Ensembl Genomes 2020—enabling non-vertebrate genomic research

by Howe, Kevin L, Contreras-Moreira, Bruno, De Silva, Nishadi, Maslen, Gareth, Akanni, Wasiu, Allen, James, Alvarez-Jarreta, Jorge, Barba, Matthieu, Bolser, Dan M, Cambell, Lahcen, Carbajo, Manuel, Chakiachvili, Marc, Christensen, Mikkel, Cummins, Carla, Cuzick, Alayne, Davis, Paul, Fexova, Silvie, Gall, Astrid, George, Nancy, Gil, Laurent, Gupta, Parul, Hammond-Kosack, Kim E, Haskell, Erin, Hunt, Sarah E, Jaiswal, Pankaj, Janacek, Sophie H, Kersey, Paul J, Langridge, Nick, Maheswari, Uma, Maurel, Thomas, McDowall, Mark D, Moore, Ben, Muffato, Matthieu, Naamati, Guy, Naithani, Sushma, Olson, Andrew, Papatheodorou, Irene, Patricio, Mateus, Paulini, Michael, Pedro, Helder, Perry, Emily, Preece, Justin, Rosello, Marc, Russell, Matthew, Sitnik, Vasily, Staines, Daniel M, Stein, Joshua, Tello-Ruiz, Marcela K, Trevanion, Stephen J, Urban, Martin, Wei, Sharon, Ware, Doreen, Williams, Gary, Yates, Andrew D, Flicek, Paul
Published in Nucleic acids research

An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations

by Clavijo, Bernardo J, Venturini, Luca, Schudoma, Christian, Accinelli, Gonzalo Garcia, Kaithakottil, Gemy, Wright, Jonathan, Borrill, Philippa, Kettleborough, George, Heavens, Darren, Chapman, Helen, Lipscombe, James, Barker, Tom, Lu, Fu-Hao, McKenzie, Neil, Raats, Dina, Ramirez-Gonzalez, Ricardo H, Coince, Aurore, Peel, Ned, Percival-Alwyn, Lawrence, Duncan, Owen, Trösch, Josua, Yu, Guotai, Bolser, Dan M, Namaati, Guy, Kerhornou, Arnaud, Spannagl, Manuel, Gundlach, Heidrun, Haberer, Georg, Davey, Robert P, Fosker, Christine, Palma, Federica Di, Phillips, Andrew L, Millar, A Harvey, Kersey, Paul J, Uauy, Cristobal, Krasileva, Ksenia V, Swarbreck, David, Bevan, Michael W, Clark, Matthew D
Published in Genome research

Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species

by Kersey, Paul Julian, Allen, James E, Allot, Alexis, Barba, Matthieu, Boddu, Sanjay, Bolt, Bruce J, Carvalho-Silva, Denise, Christensen, Mikkel, Davis, Paul, Grabmueller, Christoph, Kumar, Navin, Liu, Zicheng, Maurel, Thomas, Moore, Ben, McDowall, Mark D, Maheswari, Uma, Naamati, Guy, Newman, Victoria, Ong, Chuang Kee, Paulini, Michael, Pedro, Helder, Perry, Emily, Russell, Matthew, Sparrow, Helen, Tapanari, Electra, Taylor, Kieron, Vullo, Alessandro, Williams, Gareth, Zadissia, Amonida, Olson, Andrew, Stein, Joshua, Wei, Sharon, Tello-Ruiz, Marcela, Ware, Doreen, Luciani, Aurelien, Potter, Simon, Finn, Robert D, Urban, Martin, Hammond-Kosack, Kim E, Bolser, Dan M, De Silva, Nishadi, Howe, Kevin L, Langridge, Nicholas, Maslen, Gareth, Staines, Daniel Michael, Yates, Andrew
Published in Nucleic acids research

Triticeae resources in Ensembl Plants

by Bolser, Dan M, Kerhornou, Arnaud, Walts, Brandon, Kersey, Paul
Published in Plant and cell physiology

A protein domain interaction interface database: InterPare

by Gong, Sungsam, Park, Changbum, Choi, Hansol, Ko, Junsu, Jang, Insoo, Lee, Jungsul, Bolser, Dan M, Oh, Donghoon, Kim, Deok-Soo, Bhak, Jong
Published in BMC bioinformatics

Large-scale co-evolution analysis of protein structural interlogues using the global protein structural interactome map (PSIMAP)

by Kim, Wan K., Bolser, Dan M., Park, Jong H.
Published in Bioinformatics

Comparative analysis of 7 short-read sequencing platforms using the Korean Reference Genome: MGI and Illumina sequencing benchmark for whole-genome sequencing

by Kim, Hak-Min, Jeon, Sungwon, Chung, Oksung, Jun, Je Hoon, Kim, Hui-Su, Blazyte, Asta, Lee, Hwang-Yeol, Yu, Youngseok, Cho, Yun Sung, Bolser, Dan M, Bhak, Jong
Published in GigaScience

