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Volkan Atalay
Researcher at Middle East Technical University
Publications - 80
Citations - 2304
Volkan Atalay is an academic researcher from Middle East Technical University. The author has contributed to research in topics: Deep learning & Computer science. The author has an hindex of 20, co-authored 76 publications receiving 1629 citations. Previous affiliations of Volkan Atalay include Virginia Tech & Paris Descartes University.
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Journal ArticleDOI
Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases.
Ahmet Sureyya Rifaioglu,Heval Atas,Maria Jesus Martin,Rengul Cetin-Atalay,Volkan Atalay,Tunca Doğan +5 more
TL;DR: The objective of this study is to examine and discuss the recent applications of machine learning techniques in VS, including deep learning, which became highly popular after giving rise to epochal developments in the fields of computer vision and natural language processing.
Journal ArticleDOI
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
Naihui Zhou,Yuxiang Jiang,Timothy Bergquist,Alexandra J. Lee,Balint Z. Kacsoh,Alex W. Crocker,Kimberley A. Lewis,George Georghiou,Huy N Nguyen,Nafiz Hamid,Larry Davis,Tunca Doğan,Tunca Doğan,Volkan Atalay,Ahmet Sureyya Rifaioglu,Alperen Dalkiran,Rengul Cetin Atalay,Chengxin Zhang,Rebecca L. Hurto,Peter L. Freddolino,Yang Zhang,Prajwal Bhat,Fran Supek,José M. Fernández,Branislava Gemovic,Vladimir Perovic,Radoslav Davidovic,Neven Sumonja,Nevena Veljkovic,Ehsaneddin Asgari,Mohammad R. K. Mofrad,Giuseppe Profiti,Giuseppe Profiti,Castrense Savojardo,Pier Luigi Martelli,Rita Casadio,Florian Boecker,Heiko Schoof,Indika Kahanda,Natalie Thurlby,Alice C. McHardy,Alexandre Renaux,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,Haixuan Yang,Tatyana Goldberg,Chenguang Zhao,Liisa Holm,Petri Törönen,Alan Medlar,Elaine Zosa,Itamar Borukhov,Ilya Novikov,Angela D. Wilkins,Olivier Lichtarge,Po-Han Chi,Wei-Cheng Tseng,Michal Linial,Peter W. Rose,Christophe Dessimoz,Christophe Dessimoz,Christophe Dessimoz,Vedrana Vidulin,Saso Dzeroski,Ian Sillitoe,Sayoni Das,Jonathan G. Lees,Jonathan G. Lees,David T. Jones,David T. Jones,Cen Wan,Cen Wan,Domenico Cozzetto,Domenico Cozzetto,Rui Fa,Rui Fa,Mateo Torres,Alex Warwick Vesztrocy,Alex Warwick Vesztrocy,Jose Manuel Rodriguez,Michael L. Tress,Marco Frasca,Marco Notaro,Giuliano Grossi,Alessandro Petrini,Matteo Re,Giorgio Valentini,Marco Mesiti,Marco Mesiti,Daniel B. Roche,Jonas Reeb,David W. Ritchie,Sabeur Aridhi,Seyed Ziaeddin Alborzi,Seyed Ziaeddin Alborzi,Marie-Dominique Devignes,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,Qizhong Mao,Shanshan Zhang,Slobodan Vucetic,Gage S. Black,Dane Jo,Erica Suh,Jonathan B. Dayton,Dallas J. Larsen,Ashton 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,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,Suwisa Kaewphan,Jari Björne,Jari Björne,Hans Moen,Martti Tolvanen,Tapio Salakoski,Tapio Salakoski,Daisuke Kihara,Daisuke Kihara,Aashish Jain,Tomislav Šmuc,Adrian M. Altenhoff,Adrian M. Altenhoff,Asa Ben-Hur,Burkhard Rost,Steven E. Brenner,Christine A. Orengo,Constance J. Jeffery,Giovanni Bosco,Deborah A. Hogan,Maria Jesus Martin,Claire O'Donovan,Sean D. Mooney,Casey S. Greene,Predrag Radivojac,Iddo Friedberg +188 more
TL;DR: 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, concluded that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not.
