Lack of evidence for conserved secondary structure in long noncoding RNAs

by Rivas, Elena, Clements, Jody, Eddy, Sean R.
Published in Nat Methods (2016)

Estimating the power of sequence covariation for detecting conserved RNA structure

by Rivas, Elena, Clements, Jody, Eddy, Sean R
Published in Bioinformatics (2020)

HMMER web server: interactive sequence similarity searching

by Finn, Robert D., Clements, Jody, Eddy, Sean R.
Published 2011

Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models

by Wheeler, Travis J, Clements, Jody, Finn, Robert D
Published 2014

iPfam: a database of protein family and domain interactions found in the Protein Data Bank

by Finn, Robert D., Miller, Benjamin L., Clements, Jody, Bateman, Alex
Published 2014

ProServer: a simple, extensible Perl DAS server

by Finn, Robert D., Stalker, James W., Jackson, David K., Kulesha, Eugene, Clements, Jody, Pettett, Roger
Published 2007

Extensive and spatially variable within-cell-type heterogeneity across the basolateral amygdala

by O'Leary, Timothy P, Sullivan, Kaitlin E, Wang, Lihua, Clements, Jody, Lemire, Andrew L, Cembrowski, Mark S
Published in eLife (2020)

The subiculum is a patchwork of discrete subregions

by Cembrowski, Mark S, Wang, Lihua, Lemire, Andrew L, Copeland, Monique, DiLisio, Salvatore F, Clements, Jody, Spruston, Nelson
Published in eLife (2018)

HMMER web server: 2015 update

by Finn, Robert D., Clements, Jody, Arndt, William, Miller, Benjamin L., Wheeler, Travis J., Schreiber, Fabian, Bateman, Alex, Eddy, Sean R.
Published in Nucleic Acids Res (2015)

Dfam: a database of repetitive DNA based on profile hidden Markov models

by Wheeler, Travis J., Clements, Jody, Eddy, Sean R., Hubley, Robert, Jones, Thomas A., Jurka, Jerzy, Smit, Arian F. A., Finn, Robert D.
Published 2013

The Dfam database of repetitive DNA families

by Hubley, Robert, Finn, Robert D., Clements, Jody, Eddy, Sean R., Jones, Thomas A., Bao, Weidong, Smit, Arian F.A., Wheeler, Travis J.
Published in Nucleic Acids Res (2016)

Pfam: the protein families database

by Finn, Robert D., Bateman, Alex, Clements, Jody, Coggill, Penelope, Eberhardt, Ruth Y., Eddy, Sean R., Heger, Andreas, Hetherington, Kirstie, Holm, Liisa, Mistry, Jaina, Sonnhammer, Erik L. L., Tate, John, Punta, Marco
Published 2014

The Pfam protein families database

by Punta, Marco, Coggill, Penny C., Eberhardt, Ruth Y., Mistry, Jaina, Tate, John, Boursnell, Chris, Pang, Ningze, Forslund, Kristoffer, Ceric, Goran, Clements, Jody, Heger, Andreas, Holm, Liisa, Sonnhammer, Erik L. L., Eddy, Sean R., Bateman, Alex, Finn, Robert D.
Published 2012

Mutation analysis of 24 known cancer genes in the NCI-60 cell line set

by Ikediobi, Ogechi N., Davies, Helen, Bignell, Graham, Edkins, Sarah, Stevens, Claire, O’Meara, Sarah, Santarius, Thomas, Avis, Tim, Barthorpe, Syd, Brackenbury, Lisa, Buck, Gemma, Butler, Adam, Clements, Jody, Cole, Jennifer, Dicks, Ed, Forbes, Simon, Gray, Kristian, Halliday, Kelly, Harrison, Rachel, Hills, Katy, Hinton, Jonathan, Hunter, Chris, Jenkinson, Andy, Jones, David, Kosmidou, Vivienne, Lugg, Richard, Menzies, Andrew, Mironenko, Tatiana, Parker, Adrian, Perry, Janet, Raine, Keiran, Richardson, David, Shepherd, Rebecca, Small, Alex, Smith, Raffaella, Solomon, Helen, Stephens, Philip, Teague, Jon, Tofts, Calli, Varian, Jennifer, Webb, Tony, West, Sofie, Widaa, Sara, Yates, Andy, Reinhold, William, Weinstein, John N., Stratton, Michael R., Futreal, P. Andrew, Wooster, Richard
Published 2006

