, Rachel ; Schneider, Katharina ; Staňková, Kateřina
Publisher:United States: Public Library of Science
Journal title:PloS one, 2025-01, Vol.20 (1), p.e0310844
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Assessment of a complete and classified platelet proteome from genome-wide transcripts of human platelets and megakaryocytes covering platelet functions
Author / Creator:Huang, Jingnan ; Swieringa, Frauke ; Solari, Fiorella A. ; Provenzale, Isabella ; Grassi, Luigi ; De Simone, Ilaria ; Baaten, Constance C. F. M. J. ; Cavill, Rachel ; Sickmann, Albert ; Frontini, Mattia ; Heemskerk, Johan W. M.
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2021-06, Vol.11 (1), p.12358-18, Article 12358
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ArticlesPeer ReviewedFull Text
PSnpBind-ML: predicting the effect of binding site mutations on protein-ligand binding affinity
Author / Creator:Ammar, Ammar ; Cavill, Rachel ; Evelo, Chris ; Willighagen, Egon
Publisher:Cham: Springer International Publishing
Journal title:Journal of cheminformatics, 2023-03, Vol.15 (1), p.31-31, Article 31
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PSnpBind: a database of mutated binding site protein–ligand complexes constructed using a multithreaded virtual screening workflow
Author / Creator:Ammar, Ammar ; Cavill, Rachel ; Evelo, Chris ; Willighagen, Egon
Publisher:Cham: Springer International Publishing
Journal title:Journal of cheminformatics, 2022-02, Vol.14 (1), p.8-16, Article 8
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An agent-based approach for modelling and simulation of glycoprotein VI receptor diffusion, localisation and dimerisation in platelet lipid rafts
Author / Creator:Tantiwong, Chukiat ; Dunster, Joanne L. ; Cavill, Rachel ; Tomlinson, Michael G. ; Wierling, Christoph ; Heemskerk, Johan W. M. ; Gibbins, Jonathan M.
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2023-03, Vol.13 (1), p.3906-3906, Article 3906
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Application of transfer learning to predict drug-induced human in vivo gene expression changes using rat in vitro and in vivo data
Author / Creator:O’Donovan, Shauna D. ; Cavill, Rachel ; Wimmenauer, Florian ; Lukas, Alexander ; Stumm, Tobias ; Smirnov, Evgueni ; Lenz, Michael ; Ertaylan, Gokhan ; Jennen, Danyel G. J. ; van Riel, Natal A. W. ; Driessens, Kurt ; Peeters, Ralf L. M. ; de Kok, Theo M. C. M.
Publisher:San Francisco, CA USA: Public Library of Science
Journal title:PloS one, 2023-11, Vol.18 (11), p.e0292030-e0292030
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Deep embedded clustering generalisability and adaptation for integrating mixed datatypes: two critical care cohorts
Author / Creator:de Kok, Jip W. T. M. ; van Rosmalen, Frank ; Koeze, Jacqueline ; Keus, Frederik ; van Kuijk, Sander M. J. ; Castela Forte, José ; Schnabel, Ronny M. ; Driessen, Rob G. H. ; van Herpt, Thijs T. W. ; Sels, Jan-Willem E. M. ; Bergmans, Dennis C. J. J. ; Lexis, Chris P. H. ; van Doorn, William P. T. M. ; Meex, Steven J. R. ; Xu, Minnan ; Borrat, Xavier ; Cavill, Rachel ; van der Horst, Iwan C. C. ; van Bussel, Bas C. T.
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2024-01, Vol.14 (1), p.1045-1045, Article 1045
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DTW4Omics: Comparing Patterns in Biological Time Series
Author / Creator:Cavill, Rachel ; Kleinjans, Jos ; Briedé, Jacob-Jan
Publisher:United States: Public Library of Science
Journal title:PloS one, 2013-08, Vol.8 (8), p.e71823
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Use of deep learning methods to translate drug-induced gene expression changes from rat to human primary hepatocytes
Author / Creator:O’Donovan, Shauna D. ; Driessens, Kurt ; Lopatta, Daniel ; Wimmenauer, Florian ; Lukas, Alexander ; Neeven, Jelmer ; Stumm, Tobias ; Smirnov, Evgueni ; Lenz, Michael ; Ertaylan, Gokhan ; Jennen, Danyel G. J. ; van Riel, Natal A. W. ; Cavill, Rachel ; Peeters, Ralf L. M. ; de Kok, Theo M. C. M.
Publisher:United States: Public Library of Science
Journal title:PloS one, 2020-08, Vol.15 (8), p.e0236392
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ArticlesPeer ReviewedFull Text
Machine learning-based prediction of cognitive outcomes in de novo Parkinson’s disease
Author / Creator:Harvey, Joshua ; Reijnders, Rick A ; Cavill, Rachel ; Duits, Annelien ; Köhler, Sebastian ; Eijssen, Lars ; Rutten, Bart P. F ; Shireby, Gemma ; Torkamani, Ali ; Creese, Byron ; Leentjens, Albert F. G ; Lunnon, Katie ; Pishva, Ehsan
Publisher:London: Nature Publishing Group
Journal title:NPJ Parkinson's Disease, 2022-11, Vol.8 (1)
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Consensus-Phenotype Integration of Transcriptomic and Metabolomic Data Implies a Role for Metabolism in the Chemosensitivity of Tumour Cells
Author / Creator:Cavill, Rachel ; Kamburov, Atanas ; Ellis, James K. ; Athersuch, Toby J. ; Blagrove, Marcus S. C. ; Herwig, Ralf ; Ebbels, Timothy M. D. ; Keun, Hector C.
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2011-03, Vol.7 (3), p.e1001113-e1001113
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ArticlesPeer ReviewedFull Text
