ASaiM: a Galaxy-based framework to analyze microbiota data
Batut, Bérénice; Gravouil, Kévin; Defois, Clémence; Hiltemann, Saskia; Brugère, Jean-François; Peyretaillade, Eric; Peyret, Pierre
Erasmus MC Citations
Scientific publications that cited the Erasmus MC Galaxy instance.
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Showing 24 citations
Community-driven data analysis training for biology
Batut, Bérénice; Hiltemann, Saskia; Bagnacani, Andrea; Baker, Dannon; Bhardwaj, Vivek; Blank, Clemens; Bretaudeau, Anthony; Guéguen, Loraine; Čech, Martin; Chilton, John; others
Development and evaluation of a culture-free microbiota profiling platform (MYcrobiota) for clinical diagnostics
Boers, Stefan A; Hiltemann, Saskia D; Stubbs, Andrew P; Jansen, Ruud; Hays, John P
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update
Afgan, Enis; Baker, Dannon; Batut, Bérénice; Beek, Marius; Bouvier, Dave; Čech, Martin; Chilton, John; Clements, Dave; Coraor, Nate; Grüning, Björn; Guerler, Aysam; Hillman-Jackson, Jennifer; Hiltemann, Saskia; Jalili, Vahid; Rasche; Soranzo; Goecks, Jeremy; Taylor, James; Nekrutenko, Anton; Blankenberg, Daniel
Antigen receptor galaxy: a user-friendly, web-based tool for analysis and visualization of T and B cell receptor repertoire data
IJspeert, Hanna; Van Schouwenburg, Pauline A; Zessen, David; Pico-Knijnenburg, Ingrid; Stubbs, Andrew P; Burg, Mirjam
Antigen receptor sequencing of paired bone marrow samples shows homogeneous distribution of acute lymphoblastic leukemia subclones
Theunissen, Prisca MJ; Zessen, David; Stubbs, Andrew P; Faham, Malek; Zwaan, Christian M; Dongen, Jacques JM; Van Der Velden, Vincent HJ
Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data
Zhang, Chao; Bijlard, Jochem; Staiger, Christine; Scollen, Serena; Enckevort, David; Hoogstrate, Youri; Senf, Alexander; Hiltemann, Saskia; Repo, Susanna; Pipping, Wibo; others
The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy
Grüning, Björn A; Fallmann, Jörg; Yusuf, Dilmurat; Will, Sebastian; Erxleben, Anika; Eggenhofer, Florian; Houwaart, Torsten; Batut, Bérénice; Videm, Pavankumar; Bagnacani, Andrea; others
A comprehensive repertoire of tRNA-derived fragments in prostate cancer
Olvedy, Michael; Scaravilli, Mauro; Hoogstrate, Youri; Visakorpi, Tapio; Jenster, Guido; Martens, Elena S
Evaluation of the antigen-experienced B-cell receptor repertoire in healthy children and adults
IJspeert, Hanna; Schouwenburg, Pauline A; Zessen, David; Pico-Knijnenburg, Ingrid; Driessen, Gertjan J; Stubbs, Andrew P; Burg, Mirjam
Identification of patients with recurrent glioblastoma who may benefit from combined bevacizumab and CCNU therapy: a report from the BELOB trial
Erdem-Eraslan, Lale; Bent, Martin J; Hoogstrate, Youri; Naz-Khan, Hina; Stubbs, Andrew; Spek, Peter; Böttcher, René; Gao, Ya; De Wit, Maurice; Taal, Walter; others
Integration of EGA secure data access into Galaxy
Hoogstrate, Youri; Zhang, Chao; Senf, Alexander; Bijlard, Jochem; Hiltemann, Saskia; Enckevort, David; Repo, Susanna; Heringa, Jaap; Jenster, Guido; Fijneman, Remond JA; others
Discriminating somatic and germline mutations in tumor DNA samples without matching normals
Hiltemann, Saskia; Jenster, Guido; Trapman, Jan; Spek, Peter; Stubbs, Andrew
FuMa: reporting overlap in RNA-seq detected fusion genes
Hoogstrate, Youri; Böttcher, René; Hiltemann, Saskia; Spek, Peter J; Jenster, Guido; Stubbs, Andrew P
Next-generation sequencing reveals novel rare fusion events with functional implication in prostate cancer
Alves, I Teles; Hartjes, Thomas; McClellan, Elizabeth; Hiltemann, Saskia; Böttcher, René; Dits, Natasja; Temanni, MR; Janssen, Bart; Van Workum, W; Spek, Peter; others
CGtag: complete genomics toolkit and annotation in a cloud-based Galaxy
Hiltemann, Saskia; Mei, Hailiang; Hollander, Mattias; Palli, Ivo; Spek, Peter; Jenster, Guido; Stubbs, Andrew
ImmunoGlobulin galaxy (IGGalaxy) for simple determination and quantitation of immunoglobulin heavy chain rearrangements from NGS
Moorhouse, Michael J; Zessen, David; IJspeert, Hanna; Hiltemann, Saskia; Horsman, Sebastian; Spek, Peter J; Burg, Mirjam; Stubbs, Andrew P
iReport: a generalised Galaxy solution for integrated experimental reporting
Hiltemann, Saskia; Hoogstrate, Youri; Spek, Peter; Jenster, Guido; Stubbs, Andrew
FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data
Hoogstrate, Youri; Jenster, Guido; Martens-Uzunova, Elena S
Pollitt syndrome patients carry mutation in TTDN1
Swagemakers, Sigrid MA; Jaspers, Nicolaas GJ; Raams, Anja; Heijsman, Daphne; Vermeulen, Wim; Troelstra, Christine; Kremer, Andreas; Lincoln, Stephen E; Tearle, Rick; Hoeijmakers, Jan HJ; others
Similar recombination-activating gene (RAG) mutations result in similar immunobiological effects but in different clinical phenotypes
IJspeert, Hanna; Driessen, Gertjan J; Moorhouse, Michael J; Hartwig, Nico G; Wolska-Kusnierz, Beata; Kalwak, Krzysztof; Pituch-Noworolska, Anna; Kondratenko, Irina; Montfrans, Joris M; Mejstrikova, Ester; others
Gene fusions by chromothripsis of chromosome 5q in the VCaP prostate cancer cell line
Alves, Inês Teles; Hiltemann, Saskia; Hartjes, Thomas; Spek, Peter; Stubbs, Andrew; Trapman, Jan; Jenster, Guido
iFUSE: integrated fusion gene explorer
Hiltemann, Saskia; McClellan, Elizabeth A; Nijnatten, Jos; Horsman, Sebastiaan; Palli, Ivo; Teles Alves, Ines; Hartjes, Thomas; Trapman, Jan; Spek, Peter; Jenster, Guido; others
Huvariome: a web server resource of whole genome next-generation sequencing allelic frequencies to aid in pathological candidate gene selection
Stubbs, Andrew; McClellan, Elizabeth A; Horsman, Sebastiaan; Hiltemann, Saskia D; Palli, Ivo; Nouwens, Stephan; Koning, Anton HJ; Hoogland, Frits; Reumers, Joke; Heijsman, Daphne; others