A Hypermutation Phenotype and Somatic MSH6 Mutations in Recurrent Human Malignant Gliomas after Alkylator Chemotherapy

by Hunter, Chris, Smith, Raffaella, Cahill, Daniel P., Stephens, Philip, Stevens, Claire, Teague, Jon, Greenman, Chris, Edkins, Sarah, Bignell, Graham, Davies, Helen, O’Meara, Sarah, Parker, Adrian, Avis, Tim, Barthorpe, Syd, Brackenbury, Lisa, Buck, Gemma, Butler, Adam, Clements, Jody, Cole, Jennifer, Dicks, Ed, Forbes, Simon, Gorton, Matthew, Gray, Kristian, Halliday, Kelly, Harrison, Rachel, Hills, Katy, Hinton, Jonathon, Jenkinson, Andy, Jones, David, Kosmidou, Vivienne, Laman, Ross, Lugg, Richard, Menzies, Andrew, Perry, Janet, Petty, Robert, Raine, Keiran, Richardson, David, Shepherd, Rebecca, Small, Alexandra, Solomon, Helen, Tofts, Calli, Varian, Jennifer, West, Sofie, Widaa, Sara, Yates, Andy, Easton, Douglas F., Riggins, Gregory, Roy, Jennifer E., Levine, Kymberly K., Mueller, Wolf, Batchelor, Tracy T., Louis, David N., Stratton, Michael R., Andrew Futreal, P., Wooster, Richard
Published in Cancer Res (2006)

Sequence Analysis of the Protein Kinase Gene Family in Human Testicular Germ-Cell Tumors of Adolescents and Adults

by Bignell, Graham, Smith, Raffaella, Hunter, Chris, Stephens, Philip, Davies, Helen, Greenman, Chris, Teague, Jon, Butler, Adam, Edkins, Sarah, Stevens, Claire, O’Meara, Sarah, Parker, Adrian, Avis, Tim, Barthorpe, Syd, Brackenbury, Lisa, Buck, Gemma, Clements, Jody, Cole, Jennifer, Dicks, Ed, Edwards, Ken, Forbes, Simon, Gorton, Matthew, Gray, Kristian, Halliday, Kelly, Harrison, Rachel, Hills, Katy, Hinton, Jonathon, Jones, David, Kosmidou, Vivienne, Laman, Ross, Lugg, Richard, Menzies, Andrew, Perry, Janet, Petty, Robert, Raine, Keiran, Shepherd, Rebecca, Small, Alexandra, Solomon, Helen, Stephens, Yvonne, Tofts, Calli, Varian, Jennifer, Webb, Anthony, West, Sofie, Widaa, Sara, Yates, Andy, Gillis, Ad J. M., Stoop, Hans J., van Gurp, Ruud J. H. L. M., Oosterhuis, J. Wolter, Looijenga, Leendert H. J., Futreal, P. Andrew, Wooster, Richard, Stratton, Michael R.
Published in Genes Chromosomes Cancer (2006)

