TY  - JOUR
AU  - Abramowicz, H
AU  - Alipour Tehrani, N
AU  - Arominski, D
AU  - Benhammou, Y
AU  - Benoit, M
AU  - Blaising, J.-J.
AU  - Boronat, M
AU  - Borysov, O
AU  - Bosley, R R
AU  - Božović-Jelisavčić, Ivanka
AU  - Boyko, I
AU  - Brass, S
AU  - Brondolin, E
AU  - Bruckman de Renstrom, P.
AU  - Buckland, M
AU  - Burrows, P N
AU  - Chefdeville, M
AU  - Chekanov, S
AU  - Coates, T
AU  - Dannheim, D
AU  - Demarteau, M
AU  - Denizli, H
AU  - Durieux, G
AU  - Eigen, G
AU  - Elsener, K
AU  - Fullana, E
AU  - Fuster, J
AU  - Gabriel, M
AU  - Gaede, F
AU  - García, I
AU  - Goldstein, J
AU  - Gomis Lopez, P
AU  - Graf, C
AU  - Green, S
AU  - Grefe, C
AU  - Grojean, C
AU  - Hoang, A
AU  - Hynds, D
AU  - Joffe, A
AU  - Kalinowski, J
AU  - Kačarević, Goran
AU  - Kilian, W
AU  - van der Kolk, N
AU  - Krawczyk, M
AU  - Kucharczyk, M
AU  - Leogrande, E
AU  - Lesiak, T
AU  - Levy, A.
AU  - Levy, I
AU  - Linssen, L
AU  - Maier, A A
AU  - Makarenko, V
AU  - Marshall, J S
AU  - Martin, V
AU  - Mateu, V
AU  - Matsedonskyi, O
AU  - Metcalfe, J
AU  - Milutinović-Dumbelović, Gordana
AU  - Münker, R M
AU  - Nefedov, Yu.
AU  - Nowak, K
AU  - Nürnberg, A
AU  - Pandurović, Mila
AU  - Perelló, M
AU  - Perez Codina, E
AU  - Petric, M
AU  - Pitters, F
AU  - Price, T
AU  - Quast, T
AU  - Redford, S
AU  - Repond, J
AU  - Robson, A
AU  - Roloff, P
AU  - Ros, E
AU  - Rozwadowska, K
AU  - Ruiz-Jimeno, A
AU  - Sailer, A
AU  - Salvatore, F
AU  - Schnoor, U
AU  - Schulte, D
AU  - Senol, A
AU  - Shelkov, G
AU  - Sicking, E
AU  - Simon, F
AU  - Simoniello, R
AU  - Sopicki, P
AU  - Spannagel, S
AU  - Stapnes, S
AU  - Ström, R
AU  - Szalay, M
AU  - Thomson, M A
AU  - Turbiarz, B
AU  - Viazlo, O
AU  - Vicente, M
AU  - Vila, I
AU  - Vos, M
AU  - Vossebeld, J
AU  - Watson, M. F.
AU  - Watson, N K
AU  - Weber, M A
AU  - Weerts, H
AU  - Wells, J D
AU  - Widl, A
AU  - Williams, M
AU  - Winter, A.G.
AU  - Wojtoń, T
AU  - Wulzer, A
AU  - Xu, B
AU  - Xia, L
AU  - You, T
AU  - Żarnecki, A F
AU  - Zawiejski, L
AU  - Zhang, C.
AU  - Zhang, J.
AU  - Zhang, Y.
