TY  - JOUR
AU  - Zhou, Naihui
AU  - Jiang, Yuxiang
AU  - Bergquist, Timothy R
AU  - Lee, Alexandra J
AU  - Kacsoh, Balint Z
AU  - Crocker, Alex W
AU  - Lewis, Kimberley A
AU  - Georghiou, George
AU  - Nguyen, Huy N
AU  - Hamid, Md Nafiz
AU  - Davis, Larry
AU  - Dogan, Tunca
AU  - Atalay, Volkan
AU  - Rifaioglu, Ahmet S
AU  - Dalkıran, Alperen
AU  - Cetin Atalay, Rengul
AU  - Zhang, Chengxin
AU  - Hurto, Rebecca L
AU  - Freddolino, Peter L
AU  - Zhang, Yang
AU  - Bhat, Prajwal
AU  - Supek, Fran
AU  - Fernández, José M
AU  - Gemović, Branislava S.
AU  - Perović, Vladimir R.
AU  - Davidović, Radoslav S.
AU  - Šumonja, Neven
AU  - Veljković, Nevena V.
AU  - Asgari, Ehsaneddin
AU  - Mofrad, Mohammad R.K.
AU  - Profiti, Giuseppe
AU  - Savojardo, Castrense
AU  - Martelli, Pier Luigi
AU  - Casadio, Rita
AU  - Boecker, Florian
AU  - Schoof, Heiko
AU  - Kahanda, Indika
AU  - Thurlby, Natalie
AU  - McHardy, Alice C
AU  - Renaux, Alexandre
AU  - Saidi, Rabie
AU  - Gough, Julian
AU  - Freitas, Alex A
AU  - Antczak, Magdalena
AU  - Fabris, Fabio
AU  - Wass, Mark N
AU  - Hou, Jie
AU  - Cheng, Jianlin
AU  - Wang, Zheng
AU  - Romero, Alfonso E
AU  - Paccanaro, Alberto
AU  - Yang, Haixuan
AU  - Goldberg, Tatyana
AU  - Zhao, Chenguang
AU  - Holm, Liisa
AU  - Törönen, Petri
AU  - Medlar, Alan J
AU  - Zosa, Elaine
AU  - Borukhov, Itamar
AU  - Novikov, Ilya
AU  - Wilkins, Angela
AU  - Lichtarge, Olivier
AU  - Chi, Po-Han
AU  - Tseng, Wei-Cheng
AU  - Linial, Michal
AU  - Rose, Peter W
AU  - Dessimoz, Christophe
AU  - Vidulin, Vedrana
AU  - Dzeroski, Saso
AU  - Sillitoe, Ian
AU  - Das, Sayoni
AU  - Lees, Jonathan Gill
AU  - Jones, David T
AU  - Wan, Cen
AU  - Cozzetto, Domenico
AU  - Fa, Rui
AU  - Torres, Mateo
AU  - Warwick Vesztrocy, Alex
AU  - Rodriguez, Jose Manuel
AU  - Tress, Michael L
AU  - Frasca, Marco
AU  - Notaro, Marco
AU  - Grossi, Giuliano
AU  - Petrini, Alessandro
AU  - Re, Matteo
AU  - Valentini, Giorgio
AU  - Mesiti, Marco
AU  - Roche, Daniel B
AU  - Reeb, Jonas
AU  - Ritchie, David W
AU  - Aridhi, Sabeur
AU  - Alborzi, Seyed Ziaeddin
AU  - Devignes, Marie-Dominique
AU  - Koo, Da Chen Emily
AU  - Bonneau, Richard
AU  - Gligorijević, Vladimir
AU  - Barot, Meet
AU  - Fang, Hai
AU  - Toppo, Stefano
AU  - Lavezzo, Enrico
AU  - Falda, Marco
AU  - Berselli, Michele
AU  - Tosatto, Silvio C.E.
AU  - Carraro, Marco
AU  - Piovesan, Damiano
AU  - Ur Rehman, Hafeez
AU  - Mao, Qizhong
AU  - Zhang, Shanshan
AU  - Vucetic, Slobodan
AU  - Black, Gage S
AU  - Jo, Dane
AU  - Suh, Erica
AU  - Dayton, Jonathan B
AU  - Larsen, Dallas J
AU  - Omdahl, Ashton R
AU  - McGuffin, Liam J
AU  - Brackenridge, Danielle A
AU  - Babbitt, Patricia C
AU  - Yunes, Jeffrey M
AU  - Fontana, Paolo
AU  - Zhang, Feng
AU  - Zhu, Shanfeng
AU  - You, Ronghui
AU  - Zhang, Zihan
AU  - Dai, Suyang
AU  - Yao, Shuwei
AU  - Tian, Weidong
AU  - Cao, Renzhi
AU  - Chandler, Caleb
AU  - Amezola, Miguel
AU  - Johnson, Devon
AU  - Chang, Jia-Ming
AU  - Liao, Wen-Hung
AU  - Liu, Yi-Wei
AU  - Pascarelli, Stefano
AU  - Frank, Yotam
AU  - Hoehndorf, Robert
AU  - Kulmanov, Maxat
AU  - Boudellioua, Imane
AU  - Politano, Gianfranco
AU  - Di Carlo, Stefano
AU  - Benso, Alfredo
AU  - Hakala, Kai
AU  - Ginter, Filip
AU  - Mehryary, Farrokh
AU  - Kaewphan, Suwisa
AU  - Björne, Jari
AU  - Moen, Hans
AU  - Tolvanen, Martti E.E.
