ProServer: a simple, extensible Perl DAS server. - Robert D. Finn; James W. Stalker; David K. Jackson; Eugene Kulesha; Jody Clements; Roger Pettett (Bioinform., 2007)

HMMER web server: interactive sequence similarity searching. - Robert D. Finn; Jody Clements; Sean R. Eddy (Nucleic Acids Res., 2011)

The Pfam protein families database. - Marco Punta; Penny C. Coggill; Ruth Y. Eberhardt; Jaina Mistry; John G. Tate; Chris Boursnell; Ningze Pang; Kristoffer Forslund; Goran Ceric; Jody Clements; Andreas Heger; Liisa Holm; et al. (Nucleic Acids Res., 2012)

Dfam: a database of repetitive DNA based on profile hidden Markov models. - Travis J. Wheeler; Jody Clements; Sean R. Eddy; Robert Hubley; Thomas A. Jones; Jerzy Jurka; Arian F. A. Smit; Robert D. Finn (Nucleic Acids Res., 2013)

Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models. - Travis J. Wheeler; Jody Clements; Robert D. Finn (BMC Bioinform., 2014)

Pfam: the protein families database. - Robert D. Finn; Alex Bateman; Jody Clements; Penelope Coggill; Ruth Y. Eberhardt; Sean R. Eddy; Andreas Heger; Kirstie Hetherington; Liisa Holm; Jaina Mistry; Erik L. L. Sonnhammer; John G. Tate; et al. (Nucleic Acids Res., 2014)

iPfam: a database of protein family and domain interactions found in the Protein Data Bank. - Robert D. Finn; Benjamin L. Miller; Jody Clements; Alex Bateman (Nucleic Acids Res., 2014)

HMMER web server: 2015 update. - Robert D. Finn; Jody Clements; William Arndt; Benjamin L. Miller; Travis J. Wheeler; Fabian Schreiber; Alex Bateman; Sean R. Eddy (Nucleic Acids Res., 2015)

The Dfam database of repetitive DNA families. - Robert Hubley; Robert D. Finn; Jody Clements; Sean R. Eddy; Thomas A. Jones; Weidong Bao 004; Arian F. A. Smit; Travis J. Wheeler (Nucleic Acids Res., 2016)

Estimating the power of sequence covariation for detecting conserved RNA structure. - Elena Rivas; Jody Clements; Sean R. Eddy (Bioinform., 2020)

neuPrint: An open access tool for EM connectomics. - Stephen M. Plaza; Jody Clements; Tom Dolafi; Lowell A. Umayam; Nicole N. Neubarth; Louis K. Scheffer; Stuart E. Berg (Frontiers Neuroinformatics, 2022)

NeuronBridge: an intuitive web application for neuronal morphology search across large data sets. - Jody Clements; Cristian Goina; Philip M. Hubbard; Takashi Kawase; Donald J. Olbris; Hideo Otsuna; Robert Svirskas; Konrad Rokicki (BMC Bioinform., 2024)