Improving Gene Network Inference by Comparing Expression Time-series across Species, Developmental Stages or Tissues. - Guillaume Bourque; David Sankoff (J. Bioinform. Comput. Biol., 2004)

Maximizing Synteny Blocks to Identify Ancestral Homologs. - Guillaume Bourque; Yasmine Yacef; Nadia El-Mabrouk (Comparative Genomics, 2005)

Models and Methods in Comparative Genomics. - Guillaume Bourque; Louxin Zhang (Adv. Comput., 2006)

Recovering True Rearrangement Events on Phylogenetic Trees. - Hao Zhao; Guillaume Bourque (RECOMB-CG, 2007)

Prediction of low coverage prone regions for Illumina sequencing projects using a support vector machine. - Zejun Zheng; Bertil Schmidt; Guillaume Bourque (BIBM, 2010)

webMGR: an online tool for the multiple genome rearrangement problem. - Chi Ho Lin; Hao Zhao; Sean Harry Lowcay; Atif Shahab; Guillaume Bourque (Bioinform., 2010)

PeakSeg: constrained optimal segmentation and supervised penalty learning for peak detection in count data. - Toby Hocking; Guillem Rigaill; Guillaume Bourque (ICML, 2015)

Optimizing ChIP-seq peak detectors using visual labels and supervised machine learning. - Toby Dylan Hocking; Patricia Goerner-Potvin; Andreanne Morin; Xiaojian Shao; Tomi Pastinen; Guillaume Bourque (Bioinform., 2017)

MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis. - Jasmine Chong; Othman Soufan; Carin Li; Iurie Caraus; Shuzhao Li; Guillaume Bourque; David S. Wishart; Jianguo Xia (Nucleic Acids Res., 2018)

The use of hyperspectral remote sensing to detect PCB contaminated soils in the 0.35 to 12 micron spectral range. - Josée Lévesque; Eldon Puckrin; Luc Levert; Guillaume Bourque (IGARSS, 2019)

eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data. - Charles E. Breeze; Alex P. Reynolds; Jenny van Dongen; Ian Dunham; John Lazar; Shane J. Neph; Jeff Vierstra; Guillaume Bourque; Andrew E. Teschendorff; John A. Stamatoyannopoulos; Stephan Beck 002 (Bioinform., 2019)

The epiGenomic Efficient Correlator (epiGeEC) tool allows fast comparison of user datasets with thousands of public epigenomic datasets. - Jonathan Laperle; Simon Hébert-Deschamps; Joanny Raby; David A. de Lima Morais; Michel Barrette; David Bujold; Charlotte Bastin; Marc-Antoine Robert; Jean-François Nadeau; Marie Harel; Alexei Nordell-Markovits; Alain Veilleux; et al. (Bioinform., 2019)

Machine Learning Algorithms for Simultaneous Supervised Detection of Peaks in Multiple Samples andCell Types. - Toby Dylan Hocking; Guillaume Bourque (PSB, 2020)

Constrained Dynamic Programming and Supervised Penalty Learning Algorithms for Peak Detection in Genomic Data. - Toby Dylan Hocking; Guillem Rigaill; Paul Fearnhead; Guillaume Bourque (J. Mach. Learn. Res., 2020)

Generalized Functional Pruning Optimal Partitioning (GFPOP) for Constrained Changepoint Detection in Genomic Data. - Toby Dylan Hocking; Guillem Rigaill; Paul Fearnhead; Guillaume Bourque (J. Stat. Softw., 2022)

RNAget: an API to securely retrieve RNA quantifications. - Sean Upchurch; Emilio Palumbo; Jeremy Adams; David Bujold; Guillaume Bourque; Jared Nedzel; Keenan Graham; Meenakshi S. Kagda; Pedro Assis; Benjamin C. Hitz; Emilio Righi; Roderic Guigó; et al. (Bioinform., 2023)