AU  - Salakoski, Tapio
AU  - Kihara, Daisuke
AU  - Jain, Aashish
AU  - Šmuc, Tomislav
AU  - Altenhoff, Adrian
AU  - Ben-Hur, Asa
AU  - Rost, Burkhard
AU  - Brenner, Steven E
AU  - Orengo, Christine A
AU  - Jeffery, Constance J
AU  - Bosco, Giovanni
AU  - Hogan, Deborah A
AU  - Martin, Maria J
AU  - O’Donovan, Claire
AU  - Mooney, Sean D
AU  - Greene, Casey S
AU  - Radivojac, Predrag
AU  - Friedberg, Iddo
PY  - 2019
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/8655
AB  - 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 CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-Term memory. Conclusion: We conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens. © 2019 The Author(s).
T2  - Genome Biology
T1  - The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
VL  - 20
IS  - 1
SP  - 244
DO  - 10.1186/s13059-019-1835-8
ER  - 

@article{
author = "Zhou, Naihui and Jiang, Yuxiang and Bergquist, Timothy R and Lee, Alexandra J and Kacsoh, Balint Z and Crocker, Alex W and Lewis, Kimberley A and Georghiou, George and Nguyen, Huy N and Hamid, Md Nafiz and Davis, Larry and Dogan, Tunca and Atalay, Volkan and Rifaioglu, Ahmet S and Dalkıran, Alperen and Cetin Atalay, Rengul and Zhang, Chengxin and Hurto, Rebecca L and Freddolino, Peter L and Zhang, Yang and Bhat, Prajwal and Supek, Fran and Fernández, José M and Gemović, Branislava S. and Perović, Vladimir R. and Davidović, Radoslav S. and Šumonja, Neven and Veljković, Nevena V. and Asgari, Ehsaneddin and Mofrad, Mohammad R.K. and Profiti, Giuseppe and Savojardo, Castrense and Martelli, Pier Luigi and Casadio, Rita and Boecker, Florian and Schoof, Heiko and Kahanda, Indika and Thurlby, Natalie and McHardy, Alice C and Renaux, Alexandre and Saidi, Rabie and Gough, Julian and Freitas, Alex A and Antczak, Magdalena and Fabris, Fabio and Wass, Mark N and Hou, Jie and Cheng, Jianlin and Wang, Zheng and Romero, Alfonso E and Paccanaro, Alberto and Yang, Haixuan and Goldberg, Tatyana and Zhao, Chenguang and Holm, Liisa and Törönen, Petri and Medlar, Alan J and Zosa, Elaine and Borukhov, Itamar and Novikov, Ilya and Wilkins, Angela and Lichtarge, Olivier and Chi, Po-Han and Tseng, Wei-Cheng and Linial, Michal and Rose, Peter W and Dessimoz, Christophe and Vidulin, Vedrana and Dzeroski, Saso and Sillitoe, Ian and Das, Sayoni and Lees, Jonathan Gill and Jones, David T and Wan, Cen and Cozzetto, Domenico and Fa, Rui and Torres, Mateo and Warwick Vesztrocy, Alex and Rodriguez, Jose Manuel and Tress, Michael L and Frasca, Marco and Notaro, Marco and Grossi, Giuliano and Petrini, Alessandro and Re, Matteo and Valentini, Giorgio and Mesiti, Marco and Roche, Daniel B and Reeb, Jonas and Ritchie, David W and Aridhi, Sabeur and Alborzi, Seyed Ziaeddin and Devignes, Marie-Dominique and Koo, Da Chen Emily and Bonneau, Richard and Gligorijević, Vladimir and Barot, Meet and Fang, Hai and Toppo, Stefano and Lavezzo, Enrico and Falda, Marco and Berselli, Michele and Tosatto, Silvio C.E. and Carraro, Marco and Piovesan, Damiano and Ur Rehman, Hafeez and Mao, Qizhong and Zhang, Shanshan and Vucetic, Slobodan and Black, Gage S and Jo, Dane and Suh, Erica and Dayton, Jonathan B and Larsen, Dallas J and Omdahl, Ashton R and McGuffin, Liam J and Brackenridge, Danielle A and Babbitt, Patricia C and Yunes, Jeffrey M and Fontana, Paolo and Zhang, Feng and Zhu, Shanfeng and You, Ronghui and Zhang, Zihan and Dai, Suyang and Yao, Shuwei and Tian, Weidong and Cao, Renzhi and Chandler, Caleb and Amezola, Miguel and Johnson, Devon and Chang, Jia-Ming and Liao, Wen-Hung and Liu, Yi-Wei and Pascarelli, Stefano and Frank, Yotam and Hoehndorf, Robert and Kulmanov, Maxat