The effect of tumor composition on the success of adaptive therapy: The case of metastatic Castrate-Resistant Prostate Cancer
Author / Creator:Salvioli, Monica ; Vandelaer, Len ; Baena, Esther ; Schneider, Katharina ; Cavill, Rachel ; Staňková, Kateřina
Publisher:United States: Public Library of Science
Journal title:PloS one, 2024-09, Vol.19 (9), p.e0308173
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Identification of platelet function defects by multi-parameter assessment of thrombus formation
Author / Creator:de Witt, Susanne M. ; Swieringa, Frauke ; Cavill, Rachel ; Lamers, Moniek M. E. ; van Kruchten, Roger ; Mastenbroek, Tom ; Baaten, Constance ; Coort, Susan ; Pugh, Nicholas ; Schulz, Ansgar ; Scharrer, Inge ; Jurk, Kerstin ; Zieger, Barbara ; Clemetson, Kenneth J. ; Farndale, Richard W. ; Heemskerk, Johan W. M. ; Cosemans, Judith M.E.M.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2014-07, Vol.5 (1), p.4257-4257, Article 4257
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ArticlesPeer ReviewedFull Text
Platelet-primed interactions of coagulation and anticoagulation pathways in flow-dependent thrombus formation
Author / Creator:Brouns Sanne L N ; van Geffen Johanna P ; Campello, Elena ; Swieringa Frauke ; Spiezia Luca ; van Oerle René ; Provenzale Isabella ; Verdoold Remco ; Farndale, Richard W ; Clemetson, Kenneth J ; Spronk Henri M H ; van der Meijden Paola E J ; Cavill, Rachel ; Kuijpers Marijke J E ; Castoldi Elisabetta ; Simioni Paolo ; Heemskerk Johan W M
Publisher:London: Nature Publishing Group
Journal title:Scientific reports, 2020-07, Vol.10 (1)
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Blood‐based multivariate methylation risk score for cognitive impairment and dementia
Author / Creator:Koetsier, Jarno ; Cavill, Rachel ; Reijnders, Rick ; Harvey, Joshua ; Homann, Jan ; Kouhsar, Morteza ; Deckers, Kay ; Köhler, Sebastian ; Eijssen, Lars M. T. ; den Hove, Daniel L. A. ; Demuth, Ilja ; Düzel, Sandra ; Smith, Rebecca G. ; Smith, Adam R. ; Burrage, Joe ; Walker, Emma M. ; Shireby, Gemma ; Hannon, Eilis ; Dempster, Emma ; Frayling, Tim ; Mill, Jonathan ; Dobricic, Valerija ; Johannsen, Peter ; Wittig, Michael ; Franke, Andre ; Vandenberghe, Rik ; Schaeverbeke, Jolien ; Freund‐Levi, Yvonne ; Frölich, Lutz ; Scheltens, Philip ; Teunissen, Charlotte E. ; Frisoni, Giovanni ; Blin, Olivier ; Richardson, Jill C. ; Bordet, Régis ; Engelborghs, Sebastiaan ; Roeck, Ellen ; Martinez‐Lage, Pablo ; Tainta, Mikel ; Lleó, Alberto ; Sala, Isabel ; Popp, Julius ; Peyratout, Gwendoline ; Verhey, Frans ; Tsolaki, Magda ; Andreasson, Ulf ; Blennow, Kaj ; Zetterberg, Henrik ; Streffer, Johannes ; Vos, Stephanie J. B. ; Lovestone, Simon ; Visser, Pieter‐Jelle ; Lill, Christina M. ; Bertram, Lars ; Lunnon, Katie ; Pishva, Ehsan
Publisher:United States: Alzheimer's Association / Wiley
Journal title:Alzheimer's & dementia, 2024-10, Vol.20 (10), p.6682-6698
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Role of Platelet Glycoprotein VI and Tyrosine Kinase Syk in Thrombus Formation on Collagen-Like Surfaces
Author / Creator:Jooss, Natalie J. ; De Simone, Ilaria ; Provenzale, Isabella ; Fernández, Delia I. ; Brouns, Sanne L.N. ; Farndale, Richard W. ; Henskens, Yvonne M.C. ; Kuijpers, Marijke J.E. ; ten Cate, Hugo ; van der Meijden, Paola E.J. ; Cavill, Rachel ; Heemskerk, Johan W.M.
Publisher:Switzerland: MDPI AG
Journal title:International journal of molecular sciences, 2019-06, Vol.20 (11), p.2788
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Proteomic and metabolomic responses to connexin43 silencing in primary hepatocyte cultures
Author / Creator:Vinken, Mathieu ; Maes, Michaël ; Cavill, Rachel ; Valkenborg, Dirk ; Ellis, James K. ; Decrock, Elke ; Leybaert, Luc ; Staes, An ; Gevaert, Kris ; Oliveira, André G. ; Menezes, Gustavo B. ; Cogliati, Bruno ; Dagli, Maria Lúcia Zaidan ; Ebbels, Timothy M. D. ; Witters, Erwin ; Keun, Hector C. ; Vanhaecke, Tamara ; Rogiers, Vera
Publisher:Berlin/Heidelberg: Springer-Verlag
Journal title:Archives of toxicology, 2013-05, Vol.87 (5), p.883-894
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ArticlesPeer ReviewedFull Text
Consensus-Phenotype Integration of Transcriptomic and Metabolomic Data Implies a Role for Metabolism in the Chemosensitivity of Tumour Cells: e1001113
Author / Creator:Cavill, Rachel ; Kamburov, Atanas ; Ellis, James K ; Athersuch, Toby J ; Blagrove, Marcus SC ; Herwig, Ralf ; Ebbels, Timothy MD ; Keun, Hector C
Publisher:San Francisco: Public Library of Science
Journal title:PLoS computational biology, 2011-03, Vol.7 (3)
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ArticlesFull Text
How to use transcriptomic data for game-theoretic modeling of treatment-induced resistance in cancer cells? A case study in patient-derived glioblastoma organoids
Author / Creator:Spekking, Louise ; Lokh, Christer ; Jung, Weronika ; Verduin, Maikel ; Azimi, Sepinoud ; Hubert, Christopher G ; Vooijs, Marc ; Cavill, Rachel ; Staňková, Kateřina
Publisher:Cold Spring Harbor: Cold Spring Harbor Laboratory Press
Journal title:bioRxiv, 2024-12
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Transcriptomic and metabolomic data integration