AU  - Zhang, Z
AU  - Zhemchugov, A
PY  - 2019
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/8656
AB  - The Compact Linear Collider (CLIC) is a proposed future high-luminosity linear electron-positron collider operating at three energy stages, with nominal centre-of-mass energies s = 380 GeV, 1.5 TeV, and 3 TeV. Its aim is to explore the energy frontier, providing sensitivity to physics beyond the Standard Model (BSM) and precision measurements of Standard Model processes with an emphasis on Higgs boson and top-quark physics. The opportunities for top-quark physics at CLIC are discussed in this paper. The initial stage of operation focuses on top-quark pair production measurements, as well as the search for rare flavour-changing neutral current (FCNC) top-quark decays. It also includes a top-quark pair production threshold scan around 350 GeV which provides a precise measurement of the top-quark mass in a well-defined theoretical framework. At the higher-energy stages, studies are made of top-quark pairs produced in association with other particles. A study of t̄tH production including the extraction of the top Yukawa coupling is presented as well as a study of vector boson fusion (VBF) production, which gives direct access to high-energy electroweak interactions. Operation above 1 TeV leads to more highly collimated jet environments where dedicated methods are used to analyse the jet constituents. These techniques enable studies of the top-quark pair production, and hence the sensitivity to BSM physics, to be extended to higher energies. This paper also includes phenomenological interpretations that may be performed using the results from the extensive top-quark physics programme at CLIC. [Figure not available: see fulltext.] © 2019, The Author(s).
T2  - Journal of High Energy Physics
T1  - Top-quark physics at the CLIC electron-positron linear collider
VL  - 2019
IS  - 11
SP  - 3
DO  - 10.1007/JHEP11(2019)003
ER  - 

@article{
author = "Abramowicz, H and Alipour Tehrani, N and Arominski, D and Benhammou, Y and Benoit, M and Blaising, J.-J. and Boronat, M and Borysov, O and Bosley, R R and Božović-Jelisavčić, Ivanka and Boyko, I and Brass, S and Brondolin, E and Bruckman de Renstrom, P. and Buckland, M and Burrows, P N and Chefdeville, M and Chekanov, S and Coates, T and Dannheim, D and Demarteau, M and Denizli, H and Durieux, G and Eigen, G and Elsener, K and Fullana, E and Fuster, J and Gabriel, M and Gaede, F and García, I and Goldstein, J and Gomis Lopez, P and Graf, C and Green, S and Grefe, C and Grojean, C and Hoang, A and Hynds, D and Joffe, A and Kalinowski, J and Kačarević, Goran and Kilian, W and van der Kolk, N and Krawczyk, M and Kucharczyk, M and Leogrande, E and Lesiak, T and Levy, A. and Levy, I and Linssen, L and Maier, A A and Makarenko, V and Marshall, J S and Martin, V and Mateu, V and Matsedonskyi, O and Metcalfe, J and Milutinović-Dumbelović, Gordana and Münker, R M and Nefedov, Yu. and Nowak, K and Nürnberg, A and Pandurović, Mila and Perelló, M and Perez Codina, E and Petric, M and Pitters, F and Price, T and Quast, T and Redford, S and Repond, J and Robson, A and Roloff, P and Ros, E and Rozwadowska, K and Ruiz-Jimeno, A and Sailer, A and Salvatore, F and Schnoor, U and Schulte, D and Senol, A and Shelkov, G and Sicking, E and Simon, F and Simoniello, R and Sopicki, P and Spannagel, S and Stapnes, S and Ström, R and Szalay, M and Thomson, M A and Turbiarz, B and Viazlo, O and Vicente, M and Vila, I and Vos, M and Vossebeld, J and Watson, M. F. and Watson, N K and Weber, M A and Weerts, H and Wells, J D and Widl, A and Williams, M and Winter, A.G. and Wojtoń, T and Wulzer, A and Xu, B and Xia, L and You, T and Żarnecki, A F and Zawiejski, L and Zhang, C. and Zhang, J. and Zhang, Y. and Zhang, Z and Zhemchugov, A",
