K-OPLS package: Kernel-based orthogonal projections to latent structures for prediction and interpretation in feature space. - Max Bylesjö; Mattias Rantalainen; Jeremy K. Nicholson; Elaine Holmes; Johan Trygg (BMC Bioinform., 2008)

Piecewise multivariate modelling of sequential metabolic profiling data. - Mattias Rantalainen; Olivier Cloarec; Timothy M. D. Ebbels; Torbjörn Lundstedt; Jeremy K. Nicholson; Elaine Holmes; Johan Trygg (BMC Bioinform., 2008)

Genetic algorithms for simultaneous variable and sample selection in metabonomics. - Rachel Cavill; Hector C. Keun; Elaine Holmes; John C. Lindon; Jeremy K. Nicholson; Timothy M. D. Ebbels (Bioinform., 2009)

MetaboNetworks, an interactive Matlab-based toolbox for creating, customizing and exploring sub-networks from KEGG. - Joram M. Posma; Steven L. Robinette; Elaine Holmes; Jeremy K. Nicholson (Bioinform., 2014)

MetaboSignal: a network-based approach for topological analysis of metabotype regulation via metabolic and signaling pathways. - Andrea Rodriguez-Martinez; Rafael Ayala; Joram M. Posma; Ana Luísa Neves; Dominique Gauguier; Jeremy K. Nicholson; Marc-Emmanuel Dumas (Bioinform., 2017)

MWASTools: an R/bioconductor package for metabolome-wide association studies. - Andrea Rodriguez-Martinez; Joram M. Posma; Rafael Ayala; Ana Luísa Neves; Maryam Anwar; Enrico Petretto; Costanza Emanueli; Dominique Gauguier; Jeremy K. Nicholson; Marc-Emmanuel Dumas (Bioinform., 2018)

SPUTNIK: an R package for filtering of spatially related peaks in mass spectrometry imaging data. - Paolo Inglese; Gonçalo D. S. Correia; Zoltan Takats; Jeremy K. Nicholson; Robert C. Glen (Bioinform., 2019)

pJRES Binning Algorithm (JBA): a new method to facilitate the recovery of metabolic information from pJRES 1H NMR spectra. - Andrea Rodriguez-Martinez; Rafael Ayala; Joram M. Posma; Nikita Harvey; Beatriz Jiménez; Kazuhiro Sonomura; Taka-Aki Sato; Fumihiko Matsuda; Pierre A. Zalloua; Dominique Gauguier; Jeremy K. Nicholson; Marc-Emmanuel Dumas (Bioinform., 2019)

The nPYc-Toolbox, a Python module for the pre-processing, quality-control and analysis of metabolic profiling datasets. - Caroline J. Sands; Arnaud M. Wolfer; Gonçalo D. S. Correia; Noureddin Sadawi; Arfan Ahmed; Beatriz Jiménez; Matthew R. Lewis; Robert C. Glen; Jeremy K. Nicholson; Jake T. M. Pearce (Bioinform., 2019)

Metabolomics in the Cloud: Scaling Computational Tools to Big Data. - Jianliang Gao; Noureddin Sadawi; Ibrahim Karaman; Jake T. M. Pearce; Pablo A. Moreno; Anders Larsson; Marco Capuccini; Paul Elliott; Jeremy K. Nicholson; Timothy M. D. Ebbels; Robert C. Glen (CoRR, 2019)

Strategy for improved characterization of human metabolic phenotypes using a COmbined Multi-block Principal components Analysis with Statistical Spectroscopy (COMPASS). - Ruey Leng Loo; Queenie Chan; Henrik Antti; Jia V. Li; Hutan Ashrafian; Paul Elliott; Jeremiah Stamler; Jeremy K. Nicholson; Elaine Holmes; Julien Wist (Bioinform., 2021)