Stijn van Dongen

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Anton EnrightProfessor of RNA Biology and Genomics, Pathology Dept., University of CambridgeVerified email at cam.ac.uk
Harpreet SainiBioinformatician, European Bioinformatics InstituteVerified email at ebi.ac.uk
Cei Abreu-GoodgerUniversity of EdinburghVerified email at ed.ac.uk
Sam Griffiths-JonesFaculty of Biology, Medicine and Health. University of ManchesterVerified email at manchester.ac.uk
Alex BatemanHead of Protein Sequence Resources, EMBL-EBIVerified email at ebi.ac.uk
Allan BradleyDept of Medicine, Cambridge University, UKVerified email at cam.ac.uk
Tom C. FreemanProfessor of Systems Immunology, University of EdinburghVerified email at roslin.ed.ac.uk
Murray MJDepartment of Pathology, University of CambridgeVerified email at cam.ac.uk
Martin TurnerThe Babraham Institute, Cambridge, CB22 3AT, UK.Verified email at babraham.ac.uk
Klaus OkkenhaugDivision of Immunology, Department of Pathology, University of CambridgeVerified email at cam.ac.uk
Gordon DouganUniversity of CambridgeVerified email at cam.ac.uk
Christos Α. OuzounisAUTH, Thessalonica, Greece • CERTH, Thessalonica, GreeceVerified email at csd.auth.gr
Eric MiskaUniversity of Cambridge, Gurdon Institute & Department of GeneticsVerified email at cam.ac.uk
David VetrieUniversity of Glasgow, Institute of Cancer SciencesVerified email at glasgow.ac.uk
Antonio J. GiraldezDepartment of Genetics, Yale UniversityVerified email at yale.edu
Sarah A. TeichmannUniversity of CambridgeVerified email at cam.ac.uk
Vladimir KiselevHead of Bioinformatics @ AlethiomicsVerified email at alethiomics.com
Matias PiipariCTO at Papers / Springer Scientific + Business MediaVerified email at papersapp.com
Muzlifah HaniffaNewcastle UniversityVerified email at newcastle.ac.uk
Krzysztof PolańskiUniversity of CambridgeVerified email at cam.ac.uk

Stijn van Dongen

Senior Data Wrangler, ExpressionEdits, Cambridge UK

Verified email at expressionedits.com - Homepage

Bioinformatics pipelines scientific and numerical computing large scale network analysis cluster analysis algorithms


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miRBase: microRNA sequences, targets and gene nomenclature S Griffiths-Jones, RJ Grocock, S Van Dongen, A Bateman, AJ Enright Nucleic acids research 34 (suppl_1), D140-D144, 2006	5841	2006
miRBase: tools for microRNA genomics S Griffiths-Jones, HK Saini, S Van Dongen, AJ Enright Nucleic acids research 36 (suppl_1), D154-D158, 2007	5479	2007
An efficient algorithm for large-scale detection of protein families AJ Enright, S Van Dongen, CA Ouzounis Nucleic acids research 30 (7), 1575-1584, 2002	4087	2002
Graph clustering by flow simulation S Van Dongen PhD thesis, University of Utrecht, 2000	2597	2000
Requirement of bic/microRNA-155 for normal immune function A Rodriguez, E Vigorito, S Clare, MV Warren, P Couttet, DR Soond, ... Science 316 (5824), 608-611, 2007	2385	2007
Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs AJ Giraldez, Y Mishima, J Rihel, RJ Grocock, S Van Dongen, K Inoue, ... Science 312 (5770), 75, 2006	1954	2006
Graph clustering via a discrete uncoupling process S Van Dongen SIAM Journal on Matrix Analysis and Applications 30 (1), 121-141, 2008	680	2008
A new cluster algorithm for graphs S Van Dongen, ... Centrum voor Wiskunde en Informatica, 1998	643*	1998
Single-cell multi-omics analysis of the immune response in COVID-19 E Stephenson, G Reynolds, RA Botting, FJ Calero-Nieto, MD Morgan, ... Nature medicine 27 (5), 904-916, 2021	543	2021
Network visualization and analysis of gene expression data using BioLayout Express^3D A Theocharidis, S Van Dongen, AJ Enright, TC Freeman Nature protocols 4 (10), 1535-1550, 2009	502	2009
Kraken: a set of tools for quality control and analysis of high-throughput sequence data MPA Davis, S van Dongen, C Abreu-Goodger, N Bartonicek, AJ Enright Methods 63 (1), 41-49, 2013	443	2013
Using MCL to extract clusters from networks S Van Dongen, C Abreu-Goodger Bacterial molecular networks: Methods and protocols, 281-295, 2012	417	2012
RNA editing of human microRNAs MJ Blow, RJ Grocock, S van Dongen, AJ Enright, E Dicks, PA Futreal, ... Genome biology 7, 1-8, 2006	409	2006
An ENU-induced mutation of miR-96 associated with progressive hearing loss in mice MA Lewis, E Quint, AM Glazier, H Fuchs, MH De Angelis, C Langford, ... Nature genetics 41 (5), 614-618, 2009	377	2009
Cells of the human intestinal tract mapped across space and time R Elmentaite, N Kumasaka, K Roberts, A Fleming, E Dann, HW King, ... Nature 597 (7875), 250-255, 2021	358	2021
Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro L Garcia-Alonso, LF Handfield, K Roberts, K Nikolakopoulou, ... Nature genetics 53 (12), 1698-1711, 2021	345	2021
Detecting microRNA binding and siRNA off-target effects from expression data S Van Dongen, C Abreu-Goodger, AJ Enright Nature methods 5 (12), 1023-1025, 2008	329	2008
Performance criteria for graph clustering and Markov cluster experiments S Van Dongen Report-Information systems, 1-36, 2000	328*	2000
Construction, visualisation, and clustering of transcription networks from microarray expression data TC Freeman, L Goldovsky, M Brosch, S Van Dongen, P Mazière, ... PLoS computational biology 3 (10), e206, 2007	300	2007
Malignant germ cell tumors display common microRNA profiles resulting in global changes in expression of messenger RNA targets RD Palmer, MJ Murray, HK Saini, S van Dongen, C Abreu-Goodger, ... Cancer research 70 (7), 2911-2923, 2010	292	2010

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