Integration of molecular network data reconstructs Gene Ontology

por Gligorijević, Vladimir, Janjić, Vuk, Pržulj, Nataša
Publicado 2014

deepNF: deep network fusion for protein function prediction

por Gligorijević, Vladimir, Barot, Meet, Bonneau, Richard
Publicado 2018

NetQuilt: deep multispecies network-based protein function prediction using homology-informed network similarity

por Barot, Meet, Gligorijević, Vladimir, Cho, Kyunghyun, Bonneau, Richard
Publicado 2021

TCRconv: predicting recognition between T cell receptors and epitopes using contextualized motifs

por Jokinen, Emmi, Dumitrescu, Alexandru, Huuhtanen, Jani, Gligorijević, Vladimir, Mustjoki, Satu, Bonneau, Richard, Heinonen, Markus, Lähdesmäki, Harri
Publicado 2022

Comprehensive Functional Annotation of Metagenomes and Microbial Genomes Using a Deep Learning-Based Method

por Maranga, Mary, Szczerbiak, Pawel, Bezshapkin, Valentyn, Gligorijevic, Vladimir, Chandler, Chris, Bonneau, Richard, Xavier, Ramnik J., Vatanen, Tommi, Kosciolek, Tomasz
Publicado 2023

Structure-based protein function prediction using graph convolutional networks

por Gligorijević, Vladimir, Renfrew, P. Douglas, Kosciolek, Tomasz, Leman, Julia Koehler, Berenberg, Daniel, Vatanen, Tommi, Chandler, Chris, Taylor, Bryn C., Fisk, Ian M., Vlamakis, Hera, Xavier, Ramnik J., Knight, Rob, Cho, Kyunghyun, Bonneau, Richard
Publicado 2021

Sequence-structure-function relationships in the microbial protein universe

por Koehler Leman, Julia, Szczerbiak, Pawel, Renfrew, P. Douglas, Gligorijevic, Vladimir, Berenberg, Daniel, Vatanen, Tommi, Taylor, Bryn C., Chandler, Chris, Janssen, Stefan, Pataki, Andras, Carriero, Nick, Fisk, Ian, Xavier, Ramnik J., Knight, Rob, Bonneau, Richard, Kosciolek, Tomasz
Publicado 2023

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

por Zhou, Naihui, Jiang, Yuxiang, Bergquist, Timothy R., Lee, Alexandra J., Kacsoh, Balint Z., Crocker, Alex W., Lewis, Kimberley A., Georghiou, George, Nguyen, Huy N., Hamid, Md Nafiz, Davis, Larry, Dogan, Tunca, Atalay, Volkan, Rifaioglu, Ahmet S., Dalkıran, Alperen, Cetin Atalay, Rengul, Zhang, Chengxin, Hurto, Rebecca L., Freddolino, Peter L., Zhang, Yang, Bhat, Prajwal, Supek, Fran, Fernández, José M., Gemovic, Branislava, Perovic, Vladimir R., Davidović, Radoslav S., Sumonja, Neven, Veljkovic, Nevena, Asgari, Ehsaneddin, Mofrad, Mohammad R.K., Profiti, Giuseppe, Savojardo, Castrense, Martelli, Pier Luigi, Casadio, Rita, Boecker, Florian, Schoof, Heiko, Kahanda, Indika, Thurlby, Natalie, McHardy, Alice C., Renaux, Alexandre, Saidi, Rabie, Gough, Julian, Freitas, Alex A., Antczak, Magdalena, Fabris, Fabio, Wass, Mark N., Hou, Jie, Cheng, Jianlin, Wang, Zheng, Romero, Alfonso E., Paccanaro, Alberto, Yang, Haixuan, Goldberg, Tatyana, Zhao, Chenguang, Holm, Liisa, Törönen, Petri, Medlar, Alan J., Zosa, Elaine, Borukhov, Itamar, Novikov, Ilya, Wilkins, Angela, Lichtarge, Olivier, Chi, Po-Han, Tseng, Wei-Cheng, Linial, Michal, Rose, Peter W., Dessimoz, Christophe, Vidulin, Vedrana, Dzeroski, Saso, Sillitoe, Ian, Das, Sayoni, Lees, Jonathan Gill, Jones, David T., Wan, Cen, Cozzetto, Domenico, Fa, Rui, Torres, Mateo, Warwick Vesztrocy, Alex, Rodriguez, Jose Manuel, Tress, Michael L., Frasca, Marco, Notaro, Marco, Grossi, Giuliano, Petrini, Alessandro, Re, Matteo, Valentini, Giorgio, Mesiti, Marco, Roche, Daniel B., Reeb, Jonas, Ritchie, David W., Aridhi, Sabeur, Alborzi, Seyed Ziaeddin, Devignes, Marie-Dominique, Koo, Da Chen Emily, Bonneau, Richard, Gligorijević, Vladimir, Barot, Meet, Fang, Hai, Toppo, Stefano, Lavezzo, Enrico, Falda, Marco, Berselli, Michele, Tosatto, Silvio C.E., Carraro, Marco, Piovesan, Damiano, Ur Rehman, Hafeez, Mao, Qizhong, Zhang, Shanshan, Vucetic, Slobodan, Black, Gage S., Jo, Dane, Suh, Erica, Dayton, Jonathan B., Larsen, Dallas J., Omdahl, Ashton R., McGuffin, Liam J., Brackenridge, Danielle A., Babbitt, Patricia C., Yunes, Jeffrey M., Fontana, Paolo, Zhang, Feng, Zhu, Shanfeng, You, Ronghui, Zhang, Zihan, Dai, Suyang, Yao, Shuwei, Tian, Weidong, Cao, Renzhi, Chandler, Caleb, Amezola, Miguel, Johnson, Devon, Chang, Jia-Ming, Liao, Wen-Hung, Liu, Yi-Wei, Pascarelli, Stefano, Frank, Yotam, Hoehndorf, Robert, Kulmanov, Maxat, Boudellioua, Imane, Politano, Gianfranco, Di Carlo, Stefano, Benso, Alfredo, Hakala, Kai, Ginter, Filip, Mehryary, Farrokh, Kaewphan, Suwisa, Björne, Jari, Moen, Hans, Tolvanen, Martti E.E., Salakoski, Tapio, Kihara, Daisuke, Jain, Aashish, Šmuc, Tomislav, Altenhoff, Adrian, Ben-Hur, Asa, Rost, Burkhard, Brenner, Steven E., Orengo, Christine A., Jeffery, Constance J., Bosco, Giovanni, Hogan, Deborah A., Martin, Maria J., O’Donovan, Claire, Mooney, Sean D., Greene, Casey S., Radivojac, Predrag, Friedberg, Iddo
Publicado 2019