MetaBase-the wiki-database of biological databases

by Bolser, Dan M, Chibon, Pierre-Yves, Palopoli, Nicolas, Gong, Sungsam, Jacob, Daniel, Angel, Victoria Dominguez Del, Swan, Dan, Bassi, Sebastian, González, Virginia, Suravajhala, Prashanth, Hwang, Seungwoo, Romano, Paolo, Edwards, Rob, Bishop, Bryan, Eargle, John, Shtatland, Timur, Provart, Nicholas J, Clements, Dave, Renfro, Daniel P, Bhak, Daeui, Bhak, Jong
Published in Nucleic acids research

The SEQanswers wiki: a wiki database of tools for high-throughput sequencing analysis

by Li, Jing-Woei, Robison, Keith, Martin, Marcel, Sjödin, Andreas, Usadel, Björn, Young, Matthew, Olivares, Eric C, Bolser, Dan M
Published in Nucleic acids research

The SEQanswers wiki: a wiki database of tools for high-throughput sequencing analysis

by Li, J.-W., Robison, K., Martin, M., Sjodin, A., Usadel, B., Young, M., Olivares, E. C., Bolser, D. M.
Published in Nucleic acids research

Residue contact-count potentials are as effective as residue-residue contact-type potentials for ranking protein decoys

by Bolser, Dan M, Filippis, Ioannis, Stehr, Henning, Duarte, Jose, Lappe, Michael
Published in BMC structural biology

PDBWiki: added value through community annotation of the Protein Data Bank

by Stehr, Henning, Duarte, Jose M, Lappe, Michael, Bhak, Jong, Bolser, Dan M
Published in Database : the journal of biological databases and curation

transPLANT Resources for Triticeae Genomic Data

by Spannagl, Manuel, Alaux, Michael, Lange, Matthias, Bolser, Daniel M., Bader, Kai C., Letellier, Thomas, Kimmel, Erik, Flores, Raphael, Pommier, Cyril, Kerhornou, Arnaud, Walts, Brandon, Nussbaumer, Thomas, Grabmuller, Christoph, Chen, Jinbo, Colmsee, Christian, Beier, Sebastian, Mascher, Martin, Schmutzer, Thomas, Arend, Daniel, Thanki, Anil, Ramirez‐Gonzalez, Ricardo, Ayling, Martin, Ayling, Sarah, Caccamo, Mario, Mayer, Klaus F.X., Scholz, Uwe, Steinbach, Delphine, Quesneville, Hadi, Kersey, Paul J.
Published in The plant genome

Analysis of the bread wheat genome using whole―genome shotgun sequencing

by BRENCHLEY, Rachel, SPANNAGL, Manuel, KAY, Suzanne, WAITE, Darren, TRICK, Martin, BANCROFT, Ian, YONG GU, NAXIN HUO, LUO, Ming-Cheng, SEHGAL, Sunish, GILL, Bikram, KIANIAN, Sharyar, PFEIFER, Matthias, ANDERSON, Olin, KERSEY, Paul, DVORAK, Jan, MCCOMBIE, W. Richard, HALL, Anthony, MAYER, Klaus F. X, EDWARDS, Keith J, BEVAN, Michael W, HALL, Neil, BARKER, Gary L. A, D'AMORE, Rosalinda, ALLEN, Alexandra M, MCKENZIE, Neil, KRAMER, Melissa, KERHORNOU, Arnaud, BOLSER, Dan
Published in Nature (London)

Analysis of the breadwheat genome using whole-genome shotgun sequencing

by Brenchley, Rachel, Spannagl, Manuel, Pfeifer, Matthias, Barker, Gary L A, D'Amore, Rosalinda, Allen, Alexandra M, McKenzie, Neil, Kramer, Melissa, Kerhornou, Arnaud, Bolser, Dan, Kay, Suzanne, Waite, Darren, Trick, Martin, Bancroft, Ian, Gu, Yong, Huo, Naxin, Luo, Ming-Cheng, Sehgal, Sunish, Gill, Bikram, Kianian, Sharyar, Anderson, Olin, Kersey, Paul, Dvorak, Jan, McCombie, W Richard, Hall, Anthony, Mayer, Klaus F X, Edwards, Keith J, Bevan, Michael W, Hall, Neil
Published in Nature (London)

Construction of reference chromosome-scale pseudomolecules for potato: integrating the potato genome with genetic and physical maps

by Sharma, Sanjeev Kumar, Bolser, Daniel, de Boer, Jan, Sønderkær, Mads, Amoros, Walter, Carboni, Martin Federico, D'Ambrosio, Juan Martín, de la Cruz, German, Di Genova, Alex, Douches, David S, Eguiluz, Maria, Guo, Xiao, Guzman, Frank, Hackett, Christine A, Hamilton, John P, Li, Guangcun, Li, Ying, Lozano, Roberto, Maass, Alejandro, Marshall, David, Martinez, Diana, McLean, Karen, Mejía, Nilo, Milne, Linda, Munive, Susan, Nagy, Istvan, Ponce, Olga, Ramirez, Manuel, Simon, Reinhard, Thomson, Susan J, Torres, Yerisf, Waugh, Robbie, Zhang, Zhonghua, Huang, Sanwen, Visser, Richard G F, Bachem, Christian W B, Sagredo, Boris, Feingold, Sergio E, Orjeda, Gisella, Veilleux, Richard E, Bonierbale, Merideth, Jacobs, Jeanne M E, Milbourne, Dan, Martin, David Michael Alan, Bryan, Glenn J
Published in G3 (Bethesda, Md.)

