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Ahmet Süreyya Rifaioğlu

Institute for Computational Biomedicine

14H指数
40论文数
2.1K被引数
收录论文 13
发表时间
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SpaCEy links spatial tissue patterns to clinical outcomes using explainable graph neural networksSpaCEy利用可解释图神经网络将空间组织模式与临床结局联系起来
errNature Communications
IF15.7
err2026-09-26
err0
errOAAI
errAhmet Sureyya Rifaioglu; Egle Helene Ervin; Ahmet Sarigun; Deniz Germen; Bernd Bodenmiller; Jovan Tanevski; Julio Saez-Rodriguez
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Molecular contrastive learning with graph attention network (MoCL-GAT) for enhanced molecular representation用于增强分子表征的图注意网络 (mocl-gat) 分子对比学习
errBMC Bioinformatics
IF3.3
err2026-04-09
err0
errOAAI
errAlperen Dalkıran; Ahmet Sureyya Rifaioglu; Rengul Cetin-Atalay; Aybar C. Acar; Tunca Doğan; M. Volkan Atalay
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Target-specific de novo design of drug candidate molecules with graph-transformer-based generative adversarial networks基于图变换器生成对抗网络的靶点特异性药物候选分子从头设计
errNature Machine Intelligence
IF23.9
err2025-09-15
err0
PREAI
errAtabey Ünlü; Elif Çevrim; Melih Gökay Yiğit; Ahmet Sarıgün; Hayriye Çelikbilek; Osman Bayram; Deniz Cansen Kahraman; Abdurrahman Olğaç; Ahmet Sureyya Rifaioglu; Erden Banoğlu; Tunca Doğan
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Compartments in medulloblastoma with extensive nodularity are connected through differentiation along the granular precursor lineage
errNATURE COMMUNICATIONS
IF15.7
err2024-01-08
err0
errOAAI
errGhasemi, David R.; Okonechnikov, Konstantin; Rademacher, Anne; Tirier, Stephan; Maass, Kendra K.; Schumacher, Hanna; Joshi, Piyush; Gold, Maxwell P.; Sundheimer, Julia; Statz, Britta; Rifaioglu, Ahmet S.; Bauer, Katharina; Schumacher, Sabrina; Bortolomeazzi, Michele; Giangaspero, Felice; Ernst, Kati J.; Clifford, Steven C.; Saez-Rodriguez, Julio; Jones, David T. W.; Kawauchi, Daisuke; Fraenkel, Ernest; Mallm, Jan-Philipp; Rippe, Karsten; Korshunov, Andrey; Pfister, Stefan M.; Pajtler, Kristian W.
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ProFAB-open protein functional annotation benchmark
errBRIEFINGS IN BIOINFORMATICS
IF7.7
err2023-02-03
err0
PREAI
errOzdilek, A. Samet; Atakan, Ahmet; Ozsari, Goekhan; Acar, Aybar; Atalay, M. Volkan; Dogan, Tunca; Rifaioglu, Ahmet S.
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CROssBAR: comprehensive resource of biomedical relations with knowledge graph representations
errNUCLEIC ACIDS RESEARCH
IF13.1
err2021-06-28
err20
errOAAI
errDogan, 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
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Predicting the Specificity- Determining Positions of Receptor Tyrosine Kinase Axl
errFRONTIERS IN MOLECULAR BIOSCIENCES
IF4
err2021-06-14
err4
errOAAI
errKarakulak, Tulay; Rifaioglu, Ahmet Sureyya; Rodrigues, Joao P. G. L. M.; Karaca, Ezgi
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In vitro validation of drug-target interactions revealed in silico by Comprehensive Resource of Biomedical Relations with Network Representations and Deep Learning (CROssBAR) in HCC
errCANCER RESEARCH
IF16.6
err2020-08-15
err0
PREAI
errNalbat, Esra; Rifaioglu, Ahmet Sureyya; Dogan, Tunca; Martin, Maria Jesus; Cetin-Atalay, Rengul; Atalay, Volkan
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DEEPScreen: high performance drug-target interaction prediction with convolutional neural networks using 2-D structural compound representations
errCHEMICAL SCIENCE
IF7.4
err2020-01-01
err135
errOAAI
errRifaioglu, Ahmet Sureyya; Nalbat, Esra; Atalay, Volkan; Martin, Maria Jesus; Cetin-Atalay, Rengul; Dogan, Tunca
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The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screensCAFA challenge报告通过实验筛选改善了数百个基因的蛋白质功能预测和新功能注释
errGENOME BIOLOGY
IF9.4
err2019-11-19
err264
errOAAI
errZhou, 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.; Dalkiran, Alperen; Atalay, Rengul Cetin; Zhang, Chengxin; Hurto, Rebecca L.; Freddolino, Peter L.; Zhang, Yang; Bhat, Prajwal; Supek, Fran; Fernandez, Jose M.; Gemovic, Branislava; Perovic, Vladimir R.; Davidovic, 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; Toronen, 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; Vesztrocy, Alex Warwick; 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; Gligorijevic, Vladimir; Barot, Meet; Fang, Hai; Toppo, Stefano; Lavezzo, Enrico; Falda, Marco; Berselli, Michele; Tosatto, Silvio C. E.; Carraro, Marco; Piovesan, Damiano; Rehman, Hafeez Ur; 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; Bjorne, Jari; Moen, Hans; Tolvanen, Martti E. E.; Salakoski, Tapio; Kihara, Daisuke; Jain, Aashish; Smuc, 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
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DEEPred: Automated Protein Function Prediction with Multi-task Feed-forward Deep Neural NetworksDEEPred: 基于多任务前馈深度神经网络的自动蛋白质功能预测
errSCIENTIFIC REPORTS
IF3.9
err2019-05-14
err100
errOAAI
errRifaioglu, Ahmet Sureyya; Dogan, Tunca; Martin, Maria Jesus; Cetin-Atalay, Rengul; Atalay, Volkan
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Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases深度学习和机器智能在计算机药物发现中的最新应用: 方法，工具和数据库
errBRIEFINGS IN BIOINFORMATICS
IF7.7
err2018-07-31
err306
errOAAI
errRifaioglu, Ahmet Sureyya; Atas, Heval; Martin, Maria Jesus; Cetin-Atalay, Rengul; Atalay, Volkan; Dogan, Tunca
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Large-scale automated function prediction of protein sequences and an experimental case study validation on PTEN transcript variants
errPROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
IF2.8
err2017-11-29
err12
PREAI
errRifaioglu, Ahmet Sureyya; Dogan, Tunca; Sarac, Omer Sinan; Ersahin, Tulin; Saidi, Rabie; Atalay, Mehmet Volkan; Martin, Maria Jesus; Cetin-Atalay, Rengul
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研究方向

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