Lack of evidence for conserved secondary structure in long noncoding RNAs

door Rivas, Elena, Clements, Jody, Eddy, Sean R.
Gepubliceerd in Nat Methods (2016)

Estimating the power of sequence covariation for detecting conserved RNA structure

door Rivas, Elena, Clements, Jody, Eddy, Sean R
Gepubliceerd in Bioinformatics (2020)

HMMER web server: interactive sequence similarity searching

door Finn, Robert D., Clements, Jody, Eddy, Sean R.
Gepubliceerd in 2011

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

door Wheeler, Travis J, Clements, Jody, Finn, Robert D
Gepubliceerd in 2014

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

door Finn, Robert D., Miller, Benjamin L., Clements, Jody, Bateman, Alex
Gepubliceerd in 2014

ProServer: a simple, extensible Perl DAS server

door Finn, Robert D., Stalker, James W., Jackson, David K., Kulesha, Eugene, Clements, Jody, Pettett, Roger
Gepubliceerd in 2007

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

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

The subiculum is a patchwork of discrete subregions

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

HMMER web server: 2015 update

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

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

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

The Dfam database of repetitive DNA families

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

Pfam: the protein families database

door 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
Gepubliceerd in 2014

The Pfam protein families database

door 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.
Gepubliceerd in 2012

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

door 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
Gepubliceerd in 2006

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

door 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
Gepubliceerd in Cancer Res (2006)

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

door 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.
Gepubliceerd in Genes Chromosomes Cancer (2006)

Patterns of somatic mutation in human cancer genomes

door 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.
Gepubliceerd in 2007

A connectome and analysis of the adult Drosophila central brain

door 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
Gepubliceerd in eLife (2020)