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Validation of polymorphic Gompertzian model of cancer through in vitro and in vivo data

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Assessment of a complete and classified platelet proteome from genome-wide transcripts of human platelets and megakaryocytes covering platelet functions

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PSnpBind-ML: predicting the effect of binding site mutations on protein-ligand binding affinity

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PSnpBind: a database of mutated binding site protein–ligand complexes constructed using a multithreaded virtual screening workflow

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An agent-based approach for modelling and simulation of glycoprotein VI receptor diffusion, localisation and dimerisation in platelet lipid rafts

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Application of transfer learning to predict drug-induced human in vivo gene expression changes using rat in vitro and in vivo data

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Deep embedded clustering generalisability and adaptation for integrating mixed datatypes: two critical care cohorts

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DTW4Omics: Comparing Patterns in Biological Time Series

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Use of deep learning methods to translate drug-induced gene expression changes from rat to human primary hepatocytes

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Machine learning-based prediction of cognitive outcomes in de novo Parkinson’s disease

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Consensus-Phenotype Integration of Transcriptomic and Metabolomic Data Implies a Role for Metabolism in the Chemosensitivity of Tumour Cells

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The effect of tumor composition on the success of adaptive therapy: The case of metastatic Castrate-Resistant Prostate Cancer

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Identification of platelet function defects by multi-parameter assessment of thrombus formation

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Platelet-primed interactions of coagulation and anticoagulation pathways in flow-dependent thrombus formation

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Blood‐based multivariate methylation risk score for cognitive impairment and dementia

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Role of Platelet Glycoprotein VI and Tyrosine Kinase Syk in Thrombus Formation on Collagen-Like Surfaces

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Proteomic and metabolomic responses to connexin43 silencing in primary hepatocyte cultures

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Consensus-Phenotype Integration of Transcriptomic and Metabolomic Data Implies a Role for Metabolism in the Chemosensitivity of Tumour Cells: e1001113

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How to use transcriptomic data for game-theoretic modeling of treatment-induced resistance in cancer cells? A case study in patient-derived glioblastoma organoids

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