year = "2019",
abstract = "The Compact Linear Collider (CLIC) is a proposed future high-luminosity linear electron-positron collider operating at three energy stages, with nominal centre-of-mass energies s = 380 GeV, 1.5 TeV, and 3 TeV. Its aim is to explore the energy frontier, providing sensitivity to physics beyond the Standard Model (BSM) and precision measurements of Standard Model processes with an emphasis on Higgs boson and top-quark physics. The opportunities for top-quark physics at CLIC are discussed in this paper. The initial stage of operation focuses on top-quark pair production measurements, as well as the search for rare flavour-changing neutral current (FCNC) top-quark decays. It also includes a top-quark pair production threshold scan around 350 GeV which provides a precise measurement of the top-quark mass in a well-defined theoretical framework. At the higher-energy stages, studies are made of top-quark pairs produced in association with other particles. A study of t̄tH production including the extraction of the top Yukawa coupling is presented as well as a study of vector boson fusion (VBF) production, which gives direct access to high-energy electroweak interactions. Operation above 1 TeV leads to more highly collimated jet environments where dedicated methods are used to analyse the jet constituents. These techniques enable studies of the top-quark pair production, and hence the sensitivity to BSM physics, to be extended to higher energies. This paper also includes phenomenological interpretations that may be performed using the results from the extensive top-quark physics programme at CLIC. [Figure not available: see fulltext.] © 2019, The Author(s).",
journal = "Journal of High Energy Physics",
title = "Top-quark physics at the CLIC electron-positron linear collider",
volume = "2019",
number = "11",
pages = "3",
doi = "10.1007/JHEP11(2019)003"
}

Abramowicz, H., Alipour Tehrani, N., Arominski, D., Benhammou, Y., Benoit, M., Blaising, J.-J., Boronat, M., Borysov, O., Bosley, R. R., Božović-Jelisavčić, I., Boyko, I., Brass, S., Brondolin, E., Bruckman de Renstrom, P., Buckland, M., Burrows, P. N., Chefdeville, M., Chekanov, S., Coates, T., Dannheim, D., Demarteau, M., Denizli, H., Durieux, G., Eigen, G., Elsener, K., Fullana, E., Fuster, J., Gabriel, M., Gaede, F., García, I., Goldstein, J., Gomis Lopez, P., Graf, C., Green, S., Grefe, C., Grojean, C., Hoang, A., Hynds, D., Joffe, A., Kalinowski, J., Kačarević, G., Kilian, W., van der Kolk, N., Krawczyk, M., Kucharczyk, M., Leogrande, E., Lesiak, T., Levy, A., Levy, I., Linssen, L., Maier, A. A., Makarenko, V., Marshall, J. S., Martin, V., Mateu, V., Matsedonskyi, O., Metcalfe, J., Milutinović-Dumbelović, G., Münker, R. M., Nefedov, Yu., Nowak, K., Nürnberg, A., Pandurović, M., Perelló, M., Perez Codina, E., Petric, M., Pitters, F., Price, T., Quast, T., Redford, S., Repond, J., Robson, A., Roloff, P., Ros, E., Rozwadowska, K., Ruiz-Jimeno, A., Sailer, A., Salvatore, F., Schnoor, U., Schulte, D., Senol, A., Shelkov, G., Sicking, E., Simon, F., Simoniello, R., Sopicki, P., Spannagel, S., Stapnes, S., Ström, R., Szalay, M., Thomson, M. A., Turbiarz, B., Viazlo, O., Vicente, M., Vila, I., Vos, M., Vossebeld, J., Watson, M. F., Watson, N. K., Weber, M. A., Weerts, H., Wells, J. D., Widl, A., Williams, M., Winter, A.G., Wojtoń, T., Wulzer, A., Xu, B., Xia, L., You, T., Żarnecki, A. F., Zawiejski, L., Zhang, C., Zhang, J., Zhang, Y., Zhang, Z.,& Zhemchugov, A.. (2019). Top-quark physics at the CLIC electron-positron linear collider. in Journal of High Energy Physics, 2019(11), 3.