Journal ArticleDOI
Silhouette-based 3-D model reconstruction from multiple images
TL;DR: An algorithm to extract the rotation axis of a turn-table has been developed based on a multi-image calibration method and it can be extended to estimate robustly the initial bounding volume of the object to be modeled.
Journal ArticleDOI
DEEPScreen: high performance drug-target interaction prediction with convolutional neural networks using 2-D structural compound representations.
Ahmet Sureyya Rifaioglu,Esra Nalbat,Volkan Atalay,Maria Jesus Martin,Rengul Cetin-Atalay,Rengul Cetin-Atalay,Tunca Doğan +6 more
TL;DR: The DEEPScreen system is composed of 704 target protein specific prediction models, each independently trained using experimental bioactivity measurements against many drug candidate small molecules, and optimized according to the binding properties of the target proteins.
Posted ContentDOI
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
Naihui Zhou,Yuxiang Jiang,Timothy Bergquist,Alexandra J. Lee,Balint Z. Kacsoh,Alex W. Crocker,Kimberley A. Lewis,George Georghiou,Huy N Nguyen,Nafiz Hamid,Larry Davis,Tunca Doğan,Tunca Doğan,Volkan Atalay,Ahmet Sureyya Rifaioglu,Alperen Dalkiran,Rengul Cetin-Atalay,Chengxin Zhang,Rebecca L. Hurto,Peter L. Freddolino,Yang Zhang,Prajwal Bhat,Fran Supek,José M. Fernández,Branislava Gemovic,Vladimir Perovic,Radoslav Davidovic,Neven Sumonja,Nevena Veljkovic,Ehsaneddin Asgari,Mohammad R. K. Mofrad,Giuseppe Profiti,Giuseppe Profiti,Castrense Savojardo,Pier Luigi Martelli,Rita Casadio,Florian Boecker,Indika Kahanda,Natalie Thurlby,Alice C. McHardy,Alexandre Renaux,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 Medlar,Elaine Zosa,Itamar Borukhov,Ilya Novikov,Angela D. Wilkins,Olivier Lichtarge,Po-Han Chi,Wei-Cheng Tseng,Michal Linial,Peter W. Rose,Christophe Dessimoz,Christophe Dessimoz,Vedrana Vidulin,Saso Dzeroski,Ian Sillitoe,Sayoni Das,Jonathan G. Lees,Jonathan G. Lees,David T. Jones,David T. Jones,Cen Wan,Cen Wan,Domenico Cozzetto,Domenico Cozzetto,Rui Fa,Rui Fa,Mateo Torres,Alex Warwick Vesztrocy,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,Qizhong Mao,Shanshan Zhang,Slobodan Vucetic,Gage S. Black,Dane Jo,Dallas J. Larsen,Ashton Omdahl,Luke W Sagers,Erica Suh,Jonathan B. Dayton,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,Suwisa Kaewphan,Jari Björne,Jari Björne,Hans Moen,Martti Tolvanen,Tapio Salakoski,Tapio Salakoski,Daisuke Kihara,Daisuke Kihara,Aashish Jain,Tomislav Šmuc,Adrian M. Altenhoff,Asa Ben-Hur,Burkhard Rost,Steven E. Brenner,Christine A. Orengo,Constance J. Jeffery,Giovanni Bosco,Deborah A. Hogan,Maria Jesus Martin,Claire O'Donovan,Sean D. Mooney,Casey S. Greene,Predrag Radivojac,Iddo Friedberg +181 more
TL;DR: It is reported that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bioontologies, working together to improve functional annotation, computational function prediction, and the ability to manage big data in the era of large experimental screens.