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2024
Kapustina M, Zhang AA, Tsai JYJ, Bristow BN, Kraus L, Sullivan KE, Erwin SR, Wang L, Stach TR, Clements J et al..  2024.  The cell-type-specific spatial organization of the anterior thalamic nuclei of the mouse brain.. Cell Reports. 43(3):113842.
2023
Meissner GWilson, Nern A, Dorman Z, Depasquale GM, Forster K, Gibney T, Hausenfluck JH, He Y, Iyer NA, Jeter J et al..  2023.  A searchable image resource of Drosophila GAL4-driver expression patterns with single neuron resolution.. eLife. 12
Heinrich L, Patton W, Bennett D, Ackerman D, Park G, Bogovic JA, Eckstein N, Petruncio A, Clements J, Pang S et al..  2023.  Towards Generalizable Organelle Segmentation in Volume Electron Microscopy.. Microscopy and Microanalysis. 29(Supplement_1):975.
2022
Plaza SM, Clements J, Dolafi T, Umayam L, Neubarth NN, Scheffer LK, Berg S.  2022.  neuPrint: An open access tool for EM connectomics.. Frontiers in Neuroinformatics. 16:896292.
O’Leary TP, Kendrick RM, Bristow BN, Sullivan KE, Wang L, Clements J, Lemire AL, Cembrowski MS.  2022.  Neuronal cell types, projections, and spatial organization of the central amygdala. iScience. 25(12):105497.
2021
Erwin SR, Bristow BN, Sullivan KE, Kendrick RM, Marriott B, Wang L, Clements J, Lemire AL, Jackson J, Cembrowski MS.  2021.  Spatially patterned excitatory neuron subtypes and projections of the claustrum.. eLife. 10
Heinrich L, Bennett D, Ackerman D, Park W, Bogovic J, Eckstein N, Petruncio A, Clements J, Pang S, C Xu S et al..  2021.  Whole-cell organelle segmentation in volume electron microscopy.. Nature. 599(7883):141-46.
2020
Scheffer LK, C Xu S, Januszewski M, Lu Z, Takemura S-ya, Hayworth KJ, Huang GB, Shinomiya K, Maitlin-Shepard J, Berg S et al..  2020.  A connectome and analysis of the adult Drosophila central brain.. Elife. 9
Rivas E, Clements J, Eddy SR.  2020.  Estimating the power of sequence covariation for detecting conserved RNA structure.. Bioinformatics. 36(10):3072-76.
O'Leary TP, Sullivan KE, Wang L, Clements J, Lemire AL, Cembrowski MS.  2020.  Extensive and spatially variable within-cell-type heterogeneity across the basolateral amygdala.. eLife. 9
2018
Cembrowski MS, Wang L, Lemire AL, Copeland M, DiLisio SF, Clements J, Spruston N.  2018.  The subiculum is a patchwork of discrete subregions.. eLife. 7
2017
Rivas E, Clements J, Eddy SR.  2017.  A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs.. Nature Methods. 14(1):45-8.
2016
Hubley R, Finn RD, Clements J, Eddy SR, Jones TA, Bao W, Smit AFA, Wheeler TJ.  2016.  The Dfam database of repetitive DNA families.. Nucleic Acids Research. 44(D1):D81-9.
2015
Finn RD, Clements J, Arndt W, Miller BL, Wheeler TJ, Schreiber F, Bateman A, Eddy SR.  2015.  HMMER web server: 2015 update.. Nucleic Acids Research.
2014
Finn RD, Miller BL, Clements J, Bateman A.  2014.  iPfam: a database of protein family and domain interactions found in the Protein Data Bank.. Nucleic acids research. 42:D364-73.
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J et al..  2014.  Pfam: the protein families database.. Nucleic acids research. 42:D222-30.
Wheeler TJ, Clements J, Finn RD.  2014.  Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models.. BMC Bioinformatics. 15:7.
2013
Wheeler TJ, Clements J, Eddy SR, Hubley R, Jones TA, Jurka J, Smit AFA, Finn RD.  2013.  Dfam: a database of repetitive DNA based on profile hidden Markov models.. Nucleic Acids Research. 41:D70-82.
2012
Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J et al..  2012.  The Pfam protein families database.. Nucleic acids research. 40:D290-301.
2011
Finn RD, Clements J, Eddy SR.  2011.  HMMER web server: interactive sequence similarity searching.. Nucleic Acids Research. 39:W29-37.