BioHMM: a heterogeneous hidden Markov model for segmenting array CGH data. - John C. Marioni; Natalie P. Thorne; Simon Tavaré (Bioinform., 2006)

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. - Jacob F. Degner; John C. Marioni; Athma A. Pai; Joseph K. Pickrell; Everlyne Nkadori; Yoav Gilad; Jonathan K. Pritchard (Bioinform., 2009)

Tools for mapping high-throughput sequencing data. - Nuno A. Fonseca; Johan Rung; Alvis Brazma; John C. Marioni (Bioinform., 2012)

bioWeb3D: an online webGL 3D data visualisation tool. - Jean-Baptiste Pettit; John C. Marioni (BMC Bioinform., 2013)

Expression Atlas update - a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments. - Robert Petryszak; Tony Burdett; Benedetto Fiorelli; Nuno A. Fonseca; Mar Gonzalez-Porta; Emma Hastings; Wolfgang Huber; Simon Jupp; Maria Keays; Nataliya Kryvych; Julie A. McMurry; John C. Marioni; et al. (Nucleic Acids Res., 2014)

Identifying Cell Types from Spatially Referenced Single-Cell Expression Datasets. - Jean-Baptiste Pettit; Raju Tomer; Kaia Achim; Sylvia Richardson; Lamiae Azizi; John C. Marioni (PLoS Comput. Biol., 2014)

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data. - Catalina A. Vallejos; John C. Marioni; Sylvia Richardson (PLoS Comput. Biol., 2015)

HDTD: analyzing multi-tissue gene expression data. - Anestis Touloumis; John C. Marioni; Simon Tavaré (Bioinform., 2016)

A single-cell molecular map of mouse gastrulation and early organogenesis. - Blanca Pijuan-Sala; Jonathan A. Griffiths; Carolina Guibentif; Tom W. Hiscock; Wajid Jawaid; Fernando J. Calero-Nieto; Carla Mulas; Ximena Ibarra-Soria; Richard C. V. Tyser; Debbie Lee Lian Ho; Wolf Reik; Shankar Srinivas; et al. (Nat., 2019)

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. - Michael P. Snyder; Shin Lin; Amanda Posgai; Mark Atkinson; Aviv Regev; Jennifer Rood; Orit Rozenblatt-Rosen; Leslie Gaffney; Anna Hupalowska; Rahul Satija; Nils Gehlenborg; Jay Shendure; et al. (Nat., 2019)

12 Grand Challenges in Single-Cell Data Science. - David Laehnemann; Johannes Köster; Ewa Szczurek; Davis J. McCarthy; Stephanie C. Hicks; Mark D. Robinson; Catalina A. Vallejos; Niko Beerenwinkel; Kieran R. Campbell; Ahmed Mahfouz; Luca Pinello; Pavel Skums; et al. (PeerJ Prepr., 2019)

Expression Atlas update: from tissues to single cells. - Irene Papatheodorou; Pablo A. Moreno; Jonathan R. Manning; Alfonso Muñoz-Pomer Fuentes; Nancy George; Silvie Fexova; Nuno A. Fonseca; Anja Füllgrabe; Matthew Green 005; Ni Huang; Laura Huerta; Haider Iqbal; et al. (Nucleic Acids Res., 2020)

Expression Atlas update: gene and protein expression in multiple species. - Pablo A. Moreno; Silvie Fexova; Nancy George; Jonathan R. Manning; Zhichao Miao; Suhaib Mohammed; Alfonso Muñoz-Pomer Fuentes; Anja Füllgrabe; Yalan Bi; Natassja Bush; Haider Iqbal; Upendra Kumbham; et al. (Nucleic Acids Res., 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)