and Boudellioua, Imane and Politano, Gianfranco and Di Carlo, Stefano and Benso, Alfredo and Hakala, Kai and Ginter, Filip and Mehryary, Farrokh and Kaewphan, Suwisa and Björne, Jari and Moen, Hans and Tolvanen, Martti E.E. and Salakoski, Tapio and Kihara, Daisuke and Jain, Aashish and Šmuc, Tomislav and Altenhoff, Adrian and Ben-Hur, Asa and Rost, Burkhard and Brenner, Steven E and Orengo, Christine A and Jeffery, Constance J and Bosco, Giovanni and Hogan, Deborah A and Martin, Maria J and O’Donovan, Claire and Mooney, Sean D and Greene, Casey S and Radivojac, Predrag and Friedberg, Iddo",
year = "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 CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-Term memory. Conclusion: We conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens. © 2019 The Author(s).",
journal = "Genome Biology",
title = "The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens",
volume = "20",
number = "1",
pages = "244",
doi = "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., Dalkıran, A., Cetin Atalay, R., Zhang, C., Hurto, R. L., Freddolino, P. L., Zhang, Y., Bhat, P., Supek, F., Fernández, J. M., Gemović, B. S., Perović, V. R., Davidović, R. S., Šumonja, N., Veljković, N. V., 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., Tseng, W., 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., 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., Liao, W., Liu, Y., 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. in Genome Biology, 20(1), 244.
https://doi.org/10.1186/s13059-019-1835-8

Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, Lewis KA, Georghiou G, Nguyen HN, Hamid MN, Davis L, Dogan T, Atalay V, Rifaioglu AS, Dalkıran A, Cetin Atalay R, Zhang C, Hurto RL, Freddolino PL, Zhang Y, Bhat P, Supek F, Fernández JM, Gemović BS, Perović VR, Davidović RS, Šumonja N, Veljković NV, Asgari E, Mofrad MR, Profiti G, Savojardo C, Martelli PL, Casadio R, Boecker F, Schoof H, Kahanda I, Thurlby N, McHardy AC, Renaux A, Saidi R, Gough J, Freitas AA, Antczak M, Fabris F, Wass MN, Hou J, Cheng J, Wang Z, Romero AE, Paccanaro A, Yang H, Goldberg T, Zhao C, Holm L, Törönen P, Medlar AJ, Zosa E, Borukhov I, Novikov I, Wilkins A, Lichtarge O, Chi P, Tseng W, Linial M, Rose PW, Dessimoz C, Vidulin V, Dzeroski S, Sillitoe I, Das S, Lees JG, Jones DT, Wan C, Cozzetto D, Fa R, Torres M, Warwick Vesztrocy A, Rodriguez JM, Tress ML, Frasca M, Notaro M, Grossi G, Petrini A, Re M, Valentini G, Mesiti M, Roche DB, Reeb J, Ritchie DW, Aridhi S, Alborzi SZ, Devignes M, Koo DCE, Bonneau R, Gligorijević V, Barot M, Fang H, Toppo S, Lavezzo E, Falda M, Berselli M, Tosatto SC, Carraro M, Piovesan D, Ur Rehman H, Mao Q, Zhang S, Vucetic S, Black GS, Jo D, Suh E, Dayton JB, Larsen DJ, Omdahl AR, McGuffin LJ, Brackenridge DA, Babbitt PC, Yunes JM, 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, Liao W, Liu Y, 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 ME, Salakoski T, Kihara D, Jain A, Šmuc T, Altenhoff A, Ben-Hur A, Rost B, Brenner SE, Orengo CA, Jeffery CJ, Bosco G, Hogan DA, Martin MJ, O’Donovan C, Mooney SD, Greene CS, Radivojac P, Friedberg I. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. in Genome Biology. 2019;20(1):244.
doi:10.1186/s13059-019-1835-8 .

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, Gemović, Branislava S., Perović, Vladimir R., Davidović, Radoslav S., Šumonja, Neven, Veljković, Nevena V., 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, "The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens" in Genome Biology, 20, no. 1 (2019):244,
https://doi.org/10.1186/s13059-019-1835-8 . .