Chromosomal Breakpoint Detection in Human Cancer. - Kees Jong; Elena Marchiori; Aad van der Vaart; Bauke Ylstra; Marjan Weiss; Gerrit Meijer (EvoWorkshops, 2003)

Breakpoint identification and smoothing of array comparative genomic hybridization data. - Kees Jong; Elena Marchiori; Gerrit Meijer; Aad van der Vaart; Bauke Ylstra (Bioinform., 2004)

CGHMultiArray: exact P-values for multi-array comparative genomic hybridization data. - Mark A. van de Wiel; Serge J. Smeets; Ruud H. Brakenhoff; Bauke Ylstra (Bioinform., 2005)

ACE-it: a tool for genome-wide integration of gene dosage and RNA expression data. - Wessel N. van Wieringen; Jeroen A. M. Beliën; Sjoerd J. Vosse; Eskeatnaf M. Achame; Bauke Ylstra (Bioinform., 2006)

CGHcall: calling aberrations for array CGH tumor profiles. - Mark A. van de Wiel; Kyung In Kim; Sjoerd J. Vosse; Wessel N. van Wieringen; Saskia M. Wilting; Bauke Ylstra (Bioinform., 2007)

Smoothing waves in array CGH tumor profiles. - Mark A. van de Wiel; Rebecca Brosens; Paul H. C. Eilers; Candy Kumps; Gerrit Meijer; Björn Menten; Erik Sistermans; Frank Speleman; Marieke E. Timmerman; Bauke Ylstra (Bioinform., 2009)

CGHpower: exploring sample size calculations for chromosomal copy number experiments. - Ilari Scheinin; Jose A. Ferreira; Sakari Knuutila; Gerrit Meijer; Mark A. van de Wiel; Bauke Ylstra (BMC Bioinform., 2010)

Preprocessing and downstream analysis of microarray DNA copy number profiles. - Mark A. van de Wiel; Franck Picard; Wessel N. van Wieringen; Bauke Ylstra (Briefings Bioinform., 2011)

Matching of array CGH and gene expression microarray features for the purpose of integrative genomic analyses. - Wessel N. van Wieringen; Kristian Unger; Gwenaël G. R. Leday; Oscar Krijgsman; Renée X. de Menezes; Bauke Ylstra; Mark A. van de Wiel (BMC Bioinform., 2012)

GeneBreak: detection of recurrent DNA copy number aberration-associated chromosomal breakpoints within genes. - Evert van den Broek; Stef van Lieshout; Christian Rausch; Bauke Ylstra; Mark A. van de Wiel; Gerrit A. Meijer; Remond J. A. Fijneman; Sanne Abeln (F1000Research, 2016)

ACE: absolute copy number estimation from low-coverage whole-genome sequencing data. - Jos B. Poell; Matias Mendeville; Daoud Sie; Arjen Brink; Ruud H. Brakenhoff; Bauke Ylstra (Bioinform., 2019)

The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research. - David Salgado; Irina M. Armean; Michael Baudis; Sergi Beltran; Salvador Capella-Gutiérrez; Denise Carvalho-Silva; Victoria Dominguez Del Angel; Joaquín Dopazo; Laura I. Furlong; Bo Gao; Leyla Jael García Castro; Dietlind Gerloff; et al. (F1000Research, 2020)