Inferring horizontal gene transfer by Ravenhall, Matt, Škunca, Nives, Lassalle, Florent, Dessimoz, Christophe

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Quality of computationally inferred gene ontology annotations by Skunca, Nives, Altenhoff, Adrian, Dessimoz, Christophe

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The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements by Altenhoff, Adrian M, Škunca, Nives, Glover, Natasha, Train, Clément-Marie, Sueki, Anna, Piližota, Ivana, Gori, Kevin, Tomiczek, Bartlomiej, Müller, Steven, Redestig, Henning, Gonnet, Gaston H, Dessimoz, Christophe

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Phylogenetic profiling: how much input data is enough? by Škunca, Nives, Dessimoz, Christophe

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A Transcriptomic-Phylogenomic Analysis of the Evolutionary Relationships of Flatworms by Egger, Bernhard, Lapraz, François, Tomiczek, Bartłomiej, Müller, Steven, Dessimoz, Christophe, Girstmair, Johannes, Škunca, Nives, Rawlinson, Kate A., Cameron, Christopher B., Beli, Elena, Todaro, M. Antonio, Gammoudi, Mehrez, Noreña, Carolina, Telford, Maximilian J.

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REVIGO summarizes and visualizes long lists of gene ontology terms by Supek, Fran, Bošnjak, Matko, Škunca, Nives, Šmuc, Tomislav

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CAFA and the Open World of protein function predictions by Dessimoz, Christophe, Škunca, Nives, Thomas, Paul D

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The what, where, how and why of gene ontology-a primer for bioinformaticians by du Plessis, Louis, Škunca, Nives, Dessimoz, Christophe

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Translational selection is ubiquitous in prokaryotes by Supek, Fran, Skunca, Nives, Repar, Jelena, Vlahovicek, Kristian, Smuc, Tomislav

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Phyletic profiling with cliques of orthologs is enhanced by signatures of paralogy relationships by Skunca, Nives, Bošnjak, Matko, Kriško, Anita, Panov, Panče, Džeroski, Sašo, Smuc, Tomislav, Supek, Fran

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The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease by Peng, Xinxia, Alföldi, Jessica, Gori, Kevin, Eisfeld, Amie J, Tyler, Scott R, Tisoncik-Go, Jennifer, Brawand, David, Law, G Lynn, Skunca, Nives, Hatta, Masato, Gasper, David J, Kelly, Sara M, Chang, Jean, Thomas, Matthew J, Johnson, Jeremy, Berlin, Aaron M, Lara, Marcia, Russell, Pamela, Swofford, Ross, Turner-Maier, Jason, Young, Sarah, Hourlier, Thibaut, Aken, Bronwen, Searle, Steve, Sun, Xingshen, Yi, Yaling, Suresh, M, Tumpey, Terrence M, Siepel, Adam, Wisely, Samantha M, Dessimoz, Christophe, Kawaoka, Yoshihiro, Birren, Bruce W, Lindblad-Toh, Kerstin, Di Palma, Federica, Engelhardt, John F, Palermo, Robert E, Katze, Michael G

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Big data and other challenges in the quest for orthologs by Sonnhammer, Erik L L, Gabaldón, Toni, Sousa da Silva, Alan W, Martin, Maria, Robinson-Rechavi, Marc, Boeckmann, Brigitte, Thomas, Paul D, Dessimoz, Christophe

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Gearing up to handle the mosaic nature of life in the quest for orthologs by Forslund, Kristoffer, Pereira, Cecile, Capella-Gutierrez, Salvador, da Silva, Alan Sousa, Altenhoff, Adrian, Huerta-Cepas, Jaime, Muffato, Matthieu, Patricio, Mateus, Vandepoele, Klaas, Ebersberger, Ingo, Blake, Judith, Fernández Breis, Jesualdo Tomás, Boeckmann, Brigitte, Gabaldón, Toni, Sonnhammer, Erik, Dessimoz, Christophe, Lewis, Suzanna

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Toward community standards in the quest for orthologs by Dessimoz, Christophe, Gabaldón, Toni, Roos, David S, Sonnhammer, Erik L. L, Herrero, Javier