De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum

by Fox, Samuel E, Geniza, Matthew, Hanumappa, Mamatha, Naithani, Sushma, Sullivan, Chris, Preece, Justin, Tiwari, Vijay K, Elser, Justin, Leonard, Jeffrey M, Sage, Abigail, Gresham, Cathy, Kerhornou, Arnaud, Bolser, Dan, McCarthy, Fiona, Kersey, Paul, Lazo, Gerard R, Jaiswal, Pankaj
Published in PloS one

Genome sequence and analysis of the tuber crop potato

by Xu, Xun, Pan, Shengkai, Cheng, Shifeng, Zhang, Bo, Mu, Desheng, Ni, Peixiang, Zhang, Gengyun, Yang, Shuang, Li, Ruiqiang, Wang, Jun, Orjeda, Gisella, Guzman, Frank, Torres, Michael, Lozano, Roberto, Ponce, Olga, Martinez, Diana, De la Cruz, Germán, Chakrabarti, S K, Patil, Virupaksh U, Skryabin, Konstantin G, Kuznetsov, Boris B, Ravin, Nikolai V, Kolganova, Tatjana V, Beletsky, Alexey V, Mardanov, Andrei V, Di Genova, Alex, Bolser, Daniel M, Martin, David M A, Li, Guangcun, Yang, Yu, Kuang, Hanhui, Hu, Qun, Xiong, Xingyao, Bishop, Gerard J, Sagredo, Boris, Mejía, Nilo, Zagorski, Wlodzimierz, Gromadka, Robert, Gawor, Jan, Szczesny, Pawel, Huang, Sanwen, Zhang, Zhonghua, Liang, Chunbo, He, Jun, Li, Ying, He, Ying, Xu, Jianfei, Zhang, Youjun, Xie, Binyan, Du, Yongchen, Qu, Dongyu, Bonierbale, Merideth, Ghislain, Marc, Herrera, Maria del Rosario, Giuliano, Giovanni, Pietrella, Marco, Perrotta, Gaetano, Facella, Paolo, O'Brien, Kimberly, Feingold, Sergio E, Barreiro, Leandro E, Massa, Gabriela A, Diambra, Luis, Whitty, Brett R, Vaillancourt, Brieanne, Lin, Haining, Massa, Alicia N, Geoffroy, Michael, Lundback, Steven, DellaPenna, Dean, Buell, C Robin, Sharma, Sanjeev Kumar, Marshall, David F, Waugh, Robbie, Bryan, Glenn J, Destefanis, Marialaura, Nagy, Istvan, Milbourne, Dan, Thomson, Susan J, Fiers, Mark, Jacobs, Jeanne M E, Nielsen, Kåre L, Sønderkær, Mads, Iovene, Marina, Torres, Giovana A, Jiang, Jiming, Veilleux, Richard E, Bachem, Christian W B, de Boer, Jan, Borm, Theo, Kloosterman, Bjorn, van Eck, Herman, Datema, Erwin, Hekkert, Bas te Lintel, Goverse, Aska, van Ham, Roeland C H J, Visser, Richard G F
Published in Nature (London)

PSIbase: a database of Protein Structural Interactome map (PSIMAP)

by Gong, Sungsam, Yoon, Giseok, Jang, Insoo, Bolser, Dan, Dafas, Panos, Schroeder, Michael, Choi, Hansol, Cho, Yoobok, Han, Kyungsook, Lee, Sunghoon, Choi, Hwanho, Lappe, Michael, Holm, Liisa, Kim, Sangsoo, Oh, Donghoon, Bhak, Jonghwa
Published in Bioinformatics

Gramene 2013: comparative plant genomics resources

by Monaco, Marcela K., Stein, Joshua, Naithani, Sushma, Wei, Sharon, Dharmawardhana, Palitha, Kumari, Sunita, Amarasinghe, Vindhya, Youens-Clark, Ken, Thomason, James, Preece, Justin, Pasternak, Shiran, Olson, Andrew, Jiao, Yinping, Lu, Zhenyuan, Bolser, Dan, Kerhornou, Arnaud, Staines, Dan, Walts, Brandon, Wu, Guanming, D’Eustachio, Peter, Haw, Robin, Croft, David, Kersey, Paul J., Stein, Lincoln, Jaiswal, Pankaj, Ware, Doreen
Published in Nucleic acids research