P
Paul P. Eijk
Researcher at VU University Medical Center
Publications - 63
Citations - 3756
Paul P. Eijk is an academic researcher from VU University Medical Center. The author has contributed to research in topics: Haemophilus influenzae & Comparative genomic hybridization. The author has an hindex of 32, co-authored 63 publications receiving 3420 citations. Previous affiliations of Paul P. Eijk include University of Amsterdam & Utrecht University.
Papers
More filters
Journal ArticleDOI
Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures
Catherine Naughton,Nicolaos Avlonitis,Samuel Corless,James G. D. Prendergast,Ioulia K. Mati,Paul P. Eijk,Scott L. Cockroft,Mark Bradley,Bauke Ylstra,Nick Gilbert +9 more
TL;DR: It is suggested that supercoiling domains create a topological environment that facilitates gene activation, providing an evolutionary purpose for clustering genes along chromosomes.
Journal ArticleDOI
DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly
Ilari Scheinin,Daoud Sie,Henrik Bengtsson,Mark A. van de Wiel,Adam B. Olshen,Hinke F. van Thuijl,Hendrik F. van Essen,Paul P. Eijk,François Rustenburg,Gerrit A. Meijer,Jaap C. Reijneveld,Pieter Wesseling,Daniel Pinkel,Donna G. Albertson,Bauke Ylstra +14 more
TL;DR: This work improves on previous methods by first implementing a combined correction for sequence mappability and GC content, and second, by applying this procedure to sequence data from the 1000 Genomes Project in order to develop a blacklist of problematic genome regions.
Journal ArticleDOI
Human and mouse oligonucleotide-based array CGH
Paul van den IJssel,Marianne Tijssen,Suet-Feung Chin,Paul P. Eijk,Beatriz Carvalho,Erik S. Hopmans,Henne Holstege,Dhinoth Kumar Bangarusamy,Jos Jonkers,Gerrit A. Meijer,Carlos Caldas,Bauke Ylstra +11 more
TL;DR: This oligo-based platform using ‘off-the-shelf’ oligo libraries provides an easy accessible alternative to BAC arrays for CGH, which is cost-effective, available at high resolution and easily implemented for any sequenced organism without compromising the quality of the results.
Journal ArticleDOI
Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping
Paula J P de Vree,Elzo de Wit,Mehmet Yilmaz,Monique van de Heijning,Petra Klous,Marjon J.A.M. Verstegen,Yi Wan,Hans Teunissen,Peter H.L. Krijger,Geert Geeven,Paul P. Eijk,Daoud Sie,Bauke Ylstra,Lorette O M Hulsman,Marieke F. van Dooren,Laura J. C. M. van Zutven,Ans M.W. van den Ouweland,Sjef Verbeek,Ko Willems van Dijk,Marion Cornelissen,Atze T. Das,Ben Berkhout,Birgit Sikkema-Raddatz,Eva van den Berg,Pieter van der Vlies,Desiree Weening,Johan T. den Dunnen,Magdalena Matusiak,Mohamed Lamkanfi,Marjolijn J. L. Ligtenberg,Petra ter Brugge,Jos Jonkers,John A. Foekens,John W. M. Martens,Rob B. van der Luijt,Hans Kristian Ploos van Amstel,Max van Min,Erik Splinter,Wouter de Laat +38 more
TL;DR: Target locus amplification (TLA) is presented, a strategy to selectively amplify and sequence entire genes on the basis of the crosslinking of physically proximal sequences that enables robust detection of single nucleotide variants, structural variants and gene fusions in clinically relevant genes, and enables haplotyping.
Journal ArticleDOI
The genomic profile of human malignant glioma is altered early in primary cell culture and preserved in spheroids
P. C. de Witt Hamer,A A G Van Tilborg,Paul P. Eijk,Peter Sminia,Dirk Troost,C. J. F. Van Noorden,Bauke Ylstra,Sieger Leenstra +7 more
TL;DR: It is concluded that genomic profiles of primary cell cultures from glioblastoma are frequently deviant from parental tumor profiles, whereas spheroids are genetically more representative of the gliOBlastoma.