DEEPred: Automated Protein Function Prediction with Multi-task Feed-forward Deep Neural Networks

por Sureyya Rifaioglu, Ahmet, Doğan, Tunca, Jesus Martin, Maria, Cetin-Atalay, Rengul, Atalay, Volkan
Publicado 2019

Predicting the Specificity- Determining Positions of Receptor Tyrosine Kinase Axl

por Karakulak, Tülay, Rifaioglu, Ahmet Sureyya, Rodrigues, João P. G. L. M., Karaca, Ezgi
Publicado 2021

ECPred: a tool for the prediction of the enzymatic functions of protein sequences based on the EC nomenclature

por Dalkiran, Alperen, Rifaioglu, Ahmet Sureyya, Martin, Maria Jesus, Cetin-Atalay, Rengul, Atalay, Volkan, Doğan, Tunca
Publicado 2018

Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases

por Rifaioglu, Ahmet Sureyya, Atas, Heval, Martin, Maria Jesus, Cetin-Atalay, Rengul, Atalay, Volkan, Doğan, Tunca
Publicado 2018

DEEPScreen: high performance drug–target interaction prediction with convolutional neural networks using 2-D structural compound representations

por Rifaioglu, Ahmet Sureyya, Nalbat, Esra, Atalay, Volkan, Martin, Maria Jesus, Cetin-Atalay, Rengul, Doğan, Tunca
Publicado 2020

Transfer learning for drug–target interaction prediction

por Dalkıran, Alperen, Atakan, Ahmet, Rifaioğlu, Ahmet S, Martin, Maria J, Atalay, Rengül Çetin, Acar, Aybar C, Doğan, Tunca, Atalay, Volkan
Publicado 2023

CROssBAR: comprehensive resource of biomedical relations with knowledge graph representations

por Doğan, Tunca, Atas, Heval, Joshi, Vishal, Atakan, Ahmet, Rifaioglu, Ahmet Sureyya, Nalbat, Esra, Nightingale, Andrew, Saidi, Rabie, Volynkin, Vladimir, Zellner, Hermann, Cetin-Atalay, Rengul, Martin, Maria, Atalay, Volkan
Publicado 2021

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