Making sense of EST sequences by CLOBBing them. - John Parkinson; David B. Guiliano; Mark L. Blaxter (BMC Bioinform., 2002)

SimiTri-visualizing similarity relationships for groups of sequences. - John Parkinson; Mark L. Blaxter (Bioinform., 2003)

PartiGene-constructing partial genomes. - John Parkinson; Alasdair Anthony; James Wasmuth; Ralf Schmid; Ann Hedley; Mark L. Blaxter (Bioinform., 2004)

prot4EST: Translating Expressed Sequence Tags from neglected genomes. - James Wasmuth; Mark L. Blaxter (BMC Bioinform., 2004)

NEMBASE: a resource for parasitic nematode ESTs. - John Parkinson; Claire Whitton; Ralf Schmid; Marian Thomson; Mark L. Blaxter (Nucleic Acids Res., 2004)

Exploring Parasite Gene Space. - James Wasmuth; Ralf Schmid; Alasdair Anthony; John Parkinson; Mark L. Blaxter (BMC Bioinform., 2005)

TaxMan: a taxonomic database manager. - Martin O. Jones; Mark L. Blaxter (BMC Bioinform., 2006)

annot8r: GO, EC and KEGG annotation of EST datasets. - Ralf Schmid; Mark L. Blaxter (BMC Bioinform., 2008)

ButterflyBase: a platform for lepidopteran genomics. - Alexie Papanicolaou; Steffi Gebauer-Jung; Mark L. Blaxter; W. Owen McMillan; Chris D. Jiggins (Nucleic Acids Res., 2008)

Linking toxicant physiological mode of action with induced gene expression changes in Caenorhabditis elegans. - Suresh Swain; Jodie F. Wren; Stephen R. Stürzenbaum; Peter Kille; A. John Morgan; Tjalling Jager; Martijs J. Jonker; Peter K. Hankard; Claus Svendsen; Jenifer Owen; Ann Hedley; Mark L. Blaxter; et al. (BMC Syst. Biol., 2010)

iPhy: an integrated phylogenetic workbench for supermatrix analyses. - Martin O. Jones; Georgios D. Koutsovoulos; Mark L. Blaxter (BMC Bioinform., 2011)

959 Nematode Genomes: a semantic wiki for coordinating sequencing projects. - Sujai Kumar; Philipp H. Schiffer; Mark L. Blaxter (Nucleic Acids Res., 2012)

Badger - an accessible genome exploration environment. - Ben Elsworth; Martin O. Jones; Mark L. Blaxter (Bioinform., 2013)

afterParty: turning raw transcriptomes into permanent resources. - Martin O. Jones; Mark L. Blaxter (BMC Bioinform., 2013)

Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment. - Marek Gierlinski; Christian Cole; Pietà Schofield; Nicholas J. Schurch; Alexander Sherstnev; Vijender Singh; Nicola Wrobel; Karim Gharbi; Gordon G. Simpson; Tom Owen-Hughes; Mark L. Blaxter; Geoffrey J. Barton (Bioinform., 2015)

poRe: an R package for the visualization and analysis of nanopore sequencing data. - Mick Watson; Marian Thomson; Judith E. Risse; Richard Talbot; Javier Santoyo-Lopez; Karim Gharbi; Mark L. Blaxter (Bioinform., 2015)

ReproPhylo: An Environment for Reproducible Phylogenomics. - Amir Szitenberg; Max John; Mark L. Blaxter; David H. Lunt (PLoS Comput. Biol., 2015)

GenomeHubs: simple containerized setup of a custom Ensembl database and web server for any species. - Richard J. Challis; Sujai Kumar; Lewis Stevens; Mark L. Blaxter (Database J. Biol. Databases Curation, 2017)

BlobTools: Interrogation of genome assemblies. - Dominik R. Laetsch; Mark L. Blaxter (F1000Research, 2017)

MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads. - Marcela Uliano-Silva; João Gabriel R. N. Ferreira; Ksenia Krasheninnikova; Mark L. Blaxter; Nova Mieszkowska; Neil Hall; Peter Holland; Richard Durbin; Thomas Richards; Paul J. Kersey; Peter Hollingsworth; Willie Wilson; et al. (BMC Bioinform., 2023)