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Gearing up to handle the mosaic nature of life in the quest for orthologs by Forslund, Kristoffer, Pereira, Cecile, Capella-Gutierrez, Salvador, da Silva, Alan Sousa, Altenhoff, Adrian, Huerta-Cepas, Jaime, Muffato, Matthieu, Patricio, Mateus, Vandepoele, Klaas, Ebersberger, Ingo, Blake, Judith, Fernández Breis, Jesualdo Tomás, Boeckmann, Brigitte, Gabaldón, Toni, Sonnhammer, Erik, Dessimoz, Christophe, Lewis, Suzanna, Bello, Carla, Briois, Sébastien, Capella-Gutierrez, Salvador, Chalstrey, Edward, Chiba, Hirokazu, Conchillo-Solé, Oscar, Daubin, Vincent, Deluca, Todd, Dufayard, Jean-Francois, Durand, Dannie, Fernández-Breis, Jesualdo Tomás, Forslund, Kristoffer, Glover, Natasha, Hauser, Alexander, Heller, Davide, Kaduk, Mateusz, Koch, Jan, Koonin, Eugene, Kriventseva, Evgenia, Kuraku, Shigehiro, Lecompte, Odile, Lespinet, Olivier, Levy, Jeremy, Liebeskind, Benjamin, Linard, Benjamin, Marcet-Houben, Marina, Martin, Maria, Mcwhite, Claire, Mekhedov, Sergei, Moretti, Sebastien, Müller, Steven, Nadia, El-Mabrouk, Notredame, Cédric, Penel, Simon, Pereira, Cécile, Pilizota, Ivana, Redestig, Henning, Robinson-Rechavi, Marc, Schreiber, Fabian, Sjölander, Kimmen, Škunca, Nives, Steinegger, Martin, Szklarczyk, Damian, Thomas, Paul, Thuer, Ernst, Train, Clément, Uchiyama, Ikuo, Wittwer, Lucas, Xenarios, Ioannis, Yates, Bethan, Zdobnov, Evgeny, Waterhouse, Robert

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An expanded evaluation of protein function prediction methods shows an improvement in accuracy by Jiang, Yuxiang, Oron, Tal Ronnen, Clark, Wyatt T, Bankapur, Asma R, D'Andrea, Daniel, Lepore, Rosalba, Funk, Christopher S, Kahanda, Indika, Verspoor, Karin M, Ben-Hur, Asa, Koo, Da Chen Emily, Penfold-Brown, Duncan, Shasha, Dennis, Youngs, Noah, Bonneau, Richard, Lin, Alexandra, Sahraeian, Sayed M E, Martelli, Pier Luigi, Profiti, Giuseppe, Casadio, Rita, Cao, Renzhi, Zhong, Zhaolong, Cheng, Jianlin, Altenhoff, Adrian, Skunca, Nives, Dessimoz, Christophe, Dogan, Tunca, Hakala, Kai, Kaewphan, Suwisa, Mehryary, Farrokh, Salakoski, Tapio, Ginter, Filip, Fang, Hai, Smithers, Ben, Oates, Matt, Gough, Julian, Törönen, Petri, Koskinen, Patrik, Holm, Liisa, Chen, Ching-Tai, Hsu, Wen-Lian, Bryson, Kevin, Cozzetto, Domenico, Minneci, Federico, Jones, David T, Chapman, Samuel, Bkc, Dukka, Khan, Ishita K, Kihara, Daisuke, Ofer, Dan, Rappoport, Nadav, Stern, Amos, Cibrian-Uhalte, Elena, Denny, Paul, Foulger, Rebecca E, Hieta, Reija, Legge, Duncan, Lovering, Ruth C, Magrane, Michele, Melidoni, Anna N, Mutowo-Meullenet, Prudence, Pichler, Klemens, Shypitsyna, Aleksandra, Li, Biao, Zakeri, Pooya, ElShal, Sarah, Tranchevent, Léon-Charles, Das, Sayoni, Dawson, Natalie L, Lee, David, Lees, Jonathan G, Sillitoe, Ian, Bhat, Prajwal, Nepusz, Tamás, Romero, Alfonso E, Sasidharan, Rajkumar, Yang, Haixuan, Paccanaro, Alberto, Gillis, Jesse, Sedeño-Cortés, Adriana E, Pavlidis, Paul, Feng, Shou, Cejuela, Juan M, Goldberg, Tatyana, Hamp, Tobias, Richter, Lothar, Salamov, Asaf, Gabaldon, Toni, Marcet-Houben, Marina, Supek, Fran, Gong, Qingtian, Ning, Wei, Zhou, Yuanpeng, Tian, Weidong, Falda, Marco, Fontana, Paolo, Lavezzo, Enrico, Toppo, Stefano, Ferrari, Carlo, Giollo, Manuel

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Inferring Horizontal Gene Transfer: e1004095 by Ravenhall, Matt, Skunca, Nives, Lassalle, Florent, Dessimoz, Christophe

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Phylogenetic Profiling: How Much Input Data Is Enough?: e0114701 by Skunca, Nives, Dessimoz, Christophe

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The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations by Bastian, Frederic B, Chibucos, Marcus C, Gaudet, Pascale, Giglio, Michelle, Holliday, Gemma L, Huang, Hong, Lewis, Suzanna E, Niknejad, Anne, Orchard, Sandra, Poux, Sylvain, Skunca, Nives, Robinson-Rechavi, Marc

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Visualizing Gene Ontology annotations by Supek, Fran, Škunca, Nives

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