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Author Title [ Type(Desc)] Year
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Journal Article
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.
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
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.
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.
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
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.
Finn RD, Clements J, Eddy SR.  2011.  HMMER web server: interactive sequence similarity searching.. Nucleic Acids Research. 39:W29-37.
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.
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.
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.
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.
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
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.
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
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.
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
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.
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.