https://doi.org/10.1007/JHEP11(2019)003

Abramowicz H, Alipour Tehrani N, Arominski D, Benhammou Y, Benoit M, Blaising J, Boronat M, Borysov O, Bosley RR, Božović-Jelisavčić I, Boyko I, Brass S, Brondolin E, Bruckman de Renstrom P, Buckland M, Burrows PN, Chefdeville M, Chekanov S, Coates T, Dannheim D, Demarteau M, Denizli H, Durieux G, Eigen G, Elsener K, Fullana E, Fuster J, Gabriel M, Gaede F, García I, Goldstein J, Gomis Lopez P, Graf C, Green S, Grefe C, Grojean C, Hoang A, Hynds D, Joffe A, Kalinowski J, Kačarević G, Kilian W, van der Kolk N, Krawczyk M, Kucharczyk M, Leogrande E, Lesiak T, Levy A, Levy I, Linssen L, Maier AA, Makarenko V, Marshall JS, Martin V, Mateu V, Matsedonskyi O, Metcalfe J, Milutinović-Dumbelović G, Münker RM, Nefedov Y, Nowak K, Nürnberg A, Pandurović M, Perelló M, Perez Codina E, Petric M, Pitters F, Price T, Quast T, Redford S, Repond J, Robson A, Roloff P, Ros E, Rozwadowska K, Ruiz-Jimeno A, Sailer A, Salvatore F, Schnoor U, Schulte D, Senol A, Shelkov G, Sicking E, Simon F, Simoniello R, Sopicki P, Spannagel S, Stapnes S, Ström R, Szalay M, Thomson MA, Turbiarz B, Viazlo O, Vicente M, Vila I, Vos M, Vossebeld J, Watson MF, Watson NK, Weber MA, Weerts H, Wells JD, Widl A, Williams M, Winter A, Wojtoń T, Wulzer A, Xu B, Xia L, You T, Żarnecki AF, Zawiejski L, Zhang C, Zhang J, Zhang Y, Zhang Z, Zhemchugov A. Top-quark physics at the CLIC electron-positron linear collider. in Journal of High Energy Physics. 2019;2019(11):3.
doi:10.1007/JHEP11(2019)003 .

Abramowicz, H, Alipour Tehrani, N, Arominski, D, Benhammou, Y, Benoit, M, Blaising, J.-J., Boronat, M, Borysov, O, Bosley, R R, Božović-Jelisavčić, Ivanka, Boyko, I, Brass, S, Brondolin, E, Bruckman de Renstrom, P., Buckland, M, Burrows, P N, Chefdeville, M, Chekanov, S, Coates, T, Dannheim, D, Demarteau, M, Denizli, H, Durieux, G, Eigen, G, Elsener, K, Fullana, E, Fuster, J, Gabriel, M, Gaede, F, García, I, Goldstein, J, Gomis Lopez, P, Graf, C, Green, S, Grefe, C, Grojean, C, Hoang, A, Hynds, D, Joffe, A, Kalinowski, J, Kačarević, Goran, Kilian, W, van der Kolk, N, Krawczyk, M, Kucharczyk, M, Leogrande, E, Lesiak, T, Levy, A., Levy, I, Linssen, L, Maier, A A, Makarenko, V, Marshall, J S, Martin, V, Mateu, V, Matsedonskyi, O, Metcalfe, J, Milutinović-Dumbelović, Gordana, Münker, R M, Nefedov, Yu., Nowak, K, Nürnberg, A, Pandurović, Mila, Perelló, M, Perez Codina, E, Petric, M, Pitters, F, Price, T, Quast, T, Redford, S, Repond, J, Robson, A, Roloff, P, Ros, E, Rozwadowska, K, Ruiz-Jimeno, A, Sailer, A, Salvatore, F, Schnoor, U, Schulte, D, Senol, A, Shelkov, G, Sicking, E, Simon, F, Simoniello, R, Sopicki, P, Spannagel, S, Stapnes, S, Ström, R, Szalay, M, Thomson, M A, Turbiarz, B, Viazlo, O, Vicente, M, Vila, I, Vos, M, Vossebeld, J, Watson, M. F., Watson, N K, Weber, M A, Weerts, H, Wells, J D, Widl, A, Williams, M, Winter, A.G., Wojtoń, T, Wulzer, A, Xu, B, Xia, L, You, T, Żarnecki, A F, Zawiejski, L, Zhang, C., Zhang, J., Zhang, Y., Zhang, Z, Zhemchugov, A, "Top-quark physics at the CLIC electron-positron linear collider" in Journal of High Energy Physics, 2019, no. 11 (2019):3,
https://doi.org/10.1007/JHEP11(2019)003 . .

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 . .