VAMP: Visualization and analysis of array-CGH, transcriptome and other molecular profiles. - Philippe La Rosa; Eric Viara; Philippe Hupé; Gaëlle Pierron; Stéphane Liva; Pierre Neuvial; Isabel Brito 002; Séverine Lair; Nicolas Servant; Nicolas Robine; Elodie Manié; Caroline Brennetot; et al. (Bioinform., 2006)

SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data. - Bruno Zeitouni; Valentina Boeva; Isabelle Janoueix-Lerosey; Sophie Loeillet; Patricia Legoix-né; Alain Nicolas; Olivier Delattre; Emmanuel Barillot (Bioinform., 2010)

Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization. - Valentina Boeva; Andrei Yu. Zinovyev; Kevin Bleakley; Jean-Philippe Vert; Isabelle Janoueix-Lerosey; Olivier Delattre; Emmanuel Barillot (Bioinform., 2011)

Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data. - Valentina Boeva; Tatiana G. Popova; Kevin Bleakley; Pierre Chiche; Julie Cappo; Gudrun Schleiermacher; Isabelle Janoueix-Lerosey; Olivier Delattre; Emmanuel Barillot (Bioinform., 2012)

Learning smoothing models of copy number profiles using breakpoint annotations. - Toby Dylan Hocking; Gudrun Schleiermacher; Isabelle Janoueix-Lerosey; Valentina Boeva; Julie Cappo; Olivier Delattre; Francis R. Bach; Jean-Philippe Vert (BMC Bioinform., 2013)

SegAnnDB: interactive Web-based genomic segmentation. - Toby Dylan Hocking; Valentina Boeva; Guillem Rigaill; Gudrun Schleiermacher; Isabelle Janoueix-Lerosey; Olivier Delattre; Wilfrid Richer; Franck Bourdeaut; Miyuki Suguro; Masao Seto; Francis R. Bach; Jean-Philippe Vert (Bioinform., 2014)

SV-Bay: structural variant detection in cancer genomes using a Bayesian approach with correction for GC-content and read mappability. - Daria Iakovishina; Isabelle Janoueix-Lerosey; Emmanuel Barillot; Mireille Régnier; Valentina Boeva (Bioinform., 2016)

QuantumClone: clonal assessment of functional mutations in cancer based on a genotype-aware method for clonal reconstruction. - Paul Deveau; Leo Colmet Daage; Derek Oldridge; Virginie Bernard; Angela Bellini; Mathieu Chicard; Nathalie Clement; Eve Lapouble; Valerie Combaret; Anne Boland; Vincent Meyer; Jean-Francois Deleuze; et al. (Bioinform., 2018)