Patterns of somatic mutation in human cancer genomes

by Greenman, Christopher, Stephens, Philip, Smith, Raffaella, Dalgliesh, Gillian L., Hunter, Christopher, Bignell, Graham, Davies, Helen, Teague, Jon, Butler, Adam, Stevens, Claire, Edkins, Sarah, O'Meara, Sarah, Vastrik, Imre, Schmidt, Esther E., Avis, Tim, Barthorpe, Syd, Bhamra, Gurpreet, Buck, Gemma, Choudhury, Bhudipa, Clements, Jody, Cole, Jennifer, Dicks, Ed, Forbes, Simon, Gray, Kris, Halliday, Kelly, Harrison, Rachel, Hills, Katy, Hinton, Jon, Jenkinson, Andy, Jones, David, Menzies, Andy, Mironenko, Tatiana, Perry, Janet, Raine, Keiran, Richardson, Dave, Shepherd, Rebecca, Small, Alexandra, Tofts, Calli, Varian, Jennifer, Webb, Tony, West, Sofie, Widaa, Sara, Yates, Andy, Cahill, Daniel P., Louis, David N., Goldstraw, Peter, Nicholson, Andrew G., Brasseur, Francis, Looijenga, Leendert, Weber, Barbara L., Chiew, Yoke-Eng, deFazio, Anna, Greaves, Mel F., Green, Anthony R., Campbell, Peter, Birney, Ewan, Easton, Douglas F., Chenevix-Trench, Georgia, Tan, Min-Han, Khoo, Sok Kean, Teh, Bin Tean, Yuen, Siu Tsan, Leung, Suet Yi, Wooster, Richard, Futreal, P. Andrew, Stratton, Michael R.
Published 2007

A connectome and analysis of the adult Drosophila central brain

by Scheffer, Louis K, Xu, C Shan, Januszewski, Michal, Lu, Zhiyuan, Takemura, Shin-ya, Hayworth, Kenneth J, Huang, Gary B, Shinomiya, Kazunori, Maitlin-Shepard, Jeremy, Berg, Stuart, Clements, Jody, Hubbard, Philip M, Katz, William T, Umayam, Lowell, Zhao, Ting, Ackerman, David, Blakely, Tim, Bogovic, John, Dolafi, Tom, Kainmueller, Dagmar, Kawase, Takashi, Khairy, Khaled A, Leavitt, Laramie, Li, Peter H, Lindsey, Larry, Neubarth, Nicole, Olbris, Donald J, Otsuna, Hideo, Trautman, Eric T, Ito, Masayoshi, Bates, Alexander S, Goldammer, Jens, Wolff, Tanya, Svirskas, Robert, Schlegel, Philipp, Neace, Erika, Knecht, Christopher J, Alvarado, Chelsea X, Bailey, Dennis A, Ballinger, Samantha, Borycz, Jolanta A, Canino, Brandon S, Cheatham, Natasha, Cook, Michael, Dreher, Marisa, Duclos, Octave, Eubanks, Bryon, Fairbanks, Kelli, Finley, Samantha, Forknall, Nora, Francis, Audrey, Hopkins, Gary Patrick, Joyce, Emily M, Kim, SungJin, Kirk, Nicole A, Kovalyak, Julie, Lauchie, Shirley A, Lohff, Alanna, Maldonado, Charli, Manley, Emily A, McLin, Sari, Mooney, Caroline, Ndama, Miatta, Ogundeyi, Omotara, Okeoma, Nneoma, Ordish, Christopher, Padilla, Nicholas, Patrick, Christopher M, Paterson, Tyler, Phillips, Elliott E, Phillips, Emily M, Rampally, Neha, Ribeiro, Caitlin, Robertson, Madelaine K, Rymer, Jon Thomson, Ryan, Sean M, Sammons, Megan, Scott, Anne K, Scott, Ashley L, Shinomiya, Aya, Smith, Claire, Smith, Kelsey, Smith, Natalie L, Sobeski, Margaret A, Suleiman, Alia, Swift, Jackie, Takemura, Satoko, Talebi, Iris, Tarnogorska, Dorota, Tenshaw, Emily, Tokhi, Temour, Walsh, John J, Yang, Tansy, Horne, Jane Anne, Li, Feng, Parekh, Ruchi, Rivlin, Patricia K, Jayaraman, Vivek, Costa, Marta, Jefferis, Gregory SXE, Ito, Kei, Saalfeld, Stephan, George, Reed, Meinertzhagen, Ian A, Rubin, Gerald M, Hess, Harald F, Jain, Viren, Plaza, Stephen M
Published in eLife (2020)