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

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

Publikováno v: Genome Biology, Vol 20, Iss 1, Pp 1-23 (2019)

Abstract Background The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Results Here, we report on the results of the third C

Externí odkaz: https://doaj.org/article/4c2b017b155b41ceab8d6d078186cafa

Neural Network and Random Forest Models in Protein Function Prediction

Autor: Kai, Hakala, Suwisa, Kaewphan, Jari, Bjorne, Farrokh, Mehryary, Hans, Moen, Martti, Tolvanen, Tapio, Salakoski, Filip, Ginter

Publikováno v: IEEE/ACM transactions on computational biology and bioinformatics. 19(3)

Over the past decade, the demand for automated protein function prediction has increased due to the volume of newly sequenced proteins. In this paper, we address the function prediction task by developing an ensemble system automatically assigning Ge

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::d3b7f9eb0e7ff34dc0e5a10e050c74cb
https://pubmed.ncbi.nlm.nih.gov/33306472

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

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

The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Here we report on the results of the third CAFA challenge, CAFA3, that fe

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4041959032930476de14481a887bcd78

The Cafa Challenge Reports Improved Protein Function Prediction And New Functional Annotations For Hundreds Of Genes Through Experimental Screens

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

Publikováno v: Repisalud
Instituto de Salud Carlos III (ISCIII)
Genome Biology
Genome Biology, BioMed Central, 2019, 20 (1), ⟨10.1186/s13059-019-1835-8⟩
Zhou, N, Jiang, Y, Bergquist, T R, Lee, A J, Kacsoh, B Z, Crocker, A W, Lewis, K A, Georghiou, G, Nguyen, H N, Hamid, M N, Davis, L, Dogan, T, Atalay, V, Rifaioglu, A S, Dalklran, A, Cetin Atalay, R, Zhang, C, Hurto, R L, Freddolino, P L, Zhang, Y, Bhat, P, Supek, F, Fernández, J M, Gemovic, B, Perovic, V R, Davidović, R S, Sumonja, N, Veljkovic, N, Asgari, E, Mofrad, M R K, Profiti, G, Savojardo, C, Martelli, P L, Casadio, R, Boecker, F, Schoof, H, Kahanda, I, Thurlby, N, McHardy, A C, Renaux, A, Saidi, R, Gough, J, Freitas, A A, Antczak, M, Fabris, F, Wass, M N, Hou, J, Cheng, J, Wang, Z, Romero, A E, Paccanaro, A, Yang, H, Goldberg, T, Zhao, C, Holm, L, Törönen, P, Medlar, A J, Zosa, E, Borukhov, I, Novikov, I, Wilkins, A, Lichtarge, O, Chi, P H, Tseng, W C, Linial, M, Rose, P W, Dessimoz, C, Vidulin, V, Dzeroski, S, Sillitoe, I, Das, S, Lees, J G, Jones, D T, Wan, C, Cozzetto, D, Fa, R, Torres, M, Warwick Vesztrocy, A, Rodriguez, J M, Tress, M L, Frasca, M, Notaro, M, Grossi, G, Petrini, A, Re, M, Valentini, G, Mesiti, M, Roche, D B, Reeb, J, Ritchie, D W, Aridhi, S, Alborzi, S Z, Devignes, M D, Koo, D C E, Bonneau, R, Gligorijević, V, Barot, M, Fang, H, Toppo, S, Lavezzo, E, Falda, M, Berselli, M, Tosatto, S C E, Carraro, M, Piovesan, D, Ur Rehman, H, Mao, Q, Zhang, S, Vucetic, S, Black, G S, Jo, D, Suh, E, Dayton, J B, Larsen, D J, Omdahl, A R, McGuffin, L J, Brackenridge, D A, Babbitt, P C, Yunes, J M, Fontana, P, Zhang, F, Zhu, S, You, R, Zhang, Z, Dai, S, Yao, S, Tian, W, Cao, R, Chandler, C, Amezola, M, Johnson, D, Chang, J M, Liao, W H, Liu, Y W, Pascarelli, S, Frank, Y, Hoehndorf, R, Kulmanov, M, Boudellioua, I, Politano, G, Di Carlo, S, Benso, A, Hakala, K, Ginter, F, Mehryary, F, Kaewphan, S, Björne, J, Moen, H, Tolvanen, M E E, Salakoski, T, Kihara, D, Jain, A, Šmuc, T, Altenhoff, A, Ben-Hur, A, Rost, B, Brenner, S E, Orengo, C A, Jeffery, C J, Bosco, G, Hogan, D A, Martin, M J, O'Donovan, C, Mooney, S D, Greene, C S, Radivojac, P & Friedberg, I 2019, ' The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens ', Genome Biology, vol. 20, no. 1, 244 (2019) . https://doi.org/10.1186/s13059-019-1835-8
Genome biology
Genome Biology, Vol 20, Iss 1, Pp 1-23 (2019)
Genome Biology, 2019, 20 (1), ⟨10.1186/s13059-019-1835-8⟩

Tosatto, Silvio/0000-0003-4525-7793; Zhang, Feng/0000-0003-3447-897X; Gonzalez, Jose Maria Fernandez/0000-0002-4806-5140; Devignes, Marie-Dominique/0000-0002-0399-8713; Wass, Mark/0000-0001-5428-6479; Falda, Marco/0000-0003-2642-519X; Thurlby, Natali

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::99caa2a2ab2b36bdcf4f44143c8015a5
http://hdl.handle.net/11655/24591

Wide-scope biomedical named entity recognition and normalization with CRFs, fuzzy matching and character level modeling

Autor: Suwisa, Kaewphan, Kai, Hakala, Niko, Miekka, Tapio, Salakoski, Filip, Ginter

Publikováno v: Database : the journal of biological databases and curation. 2018

We present a system for automatically identifying a multitude of biomedical entities from the literature. This work is based on our previous efforts in the BioCreative VI: Interactive Bio-ID Assignment shared task in which our system demonstrated sta

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::297165e5dcacac15b2b3b1c84e977de6
https://pubmed.ncbi.nlm.nih.gov/30239666